Identification of Acinetobacter species: is Bruker biotyper MALDI-TOF mass spectrometry a good alternative to molecular techniques?

PubMed

Alvarez-Buylla, Adela; Culebras, Esther; Picazo, Juan J

2012-03-01

Acinetobacter spp. has become a leading cause of nosocomial infection in recent years. Phenotypic similarities between the species in the genus have made it difficult to identify them clearly using routine diagnostic methods. Consequently, more relevant species have been grouped together as Acinetobacter calcoaceticus-Acinetobacter baumannii complex (A. baumannii, A. calcoaceticus, Acinetobacter genospecies 3 and A. genospecies 13TU). However, there are other species that may also have clinical significance. The aims of this study were to establish the usefulness of matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) for the identification of Acinetobacter species by comparison with two molecular techniques, as well as determine the role of species other than A. baumannii play in nosocomial infections.The study sample comprised 109 clinical isolates of Acinetobacter. They were all identified using MALDI-TOF MS. Thirty-one isolates of these were also tested using comparator amplification of bla(OXA51-like) and sequencing of the rpoB gene. Different score values in MALDI-TOF MS revealed 87 A. baumannii, 19 A. genospecies 3, 1 Acinetobacter junii, 1 Acinetobacter baylyi and 1 Acinetobacter tjernbergiae. Amplification of bla(OXA-51)(-like) showed products in 85 isolates. Sequencing of the rpoB gene allowed us to identify all the 31 isolates analyzed: 16 were consistent with the results of spectrometry and 15 were not. This work showed that molecular techniques are still needed to identify the different species of clinical interest within the genus Acinetobacter. Although, MALDI-TOF MS could be useful to identify A. baumannii but not other species in the genus. Copyright © 2012 Elsevier B.V. All rights reserved.

Identification of a new allelic variant of the Acinetobacter baumannii cephalosporinase, ADC-7 beta-lactamase: defining a unique family of class C enzymes.

PubMed

Hujer, Kristine M; Hamza, Nashaat S; Hujer, Andrea M; Perez, Federico; Helfand, Marion S; Bethel, Christopher R; Thomson, Jodi M; Anderson, Vernon E; Barlow, Miriam; Rice, Louis B; Tenover, Fred C; Bonomo, Robert A

2005-07-01

Acinetobacter spp. are emerging as opportunistic hospital pathogens that demonstrate resistance to many classes of antibiotics. In a metropolitan hospital in Cleveland, a clinical isolate of Acinetobacter baumannii that tested resistant to cefepime and ceftazidime (MIC = 32 microg/ml) was identified. Herein, we sought to determine the molecular basis for the extended-spectrum-cephalosporin resistance. Using analytical isoelectric focusing, a beta-lactamase with a pI of > or = 9.2 was detected. PCR amplification with specific A. baumannii cephalosporinase primers yielded a 1,152-bp product which, when sequenced, identified a novel 383-amino-acid class C enzyme. Expressed in Escherichia coli DH10B, this beta-lactamase demonstrated greater resistance against ceftazidime and cefotaxime than cefepime (4.0 microg/ml versus 0.06 microg/ml). The kinetic characteristics of this beta-lactamase were similar to other cephalosporinases found in Acinetobacter spp. In addition, this cephalosporinase was inhibited by meropenem, imipenem, ertapenem, and sulopenem (K(i) < 40 microM). The amino acid compositions of this novel enzyme and other class C beta-lactamases thus far described for A. baumannii, Acinetobacter genomic species 3, and Oligella urethralis in Europe and South Africa suggest that this cephalosporinase defines a unique family of class C enzymes. We propose a uniform designation for this family of cephalosporinases (Acinetobacter-derived cephalosporinases [ADC]) found in Acinetobacter spp. and identify this enzyme as ADC-7 beta-lactamase. The coalescence of Acinetobacter ampC beta-lactamases into a single common ancestor and the substantial phylogenetic distance separating them from other ampC genes support the logical value of developing a system of nomenclature for these Acinetobacter cephalosporinase genes.

Identification of a New Allelic Variant of the Acinetobacter baumannii Cephalosporinase, ADC-7 β-Lactamase: Defining a Unique Family of Class C Enzymes‡

PubMed Central

Hujer, Kristine M.; Hamza, Nashaat S.; Hujer, Andrea M.; Perez, Federico; Helfand, Marion S.; Bethel, Christopher R.; Thomson, Jodi M.; Anderson, Vernon E.; Barlow, Miriam; Rice, Louis B.; Tenover, Fred C.; Bonomo, Robert A.

2005-01-01

Acinetobacter spp. are emerging as opportunistic hospital pathogens that demonstrate resistance to many classes of antibiotics. In a metropolitan hospital in Cleveland, a clinical isolate of Acinetobacter baumannii that tested resistant to cefepime and ceftazidime (MIC = 32 μg/ml) was identified. Herein, we sought to determine the molecular basis for the extended-spectrum-cephalosporin resistance. Using analytical isoelectric focusing, a β-lactamase with a pI of ≥9.2 was detected. PCR amplification with specific A. baumannii cephalosporinase primers yielded a 1,152-bp product which, when sequenced, identified a novel 383-amino-acid class C enzyme. Expressed in Escherichia coli DH10B, this β-lactamase demonstrated greater resistance against ceftazidime and cefotaxime than cefepime (4.0 μg/ml versus 0.06 μg/ml). The kinetic characteristics of this β-lactamase were similar to other cephalosporinases found in Acinetobacter spp. In addition, this cephalosporinase was inhibited by meropenem, imipenem, ertapenem, and sulopenem (Ki < 40 μM). The amino acid compositions of this novel enzyme and other class C β-lactamases thus far described for A. baumannii, Acinetobacter genomic species 3, and Oligella urethralis in Europe and South Africa suggest that this cephalosporinase defines a unique family of class C enzymes. We propose a uniform designation for this family of cephalosporinases (Acinetobacter-derived cephalosporinases [ADC]) found in Acinetobacter spp. and identify this enzyme as ADC-7 β-lactamase. The coalescence of Acinetobacter ampC β-lactamases into a single common ancestor and the substantial phylogenetic distance separating them from other ampC genes support the logical value of developing a system of nomenclature for these Acinetobacter cephalosporinase genes. PMID:15980372

Draft Genome Sequence of Acinetobacter calcoaceticus Strain P23, a Plant Growth-Promoting Bacterium of Duckweed

PubMed Central

Hosoyama, Akira; Yamazoe, Atsushi; Morikawa, Masaaki

2015-01-01

Acinetobacter calcoaceticus strain P23 is a plant growth-promoting bacterium, which was isolated from the surface of duckweed. We report here the draft genome sequence of strain P23. The genome data will serve as a valuable reference for understanding the molecular mechanism of plant growth promotion in aquatic plants. PMID:25720680

Complete Genome Sequence of Acinetobacter baumannii CIP 70.10, a Susceptible Reference Strain for Comparative Genome Analyses.

PubMed

Krahn, Thomas; Wibberg, Daniel; Maus, Irena; Winkler, Anika; Pühler, Alfred; Poirel, Laurent; Schlüter, Andreas

2015-07-30

The complete genome sequence for the reference strain Acinetobacter baumannii CIP 70.10 (ATCC 15151) was established. The strain was isolated in France in 1970, is susceptible to most antimicrobial compounds, and is therefore of importance for comparative genome analyses with clinical multidrug-resistant (MDR) A. baumannii strains to study resistance development and acquisition in this emerging human pathogen. Copyright © 2015 Krahn et al.

The Genetic Analysis of an Acinetobacter johnsonii Clinical Strain Evidenced the Presence of Horizontal Genetic Transfer.

PubMed

Montaña, Sabrina; Schramm, Sareda T J; Traglia, German Matías; Chiem, Kevin; Parmeciano Di Noto, Gisela; Almuzara, Marisa; Barberis, Claudia; Vay, Carlos; Quiroga, Cecilia; Tolmasky, Marcelo E; Iriarte, Andrés; Ramírez, María Soledad

2016-01-01

Acinetobacter johnsonii rarely causes human infections. While most A. johnsonii isolates are susceptible to virtually all antibiotics, strains harboring a variety of β-lactamases have recently been described. An A. johnsonii Aj2199 clinical strain recovered from a hospital in Buenos Aires produces PER-2 and OXA-58. We decided to delve into its genome by obtaining the whole genome sequence of the Aj2199 strain. Genome comparison studies on Aj2199 revealed 240 unique genes and a close relation to strain WJ10621, isolated from the urine of a patient in China. Genomic analysis showed evidence of horizontal genetic transfer (HGT) events. Forty-five insertion sequences and two intact prophages were found in addition to several resistance determinants such as blaPER-2, blaOXA-58, blaTEM-1, strA, strB, ereA, sul1, aacC2 and a new variant of blaOXA-211, called blaOXA-498. In particular, blaPER-2 and blaTEM-1 are present within the typical contexts previously described in the Enterobacteriaceae family. These results suggest that A. johnsonii actively acquires exogenous DNA from other bacterial species and concomitantly becomes a reservoir of resistance genes.

Diversity and Antibiotic Susceptibility of Acinetobacter Strains From Milk Powder Produced in Germany

PubMed Central

Cho, Gyu-Sung; Li, Bo; Rostalsky, André; Fiedler, Gregor; Rösch, Niels; Igbinosa, Etinosa; Kabisch, Jan; Bockelmann, Wilhelm; Hammer, Philipp; Huys, Geert; Franz, Charles M. A. P.

2018-01-01

Forty-seven Acinetobacter spp. isolates from milk powder obtained from a powdered milk producer in Germany were investigated for their antibiotic resistance susceptibilities, in order to assess whether strains from food harbor multiple antibiotic resistances and whether the food route is important for dissemination of resistance genes. The strains were identified by 16S rRNA and rpoB gene sequencing, as well as by whole genome sequencing of selected isolates and their in silico DNA-DNA hybridization (DDH). Furthermore, they were genotyped by rep-PCR together with reference strains of pan-European groups I, II, and III strains of Acinetobacter baumannii. Of the 47 strains, 42 were identified as A. baumannii, 4 as Acinetobacter Pittii, and 1 as Acinetobacter calcoaceticus based on 16S rRNA gene sequencing. In silico DDH with the genome sequence data of selected strains and rpoB gene sequencing data suggested that the five non-A. baumannii strains all belonged to A. pittii, suggesting that the rpoB gene is more reliable than the 16S rRNA gene for species level identification in this genus. Rep-PCR genotyping of the A. baumannii strains showed that these could be grouped into four groups, and that some strains clustered together with reference strains of pan-European clinical group II and III strains. All strains in this study were intrinsically resistant toward chloramphenicol and oxacillin, but susceptible toward tetracycline, tobramycin, erythromycin, and ciprofloxacin. For cefotaxime, 43 strains (91.5%) were intermediate and 3 strains (6.4%) resistant, while 3 (6.4%) and 21 (44.7%) strains exhibited resistance to cefepime and streptomycin, respectively. Forty-six (97.9%) strains were susceptible to amikacin and ampicillin-sulbactam. Therefore, the strains in this study were generally not resistant to the clinically relevant antibiotics, especially tobramycin, ciprofloxacin, cefepime, and meropenem, suggesting that the food route probably poses only a low risk for multidrug resistant Acinetobacter strains or resistance genes. PMID:29636733

Reservoirs of Non-baumannii Acinetobacter Species

PubMed Central

Al Atrouni, Ahmad; Joly-Guillou, Marie-Laure; Hamze, Monzer; Kempf, Marie

2016-01-01

Acinetobacter spp. are ubiquitous gram negative and non-fermenting coccobacilli that have the ability to occupy several ecological niches including environment, animals and human. Among the different species, Acinetobacter baumannii has evolved as global pathogen causing wide range of infection. Since the implementation of molecular techniques, the habitat and the role of non-baumannii Acinetobacter in human infection have been elucidated. In addition, several new species have been described. In the present review, we summarize the recent data about the natural reservoir of non-baumannii Acinetobacter including the novel species that have been described for the first time from environmental sources and reported during the last years. PMID:26870013

Characterization of Plasmids in Extensively Drug-Resistant Acinetobacter Strains Isolated in India and Pakistan

PubMed Central

Carvalho, Maria J.; Toleman, Mark A.; White, P. Lewis; Connor, Thomas R.; Mushtaq, Ammara; Weeks, Janis L.; Kumarasamy, Karthikeyan K.; Raven, Katherine E.; Török, M. Estée; Peacock, Sharon J.; Howe, Robin A.; Walsh, Timothy R.

2014-01-01

The blaNDM-1 gene is associated with extensive drug resistance in Gram-negative bacteria. This probably spread to Enterobacteriaceae from Acinetobacter spp., and we characterized plasmids associated with blaNDM-1 in Acinetobacter spp. to gain insight into their role in this dissemination. Four clinical NDM-1-producing Acinetobacter species strains from India and Pakistan were investigated. A plasmid harboring blaNDM-1, pNDM-40-1, was characterized by whole-genome sequencing of Acinetobacter bereziniae CHI-40-1 and comparison with related plasmids. The presence of similar plasmids in strains from Pakistan was sought by PCR and sequencing of amplicons. Conjugation frequency was tested and stability of pNDM-40-1 investigated by real-time PCR of isolates passaged with and without antimicrobial selection pressure. A. bereziniae and Acinetobacter haemolyticus strains contained plasmids similar to the pNDM-BJ01-like plasmids identified in Acinetobacter spp. in China. The backbone of pNDM-40-1 was almost identical to that of pNDM-BJ01-like plasmids, but the transposon harboring blaNDM-1, Tn125, contained two short deletions. Escherichia coli and Acinetobacter pittii transconjugants were readily obtained. Transconjugants retained pNDM-40-1 after a 14-day passage experiment, although stability was greater with meropenem selection. Fragments of pNDM-BJ01-like plasmid backbones are found near blaNDM-1 in some genetic contexts from Enterobacteriaceae, suggesting that cross-genus transfer has occurred. pNDM-BJ01-like plasmids have been described in isolates originating from a wide geographical region in southern Asia. In vitro data on plasmid transfer and stability suggest that these plasmids could have contributed to the spread of blaNDM-1 into Enterobacteriaceae. PMID:25421466

Microbial Profiling of Combat Wound Infection through Detection Microarray and Next-Generation Sequencing

PubMed Central

Allen, Jonathan E.; Brown, Trevor S.; Gardner, Shea N.; McLoughlin, Kevin S.; Forsberg, Jonathan A.; Kirkup, Benjamin C.; Chromy, Brett A.; Luciw, Paul A.; Elster, Eric A.

2014-01-01

Combat wound healing and resolution are highly affected by the resident microbial flora. We therefore sought to achieve comprehensive detection of microbial populations in wounds using novel genomic technologies and bioinformatics analyses. We employed a microarray capable of detecting all sequenced pathogens for interrogation of 124 wound samples from extremity injuries in combat-injured U.S. service members. A subset of samples was also processed via next-generation sequencing and metagenomic analysis. Array analysis detected microbial targets in 51% of all wound samples, with Acinetobacter baumannii being the most frequently detected species. Multiple Pseudomonas species were also detected in tissue biopsy specimens. Detection of the Acinetobacter plasmid pRAY correlated significantly with wound failure, while detection of enteric-associated bacteria was associated significantly with successful healing. Whole-genome sequencing revealed broad microbial biodiversity between samples. The total wound bioburden did not associate significantly with wound outcome, although temporal shifts were observed over the course of treatment. Given that standard microbiological methods do not detect the full range of microbes in each wound, these data emphasize the importance of supplementation with molecular techniques for thorough characterization of wound-associated microbes. Future application of genomic protocols for assessing microbial content could allow application of specialized care through early and rapid identification and management of critical patterns in wound bioburden. PMID:24829242

Genome Sequence of Acinetobacter sp. Strain HA, Isolated from the Gut of the Polyphagous Insect Pest Helicoverpa armigera

PubMed Central

Malhotra, Jaya; Dua, Ankita; Saxena, Anjali; Sangwan, Naseer; Mukherjee, Udita; Pandey, Neeti; Rajagopal, Raman; Khurana, Paramjit; Khurana, Jitendra P.

2012-01-01

In this study, Acinetobacter sp. strain HA was isolated from the midgut of a fifth-instar larva of Helicoverpa armigera. Here, we report the draft genome sequence (3,125,085 bp) of this strain that consists of 102 contigs, 2,911 predicted coding sequences, and a G+C content of 41%. PMID:22933775

Annual Surveillance Summary: Acinetobacter Infections in the Military Health System, 2015

DTIC Science & Technology

2017-05-01

pharmacy data to assess prescription practices, the Standard Inpatient Data Record to determine healthcare-associated exposures, Defense Manpower ...7 Results ...System (CHCS) microbiology data were used to identify positive Acinetobacter species laboratory results . A unique Acinetobacter species infection

Comparative genomic analysis of Acinetobacter strains isolated from murine colonic crypts.

PubMed

Saffarian, Azadeh; Touchon, Marie; Mulet, Céline; Tournebize, Régis; Passet, Virginie; Brisse, Sylvain; Rocha, Eduardo P C; Sansonetti, Philippe J; Pédron, Thierry

2017-07-11

A restricted set of aerobic bacteria dominated by the Acinetobacter genus was identified in murine intestinal colonic crypts. The vicinity of such bacteria with intestinal stem cells could indicate that they protect the crypt against cytotoxic and genotoxic signals. Genome analyses of these bacteria were performed to better appreciate their biodegradative capacities. Two taxonomically different clusters of Acinetobacter were isolated from murine proximal colonic crypts, one was identified as A. modestus and the other as A. radioresistens. Their identification was performed through biochemical parameters and housekeeping gene sequencing. After selection of one strain of each cluster (A. modestus CM11G and A. radioresistens CM38.2), comparative genomic analysis was performed on whole-genome sequencing data. The antibiotic resistance pattern of these two strains is different, in line with the many genes involved in resistance to heavy metals identified in both genomes. Moreover whereas the operon benABCDE involved in benzoate metabolism is encoded by the two genomes, the operon antABC encoding the anthranilate dioxygenase, and the phenol hydroxylase gene cluster are absent in the A. modestus genomic sequence, indicating that the two strains have different capacities to metabolize xenobiotics. A common feature of the two strains is the presence of a type IV pili system, and the presence of genes encoding proteins pertaining to secretion systems such as Type I and Type II secretion systems. Our comparative genomic analysis revealed that different Acinetobacter isolated from the same biological niche, even if they share a large majority of genes, possess unique features that could play a specific role in the protection of the intestinal crypt.

Draft Genome Sequence of Acinetobacter calcoaceticus Strain GK1, a Hydrocarbon-Degrading Plant Growth-Promoting Rhizospheric Bacterium.

PubMed

Gkorezis, Panagiotis; Bottos, Eric M; Van Hamme, Jonathan D; Franzetti, Andrea; Abbamondi, Gennaro Roberto; Balseiro-Romero, Maria; Weyens, Nele; Rineau, Francois; Vangronsveld, Jaco

2015-08-13

The 3.94-Mb draft genome of Acinetobacter calcoaceticus GK1, a hydrocarbonoclastic plant growth-promoting Gram-negative rhizospheric bacterium, is presented here. Isolated at the Ford Motor Company site in Genk, Belgium, from poplar trees planted on a diesel-contaminated plume, GK1 is useful for enhancing hydrocarbon phytoremediation. Copyright © 2015 Gkorezis et al.

Draft Genome Sequences of Six Multidrug-Resistant Clinical Strains of Acinetobacter baumannii, Isolated at Two Major Hospitals in Kuwait.

PubMed

Nasser, Kother; Mustafa, Abu Salim; Khan, Mohd Wasif; Purohit, Prashant; Al-Obaid, Inaam; Dhar, Rita; Al-Fouzan, Wadha

2018-04-19

Acinetobacter baumannii is an important opportunistic pathogen in global health care settings. Its dissemination and multidrug resistance pose an issue with treatment and outbreak control. Here, we present draft genome assemblies of six multidrug-resistant clinical strains of A. baumannii isolated from patients admitted to one of two major hospitals in Kuwait. Copyright © 2018 Nasser et al.

Relatedness of three species of "false neisseriae," Neisseria caviae, Neisseria cuniculi, and Neisseria ovis, by DNA-DNA hybridizations and fatty acid analysis.

PubMed

Véron, M; Lenvoisé-Furet, A; Coustère, C; Ged, C; Grimont, F

1993-04-01

DNA-DNA hybridization was used to determine the levels of genomic relatedness of the three species of "false neisseriae," Neisseria caviae, Neisseria cuniculi, and Neisseria ovis. The reference strains of these species exhibited high levels of intraspecies relatedness (93 to 100% for N. caviae, 79 to 100% for N. cuniculi, and 68 to 100% for N. ovis) but low levels of interspecific relatedness (less than 34%) to each other and to various species belonging to the beta subclass of the Proteobacteria (Kingella kingae, Neisseria gonorrhoeae, Neisseria meningitidis, and Oligella urethralis) or to the gamma subclass (Branhamella catarrhalis, Kingella indologenes, Moraxella atlantae, Moraxella bovis, Moraxella lacunata subsp. lacunata, Moraxella lacunata subsp. liquefaciens, Moraxella nonliquefaciens, Moraxella osloensis, and Moraxella phenylpyruvica). However, the levels of DNA-DNA hybridization for the three species of "false neisseriae" were significantly higher with the species belonging to the gamma subclass (average, 13.7%) than with the species belonging to the beta subclass (average, 4.5%). These data suggest that N. caviae, N. cuniculi, and N. ovis are three separate genomic species in the gamma subclass. An ascendant hierarchical classification based only on fatty acid profiles distinguished four main classes containing (i) most of the "classical moraxellae," the "false neisseriae," and B. catarrhalis, (ii) only Acinetobacter spp., (iii) M. nonliquefaciens and "misnamed moraxellae" (M. atlantae, M. osloensis, and M. phenylpyruvica), and (iv) the "true neisseriae," the three Kingella species, and O. urethralis. Fatty acids that distinguish these four classes were identified. The fatty acid profiles of the two strains of Psychrobacter immobilis which we studied are not very similar to the profiles of the other taxa. Our results support the hypothesis that the three species of "false neisseriae," B. catarrhalis, the "classical moraxellae," and Acinetobacter spp. should be included in the same family.

Draft Genome Sequences of Pseudomonas aeruginosa Isolates from Wounded Military Personnel.

PubMed

Arivett, Brock A; Ream, Dave C; Fiester, Steven E; Kidane, Destaalem; Actis, Luis A

2016-08-11

Pseudomonas aeruginosa, a Gram-negative bacterium that causes severe hospital-acquired infections, is grouped as an ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) pathogen because of its extensive drug resistance phenotypes and effects on human health worldwide. Five multidrug resistant P. aeruginosa strains isolated from wounded military personnel were sequenced and annotated in this work. Copyright © 2016 Arivett et al.

Development of a dry-reagent mix-based polymerase chain reaction as a novel tool for the identification of Acinetobacter species and its comparison with conventional polymerase chain reaction

PubMed Central

Kulkarni, Raghavendra D.; Mishra, Mukti Nath; Mohanraj, Jeevanandam; Chandrasekhar, Arun; Ajantha, G. S.; Kulkani, Sheetal; Bhat, Shama

2018-01-01

BACKGROUND: Nosocomial infections are often caused by multidrug-resistant bacteria and the incidence is increasing. Acinetobacter, a Gram-negative bacillus, is commonly associated with the use of intravascular catheterization and airway intubation. Polymerase chain reaction (PCR) for identification of Acinetobacter baumannii from samples has been standardized that use conventional wet-reagent mix. We have designed and optimized a dry-reagent mix for identification of Acinetobacter species by PCR. The dry-reagent mix can be stored at room temperature, has less chances of contamination, and thus can be used at point-of-care diagnosis. AIM AND OBJECTIVE: The present work was focused on comparing the sensitivity and specificity of dry-reagent PCR mix over conventional wet-reagent PCR mix for identification of Acinetobacter species. MATERIALS AND METHODS: Conventional wet-reagent mix based and dry-reagent mix based PCR were carried out for the DNA isolated from Acinetobacter species. The latter was also applied directly on bacterial growth without prior DNA extraction process. Equal numbers of bacterial isolates other than Acinetobacter species were also subjected to identification by the same protocols for determining the sensitivity and specificity of the test. RESULTS: The Acinetobacter species showed amplification of the target rpoB gene and the band was observed at 397 bp. The dry-reagent PCR mix results matched completely with the conventional wet-reagent PCR mix assay. All the non-Acinetobacter isolates were negative for the PCR. This indicates that the test is highly specific. The dry-reagent mix also contained an enzyme resistant to PCR inhibitors and capable of amplifying DNA directly from cells. CONCLUSION: Performance of dry-reagent PCR mix without the need for DNA extraction and preparation of a PCR mix proved to be more sensitive and reduce the handling error, minimizes the time, manual work, and skilled labor. PMID:29403209

Complete genome analysis of three Acinetobacter baumannii clinical isolates in China for insight into the diversification of drug resistance elements.

PubMed

Zhu, Lingxiang; Yan, Zhongqiang; Zhang, Zhaojun; Zhou, Qiming; Zhou, Jinchun; Wakeland, Edward K; Fang, Xiangdong; Xuan, Zhenyu; Shen, Dingxia; Li, Quan-Zhen

2013-01-01

The emergence and rapid spreading of multidrug-resistant Acinetobacter baumannii strains has become a major health threat worldwide. To better understand the genetic recombination related with the acquisition of drug-resistant elements during bacterial infection, we performed complete genome analysis on three newly isolated multidrug-resistant A. baumannii strains from Beijing using next-generation sequencing technology. Whole genome comparison revealed that all 3 strains share some common drug resistant elements including carbapenem-resistant bla OXA-23 and tetracycline (tet) resistance islands, but the genome structures are diversified among strains. Various genomic islands intersperse on the genome with transposons and insertions, reflecting the recombination flexibility during the acquisition of the resistant elements. The blood-isolated BJAB07104 and ascites-isolated BJAB0868 exhibit high similarity on their genome structure with most of the global clone II strains, suggesting these two strains belong to the dominant outbreak strains prevalent worldwide. A large resistance island (RI) of about 121-kb, carrying a cluster of resistance-related genes, was inserted into the ATPase gene on BJAB07104 and BJAB0868 genomes. A 78-kb insertion element carrying tra-locus and bla OXA-23 island, can be either inserted into one of the tniB gene in the 121-kb RI on the chromosome, or transformed to conjugative plasmid in the two BJAB strains. The third strains of this study, BJAB0715, which was isolated from spinal fluid, exhibit much more divergence compared with above two strains. It harbors multiple drug-resistance elements including a truncated AbaR-22-like RI on its genome. One of the unique features of this strain is that it carries both bla OXA-23 and bla OXA-58 genes on its genome. Besides, an Acinetobacter lwoffii adeABC efflux element was found inserted into the ATPase position in BJAB0715. Our comparative analysis on currently completed Acinetobacter baumannii genomes revealed extensive and dynamic genome organizations, which may facilitate the bacteria to acquire drug-resistance elements into their genomes.

Identification of antibiotic resistance genes in the multidrug-resistant Acinetobacter baumannii strain, MDR-SHH02, using whole-genome sequencing.

PubMed

Wang, Hualiang; Wang, Jinghua; Yu, Peijuan; Ge, Ping; Jiang, Yanqun; Xu, Rong; Chen, Rong; Liu, Xuejie

2017-02-01

This study aimed to investigate antibiotic resistance genes in the multidrug-resistant (MDR) Acinetobacter baumannii (A. baumanii) strain, MDR-SHH02, using whole‑genome sequencing (WGS). The antibiotic resistance of MDR-SHH02 isolated from a patient with breast cancer to 19 types of antibiotics was determined using the Kirby‑Bauer method. WGS of MDR-SHH02 was then performed. Following quality control and transcriptome assembly, functional annotation of genes was conducted, and the phylogenetic tree of MDR-SHH02, along with another 5 A. baumanii species and 2 Acinetobacter species, was constructed using PHYLIP 3.695 and FigTree v1.4.2. Furthermore, pathogenicity islands (PAIs) were predicted by the pathogenicity island database. Potential antibiotic resistance genes in MDR-SHH02 were predicted based on the information in the Antibiotic Resistance Genes Database (ARDB). MDR-SHH02 was found to be resistant to all of the tested antibiotics. The total draft genome length of MDR-SHH02 was 4,003,808 bp. There were 74.25% of coding sequences to be annotated into 21 of the Clusters of Orthologous Groups (COGs) of protein terms, such as 'transcription' and 'amino acid transport and metabolism'. Furthermore, there were 45 PAIs homologous to the sequence MDRSHH02000806. Additionally, a total of 12 gene sequences in MDR-SHH02 were highly similar to the sequences of antibiotic resistance genes in ARDB, including genes encoding aminoglycoside‑modifying enzymes [e.g., aac(3)-Ia, ant(2'')‑Ia, aph33ib and aph(3')-Ia], β-lactamase genes (bl2b_tem and bl2b_tem1), sulfonamide-resistant dihydropteroate synthase genes (sul1 and sul2), catb3 and tetb. These results suggest that numerous genes mediate resistance to various antibiotics in MDR-SHH02, and provide a clinical guidance for the personalized therapy of A. baumannii-infected patients.

Comparative genomics of multidrug resistance in Acinetobacter baumannii.

PubMed

Fournier, Pierre-Edouard; Vallenet, David; Barbe, Valérie; Audic, Stéphane; Ogata, Hiroyuki; Poirel, Laurent; Richet, Hervé; Robert, Catherine; Mangenot, Sophie; Abergel, Chantal; Nordmann, Patrice; Weissenbach, Jean; Raoult, Didier; Claverie, Jean-Michel

2006-01-01

Acinetobacter baumannii is a species of nonfermentative gram-negative bacteria commonly found in water and soil. This organism was susceptible to most antibiotics in the 1970s. It has now become a major cause of hospital-acquired infections worldwide due to its remarkable propensity to rapidly acquire resistance determinants to a wide range of antibacterial agents. Here we use a comparative genomic approach to identify the complete repertoire of resistance genes exhibited by the multidrug-resistant A. baumannii strain AYE, which is epidemic in France, as well as to investigate the mechanisms of their acquisition by comparison with the fully susceptible A. baumannii strain SDF, which is associated with human body lice. The assembly of the whole shotgun genome sequences of the strains AYE and SDF gave an estimated size of 3.9 and 3.2 Mb, respectively. A. baumannii strain AYE exhibits an 86-kb genomic region termed a resistance island--the largest identified to date--in which 45 resistance genes are clustered. At the homologous location, the SDF strain exhibits a 20 kb-genomic island flanked by transposases but devoid of resistance markers. Such a switching genomic structure might be a hotspot that could explain the rapid acquisition of resistance markers under antimicrobial pressure. Sequence similarity and phylogenetic analyses confirm that most of the resistance genes found in the A. baumannii strain AYE have been recently acquired from bacteria of the genera Pseudomonas, Salmonella, or Escherichia. This study also resulted in the discovery of 19 new putative resistance genes. Whole-genome sequencing appears to be a fast and efficient approach to the exhaustive identification of resistance genes in epidemic infectious agents of clinical significance.

A distinct alleles and genetic recombination of pmrCAB operon in species of Acinetobacter baumannii complex isolates.

PubMed

Kim, Dae Hun; Ko, Kwan Soo

2015-07-01

To investigate pmrCAB sequence divergence in 5 species of Acinetobacter baumannii complex, a total of 80 isolates from a Korean hospital were explored. We evaluated nucleotide and amino acid polymorphisms of pmrCAB operon, and phylogenetic trees were constructed for each gene of prmCAB operon. Colistin and polymyxin B susceptibility was determined for all isolates, and multilocus sequence typing was also performed for A. baumannii isolates. Our results showed that each species of A. baumannii complex has divergent pmrCAB operon sequences. We identified a distinct pmrCAB allele allied with Acinetobacter nosocomialis in gene trees. Different grouping in each gene tree suggests sporadic recombination or emergence of pmrCAB genes among Acinetobacter species. Sequence polymorphisms among Acinetobacter species might not be associated with colistin resistance. We revealed that a distinct pmrCAB allele may be widespread across the continents such as North America and Asia and that sporadic genetic recombination or emergence of pmrCAB genes might occur. Copyright © 2015 Elsevier Inc. All rights reserved.

Insight into Identification of Acinetobacter Species by Matrix-Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry (MALDI-TOF MS) in the Clinical Laboratory

NASA Astrophysics Data System (ADS)

Li, Xiuyuan; Tang, Yanyan; Lu, Xinxin

2018-04-01

Currently, the capability of identification for Acinetobacter species using MALDI-TOF MS still remains unclear in clinical laboratories due to certain elusory phenomena. Thus, we conducted this research to evaluate this technique and reveal the causes of misidentification. Briefly, a total of 788 Acinetobacter strains were collected and confirmed at the species level by 16S rDNA and rpoB sequencing, and subsequently compared to the identification by MALDI-TOF MS using direct smear and bacterial extraction pretreatments. Cluster analysis was performed based on the mass spectra and 16S rDNA to reflect the diversity among different species. Eventually, 19 Acinetobacter species were confirmed, including 6 species unavailable in Biotyper 3.0 database. Another novel species was observed, temporarily named A. corallinus. The accuracy of identification for Acinetobacter species using MALDI-TOF MS was 97.08% (765/788), regardless of which pretreatment was applied. The misidentification only occurred on 3 A. parvus strains and 20 strains of species unavailable in the database. The proportions of strains with identification score ≥ 2.000 using direct smear and bacterial extraction pretreatments were 86.04% (678/788) and 95.43% (752/788), χ 2 = 41.336, P < 0.001. The species similar in 16 rDNA were discriminative from the mass spectra, such as A. baumannii & A. junii, A. pittii & A. calcoaceticus, and A. nosocomialis & A. seifertii. Therefore, using MALDI-TOF MS to identify Acinetobacter strains isolated from clinical samples was deemed reliable. Misidentification occurred occasionally due to the insufficiency of the database rather than sample extraction failure. We suggest gene sequencing should be performed when the identification score is under 2.000 even when using bacterial extraction pretreatment. [Figure not available: see fulltext.

Insight into Identification of Acinetobacter Species by Matrix-Assisted Laser Desorption/Ionization Time of Flight Mass Spectrometry (MALDI-TOF MS) in the Clinical Laboratory.

PubMed

Li, Xiuyuan; Tang, Yanyan; Lu, Xinxin

2018-04-09

Currently, the capability of identification for Acinetobacter species using MALDI-TOF MS still remains unclear in clinical laboratories due to certain elusory phenomena. Thus, we conducted this research to evaluate this technique and reveal the causes of misidentification. Briefly, a total of 788 Acinetobacter strains were collected and confirmed at the species level by 16S rDNA and rpoB sequencing, and subsequently compared to the identification by MALDI-TOF MS using direct smear and bacterial extraction pretreatments. Cluster analysis was performed based on the mass spectra and 16S rDNA to reflect the diversity among different species. Eventually, 19 Acinetobacter species were confirmed, including 6 species unavailable in Biotyper 3.0 database. Another novel species was observed, temporarily named A. corallinus. The accuracy of identification for Acinetobacter species using MALDI-TOF MS was 97.08% (765/788), regardless of which pretreatment was applied. The misidentification only occurred on 3 A. parvus strains and 20 strains of species unavailable in the database. The proportions of strains with identification score ≥ 2.000 using direct smear and bacterial extraction pretreatments were 86.04% (678/788) and 95.43% (752/788), χ 2  = 41.336, P < 0.001. The species similar in 16 rDNA were discriminative from the mass spectra, such as A. baumannii & A. junii, A. pittii & A. calcoaceticus, and A. nosocomialis & A. seifertii. Therefore, using MALDI-TOF MS to identify Acinetobacter strains isolated from clinical samples was deemed reliable. Misidentification occurred occasionally due to the insufficiency of the database rather than sample extraction failure. We suggest gene sequencing should be performed when the identification score is under 2.000 even when using bacterial extraction pretreatment. Graphical Abstract ᅟ.

Acinetobacter phage genome is similar to Sphinx 2.36, the circular DNA copurified with TSE infected particles.

PubMed

Longkumer, Toshisangba; Kamireddy, Swetha; Muthyala, Venkateswar Reddy; Akbarpasha, Shaikh; Pitchika, Gopi Krishna; Kodetham, Gopinath; Ayaluru, Murali; Siddavattam, Dayananda

2013-01-01

While analyzing plasmids of Acinetobacter sp. DS002 we have detected a circular DNA molecule pTS236, which upon further investigation is identified as the genome of a phage. The phage genome has shown sequence similarity to the recently discovered Sphinx 2.36 DNA sequence co-purified with the Transmissible Spongiform Encephalopathy (TSE) particles isolated from infected brain samples collected from diverse geographical regions. As in Sphinx 2.36, the phage genome also codes for three proteins. One of them codes for RepA and is shown to be involved in replication of pTS236 through rolling circle (RC) mode. The other two translationally coupled ORFs, orf106 and orf96, code for coat proteins of the phage. Although an orf96 homologue was not previously reported in Sphinx 2.36, a closer examination of DNA sequence of Sphinx 2.36 revealed its presence downstream of orf106 homologue. TEM images and infection assays revealed existence of phage AbDs1 in Acinetobacter sp. DS002.

Acinetobacter phage genome is similar to Sphinx 2.36, the circular DNA copurified with TSE infected particles

PubMed Central

Longkumer, Toshisangba; Kamireddy, Swetha; Muthyala, Venkateswar Reddy; Akbarpasha, Shaikh; Pitchika, Gopi Krishna; Kodetham, Gopinath; Ayaluru, Murali; Siddavattam, Dayananda

2013-01-01

While analyzing plasmids of Acinetobacter sp. DS002 we have detected a circular DNA molecule pTS236, which upon further investigation is identified as the genome of a phage. The phage genome has shown sequence similarity to the recently discovered Sphinx 2.36 DNA sequence co-purified with the Transmissible Spongiform Encephalopathy (TSE) particles isolated from infected brain samples collected from diverse geographical regions. As in Sphinx 2.36, the phage genome also codes for three proteins. One of them codes for RepA and is shown to be involved in replication of pTS236 through rolling circle (RC) mode. The other two translationally coupled ORFs, orf106 and orf96, code for coat proteins of the phage. Although an orf96 homologue was not previously reported in Sphinx 2.36, a closer examination of DNA sequence of Sphinx 2.36 revealed its presence downstream of orf106 homologue. TEM images and infection assays revealed existence of phage AbDs1 in Acinetobacter sp. DS002. PMID:23867905

Draft Genome Sequence of Acinetobacter oleivorans PF1, a Diesel-Degrading and Plant-Growth-Promoting Endophytic Strain Isolated from Poplar Trees Growing on a Diesel-Contaminated Plume.

PubMed

Gkorezis, Panagiotis; Rineau, Francois; Van Hamme, Jonathan; Franzetti, Andrea; Daghio, Matteo; Thijs, Sofie; Weyens, Nele; Vangronsveld, Jaco

2015-02-05

We report the 3.7-Mb draft genome of Acinetobacter oleivorans strain PF1, a hydrocarbonoclastic Gram-negative bacterium in the class Gammaproteobacteria, isolated from poplar trees growing on a diesel-contaminated plume at the Ford Motor Company site in Genk, Belgium. Strain PF1 is a potent plant-growth promoter, useful for diesel fuel phytoremediation applications. Copyright © 2015 Gkorezis et al.

Genomic and proteomic evidences unravel the UV-resistome of the poly-extremophile Acinetobacter sp. Ver3

PubMed Central

Kurth, Daniel; Belfiore, Carolina; Gorriti, Marta F.; Cortez, Néstor; Farias, María E.; Albarracín, Virginia H.

2015-01-01

Ultraviolet radiation can damage biomolecules, with detrimental or even lethal effects for life. Even though lower wavelengths are filtered by the ozone layer, a significant amount of harmful UV-B and UV-A radiation reach Earth’s surface, particularly in high altitude environments. high-altitude Andean lakes (HAALs) are a group of disperse shallow lakes and salterns, located at the Dry Central Andes region in South America at altitudes above 3,000 m. As it is considered one of the highest UV-exposed environments, HAAL microbes constitute model systems to study UV-resistance mechanisms in environmental bacteria at various complexity levels. Herein, we present the genome sequence of Acinetobacter sp. Ver3, a gammaproteobacterium isolated from Lake Verde (4,400 m), together with further experimental evidence supporting the phenomenological observations regarding this bacterium ability to cope with increased UV-induced DNA damage. Comparison with the genomes of other Acinetobacter strains highlighted a number of unique genes, such as a novel cryptochrome. Proteomic profiling of UV-exposed cells identified up-regulated proteins such as a specific cytoplasmic catalase, a putative regulator, and proteins associated to amino acid and protein synthesis. Down-regulated proteins were related to several energy-generating pathways such as glycolysis, beta-oxidation of fatty acids, and electronic respiratory chain. To the best of our knowledge, this is the first report on a genome from a polyextremophilic Acinetobacter strain. From the genomic and proteomic data, an “UV-resistome” was defined, encompassing the genes that would support the outstanding UV-resistance of this strain. PMID:25954258

Genomic and proteomic evidences unravel the UV-resistome of the poly-extremophile Acinetobacter sp. Ver3.

PubMed

Kurth, Daniel; Belfiore, Carolina; Gorriti, Marta F; Cortez, Néstor; Farias, María E; Albarracín, Virginia H

2015-01-01

Ultraviolet radiation can damage biomolecules, with detrimental or even lethal effects for life. Even though lower wavelengths are filtered by the ozone layer, a significant amount of harmful UV-B and UV-A radiation reach Earth's surface, particularly in high altitude environments. high-altitude Andean lakes (HAALs) are a group of disperse shallow lakes and salterns, located at the Dry Central Andes region in South America at altitudes above 3,000 m. As it is considered one of the highest UV-exposed environments, HAAL microbes constitute model systems to study UV-resistance mechanisms in environmental bacteria at various complexity levels. Herein, we present the genome sequence of Acinetobacter sp. Ver3, a gammaproteobacterium isolated from Lake Verde (4,400 m), together with further experimental evidence supporting the phenomenological observations regarding this bacterium ability to cope with increased UV-induced DNA damage. Comparison with the genomes of other Acinetobacter strains highlighted a number of unique genes, such as a novel cryptochrome. Proteomic profiling of UV-exposed cells identified up-regulated proteins such as a specific cytoplasmic catalase, a putative regulator, and proteins associated to amino acid and protein synthesis. Down-regulated proteins were related to several energy-generating pathways such as glycolysis, beta-oxidation of fatty acids, and electronic respiratory chain. To the best of our knowledge, this is the first report on a genome from a polyextremophilic Acinetobacter strain. From the genomic and proteomic data, an "UV-resistome" was defined, encompassing the genes that would support the outstanding UV-resistance of this strain.

Acinetobacter bacteraemia in Thailand: evidence for infections outside the hospital setting

PubMed Central

PORTER, K. A.; RHODES, J.; DEJSIRILERT, S.; HENCHAICHON, S.; SILUDJAI, D.; THAMTHITIWAT, S.; PRAPASIRI, P.; JORAKATE, P.; KAEWPAN, A.; PERUSKI, L. F.; KERDSIN, A.; PRASERT, K.; YUENPRAKONE, S.; MALONEY, S. A.; BAGGETT, H. C.

2015-01-01

SUMMARY Acinetobacter is a well-recognized nosocomial pathogen. Previous reports of community-associated Acinetobacter infections have lacked clear case definitions and assessment of healthcare-associated (HCA) risk factors. We identified Acinetobacter bacteraemia cases from blood cultures obtained <3 days after hospitalization in rural Thailand and performed medical record reviews to assess HCA risk factors in the previous year and compare clinical and microbiological characteristics between cases with and without HCA risk factors. Of 72 Acinetobacter cases, 32 (44%) had no HCA risk factors. Compared to HCA infections, non-HCA infections were more often caused by Acinetobacter species other than calcoaceticus–baumannii complex species and by antibiotic-susceptible organisms. Despite similar symptoms, the case-fatality proportion was lower in non-HCA than HCA cases (9% vs. 45%, P < 0·01). Clinicians should be aware of Acinetobacter as a potential cause of community-associated infections in Thailand; prospective studies are needed to improve understanding of associated risk factors and disease burden. PMID:24001479

Acinetobacter spp. Infections in Malaysia: A Review of Antimicrobial Resistance Trends, Mechanisms and Epidemiology

PubMed Central

Mohd. Rani, Farahiyah; A. Rahman, Nor Iza; Ismail, Salwani; Alattraqchi, Ahmed Ghazi; Cleary, David W.; Clarke, Stuart C.; Yeo, Chew Chieng

2017-01-01

Acinetobacter spp. are important nosocomial pathogens, in particular the Acinetobacter baumannii-calcoaceticus complex, which have become a global public health threat due to increasing resistance to carbapenems and almost all other antimicrobial compounds. High rates of resistance have been reported among countries in Southeast Asia, including Malaysia. In this review, we examine the antimicrobial resistance profiles of Acinetobacter spp. hospital isolates from Malaysia over a period of nearly three decades (1987–2016) with data obtained from various peer-reviewed publications as well as the Malaysian National Surveillance on Antibiotic Resistance (NSAR). NSAR data indicated that for most antimicrobial compounds, including carbapenems, the peak resistance rates were reached around 2008–2009 and thereafter, rates have remained fairly constant (e.g., 50–60% for carbapenems). Individual reports from various hospitals in Peninsular Malaysia do not always reflect the nationwide resistance rates and often showed higher rates of resistance. We also reviewed the epidemiology and mechanisms of resistance that have been investigated in Malaysian Acinetobacter spp. isolates, particularly carbapenem resistance and found that blaOXA-23 is the most prevalent acquired carbapenemase-encoding gene. From the very few published reports and whole genome sequences that are available, most of the Acinetobacter spp. isolates from Malaysia belonged to the Global Clone 2 (GC2) CC92 group with ST195 being the predominant sequence type. The quality of data and analysis in the national surveillance reports could be improved and more molecular epidemiology and genomics studies need to be carried out for further in-depth understanding of Malaysian Acinetobacter spp. isolates. PMID:29312188

Acinetobacter spp. Infections in Malaysia: A Review of Antimicrobial Resistance Trends, Mechanisms and Epidemiology.

PubMed

Mohd Rani, Farahiyah; A Rahman, Nor Iza; Ismail, Salwani; Alattraqchi, Ahmed Ghazi; Cleary, David W; Clarke, Stuart C; Yeo, Chew Chieng

2017-01-01

Acinetobacter spp. are important nosocomial pathogens, in particular the Acinetobacter baumannii - calcoaceticus complex, which have become a global public health threat due to increasing resistance to carbapenems and almost all other antimicrobial compounds. High rates of resistance have been reported among countries in Southeast Asia, including Malaysia. In this review, we examine the antimicrobial resistance profiles of Acinetobacter spp. hospital isolates from Malaysia over a period of nearly three decades (1987-2016) with data obtained from various peer-reviewed publications as well as the Malaysian National Surveillance on Antibiotic Resistance (NSAR). NSAR data indicated that for most antimicrobial compounds, including carbapenems, the peak resistance rates were reached around 2008-2009 and thereafter, rates have remained fairly constant (e.g., 50-60% for carbapenems). Individual reports from various hospitals in Peninsular Malaysia do not always reflect the nationwide resistance rates and often showed higher rates of resistance. We also reviewed the epidemiology and mechanisms of resistance that have been investigated in Malaysian Acinetobacter spp. isolates, particularly carbapenem resistance and found that bla OXA-23 is the most prevalent acquired carbapenemase-encoding gene. From the very few published reports and whole genome sequences that are available, most of the Acinetobacter spp. isolates from Malaysia belonged to the Global Clone 2 (GC2) CC92 group with ST195 being the predominant sequence type. The quality of data and analysis in the national surveillance reports could be improved and more molecular epidemiology and genomics studies need to be carried out for further in-depth understanding of Malaysian Acinetobacter spp. isolates.

Homologs of the Acinetobacter baumannii AceI transporter represent a new family of bacterial multidrug efflux systems.

PubMed

Hassan, Karl A; Liu, Qi; Henderson, Peter J F; Paulsen, Ian T

2015-02-10

Multidrug efflux systems are a major cause of resistance to antimicrobials in bacteria, including those pathogenic to humans, animals, and plants. These proteins are ubiquitous in these pathogens, and five families of bacterial multidrug efflux systems have been identified to date. By using transcriptomic and biochemical analyses, we recently identified the novel AceI (Acinetobacter chlorhexidine efflux) protein from Acinetobacter baumannii that conferred resistance to the biocide chlorhexidine, via an active efflux mechanism. Proteins homologous to AceI are encoded in the genomes of many other bacterial species and are particularly prominent within proteobacterial lineages. In this study, we expressed 23 homologs of AceI and examined their resistance and/or transport profiles. MIC analyses demonstrated that, like AceI, many of the homologs conferred resistance to chlorhexidine. Many of the AceI homologs conferred resistance to additional biocides, including benzalkonium, dequalinium, proflavine, and acriflavine. We conducted fluorimetric transport assays using the AceI homolog from Vibrio parahaemolyticus and confirmed that resistance to both proflavine and acriflavine was mediated by an active efflux mechanism. These results show that this group of AceI homologs represent a new family of bacterial multidrug efflux pumps, which we have designated the proteobacterial antimicrobial compound efflux (PACE) family of transport proteins. Bacterial multidrug efflux pumps are an important class of resistance determinants that can be found in every bacterial genome sequenced to date. These transport proteins have important protective functions for the bacterial cell but are a significant problem in the clinical setting, since a single efflux system can mediate resistance to many structurally and mechanistically diverse antibiotics and biocides. In this study, we demonstrate that proteins related to the Acinetobacter baumannii AceI transporter are a new class of multidrug efflux systems which are very common in Proteobacteria: the proteobacterial antimicrobial compound efflux (PACE) family. This is the first new family of multidrug efflux pumps to be described in 15 years. Copyright © 2015 Hassan et al.

Acinetobacter kookii sp. nov., isolated from soil.

PubMed

Choi, Ji Young; Ko, Gwangpyo; Jheong, Weonghwa; Huys, Geert; Seifert, Harald; Dijkshoorn, Lenie; Ko, Kwan Soo

2013-12-01

Two Gram-stain-negative, non-fermentative bacterial strains, designated 11-0202(T) and 11-0607, were isolated from soil in South Korea, and four others, LUH 13522, LUH 8638, LUH 10268 and LUH 10288, were isolated from a beet field in Germany, soil in the Netherlands, and sediment of integrated fish farms in Malaysia and Thailand, respectively. Based on 16S rRNA, rpoB and gyrB gene sequences, they are considered to represent a novel species of the genus Acinetobacter. Their 16S rRNA gene sequences showed greatest pairwise similarity to Acinetobacter beijerinckii NIPH 838(T) (97.9-98.4 %). They shared highest rpoB and gyrB gene sequence similarity with Acinetobacter johnsonii DSM 6963(T) and Acinetobacter bouvetii 4B02(T) (85.4-87.6 and 78.1-82.7 %, respectively). Strain 11-0202(T) displayed low DNA-DNA reassociation values (<40 %) with the most closely related species of the genus Acinetobacter. The six strains utilized azelate, 2,3-butanediol, ethanol and dl-lactate as sole carbon sources. Cellular fatty acid analyses showed similarities to profiles of related species of the genus Acinetobacter: summed feature 3 (C16 : 1ω7c, C16 : 1ω6c; 24.3-27.2 %), C18 : 1ω9c (19.9-22.1 %), C16 : 0 (15.2-22.0 %) and C12 : 0 (9.2-14.2 %). On the basis of the current findings, it is concluded that the six strains represent a novel species, for which the name Acinetobacter kookii sp. nov. is proposed. The type strain is 11-0202(T) ( = KCTC 32033(T) = JCM 18512(T)).

Isolation and identification of Acinetobacter spp. from healthy canine skin.

PubMed

Mitchell, Kayleigh E; Turton, Jane F; Lloyd, David H

2018-06-01

Acinetobacter species can exhibit widespread resistance to antimicrobial agents. They are already recognized as important nosocomial pathogens of humans, but are becoming increasingly recognized in opportunistic infections of animals. This study aimed to determine whether Acinetobacter spp. are carried on skin of healthy dogs and, if present, to identify the species. Forty dogs were sampled at veterinary practices and rescue centres. They were free from skin disease and receiving no systemic or topical treatments. Skin swab samples were collected from four sites on each dog and cultured. Acinetobacter spp. isolates were detected by biochemical tests and gas chromatography. The species was determined by sequencing the RNA polymerase β-subunit (rpoB) gene. Isolates were screened for OXA carbapenemase genes and class 1 integrons capable of carrying resistance genes, and subjected to antimicrobial susceptibility tests. For 25% dogs sampled (10 of 40), Acinetobacter spp. were isolated at one or more skin sites. Thirteen Acinetobacter spp. isolates were recovered from 160 samples. The most frequently cultured was A. lwoffii (seven of 13), followed by A. baumannii (two of 13), A. junii (one of 13), A. calcoaceticus (one of 13), A. pittii (one of 13) and a novel Acinetobacter species (one of 13). Class 1 integrons and bla OXA -23-like were not detected. Isolates were susceptible to most antibiotics. The study confirms that Acinetobacter spp. can survive on canine skin, where they may be potential reservoirs for infection. This highlights the importance of good hygiene in veterinary practice, adhering to aseptic principles in surgery, and treatment based on culture and susceptibility testing where possible. © 2018 ESVD and ACVD.

Bioinformatic analysis of phage AB3, a phiKMV-like virus infecting Acinetobacter baumannii.

PubMed

Zhang, J; Liu, X; Li, X-J

2015-01-16

The phages of Acinetobacter baumannii has drawn increasing attention because of the multi-drug resistance of A. baumanni. The aim of this study was to sequence Acinetobacter baumannii phage AB3 and conduct bioinformatic analysis to lay a foundation for genome remodeling and phage therapy. We isolated and sequenced A. baumannii phage AB3 and attempted to annotate and analyze its genome. The results showed that the genome is a double-stranded DNA with a total length of 31,185 base pairs (bp) and 97 open reading frames greater than 100 bp. The genome includes 28 predicted genes, of which 24 are homologous to phage AB1. The entire coding sequence is located on the negative strand, representing 90.8% of the total length. The G+C mol% was 39.18%, without areas of high G+C content over 200 bp in length. No GC island, tRNA gene, or repeated sequence was identified. Gene lengths were 120-3099 bp, with an average of 1011 bp. Six genes were found to be greater than 2000 bp in length. Genomic alignment and phylogenetic analysis of the RNA polymerase gene showed that similar to phage AB1, phage AB3 is a phiKMV-like virus in the T7 phage family.

Nanoparticles for Control of Biofilms of Acinetobacter Species

PubMed Central

Singh, Richa; Nadhe, Shradhda; Wadhwani, Sweety; Shedbalkar, Utkarsha; Chopade, Balu Ananda

2016-01-01

Biofilms are the cause of 80% of microbial infections. Acinetobacter species have emerged as multi- and pan-drug-resistant bacteria and pose a great threat to human health. These act as nosocomial pathogens and form excellent biofilms, both on biotic and abiotic surfaces, leading to severe infections and diseases. Various methods have been developed for treatment and control of Acinetobacter biofilm including photodynamic therapy, radioimmunotherapy, prophylactic vaccines and antimicrobial peptides. Nanotechnology, in the present scenario, offers a promising alternative. Nanomaterials possess unique properties, and multiple bactericidal mechanisms render them more effective than conventional drugs. This review intends to provide an overview of Acinetobacter biofilm and the significant role of various nanoparticles as anti-biofouling agents, surface-coating materials and drug-delivery vehicles for biofilm control and treatment of Acinetobacter infections. PMID:28773507

Characteristics of invasive Acinetobacter species isolates recovered in a pediatric academic center.

PubMed

Jain, Avish L; Harding, Christian M; Assani, Kaivon; Shrestha, Chandra L; Haga, Mercedees; Leber, Amy; Munson, Robert S; Kopp, Benjamin T

2016-07-22

Acinetobacter species are associated with increasing mortality due to emerging drug-resistance. Pediatric Acinetobacter infections are largely undefined in developed countries and clinical laboratory identification methods do not reliably differentiate between members of the Acinetobacter calcoaceticus-baumannii complex, leading to improper identification. Therefore we aimed to determine risk factors for invasive Acinetobacter infections within an academic, pediatric setting as well as defining microbiologic characteristics of predominant strains. Twenty-four invasive Acinetobacter isolates were collected from 2009-2013. Comparative sequence analysis of the rpoB gene was performed coupled with phenotypic characterization of antibiotic resistance, motility, biofilm production and clinical correlation. Affected patients had a median age of 3.5 years, and 71 % had a central catheter infection source. rpoB gene sequencing revealed a predominance of A. pittii (45.8 %) and A. baumannii (33.3 %) strains. There was increasing incidence of A. pittii over the study. Two fatalities occurred in the A. pittii group. Seventeen percent of isolates were multi-drug resistant. A pittii and A. baumannii strains were similar in motility, but A pittii strains had significantly more biofilm production (P value = 0.018). A. pittii was the most isolated species highlighting the need for proper species identification. The isolated strains had limited acute mortality in children, but the occurrence of more multi-drug resistant strains in the future is a distinct possibility, justifying continued research and accurate species identification.

Acinetobacter species as model microorganisms in environmental microbiology: current state and perspectives.

PubMed

Jung, Jaejoon; Park, Woojun

2015-03-01

Acinetobacter occupies an important position in nature because of its ubiquitous presence in diverse environments such as soils, fresh water, oceans, sediments, and contaminated sites. Versatile metabolic characteristics allow species of this genus to catabolize a wide range of natural compounds, implying active participation in the nutrient cycle in the ecosystem. On the other hand, multi-drug-resistant Acinetobacter baumannii causing nosocomial infections with high mortality has been raising serious concerns in medicine. Due to the ecological and clinical importance of the genus, Acinetobacter was proposed as a model microorganism for environmental microbiological studies, pathogenicity tests, and industrial production of chemicals. For these reasons, Acinetobacter has attracted significant attention in scientific and biotechnological fields, but only limited research areas such as natural transformation and aromatic compound degradation have been intensively investigated, while important physiological characteristics including quorum sensing, motility, and stress response have been neglected. The aim of this review is to summarize the recent achievements in Acinetobacter research with a special focus on strain DR1 and to compare the similarities and differences between species or other genera. Research areas that require more attention in future research are also suggested.

Characterization of multidrug-resistant Acinetobacter ssp. strains isolated from medical intensive care units in Cali - Colombia.

PubMed Central

Castillo, Andres; Chávez-Vivas, Mónica

2017-01-01

Abstract Introduction: The extensive use of antibiotics has led to the emergence of multi-resistant strains in some species of the genus Acinetobacter. Objective: To investigate the molecular characteristics of multidrug-resistant of Acinetobacter ssp. strains isolated from 52 patients collected between March 2009 and July 2010 in medical intensive care units in Cali - Colombia. Methods: The susceptibility to various classes of antibiotics was determined by disc diffusion method, and the determination of the genomic species was carried out using amplified ribosomal DNA restriction analysis (ARDRA) and by sequencing of the 16s rDNA gene. Also, the genes of beta-lactamases as well as, integrases IntI1 and IntI2 were analyzed by PCR method. Results: The phenotypic identification showed that the isolates belong mainly to A. calcoaceticus- A. baumannii complex. All of them were multi-resistant to almost the whole antibiotics except to tigecycline and sulperazon, and they were grouped into five (I to V) different antibiotypes, being the antibiotype I the most common (50.0%). The percent of beta-lactamases detected was: blaTEM (17.3%), blaCTX-M (9.6%), blaVIM (21.2%), blaIMP (7.7%), blaOXA-58 (21.2%), and blaOXA-51 (21.2%). The phylogenetic tree analysis showed that the isolates were clustering to A. baumannii (74.1%), A. nosocomialis (11.1%) and A. calcoaceticus (7.4 %). Besides, the integron class 1 and class 2 were detected in 23.1% and 17.3% respectively. Conclusion: The isolates were identified to species A. baumanii mainly, and they were multiresistant. The resistance to beta-lactams may be by for presence of beta-lactamases in the majority of the isolates. PMID:29662260

Diversity and clinical impact of Acinetobacter baumannii colonization and infection at a military medical center.

PubMed

Petersen, Kyle; Cannegieter, Suzanne C; van der Reijden, Tanny J; van Strijen, Beppie; You, David M; Babel, Britta S; Philip, Andrew I; Dijkshoorn, Lenie

2011-01-01

The epidemiology of Acinetobacter baumannii emerging in combat casualties is poorly understood. We analyzed 65 (54 nonreplicate) Acinetobacter isolates from 48 patients (46 hospitalized and 2 outpatient trainees entering the military) from October 2004 to October 2005 for genotypic similarities, time-space relatedness, and antibiotic susceptibility. Clinical and surveillance cultures were compared by amplified fragment length polymorphism (AFLP) genomic fingerprinting to each other and to strains of a reference database. Antibiotic susceptibility was determined, and multiplex PCR was performed for OXA-23-like, -24-like, -51-like, and -58-like carbapenemases. Records were reviewed for overlapping hospital stays of the most frequent genotypes, and risk ratios were calculated for any association of genotype with severity of Acute Physiology and Chronic Health Evaluation II (APACHE II) score or injury severity score (ISS) and previous antibiotic use. Nineteen genotypes were identified; two predominated, one consistent with an emerging novel international clone and the other unique to our database. Both predominant genotypes were carbapenem resistant, were present at another hospital before patients' admission to our facility, and were associated with higher APACHE II scores, higher ISSs, and previous carbapenem antibiotics in comparison with other genotypes. One predominated in wound and respiratory isolates, and the other predominated in wound and skin surveillance samples. Several other genotypes were identified as European clones I to III. Acinetobacter genotypes from recruits upon entry to the military, unlike those in hospitalized patients, did not include carbapenem-resistant genotypes. Acinetobacter species isolated from battlefield casualties are diverse, including genotypes belonging to European clones I to III. Two carbapenem-resistant genotypes were epidemic, one of which appeared to belong to a novel international clone.

Genome shuffling improves production of the low-temperature alkalophilic lipase by Acinetobacter johnsonii.

PubMed

Wang, HaiKuan; Zhang, Jie; Wang, XiaoJie; Qi, Wei; Dai, YuJie

2012-01-01

The production of a low-temperature alkalophilic lipase from Acinetobacter johnsonii was improved using genome shuffling. The starting populations, obtained by UV irradiation and diethyl sulfate mutagenesis, were subjected to recursive protoplast fusion. The optimal conditions for protoplast formation and regeneration were 0.15 mg lysozyme/ml for 45 min at 37°C. The protoplasts were inactivated under UV for 20 min or heated at 60°C for 60 min and a fusant probability of ~98% was observed. The positive colonies were created by fusing the inactivated protoplasts. After two rounds of genome shuffling, one strain, F22, with a lipase activity of 7 U/ml was obtained.

Improvement of MALDI-TOF MS profiling for the differentiation of species within the Acinetobacter calcoaceticus-Acinetobacter baumannii complex.

PubMed

Šedo, Ondrej; Nemec, Alexandr; Křížová, Lenka; Kačalová, Magdaléna; Zdráhal, Zbyněk

2013-12-01

MALDI-TOF MS is currently becoming the method of choice for rapid identification of bacterial species in routine diagnostics. Yet, this method suffers from the inability to differentiate reliably between some closely related bacterial species including those of the Acinetobacter calcoaceticus-Acinetobacter baumannii (ACB) complex, namely A. baumannii and Acinetobacter nosocomialis. In the present study, we evaluated a protocol which was different from that used in the Bruker Daltonics identification system (MALDI BioTyper) to improve species identification using a taxonomically precisely defined set of 105 strains representing the four validly named species of the ACB complex. The novel protocol is based on the change in matrix composition from alpha-cyano-4-hydroxycinnamic acid (saturated solution in water:acetonitrile:trifluoroacetic acid, 47.5:50:2.5, v/v) to ferulic acid (12.5mgml(-1) solution in water:acetonitrile:formic acid 50:33:17, v/v), while the other steps of sample processing remain unchanged. Compared to the standard protocol, the novel one extended the range of detected compounds towards higher molecular weight, produced signals with better mass resolution, and allowed the detection of species-specific signals. As a result, differentiation of A. nosocomialis and A. baumannii strains by cluster analysis was improved and 13 A. nosocomialis strains, assigned erroneously or ambiguously by using the standard protocol, were correctly identified. Copyright © 2013 Elsevier GmbH. All rights reserved.

Molecular Survey of Head and Body Lice, Pediculus humanus, in France.

PubMed

Candy, Kerdalidec; Amanzougaghene, Nadia; Izri, Arezki; Brun, Sophie; Durand, Rémy; Louni, Meriem; Raoult, Didier; Fenollar, Florence; Mediannikov, Oleg

2018-05-01

Human lice, Pediculus humanus, are obligate blood-sucking parasites. Phylogenetically, they belong to several mitochondrial clades exhibiting some geographic differences. Currently, the body louse is the only recognized disease vector, with the head louse being proposed as an additional vector. In this article, we study the genetic diversity of head and body lice collected from Bobigny, a town located close to Paris (France), and look for louse-borne pathogens. By amplifying and sequencing the cytb gene, we confirmed the presence of clades A and B in France. Besides, by amplifying and sequencing both cytb and cox1 gene, we reported, for the first time, the presence of clade E, which has thus far only been found in lice from West Africa. DNA from Bartonella quintana was detected in 16.7% of body lice from homeless individuals, but in none of the head lice collected from 47 families. Acinetobacter DNA was detected in 11.5% of head lice belonging to all three clades and 29.1% of body lice. Six species of Acinetobacter were identified, including two potential new ones. Acinetobacter baumannii was the most prevalent, followed by Candidatus Acinetobacter Bobigny-1, Acinetobacter calcoaceticus, Acinetobacter nosocomialis, Acinetobacter junii, and Candidatus Acinetobacter Bobigny-2. Body lice were found to be infected only with A. baumannii. These findings show for the first time, the presence of clade E head lice in France. This study is also the first to report the presence of DNAs of several species of Acinetobacter in human head lice in France.

Nosocomial infections due to Acinetobacter calcoaceticus.

PubMed

Zaer, F; Deodhar, L

1989-01-01

Fifty four isolates of Acinetobacter calcoaceticus were studied in a period of 6 months. Maximum isolates were from burns cases and environmental sampling from burns ward also grew the same organism, indicating their role as nosocomial pathogen. Acinetobacter may initially be mistaken for Neisseria species. As the organisms show multidrug resistance to commonly used antibiotics their correct identification is important.

Resources for Genetic and Genomic Analysis of Emerging Pathogen Acinetobacter baumannii

PubMed Central

Ramage, Elizabeth; Weiss, Eli J.; Radey, Matthew; Hayden, Hillary S.; Held, Kiara G.; Huse, Holly K.; Zurawski, Daniel V.; Brittnacher, Mitchell J.; Manoil, Colin

2015-01-01

ABSTRACT Acinetobacter baumannii is a Gram-negative bacterial pathogen notorious for causing serious nosocomial infections that resist antibiotic therapy. Research to identify factors responsible for the pathogen's success has been limited by the resources available for genome-scale experimental studies. This report describes the development of several such resources for A. baumannii strain AB5075, a recently characterized wound isolate that is multidrug resistant and displays robust virulence in animal models. We report the completion and annotation of the genome sequence, the construction of a comprehensive ordered transposon mutant library, the extension of high-coverage transposon mutant pool sequencing (Tn-seq) to the strain, and the identification of the genes essential for growth on nutrient-rich agar. These resources should facilitate large-scale genetic analysis of virulence, resistance, and other clinically relevant traits that make A. baumannii a formidable public health threat. IMPORTANCE Acinetobacter baumannii is one of six bacterial pathogens primarily responsible for antibiotic-resistant infections that have become the scourge of health care facilities worldwide. Eliminating such infections requires a deeper understanding of the factors that enable the pathogen to persist in hospital environments, establish infections, and resist antibiotics. We present a set of resources that should accelerate genome-scale genetic characterization of these traits for a reference isolate of A. baumannii that is highly virulent and representative of current outbreak strains. PMID:25845845

iCN718, an Updated and Improved Genome-Scale Metabolic Network Reconstruction of Acinetobacter baumannii AYE.

PubMed

Norsigian, Charles J; Kavvas, Erol; Seif, Yara; Palsson, Bernhard O; Monk, Jonathan M

2018-01-01

Acinetobacter baumannii has become an urgent clinical threat due to the recent emergence of multi-drug resistant strains. There is thus a significant need to discover new therapeutic targets in this organism. One means for doing so is through the use of high-quality genome-scale reconstructions. Well-curated and accurate genome-scale models (GEMs) of A. baumannii would be useful for improving treatment options. We present an updated and improved genome-scale reconstruction of A. baumannii AYE, named iCN718, that improves and standardizes previous A. baumannii AYE reconstructions. iCN718 has 80% accuracy for predicting gene essentiality data and additionally can predict large-scale phenotypic data with as much as 89% accuracy, a new capability for an A. baumannii reconstruction. We further demonstrate that iCN718 can be used to analyze conserved metabolic functions in the A. baumannii core genome and to build strain-specific GEMs of 74 other A. baumannii strains from genome sequence alone. iCN718 will serve as a resource to integrate and synthesize new experimental data being generated for this urgent threat pathogen.

Clinical and Pathophysiological Overview of Acinetobacter Infections: a Century of Challenges

PubMed Central

Nielsen, Travis B.; Bonomo, Robert A.; Pantapalangkoor, Paul; Luna, Brian; Spellberg, Brad

2016-01-01

SUMMARY Acinetobacter is a complex genus, and historically, there has been confusion about the existence of multiple species. The species commonly cause nosocomial infections, predominantly aspiration pneumonia and catheter-associated bacteremia, but can also cause soft tissue and urinary tract infections. Community-acquired infections by Acinetobacter spp. are increasingly reported. Transmission of Acinetobacter and subsequent disease is facilitated by the organism's environmental tenacity, resistance to desiccation, and evasion of host immunity. The virulence properties demonstrated by Acinetobacter spp. primarily stem from evasion of rapid clearance by the innate immune system, effectively enabling high bacterial density that triggers lipopolysaccharide (LPS)–Toll-like receptor 4 (TLR4)-mediated sepsis. Capsular polysaccharide is a critical virulence factor that enables immune evasion, while LPS triggers septic shock. However, the primary driver of clinical outcome is antibiotic resistance. Administration of initially effective therapy is key to improving survival, reducing 30-day mortality threefold. Regrettably, due to the high frequency of this organism having an extreme drug resistance (XDR) phenotype, early initiation of effective therapy is a major clinical challenge. Given its high rate of antibiotic resistance and abysmal outcomes (up to 70% mortality rate from infections caused by XDR strains in some case series), new preventative and therapeutic options for Acinetobacter spp. are desperately needed. PMID:27974412

Acinetobacter Species Infections Among Navy and Marine Corps Beneficiaries: 2013 Annual Report

DTIC Science & Technology

2014-11-19

cases in 2013, DON providers most commonly prescribed colistin, minocycline , piperacillin/tazobactam, and trimethoprim/sulfamethoxazole. DOD...administration route, the following antibiotics were all equally common in the DON for resistant Acinetobacter cases: colistin, minocycline , piperacillin

Occurrence of bla genes encoding carbapenem-resistant Pseudomonas aeruginosa and Acinetobacter baumannii from Intensive Care Unit in a tertiary care hospital.

PubMed

Subramaniyan, Jayanthi Siva; Sundaram, Jeya Meenakshi

2018-01-01

ICU shows increasing incidence of infection associated with the use of invasive procedures for the diagnostic purpose as well as the indiscriminate use of antibiotics. Pseudomonas aeruginosa and Acinetobacter species are "very successful" pathogen and the emergence of the Metallo-β-Lactamases (MBL) is becoming a therapeutic challenge. To isolate the Nonfermenting Gram negative bacilli from the ICU samples. To identify the metallo betalactamase producers and to detect the bla gene presence among the Pseudomonas aeruginosa and Acinetobacter baumannii . The Nonfermenting Gram negative bacilli isolates from the ICU samples were taken over for 5 years (2009-2014) in a tertiary care hospital. The isolates of Pseudomonas species and Acinetobacter species were confirmed by API analyser and processed according to standard procedures. Detection of the MBL producers were done by E strip method and subjected for bla gene detection by PCR method. In our study a total of 195 isolates of NFGNB were obtained from various ICU. Of these MBL producers, 26 % were Pseudomonas aeruginosa and 25 % were Acinetobacter baumannii . The subtypes of bla VIM MBL producing P.aeruginosa were 26%. The predominant gene coding for MBL activity in A.baumannii were found to be bla OXA gene 11.9%. The gene accession numbers were KF975367, KF975372. We have to control the development and dissemination of these superbugs among the ICU's.

Complement deficiency predisposes for meningitis due to nongroupable meningococci and Neisseria-related bacteria.

PubMed

Fijen, C A; Kuijper, E J; Tjia, H G; Daha, M R; Dankert, J

1994-05-01

Nongroupable meningococci or bacteria related to the genus Neisseria rarely cause meningitis. Complement deficiency has been identified as a major predisposing factor for meningococcal disease. To assess whether patients with meningitis due to such strains have a complement deficiency, we studied 12 persons. Six patients had meningitis due to nongroupable strains of meningococci, and six patients had meningitis due to Moraxella species or Acinetobacter species. Inherited complement component C7 or C8 deficiency was found in two persons who had had meningitis due to nongroupable meningococci, and one C8-deficient person had had meningitis caused by Moraxella osloensis. Hypocomplementemia resulting from CSF drain-associated shunt nephritis was found in one person with meningitis due to Moraxella nonliquefaciens and in one person with meningitis due to Acinetobacter lwoffi. This rather high frequency of inherited or acquired complement deficiencies among patients with meningitis due to nongroupable meningococci, Moraxella species, and Acinetobacter species justifies the recommendation that such patients must be studied for complement deficiency.

Detection of the frequency of PER-1 type extended-spectrum β-lactamase-producing Acinetobacter baumannii clinical isolates in Turkey: a multicenter study.

PubMed

Aşik, Gülşah; Özdemir, Mehmet; Kurtoğlu, Muhammet Güzel; Yağci, Server; Öksüz, Lütfiye; Gül, Mustafa; Koçoğlu, Mücahide Esra; Sesli Çetin, Emel; Seyrek, Adnan; Berktaş, Mustafa; Ayyildiz, Ahmet; Çiftci, İhsan Hakkı

2014-01-01

β-Lactamases are an important resistance mechanism in Acinetobacter baumannii. Pseudomonas extended-resistance (PER-1) type β-lactamase-producing strains have been reported from various geographic locations; however, PER-1 type β-lactamases from Turkish hospitals have not been investigated extensively. The aim of this study was to determine the prevalence of PER-1 type β-lactamases in A. baumannii isolates in various regions of Turkey. A total of 763 clinical A. baumannii isolates were collected from 9 university hospitals and 2 state hospitals between 2008 and 2011. Molecular amplification of the OXA-51 gene from the A. baumannii genome was performed in order to verify identification of the species. Real-time polymerase chain reaction was used to detect blaPER-1 genes. PER-1 was detected in 24.6% of the isolates. The annual frequencies of the PER-1 enzyme were detected as 52.2%, 35.9%, and 8.3% in 2008, 2009, and 2010, respectively. PER-1 prevalence decreased gradually over time. The differences observed in PER-1 prevalence among the regions of Turkey were statistically significant (chi-square test; P < 0.001). These data demonstrate that the frequency of detection of PER-1 type β-lactamases in A. baumannii species has decreased in Turkey. However, the increased carbapenem resistance, together with multidrug resistance, has created a worrisome situation regarding this pathogen.

Acinetobacter Peritoneal Dialysis Peritonitis: A Changing Landscape over Time

PubMed Central

Chao, Chia-Ter; Lee, Szu-Ying; Yang, Wei-Shun; Chen, Huei-Wen; Fang, Cheng-Chung; Yen, Chung-Jen; Chiang, Chih-Kang; Hung, Kuan-Yu; Huang, Jenq-Wen

2014-01-01

Background Acinetobacter species are assuming an increasingly important role in modern medicine, with their persistent presence in health-care settings and antibiotic resistance. However, clinical reports addressing this issue in patients with peritoneal dialysis (PD) peritonitis are rare. Methods All PD peritonitis episodes caused by Acinetobacter that occurred between 1985 and 2012 at a single centre were retrospectively reviewed. Clinical features, microbiological data, and outcomes were analysed, with stratifications based upon temporal periods (before and after 2000). Results Acinetobacter species were responsible for 26 PD peritonitis episodes (3.5% of all episodes) in 25 patients. A. baumannii was the most common pathogen (54%), followed by A. iwoffii (35%), with the former being predominant after 2000. Significantly more episodes resulted from breaks in exchange sterility after 2000, while those from exit site infections decreased (P = 0.01). The interval between the last and current peritonitis episodes lengthened significantly after 2000 (5 vs. 13.6 months; P = 0.05). All the isolates were susceptible to cefepime, fluoroquinolone, and aminoglycosides, with a low ceftazidime resistance rate (16%). Nearly half of the patients (46%) required hospitalisation for their Acinetobacter PD-associated peritonitis, and 27% required an antibiotic switch. The overall outcome was fair, with no mortality and a 12% technique failure rate, without obvious interval differences. Conclusions The temporal change in the microbiology and origin of Acinetobacter PD-associated peritonitis in our cohort suggested an important evolutional trend. Appropriate measures, including technique re-education and sterility maintenance, should be taken to decrease the Acinetobacter peritonitis incidence in PD patients. PMID:25314341

Structure of a short-chain dehydrogenase/reductase (SDR) within a genomic island from a clinical strain of Acinetobacter baumannii

DOE Office of Scientific and Technical Information (OSTI.GOV)

Shah, Bhumika S., E-mail: bhumika.shah@mq.edu.au; Tetu, Sasha G.; Harrop, Stephen J.

2014-09-25

The structure of a short-chain dehydrogenase encoded within genomic islands of A. baumannii strains has been solved to 2.4 Å resolution. This classical SDR incorporates a flexible helical subdomain. The NADP-binding site and catalytic side chains are identified. Over 15% of the genome of an Australian clinical isolate of Acinetobacter baumannii occurs within genomic islands. An uncharacterized protein encoded within one island feature common to this and other International Clone II strains has been studied by X-ray crystallography. The 2.4 Å resolution structure of SDR-WM99c reveals it to be a new member of the classical short-chain dehydrogenase/reductase (SDR) superfamily. Themore » enzyme contains a nucleotide-binding domain and, like many other SDRs, is tetrameric in form. The active site contains a catalytic tetrad (Asn117, Ser146, Tyr159 and Lys163) and water molecules occupying the presumed NADP cofactor-binding pocket. An adjacent cleft is capped by a relatively mobile helical subdomain, which is well positioned to control substrate access.« less

Occurrence of bla genes encoding carbapenem-resistant Pseudomonas aeruginosa and Acinetobacter baumannii from Intensive Care Unit in a tertiary care hospital

PubMed Central

Subramaniyan, Jayanthi Siva; Sundaram, Jeya Meenakshi

2018-01-01

CONTEXT: ICU shows increasing incidence of infection associated with the use of invasive procedures for the diagnostic purpose as well as the indiscriminate use of antibiotics. Pseudomonas aeruginosa and Acinetobacter species are “very successful” pathogen and the emergence of the Metallo-β-Lactamases (MBL) is becoming a therapeutic challenge. AIMS: To isolate the Nonfermenting Gram negative bacilli from the ICU samples. To identify the metallo betalactamase producers and to detect the bla gene presence among the Pseudomonas aeruginosa and Acinetobacter baumannii. SETTINGS AND DESIGN: The Nonfermenting Gram negative bacilli isolates from the ICU samples were taken over for 5 years (2009-2014) in a tertiary care hospital. METHODS AND MATERIALS: The isolates of Pseudomonas species and Acinetobacter species were confirmed by API analyser and processed according to standard procedures. Detection of the MBL producers were done by E strip method and subjected for bla gene detection by PCR method. RESULTS: In our study a total of 195 isolates of NFGNB were obtained from various ICU. Of these MBL producers, 26 % were Pseudomonas aeruginosa and 25 % were Acinetobacter baumannii. The subtypes of blaVIM MBL producing P.aeruginosa were 26%. The predominant gene coding for MBL activity in A.baumannii were found to be blaOXA gene 11.9%. The gene accession numbers were KF975367, KF975372. CONCLUSIONS: We have to control the development and dissemination of these superbugs among the ICU's. PMID:29692589

Species distribution, virulence factors, and antimicrobial resistance of Acinetobacter spp. isolates from dogs and cats: a preliminary study.

PubMed

Kimura, Yui; Harada, Kazuki; Shimizu, Takae; Sato, Tomomi; Kajino, Akari; Usui, Masaru; Tamura, Yutaka; Tsuyuki, Yuzo; Miyamoto, Tadashi; Ohki, Asami; Watarai, Masahisa

2018-05-12

We investigated the prevalence of virulence factors and antimicrobial resistance among 67 Acinetobacter spp. isolates, consisting of 21 Acinetobacter baumannii and 46 non-baumannii Acinetobacter from companion animals. The PCR analysis showed that the most prevalent virulence gene was afa/draBC (29.9%), followed by papC (22.4%) and cvaC (20.9%). Antimicrobial susceptibility testing revealed that resistance to gentamicin (14.9%) and ciprofloxacin (11.9%) was relatively prevalent. Five gentamicin- and/or ciprofloxacin-resistant A. baumannii strains were assigned to ST25, ST149, ST164, ST203, and ST1198. All ciprofloxacin-resistant isolates harbored point mutations in gyrA and/or parC. This is the first preliminary monitoring of animal-origin Acinetobacter spp. in Japan. © 2018 The Societies and John Wiley & Sons Australia, Ltd.

Genome-guided Investigation of Antibiotic Substances produced by Allosalinactinospora lopnorensis CA15-2T from Lop Nor region, China

PubMed Central

Huang, Chen; Leung, Ross Ka-Kit; Guo, Min; Tuo, Li; Guo, Lin; Yew, Wing Wai; Lou, Inchio; Lee, Simon Ming Yuen; Sun, Chenghang

2016-01-01

Microbial secondary metabolites are valuable resources for novel drug discovery. In particular, actinomycetes expressed a range of antibiotics against a spectrum of bacteria. In genus level, strain Allosalinactinospora lopnorensis CA15-2T is the first new actinomycete isolated from the Lop Nor region, China. Antimicrobial assays revealed that the strain could inhibit the growth of certain types of bacteria, including Acinetobacter baumannii and Staphylococcus aureus, highlighting its clinical significance. Here we report the 5,894,259 base pairs genome of the strain, containing 5,662 predicted genes, and 832 of them cannot be detected by sequence similarity-based methods, suggesting the new species may carry a novel gene pool. Furthermore, our genome-mining investigation reveals that A. lopnorensis CA15-2T contains 17 gene clusters coding for known or novel secondary metabolites. Meanwhile, at least six secondary metabolites were disclosed from ethyl acetate (EA) extract of the fermentation broth of the strain by high-resolution UPLC-MS. Compared with reported clusters of other species, many new genes were found in clusters, and the physical chromosomal location and order of genes in the clusters are distinct. This study presents evidence in support of A. lopnorensis CA15-2T as a potent natural products source for drug discovery. PMID:26864220

Antimicrobial susceptibility pattern in nosocomial infections caused by Acinetobacter species in Asir Region, Saudi Arabia.

PubMed

Abdalla, Nazar M; Osman, Amani A; Haimour, Waleed O; Sarhan, Mohammed A A; Mohammed, Mohammed N; Zyad, Eyhab M; Al-Ghtani, Abdalla M

2013-03-15

This study aimed at evaluating the sensitivity of antibiotics towards nosocomial infections caused by Acinetobacter species. The study took place during the period Dec. 2011- Dec. 2012 at Assir Central Hospital in collaboration with the department of microbiology, college of medicine, King Khalid University, Abha. A prospective study involving 150 patients presented with nosocomial infections due to Acinetobacter species detected by bacteriological tests; direct microscopy, culture in blood agar media, fermentation test in MacConkey media and MIC (minimum inhibitory concentration) for antibiotics sensitivity using Muller Hinton media and Chemical test using API 20. A 150 nosocomial infections in this study showed gram-negative coccobacilli, non motile, glucose-negative fermentor and oxidase negative. All isolates showed 100% sensitivity to: Imipramine, Meropenem, Colistin. From the rest of tested antibiotics the higher resistant ones were; Nitrofurantoin 87% and Cefoxitin 85%. The least resistant antibiotics; Imipenem 3% and Ticarcillin 7%. While variable resistance in the rest of tested antimicrobials. A 47 patients (31.3%) have used antibiotics prior to this study. The high rate of usage occurred in elder patients. The frequency of Acinetobacter calcoaceticus baumannii complex multi-drugs resistance ABCMDR is rising including almost all commonly used antibiotics. Only few antibiotics exert 100% sensitivity towards these bacteria.

Genome organization of epidemic Acinetobacter baumannii strains.

PubMed

Di Nocera, Pier Paolo; Rocco, Francesco; Giannouli, Maria; Triassi, Maria; Zarrilli, Raffaele

2011-10-10

Acinetobacter baumannii is an opportunistic pathogen responsible for hospital-acquired infections. A. baumannii epidemics described world-wide were caused by few genotypic clusters of strains. The occurrence of epidemics caused by multi-drug resistant strains assigned to novel genotypes have been reported over the last few years. In the present study, we compared whole genome sequences of three A. baumannii strains assigned to genotypes ST2, ST25 and ST78, representative of the most frequent genotypes responsible for epidemics in several Mediterranean hospitals, and four complete genome sequences of A. baumannii strains assigned to genotypes ST1, ST2 and ST77. Comparative genome analysis showed extensive synteny and identified 3068 coding regions which are conserved, at the same chromosomal position, in all A. baumannii genomes. Genome alignments also identified 63 DNA regions, ranging in size from 4 o 126 kb, all defined as genomic islands, which were present in some genomes, but were either missing or replaced by non-homologous DNA sequences in others. Some islands are involved in resistance to drugs and metals, others carry genes encoding surface proteins or enzymes involved in specific metabolic pathways, and others correspond to prophage-like elements. Accessory DNA regions encode 12 to 19% of the potential gene products of the analyzed strains. The analysis of a collection of epidemic A. baumannii strains showed that some islands were restricted to specific genotypes. The definition of the genome components of A. baumannii provides a scaffold to rapidly evaluate the genomic organization of novel clinical A. baumannii isolates. Changes in island profiling will be useful in genomic epidemiology of A. baumannii population.

Acinetobacter baumannii: a universal threat to public health?

PubMed

Giamarellou, Helen; Antoniadou, Anastasia; Kanellakopoulou, Kyriaki

2008-08-01

Acinetobacter spp. are non-fermentative, strictly aerobic, Gram-negative microorganisms with a confusing taxonomic history. The Acinetobacter baumannii-Acinetobacter calcoaceticus complex is the species most commonly isolated from clinical specimens. It is ubiquitous in nature and has been found as part of the normal skin, throat and rectal flora as well as in food and body lice. It colonises patients in Intensive Care Units and contaminates inanimate hospital surfaces and devices as well as wounds, including war injuries. Although a frequent coloniser, Acinetobacter can be the cause of severe and sometimes lethal infections, mostly of nosocomial origin, predominantly ventilator-associated pneumonia. Bacteraemic infections are rare but may evolve to septic shock. Acinetobacter also emerges as a cause of nosocomial outbreaks and is characterised by increasing antimicrobial multiresistance. Antibiotic use, especially carbapenems and third-generation cephalosporins, is recognised as the most important risk factor for multiresistance. Described resistance mechanisms include hydrolysis by beta-lactamases, alterations in outer membrane proteins and penicillin-binding proteins, and increased activity of efflux pumps. Today, Acinetobacter resistant to carbapenems, aminoglycosides and fluoroquinolones presents a challenge to the clinician. However, sulbactam, tigecycline and colistin represent the current therapeutic approaches, which are associated with satisfactory efficacy.

Antimicrobial Resistance Prediction in PATRIC and RAST.

PubMed

Davis, James J; Boisvert, Sébastien; Brettin, Thomas; Kenyon, Ronald W; Mao, Chunhong; Olson, Robert; Overbeek, Ross; Santerre, John; Shukla, Maulik; Wattam, Alice R; Will, Rebecca; Xia, Fangfang; Stevens, Rick

2016-06-14

The emergence and spread of antimicrobial resistance (AMR) mechanisms in bacterial pathogens, coupled with the dwindling number of effective antibiotics, has created a global health crisis. Being able to identify the genetic mechanisms of AMR and predict the resistance phenotypes of bacterial pathogens prior to culturing could inform clinical decision-making and improve reaction time. At PATRIC (http://patricbrc.org/), we have been collecting bacterial genomes with AMR metadata for several years. In order to advance phenotype prediction and the identification of genomic regions relating to AMR, we have updated the PATRIC FTP server to enable access to genomes that are binned by their AMR phenotypes, as well as metadata including minimum inhibitory concentrations. Using this infrastructure, we custom built AdaBoost (adaptive boosting) machine learning classifiers for identifying carbapenem resistance in Acinetobacter baumannii, methicillin resistance in Staphylococcus aureus, and beta-lactam and co-trimoxazole resistance in Streptococcus pneumoniae with accuracies ranging from 88-99%. We also did this for isoniazid, kanamycin, ofloxacin, rifampicin, and streptomycin resistance in Mycobacterium tuberculosis, achieving accuracies ranging from 71-88%. This set of classifiers has been used to provide an initial framework for species-specific AMR phenotype and genomic feature prediction in the RAST and PATRIC annotation services.

Laboratory Maintenance of Acinetobacter baumannii.

PubMed

Jacobs, Anna C; Zurawski, Daniel V

2014-11-03

Acinetobacter baumannii has recently drawn great interest in the microbiology research community due to the increase in clinical antibiotic resistance of this organism, and persistence of this bacterial species in the hospital environment. This unit outlines protocols for the growth and maintenance of A. baumannii in the laboratory. Copyright © 2014 John Wiley & Sons, Inc.

Genomic comparison of multi-drug resistant invasive and colonizing Acinetobacter baumannii isolated from diverse human body sites reveals genomic plasticity.

PubMed

Sahl, Jason W; Johnson, J Kristie; Harris, Anthony D; Phillippy, Adam M; Hsiao, William W; Thom, Kerri A; Rasko, David A

2011-06-04

Acinetobacter baumannii has recently emerged as a significant global pathogen, with a surprisingly rapid acquisition of antibiotic resistance and spread within hospitals and health care institutions. This study examines the genomic content of three A. baumannii strains isolated from distinct body sites. Isolates from blood, peri-anal, and wound sources were examined in an attempt to identify genetic features that could be correlated to each isolation source. Pulsed-field gel electrophoresis, multi-locus sequence typing and antibiotic resistance profiles demonstrated genotypic and phenotypic variation. Each isolate was sequenced to high-quality draft status, which allowed for comparative genomic analyses with existing A. baumannii genomes. A high resolution, whole genome alignment method detailed the phylogenetic relationships of sequenced A. baumannii and found no correlation between phylogeny and body site of isolation. This method identified genomic regions unique to both those isolates found on the surface of the skin or in wounds, termed colonization isolates, and those identified from body fluids, termed invasive isolates; these regions may play a role in the pathogenesis and spread of this important pathogen. A PCR-based screen of 74 A. baumanii isolates demonstrated that these unique genes are not exclusive to either phenotype or isolation source; however, a conserved genomic region exclusive to all sequenced A. baumannii was identified and verified. The results of the comparative genome analysis and PCR assay show that A. baumannii is a diverse and genomically variable pathogen that appears to have the potential to cause a range of human disease regardless of the isolation source.

Radiation sensitivity of Acinetobacter spp. and their redicidation for preservation of meat at low temperature.

PubMed

Saha, Sahadev Chandra; Chopade, Balu Anand

2009-08-01

In recent years, interest has been growing to preserve food including meat applying gamma radiation recommended by International Atomic Energy Agency to extend the shelf-life of meat retaining the organoleptic conditions as it is. In view of this point the present study aims to check the sensitivity of Acinetobacter spp. isolated from meat to gamma radiations. Seven species of Acinetobacter viz. A. lwoffli M1; A. baumannii M8; A. calcoaceticus M19; A. junii M20; A. johnsonnii M23; A. haemolyticus M27 and A. radioresistens M25 isolated from meat were exposed to gamma radiation at the dose level of 0.1 to 10 KGy. The D10 value of Acinetobacter was found highest 1.25 KGy in A. radioresistens M25, which was 4 to 8 times higher than other genospecies of Acinetobacter. Acinetobacter radioresistens M25 contains one plasmid of 45 Kb. The radicidation dose of 4 KGy gamma radiations was found to be sufficient to eliminate the natural contamination of meat and contamination by Acinetobacter. To eliminate radiation resistant Acinetobacter contamination a dose of 4 to 5 KGy was required. Development of the radicidation process for preservation of meat to eliminate Acinetobacter as contaminants at low temperature is one of the new and interesting phenomena. Attempts of finding the appropriate radicidation dose for preservation of meat at low temperature will open up new avenues for commercial preservation of meat.

Two New Lytic Bacteriophages of the Myoviridae Family Against Carbapenem-Resistant Acinetobacter baumannii

PubMed Central

Zhou, Weilong; Feng, Yu; Zong, Zhiyong

2018-01-01

Two lytic bacteriophages, WCHABP1 and WCHABP12, were recovered from hospital sewage and were able to infect 9 and 12 out of 18 carbapenem-resistant Acinetobacter baumannii clinical strains, which belonged to different clones. Electron microscopy scan showed that both bacteriophages had the similar morphology as those of the Myoviridae family. Whole genomic sequencing revealed 45.4- or 45.8-kb genome with a 37.6% GC content for WCHABP1 and WCHABP12, both of which showed significant DNA sequence similarity with bacteriophages of the Ap22virus genus within the Myoviridae family. Taxonomic analysis was therefore performed following the proposal approved by the International Committee on Taxonomy of Viruses, which confirmed that WCHABP1 and WCHABP12 represented two new species of the Ap22virus genus. No tRNAs but 88 and 89 open reading frames (ORFs) were predicted for the two bacteriophages, among which 22 and 21 had known function and encoded proteins for morphogenesis, packaging, lysis, and nucleiotide metabolism. The C-terminal amino acids of the large unit of fiber tail proteins varied between the bacteriophages, which may explain their different host ranges. For most lytic bacteriophages, a set of holin and endolysin are required for lysis. However, no known holin-encoding genes were identified in WCHABP1 and WCHABP12, suggesting that they may use alternative, yet-to-be-identified, novel holins for host cell membrane lysis. To test the efficacy of the bacteriophages in protecting against A. baumannii infection, a Galleria mellonella larva model was used. Only <20% G. mellonella larvae survived at 96 h after being infected by carbapenem-resistant A. baumannii strains, from which the two bacteriophages were recovered. With the administration of WCHABP1 and WCHABP12, the survival of larvae increased to 75%, while the treatment of polymyxin B only slightly increased the survival rate to 25%. The isolation of two new lytic bacteriophages in this study could expand our sight on Acinetobacter bacteriophages and may offer new potential therapeutic alternatives against A. baumannii. PMID:29760690

Prevalence of carbapenem-resistant Acinetobacter baumannii from 2005 to 2016 in Switzerland.

PubMed

Ramette, A; Kronenberg, A

2018-04-03

We describe the prevalence of invasive carbapenem-resistant Acinetobacter spp. isolated from 2005 to 2016 in different regions of Switzerland. Using the Swiss Antibiotic Resistance Centre (anresis) database that includes data from 70% of all hospitalized patients and one third of all ambulatory practitioners in Switzerland, we analysed the number of carbapenem-susceptible and resistant Acinetobacter spp. isolated from blood or cerebrospinal fluid, and further described their temporal and regional fluctuations. From 2005 to 2016, 58 cases of resistant or intermediate strains to carbapenem were observed among 632 cases of invasive Acinetobacter. Multivariable analyses indicated that the number of carbapenem-resistant isolates (mean 4.8 ± sd 2.12) and carbapenem resistance rates per region per annum (8.4% ± 13.9%) were low and stable over the studied period. Large fluctuations were observed at the regional level, with e.g. the North East region displaying resistance rates twice as high as that found in other regions. Despite a relatively stable number of carbapenem-resistant Acinetobacter isolates in Switzerland, our results suggest the existence of a diverse pool of A. baumannii species in hospital settings, and confirm the implication of carbapenem-resistant Acinetobacter calcoaceticus-Acinetobacter baumannii (ACB) complex in the vast majority of clinical infections and nosocomial outbreaks with notable regional fluctuations.

Transposons and integrons in colistin-resistant clones of Klebsiella pneumoniae and Acinetobacter baumannii with epidemic or sporadic behaviour.

PubMed

Arduino, Sonia M; Quiroga, María Paula; Ramírez, María Soledad; Merkier, Andrea Karina; Errecalde, Laura; Di Martino, Ana; Smayevsky, Jorgelina; Kaufman, Sara; Centrón, Daniela

2012-10-01

Multiple transposons, integrons and carbapenemases were found in Klebsiella pneumoniae colistin-resistant isolates as well as a genomic resistance island of the AbaR type in Acinetobacter baumannii colistin-resistant isolates from different hospitals from Buenos Aires City. PFGE analysis showed a polyclonal dissemination of antimicrobial resistance mechanisms among K. pneumoniae isolates, while in A. baumannii isolates the epidemic clone 1 from South America was found. Resistance determinants associated with horizontal gene transfer are contributing to the evolution to pandrug resistance in both epidemic and sporadic clones.

Draft Genome Sequences of Acinetobacter and Bacillus Strains Isolated from Spacecraft-Associated Surfaces

PubMed Central

Seuylemezian, Arman; Vaishampayan, Parag; Cooper, Kerry

2018-01-01

ABSTRACT We report here the draft genome sequences of four strains isolated from spacecraft-associated surfaces exhibiting increased resistance to stressors such as UV radiation and exposure to H2O2. The draft genomes of strains 1P01SCT, FO-92T, 50v1, and 2P01AA had sizes of 5,500,894 bp, 4,699,376 bp, 3,174,402 bp, and 4,328,804 bp, respectively. PMID:29439046

Experimental infection of human body lice with Acinetobacter baumannii.

PubMed

Houhamdi, Linda; Raoult, Didier

2006-04-01

The human body louse is currently recognized as a vector of Rickettsia prowazekii, Borrelia recurrentis, and Bartonella quintana. Previous studies have reported the isolation of Acinetobacter baumannii from the body lice of homeless patients. To study how the body louse acquires A. baumannii, we infected a rabbit by infusing 2 x 10(6) colony-forming units of the louse strain of A. baumannii. Two hundred body lice were infected by feeding on the bacteremic rabbit and compared with 200 uninfected lice and two groups of 200 lice feeding on rabbits infected either with another strain of A. baumannii or A. lwoffii. Each louse group received maintenance feedings once a day on another seronegative rabbit. Body lice that fed on rabbits infused with each Acinetobacter species demonstrated a generalized infection. The body lice did not transmit their infection to the nurse rabbit by bite while feeding or to their progeny (eggs and larvae). The lice excreted living Acinetobacter species within their feces. Only the louse strain of A. baumannii was pathogenic for the body louse. An increased mortality rate was observed between the second and third days post-infection; however, they remained infected for their lifespan.

Phylogenetic relationships between some members of the genera Neisseria, Acinetobacter, Moraxella, and Kingella based on partial 16S ribosomal DNA sequence analysis.

PubMed

Enright, M C; Carter, P E; MacLean, I A; McKenzie, H

1994-07-01

We obtained 16S ribosomal DNA (rDNA) sequence data for strains belonging to 11 species of Proteobacteria, including the type strains of Kingella kingae, Neisseria lactamica, Neisseria meningitidis, Moraxella lacunata subsp. lacunata, [Neisseria] ovis, Moraxella catarrhalis, Moraxella osloensis, [Moraxella] phenylpyruvica, and Acinetobacter lwoffii, as well as strains of Neisseria subflava and Acinetobacter calcoaceticus. The data in a distance matrix constructed by comparing the sequences supported the proposal that the genera Acinetobacter and Moraxella and [N.] ovis should be excluded from the family Neisseriaceae. Our results are consistent with hybridization data which suggest that these excluded taxa should be part of a new family, the Moraxellaceae. The strains that we studied can be divided into the following five groups: (i) M. lacunata subsp. lacunata, [N.] ovis, and M. catarrhalis; (ii) M. osloensis; (iii) [M.] phenylpyruvica; (iv) A. calcoaceticus and A. lwoffii; and (v) N. meningitidis, N. subflava, N. lactamica, and K. kingae. We agree with the previous proposal that [N.] ovis should be renamed Moraxella ovis, as this organism is closely related to Moraxella species and not to Neisseria species. The generically misnamed taxon [M.] phenylpyruvica belongs to the proposed family Moraxellaceae, but it is sufficiently different to warrant exclusion from the genus Moraxella. Further work needs to be done to investigate genetically similar species, such as Psychrobacter immobilis, before the true generic position of this organism can be determined. Automated 16S rDNA sequencing with the PCR allows workers to accurately determine phylogenetic relationships between groups of organisms.(ABSTRACT TRUNCATED AT 250 WORDS)

Acinetobacter apis sp. nov., isolated from the intestinal tract of a honey bee, Apis mellifera.

PubMed

Kim, Pil Soo; Shin, Na-Ri; Kim, Joon Yong; Yun, Ji-Hyun; Hyun, Dong-Wook; Bae, Jin-Woo

2014-08-01

A novel Gram-negative, obligate aerobic, non-motile, and both coccobacillus- and bacillus-shaped bacterium, designated strain HYN18(T), was isolated from the intestinal tract of a honey bee (Apis mellifera). The isolate was oxidase-negative and catalase-positive. Strain HYN18(T) showed optimum growth at 25°C, pH 6-7, and in the presence of 1% (w/v) NaCl in trypticase soy broth medium. The isolate was negative for hydrolyses of starch, casein, gelatin and urea, indole production from tryptone and hemolysis on sheep blood agar. A phylogenetic analysis based on the 16S rRNA gene and rpoB gene sequence showed that strain HYN18(T) was most closely related to Acinetobacter nectaris SAP 763.2(T) and A. boissieri SAP 284.1(T) with 98.3% and 98.1% similarity (16S rRNA gene), respectively, and 84.4% similarity with Acinetobacter nectaris SAP 763.2(T) (rpoB gene). The major cellular fatty acids were summed features 3 (comprising C16:1ω7c /C16:1ω6c ), C12:0 and C16:0. The main isoprenoid quinone was ubiquinone-9 (Q-9). The polar lipids of strain HYN18(T) were phosphatidylethanolamine, three unidentified lipids, an unidentified phospholipid and an unidentified glycolipid. The DNA G+C content was 40.6 mol%. DNA-DNA hybridization experiments indicated less than 33 ± 10% relatedness to the closest phylogenetic species, Acinetobacter nectaris SAP 763.2(T). Thus, the phenotypic, phylogenetic and genotypic analyses indicate that strain HYN18(T) is a novel species within the genus Acinetobacter, for which the name Acinetobacter apis is proposed. The type strain is HYN18(T) (=KACC 16906(T) =JCM 18575(T)).

Isolation and Whole-genome Sequence Analysis of the Imipenem Heteroresistant Acinetobacter baumannii Clinical Isolate HRAB-85.

PubMed

Li, Puyuan; Huang, Yong; Yu, Lan; Liu, Yannan; Niu, Wenkai; Zou, Dayang; Liu, Huiying; Zheng, Jing; Yin, Xiuyun; Yuan, Jing; Yuan, Xin; Bai, Changqing

2017-09-01

Heteroresistance is a phenomenon in which there are various responses to antibiotics from bacterial cells within the same population. Here, we isolated and characterised an imipenem heteroresistant Acinetobacter baumannii strain (HRAB-85). The genome of strain HRAB-85 was completely sequenced and analysed to understand its antibiotic resistance mechanisms. Population analysis and multilocus sequence typing were performed. Subpopulations grew in the presence of imipenem at concentrations of up to 64μg/mL, and the strain was found to belong to ST208. The total length of strain HRAB-85 was 4,098,585bp with a GC content of 39.98%. The genome harboured at least four insertion sequences: the common ISAba1, ISAba22, ISAba24, and newly reported ISAba26. Additionally, 19 antibiotic-resistance genes against eight classes of antimicrobial agents were found, and 11 genomic islands (GIs) were identified. Among them, GI3, GI10, and GI11 contained many ISs and antibiotic-resistance determinants. The existence of imipenem heteroresistant phenotypes in A. baumannii was substantiated in this hospital, and imipenem pressure, which could induce imipenem-heteroresistant subpopulations, may select for highly resistant strains. The complete genome sequencing and bioinformatics analysis of HRAB-85 could improve our understanding of the epidemiology and resistance mechanisms of carbapenem-heteroresistant A. baumannii. Copyright © 2017. Published by Elsevier Ltd.

Widespread Fosfomycin Resistance in Gram-Negative Bacteria Attributable to the Chromosomal fosA Gene

PubMed Central

Ito, Ryota; Tomich, Adam D.; Callaghan, Jake D.; McElheny, Christi L.; Mettus, Roberta T.; Sluis-Cremer, Nicolas

2017-01-01

ABSTRACT Fosfomycin is a decades-old antibiotic which is being revisited because of its perceived activity against many extensively drug-resistant Gram-negative pathogens. FosA proteins are Mn2+ and K+-dependent glutathione S-transferases which confer fosfomycin resistance in Gram-negative bacteria by conjugation of glutathione to the antibiotic. Plasmid-borne fosA variants have been reported in fosfomycin-resistant Escherichia coli strains. However, the prevalence and distribution of fosA in other Gram-negative bacteria are not known. We systematically surveyed the presence of fosA in Gram-negative bacteria in over 18,000 published genomes from 18 Gram-negative species and investigated their contribution to fosfomycin resistance. We show that FosA homologues are present in the majority of genomes in some species (e.g., Klebsiella spp., Enterobacter spp., Serratia marcescens, and Pseudomonas aeruginosa), whereas they are largely absent in others (e.g., E. coli, Acinetobacter baumannii, and Burkholderia cepacia). FosA proteins in different bacterial pathogens are highly divergent, but key amino acid residues in the active site are conserved. Chromosomal fosA genes conferred high-level fosfomycin resistance when expressed in E. coli, and deletion of chromosomal fosA in S. marcescens eliminated fosfomycin resistance. Our results indicate that FosA is encoded by clinically relevant Gram-negative species and contributes to intrinsic fosfomycin resistance. PMID:28851843

Antimicrobial resistance prediction in PATRIC and RAST

DOE Office of Scientific and Technical Information (OSTI.GOV)

Davis, James J.; Boisvert, Sebastien; Brettin, Thomas

The emergence and spread of antimicrobial resistance (AMR) mechanisms in bacterial pathogens, coupled with the dwindling number of effective antibiotics, has created a global health crisis. Being able to identify the genetic mechanisms of AMR and predict the resistance phenotypes of bacterial pathogens prior to culturing could inform clinical decision-making and improve reaction time. At PATRIC (http://patricbrc.org/), we have been collecting bacterial genomes with AMR metadata for several years. In order to advance phenotype prediction and the identification of genomic regions relating to AMR, we have updated the PATRIC FTP server to enable access to genomes that are binned bymore » their AMR phenotypes, as well as metadata including minimum inhibitory concentrations. Using this infrastructure, we custom built AdaBoost (adaptive boosting) machine learning classifiers for identifying carbapenem resistance in Acinetobacter baumannii, methicillin resistance in Staphylococcus aureus, and beta-lactam and co-trimoxazole resistance in Streptococcus pneumoniae with accuracies ranging from 88–99%. We also did this for isoniazid, kanamycin, ofloxacin, rifampicin, and streptomycin resistance in Mycobacterium tuberculosis, achieving accuracies ranging from 71–88%. Lastly, this set of classifiers has been used to provide an initial framework for species-specific AMR phenotype and genomic feature prediction in the RAST and PATRIC annotation services.« less

Antimicrobial resistance prediction in PATRIC and RAST

DOE PAGES

Davis, James J.; Boisvert, Sebastien; Brettin, Thomas; ...

2016-06-14

The emergence and spread of antimicrobial resistance (AMR) mechanisms in bacterial pathogens, coupled with the dwindling number of effective antibiotics, has created a global health crisis. Being able to identify the genetic mechanisms of AMR and predict the resistance phenotypes of bacterial pathogens prior to culturing could inform clinical decision-making and improve reaction time. At PATRIC (http://patricbrc.org/), we have been collecting bacterial genomes with AMR metadata for several years. In order to advance phenotype prediction and the identification of genomic regions relating to AMR, we have updated the PATRIC FTP server to enable access to genomes that are binned bymore » their AMR phenotypes, as well as metadata including minimum inhibitory concentrations. Using this infrastructure, we custom built AdaBoost (adaptive boosting) machine learning classifiers for identifying carbapenem resistance in Acinetobacter baumannii, methicillin resistance in Staphylococcus aureus, and beta-lactam and co-trimoxazole resistance in Streptococcus pneumoniae with accuracies ranging from 88–99%. We also did this for isoniazid, kanamycin, ofloxacin, rifampicin, and streptomycin resistance in Mycobacterium tuberculosis, achieving accuracies ranging from 71–88%. Lastly, this set of classifiers has been used to provide an initial framework for species-specific AMR phenotype and genomic feature prediction in the RAST and PATRIC annotation services.« less

Colistin-Resistant Acinetobacter baumannii Clinical Strains with Deficient Biofilm Formation

PubMed Central

Dafopoulou, Konstantina; Xavier, Basil Britto; Hotterbeekx, An; Janssens, Lore; Lammens, Christine; Dé, Emmanuelle; Goossens, Herman; Tsakris, Athanasios; Malhotra-Kumar, Surbhi

2015-01-01

In two pairs of clinical colistin-susceptible/colistin-resistant (Csts/Cstr) Acinetobacter baumannii strains, the Cstr strains showed significantly decreased biofilm formation in static and dynamic assays (P < 0.001) and lower relative fitness (P < 0.05) compared with those of the Csts counterparts. The whole-genome sequencing comparison of strain pairs identified a mutation converting a stop codon to lysine (*241K) in LpsB (involved in lipopolysaccharide [LPS] synthesis) in one Cstr strain and a frameshift mutation in CarO and the loss of a 47,969-bp element containing multiple genes associated with biofilm production in the other. PMID:26666921

First Description of Two Sequence Type 2 Acinetobacter baumannii Isolates Carrying OXA-23 Carbapenemase in Pagellus acarne Fished from the Mediterranean Sea near Bejaia, Algeria

PubMed Central

Brahmi, Soumia; Touati, Abdelaziz; Cadière, Axelle; Djahmi, Nassima; Pantel, Alix; Sotto, Albert; Dunyach-Remy, Catherine

2016-01-01

To determine the occurrence of carbapenem-resistant Acinetobacter baumannii in fish fished from the Mediterranean Sea near the Bejaia coast (Algeria), we studied 300 gills and gut samples that had been randomly and prospectively collected during 1 year. After screening on selective agar media, using PCR arrays and whole-genome sequencing, we identified for the first time two OXA-23-producing A. baumannii strains belonging to the widespread sequence type 2 (ST2)/international clone II and harboring aminoglycoside-modifying enzymes [aac(6′)-Ib and aac(3′)-I genes]. PMID:26787693

KatG and KatE Confer Acinetobacter Resistance to Hydrogen Peroxide but Sensitize Bacteria to Killing by Phagocytic Respiratory Burst

PubMed Central

Sun, Daqing; Crowell, Sara A.; Harding, Christian M.; De Silva, P. Malaka; Harrison, Alistair; Fernando, Dinesh M.; Mason, Kevin M.; Santana, Estevan; Loewen, Peter C.; Kumar, Ayush; Liu, Yusen

2016-01-01

Aims Catalase catalyzes the degradation of H2O2. Acinetobacter species have four predicted catalase genes, katA, katE, katG, and katX. The aims of the present study seek to determine which catalase(s) plays a predominant role in determining the resistance to H2O2, and to assess the role of catalase in Acinetobacter virulence. Main Methods Mutants of A. baumannii and A. nosocomialis with deficiencies in katA, katE, katG, and katX were tested for sensitivity to H2O2, either by halo assays or by liquid culture assays. Respiratory burst of neutrophils, in response to A. nosocomialis, was assessed by chemiluminescence to examine the effects of catalase on the production of reactive oxygen species (ROS)1 in neutrophils. Bacterial virulence was assessed using a Galleria mellonella larva infection model. Key findings The capacities of A. baumannii and A. nosocomialis to degrade H2O2 are largely dependent on katE. The resistance of both A. baumannii and A. nosocomialis to H2O2 is primarily determined by the katG gene, although katE also plays a minor role in H2O2 resistance. Bacteria lacking both the katG and katE genes exhibit the highest sensitivity to H2O2. While A. nosocomialis bacteria with katE and/or katG were able to decrease ROS production by neutrophils, these cells also induced a more robust respiratory burst in neutrophils than did cells deficient in both katE and katG. We also found that A. nosocomialis deficient in both katE and katG was more virulent than the wildtype A. nosocomialis strain. Significance Our findings suggest that inhibition of Acinetobacter catalase may help to overcome the resistance of Acinetobacter species to microbicidal H2O2 and facilitate bacterial disinfection. PMID:26860891

Antibacterial Discovery and Development: From Gene to Product and Back

PubMed Central

Fedorenko, Victor; Genilloud, Olga; Horbal, Liliya; Marcone, Giorgia Letizia; Marinelli, Flavia; Paitan, Yossi; Ron, Eliora Z.

2015-01-01

Concern over the reports of antibiotic-resistant bacterial infections in hospitals and in the community has been publicized in the media, accompanied by comments on the risk that we may soon run out of antibiotics as a way to control infectious disease. Infections caused by Enterococcus faecium, Staphylococcus aureus, Klebsiella species, Clostridium difficile, Acinetobacter baumannii, Pseudomonas aeruginosa, Escherichia coli, and other Enterobacteriaceae species represent a major public health burden. Despite the pharmaceutical sector's lack of interest in the topic in the last decade, microbial natural products continue to represent one of the most interesting sources for discovering and developing novel antibacterials. Research in microbial natural product screening and development is currently benefiting from progress that has been made in other related fields (microbial ecology, analytical chemistry, genomics, molecular biology, and synthetic biology). In this paper, we review how novel and classical approaches can be integrated in the current processes for microbial product screening, fermentation, and strain improvement. PMID:26339625

Reduced Mutation Rate and Increased Transformability of Transposon-Free Acinetobacter baylyi ADP1-ISx.

PubMed

Suárez, Gabriel A; Renda, Brian A; Dasgupta, Aurko; Barrick, Jeffrey E

2017-09-01

The genomes of most bacteria contain mobile DNA elements that can contribute to undesirable genetic instability in engineered cells. In particular, transposable insertion sequence (IS) elements can rapidly inactivate genes that are important for a designed function. We deleted all six copies of IS 1236 from the genome of the naturally transformable bacterium Acinetobacter baylyi ADP1. The natural competence of ADP1 made it possible to rapidly repair deleterious point mutations that arose during strain construction. In the resulting ADP1-ISx strain, the rates of mutations inactivating a reporter gene were reduced by 7- to 21-fold. This reduction was higher than expected from the incidence of new IS 1236 insertions found during a 300-day mutation accumulation experiment with wild-type ADP1 that was used to estimate spontaneous mutation rates in the strain. The extra improvement appears to be due in part to eliminating large deletions caused by IS 1236 activity, as the point mutation rate was unchanged in ADP1-ISx. Deletion of an error-prone polymerase ( dinP ) and a DNA damage response regulator ( umuD Ab [the umuD gene of A. baylyi ]) from the ADP1-ISx genome did not further reduce mutation rates. Surprisingly, ADP1-ISx exhibited increased transformability. This improvement may be due to less autolysis and aggregation of the engineered cells than of the wild type. Thus, deleting IS elements from the ADP1 genome led to a greater than expected increase in evolutionary reliability and unexpectedly enhanced other key strain properties, as has been observed for other clean-genome bacterial strains. ADP1-ISx is an improved chassis for metabolic engineering and other applications. IMPORTANCE Acinetobacter baylyi ADP1 has been proposed as a next-generation bacterial host for synthetic biology and genome engineering due to its ability to efficiently take up DNA from its environment during normal growth. We deleted transposable elements that are capable of copying themselves, inserting into other genes, and thereby inactivating them from the ADP1 genome. The resulting "clean-genome" ADP1-ISx strain exhibited larger reductions in the rates of inactivating mutations than expected from spontaneous mutation rates measured via whole-genome sequencing of lineages evolved under relaxed selection. Surprisingly, we also found that IS element activity reduces transformability and is a major cause of cell aggregation and death in wild-type ADP1 grown under normal laboratory conditions. More generally, our results demonstrate that domesticating a bacterial genome by removing mobile DNA elements that have accumulated during evolution in the wild can have unanticipated benefits. Copyright © 2017 American Society for Microbiology.

Genomic epidemiology of a protracted hospital outbreak caused by multidrug-resistant Acinetobacter baumannii in Birmingham, England.

PubMed

Halachev, Mihail R; Chan, Jacqueline Z-M; Constantinidou, Chrystala I; Cumley, Nicola; Bradley, Craig; Smith-Banks, Matthew; Oppenheim, Beryl; Pallen, Mark J

2014-01-01

Multidrug-resistant Acinetobacter baumannii commonly causes hospital outbreaks. However, within an outbreak, it can be difficult to identify the routes of cross-infection rapidly and accurately enough to inform infection control. Here, we describe a protracted hospital outbreak of multidrug-resistant A. baumannii, in which whole-genome sequencing (WGS) was used to obtain a high-resolution view of the relationships between isolates. To delineate and investigate the outbreak, we attempted to genome-sequence 114 isolates that had been assigned to the A. baumannii complex by the Vitek2 system and obtained informative draft genome sequences from 102 of them. Genomes were mapped against an outbreak reference sequence to identify single nucleotide variants (SNVs). We found that the pulsotype 27 outbreak strain was distinct from all other genome-sequenced strains. Seventy-four isolates from 49 patients could be assigned to the pulsotype 27 outbreak on the basis of genomic similarity, while WGS allowed 18 isolates to be ruled out of the outbreak. Among the pulsotype 27 outbreak isolates, we identified 31 SNVs and seven major genotypic clusters. In two patients, we documented within-host diversity, including mixtures of unrelated strains and within-strain clouds of SNV diversity. By combining WGS and epidemiological data, we reconstructed potential transmission events that linked all but 10 of the patients and confirmed links between clinical and environmental isolates. Identification of a contaminated bed and a burns theatre as sources of transmission led to enhanced environmental decontamination procedures. WGS is now poised to make an impact on hospital infection prevention and control, delivering cost-effective identification of routes of infection within a clinically relevant timeframe and allowing infection control teams to track, and even prevent, the spread of drug-resistant hospital pathogens.

Reduced Mutation Rate and Increased Transformability of Transposon-Free Acinetobacter baylyi ADP1-ISx

PubMed Central

Suárez, Gabriel A.; Renda, Brian A.; Dasgupta, Aurko

2017-01-01

ABSTRACT The genomes of most bacteria contain mobile DNA elements that can contribute to undesirable genetic instability in engineered cells. In particular, transposable insertion sequence (IS) elements can rapidly inactivate genes that are important for a designed function. We deleted all six copies of IS1236 from the genome of the naturally transformable bacterium Acinetobacter baylyi ADP1. The natural competence of ADP1 made it possible to rapidly repair deleterious point mutations that arose during strain construction. In the resulting ADP1-ISx strain, the rates of mutations inactivating a reporter gene were reduced by 7- to 21-fold. This reduction was higher than expected from the incidence of new IS1236 insertions found during a 300-day mutation accumulation experiment with wild-type ADP1 that was used to estimate spontaneous mutation rates in the strain. The extra improvement appears to be due in part to eliminating large deletions caused by IS1236 activity, as the point mutation rate was unchanged in ADP1-ISx. Deletion of an error-prone polymerase (dinP) and a DNA damage response regulator (umuDAb [the umuD gene of A. baylyi]) from the ADP1-ISx genome did not further reduce mutation rates. Surprisingly, ADP1-ISx exhibited increased transformability. This improvement may be due to less autolysis and aggregation of the engineered cells than of the wild type. Thus, deleting IS elements from the ADP1 genome led to a greater than expected increase in evolutionary reliability and unexpectedly enhanced other key strain properties, as has been observed for other clean-genome bacterial strains. ADP1-ISx is an improved chassis for metabolic engineering and other applications. IMPORTANCE Acinetobacter baylyi ADP1 has been proposed as a next-generation bacterial host for synthetic biology and genome engineering due to its ability to efficiently take up DNA from its environment during normal growth. We deleted transposable elements that are capable of copying themselves, inserting into other genes, and thereby inactivating them from the ADP1 genome. The resulting “clean-genome” ADP1-ISx strain exhibited larger reductions in the rates of inactivating mutations than expected from spontaneous mutation rates measured via whole-genome sequencing of lineages evolved under relaxed selection. Surprisingly, we also found that IS element activity reduces transformability and is a major cause of cell aggregation and death in wild-type ADP1 grown under normal laboratory conditions. More generally, our results demonstrate that domesticating a bacterial genome by removing mobile DNA elements that have accumulated during evolution in the wild can have unanticipated benefits. PMID:28667117

Annual Surveillance Summary: Acinetobacter Species Infections in the Military Health System (MHS), 2016

DTIC Science & Technology

2017-06-01

exposures, Defense Manpower Data Center (DMDC) rosters to determine burden among Department of Defense (DOD) active duty (AD) service members, and the...above weighted historic IRs with the exception of the Marine Corps and Department of Defense (DOD) active duty (AD) populations. All current rates... Active Duty 119 8.7 Family Members 218 4.0 Retired 80 3.7 Othera 84 -- Gender Age Group (in Years) Beneficiary Type 4 Acinetobacter in the

Molecular Epidemiology and Clinical Impact of Acinetobacter calcoaceticus-baumannii Complex in a Belgian Burn Wound Center

PubMed Central

Bilocq, Florence; Jennes, Serge; Verbeken, Gilbert; Rose, Thomas; Keersebilck, Elkana; Bosmans, Petra; Pieters, Thierry; Hing, Mony; Heuninckx, Walter; De Pauw, Frank; Soentjens, Patrick; Merabishvili, Maia; Deschaght, Pieter; Vaneechoutte, Mario; Bogaerts, Pierre; Glupczynski, Youri; Pot, Bruno; van der Reijden, Tanny J.; Dijkshoorn, Lenie

2016-01-01

Multidrug resistant Acinetobacter baumannii and its closely related species A. pittii and A. nosocomialis, all members of the Acinetobacter calcoaceticus-baumannii (Acb) complex, are a major cause of hospital acquired infection. In the burn wound center of the Queen Astrid military hospital in Brussels, 48 patients were colonized or infected with Acb complex over a 52-month period. We report the molecular epidemiology of these organisms, their clinical impact and infection control measures taken. A representative set of 157 Acb complex isolates was analyzed using repetitive sequence-based PCR (rep-PCR) (DiversiLab) and a multiplex PCR targeting OXA-51-like and OXA-23-like genes. We identified 31 rep-PCR genotypes (strains). Representatives of each rep-type were identified to species by rpoB sequence analysis: 13 types to A. baumannii, 10 to A. pittii, and 3 to A. nosocomialis. It was assumed that isolates that belonged to the same rep-type also belonged to the same species. Thus, 83.4% of all isolates were identified to A. baumannii, 9.6% to A. pittii and 4.5% to A. nosocomialis. We observed 12 extensively drug resistant Acb strains (10 A. baumannii and 2 A. nosocomialis), all carbapenem-non-susceptible/colistin-susceptible and imported into the burn wound center through patients injured in North Africa. The two most prevalent rep-types 12 and 13 harbored an OXA-23-like gene. Multilocus sequence typing allocated them to clonal complex 1 corresponding to EU (international) clone I. Both strains caused consecutive outbreaks, interspersed with periods of apparent eradication. Patients infected with carbapenem resistant A. baumannii were successfully treated with colistin/rifampicin. Extensive infection control measures were required to eradicate the organisms. Acinetobacter infection and colonization was not associated with increased attributable mortality. PMID:27223476

Molecular Epidemiology and Clinical Impact of Acinetobacter calcoaceticus-baumannii Complex in a Belgian Burn Wound Center.

PubMed

De Vos, Daniel; Pirnay, Jean-Paul; Bilocq, Florence; Jennes, Serge; Verbeken, Gilbert; Rose, Thomas; Keersebilck, Elkana; Bosmans, Petra; Pieters, Thierry; Hing, Mony; Heuninckx, Walter; De Pauw, Frank; Soentjens, Patrick; Merabishvili, Maia; Deschaght, Pieter; Vaneechoutte, Mario; Bogaerts, Pierre; Glupczynski, Youri; Pot, Bruno; van der Reijden, Tanny J; Dijkshoorn, Lenie

2016-01-01

Multidrug resistant Acinetobacter baumannii and its closely related species A. pittii and A. nosocomialis, all members of the Acinetobacter calcoaceticus-baumannii (Acb) complex, are a major cause of hospital acquired infection. In the burn wound center of the Queen Astrid military hospital in Brussels, 48 patients were colonized or infected with Acb complex over a 52-month period. We report the molecular epidemiology of these organisms, their clinical impact and infection control measures taken. A representative set of 157 Acb complex isolates was analyzed using repetitive sequence-based PCR (rep-PCR) (DiversiLab) and a multiplex PCR targeting OXA-51-like and OXA-23-like genes. We identified 31 rep-PCR genotypes (strains). Representatives of each rep-type were identified to species by rpoB sequence analysis: 13 types to A. baumannii, 10 to A. pittii, and 3 to A. nosocomialis. It was assumed that isolates that belonged to the same rep-type also belonged to the same species. Thus, 83.4% of all isolates were identified to A. baumannii, 9.6% to A. pittii and 4.5% to A. nosocomialis. We observed 12 extensively drug resistant Acb strains (10 A. baumannii and 2 A. nosocomialis), all carbapenem-non-susceptible/colistin-susceptible and imported into the burn wound center through patients injured in North Africa. The two most prevalent rep-types 12 and 13 harbored an OXA-23-like gene. Multilocus sequence typing allocated them to clonal complex 1 corresponding to EU (international) clone I. Both strains caused consecutive outbreaks, interspersed with periods of apparent eradication. Patients infected with carbapenem resistant A. baumannii were successfully treated with colistin/rifampicin. Extensive infection control measures were required to eradicate the organisms. Acinetobacter infection and colonization was not associated with increased attributable mortality.

Substitutions of short heterologous DNA segments of intragenomic or extragenomic origins produce clustered genomic polymorphisms

PubMed Central

Harms, Klaus; Lunnan, Asbjørn; Hülter, Nils; Mourier, Tobias; Vinner, Lasse; Andam, Cheryl P.; Marttinen, Pekka; Fridholm, Helena; Hansen, Anders Johannes; Hanage, William P.; Nielsen, Kaare Magne; Willerslev, Eske; Johnsen, Pål Jarle

2016-01-01

In a screen for unexplained mutation events we identified a previously unrecognized mechanism generating clustered DNA polymorphisms such as microindels and cumulative SNPs. The mechanism, short-patch double illegitimate recombination (SPDIR), facilitates short single-stranded DNA molecules to invade and replace genomic DNA through two joint illegitimate recombination events. SPDIR is controlled by key components of the cellular genome maintenance machinery in the gram-negative bacterium Acinetobacter baylyi. The source DNA is primarily intragenomic but can also be acquired through horizontal gene transfer. The DNA replacements are nonreciprocal and locus independent. Bioinformatic approaches reveal occurrence of SPDIR events in the gram-positive human pathogen Streptococcus pneumoniae and in the human genome. PMID:27956618

PER-8, a Novel Extended-Spectrum β-Lactamase PER Variant, from an Acinetobacter baumannii Clinical Isolate in Nepal.

PubMed

Tada, Tatsuya; Shrestha, Shovita; Shimada, Kayo; Ohara, Hiroshi; Sherchand, Jeevan B; Pokhrel, Bharat M; Kirikae, Teruo

2017-03-01

A novel PER-type extended-spectrum β-lactamase, PER-8, was identified in an Acinetobacter baumannii clinical isolate obtained in Nepal. The amino acid sequence of PER-8 has a substitution at position 39 (Gly to Glu) compared with that of PER-7. The k cat / K m ratio of PER-8 for aztreonam was lower than that of PER-7, while the k cat / K m ratio of PER-8 for imipenem was higher than that of PER-7. The genomic environment surrounding bla PER-8 was intI1 bla PSE-1 qacEDI sulI IS CR1-bla PER-8 gts sulI orfX on a 100-kb plasmid. Copyright © 2017 American Society for Microbiology.

Antibiotic-Resistant Acinetobacter baumannii Increasing Success Remains a Challenge as a Nosocomial Pathogen

PubMed Central

Gonzalez-Villoria, Ana Maria; Valverde-Garduno, Veronica

2016-01-01

Antibiotic-resistant infectious bacteria currently imply a high risk and therefore constitute a strong challenge when treating patients in hospital settings. Characterization of these species and of particular strains is a priority for the establishment of diagnostic tests and preventive procedures. The relevance of Acinetobacter baumannii as a problematic microorganism in inpatient facilities, particularly intensive care units, has increased over time. This review aims to draw attention to (i) the historical emergence of carbapenem-resistant Acinetobacter baumannii, (ii) the current status of surveillance needs in Latin America, and (iii) recent data suggesting that A. baumannii continues to spread and evolve in hospital settings. First, we present synopsis of the series of events leading to the discovery and precise identification of this microorganism in hospital settings. Then key events in the acquisition of antibiotic-resistant genes by this microorganism are summarized, highlighting the race between new antibiotic generation and emergence of A. baumannii resistant strains. Here we review the historical development of this species as an infectious threat, the current state of its distribution, and antibiotic resistance characteristics, and we discuss future prospects for its control. PMID:26966582

Isolation and characterization of a virulent bacteriophage infecting Acinetobacter johnsonii from activated sludge.

PubMed

Fan, Niansi; Qi, Rong; Yang, Min

2017-06-01

A double-stranded DNA phage named AJO1, infecting Acinetobacter johnsonii, which plays an important role in wastewater treatment, was isolated from activated sludge in a full-scale municipal wastewater treatment plant. Based on morphological taxonomy, AJO1, with an icosahedral head 55 ± 2 nm in diameter and a non-contractile tail 8 ± 2 nm in length, was classified as a member of the Podoviridae family. Bacterial infection characteristics were as follows: no polyvalent infectivity, optimal multiplicity of infection of 10 -2 ; eclipse and burst size of 30 min and 51.2 PFU-infected cells -1 , respectively. It showed considerable infectivity under a neutral pH condition (pH 6.0-9.0) and relatively high temperature (55 °C). Whole-genome sequencing of AJO1 revealed a linearly permuted DNA (41 437 bp) carrying 54 putative open reading frames and 4 repeats. This is the first report of isolation of an A. johnsonii phage, whose bacteriophage distribution and population dynamics are not well known. The results of this study could contribute to subsequent research on the interaction between bacteriophages and their hosts during wastewater treatment. In addition, AJO1 may become a candidate for potential therapy against A. johnsonii infection in clinical applications, since this species is an opportunistic pathogen. Copyright © 2017 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

Microbial urate catabolism: characterization of HpyO, a non-homologous isofunctional isoform of the flavoprotein urate hydroxylase HpxO.

PubMed

Michiel, Magalie; Perchat, Nadia; Perret, Alain; Tricot, Sabine; Papeil, Aude; Besnard, Marielle; de Berardinis, Véronique; Salanoubat, Marcel; Fischer, Cécile

2012-12-01

In aerobic cells, urate is oxidized to 5-hydroxyisourate by two distinct enzymes: a coenzyme-independent urate oxidase (EC 1.7.3.3) found in eukaryotes and bacteria like Bacillus subtilis and a prokaryotic flavoprotein urate hydroxylase (HpxO) originally found in some Klebsiella species. More cases of analogous or non-homologous isofunctional enzymes (NISE) for urate catabolism have been hypothesized by inspecting bacterial genomes. Here, we used a functional complementation approach in which a candidate gene for urate oxidation is integrated by homologous recombination in the Acinetobacter baylyi ADP1 genome at the locus of its original hpxO gene. Catabolism of urate was restored in A. baylyi ADP1 expressing a FAD-dependent protein from Xanthomonas campestris, representing a new urate hydroxylase family that we called HpyO. This enzyme was kinetically characterized and compared with other HpxO enzymes. In contrast to the latter, HpyO is a typical Michaelian enzyme. This work provides the first experimental evidences for the function of HpyO in bacterial urate catabolism and establishes it as a NISE of HpxO. © 2012 Society for Applied Microbiology and Blackwell Publishing Ltd.

Cultural and chemical characterization of CDC groups EO-2, M-5, and M-6, Moraxella (Moraxella) species, Oligella urethralis, Acinetobacter species, and Psychrobacter immobilis.

PubMed

Moss, C W; Wallace, P L; Hollis, D G; Weaver, R E

1988-03-01

We determined phenotypic characteristics, cellular fatty acid composition, and isoprenoid quinone content of representative strains of CDC groups EO-2, M-5, and M-6, Moraxella (Moraxella) species, Oligella urethralis, Acinetobacter species, and Psychrobacter immobilis. All organisms contained ubiquinone with eight isoprene units as the major isoprenolog, but distinct differences were observed in fatty acid composition. Twenty-eight of the original collection of CDC group EO-2 strains were further identified as P. immobilis, EO-2, or EO-3 by distinctive cellular fatty acid profiles, cellular morphology, and pigment production. The cellular fatty acid compositions of M-5 and M-6 were similar but were clearly different from those of other organisms. The genus Acinetobacter was differentiated from other organisms in the study by small amounts of 2-hydroxydodecanoic acid (2-OH-12:0), and P. immobilis was differentiated by small amounts of decanoic acid (10:0) and a branched-chain 17-carbon acid (i-17:0). All Moraxella species were distinguished by small amounts of decanoic acid (10:0) and the absence of i-17:0. M. bovis, M. nonliquefaciens, and some strains of M. lacunata formed a single fatty acid group, while M. osloensis, M. phenylpyruvica, M. atlantae, and other strains of M. lacunata (M. lacunata II) had species-specific fatty acid profiles. O. urethralis differed from Moraxella species by the presence of large amounts (49%) of cis-vaccenic acid (18:1 omega 7c), small amounts (1%) of 3-hydroxyhexadecanoate (3-OH-16:0), and the absence of 10:0 and 3-hydroxydodecanoate (3-OH-12:0). The combined use of chemical data and a small number of conventional tests permitted rapid identification and differentiation of these organisms from each other and from related organisms.

Cultural and chemical characterization of CDC groups EO-2, M-5, and M-6, Moraxella (Moraxella) species, Oligella urethralis, Acinetobacter species, and Psychrobacter immobilis.

PubMed Central

Moss, C W; Wallace, P L; Hollis, D G; Weaver, R E

1988-01-01

We determined phenotypic characteristics, cellular fatty acid composition, and isoprenoid quinone content of representative strains of CDC groups EO-2, M-5, and M-6, Moraxella (Moraxella) species, Oligella urethralis, Acinetobacter species, and Psychrobacter immobilis. All organisms contained ubiquinone with eight isoprene units as the major isoprenolog, but distinct differences were observed in fatty acid composition. Twenty-eight of the original collection of CDC group EO-2 strains were further identified as P. immobilis, EO-2, or EO-3 by distinctive cellular fatty acid profiles, cellular morphology, and pigment production. The cellular fatty acid compositions of M-5 and M-6 were similar but were clearly different from those of other organisms. The genus Acinetobacter was differentiated from other organisms in the study by small amounts of 2-hydroxydodecanoic acid (2-OH-12:0), and P. immobilis was differentiated by small amounts of decanoic acid (10:0) and a branched-chain 17-carbon acid (i-17:0). All Moraxella species were distinguished by small amounts of decanoic acid (10:0) and the absence of i-17:0. M. bovis, M. nonliquefaciens, and some strains of M. lacunata formed a single fatty acid group, while M. osloensis, M. phenylpyruvica, M. atlantae, and other strains of M. lacunata (M. lacunata II) had species-specific fatty acid profiles. O. urethralis differed from Moraxella species by the presence of large amounts (49%) of cis-vaccenic acid (18:1 omega 7c), small amounts (1%) of 3-hydroxyhexadecanoate (3-OH-16:0), and the absence of 10:0 and 3-hydroxydodecanoate (3-OH-12:0). The combined use of chemical data and a small number of conventional tests permitted rapid identification and differentiation of these organisms from each other and from related organisms. Images PMID:3356788

Small, Enigmatic Plasmids of the Nosocomial Pathogen, Acinetobacter baumannii: Good, Bad, Who Knows?

PubMed Central

Lean, Soo Sum; Yeo, Chew Chieng

2017-01-01

Acinetobacter baumannii is a Gram-negative nosocomial pathogen that has become a serious healthcare concern within a span of two decades due to its ability to rapidly acquire resistance to all classes of antimicrobial compounds. One of the key features of the A. baumannii genome is an open pan genome with a plethora of plasmids, transposons, integrons, and genomic islands, all of which play important roles in the evolution and success of this clinical pathogen, particularly in the acquisition of multidrug resistance determinants. An interesting genetic feature seen in majority of A. baumannii genomes analyzed is the presence of small plasmids that usually ranged from 2 to 10 kb in size, some of which harbor antibiotic resistance genes and homologs of plasmid mobilization genes. These plasmids are often overlooked when compared to their larger, conjugative counterparts that harbor multiple antibiotic resistance genes and transposable elements. In this mini-review, we will examine our current knowledge of these small A. baumannii plasmids and look into their genetic diversity and phylogenetic relationships. Some of these plasmids, such as the Rep-3 superfamily group and the pRAY-type, which has no recognizable replicase genes, are quite widespread among diverse A. baumannii clinical isolates worldwide, hinting at their usefulness to the lifestyle of this pathogen. Other small plasmids especially those from the Rep-1 superfamily are truly enigmatic, encoding only hypothetical proteins of unknown function, leading to the question of whether these small plasmids are “good” or “bad” to their host A. baumannii. PMID:28861061

Detection of Multi-drug Resistant Acinetobacter Lwoffii Isolated from Soil of Mink Farm.

PubMed

Sun, Na; Wen, Yong Jun; Zhang, Shu Qin; Zhu, Hong Wei; Guo, Li; Wang, Feng Xue; Chen, Qiang; Ma, Hong Xia; Cheng, Shi Peng

2016-07-01

There were 4 Acinetobacter lwoffii obtained from soil samples. The antimicrobial susceptibility of the strains to 16 antimicrobial agents was investigated using K-B method. Three isolates showed the multi-drug resistance. The presence of resistance genes and integrons was determined using PCR. The aadA1, aac(3')-IIc, aph(3')-VII, aac(6')-Ib, sul2, cat2, floR, and tet(K) genes were detected, respectively. Three class 1 integrons were obtained. The arr-3-aacA4 and blaPSE-1 gene cassette, which cause resistance to aminoglycoside and beta-lactamase antibiotics. Our results reported the detection of multi-drug resistant and carried resistant genes Acinetobacter lwoffii from soil. The findings suggested that we should pay close attention to the prevalence of multi-drug resistant bacterial species of environment. Copyright © 2016 The Editorial Board of Biomedical and Environmental Sciences. Published by China CDC. All rights reserved.

Prolonged and high dosage of tigecycline - successful treatment of spondylodiscitis caused by multidrug-resistant Acinetobacter baumannii: a case report.

PubMed

Tsachouridou, Olga; Georgiou, Adamantini; Nanoudis, Sideris; Chrysanthidis, Theofilos; Loli, Georgia; Morfesis, Petros; Zebekakis, Pantelis; Metallidis, Symeon

2017-07-08

The incidence of infectious spondylodiscitis has been increasing over the last few years. This reflects the expanding elderly and immunocompromised populations and the rising implementation of invasive spinal procedures. Infection may be inoculated into the disc space directly during invasive spinal procedures. Osteomyelitis caused by Acinetobacter species is rare and mainly caused by multidrug-resistant strains. We present the case of a 72-year-old Greek woman with postoperative spondylodiscitis caused by a multidrug-resistant Acinetobacter baumannii strain that was successfully treated, after she declined surgical treatment, with prolonged and high dosage of tigecycline. She received intravenously administered tigecycline 200 mg per day for 60 days and then 100 mg per day for a total of 102 days and was infection-free. We reviewed the literature on the role of Acinetobacter baumannii as a cause of osteomyelitis, emphasizing the difficulty of treatment and the potential role of tigecycline in conservative treatment of the infection. We believe that 102 days in total is the longest time that any patient has received tigecycline in the literature, thus our patient is a unique case of successful treatment of spondylodiscitis.

Distribution and Molecular Characterization of Acinetobacter baumannii International Clone II Lineage in Japan.

PubMed

Matsui, Mari; Suzuki, Masato; Suzuki, Masahiro; Yatsuyanagi, Jun; Watahiki, Masanori; Hiraki, Yoichi; Kawano, Fumio; Tsutsui, Atsuko; Shibayama, Keigo; Suzuki, Satowa

2018-02-01

Multidrug-resistant (MDR) Acinetobacter spp. have been globally disseminated in association with the successful clonal lineage Acinetobacter baumannii international clone II (IC II). Because the prevalence of MDR Acinetobacter spp. in Japan remains very low, we characterized all Acinetobacter spp. ( n = 866) from 76 hospitals between October 2012 and March 2013 to describe the entire molecular epidemiology of Acinetobacter spp. The most prevalent species was A. baumannii ( n = 645; 74.5%), with A. baumannii IC II ( n = 245) accounting for 28.3% of the total. Meropenem-resistant isolates accounted for 2.0% ( n = 17) and carried IS Aba1-bla OXA-23-like ( n = 10), bla IMP ( n = 4), or IS Aba1-bla OXA-51-like ( n = 3). Multilocus sequence typing of 110 representative A. baumannii isolates revealed the considerable prevalence of domestic sequence types (STs). A. baumannii IC II isolates were divided into the domestic sequence type 469 (ST469) ( n = 18) and the globally disseminated STs ST208 ( n = 14) and ST219 ( n = 4). ST469 isolates were susceptible to more antimicrobial agents, while ST208 and ST219 overproduced the intrinsic AmpC β-lactamase. A. baumannii IC II and some A. baumannii non-IC II STs (e.g., ST149 and ST246) were associated with fluoroquinolone resistance. This study revealed that carbapenem-susceptible A. baumannii IC II was moderately disseminated in Japan. The low prevalence of acquired carbapenemase genes and presence of domestic STs could contribute to the low prevalence of MDR A. baumannii A similar epidemiology might have appeared before the global dissemination of MDR epidemic lineages. In addition, fluoroquinolone resistance associated with A. baumannii IC II may provide insight into the significance of A. baumannii epidemic clones. Copyright © 2018 American Society for Microbiology.

Diversity within the O-linked protein glycosylation systems of acinetobacter species.

PubMed

Scott, Nichollas E; Kinsella, Rachel L; Edwards, Alistair V G; Larsen, Martin R; Dutta, Sucharita; Saba, Julian; Foster, Leonard J; Feldman, Mario F

2014-09-01

The opportunistic human pathogen Acinetobacter baumannii is a concern to health care systems worldwide because of its persistence in clinical settings and the growing frequency of multiple drug resistant infections. To combat this threat, it is necessary to understand factors associated with disease and environmental persistence of A. baumannii. Recently, it was shown that a single biosynthetic pathway was responsible for the generation of capsule polysaccharide and O-linked protein glycosylation. Because of the requirement of these carbohydrates for virulence and the non-template driven nature of glycan biogenesis we investigated the composition, diversity, and properties of the Acinetobacter glycoproteome. Utilizing global and targeted mass spectrometry methods, we examined 15 strains and found extensive glycan diversity in the O-linked glycoproteome of Acinetobacter. Comparison of the 26 glycoproteins identified revealed that different A. baumannii strains target similar protein substrates, both in characteristics of the sites of O-glycosylation and protein identity. Surprisingly, glycan micro-heterogeneity was also observed within nearly all isolates examined demonstrating glycan heterogeneity is a widespread phenomena in Acinetobacter O-linked glycosylation. By comparing the 11 main glycoforms and over 20 alternative glycoforms characterized within the 15 strains, trends within the glycan utilized for O-linked glycosylation could be observed. These trends reveal Acinetobacter O-linked glycosylation favors short (three to five residue) glycans with limited branching containing negatively charged sugars such as GlcNAc3NAcA4OAc or legionaminic/pseudaminic acid derivatives. These observations suggest that although highly diverse, the capsule/O-linked glycan biosynthetic pathways generate glycans with similar characteristics across all A. baumannii. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

Evaluation of High-Resolution Melting Curve Analysis of Ligation-Mediated Real-Time PCR, a Rapid Method for Epidemiological Typing of ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter Species) Pathogens

PubMed Central

Ryberg, Anna; Billström, Hanna; Hällgren, Anita; Nilsson, Lennart E.; Marklund, Britt-Inger; Olsson-Liljequist, Barbro; Schön, Thomas

2014-01-01

A single-tube method, ligation-mediated real-time PCR high-resolution melt analysis (LMqPCR HRMA), was modified for the rapid typing of Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp. (ESKAPE) pathogens. A 97% agreement (60/62 isolates) was achieved in comparison to pulsed-field gel electrophoresis (PFGE) results, which indicates that LMqPCR HRMA is a rapid and accurate screening tool for monitoring nosocomial outbreaks. PMID:25232168

Comparison of the Virulence-Associated Phenotypes of Five Species of Acinetobacter baumannii Complex.

PubMed

Na, In Young; Chung, Eun Seon; Jung, Chang-Yun; Kim, Dae Hun; Shin, Juyoun; Kang, KyeongJin; Kim, Seong-Tae; Ko, Kwan Soo

2016-01-01

In this study, we compared the virulence-associated factors of Acinetobacter baumannii complex species. Sixty-three isolates of five A. baumannii complex species, including 19 A. baumannii, 15 A. nosocomialis, 13 A. seifertii, 13 A. pittii, and 3 A. calcoaceticus isolates, were included in this study. For all isolates, biofilm formation, A549 cell adherence, resistance to normal human serum, and motility were evaluated. A. baumannii complex isolates showed diversity in biofilm formation, A549 cell adherence, and serum resistance, and no strong positive relationships among these virulence characteristics. However, A. seifertii showed relatively consistent virulence-associated phenotypes. In addition, A. baumannii clone ST110 exhibited consistently high virulence-associated phenotypes. Motility was observed in seven isolates, and all four A. baumannii ST110 isolates showed twitching motility. Although some inconsistencies in virulence-associated phenotypes were seen, high virulence characteristics were observed in A. seifertii, which has been mainly reported in Korea and shows high rates of colistin resistance.

Molecular detection of six (endo-) symbiotic bacteria in Belgian mosquitoes: first step towards the selection of appropriate paratransgenesis candidates.

PubMed

Raharimalala, Fara Nantenaina; Boukraa, S; Bawin, T; Boyer, S; Francis, F

2016-04-01

Actually, the use of symbiotic bacteria is one of alternative solution to avoid vector resistance to pesticides. In Belgium, among 31 identified mosquito species, 10 were considered as potential vectors. Given to introduction risks of arbovirosis, the purpose of this study was to investigate the presence of symbiosis bacteria in potential mosquito vectors. Eleven species caught from 12 sites in Belgium were used: Culex pipiens s.l., Culex torrentium, Culex hortensis, Anopheles claviger, Anopheles maculipennis s.l., Anopheles plumbeus, Culiseta annulata, Ochlerotatus geniculatus, Ochlerotatus dorsalis, Aedes albopictus, and Coquillettidia richiardii. Six genera of symbiotic bacteria were screened: Wolbachia sp., Comamonas sp, Delftia sp., Pseudomonas sp., Acinetobacter sp., and Asaia sp. A total of 173 mosquito individuals (144 larvae and 29 adults) were used for the polymerase chain reaction screening. Wolbachia was not found in any Anopheles species nor Cx. torrentium. A total absence of Comamonas and Delftia was observed in all species. Acinetobacter, Pseudomonas, and Asaia were found in most of species with a high prevalence for Pseudomonas. These results were discussed to develop potential strategy and exploit the variable occurrence of symbiotic bacteria to focus on them to propose biological ways of mosquito control.

Nature, nomenclature and taxonomy of obligate methanol utilizing strains.

PubMed

Cercel, M

1999-01-01

In a screening program, a number of different bacterial strains with the ability to utilize methanol as a sole carbon and energy source were isolated and described. They are well known methanol utilizing genera Pseudomonas, Klebsiella, Micrococcus, Methylomonas or, on the contrary, the new, unknown genera and species of methylotrophic bacteria. In the last category, Acinetobacter and Alcaligenes are the new reported genera of organisms able to use methanol as a sole carbon and energy source. The present paper reports the very complex physiological and biochemical modifications when very versatile bacteria such as Pseudomonas aeruginosa and Acinetobacter calcoaceticus are cultured on methanol and when the obligate methylotrophic state is compared with the facultative methylotrophic state of the same bacterial strain. Based on experiments and comparisons with literature data, it seems that Methylomonas methanica is the obligate methylotrophic state of Pseudomonas aeruginosa and that Acinetobacter calcoaceticus is the facultative methylotrophic state of Methylococcus capsulatus, an obligate methylotroph. The relationship of the obligate to the facultative and of the facultative to the obligate methylotrophy were established. These new methylotrophic genera and species, the profound physiological and biochemical modifications as well as the new data concerning nature, nomenclature and taxonomy of methanol utilizing bateria were reported for the first time in 1983.

Five-Year Antimicrobial Susceptibility Trends Among Bacterial Isolates from a Tertiary Health-Care Facility in Kigali, Rwanda.

PubMed

Carroll, Makeda; Rangaiahagari, Ashok; Musabeyezu, Emmanuel; Singer, Donald; Ogbuagu, Onyema

2016-12-07

Antimicrobial resistance (AMR) is a global public health threat. There is limited information from Rwanda on AMR trends. This longitudinal study aimed to describe temporal trends of antibiotic susceptibility among common bacteria. We collated the antimicrobial susceptibility results of bacteria cultured from clinical specimens collected from inpatients and outpatients and submitted to the microbiology laboratory at King Faisal Hospital, Kigali, Rwanda, from January 1, 2009, to December 31, 2013. Differences in antimicrobial susceptibility between the first and fifth year of the study for each bacterial species was assessed using χ 2 test. Of 5,296 isolates collected, 46.7% were Escherichia coli, 18.4% were Klebsiella spp., 5.9% were Acinetobacter spp., 7.1% were Pseudomonas spp., 11.7% were Staphylococcus aureus, and 10.3% were Enterococcus spp. Colistin and imipenem had greatest activity against gram-negative bacteria. Acinetobacter spp. showed the greatest resistance profile to antimicrobials tested, relative to other gram-negative bacteria. Vancomycin retained excellent activity against S. aureus and Enterococcus species (average susceptibility was 100% and 99.4%, respectively). Trend analysis determined that resistance to imipenem increased significantly among Klebsiella, E. coli, Pseudomonas, and Acinetobacter isolates; there was also rising resistance to colistin among E. coli and Pseudomonas species. Only E. coli demonstrated increased resistance to gentamicin. For gram-positive pathogens, vancomycin susceptibility increased over time for Enterococcus species, but was unchanged for S. aureus Our data suggest that resistance to imipenem and colistin are rising among gram-negative bacteria in Rwanda. Proper infection control practices and antimicrobial stewardship will be important to address this emerging threat. © The American Society of Tropical Medicine and Hygiene.

Identification of Lama glama as Reservoirs for Acinetobacter lwoffii

PubMed Central

Ledesma, Martín M.; Díaz, Ailén M.; Barberis, Claudia; Vay, Carlos; Manghi, Marcela A.; Leoni, Juliana; Castro, Marisa S.; Ferrari, Alejandro

2017-01-01

South American Camelids have an increasing relevance in local economies, worldwide. These animals are bred for their meat, fur and as companion and therapy animals. Thus, their sanitary status should be well-established. According to the OIE (World Organization for Animal Health), respiratory infections mainly produced by Pasteurella spp. have been reported for camelids. It has been stated that this microorganism causes a mild disease, although many authors report it is an important cause of mortality among alpacas. Nevertheless, the incidence of infection by Pasteurella spp. in camelids still needs to be investigated. The aim of the present study was to analyze the occurrence of nasopharyngeal colonization of Lama glama by respiratory bacteria, and to assess the usefulness of serological tests for clinical diagnosis. The colonization was studied by culture techniques carried out with material taken by nasopharyngeal swabs. Bacterial isolates were first phenotypically characterized and then identified by MALDI/TOF-MS. The presence of specific serum antibodies was studied by ELISA and Western blot. In the present work Pasteurella spp. was not found. Nevertheless, we report for the first time, the colonization of L. glama by bacteria of the Acinetobacter lwoffii, at a reliable level in 19.4% of the animals. Acinetobacter species are found in different environmental sources, as well as vegetables, animals, and humans, and their role in infections has recently gained relevance. The results presented herein contribute to a better understanding of the respiratory microbiota in camelids, and increase the knowledge about environmental distribution of Acinetobacter non-baumanii species. Given that these respiratory bacteria might be the cause of infection among cattle, and even humans, this report highlights the need for further research. PMID:28303121

Evaluation of high-resolution melting curve analysis of ligation-mediated real-time PCR, a rapid method for epidemiological typing of ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter Species) pathogens.

PubMed

Woksepp, Hanna; Ryberg, Anna; Billström, Hanna; Hällgren, Anita; Nilsson, Lennart E; Marklund, Britt-Inger; Olsson-Liljequist, Barbro; Schön, Thomas

2014-12-01

A single-tube method, ligation-mediated real-time PCR high-resolution melt analysis (LMqPCR HRMA), was modified for the rapid typing of Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp. (ESKAPE) pathogens. A 97% agreement (60/62 isolates) was achieved in comparison to pulsed-field gel electrophoresis (PFGE) results, which indicates that LMqPCR HRMA is a rapid and accurate screening tool for monitoring nosocomial outbreaks. Copyright © 2014, American Society for Microbiology. All Rights Reserved.

Metagenomic analysis of medicinal Cannabis samples; pathogenic bacteria, toxigenic fungi, and beneficial microbes grow in culture-based yeast and mold tests.

PubMed

McKernan, Kevin; Spangler, Jessica; Helbert, Yvonne; Lynch, Ryan C; Devitt-Lee, Adrian; Zhang, Lei; Orphe, Wendell; Warner, Jason; Foss, Theodore; Hudalla, Christopher J; Silva, Matthew; Smith, Douglas R

2016-01-01

Background : The presence of bacteria and fungi in medicinal or recreational Cannabis poses a potential threat to consumers if those microbes include pathogenic or toxigenic species. This study evaluated two widely used culture-based platforms for total yeast and mold (TYM) testing marketed by 3M Corporation and Biomérieux, in comparison with a quantitative PCR (qPCR) approach marketed by Medicinal Genomics Corporation. Methods : A set of 15 medicinal Cannabis samples were analyzed using 3M and Biomérieux culture-based platforms and by qPCR to quantify microbial DNA. All samples were then subjected to next-generation sequencing and metagenomics analysis to enumerate the bacteria and fungi present before and after growth on culture-based media. Results : Several pathogenic or toxigenic bacterial and fungal species were identified in proportions of >5% of classified reads on the samples, including Acinetobacter baumannii, Escherichia coli, Pseudomonas aeruginosa, Ralstonia pickettii, Salmonella enterica, Stenotrophomonas maltophilia, Aspergillus ostianus, Aspergillus sydowii, Penicillium citrinum and Penicillium steckii. Samples subjected to culture showed substantial shifts in the number and diversity of species present, including the failure of Aspergillus species to grow well on either platform. Substantial growth of Clostridium botulinum and other bacteria were frequently observed on one or both of the culture-based TYM platforms. The presence of plant growth promoting (beneficial) fungal species further influenced the differential growth of species in the microbiome of each sample. Conclusions : These findings have important implications for the Cannabis and food safety testing industries.

Metagenomic analysis of medicinal Cannabis samples; pathogenic bacteria, toxigenic fungi, and beneficial microbes grow in culture-based yeast and mold tests

PubMed Central

McKernan, Kevin; Spangler, Jessica; Helbert, Yvonne; Lynch, Ryan C.; Devitt-Lee, Adrian; Zhang, Lei; Orphe, Wendell; Warner, Jason; Foss, Theodore; Hudalla, Christopher J.; Silva, Matthew; Smith, Douglas R.

2016-01-01

Background: The presence of bacteria and fungi in medicinal or recreational Cannabis poses a potential threat to consumers if those microbes include pathogenic or toxigenic species. This study evaluated two widely used culture-based platforms for total yeast and mold (TYM) testing marketed by 3M Corporation and Biomérieux, in comparison with a quantitative PCR (qPCR) approach marketed by Medicinal Genomics Corporation. Methods: A set of 15 medicinal Cannabis samples were analyzed using 3M and Biomérieux culture-based platforms and by qPCR to quantify microbial DNA. All samples were then subjected to next-generation sequencing and metagenomics analysis to enumerate the bacteria and fungi present before and after growth on culture-based media. Results: Several pathogenic or toxigenic bacterial and fungal species were identified in proportions of >5% of classified reads on the samples, including Acinetobacter baumannii, Escherichia coli, Pseudomonas aeruginosa, Ralstonia pickettii, Salmonella enterica, Stenotrophomonas maltophilia, Aspergillus ostianus, Aspergillus sydowii, Penicillium citrinum and Penicillium steckii. Samples subjected to culture showed substantial shifts in the number and diversity of species present, including the failure of Aspergillus species to grow well on either platform. Substantial growth of Clostridium botulinum and other bacteria were frequently observed on one or both of the culture-based TYM platforms. The presence of plant growth promoting (beneficial) fungal species further influenced the differential growth of species in the microbiome of each sample. Conclusions: These findings have important implications for the Cannabis and food safety testing industries. PMID:27853518

Extremophilic Acinetobacter strains from high-altitude lakes in Argentinean Puna: remarkable UV-B resistance and efficient DNA damage repair.

PubMed

Albarracín, Virginia Helena; Pathak, Gopal P; Douki, Thierry; Cadet, Jean; Borsarelli, Claudio Darío; Gärtner, Wolfgang; Farias, María Eugenia

2012-06-01

High-Altitude Andean Lakes (HAAL) of the South American Andes are almost unexplored ecosystems of shallow lakes. The HAAL are recognized by a remarkably high UV exposure, strong changes in temperature and salinity, and a high content of toxic elements, especially arsenic. Being exposed to remarkably extreme conditions, they have been classified as model systems for the study of life on other planets. Particularly, Acinetobacter strains isolated from the HAAL were studied for their survival competence under strong UV-B irradiation. Clinical isolates, Acinetobacter baumannii and Acinetobacter johnsonii, served as reference material. Whereas the reference strains rapidly lost viability under UV-B irradiation, most HAAL-derived strains readily survived this exposure and showed less change in cell number after the treatment. Controls for DNA repair activity, comparing dark repair (DR) or photo repair (PR), gave evidence for the involvement of photolyases in the DNA repair. Comparative measurements by HPLC-mass spectrometry detected the number of photoproducts: bipyrimidine dimers under both PR and DR treatments were more efficiently repaired in the HAAL strains (up to 85 % PR and 38 % DR) than in the controls (31 % PR and zero DR ability). Analysis of cosmid-cloned total genomic DNA from the most effective DNA-photorepair strain (Ver3) yielded a gene (HQ443199) encoding a protein with clear photolyase signatures belonging to class I CPD-photolyases. Despite the relatively low sequence similarity of 41 % between the enzymes from Ver3 and from E. coli (PDB 1DNPA), a model-building approach revealed a high structural homology to the CPD-photolyase of E. coli.

New insights into Acinetobacter baumannii pathogenesis revealed by high-density pyrosequencing and transposon mutagenesis.

PubMed

Smith, Michael G; Gianoulis, Tara A; Pukatzki, Stefan; Mekalanos, John J; Ornston, L Nicholas; Gerstein, Mark; Snyder, Michael

2007-03-01

Acinetobacter baumannii has emerged as an important and problematic human pathogen as it is the causative agent of several types of infections including pneumonia, meningitis, septicemia, and urinary tract infections. We explored the pathogenic content of this harmful pathogen using a combination of DNA sequencing and insertional mutagenesis. The genome of this organism was sequenced using a strategy involving high-density pyrosequencing, a novel, rapid method of high-throughput sequencing. Excluding the rDNA repeats, the assembled genome is 3,976,746 base pairs (bp) and has 3830 ORFs. A significant fraction of ORFs (17.2%) are located in 28 putative alien islands, indicating that the genome has acquired a large amount of foreign DNA. Consistent with its role in pathogenesis, a remarkable number of the islands (16) contain genes implicated in virulence, indicating the organism devotes a considerable portion of its genes to pathogenesis. The largest island contains elements homologous to the Legionella/Coxiella Type IV secretion apparatus. Type IV secretion systems have been demonstrated to be important for virulence in other organisms and thus are likely to help mediate pathogenesis of A. baumannii. Insertional mutagenesis generated avirulent isolates of A. baumannii and verified that six of the islands contain virulence genes, including two novel islands containing genes that lacked homology with others in the databases. The DNA sequencing approach described in this study allows the rapid elucidation of the DNA sequence of any microbe and, when combined with genetic screens, can identify many novel genes important for microbial pathogenesis.

Molecular mechanisms of antibiotic resistance in Acinetobacter baumannii with a special focus on its epidemiology in Lebanon.

PubMed

Jamal, Sabah; Atrouni, Ahmad Al; Rafei, Rayane; Dabboussi, Fouad; Hamze, Monzer; Osman, Marwan

2018-05-30

Acinetobacter baumannii is an opportunistic bacterium involved in several types of infection with high mortality and morbidity, especially in intensive care units. Treatment of these infections remains a challenge due to the worldwide emergence of broad-spectrum resistance to many antibiotics. Following the implementation of molecular techniques to study A. baumannii outbreaks, it has been shown that they are mainly caused by specific clones like international clone 1, 2 and 3. The present work aims to review the available data on the mechanisms underlying the antimicrobial resistance in A. baumannii with a special focus on the molecular epidemiology of this species in Lebanon. Copyright © 2018. Published by Elsevier Ltd.

Antimicrobial Susceptibility as a Diagnostic Aid in the Identification of Nonfermenting Gram-Negative Bacteria

PubMed Central

Gilardi, G. L.

1971-01-01

Antimicrobial susceptibility data regarding nonfermentative, gram-negative bacteria (Pseudomonas, Alcaligenes, Acinetobacter, Moraxella, Flavobacterium) are presented showing that the antibiograms of most species examined can be used as an important auxillary aid in their differentiation. PMID:5132093

Loss of LPS is involved in the virulence and resistance to colistin of colistin-resistant Acinetobacter nosocomialis mutants selected in vitro.

PubMed

Vila-Farrés, Xavier; Ferrer-Navarro, Mario; Callarisa, Anna Elena; Martí, Sara; Espinal, Paula; Gupta, Sushim; Rolain, Jean-Marc; Giralt, Ernest; Vila, Jordi

2015-11-01

Acinetobacter nosocomialis has increasingly been reported as an opportunistic pathogen causing nosocomial infections. Although it is more susceptible to all antimicrobial agents than Acinetobacter baumannii, MDR clinical isolates have also been described. In addition, several studies have shown a high percentage of resistance to colistin. Therefore, in the present study we investigated the mechanism of resistance to colistin in this microorganism. Colistin-resistant strains were selected from the original colistin-susceptible A. nosocomialis strain following multi-step mutant selection. Comparative genomic and proteomic analyses of both colistin-susceptible and colistin-resistant A. nosocomialis strains were performed. In addition, virulence was investigated using the Caenorhabditis elegans assay. The colistin-resistant mutants selected showed a lower resistance profile for other types of antibacterial agents together with a significant decrease in virulence. The LT50 (i.e. time required to kill 50% of the nematodes) for the colistin-susceptible strain (WT) was 7 days compared with 9 days for the colistin-resistant strain (256) (P < 0.0001). In the genomic studies, several mutations were observed in the lpxD genes, leading to the loss of LPS in the colistin-resistant strains. The proteomic studies showed several up- and down-regulated proteins that may be involved in colistin resistance or in a decrease in the resistance profile for several antibiotics. This study shows that the mechanism of resistance to colistin by A. nosocomialis is mainly associated with the loss of LPS due to mutations in the lpxD gene, although changes in the expression of some proteins cannot be ruled out. In addition, the acquisition of colistin resistance is related to a decrease in virulence. © The Author 2015. Published by Oxford University Press on behalf of the British Society for Antimicrobial Chemotherapy. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

High Prevalence of Ceftazidime-Resistant Klebsiella pneumoniae and Increase of Imipenem-Resistant Pseudomonas aeruginosa and Acinetobacter spp. in Korea: a KONSAR Program in 2004

PubMed Central

Lee, Kyungwon; Lim, Chang Hyun; Cho, Ji Hyun; Lee, Wee Gyo; Uh, Young; Kim, Hwi Jun; Yong, Dongeun

2006-01-01

A nationwide antimicrobial resistance surveillance has been conducted since 1997 in Korea. In this study, susceptibility test data generated in 2004 by KONSAR group hospitals were analyzed and compared to those at a commercial laboratory. In hospitals, the rank orders of organisms in 2004 were identical to those in 2003. The most prevalent species was Staphylococcus aureus (20.2%) in hospitals, but Escherichia coli (29.7%) in the commercial laboratory. The proportions of Enterococcus faecium to all isolates of Enterococcus faecalis plus E. faecium were 47.2% in hospitals and 24.9% in the commercial laboratory. The mean resistance rates of significant antimicrobial-organism combinations in hospitals were: oxacillin-resistant S. aureus (68%), oxacillin-resistant (penicillin-nonsusceptible) Streptococcus pneumoniae (68%), vancomycin-resistant E. faecium (25%), cefotaxime-resistant E. coli (14%), ceftazidime- and cefoxitin-resistant Klebsiella pneumoniae (34% and 32%, respectively), and imipenem-resistant Acinetobacter spp. and Pseudomonas aeruginosa (17% and 24%, respectively). In conclusion, oxacillin-resistant staphylococci, expanded-spectrum cephalosporin-resistant K. pneumoniae, and imipenem-resistant Acinetobacter spp. and P. aeruginosa were prevalent in 2004. Increasing trends were observed for vancomycin-resistant E. faecium, cefoxitin-resistant E. coli and K. pneumoniae, and imipenem-resistant Acinetobacter spp. and P. aeruginosa. Certain antimicrobial-organism combinations were also prevalent among the commercial laboratory-tested strains. PMID:17066507

Biological floating bed and bio-contact oxidation processes for landscape water treatment: simultaneous removal of Microcystis aeruginosa, TOC, nitrogen and phosphorus.

PubMed

Su, Jun Feng; Liang, Dong Hui; Fu, Le; Wei, Li; Ma, Min

2018-06-13

The aim of this study was to identify algicidal bacteria J25 against the Microcystis aeruginosa (90.14%), Chlorella (78.75%), Scenedesmus (not inhibited), and Oscillatoria (90.12%). Meanwhile, we evaluate the SOD activity and efficiency of denitrification characteristics with Acinetobacter sp. J25. A novel hybrid bioreactor combined biological floating bed with bio-contact oxidation (BFBO) was designed for treating the landscape water, and the average removal efficiencies of nitrate-N, ammonia-N, nitrite-N, TN, TP, TOC, and algal cells were 91.14, 50, 87.86, 88.83, 33.07, 53.95, and 53.43%, respectively. A 454-pyrosequencing technology was employed to investigate the microbial communities of the BFBO reactor samples. The results showed that Acinetobacter sp. J25 was the dominant contributor for effective removal of N, algal cells, and TOC in the BFBO reactor. And the relative abundance of Acinetobacter showed increase trend with the delay of reaction time. Graphical abstract Biological floating bed and bio-contact oxidation (BFBO) as a novel hybrid bioreactor designed for simultaneous removal Microcystis aeruginosa, TOC, nitrogen, and phosphorus. And high-throughput sequencing data demonstrated that Acinetobacter sp. J25 was the dominate species in the reactor and played key roles in the removal of N, TOC, and M. aeruginosa. Proposed reaction mechanism of the BFBO.

Rapid Molecular Characterization of Acinetobacter baumannii Clones with rep-PCR and Evaluation of Carbapenemase Genes by New Multiplex PCR in Hospital District of Helsinki and Uusimaa

PubMed Central

Pasanen, Tanja; Koskela, Suvi; Mero, Sointu; Tarkka, Eveliina; Tissari, Päivi; Vaara, Martti; Kirveskari, Juha

2014-01-01

Multidrug-resistant Acinetobacter baumannii (MDRAB) is an increasing problem worldwide. Prevalence of carbapenem resistance in Acinetobacter spp. due to acquired carbapenemase genes is not known in Finland. The purpose of this study was to examine prevalence and clonal spread of multiresistant A. baumannii group species, and their carbapenemase genes. A total of 55 Acinetobacter isolates were evaluated with repetitive PCR (DiversiLab) to analyse clonality of isolates, in conjunction with antimicrobial susceptibility profile for ampicillin/sulbactam, colistin, imipenem, meropenem, rifampicin and tigecycline. In addition, a new real-time PCR assay, detecting most clinically important carbapenemase genes just in two multiplex reactions, was developed. The assay detects genes for KPC, VIM, IMP, GES-1/-10, OXA-48, NDM, GIM-1, SPM-1, IMI/NMC-A, SME, CMY-10, SFC-1, SIM-1, OXA-23-like, OXA-24/40-like, OXA-58 and ISAbaI-OXA-51-like junction, and allows confident detection of isolates harbouring acquired carbapenemase genes. There was a time-dependent, clonal spread of multiresistant A. baumannii strongly correlating with carbapenamase gene profile, at least in this geographically restricted study material. The new carbapenemase screening assay was able to detect all the genes correctly suggesting it might be suitable for epidemiologic screening purposes in clinical laboratories. PMID:24465749

CRISPR-cas subtype I-Fb in Acinetobacter baumannii: evolution and utilization for strain subtyping.

PubMed

Karah, Nabil; Samuelsen, Ørjan; Zarrilli, Raffaele; Sahl, Jason W; Wai, Sun Nyunt; Uhlin, Bernt Eric

2015-01-01

Clustered regularly interspaced short palindromic repeats (CRISPR) are polymorphic elements found in the genome of some or all strains of particular bacterial species, providing them with a system of acquired immunity against invading bacteriophages and plasmids. Two CRISPR-Cas systems have been identified in Acinetobacter baumannii, an opportunistic pathogen with a remarkable capacity for clonal dissemination. In this study, we investigated the mode of evolution and diversity of spacers of the CRISPR-cas subtype I-Fb locus in a global collection of 76 isolates of A. baumannii obtained from 14 countries and 4 continents. The locus has basically evolved from a common ancestor following two main lineages and several pathways of vertical descent. However, this vertical passage has been interrupted by occasional events of horizontal transfer of the whole locus between distinct isolates. The isolates were assigned into 40 CRISPR-based sequence types (CST). CST1 and CST23-24 comprised 18 and 9 isolates, representing two main sub-clones of international clones CC1 and CC25, respectively. Epidemiological data showed that some of the CST1 isolates were acquired or imported from Iraq, where it has probably been endemic for more than one decade and occasionally been able to spread to USA, Canada, and Europe. CST23-24 has shown a remarkable ability to cause national outbreaks of infections in Sweden, Argentina, UAE, and USA. The three isolates of CST19 were independently imported from Thailand to Sweden and Norway, raising a concern about the prevalence of CST19 in Thailand. Our study highlights the dynamic nature of the CRISPR-cas subtype I-Fb locus in A. baumannii, and demonstrates the possibility of using a CRISPR-based approach for subtyping a significant part of the global population of A. baumannii.

CRISPR-cas Subtype I-Fb in Acinetobacter baumannii: Evolution and Utilization for Strain Subtyping

PubMed Central

Karah, Nabil; Samuelsen, Ørjan; Zarrilli, Raffaele; Sahl, Jason W.; Wai, Sun Nyunt; Uhlin, Bernt Eric

2015-01-01

Clustered regularly interspaced short palindromic repeats (CRISPR) are polymorphic elements found in the genome of some or all strains of particular bacterial species, providing them with a system of acquired immunity against invading bacteriophages and plasmids. Two CRISPR-Cas systems have been identified in Acinetobacter baumannii, an opportunistic pathogen with a remarkable capacity for clonal dissemination. In this study, we investigated the mode of evolution and diversity of spacers of the CRISPR-cas subtype I-Fb locus in a global collection of 76 isolates of A. baumannii obtained from 14 countries and 4 continents. The locus has basically evolved from a common ancestor following two main lineages and several pathways of vertical descent. However, this vertical passage has been interrupted by occasional events of horizontal transfer of the whole locus between distinct isolates. The isolates were assigned into 40 CRISPR-based sequence types (CST). CST1 and CST23-24 comprised 18 and 9 isolates, representing two main sub-clones of international clones CC1 and CC25, respectively. Epidemiological data showed that some of the CST1 isolates were acquired or imported from Iraq, where it has probably been endemic for more than one decade and occasionally been able to spread to USA, Canada, and Europe. CST23-24 has shown a remarkable ability to cause national outbreaks of infections in Sweden, Argentina, UAE, and USA. The three isolates of CST19 were independently imported from Thailand to Sweden and Norway, raising a concern about the prevalence of CST19 in Thailand. Our study highlights the dynamic nature of the CRISPR-cas subtype I-Fb locus in A. baumannii, and demonstrates the possibility of using a CRISPR-based approach for subtyping a significant part of the global population of A. baumannii. PMID:25706932

Identification of Variable-Number Tandem-Repeat (VNTR) Sequences in Acinetobacter baumannii and Interlaboratory Validation of an Optimized Multiple-Locus VNTR Analysis Typing Scheme▿†

PubMed Central

Pourcel, Christine; Minandri, Fabrizia; Hauck, Yolande; D'Arezzo, Silvia; Imperi, Francesco; Vergnaud, Gilles; Visca, Paolo

2011-01-01

Acinetobacter baumannii is an important opportunistic pathogen responsible for nosocomial outbreaks, mostly occurring in intensive care units. Due to the multiplicity of infection sources, reliable molecular fingerprinting techniques are needed to establish epidemiological correlations among A. baumannii isolates. Multiple-locus variable-number tandem-repeat analysis (MLVA) has proven to be a fast, reliable, and cost-effective typing method for several bacterial species. In this study, an MLVA assay compatible with simple PCR- and agarose gel-based electrophoresis steps as well as with high-throughput automated methods was developed for A. baumannii typing. Preliminarily, 10 potential polymorphic variable-number tandem repeats (VNTRs) were identified upon bioinformatic screening of six annotated genome sequences of A. baumannii. A collection of 7 reference strains plus 18 well-characterized isolates, including unique types and representatives of the three international A. baumannii lineages, was then evaluated in a two-center study aimed at validating the MLVA assay and comparing it with other genotyping assays, namely, macrorestriction analysis with pulsed-field gel electrophoresis (PFGE) and PCR-based sequence group (SG) profiling. The results showed that MLVA can discriminate between isolates with identical PFGE types and SG profiles. A panel of eight VNTR markers was selected, all showing the ability to be amplified and good amounts of polymorphism in the majority of strains. Independently generated MLVA profiles, composed of an ordered string of allele numbers corresponding to the number of repeats at each VNTR locus, were concordant between centers. Typeability, reproducibility, stability, discriminatory power, and epidemiological concordance were excellent. A database containing information and MLVA profiles for several A. baumannii strains is available from http://mlva.u-psud.fr/. PMID:21147956

Antimicrobial Resistance Gene Transfer in Drug Resistant Acinetobacter Species

USDA-ARS?s Scientific Manuscript database

Abstract: Antibiotic resistance is rapidly developing into one of the most formidable challenges for healthcare providers and researchers alike. To combat the rapid evolution of resistance, it will be important to uncover different mechanisms that bacteria use to acquire drug resistance genes. Acine...

Abundance of three bacterial populations in selected streams

Treesearch

O.A. Olapade; X. Gao; L.G. LEff

2005-01-01

The population sizes of three bacterial species, Acinetobacter calcoaceticw, Burkholderia cepacia, and Pseudomonas putida, were examined in water and sediment from nine streams in different parts of the United States using fluorescent in situ hybridization (FISH). Population sizes were determined from three sites (upstream,...

Trehalose, a temperature- and salt-induced solute with implications in pathobiology of Acinetobacter baumannii.

PubMed

Zeidler, Sabine; Hubloher, Josephine; Schabacker, Kim; Lamosa, Pedro; Santos, Helena; Müller, Volker

2017-12-01

Acinetobacter baumannii is an opportunistic human pathogen that has become a global threat to healthcare institutions worldwide. A major factor contributing to success of this bacterium is its outstanding ability to survive on dry surfaces. The molecular basis for desiccation resistance is not completely understood. This study focused on growth under osmotic stress and aimed to identify the pool of compatible solutes synthesized in response to these low water activity conditions. A. baumannii produced mannitol as compatible solute, but in contrast to Acinetobacter baylyi, also trehalose was accumulated in response to increasing NaCl concentrations. The genome of A. baumannii encodes a trehalose-6-phosphate phosphatase (OtsB) and a trehalose-6-phosphate synthase (OtsA). Deletion of otsB abolished trehalose formation, demonstrating that otsB is essential for trehalose biosynthesis. Growth of the mutant was neither impaired at low salt nor at 500 mM NaCl, but it did not grow at high temperatures, indicating a dual function of trehalose in osmo- and thermoprotection. This led us to analyse temperature dependence of trehalose formation. Indeed, expression of otsB was not only induced by high osmolarity but also by high temperature. Concurrently, trehalose was accumulated in cells grown at high temperature. Taken together, these data point to an important role of trehalose in A. baumannii beyond osmoprotection. © 2017 Society for Applied Microbiology and John Wiley & Sons Ltd.

Use of the accessory genome for characterization and typing of Acinetobacter baumannii.

PubMed

Turton, Jane F; Baddal, Buket; Perry, Claire

2011-04-01

Outbreak strains of Acinetobacter baumannii are highly clonal, and cross-infection investigations can be difficult. We sought targets based on AbaR resistance islands and on other genes found in some, but not all, sequenced isolates of A. baumannii among a set of clinical isolates (n = 70) that included multiple representatives of a number of pulsed-field gel electrophoresis (PFGE)-defined types. These included representatives that varied in their profiles at two variable-number tandem repeat (VNTR) loci, which can provide discrimination within a PFGE cluster. Detection, or not, of each element sought provided some degree of discrimination among the set, with the presence or absence of genes coding for a phage terminase (ACICU_02185), a sialic acid synthase (ACICU_00080), a polysaccharide biosynthesis protein (AB57_0094), aphA1, bla(TEM), and integron-associated orfX (Kyoto Encyclopedia of Genes and Genomes [KEGG] no. K03830) proving the most helpful in discriminating between closely related isolates in our panel. The results support VNTR data in describing distinct populations of highly similar isolates. Such analysis, in combination with other typing methods, can inform epidemiological investigations and provide additional characterization of isolates. Most genotypes carrying bla(OXA-23-like) were PCR positive for a yeeA-bla(OXA-23) fragment found in an AbaR4-type island, suggesting that this is widespread.

Resistance of Permafrost and Modern Acinetobacter lwoffii Strains to Heavy Metals and Arsenic Revealed by Genome Analysis.

PubMed

Mindlin, Sofia; Petrenko, Anatolii; Kurakov, Anton; Beletsky, Alexey; Mardanov, Andrey; Petrova, Mayya

2016-01-01

We performed whole-genome sequencing of five permafrost strains of Acinetobacter lwoffii (frozen for 15-3000 thousand years) and analyzed their resistance genes found in plasmids and chromosomes. Four strains contained multiple plasmids (8-12), which varied significantly in size (from 4,135 to 287,630 bp) and genetic structure; the fifth strain contained only two plasmids. All large plasmids and some medium-size and small plasmids contained genes encoding resistance to various heavy metals, including mercury, cobalt, zinc, cadmium, copper, chromium, and arsenic compounds. Most resistance genes found in the ancient strains of A . lwoffii had their closely related counterparts in modern clinical A . lwoffii strains that were also located on plasmids. The vast majority of the chromosomal resistance determinants did not possess complete sets of the resistance genes or contained truncated genes. Comparative analysis of various A . lwoffii and of A . baumannii strains discovered a number of differences between them: (i) chromosome sizes in A . baumannii exceeded those in A . lwoffii by about 20%; (ii) on the contrary, the number of plasmids in A . lwoffii and their total size were much higher than those in A . baumannii ; (iii) heavy metal resistance genes in the environmental A . lwoffii strains surpassed those in A . baumannii strains in the number and diversity and were predominantly located on plasmids. Possible reasons for these differences are discussed.

Resistance of Permafrost and Modern Acinetobacter lwoffii Strains to Heavy Metals and Arsenic Revealed by Genome Analysis

PubMed Central

Kurakov, Anton; Beletsky, Alexey; Mardanov, Andrey

2016-01-01

We performed whole-genome sequencing of five permafrost strains of Acinetobacter lwoffii (frozen for 15–3000 thousand years) and analyzed their resistance genes found in plasmids and chromosomes. Four strains contained multiple plasmids (8–12), which varied significantly in size (from 4,135 to 287,630 bp) and genetic structure; the fifth strain contained only two plasmids. All large plasmids and some medium-size and small plasmids contained genes encoding resistance to various heavy metals, including mercury, cobalt, zinc, cadmium, copper, chromium, and arsenic compounds. Most resistance genes found in the ancient strains of A. lwoffii had their closely related counterparts in modern clinical A. lwoffii strains that were also located on plasmids. The vast majority of the chromosomal resistance determinants did not possess complete sets of the resistance genes or contained truncated genes. Comparative analysis of various A. lwoffii and of A. baumannii strains discovered a number of differences between them: (i) chromosome sizes in A. baumannii exceeded those in A. lwoffii by about 20%; (ii) on the contrary, the number of plasmids in A. lwoffii and their total size were much higher than those in A. baumannii; (iii) heavy metal resistance genes in the environmental A. lwoffii strains surpassed those in A. baumannii strains in the number and diversity and were predominantly located on plasmids. Possible reasons for these differences are discussed. PMID:27795957

Whole-Cell Biocatalytic Synthesis of Cinnamyl Acetate with a Novel Esterase from the DNA Library of Acinetobacter hemolyticus.

PubMed

Dong, Hao; Secundo, Francesco; Xue, Changhu; Mao, Xiangzhao

2017-03-15

Cinnamyl acetate has a wide application in the flavor and fragrance industry because of its sweet, balsamic, and floral odor. Up to now, lipases have been mainly used in enzyme-mediated synthesis of cinnamyl acetate, whereas esterases are used in only a few cases. Moreover, the use of purified enzymes is often a disadvantage, which leads to increases of the production costs. In this paper, a genomic DNA library of Acinetobacter hemolyticus was constructed, and a novel esterase (EstK1) was identified. After expression in Escherichia coli, the whole-cell catalyst of EstK1 displayed high transesterification activity to produce cinnamyl acetate in nonaqueous systems. Furthermore, under optimal conditions (vinyl acetate as acyl donor, isooctane as solvent, molar ratio 1:4, temperature 40 °C), the conversion ratio of cinnamyl alcohol could be up to 94.1% at 1 h, and it reached an even higher level (97.1%) at 2 h.

Disruption of tetR type regulator adeN by mobile genetic element confers elevated virulence in Acinetobacter baumannii.

PubMed

Saranathan, Rajagopalan; Pagal, Sudhakar; Sawant, Ajit R; Tomar, Archana; Madhangi, M; Sah, Suresh; Satti, Annapurna; Arunkumar, K P; Prashanth, K

2017-10-03

Acinetobacter baumannii is an important human pathogen and considered as a major threat due to its extreme drug resistance. In this study, the genome of a hyper-virulent MDR strain PKAB07 of A. baumannii isolated from an Indian patient was sequenced and analyzed to understand its mechanisms of virulence, resistance and evolution. Comparative genome analysis of PKAB07 revealed virulence and resistance related genes scattered throughout the genome, instead of being organized as an island, indicating the highly mosaic nature of the genome. Many intermittent horizontal gene transfer events, insertion sequence (IS) element insertions identified were augmenting resistance machinery and elevating the SNP densities in A. baumannii eventually aiding in their swift evolution. ISAba1, the most widely distributed insertion sequence in A. baumannii was found in multiple sites in PKAB07. Out of many ISAba1 insertions, we identified novel insertions in 9 different genes wherein insertional inactivation of adeN (tetR type regulator) was significant. To assess the significance of this disruption in A. baumannii, adeN mutant and complement strains were constructed in A. baumannii ATCC 17978 strain and studied. Biofilm levels were abrogated in the adeN knockout when compared with the wild type and complemented strain of adeN knockout. Virulence of the adeN knockout mutant strain was observed to be high, which was validated by in vitro experiments and Galleria mellonella infection model. The overexpression of adeJ, a major component of AdeIJK efflux pump observed in adeN knockout strain could be the possible reason for the elevated virulence in adeN mutant and PKB07 strain. Knocking out of adeN in ATCC strain led to increased resistance and virulence at par with the PKAB07. Disruption of tetR type regulator adeN by ISAba1 consequently has led to elevated virulence in this pathogen.

Human head lice and pubic lice reveal the presence of several Acinetobacter species in Algiers, Algeria.

PubMed

Mana, Nassima; Louni, Meriem; Parola, Philippe; Bitam, Idir

2017-08-01

There are two majorspecies of medically important lice that parasitize humans: Phthirus pubis, found in pubic hair, and Pediculus humanus. Pediculus humanus consists of two eco types that live in specific niches on the human host: body lice (Pediculus humanus humanus), found on the human body and clothing, and head lice (Pediculus humanus capitis), found on the scalp. To date, only body lice are known to be vectors of human disease; however, it has recently been reported that the DNA of several bacterial agents has been detected in head lice, raising questions about their role in the transmission of pathogens. This issue caught our attention, in addition to the fact that the pathogenic bacteria associated with P. pubis and P. humanus capitis have never been investigated in Algeria. To investigate this,molecular techniques (real-time PCR) were used to screen for the presence of Acinetobacter spp., Bartonella spp., Borrelia spp. and Rickettsia prowazekii DNA from P. humanus capitis (64 lice) collected from schoolchildren,and P. pubis (4 lice),collected from one adultman living in Algiers. Positive samples for Acinetobacter spp.were identified by sequencing therpoBgene. Conventional PCR targeting the partial Cytb gene was used to determine the phylogenetic clade of the collected lice. Of the 64 samples collected, Acinetobacter spp. DNA was detected in 17/64 (27%) of head lice, identified as: A. baumannii (14%), A. johnsonii (11%) and A. variabilis (2%). Of the four P. pubissamples, 2(50%) were positive for A. johnsonii. The phylogenetic tree based on the Cytb gene revealed that P. humanus capitis were grouped into clades A and B. In this study, we report andidentify for the first time Acinetobacter spp.in Algerian P. pubis and P. humanus capitis. The detection of the genus Acinetobacter in lice should not be underestimated, especially in P. humanus capitis, which is distributed worldwide. However, additional epidemiological data are required to determine if human lice may act as an environmental reservoir and are actively involved in the propagation of these bacteria to humans. Copyright © 2017 Elsevier Ltd. All rights reserved.

Acinetobacter baumannii Is Dependent on the Type II Secretion System and Its Substrate LipA for Lipid Utilization and In Vivo Fitness

PubMed Central

Johnson, Tanya L.; Waack, Ursula; Smith, Sara; Mobley, Harry

2015-01-01

ABSTRACT Gram-negative bacteria express a number of sophisticated secretion systems to transport virulence factors across the cell envelope, including the type II secretion (T2S) system. Genes for the T2S components GspC through GspN and PilD are conserved among isolates of Acinetobacter baumannii, an increasingly common nosocomial pathogen that is developing multidrug resistance at an alarming rate. In contrast to most species, however, the T2S genes are dispersed throughout the genome rather than linked into one or two operons. Despite this unique genetic organization, we show here that the A. baumannii T2S system is functional. Deletion of gspD or gspE in A. baumannii ATCC 17978 results in loss of secretion of LipA, a lipase that breaks down long-chain fatty acids. Due to a lack of extracellular lipase, the gspD mutant, the gspE mutant, and a lipA deletion strain are incapable of growth on long-chain fatty acids as a sole source of carbon, while their growth characteristics are indistinguishable from those of the wild-type strain in nutrient-rich broth. Genetic inactivation of the T2S system and its substrate, LipA, also has a negative impact on in vivo fitness in a neutropenic murine model for bacteremia. Both the gspD and lipA mutants are outcompeted by the wild-type strain as judged by their reduced numbers in spleen and liver following intravenous coinoculation. Collectively, our findings suggest that the T2S system plays a hitherto-unrecognized role in in vivo survival of A. baumannii by transporting a lipase that may contribute to fatty acid metabolism. IMPORTANCE Infections by multidrug-resistant Acinetobacter baumannii are a growing health concern worldwide, underscoring the need for a better understanding of the molecular mechanisms by which this pathogen causes disease. In this study, we demonstrated that A. baumannii expresses a functional type II secretion (T2S) system that is responsible for secretion of LipA, an extracellular lipase required for utilization of exogenously added lipids. The T2S system and the secreted lipase support in vivo colonization and thus contribute to the pathogenic potential of A. baumannii. PMID:26668261

Characterization of hydrogen peroxide-resistant Acinetobacter species isolated during the Mars Phoenix spacecraft assembly.

PubMed

Derecho, I; McCoy, K B; Vaishampayan, P; Venkateswaran, K; Mogul, R

2014-10-01

The microbiological inventory of spacecraft and the associated assembly facility surfaces represent the primary pool of forward contaminants that may impact the integrity of life-detection missions. Herein, we report on the characterization of several strains of hydrogen peroxide-resistant Acinetobacter, which were isolated during the Mars Phoenix lander assembly. All Phoenix-associated Acinetobacter strains possessed very high catalase specific activities, and the specific strain, A. gyllenbergii 2P01AA, displayed a survival against hydrogen peroxide (no loss in 100 mM H2O2 for 1 h) that is perhaps the highest known among Gram-negative and non-spore-forming bacteria. Proteomic characterizations reveal a survival mechanism inclusive of proteins coupled to peroxide degradation (catalase and alkyl hydroperoxide reductase), energy/redox management (dihydrolipoamide dehydrogenase), protein synthesis/folding (EF-G, EF-Ts, peptidyl-tRNA hydrolase, DnaK), membrane functions (OmpA-like protein and ABC transporter-related protein), and nucleotide metabolism (HIT family hydrolase). Together, these survivability and biochemical parameters support the hypothesis that oxidative tolerance and the related biochemical features are the measurable phenotypes or outcomes for microbial survival in the spacecraft assembly facilities, where the low-humidity (desiccation) and clean (low-nutrient) conditions may serve as selective pressures. Hence, the spacecraft-associated Acinetobacter, due to the conferred oxidative tolerances, may ultimately hinder efforts to reduce spacecraft bioburden when using chemical sterilants, thus suggesting that non-spore-forming bacteria may need to be included in the bioburden accounting for future life-detection missions.

Proliferation of spacecraft-associated Acinetobacter on alcohol solvents

NASA Astrophysics Data System (ADS)

Mogul, Rakesh; Cepeda, Ivonne; Brasali, Hania; Gornick, Trevor; Jain, Chirag; Kim, Eun Jin; Nguyen, Vinh Bao; Oei, Alex; Rodriguez, Joseph; Walker, Jillian; Savla, Gautam

The Acinetobacter are the most abundant Gram-negative and non-spore forming bacteria found in the cleanroom facilities for Mars spacecraft. The spacecraft-associated Acinetobacter are extremotolerant towards hydrogen peroxide and have been shown to increase in abundance as a result of the spacecraft assembly process. To better understand the oligotrophic growth in the cleanroom environments, we have measured the growth of several Acinetobacter strains against ethanol and isopropanol, which are cleaning solvents used in the spacecraft assembly process. Our studies show that A. radioresistens 50v1, which was isolated from Mars Odyssey orbiter, optimally proliferates on 300 mM ethanol under minimal conditions at a growth rate that is 2-fold higher than that of the A. radioresistens type strain (strain 43998 (T) ). The impact of transition metals on the growth rates followed the trend of Fe (2+) > Mn (2+) > Zn (2+) , where Zn (2+) was inhibitory. In contrast, no growth on ethanol was observed for the novel species A. phoenicis 2P01AA, which was isolated from the facilities for the Mars Phoenix lander. Alcohol dehydrogenase activities measured in rich and minimal media paralleled these observations with the 50v1 strain possessing higher specific activities than the type strain, and the 2P01AA strain displaying no measurable activity in rich media. Preliminary studies indicate that isopropanol is insufficient as an energy source when in culture. The significance of these results as well as the observed differences between the Odyssey and Phoenix-associated strains will be discussed.

First Comprehensive Evaluation of the M.I.C. Evaluator Device Compared to Etest and CLSI Broth Microdilution for MIC Testing of Aerobic Gram-Positive and Gram-Negative Bacterial Species

PubMed Central

Turnbull, L.; Brosnikoff, C.; Cloke, J.

2012-01-01

The M.I.C. Evaluator strip (Thermo Fisher Scientific, Basingstoke, United Kingdom) uses a methodology similar to that of Etest. In this first assessment of the M.I.C. Evaluator device, 409 strains of aerobic Gram-positive bacteria (staphylococci, streptococci, and enterococci) and 325 strains of Enterobacteriaceae, Pseudomonas species, and Acinetobacter species were tested by M.I.C. Evaluator strip, Etest, and broth microdilution as a reference standard. The Gram-positive bacteria included staphylococci (methicillin-resistant Staphylococcus aureus, methicillin-susceptible S. aureus, and coagulase-negative staphylococci), Streptococcus pneumoniae, beta-hemolytic streptococci and viridians group strains, vancomycin-resistant enterococci, and other enterococci. The Gram-negative bacteria included 250 strains of 60 Enterobacteriaceae species plus 50 Pseudomonas and 25 Acinetobacter species. A total of 14 antimicrobial agents (depending on the species) were included. The same methodology and reading format were used for M.I.C. Evaluator strips and Etest. Broth microdilution methodology was performed according to CLSI document M07-A8. For the clinical strains, >95% of results were plus or minus one doubling dilution for all species. There were fewer than 5% minor errors, fewer than 3% major errors, and fewer than 1% very major errors. M.I.C. Evaluator strips and Etest often reported higher MICs than the reference broth microdilution method. The M.I.C. Evaluator strips provided results comparable to those of the predicate Etest device and are of value for the accurate testing of MICs for these important pathogens. PMID:22238441

Bacteria-Human Somatic Cell Lateral Gene Transfer Is Enriched in Cancer Samples

PubMed Central

Robinson, Kelly M.; White, James Robert; Ganesan, Ashwinkumar; Nourbakhsh, Syrus; Dunning Hotopp, Julie C.

2013-01-01

There are 10× more bacterial cells in our bodies from the microbiome than human cells. Viral DNA is known to integrate in the human genome, but the integration of bacterial DNA has not been described. Using publicly available sequence data from the human genome project, the 1000 Genomes Project, and The Cancer Genome Atlas (TCGA), we examined bacterial DNA integration into the human somatic genome. Here we present evidence that bacterial DNA integrates into the human somatic genome through an RNA intermediate, and that such integrations are detected more frequently in (a) tumors than normal samples, (b) RNA than DNA samples, and (c) the mitochondrial genome than the nuclear genome. Hundreds of thousands of paired reads support random integration of Acinetobacter-like DNA in the human mitochondrial genome in acute myeloid leukemia samples. Numerous read pairs across multiple stomach adenocarcinoma samples support specific integration of Pseudomonas-like DNA in the 5′-UTR and 3′-UTR of four proto-oncogenes that are up-regulated in their transcription, consistent with conversion to an oncogene. These data support our hypothesis that bacterial integrations occur in the human somatic genome and may play a role in carcinogenesis. We anticipate that the application of our approach to additional cancer genome projects will lead to the more frequent detection of bacterial DNA integrations in tumors that are in close proximity to the human microbiome. PMID:23840181

Extrahuman Epidemiology of Acinetobacter baumannii in Lebanon

PubMed Central

Rafei, Rayane; Hamze, Monzer; Pailhoriès, Hélène; Eveillard, Matthieu; Marsollier, Laurent; Joly-Guillou, Marie-Laure; Dabboussi, Fouad

2015-01-01

The presence of Acinetobacter baumannii outside hospitals is still a controversial issue. The objective of our study was to explore the extrahospital epidemiology of A. baumannii in Lebanon. From February 2012 to October 2013, a total of 73 water samples, 51 soil samples, 37 raw cow milk samples, 50 cow meat samples, 7 raw cheese samples, and 379 animal samples were analyzed by cultural methods for the presence of A. baumannii. Species identification was performed by rpoB gene sequencing. Antibiotic susceptibility was investigated, and the A. baumannii population was studied by two genotyping approaches: multilocus sequence typing (MLST) and blaOXA-51 sequence-based typing (SBT). A. baumannii was detected in 6.9% of water samples, 2.7% of milk samples, 8.0% of meat samples, 14.3% of cheese samples, and 7.7% of animal samples. All isolates showed a susceptible phenotype against most of the antibiotics tested and lacked carbapenemase-encoding genes, except one that harbored a blaOXA-143 gene. MLST analysis revealed the presence of 36 sequence types (STs), among which 24 were novel STs reported for the first time in this study. blaOXA-51 SBT showed the presence of 34 variants, among which 21 were novel and all were isolated from animal origins. Finally, 30 isolates had new partial rpoB sequences and were considered putative new Acinetobacter species. In conclusion, animals can be a potential reservoir for A. baumannii and the dissemination of new emerging carbapenemases. The roles of the novel animal clones identified in community-acquired infections should be investigated. PMID:25616788

High prevalence of the PER-1 gene among carbapenem-resistant Acinetobacter baumannii in Riyadh, Saudi Arabia.

PubMed

Aly, M M; Abu Alsoud, N M; Elrobh, M S; Al Johani, S M; Balkhy, H H

2016-11-01

The prevalence of carbapenem-resistant Acinetobacter baumannii in Saudi Arabia and their resistance genetic mechanisms are yet to be identified. We studied the prevalence and genetic diversity of extended-spectrum beta-lactamase genes, particularly the PER-1 gene, among carbapenem-resistant A. baumannii strains from patients at a tertiary care hospital in Riyadh, Saudi Arabia between 2006 and 2014. Fresh subcultured samples were tested for antimicrobial susceptibility minimum inhibitory concentration (MIC). Total genomic DNA was extracted from each isolate and further used for polymerase chain reaction (PCR) genotyping, sequence-based typing (SBT) of PER-1 and OXA-51-like gene, and multilocus sequence typing (MLST) of positive isolates. Randomly selected clinical isolates (n = 100) were subjected to MLST. A total of 503 isolates were characterized as multidrug-resistant (MDR) using the MIC. Isolates were further PCR tested for bla -TEM and bla -PER-1 resistance genes (n = 503). The genotyping results showed that 68/503 (14 %) isolates were positive to bla TEM. The genotyping results of PER-1-like genes showed that 384/503 (76.3 %) were positive among MDR Acinetobacter isolates. Based on SBT, the majority of these isolates were clustered into three main groups including isolates harboring PER-1: AB11 (bla -PER-1 ), isolate AB16 (bla -PER-1 ), and, finally, the plasmid pAB154 (bla -PER-7 ). Remarkably, many isolates were concealing the PER-1 gene and harboring the TEM resistance genes as well. MLST results for selected isolates (n = 100) identified four main sequence types (STs: 2, 19, 20, and 25) and four novel isolates (ST 486-489). We report 76.3 % prevalence of the PER-1 resistance gene among Acinetobacter clinical isolates from Riyadh, Saudi Arabia. Further work is needed to explore the clinical risks and patient outcome with such resistance related to healthcare-associated infections and investigate the genetic and molecular mechanisms that confer the MDR phenotype.

Multi-drug-resistant Acinetobacter calcoaceticus-Acinetobacter baumannii complex infection outbreak in dogs and cats in a veterinary hospital.

PubMed

Kuzi, S; Blum, S E; Kahane, N; Adler, A; Hussein, O; Segev, G; Aroch, I

2016-11-01

Members of the Acinetobacter calcoaceticus-Acinetobacter baumannii complex cause severe outbreaks in humans, and are increasingly reported in animals. A retrospective study, describing a severe outbreak in dogs and cats caused by a multidrug resistant member of the Acinetobacter calcoaceticus-Acinetobacter baumannii complex in a veterinary hospital, between July 2010 and November 2012. The study included 19 dogs and 4 cats. Acinetobacter calcoaceticus-Acinetobacter baumannii complex bacteria were isolated from urine (9 animals), respiratory tract (11), tissues (3) and blood (1). The most common infection-associated findings included fever, purulent discharge from endotracheal tubes, hypotension, and neutropaenia. Infections led to pneumonia, urinary tract infection, cellulitis and sepsis. Infection was transmitted in the intensive care unit, where 22 of 23 animals were initially hospitalised. The mortality rate was 70% (16 of 23 animals), and was higher in cases of respiratory infection compared to other infections. Aggressive environmental cleaning and disinfection, with staff education for personal hygiene and antisepsis, sharply decreased the infection incidence. Health care-associated outbreaks with multidrug resistant Acinetobacter calcoaceticus-Acinetobacter baumannii complex in dogs and cats are potentially highly fatal and difficult to eradicate, warranting monitoring, antiseptic techniques and judicious antibiotic use. © 2016 British Small Animal Veterinary Association.

Antibiotic Resistance of Bacteria Isolated from the Internal Organs of Edible Snow Crabs

PubMed Central

Kim, Misoon; Kwon, Tae-Hyung; Jung, Su-Mi; Cho, Seung-Hak; Jin, Seon Yeong; Park, Nyun-Ho; Kim, Choong-Gon; Kim, Jong-Shik

2013-01-01

Antibiotic resistance and microbiota within edible snow crabs are important for the Chionoecetes (snow crab) fishing industry. We investigated these parameters using culture methods and antibiotic susceptibility tests with six internal organs from three species of Chionoecetes. Each sample revealed many unexpected microbial species within Chionoecetes internal organs. On the basis of 16S rRNA sequence analysis of 381 isolates, the most abundant genera identified in Chionoecetes opilio were Acinetobacter spp. (24%), Bacillus spp. (4%), Pseudomonas spp. (34%), Stenotrophomonas spp. (28%), and Agreia spp. (11%). In Chionoecetes sp. crabs, Acinetobacter spp. (23%), Bacillus spp. (12%), and Psychrobacter spp. (20%) were most prevalent, while Agreia spp. (11%), Bacillus spp. (31%), Microbacterium spp. (10%), Rhodococcus spp. (12%), and Agrococcus spp. (6%) were most abundant in C. japonicus. Our antibiotic resistance test found resistance to all nine antibiotics tested in 19, 14, and two of the isolates from C. opilio, Chionoecetes sp., and, C. japonicus respectively. Our results are the first to show that microbes with antibiotic resistance are widely distributed throughout the internal organs of natural snow crabs. PMID:23990916

Bacterial communities in ancient permafrost profiles of Svalbard, Arctic.

PubMed

Singh, Purnima; Singh, Shiv M; Singh, Ram N; Naik, Simantini; Roy, Utpal; Srivastava, Alok; Bölter, Manfred

2017-12-01

Permafrost soils are unique habitats in polar environment and are of great ecological relevance. The present study focuses on the characterization of bacterial communities from permafrost profiles of Svalbard, Arctic. Counts of culturable bacteria range from 1.50 × 10 3 to 2.22 × 10 5 CFU g -1 , total bacterial numbers range from 1.14 × 10 5 to 5.52 × 10 5 cells g -1 soil. Bacterial isolates are identified through 16S rRNA gene sequencing. Arthrobacter and Pseudomonas are the most dominant genera, and A. sulfonivorans, A. bergeri, P. mandelii, and P. jessenii as the dominant species. Other species belong to genera Acinetobacter, Bacillus, Enterobacter, Nesterenkonia, Psychrobacter, Rhizobium, Rhodococcus, Sphingobacterium, Sphingopyxis, Stenotrophomonas, and Virgibacillus. To the best of our knowledge, genera Acinetobacter, Enterobacter, Nesterenkonia, Psychrobacter, Rhizobium, Sphingobacterium, Sphingopyxis, Stenotrophomonas, and Virgibacillus are the first northernmost records from Arctic permafrost. The present study fills the knowledge gap of culturable bacterial communities and their chronological characterization from permafrost soils of Ny-Ålesund (79°N), Arctic. © 2017 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Diversity and Evolution of AbaR Genomic Resistance Islands in Acinetobacter baumannii Strains of European Clone I▿†

PubMed Central

Krizova, Lenka; Dijkshoorn, Lenie; Nemec, Alexandr

2011-01-01

To assess the diversity of AbaR genomic resistance islands in Acinetobacter baumannii European clone I (MLST clonal complex 1), we investigated 26 multidrug-resistant strains of this major clone isolated from hospitals in 21 cities of 10 European countries between 1984 and 2005. Each strain harbored an AbaR structure integrated at the same position in the chromosomal ATPase gene. AbaR3, including four subtypes based on variations in class 1 integron cassettes, and AbaR10 were found in 15 and 2 strains, respectively, whereas a new, unique AbaR variant was discovered in each of the other 9 strains. These new variants, designated AbaR11 to AbaR19 (19.8 kb to 57.5 kb), seem to be truncated derivatives of AbaR3, likely resulting from the deletions of its internal parts mediated by either IS26 elements (AbaR12 to AbaR19) or homologous recombination (AbaR11). AbaR3 was detected in all 10 strains isolated in 1984 to 1991, while AbaR11 to AbaR19 were carried only by strains isolated since 1997. Our results and those from previous publications suggest that AbaR3 is the original form of AbaR in European clone I, which may have provided strains of the lineage with a selective advantage facilitating their spread in European hospitals in the 1980s or before. PMID:21537009

Deciphering Multifactorial Resistance Phenotypes in Acinetobacter baumannii by Genomics and Targeted Label-free Proteomics.

PubMed

Cecchini, Tiphaine; Yoon, Eun-Jeong; Charretier, Yannick; Bardet, Chloé; Beaulieu, Corinne; Lacoux, Xavier; Docquier, Jean-Denis; Lemoine, Jerome; Courvalin, Patrice; Grillot-Courvalin, Catherine; Charrier, Jean-Philippe

2018-03-01

Resistance to β-lactams in Acinetobacter baumannii involves various mechanisms. To decipher them, whole genome sequencing (WGS) and real-time quantitative polymerase chain reaction (RT-qPCR) were complemented by mass spectrometry (MS) in selected reaction monitoring mode (SRM) in 39 clinical isolates. The targeted label-free proteomic approach enabled, in one hour and using a single method, the quantitative detection of 16 proteins associated with antibiotic resistance: eight acquired β-lactamases ( i.e. GES, NDM-1, OXA-23, OXA-24, OXA-58, PER, TEM-1, and VEB), two resident β-lactamases ( i.e. ADC and OXA-51-like) and six components of the two major efflux systems ( i.e. AdeABC and AdeIJK). Results were normalized using "bacterial quantotypic peptides," i.e. peptide markers of the bacterial quantity, to obtain precise protein quantitation (on average 8.93% coefficient of variation for three biological replicates). This allowed to correlate the levels of resistance to β-lactam with those of the production of acquired as well as resident β-lactamases or of efflux systems. SRM detected enhanced ADC or OXA-51-like production and absence or increased efflux pump production. Precise protein quantitation was particularly valuable to detect resistance mechanisms mediated by regulated genes or by overexpression of chromosomal genes. Combination of WGS and MS, two orthogonal and complementary techniques, allows thereby interpretation of the resistance phenotypes at the molecular level. © 2018 by The American Society for Biochemistry and Molecular Biology, Inc.

Copper Resistance of the Emerging Pathogen Acinetobacter baumannii

PubMed Central

Williams, Caitlin L.; Neu, Heather M.; Gilbreath, Jeremy J.; Michel, Sarah L. J.; Zurawski, Daniel V.

2016-01-01

ABSTRACT Acinetobacter baumannii is an important emerging pathogen that is capable of causing many types of severe infection, especially in immunocompromised hosts. Since A. baumannii can rapidly acquire antibiotic resistance genes, many infections are on the verge of being untreatable, and novel therapies are desperately needed. To investigate the potential utility of copper-based antibacterial strategies against Acinetobacter infections, we characterized copper resistance in a panel of recent clinical A. baumannii isolates. Exposure to increasing concentrations of copper in liquid culture and on solid surfaces resulted in dose-dependent and strain-dependent effects; levels of copper resistance varied broadly across isolates, possibly resulting from identified genotypic variation among strains. Examination of the growth-phase-dependent effect of copper on A. baumannii revealed that resistance to copper increased dramatically in stationary phase. Moreover, A. baumannii biofilms were more resistant to copper than planktonic cells but were still susceptible to copper toxicity. Exposure of bacteria to subinhibitory concentrations of copper allowed them to better adapt to and grow in high concentrations of copper; this copper tolerance response is likely achieved via increased expression of copper resistance mechanisms. Indeed, genomic analysis revealed numerous putative copper resistance proteins that share amino acid homology to known proteins in Escherichia coli and Pseudomonas aeruginosa. Transcriptional analysis revealed significant upregulation of these putative copper resistance genes following brief copper exposure. Future characterization of copper resistance mechanisms may aid in the search for novel antibiotics against Acinetobacter and other highly antibiotic-resistant pathogens. IMPORTANCE Acinetobacter baumannii causes many types of severe nosocomial infections; unfortunately, some isolates have acquired resistance to almost every available antibiotic, and treatment options are incredibly limited. Copper is an essential nutrient but becomes toxic at high concentrations. The inherent antimicrobial properties of copper give it potential for use in novel therapeutics against drug-resistant pathogens. We show that A. baumannii clinical isolates are sensitive to copper in vitro, both in liquid and on solid metal surfaces. Since bacterial resistance to copper is mediated though mechanisms of efflux and detoxification, we identified genes encoding putative copper-related proteins in A. baumannii and showed that expression of some of these genes is regulated by the copper concentration. We propose that the antimicrobial effects of copper may be beneficial in the development of future therapeutics that target multidrug-resistant bacteria. PMID:27520808

Emergence of carbapenem-resistant Acinetobacter baumannii as the major cause of ventilator-associated pneumonia in intensive care unit patients at an infectious disease hospital in southern Vietnam

PubMed Central

Nhu, Nguyen Thi Khanh; Lan, Nguyen Phu Huong; Campbell, James I.; Parry, Christopher M.; Thompson, Corinne; Tuyen, Ha Thanh; Hoang, Nguyen Van Minh; Tam, Pham Thi Thanh; Le, Vien Minh; Nga, Tran Vu Thieu; Nhu, Tran Do Hoang; Van Minh, Pham; Nga, Nguyen Thi Thu; Thuy, Cao Thu; Dung, Le Thi; Yen, Nguyen Thi Thu; Van Hao, Nguyen; Loan, Huynh Thi; Yen, Lam Minh; Nghia, Ho Dang Trung; Hien, Tran Tinh; Thwaites, Louise; Thwaites, Guy; Chau, Nguyen Van Vinh

2014-01-01

Ventilator-associated pneumonia (VAP) is a serious healthcare-associated infection that affects up to 30 % of intubated and mechanically ventilated patients in intensive care units (ICUs) worldwide. The bacterial aetiology and corresponding antimicrobial susceptibility of VAP is highly variable, and can differ between countries, national provinces and even between different wards in the same hospital. We aimed to understand and document changes in the causative agents of VAP and their antimicrobial susceptibility profiles retrospectively over an 11 year period in a major infectious disease hospital in southern Vietnam. Our analysis outlined a significant shift from Pseudomonas aeruginosa to Acinetobacter spp. as the most prevalent bacteria isolated from quantitative tracheal aspirates in patients with VAP in this setting. Antimicrobial resistance was common across all bacterial species and we found a marked proportional annual increase in carbapenem-resistant Acinetobacter spp. over a 3 year period from 2008 (annual trend; odds ratio 1.656, P = 0.010). We further investigated the possible emergence of a carbapenem-resistant Acinetobacter baumannii clone by multiple-locus variable number tandem repeat analysis, finding a blaOXA-23-positive strain that was associated with an upsurge in the isolation of this pathogen. We additionally identified a single blaNDM-1-positive A. baumannii isolate. This work highlights the emergence of a carbapenem-resistant clone of A. baumannii and a worrying trend of antimicrobial resistance in the ICU of the Hospital for Tropical Diseases in Ho Chi Minh City, Vietnam. PMID:25038137

Escherichia coli Overexpressing a Baeyer-Villiger Monooxygenase from Acinetobacter radioresistens Becomes Resistant to Imipenem

PubMed Central

Minerdi, Daniela; Zgrablic, Ivan; Castrignanò, Silvia; Catucci, Gianluca; Medana, Claudio; Terlizzi, Maria Elena; Gribaudo, Giorgio; Gilardi, Gianfranco

2015-01-01

Antimicrobial resistance is a global issue currently resulting in the deaths of hundreds of thousands of people a year worldwide. Data present in the literature illustrate the emergence of many bacterial species that display resistance to known antibiotics; Acinetobacter spp. are a good example of this. We report here that Acinetobacter radioresistens has a Baeyer-Villiger monooxygenase (Ar-BVMO) with 100% amino acid sequence identity to the ethionamide monooxygenase of multidrug-resistant (MDR) Acinetobacter baumannii. Both enzymes are only distantly phylogenetically related to other canonical bacterial BVMO proteins. Ar-BVMO not only is capable of oxidizing two anticancer drugs metabolized by human FMO3, danusertib and tozasertib, but also can oxidize other synthetic drugs, such as imipenem. The latter is a member of the carbapenems, a clinically important antibiotic family used in the treatment of MDR bacterial infections. Susceptibility tests performed by the Kirby-Bauer disk diffusion method demonstrate that imipenem-sensitive Escherichia coli BL21 cells overexpressing Ar-BVMO become resistant to this antibiotic. An agar disk diffusion assay proved that when imipenem reacts with Ar-BVMO, it loses its antibiotic property. Moreover, an NADPH consumption assay with the purified Ar-BVMO demonstrates that this antibiotic is indeed a substrate, and its product is identified by liquid chromatography-mass spectrometry to be a Baeyer-Villiger (BV) oxidation product of the carbonyl moiety of the β-lactam ring. This is the first report of an antibiotic-inactivating BVMO enzyme that, while mediating its usual BV oxidation, also operates by an unprecedented mechanism of carbapenem resistance. PMID:26459905

Escherichia coli Overexpressing a Baeyer-Villiger Monooxygenase from Acinetobacter radioresistens Becomes Resistant to Imipenem.

PubMed

Minerdi, Daniela; Zgrablic, Ivan; Castrignanò, Silvia; Catucci, Gianluca; Medana, Claudio; Terlizzi, Maria Elena; Gribaudo, Giorgio; Gilardi, Gianfranco; Sadeghi, Sheila J

2016-01-01

Antimicrobial resistance is a global issue currently resulting in the deaths of hundreds of thousands of people a year worldwide. Data present in the literature illustrate the emergence of many bacterial species that display resistance to known antibiotics; Acinetobacter spp. are a good example of this. We report here that Acinetobacter radioresistens has a Baeyer-Villiger monooxygenase (Ar-BVMO) with 100% amino acid sequence identity to the ethionamide monooxygenase of multidrug-resistant (MDR) Acinetobacter baumannii. Both enzymes are only distantly phylogenetically related to other canonical bacterial BVMO proteins. Ar-BVMO not only is capable of oxidizing two anticancer drugs metabolized by human FMO3, danusertib and tozasertib, but also can oxidize other synthetic drugs, such as imipenem. The latter is a member of the carbapenems, a clinically important antibiotic family used in the treatment of MDR bacterial infections. Susceptibility tests performed by the Kirby-Bauer disk diffusion method demonstrate that imipenem-sensitive Escherichia coli BL21 cells overexpressing Ar-BVMO become resistant to this antibiotic. An agar disk diffusion assay proved that when imipenem reacts with Ar-BVMO, it loses its antibiotic property. Moreover, an NADPH consumption assay with the purified Ar-BVMO demonstrates that this antibiotic is indeed a substrate, and its product is identified by liquid chromatography-mass spectrometry to be a Baeyer-Villiger (BV) oxidation product of the carbonyl moiety of the β-lactam ring. This is the first report of an antibiotic-inactivating BVMO enzyme that, while mediating its usual BV oxidation, also operates by an unprecedented mechanism of carbapenem resistance. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

Surface Enhanced Raman Spectroscopy for the Rapid Detection and Identification of Microbial Pathogens in Human Serum

DTIC Science & Technology

2014-12-11

and 1 mm depth. Bacterial culture and cell count determination Bacterial species of Acinetobacter baumannii (A. baumannii, ST-3), Escherichia coli...remove all broth components followed by a final resuspension of the pellet in ddH2O back to 1 OD. Cell count was determined by plating the 10 4 , 10 3...10 2 and 10 1 cell dilutions on TSB Nutrient Agar media. Colony forming units (CFU) were counted the following day to confirm bacterial species

Bacterial genus is a risk factor for major amputation in patients with diabetic foot.

PubMed

Cardoso, Natália Anício; Cisneiros, Lígia DE Loiola; Machado, Carla Jorge; Cenedezi, Juliana Merlin; Procópio, Ricardo Jayme; Navarro, Túlio Pinho

2017-01-01

to evaluate whether bacterial genus is a risk factor for major amputation in patients with diabetic foot and infected ulcer. we conducted a case-control, observational study of 189 patients with infected ulcers in diabetic feet admitted to the Vascular Surgery Service of the Risoleta Tolentino Neves Hospital, from January 2007 to December 2012. The bacteriological evaluation was performed in deep tissue cultures from the lesions and amputation was considered major when performed above the foot'smiddle tarsus. the patients'mean age was 61.9±12.7 years; 122 (64.6%) were men. The cultures were positive in 86.8%, being monomicrobial in 72% of the cases. In patients with major amputation, Acinetobacter spp. (24.4%), Morganella spp. (24.4%), Proteus spp. (23.1%) and Enterococcus spp. (19.2%) were the most frequent types of bacteria. The most commonly isolated species were Acinetobacter baumannii, Morganella morganii, Pseudomonas aeruginosa and Proteus mirabilis. As predictors of major amputation, we identified the isolation of the generaAcinetobacter spp. and Klebsiella spp., serum creatinine ≥1.3mg/dl and hemoglobin <11g/dl. the bacterial genera Acinetobacter spp. and Klebsiella spp. identified in infected ulcers of patients with diabetic foot were associated with a higher incidence of major amputation. avaliar se gênero bacteriano é fator de risco para amputação maior em pacientes com pé diabético e úlcera infectada. estudo observacional do tipo caso-controle de 189 pacientes com úlcera infectada em pé diabético admitidos pelo Serviço de Cirurgia Vascular do Hospital Risoleta Tolentino Neves, no período de janeiro de 2007 a dezembro de 2012. A avaliação bacteriológica foi realizada em cultura de tecido profundo das lesões e a amputação foi considerada como maior quando realizada acima do médio tarso do pé. a média de idade dos pacientes foi 61,9±12,7 anos e 122 (64,6%) eram homens. As culturas foram positivas em 86,8%, sendo monomicrobianas em 72% dos casos. Nos pacientes com amputação maior, os gêneros de bactérias mais frequentes foram Acinetobacter spp. (24,4%), Morganella spp. (24,4%), Proteus spp. (23,1%) e Enterococcus spp. (19,2%) e as espécies mais isoladas foram Acinetobacter baumannii, Morganella morganii, Pseudomonas aeruginosa e Proteus mirabilis. Identificou-se como fatores preditivos para amputação maior o isolamento dos gêneros Acinetobacter spp. e Klebsiella spp.,e níveis séricos de creatinina ≥1,3mg/dl e de hemoglobina <11g/dl. os gêneros bacterianos Acinetobacter spp. e Klebsiella spp. identificados nas úlceras infectadas dos pacientes com pé diabético associaram-se a maior incidência de amputação maior.

Kinetic analysis of simultaneous denitrification and biomineralization of novel Acinetobacter sp. CN86.

PubMed

Su, Jun-Feng; Shi, Jing-Xin; Huang, Ting-Lin; Ma, Fang

2016-08-15

A novel aerobic denitrification and biomineralization strain CN86 was isolated from the Qu Jiang artificial lake. Based on phylogenetic characteristics, the isolated strain was identified as Acinetobacter species. Strain CN86 was confirmed to have the ability to perform simultaneous denitrification and biomineralization. Exponential decay equation was used for the matching of kinetic processes on denitrification and biomineralization. A highest nitrate removal rate was achieved at the pH7.0, organic concentration of 1.5g/L and temperature of 30°C. An optimal hardness removal rate was obtained at the pH9.0, organic concentration of 2.0g/L and temperature of 30°C. Strain CN86 is a suitable candidate for the simultaneous removal of nitrate and hardness in groundwater treatment. Copyright © 2016 Elsevier Ltd. All rights reserved.

Acinetobacter Species Infections among Navy and Marine Corps Beneficiaries: 2014 Annual Report

DTIC Science & Technology

2015-07-20

cefazolin; DOD providers most commonly prescribed c iprofloxac in and trimethoprim /sulfamethoxazole for these cases. Although s lightly different...often prescribed trimethoprim /sulfamethoxazole, consistent with 2012 observations. For multidrug-resistant cases in 2014, DON providers most commonly...prescribed cefazolin; DOD providers most commonly prescribed ciprofloxacin and trimethoprim /sulfamethoxazole for these cases. Although slightly

Distribution, genetic diversity and antibiotic resistance of clinically important bacteria from the environment of a tertiary hospital.

PubMed

Phoon, Hannah Y P; Hussin, Hazilawati; Hussain, Baizurah Mohd; Lim, Shu Yong; Woon, Jia Jie; Er, Yi Xian; Thong, Kwai Lin

2018-03-11

Hospital environments are potential reservoirs of bacteria associated with nosocomial infections. Here, we determined the distribution of cultivable environmental bacteria of clinical importance from a Malaysian tertiary hospital and to investigate their resistotypes and genotypes. Swab and fluid samples (n=358) from healthcare workers' hands, frequently touched surfaces, medical equipment, patients' immediate surroundings, ward sinks and toilets and solutions or fluids of 12 selected wards were collected. Biochemical tests, PCR and 16S rRNA sequencing were used for identification after isolation from CHROMagar TM Orientation medium. Clinically important bacteria such as Enterococcus spp., Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter spp., Pseudomonas aeruginosa, and Enterobacter spp. were further characterised by disk diffusion method and REP-PCR. The 32 Gram negative and 21 Gram positive bacteria species identified were widely distributed in the hospital environment. Staphylococci were predominant followed by Bacillus spp., and P. aeruginosa. Frequently touched surfaces, medical equipment and ward sinks and toilets were the top three sources of bacterial species. Nine S. aureus, four Acinetobacter spp., one K. pneumoniae, and one Enterobacter spp., were multidrug resistant (MDR). The ESKAPE organisms were genetically diverse and widely dispersed across the hospital wards. An MDR MRSA clone was detected in a surgical ward isolation room. The large variety of cultivable, clinically important bacteria, especially the genetically related MDR S. aureus, K. pneumoniae, Acinetobacter spp., and Enterobacter spp. from various sampling sites indicated that the surfaces and fomites in the hospital were potential exogenous sources of nosocomial infections in the hospital. Copyright © 2018 International Society for Chemotherapy of Infection and Cancer. Published by Elsevier Ltd. All rights reserved.

Characterisation of Pellicles Formed by Acinetobacter baumannii at the Air-Liquid Interface

PubMed Central

Nait Chabane, Yassine; Marti, Sara; Rihouey, Christophe; Alexandre, Stéphane; Hardouin, Julie; Lesouhaitier, Olivier; Vila, Jordi; Kaplan, Jeffrey B.; Jouenne, Thierry; Dé, Emmanuelle

2014-01-01

The clinical importance of Acinetobacter baumannii is partly due to its natural ability to survive in the hospital environment. This persistence may be explained by its capacity to form biofilms and, interestingly, A. baumannii can form pellicles at the air-liquid interface more readily than other less pathogenic Acinetobacter species. Pellicles from twenty-six strains were morphologically classified into three groups: I) egg-shaped (27%); II) ball-shaped (50%); and III) irregular pellicles (23%). One strain representative of each group was further analysed by Brewster’s Angle Microscopy to follow pellicle development, demonstrating that their formation did not require anchoring to a solid surface. Total carbohydrate analysis of the matrix showed three main components: Glucose, GlcNAc and Kdo. Dispersin B, an enzyme that hydrolyzes poly-N-acetylglucosamine (PNAG) polysaccharide, inhibited A. baumannii pellicle formation, suggesting that this exopolysaccharide contributes to pellicle formation. Also associated with the pellicle matrix were three subunits of pili assembled by chaperon-usher systems: the major CsuA/B, A1S_1510 (presented 45% of identity with the main pilin F17-A from enterotoxigenic Escherichia coli pili) and A1S_2091. The presence of both PNAG polysaccharide and pili systems in matrix of pellicles might contribute to the virulence of this emerging pathogen. PMID:25360550

Characterization of Two Novel Propachlor Degradation Pathways in Two Species of Soil Bacteria

PubMed Central

Martin, Margarita; Mengs, Gerardo; Allende, Jose Luis; Fernandez, Javier; Alonso, Ramon; Ferrer, Estrella

1999-01-01

Propachlor (2-chloro-N-isopropylacetanilide) is an acetamide herbicide used in preemergence. In this study, we isolated and characterized a soil bacterium, Acinetobacter strain BEM2, that was able to utilize this herbicide as the sole and limiting carbon source. Identification of the intermediates of propachlor degradation by this strain and characterization of new metabolites in the degradation of propachlor by a previously reported strain of Pseudomonas (PEM1) support two different propachlor degradation pathways. Washed-cell suspensions of strain PEM1 with propachlor accumulated N-isopropylacetanilide, acetanilide, acetamide, and catechol. Pseudomonas strain PEM1 grew on propachlor with a generation time of 3.4 h and a Ks of 0.17 ± 0.04 mM. Acinetobacter strain BEM2 grew on propachlor with a generation time of 3.1 h and a Ks of 0.3 ± 0.07 mM. Incubations with strain BEM2 resulted in accumulation of N-isopropylacetanilide, N-isopropylaniline, isopropylamine, and catechol. Both degradative pathways were inducible, and the principal product of the carbon atoms in the propachlor ring was carbon dioxide. These results and biodegradation experiments with the identified metabolites indicate that metabolism of propachlor by Pseudomonas sp. strain PEM1 proceeds through a different pathway from metabolism by Acinetobacter sp. strain BEM2. PMID:9925619

Evaluation of CHROMagar Acinetobacter for Detection of Enteric Carriage of Multidrug-Resistant Acinetobacter baumannii in Samples from Critically Ill Patients▿

PubMed Central

Gordon, N. C.; Wareham, D. W.

2009-01-01

CHROMagar Acinetobacter was used to screen stool and perineal swabs for enteric carriage of multidrug-resistant Acinetobacter baumannii in samples from critically ill patients. Results were compared with a molecular assay resulting in sensitivity and specificity of culture compared to PCR of 91.7% and 89.6%, respectively. PMID:19439546

Misinterpretation of Gram Stain from the Stationary Growth Phase of Positive Blood Cultures for Brucella and Acinetobacter Species.

PubMed

Bazzi, Ali M; Al-Tawfiq, Jaffar A; Rabaan, Ali A

2017-01-01

Acinetobacter baumannii and Brucella species are Gram-negative organisms that are vulnerable to misinterpretation as Gram-positive or Gram-variable in blood cultures. We assess the random errors in gram stain interpretation to reduce the likelihood of such errors and therefore patient harm. Aerobic and anaerobic blood cultures from two patients in an acute care facility in Saudi Arabia were subjected to preliminary Gram-staining. In case 1, VITEK-2 Anaerobe Identification, repeat Gram staining from a blood agar plate, Remel BactiDrop™ Oxidase test, Urea Agar urease test and real-time PCR were used to confirm presence of Brucella and absence of Coryneform species. In case 2, repeat Gram- staining from the plate and the vials, VITEK-2 Gram-Negative Identification, real-time PCR and subculture on to Columbia agar, blood agar, and MacConkey agar were carried out to identify A. baumannii . In case 1, initially pleomorphic Gram-positive bacteria were identified. Coryneform species were suspected. Tiny growth was observed after 24 h on blood agar plates, and good growth by 48 h. Presence of Brucella species was ultimately confirmed. In case 2, preliminary Gram-stain results suggested giant Gram-positive oval cocci. Further testing over 18-24 h identified A. baumannii . Oxidase test from the plate and urease test from the culture vial is recommended after apparent identification of pleomorphic Gram-positive bacilli from blood culture, once tiny growth is observed, to distinguish Brucella from Corynebacterium species. If giant Gram-positive oval cocci are indicated by preliminary Gram-staining, it is recommended that the Gram stain be repeated from the plate after 4-6 h, or culture should be tested in Triple Sugar Iron (TSI) medium and the Gram stain repeated after 2-4 h incubation.

Occurrence of Diverse AbGRI1-Type Genomic Islands in Acinetobacter baumannii Global Clone 2 Isolates from South Korea.

PubMed

Kim, Dae Hun; Jung, Sook-In; Kwon, Ki Tae; Ko, Kwan Soo

2017-02-01

In this study, we analyzed the frequency of the AbGRI1-type genomic island (GI) and its association with genotypes. We obtained 130 Acinetobacter baumannii isolates causing bloodstream infections from patients in South Korea. Antimicrobial susceptibility testing and multilocus sequence typing were performed. The presence of AbGRI1-type GIs and their structures were determined by sequential PCR and sequencing. Ninety-eight isolates (75.3%) representing 14 sequence types (STs) belonged to clonal complex 208 (CC208), corresponding to global clone 2 (GC2). AbGRI1-type GIs interrupted the comM gene in 107 isolates (82.4%). Four types of GIs were identified: Tn6022 (50 isolates; 46.7%), AbaR4 (23 isolates; 21.5%), Tn6166 (10 isolates; 9.3%), and Tn6166/Tn2006 (24 isolates; 22.4%). In the 50 isolates with Tn6022, Tn2006 or Tn2008B, both containing ISAba1-bla OXA-23 , was present in sites other than GIs in 3 or 28 isolates, respectively. In the 10 isolates with Tn6166, Tn2008B was identified in one isolate. AbGRI1-type GIs were identified nearly exclusively in CC208 isolates, with the exception of nine non-CC208 isolates (AbaR4 in eight ST229 isolates and Tn6022 in one ST1244 isolate). Within CC208 isolates, there was evidence of frequent recombination events, in both housekeeping genes and AbGRI1-type GIs, contributing to genotype diversification and the emergence of carbapenem resistance. Copyright © 2017 American Society for Microbiology.

Metabolic capability and in situ activity of microorganisms in an oil reservoir.

PubMed

Liu, Yi-Fan; Galzerani, Daniela Domingos; Mbadinga, Serge Maurice; Zaramela, Livia S; Gu, Ji-Dong; Mu, Bo-Zhong; Zengler, Karsten

2018-01-05

Microorganisms have long been associated with oxic and anoxic degradation of hydrocarbons in oil reservoirs and oil production facilities. While we can readily determine the abundance of microorganisms in the reservoir and study their activity in the laboratory, it has been challenging to resolve what microbes are actively participating in crude oil degradation in situ and to gain insight into what metabolic pathways they deploy. Here, we describe the metabolic potential and in situ activity of microbial communities obtained from the Jiangsu Oil Reservoir (China) by an integrated metagenomics and metatranscriptomics approach. Almost complete genome sequences obtained by differential binning highlight the distinct capability of different community members to degrade hydrocarbons under oxic or anoxic condition. Transcriptomic data delineate active members of the community and give insights that Acinetobacter species completely oxidize alkanes into carbon dioxide with the involvement of oxygen, and Archaeoglobus species mainly ferment alkanes to generate acetate which could be consumed by Methanosaeta species. Furthermore, nutritional requirements based on amino acid and vitamin auxotrophies suggest a complex network of interactions and dependencies among active community members that go beyond classical syntrophic exchanges; this network defines community composition and microbial ecology in oil reservoirs undergoing secondary recovery. Our data expand current knowledge of the metabolic potential and role in hydrocarbon metabolism of individual members of thermophilic microbial communities from an oil reservoir. The study also reveals potential metabolic exchanges based on vitamin and amino acid auxotrophies indicating the presence of complex network of interactions between microbial taxa within the community.

Identification of molecular species of polyol oils produced from soybean oil by Pseudomonas aeruginosa e03-12 nrrl b-59991

USDA-ARS?s Scientific Manuscript database

The objective of this study is to develop a bioprocess for the production of polyol oils directly from soybean oil. We reported earlier methods for microbial screening and production of polyol oils from soybean oil (Hou and Lin, 2013). The polyol oil produced by Acinetobacter haemolyticus A01-35 (NR...

Epidemiology of nosocomial colonization/infection caused by Acinetobacter spp. in patients of six surgical clinics in war and peacetime.

PubMed

Suljagić, Vesna; Jevtić, Miodrag; Djordjević, Boban; Romić, Predrag; Ilić, Radoje; Stanković, Nebojsa; Milović, Novak; Novaković, Marijan; Kozarski, Jefta; Roganović, Zoran; Popović, Zoran; Jovelić, Aleksandra

2011-08-01

Acinetobacter spp. has emerged as nosocomial pathogen during the past few decades in hospitals all over the world, but it has increasingly been implicated as a serious nosocomial pathogen in military hospitals. The aim of this study was to analyse and compare the surveillance data on Acinetobacter nosocomial colonization/infection (NCI) collected during the wartime with the data collected in peacetime. We conducted a prospective study of incidence of Acinetobacter spp. colonization/infection. Also, the two nested case-control studies were conducted. The patients with nosocomial infection (cases) were compared with those with nosocomial colonization (controls) during the two different periods, wartime and peacetime. The patients with NCI by Acinetobacter spp. were identified by the case-based surveillance. The surveillance covered all the patients in 6 surgical clinics. During the study periods a total of 166 patients had cultures that grew Acinetobacter spp. and the pooled rates of Acinetobacter spp. colonization and infection were significantly higher in wartime. When patients with NCI in wartime were compared with those with NCI in peacetime significant differences were observed. In the war year, the patients were more significantly males (p < 0.000). In a period of peace, most of the colonization/infections were reported from patients with certain chronic diseases (p = 0.020) and the survival of patients was more significant (p = 0.049). During the peacetime, proportions of Acinetobacter isolates resistent to ciprofloksacin, imipenem and meropenem were significantly higher (p < 0.001). This study provides additional important information about the risk factors of nosocomial Acinetobacter spp. infections in a large cohort of surgical patients. This is also the first study that directly examines epidemiological differences between NCI caused by Acinetobacter spp. during the war and peace period.

Transcriptome Analysis of Porphyromonas gingivalis and Acinetobacter baumannii in Polymicrobial Communities.

PubMed

Miller, Daniel P; Wang, Qian; Weinberg, Aaron; Lamont, Richard J

2018-06-25

Acinetobacter baumannii is a nosocomial, opportunistic pathogen that causes several serious conditions such as meningitis, septicemia, endocarditis and pneumonia. It can be found in the oral biofilm, which may be a reservoir for pneumonia and chronic obstructive pulmonary disease. Subgingival colonization by A. baumannii is associated with chronic and aggressive periodontitis as well as refractory periodontal disease. Porphyromonas gingivalis, a keystone periodontal pathogen localized to subgingival plaque, is also implicated in several chronic conditions including aspiration pneumonia. While both bacteria are found together in subgingival plaque and can cause multiple polymicrobial infections, nothing is known about the interactions between these two important human pathogens. In this study, we used RNA sequencing to understand the transcriptional response of both species as they adapt to heterotypic communities. Among the differentially regulated genes were those encoding a number of important virulence factors for both species including adhesion, biofilm formation, and protein secretion. Additionally, the presence of A. baumannii increased the abundance of P. gingivalis in model dual species communities Collectively these results suggest that both P. gingivalis and A. baumannii adapt to each other and have synergistic potential for increased pathogenicity. In identifying the mechanisms that promote pathogenicity and refractory disease, novel approaches to mitigate polymicrobial synergistic interactions may be developed to treat or prevent associated diseases. This article is protected by copyright. All rights reserved. This article is protected by copyright. All rights reserved.

Novel Therapies for Acinetobacter Osteomyelitis

DTIC Science & Technology

2009-01-01

deployed soldiers. An additional problem is that while there are some effective antibiotics against Acinetobacter (i.e. Colistin and Imipenem ), they are...of Acinetobacter baumannii with confirmed resistance to amikacin, ampicillin, aztraeonam, ceftriaxone, ciprofloxacin, gentamicin, imipenem

Isolation and characterization of diesel degrading bacteria, Sphingomonas sp. and Acinetobacter junii from petroleum contaminated soil

NASA Astrophysics Data System (ADS)

Zhang, Qiuzhuo; Wang, Duanchao; Li, Mengmeng; Xiang, Wei-Ning; Achal, Varenyam

2014-03-01

Two indigenous bacteria of petroleum contaminated soil were characterized to utilize diesel fuel as the sole carbon and energy sources in this work. 16S rRNA gene sequence analysis identified these bacteria as Sphingomonas sp. and Acinetobacter junii. The ability to degrade diesel fuel has been demonstrated for the first time by these isolates. The results of IR analyses showed that Sphingomonas sp. VA1 and A. junii VA2 degraded up to 82.6% and 75.8% of applied diesel over 15 days, respectively. In addition, Sphingomonas sp. VA1 possessed the higher cellular hydrophobicities of 94% for diesel compared to 81% by A. junii VA2. The isolates Sphingomonas sp. VA1 and A. junii VA2 exhibited 24% and 18%, respectively emulsification activity. This study reports two new diesel degrading bacterial species, which can be effectively used for bioremediation of petroleum contaminated sites.

Patterns of cell division, DNA base compositions, and fine structures of some radiation-resistant vegetative bacteria found in food

DOE Office of Scientific and Technical Information (OSTI.GOV)

Sanders, S.W.; Maxcy, R.B.

1979-01-01

Representative highly radiation-resistant Moraxella-Acinetobacter (M-A), Pseudomonas radiora, Micrococcus radiodurans, and Micrococcus radiophilus exhibited a wide variety of division systems and cell wall characteristics. However, the more resistant M-A possessed unusually thick cell walls, indicating a possible role of the cell wall in radiation resistance in the M-A. Thick septation was present in most of the bacteria studied, but was absent in P. radiora, thus excluding this as a necessity for high resistance. Reliable determination of the number of division planes of the M-A for use as a taxonomic criterion was achieved by the direct observation of dividing cells. The highlymore » resistant M-A were found to divide in multiple planes and had base compositions of 54.0 to 57.5%, unlike typical Moraxella and/or Acinetobacter species. The taxonomic position of most highly resistant bacteria remains unclear.« less

Identification of genus Acinetobacter: Standardization of in-house PCR and its comparison with conventional phenotypic methods.

PubMed

Kulkarni, Sughosh S; Madalgi, Radhika; Ajantha, Ganavalli S; Kulkarni, Raghavendra D

2017-01-01

Acinetobacter is grouped under nonfermenting Gram-negative bacilli. It is increasingly isolated from pathological samples. The ability of this genus to acquire drug resistance and spread in the hospital settings is posing a grave problem in healthcare. Specific treatment protocols are advocated for Acinetobacter infections. Hence, rapid identification and drug susceptibility profiling are critical in the management of these infections. To standardize an in-house polymerase chain reaction (PCR) for identification of genus Acinetobacter and to compare PCR with two protocols for its phenotypic identification. A total of 96 clinical isolates of Acinetobacter were included in the study. An in-house PCR for genus level identification of Acinetobacter was standardized. All the isolates were phenotypically identified by two protocols. The results of PCR and phenotypic identification protocols were compared. The in-house PCR standardized was highly sensitive and specific for the genus Acinetobacter . There was 100% agreement between the phenotypic and molecular identification of the genus. The preliminary identification tests routinely used in clinical laboratories were also in complete agreement with phenotypic and molecular identification. The in-house PCR for genus level identification is specific and sensitive. However, it may not be essential for routine identification as the preliminary phenotypic identification tests used in the clinical laboratory reliably identify the genus Acinetobacter .

Quantitative proteomics to study carbapenem resistance in Acinetobacter baumannii

PubMed Central

Tiwari, Vishvanath; Tiwari, Monalisa

2014-01-01

Acinetobacter baumannii is an opportunistic pathogen causing pneumonia, respiratory infections and urinary tract infections. The prevalence of this lethal pathogen increases gradually in the clinical setup where it can grow on artificial surfaces, utilize ethanol as a carbon source. Moreover it resists desiccation. Carbapenems, a β-lactam, are the most commonly prescribed drugs against A. baumannii. Resistance against carbapenem has emerged in Acinetobacter baumannii which can create significant health problems and is responsible for high morbidity and mortality. With the development of quantitative proteomics, a considerable progress has been made in the study of carbapenem resistance of Acinetobacter baumannii. Recent updates showed that quantitative proteomics has now emerged as an important tool to understand the carbapenem resistance mechanism in Acinetobacter baumannii. Present review also highlights the complementary nature of different quantitative proteomic methods used to study carbapenem resistance and suggests to combine multiple proteomic methods for understanding the response to antibiotics by Acinetobacter baumannii. PMID:25309531

Costs and benefits of natural transformation in Acinetobacter baylyi.

PubMed

Hülter, Nils; Sørum, Vidar; Borch-Pedersen, Kristina; Liljegren, Mikkel M; Utnes, Ane L G; Primicerio, Raul; Harms, Klaus; Johnsen, Pål J

2017-02-15

Natural transformation enables acquisition of adaptive traits and drives genome evolution in prokaryotes. Yet, the selective forces responsible for the evolution and maintenance of natural transformation remain elusive since taken-up DNA has also been hypothesized to provide benefits such as nutrients or templates for DNA repair to individual cells. We investigated the immediate effects of DNA uptake and recombination on the naturally competent bacterium Acinetobacter baylyi in both benign and genotoxic conditions. In head-to-head competition experiments between DNA uptake-proficient and -deficient strains, we observed a fitness benefit of DNA uptake independent of UV stress. This benefit was found with both homologous and heterologous DNA and was independent of recombination. Recombination with taken-up DNA reduced survival of transformed cells with increasing levels of UV-stress through interference with nucleotide excision repair, suggesting that DNA strand breaks occur during recombination attempts with taken-up DNA. Consistent with this, we show that absence of RecBCD and RecFOR recombinational DNA repair pathways strongly decrease natural transformation. Our data show a physiological benefit of DNA uptake unrelated to recombination. In contrast, recombination during transformation is a strand break inducing process that represents a previously unrecognized cost of natural transformation.

2-DE analysis indicates that Acinetobacter baumannii displays a robust and versatile metabolism

PubMed Central

Soares, Nelson C; Cabral, Maria P; Parreira, José R; Gayoso, Carmen; Barba, Maria J; Bou, Germán

2009-01-01

Background Acinetobacter baumannii is a nosocomial pathogen that has been associated with outbreak infections in hospitals. Despite increasing awareness about this bacterium, its proteome remains poorly characterised, however recently the complete genome of A. baumannii reference strain ATCC 17978 has been sequenced. Here, we have used 2-DE and MALDI-TOF/TOF approach to characterise the proteome of this strain. Results The membrane and cytoplasmatic protein extracts were analysed separately, these analyses revealed the reproducible presence of 239 and 511 membrane and cytoplamatic protein spots, respectively. MALDI-TOF/TOF characterisation identified a total of 192 protein spots (37 membrane and 155 cytoplasmatic) and revealed that the identified membrane proteins were mainly transport-related proteins, whereas the cytoplasmatic proteins were of diverse nature, although mainly related to metabolic processes. Conclusion This work indicates that A. baumannii has a versatile and robust metabolism and also reveal a number of proteins that may play a key role in the mechanism of drug resistance and virulence. The data obtained complements earlier reports of A. baumannii proteome and provides new tools to increase our knowledge on the protein expression profile of this pathogen. PMID:19785748

Zinc stress induces copper depletion in Acinetobacter baumannii.

PubMed

Hassan, Karl A; Pederick, Victoria G; Elbourne, Liam D H; Paulsen, Ian T; Paton, James C; McDevitt, Christopher A; Eijkelkamp, Bart A

2017-03-11

The first row transition metal ions zinc and copper are essential to the survival of many organisms, although in excess these ions are associated with significant toxicity. Here, we examined the impact of zinc and copper stress on Acinetobacter baumannii, a common opportunistic pathogen. We show that extracellular zinc stress induces a copper-specific depletion phenotype in A. baumannii ATCC 17978. Supplementation with copper not only fails to rescue this phenotype, but further exacerbates the copper depletion. Extensive analysis of the A. baumannii ATCC 17978 genome identified 13 putative zinc/copper resistance efflux pumps. Transcriptional analyses show that four of these transporters are responsive to zinc stress, five to copper stress and seven to the combination of zinc and copper stress, thereby revealing a likely foundation for the zinc-induced copper starvation in A. baumannii. In addition, we show that zinc and copper play crucial roles in management of oxidative stress and the membrane composition of A. baumannii. Further, we reveal that zinc and copper play distinct roles in macrophage-mediated killing of this pathogen. Collectively, this study supports the targeting of metal ion homeostatic mechanisms as an effective antimicrobial strategy against multi-drug resistant bacterial pathogens.

Evaluation of Etest MBL for Detection of blaIMP-1 and blaVIM-2 Allele-Positive Clinical Isolates of Pseudomonas spp. and Acinetobacter spp.

PubMed Central

Lee, Kyungwon; Yong, Dongeun; Yum, Jong Hwa; Lim, Yong Sik; Bolmström, Anne; Qwärnström, Anette; Karlsson, Åsa; Chong, Yunsop

2005-01-01

The Etest MBL (AB BIODISK, Solna, Sweden) correctly differentiated all 57 isolates of Acinetobacter spp. and Pseudomonas aeruginosa with the blaIMP-1 allele and 135 of 137 (98.5%) Acinetobacter spp. and Pseudomonas spp. isolates with the blaVIM-2 allele. The Etest MBL was reliable for detecting the IMP-1- and VIM-2-producing Pseudomonas and Acinetobacter isolates. PMID:15695713

Biological phosphorus removal in wastewater treatment.

PubMed

Timmerman, M W

1984-09-01

Several commercially available systems claim to remove phosphate biologically from municipal wastewater. Techniques such as scanning electron microscopy, transmission electron microscopy and 31P nuclear magnetic resonance (NMR) have demonstrated that the phosphate removed is stored within bacterial cells as polyphosphate. Acinetobacter species are usually isolated from phosphate-removing systems although there is a great deal of evidence which casts doubt on the exclusive role of these organisms.

Phosphatase activity of aerobic and facultative anaerobic bacteria.

PubMed

Pácová, Z; Kocur, M

1978-10-01

1115 strains of aerobic and facultatively anaerobic bacteria were tested for phosphatase activity by a conventional plate method and a microtest. The microtest was devised to allow results to be read after 4 h cultivation. Phosphatase activity was found in wide range of species and strains. Besides staphylococci, where the test for phosphatase is successfully used, it may be applied as one of the valuable tests for the differentiation of the following species: Bacillus cereus, B. licheniformis, Aeromonas spp., Vibrio parahaemolyticus, Actinobacillus spp., Pasteurella spp., Xanthomonas spp., Flavobacterium spp., Alteromonas putrefaciens, Pseudomonas maltophilia, Ps. cepacia, and some other species of Pseudomonas. The species which gave uniformly negative phosphatase reaction were as follows: Staph. saprophyticus, Acinetobacter calcoaceticus, Alcaligenes faecalis, and Bordetella bronchiseptica.

Tetracycline Susceptibility Testing and Resistance Genes in Isolates of Acinetobacter baumannii-Acinetobacter calcoaceticus Complex from a U.S. Military Hospital

DTIC Science & Technology

2009-06-01

marcescens . Appl. Environ. Microbiol. 73:2199– 2206. 12. Turton, J. F., N. Woodford, J. Glover, S . Yarde, M. E. Kaufmann, and T. L. Pitt. 2006...Susceptibility Testing and Resistance Genes in Isolates of Acinetobacter baumannii-Acinetobacter calcoaceticus Complex from a U.S. Military Hospital Kevin S ...3 2 8 29 9 30 7 a S , susceptible. 2693 Report Documentation Page Form ApprovedOMB No. 0704-0188 Public reporting burden for the collection of

Epidemiology and Clinical Characteristics of Acinetobacter Peritoneal Dialysis-Related Peritonitis in Hong Kong-With a Perspective on Multi-Drug and Carbapenem Resistance.

PubMed

Li, Philip Hei; Cheng, Vincent C C; Yip, Terence; Yap, Desmond Y H; Lui, Sing-Leung; Lo, Wai-Kei

2017-01-01

♦ BACKGROUND: Acinetobacter spp. is an important cause of peritoneal dialysis (PD)-related peritonitis, but studies on Acinetobacter peritonitis have been scarce. In view of the rising concern of carbapenem-resistant Acinetobacter (CRA) and multidrug-resistant Acinetobacter (MDRA) infections, we conducted this study on the incidence of Acinetobacter peritonitis and the impact of CRA and MDRA on its outcome. ♦ METHODS: We retrospectively evaluated the clinical characteristics, prevalence, antibiotic sensitivity patterns, outcomes, and factors associated with treatment failure over the past 16 years in our patients with Acinetobacter PD-related peritonitis. ♦ RESULTS: Out of 2,389 episodes of peritonitis, there were 66 episodes (3%) of Acinetobacter peritonitis occurring in 59 patients. Twelve episodes were caused by MDRA (18%), of which 5 were CRA (8%). There was a progressive increase in the incidence of MDRA and CRA infections over the study period. Most isolates were sensitive to sulbactam combinations (ampicillin-sulbactam [95.4%] and cefoperazone-sulbactam [93.9%]), aminoglycosides (amikacin [92.4%], tobramycin [90.9%], and gentamicin [89.4%]), and carbapenems (imipenem [92.2%]). There was 1 case of relapse. Fifteen episodes resulted in catheter removal (23%), and 7 patients died (11%). Hypoalbuminemia (odds ratio [OR] = 0.85, p = 0.006) and carbapenem resistance (OR = 18.2, p = 0.049) were significantly associated with higher rates of treatment failure. ♦ CONCLUSION: Both carbapenem resistance and hypoalbuminemia were significantly associated with treatment failure. Up to 80% of peritonitis episodes by CRA resulted in catheter loss or mortality. Sulbactam combinations and/or aminoglycosides remained effective for the majority of Acinetobacter isolates. There seemed to be an increasing relative incidence of MDRA and CRA infections over the past 16 years. Copyright © 2017 International Society for Peritoneal Dialysis.

[The use of 16S rDNA sequencing in species diversity analysis for sputum of patients with ventilator-associated pneumonia].

PubMed

Yang, Xiaojun; Wang, Xiaohong; Liang, Zhijuan; Zhang, Xiaoya; Wang, Yanbo; Wang, Zhenhai

2014-05-01

To study the species and amount of bacteria in sputum of patients with ventilator-associated pneumonia (VAP) by using 16S rDNA sequencing analysis, and to explore the new method for etiologic diagnosis of VAP. Bronchoalveolar lavage sputum samples were collected from 31 patients with VAP. Bacterial DNA of the samples were extracted and identified by polymerase chain reaction (PCR). At the same time, sputum specimens were processed for routine bacterial culture. The high flux sequencing experiment was conducted on PCR positive samples with 16S rDNA macro genome sequencing technology, and sequencing results were analyzed using bioinformatics, then the results between the sequencing and bacteria culture were compared. (1) 550 bp of specific DNA sequences were amplified in sputum specimens from 27 cases of the 31 patients with VAP, and they were used for sequencing analysis. 103 856 sequences were obtained from those sputum specimens using 16S rDNA sequencing, yielding approximately 39 Mb of raw data. Tag sequencing was able to inform genus level in all 27 samples. (2) Alpha-diversity analysis showed that sputum samples of patients with VAP had significantly higher variability and richness in bacterial species (Shannon index values 1.20, Simpson index values 0.48). Rarefaction curve analysis showed that there were more species that were not detected by sequencing from some VAP sputum samples. (3) Analysis of 27 sputum samples with VAP by using 16S rDNA sequences yielded four phyla: namely Acitinobacteria, Bacteroidetes, Firmicutes, Proteobacteria. With genus as a classification, it was found that the dominant species included Streptococcus 88.9% (24/27), Limnohabitans 77.8% (21/27), Acinetobacter 70.4% (19/27), Sphingomonas 63.0% (17/27), Prevotella 63.0% (17/27), Klebsiella 55.6% (15/27), Pseudomonas 55.6% (15/27), Aquabacterium 55.6% (15/27), and Corynebacterium 55.6% (15/27). (4) Pyrophosphate sequencing discovered that Prevotella, Limnohabitans, Aquabacterium, Sphingomonas might not be detected by routine bacteria culture. Among seven species which were identified by both methods, pyrophosphate sequencing yielded higher positive rate than that of ordinary bacteria culture [Streptococcus: 88.9% (24/27) vs. 18.5% (5/27), Klebsiella: 55.6% (15/27) vs. 18.5% (5/27), Acinetobacter: 70.4% (19/27) vs. 37.0% (10/27), Corynebacterium: 55.6% (15/27) vs. 7.4% (2/27), P<0.05 or P<0.01]. Sequencing positive rate was found to increase positive rate for culture of Pseudomonas [55.6% (15/27) vs. 25.9% (7/27), P=0.050]. No significant differences were observed between sequencing and ordinary bacteria culture for detection Staphylococcus [7.4% (2/27) vs. 11.1% (3/27)] and Neisseria bacteria genera [18.5% (5/27) vs. 3.7% (1/27), both P>0.05]. 16S rDNA sequencing analysis confirmed that pathogenic bacteria in sputum of VAP were complicated with multiple drug resistant strains. Compared with routine bacterial culture, pyrophosphate sequencing had higher positive rate in detecting pathogens. 16S rDNA gene sequencing technology may become a new method for etiological diagnosis of VAP.

Genomic Epidemiology of NDM-1-Encoding Plasmids in Latin American Clinical Isolates Reveals Insights into the Evolution of Multidrug Resistance

PubMed Central

Marquez-Ortiz, Ricaurte Alejandro; Haggerty, Leanne; Olarte, Narda; Duarte, Carolina; Garza-Ramos, Ulises; Silva-Sanchez, Jesus; Castro, Betsy E.; Sim, Eby M.; Beltran, Mauricio; Moncada, María V.; Valderrama, Alberto; Castellanos, Jaime E.; Charles, Ian G.; Vanegas, Natasha

2017-01-01

Abstract Bacteria that produce the broad-spectrum Carbapenem antibiotic New Delhi Metallo-β-lactamase (NDM) place a burden on health care systems worldwide, due to the limited treatment options for infections caused by them and the rapid global spread of this antibiotic resistance mechanism. Although it is believed that the associated resistance gene blaNDM-1 originated in Acinetobacter spp., the role of Enterobacteriaceae in its dissemination remains unclear. In this study, we used whole genome sequencing to investigate the dissemination dynamics of blaNDM-1-positive plasmids in a set of 21 clinical NDM-1-positive isolates from Colombia and Mexico (Providencia rettgeri, Klebsiella pneumoniae, and Acinetobacter baumannii) as well as six representative NDM-1-positive Escherichia coli transconjugants. Additionally, the plasmids from three representative P. rettgeri isolates were sequenced by PacBio sequencing and finished. Our results demonstrate the presence of previously reported plasmids from K. pneumoniae and A. baumannii in different genetic backgrounds and geographically distant locations in Colombia. Three new previously unclassified plasmids were also identified in P. rettgeri from Colombia and Mexico, plus an interesting genetic link between NDM-1-positive P. rettgeri from distant geographic locations (Canada, Mexico, Colombia, and Israel) without any reported epidemiological links was discovered. Finally, we detected a relationship between plasmids present in P. rettgeri and plasmids from A. baumannii and K. pneumoniae. Overall, our findings suggest a Russian doll model for the dissemination of blaNDM-1 in Latin America, with P. rettgeri playing a central role in this process, and reveal new insights into the evolution and dissemination of plasmids carrying such antibiotic resistance genes. PMID:28854628

Genetic environment of the KPC gene in Acinetobacter baumannii ST2 clone from Puerto Rico and genomic insights into its drug resistance

PubMed Central

Martinez, Teresa; Martinez, Idali; Vazquez, Guillermo J.; Aquino, Edna E.

2016-01-01

Carbapenems are considered the last-resort antibiotics to treat infections caused by multidrug-resistant Gram-negative bacilli. The Klebsiella pneumoniae carbapenemase (KPC) enzyme hydrolyses β-lactam antibiotics including the carbapenems. KPC has been detected worldwide in Enterobacteriaceae and Pseudomonas aeruginosa isolates associated with transposon Tn4401 commonly located in plasmids. Acinetobacter baumannii has become an important multidrug-resistant nosocomial pathogen. KPC-producing A. baumannii has been reported to date only in Puerto Rico. The objective of this study was to determine the whole genomic sequence of a KPC-producing A. baumannii in order to (i) define its allelic diversity, (ii) identify the location and genetic environment of the blaKPC and (iii) detect additional mechanisms of antimicrobial resistance. Next-generation sequencing, Southern blot, PFGE, multilocus sequence typing and bioinformatics analysis were performed. The organism was assigned to the international ST2 clone. The blaKPC-2 was identified on a novel truncated version of Tn4401e (tentatively named Tn4401h), located in the chromosome within an IncA/C plasmid fragment derived from an Enterobacteriaceae, probably owing to insertion sequence IS26. A chromosomally located truncated Tn1 transposon harbouring a blaTEM-1 was found in a novel genetic environment within an antimicrobial resistance cluster. Additional resistance mechanisms included efflux pumps, non-β-lactam antibiotic inactivating enzymes within and outside a resistance island, two class 1 integrons, In439 and the novel In1252, as well as mutations in the topoisomerase and DNA gyrase genes which confer resistance to quinolones. The presence of the blaKPC in an already globally disseminated A. baumannii ST2 presents a serious threat of further dissemination. PMID:27259867

Antimicrobial activity of essential oil from Schinus molle Linn.

PubMed

Gundidza, M

1993-11-01

The essential oil from the fresh leaves of Schinus molle isolated by hydrodistillation was tested for antibacterial activity using the hole plate diffusion method and for antifungal activity using the mycelium or single cell growth inhibition method. Results obtained showed that the volatile oil exhibited significant activity against the following bacterial species: Klebsiella pneumoniae, Alcaligenes faecalis, Pseudomonas aeruginosa, Leuconostoc cremoris, Enterobacter aerogenes, Proteus vulgaris, Clostridium sporogenes, Acinetobacter calcoacetica, Escherichia coli, Beneckea natriegens, Citrobacter freundii, Serratia marcescens, Bacillus subtilis and Brochothrix thermosphacata. The fungal species Aspergillus ochraceus, Aspergillus parasiticus, Fusarium culmorum and Alternaria alternata exhibited significant sensitivity to the volatile oil.

Acinetobacter Species Infections among Navy and Marine Corps Beneficiaries: 2012 Annual Report

DTIC Science & Technology

2013-11-18

with a large number of Infections, have the ability to easily acquire resistance determinants , and quickly develop resistance to multiple antibiotics...have the ability to easily acquire resistance determinants , and quickly develop resistance to multiple antibiotics, leaving few, if any, treatment...resistant (XDR) organisms accounted for 1.3% of DON cases. For non-MDR cases in the DON, providers most commonly prescribed trimethoprim /sulfamethoxazole

Bioaerosol Exposure to Filtering Facepiece Respirators in a Clinical Environment (Author’s Final Manuscript)

DTIC Science & Technology

2013-03-11

Gram-positive staphylococci and Micrococcus spp . 73% of the Gram-positive and 67% of the Gram-negative isolates were resistant to oxacillin...staphylococci and Micrococcus spp . 73% of the Gram-positive and 67% of the Gram-negative isolates were resistant to oxacillin. Vancomycin...identified 26 species, primarily coagulase- negative staphylococci (CNS) and Micrococcus spp. Acinetobacter baumanii/calcoaceticus and S. aureus were

Analysis of drug resistance in 1,861 strains of Acinetobacter baumannii.

PubMed

Jin, Hao; Qiu, Fan; Ji, Hong Jian; Lu, Qiang

2016-04-01

Acinetobacter baumannii is an emerging human pathogen that causes hospital-acquired infections. The trend in increased antimicrobial resistance limits the choice of effective antimicrobial agents. The present study reports the resistance to Acinetobacter baumannii and analyzes the associations between antibiotic use and resistance rates at a general hospital between 2010 and 2014. A total of 1,861 isolates were obtained from clinical cultures, accounting for 10.33% of all detected bacteria (1,861/18,016). The strains were mainly from respiratory samples (1,628 isolates, 87.5%) and the intensive care unit (696 isolates, 37.4%). The resistance rates of Acinetobacter baumannii to the majority of antibiotics were >50%, particularly the resistance rate to cefoperazone/sulbactam increased from 47.37 in 2011 to 89.25% in 2014. However, the rates of imipenem and cilastatin sodium decreased from 81.03 to 69.44% due to the antibiotic policy. There were Pearson significant associations between the use of three antibiotics and resistance in Acinetobacter baumannii to this drug, piperacillin/tazobactam (r=0.976, P<0.01), gentamicin (r=0.870, P<0.01) and cefoxitin (r=0.741, P<0.05). Therefore, a combination of drugs should be adopted to treat Acinetobacter baumannii infections. Microbiology laboratory support and surveillance policies are essential to control the emergence of multidrug-resistance Acinetobacter baumannii .

Influence of relative humidity and suspending menstrua on survival of Acinetobacter spp. on dry surfaces.

PubMed Central

Jawad, A; Heritage, J; Snelling, A M; Gascoyne-Binzi, D M; Hawkey, P M

1996-01-01

Acinetobacter spp. are being reported with increasing frequency as a cause of nosocomial infection and have been isolated from the skin of healthy individuals, patients, hospital staff, dry nonbiotic objects, and different pieces of medical equipment. Factors affecting the survival of Acinetobacter spp. under conditions closely similar to those found in the hospital environment were investigated in the present study to help us understand the epidemiology of nosocomial Acinetobacter infection. Bacterial cells were suspended in distilled water or bovine serum albumin and were dried onto glass coverslips and kept at different relative humidities. Cells washed from coverslips were used to determined viable counts. Freshly isolated strains of Acinetobacter spp. belonging to the clinically important Acinetobacter calcoaceticus-Acinetobacter baumannii complex were found to be more resistant to drying conditions (e.g., 30 days for A. baumannii 16/49) than American Type Culture Collection strains (e.g., 2 days for A. baumannii ATCC 9955). The majority of strains belonging to the Acb complex had survival times similar to those observed for the gram-positive organism Staphylococcus aureus tested in the experiment. Survival times were prolonged for almost all the strains tested when they were suspended in bovine serum albumin (e.g., 60 days for A. baumannii R 447) compared with those for strains suspended in distilled water (11 days for R 447). The survival times for strains at higher relative humidity (31 or 93%) were longer than those for strains of Acinetobacter kept at a relative humidity of 10% (11 days at 31% relative humidity and 4 days at 10% relative humidity for R447). These findings are consistent with the observed tendency of Acinetobacter spp. to survive on dry surfaces, and they can be transferred not only by moist vectors but also under dry conditions in a hospital environment during nosocomial infection outbreaks. The results obtained in the experiment support the previously suggested airborne spread of Acinetobacter spp. in hospital wards and repeated outbreaks after incomplete disinfection of contaminated dry surfaces. PMID:8940416

Isolation of a bacterial strain, Acinetobacter sp. from centrate wastewater and study of its cooperation with algae in nutrients removal.

PubMed

Liu, Hui; Lu, Qian; Wang, Qin; Liu, Wen; Wei, Qian; Ren, Hongyan; Ming, Caibing; Min, Min; Chen, Paul; Ruan, Roger

2017-07-01

Algae were able to grow healthy on bacteria-containing centrate wastewater in a pilot-scale bioreactor. The batch experiment indicated that the co-cultivation of algae and wastewater-borne bacteria improved the removal efficiencies of chemical oxygen demand and total phosphorus in centrate wastewater to 93.01% and 98.78%, respectively. A strain of beneficial aerobic bacteria, Acinetobacter sp., was isolated and its biochemical characteristics were explored. Synergistic cooperation was observed in the growth of algae and Acinetobacter sp. Removal efficiencies of some nutrients were improved significantly by the co-cultivation of algae and Acinetobacter sp. After treatment, residual nutrients in centrate wastewater reached the permissible discharge limit. The cooperation between algae and Acinetobacter sp. was in part attributed to the exchange of carbon dioxide and oxygen between the algae and bacteria. This synergetic relationship between algae and Acinetobacter sp. provided a promising way to treat the wastewater by improving the nutrients removal and biomass production. Copyright © 2017 Elsevier Ltd. All rights reserved.

Acinetobacter baumannii producing OXA-23 detected in the Czech Republic.

PubMed

Senkyrikova, Marketa; Husickova, Vendula; Chroma, Magdalena; Sauer, Pavel; Bardon, Jan; Kolar, Milan

2013-12-01

Acinetobacter baumannii is an opportunistic pathogen posing an increased risk to hospitalized persons, causing nosocomial pneumonias, urinary tract infections and postoperative infections. Between 1 December 2011 and 30 September 2012, strains of Acinetobacter spp. were isolated from clinical samples obtained from hospitalized patients. Susceptibility to antibiotics was determined by the standard microdilution method and phenotypic testing was used to detect the presence of serine carbapenemases and metallo-beta-lactamases. The polymerase chain reaction was used to detect the genes encoding carbapenemases. Pulsed field gel electrophoresis was used to investigate the genetic relationship among the carbapenem resistant isolates of Acinetobacter baumannii. In three strains of Acinetobacter baumannii enzyme OXA-23 was detected. This positive result was confirmed by restriction analysis and sequencing. The study reported an OXA-23-producing strains of Acinetobacter baumannii in the Czech Republic. All three strains isolated from Military Hospital patients had a completely identical restriction profile, indicating clonal spread of a strain carrying serine carbapenemase OXA-23 in this health care facility. Moreover this was the first time the strain was detected in the country in patients who had not stayed abroad.

Detection of Acinetobacter baumannii in human head and body lice from Ethiopia and identification of new genotypes.

PubMed

Kempf, Marie; Abdissa, Alemseged; Diatta, Georges; Trape, Jean-François; Angelakis, Emmanouil; Mediannikov, Oleg; La Scola, Bernard; Raoult, Didier

2012-09-01

Acinetobacter baumannii has previously been detected and genotyped in human body lice. The objectives of this study were to determine the presence of this bacterium in head and body lice collected from healthy individuals in Ethiopia by molecular methods and to characterize the genotype. Human lice from locations at different altitudes in Ethiopia were screened for the presence of Acinetobacter sp by targeting the rpoB gene. Acinetobacter baumannii was detected and genotyped using recA PCR amplification. A total of 115 head and 109 body lice were collected from 134 healthy individuals. Acinetobacter sp were found in 54 head (47%) and 77 body (71%) lice. The recA gene was sequenced for 60 of the Acinetobacter sp and 67% were positive for A. baumannii; genotype 1 was retrieved the most frequently. Our study is the first to show the presence of A. baumannii in human body lice, and also in head lice, in Ethiopia. Copyright © 2012 International Society for Infectious Diseases. Published by Elsevier Ltd. All rights reserved.

Antimicrobial Resistance and Resistance Genes in Aerobic Bacteria Isolated from Pork at Slaughter.

PubMed

Li, Lili; Heidemann Olsen, Rikke; Ye, Lei; Yan, He; Nie, Qing; Meng, Hecheng; Shi, Lei

2016-04-01

The aim of this study was to investigate the phenotypic and genotypic antimicrobial resistance, integrons, and transferability of resistance markers in 243 aerobic bacteria recovered from pork at slaughter in the People's Republic of China. The organisms belonged to 22 genera of gram-negative bacteria (92.2%) and gram-positive bacteria (7.8%). High levels of resistance were detected to tetracycline, trimethoprim-sulfamethoxazole, and ampicillin (36.2 to 54.3%), and lower levels were detected to nitrofurantoin, cefotaxime, gentamicin, ciprofloxacin, and chloramphenicol (7.8 to 29.2%). Across species, genes conferring antimicrobial resistance were observed with the following frequencies: blaTEM, 40.7%; blaCMY-2, 15.2%; blaCTX-M, 11.5%; sul2, 27.2%; sul1, 14.4%; tet(A), 5.4%; tet(L), 5.4%; tet(M), 5.0%; tet(E), 3.7%; tet(C), 3.3%; tet(S), 2.5%; and tet(K), 0.8%. Various antimicrobial resistance genes were found in new carriers: blaTEM in Lactococcus garvieae, Myroides odoratimimus, Aeromonas hydrophila, Staphylococcus sciuri, Raoultella terrigena, Macrococcus caseolyticus, Acinetobacter ursingii, Sphingobacterium sp., and Oceanobacillus sp.; blaCMY-2 in Lactococcus lactis, Klebsiella oxytoca, Serratia marcescens, Acinetobacter baumannii, and Myroides phaeus; tet(L) in M. caseolyticus; sul1 in Vibrio cincinnatiensis; sul2 in Acinetobacter bereziniae, Acinetobacter johnsonii, and V. cincinnatiensis; and the class 1 integron and gene cassette aadA2 in V. cincinnatiensis. Approximately 6.6% of isolates contained class 1 integrons, and one isolate harbored class 2 integrons. Plasmid associated intI1 and androgen receptor- encoding genes were transferred into Escherichia coli J53 and E. coli DH5α by conjugation and transformation experiments, respectively. Our study highlights the importance of aerobic bacteria from pork as reservoirs for antimicrobial resistance genes and mobile genetic elements that can readily be transferred intra- and interspecies.

Characterization of wound infections among patients injured during the 2011 Libyan conflict.

PubMed

Dau, A A; Tloba, S; Daw, M A

2013-04-01

Few studies have analysed the bacterial pathogenesis of infections associated with war-wound in the Eastern Mediterranean region. We analysed surgical wound infections of 1200 patients injured during the Libyan conflict in 2011 and admitted to the emergency services at Tripoli medical centre. Culture swabs or surgical wound debridement samples were collected and cultures were identified and tested for antimicrobial resistance. Of the 1200 patients studied, 498 (42%) were infected with at least 1 pathogen and 57 with >2 pathogens. The most common species were Acinetobacter spp. (isolated from 144 patients), coagulase-negative staphylococci (122), Escherichia coli (107), Pseudomnonas aeruginosa (92) and Klebsiella spp. (86). A high level of resistance to the antibiotics tested was found, especially among Acinetobacter spp. Multi-drug-resistant Gram-negative bacilli were an important complicating factor in wound infections associated with war injuries among injured patients in Libya. Effective policies are needed to control and treat such infections particularly in trauma and emergency services.

Can Pharmacokinetic and Pharmacodynamic Principles Be Applied to the Treatment of Multidrug-Resistant Acinetobacter?

PubMed

Cooper, Travis W; Pass, Steven E; Brouse, Sara D; Hall, Ronald G

2011-02-01

To discuss treatment options that can be used for treatment of Acinetobac/erinfections. A MEDLINE search (1966-November 2010) was conducted to identify English-language literature on pharmacotherapy of Acinetobacter and the bibliographies of pertinent articles. Programs and abstracts from infectious diseases meetings were also searched. Search terms included Acinetobacter, multidrug resistance, pharmacokinetics, pharmacodynamics, Monte Carlo simulation, nosocomial pneumonia, carbapenems, polymyxins, sulbactam, aminoglycosides, tetracyclines, tigecycline, rifampin, and fluoroquinolones. All articles were critically evaluated and all pertinent information was included in this review. Multidrug resistant (MDR) Acinetobacter, defined as resistance to 3 or more antimicrobial classes, has increased over the past decade. The incidence of carbapenem-resistant Acinetobacter is also increasing, leading to an increased use of dose optimization techniques and/or alternative antimicrobials, which is driven by local susceptibility patterns. However, Acinetobacter infections that are resistant to all commercially available antibiotics have been reported. General principles are available to guide dose optimization of aminoglycosides, β-lactams, fluoroquinolones, and tigecycline for infections due to gram-negative pathogens. Unfortunately, data specific to patients with Acinetobacter infections are limited. Recent pharmacokinetic-pharmacodynamic information has shed light on colistin dosing. The dilemma with colistin is its concentration-dependent killing, which makes once-daily dosing seem like an attractive option, but its short postantibiotic effect limits a clinician's ability to extend the dosing interval. Localized delivery of antimicrobials is also an attractive option due to the ability to increase drug concentration at the infection site while minimizing systemic adverse events, but more data are needed regarding this approach. Increased reliance on dosage optimization, combination therapy, and localized delivery of antimicrobials are methods to pursue positive clinical outcomes in MDR Acinetobacter infections since novel antimicrobials will not be available for several years. Well-designed clinical trials with MDR Acinetobacter are needed to define the best treatment options for these patients. © 2011 SAGE Publications.

Prevalence of Pseudomonas aeruginosa and Acinetobacter spp. in subgingival biofilm and saliva of subjects with chronic periodontal infection.

PubMed

Souto, Renata; Silva-Boghossian, Carina M; Colombo, Ana Paula Vieira

2014-01-01

P. aeruginosa and Acinetobacter spp. are important pathogens associated with late nosocomial pneumonia in hospitalized and institutionalized individuals. The oral cavity may be a major source of these respiratory pathogens, particularly in the presence of poor oral hygiene and periodontal infection. This study investigated the prevalence of P. aeruginosa and Acinetobacter spp. in subgingival biofilm and saliva of subjects with periodontal disease or health. Samples were obtained from 55 periodontally healthy (PH) and 169 chronic periodontitis (CP) patients. DNA was obtained from the samples and detection of P. aeruginosa and Acinetobacter spp. was carried out by multiplex and nested PCR. P. aeruginosa and Acinetobacter spp. were detected in 40% and 45% of all samples, respectively. No significant differences in the distribution of these microorganisms between men and women, subgingival biofilm and saliva samples, patients ≤ 35 and > 35 years of age, and smokers and non-smokers were observed regardless periodontal status (p > 0.05). In contrast, the frequencies of P. aeruginosa and Acinetobacter spp. in saliva and biofilm samples were significantly greater in CP than PH patients (p < 0.01). Smokers presenting P. aeruginosa and high frequencies of supragingival plaque were more likely to present CP than PH. P. aeruginosa and Acinetobacter spp. are frequently detected in the oral microbiota of CP. Poor oral hygiene, smoking and the presence of P. aeruginosa are strongly associated with periodontitis.

Prevalence of Pseudomonas aeruginosa and Acinetobacter spp. in subgingival biofilm and saliva of subjects with chronic periodontal infection

PubMed Central

Souto, Renata; Silva-Boghossian, Carina M.; Colombo, Ana Paula Vieira

2014-01-01

P. aeruginosa and Acinetobacter spp. are important pathogens associated with late nosocomial pneumonia in hospitalized and institutionalized individuals. The oral cavity may be a major source of these respiratory pathogens, particularly in the presence of poor oral hygiene and periodontal infection. This study investigated the prevalence of P. aeruginosa and Acinetobacter spp. in subgingival biofilm and saliva of subjects with periodontal disease or health. Samples were obtained from 55 periodontally healthy (PH) and 169 chronic periodontitis (CP) patients. DNA was obtained from the samples and detection of P. aeruginosa and Acinetobacter spp. was carried out by multiplex and nested PCR. P. aeruginosa and Acinetobacter spp. were detected in 40% and 45% of all samples, respectively. No significant differences in the distribution of these microorganisms between men and women, subgingival biofilm and saliva samples, patients ≤ 35 and > 35 years of age, and smokers and non-smokers were observed regardless periodontal status (p > 0.05). In contrast, the frequencies of P. aeruginosa and Acinetobacter spp. in saliva and biofilm samples were significantly greater in CP than PH patients (p < 0.01). Smokers presenting P. aeruginosa and high frequencies of supragingival plaque were more likely to present CP than PH. P. aeruginosa and Acinetobacter spp. are frequently detected in the oral microbiota of CP. Poor oral hygiene, smoking and the presence of P. aeruginosa are strongly associated with periodontitis. PMID:25242933

Genome size variation in the genus Avena.

PubMed

Yan, Honghai; Martin, Sara L; Bekele, Wubishet A; Latta, Robert G; Diederichsen, Axel; Peng, Yuanying; Tinker, Nicholas A

2016-03-01

Genome size is an indicator of evolutionary distance and a metric for genome characterization. Here, we report accurate estimates of genome size in 99 accessions from 26 species of Avena. We demonstrate that the average genome size of C genome diploid species (2C = 10.26 pg) is 15% larger than that of A genome species (2C = 8.95 pg), and that this difference likely accounts for a progression of size among tetraploid species, where AB < AC < CC (average 2C = 16.76, 18.60, and 21.78 pg, respectively). All accessions from three hexaploid species with the ACD genome configuration had similar genome sizes (average 2C = 25.74 pg). Genome size was mostly consistent within species and in general agreement with current information about evolutionary distance among species. Results also suggest that most of the polyploid species in Avena have experienced genome downsizing in relation to their diploid progenitors. Genome size measurements could provide additional quality control for species identification in germplasm collections, especially in cases where diploid and polyploid species have similar morphology.

Development and Characterization of an Unmarked hemO Cluster Knockout in Hypervirulent Acinetobacter Baumannii LAC-4

DTIC Science & Technology

2016-03-01

decade since the First World War when Alexander Fleming discovered the inhibitory, antibacterial properties of a substance excreted by the mold...was treated with penicillin, what appeared to be resistance was noted by researchers and later discovered to be penicillinase activity (Abraham et...In particular, innovations in the treatment of Gram-negative species have shown little progress with a near absence of any drug candidate active

Stable bioemulsifiers are produced by Acinetobacter bouvetii UAM25 growing in different carbon sources.

PubMed

Ortega-de la Rosa, Nestor D; Vázquez-Vázquez, Jose L; Huerta-Ochoa, Sergio; Gimeno, Miquel; Gutiérrez-Rojas, Mariano

2018-06-01

Acinetobacter species are identified as producing surface-active and emulsifying molecules known as bioemulsifiers. Production, characterization and stability of bioemulsifiers produced by Acinetobacter bouvetii UAM25 were studied. A. bouvetii UAM25 grew in three different carbon and energy sources: ethanol, a glycerol-hexadecane mixture and waste cooking oil in an airlift bioreactor, showing that bioemulsifier production was growth associated. The three purified bioemulsifiers were lipo-heteropolysaccharides of high molecular weight (4866 ± 533 and 462 ± 101 kDa). The best carbon source and energy for bioemulsifier production was wasted cooking oil, with a highest emulsifying capacity (76.2 ± 3.5 EU mg -1 ) as compared with ethanol (46.6 ± 7.1 EU mg -1 ) and the glycerol-hexadecane mixture (49.5 ± 4.2 EU mg -1 ). The three bioemulsifiers in our study displayed similar macromolecular structures, regardless of the nature (hydrophobic or hydrophilic) of the carbon and energy source. Bioemulsifiers did not decrease surface tension, but the emulsifying capacity of all of them was retained under extreme variation in salinity (0-50 g NaCl L -1 ), pH (3-10) and temperature (25-121 °C), indicative of remarkable stability. These findings contribute to understanding of the relationship between: production, physical properties, chemical composition and stability of bioemulsifiers for their potential applications in biotechnology, such as bioremediation of hydrocarbon-contaminated soil and water.

Biofilm and metallo beta-lactamase production among the strains of Pseudomonas aeruginosa and Acinetobacter spp. at a Tertiary Care Hospital in Kathmandu, Nepal.

PubMed

Baniya, Bandana; Pant, Narayan Dutt; Neupane, Sanjeev; Khatiwada, Saroj; Yadav, Uday Narayan; Bhandari, Nisha; Khadka, Rama; Bhatta, Sabita; Chaudhary, Raina

2017-11-02

Pseudomonas aeruginosa and Acinetobacter spp. are found to be associated with biofilm and metallo-β-lactamase production and are the common causes of serious infections mainly in hospitalized patients. So, the main aims of this study were to determine the rates of biofilm production and metallo beta-lactamase production (MBL) among the strains of Pseudomonas aeruginosa and Acinetobacter spp. isolated from hospitalized patients. A total of 85 P. aeruginosa isolates and 50 Acinetobacter spp. isolates isolated from different clinical specimens from patients admitted to Shree Birendra Hospital, Kathmandu, Nepal from July 2013 to May 2014 were included in this study. The bacterial isolates were identified with the help of biochemical tests. Modified Kirby-Bauer disc diffusion technique was used for antimicrobial susceptibility testing. Combined disc diffusion technique was used for the detection of MBL production, while Congo red agar method and tube adherence method were used for detection of biofilm production. Around 16.4% of P. aeruginosa isolates and 22% of the strains of Acinetobacter spp. were metallo β-lactamase producers. Out of 85 P. aeruginosa isolates, 23 (27.05%) were biofilm producers according to tube adherence test while, only 13 (15.29%) were biofilm producers as per Congo red agar method. Similarly, out of 50 Acinetobacter spp. 7 (14%) isolates were biofilm producers on the basis of tube adherence test, while only 5 (10%) were positive for biofilm production by Congo red agar method. Highest rates of susceptibility of P. aeruginosa as well as Acinetobacter spp. were seen toward colistin. In our study, biofilm production and metallo beta-lactamase production were observed among Pseudomonas aeruginosa and Acinetobacter spp. However, no statistically significant association could be established between biofilm production and metallo beta-lactamase production.

Comparative Genomics of Two ST 195 Carbapenem-Resistant Acinetobacter baumannii with Different Susceptibility to Polymyxin Revealed Underlying Resistance Mechanism.

PubMed

Lean, Soo-Sum; Yeo, Chew Chieng; Suhaili, Zarizal; Thong, Kwai-Lin

2015-01-01

Acinetobacter baumannii is a Gram-negative nosocomial pathogen of importance due to its uncanny ability to acquire resistance to most antimicrobials. These include carbapenems, which are the drugs of choice for treating A. baumannii infections, and polymyxins, the drugs of last resort. Whole genome sequencing was performed on two clinical carbapenem-resistant A. baumannii AC29 and AC30 strains which had an indistinguishable ApaI pulsotype but different susceptibilities to polymyxin. Both genomes consisted of an approximately 3.8 Mbp circular chromosome each and several plasmids. AC29 (susceptible to polymyxin) and AC30 (resistant to polymyxin) belonged to the ST195 lineage and are phylogenetically clustered under the International Clone II (IC-II) group. An AbaR4-type resistance island (RI) interrupted the comM gene in the chromosomes of both strains and contained the bla OXA-23 carbapenemase gene and determinants for tetracycline and streptomycin resistance. AC29 harbored another copy of bla OXA-23 in a large (~74 kb) conjugative plasmid, pAC29b, but this gene was absent in a similar plasmid (pAC30c) found in AC30. A 7 kb Tn1548::armA RI which encodes determinants for aminoglycoside and macrolide resistance, is chromosomally-located in AC29 but found in a 16 kb plasmid in AC30, pAC30b. Analysis of known determinants for polymyxin resistance in AC30 showed mutations in the pmrA gene encoding the response regulator of the two-component pmrAB signal transduction system as well as in the lpxD, lpxC, and lpsB genes that encode enzymes involved in the biosynthesis of lipopolysaccharide (LPS). Experimental evidence indicated that impairment of LPS along with overexpression of pmrAB may have contributed to the development of polymyxin resistance in AC30. Cloning of a novel variant of the bla AmpC gene from AC29 and AC30, and its subsequent expression in E. coli also indicated its likely function as an extended-spectrum cephalosporinase.

Insertion sequence transposition determines imipenem resistance in Acinetobacter baumannii.

PubMed

Kuo, Han-Yueh; Chang, Kai-Chih; Liu, Chih-Chin; Tang, Chuan Yi; Peng, Jhih-Hua; Lu, Chia-Wei; Tu, Chi-Chao; Liou, Ming-Li

2014-10-01

This study employed genomewide analysis to investigate potential resistance mechanisms in Acinetobacter baumannii following imipenem exposure. Imipenem-selected mutants were generated from the imipenem-susceptible strain ATCC 17978 by multistep selection resistance. Antibiotic susceptibilities were examined, and the selected mutants originated from the ATCC 17978 strain were confirmed by pulsed-field gel electrophoresis. The genomic sequence of a resistant mutant was analyzed using a next-generation sequencing platform, and genetic recombination was further confirmed by PCR. The result showed that phenotypic resistance was observed with carbapenem upon exposure to various concentrations of imipenem. Genomewide analysis showed that ISAba1 transposition was initiated by imipenem exposure at concentrations up to 0.5 mg/L. Transposition of ISAba1 upstream of blaOXA-95 was detected in all the selected mutants. The expression of blaOXA-95 was further analyzed by quantitative PCR, and the results demonstrated that a 200-fold increase in gene expression was required for resistance to imipenem. This study concluded that imipenem exposure at a concentration of 0.5 mg/L mediated the transposition of ISAba1 upstream of the blaOXA-95 gene and resulted in the overexpression of blaOXA-95 gene, which may play a major role in the resistance to imipenem in A. baumannii.

Isolation of Acinetobacter from Soil and Water

PubMed Central

Baumann, Paul

1968-01-01

An enrichment culture procedure for isolating members of the genus Acinetobacter from soil and water is described. It involves the use of vigorously aerated mineral media at relative low pH, supplemented with acetate or other suitable carbon source and nitrate as nitrogen source. With this method, virtually all samples of soil and water yielded representatives of this genus. Semiquantitative comparisons of the numbers of Acinetobacter and of all bacteria capable of aerobic growth in a complex medium revealed that Acinetobacter constituted no less than 0.001% of the total heterotrophic aerobic population in soil and water and was one of the predominant organisms in some water samples. PMID:4874313

Production of Cell-Cell Signaling Molecules by Bacteria Isolated From Human Chronic Wounds

PubMed Central

Rickard, Alexander H.; Colacino, Katelyn R.; Manton, Katelynn M.; Morton, Robert I.; Pulcini, Elinor; Pfeil, Joanne; Rhoads, Daniel; Wolcott, Randall D.; James, Garth

2009-01-01

AIM To (i) identify chronic wound bacteria and to test their ability to produce acyl-homoserine-lactones (AHLs) and autoinducer-2 (AI-2) cell-cell signaling molecules and (ii) determine if chronic wound debridement samples might contain these molecules. METHODS AND RESULTS Partial 16S rRNA gene sequencing revealed the identity of 46 chronic wound strains as belonging to nine genera. Using bio-reporter assays, 69.6% of the chronic wound strains were inferred to produce AI-2 while 19.6% were inferred to produced AHL molecules. At-least one strain from every genus, except those belonging to the genera Acinetobacter and Pseudomonas, were indicated to produce AI-2. Production of AI-2 in batch-cultures was growth-phase-dependent. Cross-feeding assays demonstrated that AHLs were produced by Acinetobacter spp., Pseudomonas aeruginosa and Serratia marcescens. Independent from studies of the bacterial species isolated from wounds, AHL and/or AI-2 signaling molecules were detected in 21 of 30 debridement samples of unknown microbial composition. CONCLUSION Chronic wound bacteria produce cell-cell signaling molecules. Resident species generally produce AI-2 molecules and aggressive transient species associated with chronic wounds typically produce AHLs. Both these classes of cell-cell signals are present in human chronic wounds. SIGNIFICANCE AND IMPACT OF STUDY Inter-bacterial cell-cell signaling may be an important factor influencing wound development and the presence of AHLs and AI-2 could be used as a predictor of wound severity. Manipulation of cell −cell signaling may provide a novel strategy for improving wound healing. PMID:19840177

Nodeomics: Pathogen Detection in Vertebrate Lymph Nodes Using Meta-Transcriptomics

USGS Publications Warehouse

Wittekindt, Nicola E.; Padhi, Abinash; Schuster, Stephan C.; Qi, Ji; Zhao, Fangqing; Tomsho, Lynn P.; Kasson, Lindsay R.; Packard, Michael; Cross, Paul C.; Poss, Mary

2010-01-01

The ongoing emergence of human infections originating from wildlife highlights the need for better knowledge of the microbial community in wildlife species where traditional diagnostic approaches are limited. Here we evaluate the microbial biota in healthy mule deer (Odocoileus hemionus) by analyses of lymph node meta-transcriptomes. cDNA libraries from five individuals and two pools of samples were prepared from retropharyngeal lymph node RNA enriched for polyadenylated RNA and sequenced using Roche-454 Life Sciences technology. Protein-coding and 16S ribosomal RNA (rRNA) sequences were taxonomically profiled using protein and rRNA specific databases. Representatives of all bacterial phyla were detected in the seven libraries based on protein-coding transcripts indicating that viable microbiota were present in lymph nodes. Residents of skin and rumen, and those ubiquitous in mule deer habitat dominated classifiable bacterial species. Based on detection of both rRNA and protein-coding transcripts, we identified two new proteobacterial species; a Helicobacter closely related to Helicobacter cetorum in the Helicobacter pylori/Helicobacter acinonychis complex and an Acinetobacter related to Acinetobacter schindleri. Among viruses, a novel gamma retrovirus and other members of the Poxviridae and Retroviridae were identified. We additionally evaluated bacterial diversity by amplicon sequencing the hypervariable V6 region of 16S rRNA and demonstrate that overall taxonomic diversity is higher with the meta-transcriptomic approach. These data provide the most complete picture to date of the microbial diversity within a wildlife host. Our research advances the use of meta-transcriptomics to study microbiota in wildlife tissues, which will facilitate detection of novel organisms with pathogenic potential to human and animals.

Distribution and Persistence of Staphylococcus and Micrococcus Species and Other Aerobic Bacteria on Human Skin1

PubMed Central

Kloos, Wesley E.; Musselwhite, Margaret S.

1975-01-01

The distribution of Staphylococcus and Micrococcus species and associated coryneform bacteria, Acinetobacter, Klebsiella, Enterobacter, Bacillus, and Streptomyces on skin was determined during October 1971 from samples collected on persons living in North Carolina and New Jersey. Persistence of these organisms on skin was estimated in temporal studies conducted during the period from June 1971 to June 1972 on persons living in North Carolina. Staphylococci and coryneforms were the most predominant and persistent bacteria isolated from the nares and axillae. Staphylococci, coryneforms, micrococci, and Bacillus were the most predominant and persistent bacteria isolated from the head, legs, and arms. Acinetobacters were most frequently isolated during the warmer months of the years. Staphylococcus aureus and S. epidermidis were the most predominant and persistent staphylococci isolated from the nares, whereas S. epidermidis and S. hominis were the most predominant and persistent staphylococci isolated from the axillae, head, legs, and arms. S. capitis was often isolated from the head and arms and S. haemolyticus was often isolated from the head, legs, and arms. S. simulans, S. xylosus, S. cohnii, S. saprophyticus, S. warneri, and an unclassified coagulase-positive species were only occasionally isolated from skin. Micrococcus luteus was the most predominant and persistent Micrococcus isolated from skin and preferred regions of the head, legs, and arms. M. varians was the second most frequent Micrococcus isolated. M. lylae, M. sedentarius, M. roseus, M. kristinae, and M. nishinomiyaensis were only occasionally isolated from skin. M. lylae was most frequently isolated during the colder months of the years. PMID:810086

Comparative Genomics and Identification of an Enterotoxin-Bearing Pathogenicity Island, SEPI-1/SECI-1, in Staphylococcus epidermidis Pathogenic Strains.

PubMed

Argemi, Xavier; Nanoukon, Chimène; Affolabi, Dissou; Keller, Daniel; Hansmann, Yves; Riegel, Philippe; Baba-Moussa, Lamine; Prévost, Gilles

2018-02-25

Staphylococcus epidermidis is a leading cause of nosocomial infections, majorly resistant to beta-lactam antibiotics, and may transfer several mobile genetic elements among the members of its own species, as well as to Staphylococcus aureus ; however, a genetic exchange from S. aureus to S. epidermidis remains controversial. We recently identified two pathogenic clinical strains of S. epidermidis that produce a staphylococcal enterotoxin C3-like (SEC) similar to that by S. aureus pathogenicity islands. This study aimed to determine the genetic environment of the SEC-coding sequence and to identify the mobile genetic elements. Whole-genome sequencing and annotation of the S. epidermidis strains were performed using Illumina technology and a bioinformatics pipeline for assembly, which provided evidence that the SEC-coding sequences were located in a composite pathogenicity island that was previously described in the S. epidermidis strain FRI909, called SePI-1/SeCI-1, with 83.8-89.7% nucleotide similarity. Various other plasmids were identified, particularly p_3_95 and p_4_95, which carry antibiotic resistance genes ( hsrA and dfrG , respectively), and share homologies with SAP085A and pUSA04-2-SUR11, two plasmids described in S. aureus . Eventually, one complete prophage was identified, ΦSE90, sharing 30 out of 52 coding sequences with the Acinetobacter phage vB_AbaM_IME200. Thus, the SePI-1/SeCI-1 pathogenicity island was identified in two pathogenic strains of S. epidermidis that produced a SEC enterotoxin causing septic shock. These findings suggest the existence of in vivo genetic exchange from S. aureus to S. epidermidis .

Comparative Genomics and Identification of an Enterotoxin-Bearing Pathogenicity Island, SEPI-1/SECI-1, in Staphylococcus epidermidis Pathogenic Strains

PubMed Central

Nanoukon, Chimène; Affolabi, Dissou; Keller, Daniel; Hansmann, Yves; Riegel, Philippe; Baba-Moussa, Lamine; Prévost, Gilles

2018-01-01

Staphylococcus epidermidis is a leading cause of nosocomial infections, majorly resistant to beta-lactam antibiotics, and may transfer several mobile genetic elements among the members of its own species, as well as to Staphylococcus aureus; however, a genetic exchange from S. aureus to S. epidermidis remains controversial. We recently identified two pathogenic clinical strains of S. epidermidis that produce a staphylococcal enterotoxin C3-like (SEC) similar to that by S. aureus pathogenicity islands. This study aimed to determine the genetic environment of the SEC-coding sequence and to identify the mobile genetic elements. Whole-genome sequencing and annotation of the S. epidermidis strains were performed using Illumina technology and a bioinformatics pipeline for assembly, which provided evidence that the SEC-coding sequences were located in a composite pathogenicity island that was previously described in the S. epidermidis strain FRI909, called SePI-1/SeCI-1, with 83.8–89.7% nucleotide similarity. Various other plasmids were identified, particularly p_3_95 and p_4_95, which carry antibiotic resistance genes (hsrA and dfrG, respectively), and share homologies with SAP085A and pUSA04-2-SUR11, two plasmids described in S. aureus. Eventually, one complete prophage was identified, ΦSE90, sharing 30 out of 52 coding sequences with the Acinetobacter phage vB_AbaM_IME200. Thus, the SePI-1/SeCI-1 pathogenicity island was identified in two pathogenic strains of S. epidermidis that produced a SEC enterotoxin causing septic shock. These findings suggest the existence of in vivo genetic exchange from S. aureus to S. epidermidis. PMID:29495323

Chromosomal Amplification of the blaOXA-58 Carbapenemase Gene in a Proteus mirabilis Clinical Isolate.

PubMed

Girlich, Delphine; Bonnin, Rémy A; Bogaerts, Pierre; De Laveleye, Morgane; Huang, Daniel T; Dortet, Laurent; Glaser, Philippe; Glupczynski, Youri; Naas, Thierry

2017-02-01

Horizontal gene transfer may occur between distantly related bacteria, thus leading to genetic plasticity and in some cases to acquisition of novel resistance traits. Proteus mirabilis is an enterobacterial species responsible for human infections that may express various acquired β-lactam resistance genes, including different classes of carbapenemase genes. Here we report a Proteus mirabilis clinical isolate (strain 1091) displaying resistance to penicillin, including temocillin, together with reduced susceptibility to carbapenems and susceptibility to expanded-spectrum cephalosporins. Using biochemical tests, significant carbapenem hydrolysis was detected in P. mirabilis 1091. Since PCR failed to detect acquired carbapenemase genes commonly found in Enterobacteriaceae, we used a whole-genome sequencing approach that revealed the presence of bla OXA-58 class D carbapenemase gene, so far identified only in Acinetobacter species. This gene was located on a 3.1-kb element coharboring a bla AmpC -like gene. Remarkably, these two genes were bracketed by putative XerC-XerD binding sites and inserted at a XerC-XerD site located between the terminase-like small- and large-subunit genes of a bacteriophage. Increased expression of the two bla genes resulted from a 6-time tandem amplification of the element as revealed by Southern blotting. This is the first isolation of a clinical P. mirabilis strain producing OXA-58, a class D carbapenemase, and the first description of a XerC-XerD-dependent insertion of antibiotic resistance genes within a bacteriophage. This study revealed a new role for the XerC-XerD recombinase in bacteriophage biology. Copyright © 2017 American Society for Microbiology.

Chromosomal Amplification of the blaOXA-58 Carbapenemase Gene in a Proteus mirabilis Clinical Isolate

PubMed Central

Girlich, Delphine; Bogaerts, Pierre; De Laveleye, Morgane; Huang, Daniel T.; Glupczynski, Youri

2016-01-01

ABSTRACT Horizontal gene transfer may occur between distantly related bacteria, thus leading to genetic plasticity and in some cases to acquisition of novel resistance traits. Proteus mirabilis is an enterobacterial species responsible for human infections that may express various acquired β-lactam resistance genes, including different classes of carbapenemase genes. Here we report a Proteus mirabilis clinical isolate (strain 1091) displaying resistance to penicillin, including temocillin, together with reduced susceptibility to carbapenems and susceptibility to expanded-spectrum cephalosporins. Using biochemical tests, significant carbapenem hydrolysis was detected in P. mirabilis 1091. Since PCR failed to detect acquired carbapenemase genes commonly found in Enterobacteriaceae, we used a whole-genome sequencing approach that revealed the presence of blaOXA-58 class D carbapenemase gene, so far identified only in Acinetobacter species. This gene was located on a 3.1-kb element coharboring a blaAmpC-like gene. Remarkably, these two genes were bracketed by putative XerC-XerD binding sites and inserted at a XerC-XerD site located between the terminase-like small- and large-subunit genes of a bacteriophage. Increased expression of the two bla genes resulted from a 6-time tandem amplification of the element as revealed by Southern blotting. This is the first isolation of a clinical P. mirabilis strain producing OXA-58, a class D carbapenemase, and the first description of a XerC-XerD-dependent insertion of antibiotic resistance genes within a bacteriophage. This study revealed a new role for the XerC-XerD recombinase in bacteriophage biology. PMID:27855079

Modulation of microbial consortia enriched from different polluted environments during petroleum biodegradation.

PubMed

Omrani, Rahma; Spini, Giulia; Puglisi, Edoardo; Saidane, Dalila

2018-04-01

Environmental microbial communities are key players in the bioremediation of hydrocarbon pollutants. Here we assessed changes in bacterial abundance and diversity during the degradation of Tunisian Zarzatine oil by four indigenous bacterial consortia enriched from a petroleum station soil, a refinery reservoir soil, a harbor sediment and seawater. The four consortia were found to efficiently degrade up to 92.0% of total petroleum hydrocarbons after 2 months of incubation. Illumina 16S rRNA gene sequencing revealed that the consortia enriched from soil and sediments were dominated by species belonging to Pseudomonas and Acinetobacter genera, while in the seawater-derived consortia Dietzia, Fusobacterium and Mycoplana emerged as dominant genera. We identified a number of species whose relative abundances bloomed from small to high percentages: Dietzia daqingensis in the seawater microcosms, and three OTUs classified as Acinetobacter venetianus in all two soils and sediment derived microcosms. Functional analyses on degrading genes were conducted by comparing PCR results of the degrading genes alkB, ndoB, cat23, xylA and nidA1 with inferences obtained by PICRUSt analysis of 16S amplicon data: the two data sets were partly in agreement and suggest a relationship between the catabolic genes detected and the rate of biodegradation obtained. The work provides detailed insights about the modulation of bacterial communities involved in petroleum biodegradation and can provide useful information for in situ bioremediation of oil-related pollution.

Microbial species delineation using whole genome sequences

PubMed Central

Varghese, Neha J.; Mukherjee, Supratim; Ivanova, Natalia; Konstantinidis, Konstantinos T.; Mavrommatis, Kostas; Kyrpides, Nikos C.; Pati, Amrita

2015-01-01

Increased sequencing of microbial genomes has revealed that prevailing prokaryotic species assignments can be inconsistent with whole genome information for a significant number of species. The long-standing need for a systematic and scalable species assignment technique can be met by the genome-wide Average Nucleotide Identity (gANI) metric, which is widely acknowledged as a robust measure of genomic relatedness. In this work, we demonstrate that the combination of gANI and the alignment fraction (AF) between two genomes accurately reflects their genomic relatedness. We introduce an efficient implementation of AF,gANI and discuss its successful application to 86.5M genome pairs between 13,151 prokaryotic genomes assigned to 3032 species. Subsequently, by comparing the genome clusters obtained from complete linkage clustering of these pairs to existing taxonomy, we observed that nearly 18% of all prokaryotic species suffer from anomalies in species definition. Our results can be used to explore central questions such as whether microorganisms form a continuum of genetic diversity or distinct species represented by distinct genetic signatures. We propose that this precise and objective AF,gANI-based species definition: the MiSI (Microbial Species Identifier) method, be used to address previous inconsistencies in species classification and as the primary guide for new taxonomic species assignment, supplemented by the traditional polyphasic approach, as required. PMID:26150420

Morphine, but not Trauma, Sensitizes to Systemic Acinetobacter baumannii Infection

PubMed Central

Breslow, Jessica M.; Monroy, M. Alexandra; Daly, John M.; Meissler, Joseph J.; Gaughan, John; Adler, Martin W.; Eisenstein, Toby K.

2014-01-01

Acinetobacter baumannii is an important nosocomial pathogen in civilian intensive care units. Recently the incidence has increased in wounded military personnel. Morphine is documented in numerous animal studies to be immunosuppressive and to sensitize to infection. The hypotheses were tested that morphine, administered for analgesia in the battlefield, predisposes to Acinetobacter infection, and that the opioid may have an additive or synergistic effect with trauma. To test these hypotheses, an intraperitoneal infection model was established in mice using several Acinetobacter strains. Morphine administered for 48 hr by implantation of a slow-release morphine pellet increased mortality compared to animals receiving a placebo pellet, an effect that was blocked by the mu-opioid receptor antagonist, naltrexone. Acinetobacter burdens in the blood, spleens, livers, and lungs of morphine-treated mice, were significantly higher than those in placebo-treated animals, confirming that mortality was due to potentiated growth of the bacteria. There were also elevated levels of pro-inflammatory cytokines in morphine-treated versus placebo-treated mice. Morphine caused a reduction in the total number of cells in the peritoneal cavity, a decrease in the percentage and total numbers of neutrophils, and a decrease in the total number of macrophages. Morphine treatment also suppressed levels of the neutrophil-inducing molecules, IL-17A and KC/CXCL1. However, IL-17A−/− mice given morphine were not sensitized to Acintobacter infection to a greater degree than similarly treated wild-type mice. Trauma alone did not sensitize to Acinetobacter infection, and there was no additive effect between morphine and trauma. These results support the hypothesis that morphine potentiates Acinetobacter infection. PMID:21826405

Morphine, but not trauma, sensitizes to systemic Acinetobacter baumannii infection.

PubMed

Breslow, Jessica M; Monroy, M Alexandra; Daly, John M; Meissler, Joseph J; Gaughan, John; Adler, Martin W; Eisenstein, Toby K

2011-12-01

Acinetobacter baumannii is an important nosocomial pathogen in civilian intensive care units. Recently the incidence has increased in wounded military personnel. Morphine is documented in numerous animal studies to be immunosuppressive and to sensitize to infection. The hypotheses were tested that morphine, administered for analgesia in the battlefield, predisposes to Acinetobacter infection, and that the opioid may have an additive or synergistic effect with trauma. To test these hypotheses, an intraperitoneal infection model was established in mice using several Acinetobacter strains. Morphine administered for 48 h by implantation of a slow-release morphine pellet increased mortality compared to animals receiving a placebo pellet, an effect that was blocked by the mu-opioid receptor antagonist, naltrexone. Acinetobacter burdens in the blood, spleens, livers, and lungs of morphine-treated mice, were significantly higher than those in placebo-treated animals, confirming that mortality was due to potentiated growth of the bacteria. There were also elevated levels of pro-inflammatory cytokines in morphine-treated versus placebo-treated mice. Morphine caused a reduction in the total number of cells in the peritoneal cavity, a decrease in the percentage and total numbers of neutrophils, and a decrease in the total number of macrophages. Morphine treatment also suppressed levels of the neutrophil-inducing molecules, IL-17A and KC/CXCL1. However, IL-17A(-/-) mice given morphine were not sensitized to Acintobacter infection to a greater degree than similarly treated wild-type mice. Trauma alone did not sensitize to Acinetobacter infection, and there was no additive effect between morphine and trauma. These results support the hypothesis that morphine potentiates Acinetobacter infection.

Phenotypic and genomic characterization of the antimicrobial producer Rheinheimera sp. EpRS3 isolated from the medicinal plant Echinacea purpurea: insights into its biotechnological relevance.

PubMed

Presta, Luana; Bosi, Emanuele; Fondi, Marco; Maida, Isabel; Perrin, Elena; Miceli, Elisangela; Maggini, Valentina; Bogani, Patrizia; Firenzuoli, Fabio; Di Pilato, Vincenzo; Rossolini, Gian Maria; Mengoni, Alessio; Fani, Renato

2017-04-01

In recent years, there has been increasing interest in plant microbiota; however, despite medicinal plant relevance, very little is known about their highly complex endophytic communities. In this work, we report on the genomic and phenotypic characterization of the antimicrobial compound producer Rheinheimera sp. EpRS3, a bacterial strain isolated from the rhizospheric soil of the medicinal plant Echinacea purpurea. In particular, EpRS3 is able to inhibit growth of different bacterial pathogens (Bcc, Acinetobacter baumannii, and Klebsiella pneumoniae) which might be related to the presence of gene clusters involved in the biosynthesis of different types of secondary metabolites. The outcomes presented in this work highlight the fact that the strain possesses huge biotechnological potential; indeed, it also shows antimicrobial effects upon well-described multidrug-resistant (MDR) human pathogens, and it affects plant root elongation and morphology, mimicking indole acetic acid (IAA) action. Copyright © 2016 Institut Pasteur. Published by Elsevier Masson SAS. All rights reserved.

Novel genomes and genome constitutions identified by GISH and 5S rDNA and knotted1 genomic sequences in the genus Setaria.

PubMed

Zhao, Meicheng; Zhi, Hui; Doust, Andrew N; Li, Wei; Wang, Yongfang; Li, Haiquan; Jia, Guanqing; Wang, Yongqiang; Zhang, Ning; Diao, Xianmin

2013-04-11

The Setaria genus is increasingly of interest to researchers, as its two species, S. viridis and S. italica, are being developed as models for understanding C4 photosynthesis and plant functional genomics. The genome constitution of Setaria species has been studied in the diploid species S. viridis, S. adhaerans and S. grisebachii, where three genomes A, B and C were identified respectively. Two allotetraploid species, S. verticillata and S. faberi, were found to have AABB genomes, and one autotetraploid species, S. queenslandica, with an AAAA genome, has also been identified. The genomes and genome constitutions of most other species remain unknown, even though it was thought there are approximately 125 species in the genus distributed world-wide. GISH was performed to detect the genome constitutions of Eurasia species of S. glauca, S. plicata, and S. arenaria, with the known A, B and C genomes as probes. No or very poor hybridization signal was detected indicating that their genomes are different from those already described. GISH was also performed reciprocally between S. glauca, S. plicata, and S. arenaria genomes, but no hybridization signals between each other were found. The two sets of chromosomes of S. lachnea both hybridized strong signals with only the known C genome of S. grisebachii. Chromosomes of Qing 9, an accession formerly considered as S. viridis, hybridized strong signal only to B genome of S. adherans. Phylogenetic trees constructed with 5S rDNA and knotted1 markers, clearly classify the samples in this study into six clusters, matching the GISH results, and suggesting that the F genome of S. arenaria is basal in the genus. Three novel genomes in the Setaria genus were identified and designated as genome D (S. glauca), E (S. plicata) and F (S. arenaria) respectively. The genome constitution of tetraploid S. lachnea is putatively CCC'C'. Qing 9 is a B genome species indigenous to China and is hypothesized to be a newly identified species. The difference in genome constitution and origin of S. verticillata and S. faberi is also discussed. The new genomes and the genome constitutions of Setaria species identified in this report provide useful information for Setaria germplasm management, foxtail millet breeding, grass evolution and the development of S. viridis and S. italica as a new model for functional genomics.

Microbial genomic taxonomy

PubMed Central

2013-01-01

A need for a genomic species definition is emerging from several independent studies worldwide. In this commentary paper, we discuss recent studies on the genomic taxonomy of diverse microbial groups and a unified species definition based on genomics. Accordingly, strains from the same microbial species share >95% Average Amino Acid Identity (AAI) and Average Nucleotide Identity (ANI), >95% identity based on multiple alignment genes, <10 in Karlin genomic signature, and > 70% in silico Genome-to-Genome Hybridization similarity (GGDH). Species of the same genus will form monophyletic groups on the basis of 16S rRNA gene sequences, Multilocus Sequence Analysis (MLSA) and supertree analysis. In addition to the established requirements for species descriptions, we propose that new taxa descriptions should also include at least a draft genome sequence of the type strain in order to obtain a clear outlook on the genomic landscape of the novel microbe. The application of the new genomic species definition put forward here will allow researchers to use genome sequences to define simultaneously coherent phenotypic and genomic groups. PMID:24365132

Characterization of St and Y genome in StStYY Elymus species (Triticeae: Poaceae) using Sequential FISH and GISH

USDA-ARS?s Scientific Manuscript database

Tetraploid species possessing StY genome could be donors to hexaploid species having StYH, StYP, or StYW genome constitution in the genus Elymus, and a few of StY species have been intensely studied for inferring the origin of the Y genome. In this study, genome characterization of St and Y genome w...

Microbial species delineation using whole genome sequences.

PubMed

Varghese, Neha J; Mukherjee, Supratim; Ivanova, Natalia; Konstantinidis, Konstantinos T; Mavrommatis, Kostas; Kyrpides, Nikos C; Pati, Amrita

2015-08-18

Increased sequencing of microbial genomes has revealed that prevailing prokaryotic species assignments can be inconsistent with whole genome information for a significant number of species. The long-standing need for a systematic and scalable species assignment technique can be met by the genome-wide Average Nucleotide Identity (gANI) metric, which is widely acknowledged as a robust measure of genomic relatedness. In this work, we demonstrate that the combination of gANI and the alignment fraction (AF) between two genomes accurately reflects their genomic relatedness. We introduce an efficient implementation of AF,gANI and discuss its successful application to 86.5M genome pairs between 13,151 prokaryotic genomes assigned to 3032 species. Subsequently, by comparing the genome clusters obtained from complete linkage clustering of these pairs to existing taxonomy, we observed that nearly 18% of all prokaryotic species suffer from anomalies in species definition. Our results can be used to explore central questions such as whether microorganisms form a continuum of genetic diversity or distinct species represented by distinct genetic signatures. We propose that this precise and objective AF,gANI-based species definition: the MiSI (Microbial Species Identifier) method, be used to address previous inconsistencies in species classification and as the primary guide for new taxonomic species assignment, supplemented by the traditional polyphasic approach, as required. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Antimicrobial activity and cytotoxic effects of Magnolia dealbata and its active compounds.

PubMed

Jacobo-Salcedo, Maria del Rosario; Gonzalez-Espindola, Luis Angel; Alonso-Castro, Angel Josabad; Gonzalez-Martinez, Marisela del Rocio; Domínguez, Fabiola; Garcia-Carranca, Alejandro

2011-08-01

Multi-drug resistance is of great concern for public health worldwide and necessitates the search for new antimicrobials from sources such as plants. Several Magnolia (Magnoliaceae) species have been reported to exert antimicrobial effects on sensitive and multidrug-resistant microorganisms. However, the antimicrobial properties of Magnolia dealbata have not been experimentally evaluated. The antimicrobial effects of an ethanol extract of Magnolia dealbata seeds (MDE) and its active compounds honokiol (HK) and magnolol (MG) were tested against the phytopathogen Clavibacter michiganensis subsp. michiganensis and several human multi-drug resistant pathogens using the disk-diffusion assay. The effects of MDE and its active compounds on the viability of human peripheral blood mononuclear cells (PBMC) were evaluated using MTT assay. MDE and its active compounds had antimicrobial activity (inhibition zone > 10 mm) against C. michiganensis, Pseudomonas aeruginosa, Acinetobacter baumannii, Acinetobacter lwoffii, Candida albicans, Candida tropicalis and Trichosporon belgeii. The results suggest that M. dealbata and its active compounds have selective antimicrobial effects against drug-resistant fungal and Gram (-) bacteria and exert minimal toxic effects on human PMBC.

Identification of gram-negative bacilli using the Autobac IDX.

PubMed

Burdash, N M; Welborn, A L; Teti, G; Bannister, E R; Manos, J P

1985-01-01

The Autobac IDX is a new system for the rapid identification of clinically significant members of the Enterobacteriaceae and Aeromonas, Acinetobacter, Alcaligenes, Flavobacterium, Moraxella, and Pseudomonas species. The use of 18 differentially inhibitory compounds such as dyes and antibiotics along with a computerized algorithm based on a multivariate analysis provides the basis for the identification of 30 different groups of gram-negative bacilli. Required preliminary tests include observations on the presence or absence of swarming on a sheep blood agar plate and noting the following: growth, lactose fermentation, and bile precipitation from a MacConkey plate. Spot indole and spot oxidase tests must be performed as well. Identification by the Autobac IDX System takes 3-6 hr after completion of the preliminary tests. From a total of 403 isolates tested, the Autobac system agreed with the MicroID AND N/F systems on 382 identifications (94.8%). Four isolates, two Acinetobacter anitratus, one Serratia marcescens and one Moraxella osloensis could not be identified by IDX. Additional testing was required on 35 (8.7%) of the isolates.

Polyhexamethylene guanidine hydrochloride shows bactericidal advantages over chlorhexidine digluconate against ESKAPE bacteria.

PubMed

Zhou, Zhongxin; Wei, Dafu; Lu, Yanhua

2015-01-01

More information regarding the bactericidal properties of polyhexamethylene guanidine hydrochloride (PHMG) against clinically important antibiotic-resistant ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) pathogens needs to be provided for its uses in infection control. The bactericidal properties of PHMG and chlorhexidine digluconate (CHG) were compared based on their minimum inhibitory concentrations (MICs), minimum bactericidal concentrations, and time-course-killing curves against clinically important antibiotic-susceptible and antibiotic-resistant ESKAPE pathogens. Results showed that PHMG exhibited significantly higher bactericidal activities against methicillin-resistant Staphylococcus aureus, carbapenem-resistant Klebsiella pneumoniae, and ceftazidime-resistant Enterobacter spp. than CHG. A slight bactericidal advantage over CHG was obtained against vancomycin-resistant Enterococcus faecium, ciprofloxacin- and levofloxacin-resistant Acinetobacter spp., and multidrug-resistant Pseudomonas aeruginosa. In previous reports, PHMG had higher antimicrobial activity against almost all tested Gram-negative bacteria and several Gram-positive bacteria than CHG using MIC test. These studies support the further development of covalently bound PHMG in sterile-surface materials and the incorporation of PHMG in novel disinfectant formulas. © 2014 International Union of Biochemistry and Molecular Biology, Inc.

21 CFR 866.3010 - Acinetobacter calcoaceticus serological reagents.

Code of Federal Regulations, 2011 CFR

2011-04-01

... this bacterium from cultured isolates derived from clinical specimens. The identification aids in the diagnosis of disease caused by the bacterium Acinetobacter calcoaceticus and provides epidemiological...

21 CFR 866.3010 - Acinetobacter calcoaceticus serological reagents.

Code of Federal Regulations, 2010 CFR

2010-04-01

... this bacterium from cultured isolates derived from clinical specimens. The identification aids in the diagnosis of disease caused by the bacterium Acinetobacter calcoaceticus and provides epidemiological...

Novel genomes and genome constitutions identified by GISH and 5S rDNA and knotted1 genomic sequences in the genus Setaria

PubMed Central

2013-01-01

Background The Setaria genus is increasingly of interest to researchers, as its two species, S. viridis and S. italica, are being developed as models for understanding C4 photosynthesis and plant functional genomics. The genome constitution of Setaria species has been studied in the diploid species S. viridis, S. adhaerans and S. grisebachii, where three genomes A, B and C were identified respectively. Two allotetraploid species, S. verticillata and S. faberi, were found to have AABB genomes, and one autotetraploid species, S. queenslandica, with an AAAA genome, has also been identified. The genomes and genome constitutions of most other species remain unknown, even though it was thought there are approximately 125 species in the genus distributed world-wide. Results GISH was performed to detect the genome constitutions of Eurasia species of S. glauca, S. plicata, and S. arenaria, with the known A, B and C genomes as probes. No or very poor hybridization signal was detected indicating that their genomes are different from those already described. GISH was also performed reciprocally between S. glauca, S. plicata, and S. arenaria genomes, but no hybridization signals between each other were found. The two sets of chromosomes of S. lachnea both hybridized strong signals with only the known C genome of S. grisebachii. Chromosomes of Qing 9, an accession formerly considered as S. viridis, hybridized strong signal only to B genome of S. adherans. Phylogenetic trees constructed with 5S rDNA and knotted1 markers, clearly classify the samples in this study into six clusters, matching the GISH results, and suggesting that the F genome of S. arenaria is basal in the genus. Conclusions Three novel genomes in the Setaria genus were identified and designated as genome D (S. glauca), E (S. plicata) and F (S. arenaria) respectively. The genome constitution of tetraploid S. lachnea is putatively CCC’C’. Qing 9 is a B genome species indigenous to China and is hypothesized to be a newly identified species. The difference in genome constitution and origin of S. verticillata and S. faberi is also discussed. The new genomes and the genome constitutions of Setaria species identified in this report provide useful information for Setaria germplasm management, foxtail millet breeding, grass evolution and the development of S. viridis and S. italica as a new model for functional genomics. PMID:23577839

Acinetobacter sp. DW-1 immobilized on polyhedron hollow polypropylene balls and analysis of transcriptome and proteome of the bacterium during phenol biodegradation process.

PubMed

Gu, Qihui; Wu, Qingping; Zhang, Jumei; Guo, Weipeng; Wu, Huiqing; Sun, Ming

2017-07-07

Phenol is a hazardous chemical known to be widely distributed in aquatic environments. Biodegradation is an attractive option for removal of phenol from water sources. Acinetobacter sp. DW-1 isolated from drinking water biofilters can use phenol as a sole carbon and energy source. In this study, we found that Immobilized Acinetobacter sp. DW-1cells were effective in biodegradation of phenol. In addition, we performed proteome and transcriptome analysis of Acinetobacter sp. DW-1 during phenol biodegradation. The results showed that Acinetobacter sp. DW-1 degrades phenol mainly by the ortho pathway because of the induction of phenol hydroxylase, catechol-1,2-dioxygenase. Furthermore, some novel candidate proteins (OsmC-like family protein, MetA-pathway of phenol degradation family protein, fimbrial protein and coenzyme F390 synthetase) and transcriptional regulators (GntR/LuxR/CRP/FNR/TetR/Fis family transcriptional regulator) were successfully identified to be potentially involved in phenol biodegradation. In particular, MetA-pathway of phenol degradation family protein and fimbrial protein showed a strong positive correlation with phenol biodegradation, and Fis family transcriptional regulator is likely to exert its effect as activators of gene expression. This study provides valuable clues for identifying global proteins and genes involved in phenol biodegradation and provides a fundamental platform for further studies to reveal the phenol degradation mechanism of Acinetobacter sp.

Isolation and Characterization of Fipronil Degrading Acinetobacter calcoaceticus and Acinetobacter oleivorans from Rhizospheric Zone of Zea mays.

PubMed

Uniyal, Shivani; Paliwal, Rashmi; Verma, Megha; Sharma, R K; Rai, J P N

2016-06-01

An enrichment culture technique was used for the isolation of bacteria capable of utilizing fipronil as a sole source of carbon and energy. Based on morphological, biochemical characteristics and phylogenetic analysis of 16S rRNA sequence, the bacterial strains were identified as Acinetobacter calcoaceticus and Acinetobacter oleivorans. Biodegradation experiments were conducted in loamy sand soil samples fortified with fipronil (50 µg kg(-1)) and inoculated with Acinetobacter sp. cells (45 × 10(7) CFU mL(-1)) for 90 days. Soil samples were periodically analyzed by gas liquid chromatography equipped with electron capture detector. Biodegradation of fipronil fitted well with the pseudo first-order kinetics, with rate constant value between 0.041 and 0.051 days(-1). In pot experiments, fipronil and its metabolites fipronil sulfide, fipronil sulfone and fipronil amide were found below quantifiable limit in soil and root, shoot and leaves of Zea mays. These results demonstrated that A. calcoaceticus and A. oleivorans may serve as promising strains in the bioremediation of fipronil-contaminated soils.

Functional Features of TonB Energy Transduction Systems of Acinetobacter baumannii

PubMed Central

Zimbler, Daniel L.; Arivett, Brock A.; Beckett, Amber C.; Menke, Sharon M.

2013-01-01

Acinetobacter baumannii is an opportunistic pathogen that causes severe nosocomial infections. Strain ATCC 19606T utilizes the siderophore acinetobactin to acquire iron under iron-limiting conditions encountered in the host. Accordingly, the genome of this strain has three tonB genes encoding proteins for energy transduction functions needed for the active transport of nutrients, including iron, through the outer membrane. Phylogenetic analysis indicates that these tonB genes, which are present in the genomes of all sequenced A. baumannii strains, were acquired from different sources. Two of these genes occur as components of tonB-exbB-exbD operons and one as a monocistronic copy; all are actively transcribed in ATCC 19606T. The abilities of components of these TonB systems to complement the growth defect of Escherichia coli W3110 mutants KP1344 (tonB) and RA1051 (exbBD) under iron-chelated conditions further support the roles of these TonB systems in iron acquisition. Mutagenesis analysis of ATCC 19606T tonB1 (subscripted numbers represent different copies of genes or proteins) and tonB2 supports this hypothesis: their inactivation results in growth defects in iron-chelated media, without affecting acinetobactin biosynthesis or the production of the acinetobactin outer membrane receptor protein BauA. In vivo assays using Galleria mellonella show that each TonB protein is involved in, but not essential for, bacterial virulence in this infection model. Furthermore, we observed that TonB2 plays a role in the ability of bacteria to bind to fibronectin and to adhere to A549 cells by uncharacterized mechanisms. Taken together, these results indicate that A. baumannii ATCC 19606T produces three independent TonB proteins, which appear to provide the energy-transducing functions needed for iron acquisition and cellular processes that play a role in the virulence of this pathogen. PMID:23817614

Diagnostics of Neisseriaceae and Moraxellaceae by Ribosomal DNA Sequencing: Ribosomal Differentiation of Medical Microorganisms

PubMed Central

Harmsen, Dag; Singer, Christian; Rothgänger, Jörg; Tønjum, Tone; Sybren de Hoog, Gerrit; Shah, Haroun; Albert, Jürgen; Frosch, Matthias

2001-01-01

Fast and reliable identification of microbial isolates is a fundamental goal of clinical microbiology. However, in the case of some fastidious gram-negative bacterial species, classical phenotype identification based on either metabolic, enzymatic, or serological methods is difficult, time-consuming, and/or inadequate. 16S or 23S ribosomal DNA (rDNA) bacterial sequencing will most often result in accurate speciation of isolates. Therefore, the objective of this study was to find a hypervariable rDNA stretch, flanked by strongly conserved regions, which is suitable for molecular species identification of members of the Neisseriaceae and Moraxellaceae. The inter- and intrageneric relationships were investigated using comparative sequence analysis of PCR-amplified partial 16S and 23S rDNAs from a total of 94 strains. When compared to the type species of the genera Acinetobacter, Moraxella, and Neisseria, an average of 30 polymorphic positions was observed within the partial 16S rDNA investigated (corresponding to Escherichia coli positions 54 to 510) for each species and an average of 11 polymorphic positions was observed within the 202 nucleotides of the 23S rDNA gene (positions 1400 to 1600). Neisseria macacae and Neisseria mucosa subsp. mucosa (ATCC 19696) had identical 16S and 23S rDNA sequences. Species clusters were heterogeneous in both genes in the case of Acinetobacter lwoffii, Moraxella lacunata, and N. mucosa. Neisseria meningitidis isolates failed to cluster only in the 23S rDNA subset. Our data showed that the 16S rDNA region is more suitable than the partial 23S rDNA for the molecular diagnosis of Neisseriaceae and Moraxellaceae and that a reference database should include more than one strain of each species. All sequence chromatograms and taxonomic and disease-related information are available as part of our ribosomal differentiation of medical microorganisms (RIDOM) web-based service (http://www.ridom.hygiene.uni-wuerzburg.de/). Users can submit a sequence and conduct a similarity search against the RIDOM reference database for microbial identification purposes. PMID:11230407

Reduced representation approaches to interrogate genome diversity in large repetitive plant genomes.

PubMed

Hirsch, Cory D; Evans, Joseph; Buell, C Robin; Hirsch, Candice N

2014-07-01

Technology and software improvements in the last decade now provide methodologies to access the genome sequence of not only a single accession, but also multiple accessions of plant species. This provides a means to interrogate species diversity at the genome level. Ample diversity among accessions in a collection of species can be found, including single-nucleotide polymorphisms, insertions and deletions, copy number variation and presence/absence variation. For species with small, non-repetitive rich genomes, re-sequencing of query accessions is robust, highly informative, and economically feasible. However, for species with moderate to large sized repetitive-rich genomes, technical and economic barriers prevent en masse genome re-sequencing of accessions. Multiple approaches to access a focused subset of loci in species with larger genomes have been developed, including reduced representation sequencing, exome capture and transcriptome sequencing. Collectively, these approaches have enabled interrogation of diversity on a genome scale for large plant genomes, including crop species important to worldwide food security. © The Author 2014. Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Antibiotic resistant airborne bacteria and their multidrug resistance pattern at University teaching referral Hospital in South Ethiopia.

PubMed

Solomon, Fithamlak Bisetegen; Wadilo, Fiseha Wada; Arota, Amsalu Amache; Abraham, Yishak Leka

2017-04-12

Hospitals provide a reservoir of microorganisms, many of which are multi-resistant to antibiotics. Emergence of multi-drug resistant strains in a hospital environment, particularly in developing countries is an increasing problem to infection treatment. This study aims at assessing antibiotic resistant airborne bacterial isolates. A cross-sectional study was conducted at Wolaita Sodo university teaching and referral Hospital. Indoor air samples were collected by using passive air sampling method. Sample processing and antimicrobial susceptibility testing were done following standard bacteriological techniques. The data was analyzed using SPSS version 20. Medically important bacterial pathogens, Coagulase negative staphylococci (29.6%), Staphylococcus aureus (26.3%), Enterococci species, Enterococcus faecalis and Enterococcus faecium (16.5%), Acinetobacter species (9.5%), Escherichia coli (5.8%) and Pseudomonas aeruginosa (5.3%) were isolated. Antibiotic resistance rate ranging from 7.5 to 87.5% was detected for all isolates. Acinetobacter species showed a high rate of resistance for trimethoprim-sulfamethoxazole, gentamicin (78.2%) and ciprofloxacin (82.6%), 28 (38.9%) of S. aureus isolates were meticillin resistant, and 7.5% Enterococci isolates of were vancomycin resistant. 75.3% of all bacterial pathogen were multi-drug resistant. Among them, 74.6% were gram positive and 84% were gram negative. Multi-drug resistance were observed among 84.6% of P. aeruginosa, of 82.5% Enterococcii, E. coli 78.6%, S. aureus 76.6%, and Coagulase negative staphylococci of 73.6%. Indoor environment of the hospital was contaminated with airborne microbiotas, which are common cause of post-surgical site infection in the study area. Bacterial isolates were highly resistant to commonly used antibiotics with high multi-drug resistance percentage. So air quality of hospital environment, in restricted settings deserves attention, and requires long-term surveillance to protect both patients and healthcare workers.

Trauma-related Infections in Battlefield Casualties From Iraq

PubMed Central

Petersen, Kyle; Riddle, Mark S.; Danko, Janine R.; Blazes, David L.; Hayden, Richard; Tasker, Sybil A.; Dunne, James R.

2007-01-01

Objective: To describe risks for, and microbiology and antimicrobial resistance patterns of, war trauma associated infections from Operation Iraqi Freedom. Background: The invasion of Iraq resulted in casualties from high-velocity gunshot, shrapnel, and blunt trauma injuries as well as burns. Infectious complications of these unique war trauma injuries have not been described since the 1970s. Methods: Retrospective record review of all trauma casualties 5 to 65 years of age evacuated from the Iraqi theatre to U.S. Navy hospital ship, USNS Comfort March to May 2003.War trauma-associated infection was defined by positive culture from a wound or sterile body fluid (ie, blood, cerebrospinal fluid) and at least two of the following infection-associated signs/symptoms: fever, dehiscence, foul smell, peri-wound erythema, hypotension, and leukocytosis. A comparison of mechanisms of injury, demographics, and clinical variables was done using multivariate analysis. Results: Of 211 patients, 56 met criteria for infection. Infections were more common in blast injuries, soft tissue injuries, >3 wound sites, loss of limb, abdominal trauma, and higher Injury Severity Score (ISS). Wound infections accounted for 84% of cases, followed by bloodstream infections (38%). Infected were more likely to have had fever prior to arrival, and had higher probability of ICU admission and more surgical procedures. Acinetobacter species (36%) were the predominant organisms followed by Escherichia coli and Pseudomonas species (14% each). Conclusions: Similar to the Vietnam War experience, gram-negative rods, particularly Acinetobacter species, accounted for the majority of wound infections cared for on USNS Comfort during Operation Iraqi Freedom. Multidrug resistance was common, with the exception of the carbapenem class, limiting antibiotic therapy options. PMID:17457175

Characterization and degradation potential of diesel-degrading bacterial strains for application in bioremediation.

PubMed

Balseiro-Romero, María; Gkorezis, Panagiotis; Kidd, Petra S; Van Hamme, Jonathan; Weyens, Nele; Monterroso, Carmen; Vangronsveld, Jaco

2017-10-03

Bioremediation of polluted soils is a promising technique with low environmental impact, which uses soil organisms to degrade soil contaminants. In this study, 19 bacterial strains isolated from a diesel-contaminated soil were screened for their diesel-degrading potential, biosurfactant (BS) production, and biofilm formation abilities, all desirable characteristics when selecting strains for re-inoculation into hydrocarbon-contaminated soils. Diesel-degradation rates were determined in vitro in minimal medium with diesel as the sole carbon source. The capacity to degrade diesel range organics (DROs) of strains SPG23 (Arthobacter sp.) and PF1 (Acinetobacter oleivorans) reached 17-26% of total DROs after 10 days, and 90% for strain GK2 (Acinetobacter calcoaceticus). The amount and rate of alkane degradation decreased significantly with increasing carbon number for strains SPG23 and PF1. Strain GK2, which produced BSs and biofilms, exhibited a greater extent, and faster rate of alkane degradation compared to SPG23 and PF1. Based on the outcomes of degradation experiments, in addition to BS production, biofilm formation capacities, and previous genome characterizations, strain GK2 is a promising candidate for microbial-assisted phytoremediation of diesel-contaminated soils. These results are of particular interest to select suitable strains for bioremediation, not only presenting high diesel-degradation rates, but also other characteristics which could improve rhizosphere colonization.

Development of genome- and transcriptome-derived microsatellites in related species of snapping shrimps with highly duplicated genomes.

PubMed

Gaynor, Kaitlyn M; Solomon, Joseph W; Siller, Stefanie; Jessell, Linnet; Duffy, J Emmett; Rubenstein, Dustin R

2017-11-01

Molecular markers are powerful tools for studying patterns of relatedness and parentage within populations and for making inferences about social evolution. However, the development of molecular markers for simultaneous study of multiple species presents challenges, particularly when species exhibit genome duplication or polyploidy. We developed microsatellite markers for Synalpheus shrimp, a genus in which species exhibit not only great variation in social organization, but also interspecific variation in genome size and partial genome duplication. From the four primary clades within Synalpheus, we identified microsatellites in the genomes of four species and in the consensus transcriptome of two species. Ultimately, we designed and tested primers for 143 microsatellite markers across 25 species. Although the majority of markers were disomic, many markers were polysomic for certain species. Surprisingly, we found no relationship between genome size and the number of polysomic markers. As expected, markers developed for a given species amplified better for closely related species than for more distant relatives. Finally, the markers developed from the transcriptome were more likely to work successfully and to be disomic than those developed from the genome, suggesting that consensus transcriptomes are likely to be conserved across species. Our findings suggest that the transcriptome, particularly consensus sequences from multiple species, can be a valuable source of molecular markers for taxa with complex, duplicated genomes. © 2017 John Wiley & Sons Ltd.

Distinguishing potential bacteria-tumor associations from contamination in a secondary data analysis of public cancer genome sequence data.

PubMed

Robinson, Kelly M; Crabtree, Jonathan; Mattick, John S A; Anderson, Kathleen E; Dunning Hotopp, Julie C

2017-01-25

A variety of bacteria are known to influence carcinogenesis. Therefore, we sought to investigate if publicly available whole genome and whole transcriptome sequencing data generated by large public cancer genome efforts, like The Cancer Genome Atlas (TCGA), could be used to identify bacteria associated with cancer. The Burrows-Wheeler aligner (BWA) was used to align a subset of Illumina paired-end sequencing data from TCGA to the human reference genome and all complete bacterial genomes in the RefSeq database in an effort to identify bacterial read pairs from the microbiome. Through careful consideration of all of the bacterial taxa present in the cancer types investigated, their relative abundance, and batch effects, we were able to identify some read pairs from certain taxa as likely resulting from contamination. In particular, the presence of Mycobacterium tuberculosis complex in the ovarian serous cystadenocarcinoma (OV) and glioblastoma multiforme (GBM) samples was correlated with the sequencing center of the samples. Additionally, there was a correlation between the presence of Ralstonia spp. and two specific plates of acute myeloid leukemia (AML) samples. At the end, associations remained between Pseudomonas-like and Acinetobacter-like read pairs in AML, and Pseudomonas-like read pairs in stomach adenocarcinoma (STAD) that could not be explained through batch effects or systematic contamination as seen in other samples. This approach suggests that it is possible to identify bacteria that may be present in human tumor samples from public genome sequencing data that can be examined further experimentally. More weight should be given to this approach in the future when bacterial associations with diseases are suspected.

Genome size evolution at the speciation level: the cryptic species complex Brachionus plicatilis (Rotifera).

PubMed

Stelzer, Claus-Peter; Riss, Simone; Stadler, Peter

2011-04-07

Studies on genome size variation in animals are rarely done at lower taxonomic levels, e.g., slightly above/below the species level. Yet, such variation might provide important clues on the tempo and mode of genome size evolution. In this study we used the flow-cytometry method to study the evolution of genome size in the rotifer Brachionus plicatilis, a cryptic species complex consisting of at least 14 closely related species. We found an unexpectedly high variation in this species complex, with genome sizes ranging approximately seven-fold (haploid '1C' genome sizes: 0.056-0.416 pg). Most of this variation (67%) could be ascribed to the major clades of the species complex, i.e. clades that are well separated according to most species definitions. However, we also found substantial variation (32%) at lower taxonomic levels--within and among genealogical species--and, interestingly, among species pairs that are not completely reproductively isolated. In one genealogical species, called B. 'Austria', we found greatly enlarged genome sizes that could roughly be approximated as multiples of the genomes of its closest relatives, which suggests that whole-genome duplications have occurred early during separation of this lineage. Overall, genome size was significantly correlated to egg size and body size, even though the latter became non-significant after controlling for phylogenetic non-independence. Our study suggests that substantial genome size variation can build up early during speciation, potentially even among isolated populations. An alternative, but not mutually exclusive interpretation might be that reproductive isolation tends to build up unusually slow in this species complex.

Genome size evolution at the speciation level: The cryptic species complex Brachionus plicatilis (Rotifera)

PubMed Central

2011-01-01

Background Studies on genome size variation in animals are rarely done at lower taxonomic levels, e.g., slightly above/below the species level. Yet, such variation might provide important clues on the tempo and mode of genome size evolution. In this study we used the flow-cytometry method to study the evolution of genome size in the rotifer Brachionus plicatilis, a cryptic species complex consisting of at least 14 closely related species. Results We found an unexpectedly high variation in this species complex, with genome sizes ranging approximately seven-fold (haploid '1C' genome sizes: 0.056-0.416 pg). Most of this variation (67%) could be ascribed to the major clades of the species complex, i.e. clades that are well separated according to most species definitions. However, we also found substantial variation (32%) at lower taxonomic levels - within and among genealogical species - and, interestingly, among species pairs that are not completely reproductively isolated. In one genealogical species, called B. 'Austria', we found greatly enlarged genome sizes that could roughly be approximated as multiples of the genomes of its closest relatives, which suggests that whole-genome duplications have occurred early during separation of this lineage. Overall, genome size was significantly correlated to egg size and body size, even though the latter became non-significant after controlling for phylogenetic non-independence. Conclusions Our study suggests that substantial genome size variation can build up early during speciation, potentially even among isolated populations. An alternative, but not mutually exclusive interpretation might be that reproductive isolation tends to build up unusually slow in this species complex. PMID:21473744

Genomic Species Are Ecological Species as Revealed by Comparative Genomics in Agrobacterium tumefaciens

PubMed Central

Lassalle, Florent; Campillo, Tony; Vial, Ludovic; Baude, Jessica; Costechareyre, Denis; Chapulliot, David; Shams, Malek; Abrouk, Danis; Lavire, Céline; Oger-Desfeux, Christine; Hommais, Florence; Guéguen, Laurent; Daubin, Vincent; Muller, Daniel; Nesme, Xavier

2011-01-01

The definition of bacterial species is based on genomic similarities, giving rise to the operational concept of genomic species, but the reasons of the occurrence of differentiated genomic species remain largely unknown. We used the Agrobacterium tumefaciens species complex and particularly the genomic species presently called genomovar G8, which includes the sequenced strain C58, to test the hypothesis of genomic species having specific ecological adaptations possibly involved in the speciation process. We analyzed the gene repertoire specific to G8 to identify potential adaptive genes. By hybridizing 25 strains of A. tumefaciens on DNA microarrays spanning the C58 genome, we highlighted the presence and absence of genes homologous to C58 in the taxon. We found 196 genes specific to genomovar G8 that were mostly clustered into seven genomic islands on the C58 genome—one on the circular chromosome and six on the linear chromosome—suggesting higher plasticity and a major adaptive role of the latter. Clusters encoded putative functional units, four of which had been verified experimentally. The combination of G8-specific functions defines a hypothetical species primary niche for G8 related to commensal interaction with a host plant. This supports that the G8 ancestor was able to exploit a new ecological niche, maybe initiating ecological isolation and thus speciation. Searching genomic data for synapomorphic traits is a powerful way to describe bacterial species. This procedure allowed us to find such phenotypic traits specific to genomovar G8 and thus propose a Latin binomial, Agrobacterium fabrum, for this bona fide genomic species. PMID:21795751

Contamination of Ambient Air with Acinetobacter baumannii on Consecutive Inpatient Days.

PubMed

Shimose, Luis A; Doi, Yohei; Bonomo, Robert A; De Pascale, Dennise; Viau, Roberto A; Cleary, Timothy; Namias, Nicholas; Kett, Daniel H; Munoz-Price, L Silvia

2015-07-01

Acinetobacter-positive patients had their ambient air tested for up to 10 consecutive days. The air was Acinetobacter positive for an average of 21% of the days; the rate of contamination was higher among patients colonized in the rectum than in the airways (relative risk [RR], 2.35; P = 0.006). Of the 6 air/clinical isolate pairs available, 4 pairs were closely related according to rep-PCR results. Copyright © 2015, American Society for Microbiology. All Rights Reserved.

In vitro Antibacterial Activity of Ocimum suave Essential Oils against Uropathogens Isolated from Patients in Selected Hospitals in Bushenyi District, Uganda

PubMed Central

Tibyangye, Julius; Okech, Matilda Angela; Nyabayo, Josephat Maniga; Nakavuma, Jessica Lukanga

2015-01-01

Aims To determine antibacterial activity of Ocimum suave essential oils against bacterial uropathogens. Study Design A cross sectional and experimental study. Place and Duration of Study Six selected hospitals in Bushenyi District, Uganda between June 2012 and July 2013. Methodology Clean catch midstream urine samples were collected and inoculated on Cystine Lysine Electrolyte Deficient (CLED) agar. The plates were incubated at 37°C for 24hrs to 48hrs. The O. suave essential oils were extracted by hydrodistillation of leaves for 4hrs using a Clevenger apparatus. The oil was collected and dried over anhydrous sodium sulphate (Na2SO4) and kept at 4°C till further use. The antimicrobial activity of O. suave essential oils against isolates was determined by agar well method. The MIC of O. suave essential oil extract was carried out by microbroth dilution method. Results Of the three hundred (300) midstream urine samples collected, 67(22.33%) had significant bacterial growth. Escherichia coli is the most common isolate (61.19%, n = 41). The essential oil from O. suave showed activity against isolates of E. coli, K. pneumoniae, S. aureus, E. feacalis, M. morganii, Citrobacter species, Enterobacter species and P. aeruginosa with mean zone of inhibition (ZI) ranging from 10–22 mm. The essential oils had no inhibitory activity on Acinetobacter species. The minimum inhibitory concentration (MIC) for O. suave essential oils ranged from 0.78 to 22 μg/ml. This study showed that O. suave essential oils had MIC value of 0.78 μg/ml against S. aureus and MIC values ranging from 3 to 22 μg/ml against the other tested isolates. Conclusion The most common uropathogen was E. coli (61.19% n = 41). O. suave essential oils exhibited antibacterial activity against majority of the uropathogens, except Acinetobacter species, mean ZI of 10–22 mm and MIC of 0.78 – 22 μg/ml. PMID:26120574

Attaching NorA efflux pump inhibitors to methylene blue enhances antimicrobial photodynamic inactivation of Escherichia coli and Acinetobacter baumannii in vitro and in vivo.

PubMed

Rineh, Ardeshir; Bremner, John B; Hamblin, Michael R; Ball, Anthony R; Tegos, George P; Kelso, Michael J

2018-02-24

Resistance of bacteria to antibiotics is a public health concern worldwide due to the increasing failure of standard antibiotic therapies. Antimicrobial photodynamic inactivation (aPDI) is a promising non-antibiotic alternative for treating localized bacterial infections that uses non-toxic photosensitizers and harmless visible light to produce reactive oxygen species and kill microbes. Phenothiazinium photosensitizers like methylene blue (MB) and toluidine blue O are hydrophobic cations that are naturally expelled from bacterial cells by multidrug efflux pumps, which reduces their effectiveness. We recently reported the discovery of a NorA efflux pump inhibitor-methylene blue (EPI-MB) hybrid compound INF55-(Ac)en-MB that shows enhanced photodynamic inactivation of the Gram-positive bacterium methicillin-resistant Staphylococcus aureus (MRSA) relative to MB, both in vitro and in vivo. Here, we report the surprising observation that INF55-(Ac)en-MB and two related hybrids bearing the NorA efflux pump inhibitors INF55 and INF271 also show enhanced aPDI activity in vitro (relative to MB) against the Gram-negative bacteria Escherichia coli and Acinetobacter baumannii, despite neither species expressing the NorA pump. Two of the hybrids showed superior effects to MB in murine aPDI infection models. The findings motivate wider exploration of aPDI with EPI-MB hybrids against Gram-negative pathogens and more detailed studies into the molecular mechanisms underpinning their activity. Copyright © 2018 Elsevier Ltd. All rights reserved.

Observations of resistance through minimum inhibitory concentrations trends for respiratory specimens of commonly isolated organisms.

PubMed

Gillard, Christopher J; Al-Dahir, Sara; Brakta, Fatima

2016-03-01

The objective of this study was to determine minimum inhibitory concentration (MIC) trends among common bacterial organisms found in respiratory isolates in the trauma intensive care unit setting. In this retrospective observational study, MIC data was reviewed over a three year period from January 2009 to December 2011 for the three most frequently identified organisms isolated from respiratory specimens in a trauma intensive care unit along with corresponding hospital data. The most frequently isolated bacterial species identified were Staphylococcus aureus (229 isolates), Pseudomonas aeruginosa (129 isolates), and Acinetobacter species (87 isolates) in the analysis within our institution from 2009-2011. There was considerable variability among the MIC trends for the analyzed organisms. For Pseudomonas isolates, observed sensitivities were as high as 100% for antibiotics ciprofloxacin and imipenem in 2009, but decreased over the next two years in 2010 and 2011. There was considerable variability among the MIC trends for Acinetobacter over the three year period for the antibiotics tested. The MIC data for most Staphylococcus aureus isolates over the three years were sensitive to vancomycin with little change in the observed MIC data. The data reported is observational and indicates the need for future studies to establish a valid relationship of the MIC data over time in our institution particularly among our gram negative organisms, to monitor patterns of antimicrobial resistance. Copyright © 2016 by the American Society of Health-System Pharmacists, Inc. All rights reserved.

A brief introduction to web-based genome browsers.

PubMed

Wang, Jun; Kong, Lei; Gao, Ge; Luo, Jingchu

2013-03-01

Genome browser provides a graphical interface for users to browse, search, retrieve and analyze genomic sequence and annotation data. Web-based genome browsers can be classified into general genome browsers with multiple species and species-specific genome browsers. In this review, we attempt to give an overview for the main functions and features of web-based genome browsers, covering data visualization, retrieval, analysis and customization. To give a brief introduction to the multiple-species genome browser, we describe the user interface and main functions of the Ensembl and UCSC genome browsers using the human alpha-globin gene cluster as an example. We further use the MSU and the Rice-Map genome browsers to show some special features of species-specific genome browser, taking a rice transcription factor gene OsSPL14 as an example.

DroSpeGe: rapid access database for new Drosophila species genomes.

PubMed

Gilbert, Donald G

2007-01-01

The Drosophila species comparative genome database DroSpeGe (http://insects.eugenes.org/DroSpeGe/) provides genome researchers with rapid, usable access to 12 new and old Drosophila genomes, since its inception in 2004. Scientists can use, with minimal computing expertise, the wealth of new genome information for developing new insights into insect evolution. New genome assemblies provided by several sequencing centers have been annotated with known model organism gene homologies and gene predictions to provided basic comparative data. TeraGrid supplies the shared cyberinfrastructure for the primary computations. This genome database includes homologies to Drosophila melanogaster and eight other eukaryote model genomes, and gene predictions from several groups. BLAST searches of the newest assemblies are integrated with genome maps. GBrowse maps provide detailed views of cross-species aligned genomes. BioMart provides for data mining of annotations and sequences. Common chromosome maps identify major synteny among species. Potential gain and loss of genes is suggested by Gene Ontology groupings for genes of the new species. Summaries of essential genome statistics include sizes, genes found and predicted, homology among genomes, phylogenetic trees of species and comparisons of several gene predictions for sensitivity and specificity in finding new and known genes.

In-silico Taxonomic Classification of 373 Genomes Reveals Species Misidentification and New Genospecies within the Genus Pseudomonas.

PubMed

Tran, Phuong N; Savka, Michael A; Gan, Han Ming

2017-01-01

The genus Pseudomonas has one of the largest diversity of species within the Bacteria kingdom. To date, its taxonomy is still being revised and updated. Due to the non-standardized procedure and ambiguous thresholds at species level, largely based on 16S rRNA gene or conventional biochemical assay, species identification of publicly available Pseudomonas genomes remains questionable. In this study, we performed a large-scale analysis of all Pseudomonas genomes with species designation (excluding the well-defined P. aeruginosa ) and re-evaluated their taxonomic assignment via in silico genome-genome hybridization and/or genetic comparison with valid type species. Three-hundred and seventy-three pseudomonad genomes were analyzed and subsequently clustered into 145 distinct genospecies. We detected 207 erroneous labels and corrected 43 to the proper species based on Average Nucleotide Identity Multilocus Sequence Typing (MLST) sequence similarity to the type strain. Surprisingly, more than half of the genomes initially designated as Pseudomonas syringae and Pseudomonas fluorescens should be classified either to a previously described species or to a new genospecies. Notably, high pairwise average nucleotide identity (>95%) indicating species-level similarity was observed between P. synxantha-P. libanensis, P. psychrotolerans - P. oryzihabitans , and P. kilonensis- P. brassicacearum , that were previously differentiated based on conventional biochemical tests and/or genome-genome hybridization techniques.

Bacteria Community in the Terrestrial Deep Subsurface Microbiology Research of the Chinese Continent Scientific Drilling

NASA Astrophysics Data System (ADS)

Wang, Y.; Xia, Y.; Dong, H.; Dong, X.; Yang, K.; Dong, Z.; Huang, L.

2005-12-01

Microbial communities in the deep drill cores from the Chinese Continent Scientific Drilling were analyzed with culture-independent and dependent techniques. Genomic DNA was extracted from two metamorphic rocks: S1 from 430 and S13 from 1033 meters below the ground surface. The 16S rRNA gene was amplified by polymerase chain reaction (PCR) followed by cloning and sequencing. The total cell number was counted using the 4',6-diamidino-2-phenylindole (DAPI) staining and biomass of two specific bacteria were quantified using real-time PCR. Enrichment was set up for a rock from 3911 meters below the surface in medium for authotrophic methanogens (i.e., CO2 + H2). The total cell number in S13 was 1.0 × 104 cells per gram of rock. 16S rRNA gene analysis indicated that low G + C Gram positive sequences were dominant (50 percent of all 54 clone sequenced) followed by the alpha-, beta, and gamma-Proteobacteria. Within the low G + C Gram positive bacteria, most clone sequences were similar to species of Bacillus from various natural environments (deserts, rivers etc.). Within the Proteobacteria, our clone sequences were similar to species of Acinetobacter, Acidovorax, and Aeromonas. The RT-RCP results showed that biomass of two particular clone sequences (CCSD1305, similar to Aeromonas caviae and CCSD1307, similar to Acidovorax facilis) was 95 and 1258 cells/g, respectively. A bacterial isolate was obtained from the 3911-m rock in methanogenic medium. It was Gram negative with no flagella, immobile, and facultative anaerobic, and grows optimally at 65oC. Phylogenetic analysis indicated that it was closely related to the genus of Bacillus. Physiological tests further revealed that it was a strain of Bacillus caldotenax.

Evaluation of bacterial pathogen diversity, abundance and health risks in urban recreational water by amplicon next-generation sequencing and quantitative PCR.

PubMed

Cui, Qijia; Fang, Tingting; Huang, Yong; Dong, Peiyan; Wang, Hui

2017-07-01

The microbial quality of urban recreational water is of great concern to public health. The monitoring of indicator organisms and several pathogens alone is not sufficient to accurately and comprehensively identify microbial risks. To assess the levels of bacterial pathogens and health risks in urban recreational water, we analyzed pathogen diversity and quantified four pathogens in 46 water samples collected from waterbodies in Beijing Olympic Forest Park in one year. The pathogen diversity revealed by 16S rRNA gene targeted next-generation sequencing (NGS) showed that 16 of 40 genera and 13 of 76 reference species were present. The most abundant species were Acinetobacter johnsonii, Mycobacterium avium and Aeromonas spp. Quantitative polymerase chain reaction (qPCR) of Escherichia coli (uidA), Aeromonas (aerA), M. avium (16S rRNA), Pseudomonas aeruginosa (oaa) and Salmonella (invA) showed that the aerA genes were the most abundant, occurring in all samples with concentrations of 10 4-6 genome copies/100mL, followed by oaa, invA and M. avium. In total, 34.8% of the samples harbored all genes, indicating the prevalence of these pathogens in this recreational waterbody. Based on the qPCR results, a quantitative microbial risk assessment (QMRA) showed that the annual infection risks of Salmonella, M. avium and P. aeruginosa in five activities were mostly greater than the U.S. EPA risk limit for recreational contacts, and children playing with water may be exposed to the greatest infection risk. Our findings provide a comprehensive understanding of bacterial pathogen diversity and pathogen abundance in urban recreational water by applying both NGS and qPCR. Copyright © 2016. Published by Elsevier B.V.

Genome-wide comparative analysis of four Indian Drosophila species.

PubMed

Mohanty, Sujata; Khanna, Radhika

2017-12-01

Comparative analysis of multiple genomes of closely or distantly related Drosophila species undoubtedly creates excitement among evolutionary biologists in exploring the genomic changes with an ecology and evolutionary perspective. We present herewith the de novo assembled whole genome sequences of four Drosophila species, D. bipectinata, D. takahashii, D. biarmipes and D. nasuta of Indian origin using Next Generation Sequencing technology on an Illumina platform along with their detailed assembly statistics. The comparative genomics analysis, e.g. gene predictions and annotations, functional and orthogroup analysis of coding sequences and genome wide SNP distribution were performed. The whole genome of Zaprionus indianus of Indian origin published earlier by us and the genome sequences of previously sequenced 12 Drosophila species available in the NCBI database were included in the analysis. The present work is a part of our ongoing genomics project of Indian Drosophila species.

The Biofuel Feedstock Genomics Resource: a web-based portal and database to enable functional genomics of plant biofuel feedstock species.

PubMed

Childs, Kevin L; Konganti, Kranti; Buell, C Robin

2012-01-01

Major feedstock sources for future biofuel production are likely to be high biomass producing plant species such as poplar, pine, switchgrass, sorghum and maize. One active area of research in these species is genome-enabled improvement of lignocellulosic biofuel feedstock quality and yield. To facilitate genomic-based investigations in these species, we developed the Biofuel Feedstock Genomic Resource (BFGR), a database and web-portal that provides high-quality, uniform and integrated functional annotation of gene and transcript assembly sequences from species of interest to lignocellulosic biofuel feedstock researchers. The BFGR includes sequence data from 54 species and permits researchers to view, analyze and obtain annotation at the gene, transcript, protein and genome level. Annotation of biochemical pathways permits the identification of key genes and transcripts central to the improvement of lignocellulosic properties in these species. The integrated nature of the BFGR in terms of annotation methods, orthologous/paralogous relationships and linkage to seven species with complete genome sequences allows comparative analyses for biofuel feedstock species with limited sequence resources. Database URL: http://bfgr.plantbiology.msu.edu.

Involvement of a plasmid in growth on and dispersion of crude oil by Acinetobacter calcoaceticus RA57.

PubMed Central

Rusansky, S; Avigad, R; Michaeli, S; Gutnick, D L

1987-01-01

A crude-oil-degrading Acinetobacter species, Acinetobacter calcoaceticus RA57, was isolated by standard enrichment culture techniques on the basis of its ability to utilize the oily sludge found in the vicinity of a local gas station. Strain RA57 was found to contain four plasmids: pSR1 (5.1 kilobases [kb]), pSR2 (5.4 kb), pSR3 (10.5 kb), and pSR4 (20 kb). Both supercoiled and open circular forms of the first three plasmids were identified by two-dimensional gel electrophoresis. Restriction endonuclease analysis of pSR4 demonstrated that the plasmid contained a circular map. Colonies were isolated at random after growth in the presence of acridine orange and found to fall into two categories: (i) those which had lost the ability to grow on and disperse crude oil in liquid culture and concurrently were cured of pSR4 and (ii) those which retained the ability to both grow on and disperse crude oil and which contained pSR4. Strains from the first class continued to grow on hydrocarbon vapors, indicating that the defect associated with the curing of pSR4 was related to the physical interaction of the cells with the hydrocarbon substrate, rather than to its metabolism. No differences in either adherence to hydrocarbons or production of extracellular emulsifying activity were found between the two classes of mutants. In growth experiments on crude oil in mixed culture with strains which either contained or lacked pSR4, no sparing of the growth defect was observed. The results are consistent with the possibility that pSR4 encodes a factor(s) which is tightly associated with the cell surface. Images PMID:2821903

Evaluation of the MicroScan ESBL plus confirmation panel for detection of extended-spectrum beta-lactamases in clinical isolates of oxyimino-cephalosporin-resistant Gram-negative bacteria.

PubMed

Stürenburg, Enno; Lang, Melanie; Horstkotte, Matthias A; Laufs, Rainer; Mack, Dietrich

2004-11-01

We aimed to assess the performance of the MicroScan ESBL plus confirmation panel using a series of 87 oxyimino-cephalosporin-resistant Gram-negative bacilli of various species. Organisms tested included 57 extended-spectrum beta-lactamase (ESBL) strains comprising Enterobacter aerogenes (3), Enterobacter cloacae (10), Escherichia coli (11), Klebsiella pneumoniae (26), Klebsiella oxytoca (3) and Proteus mirabilis (4). Also included were 30 strains resistant to oxyimino cephalosporins but lacking ESBLs, which were characterized with other resistance mechanisms, such as inherent clavulanate susceptibility in Acinetobacter spp. (4), hyperproduction of AmpC enzyme in Citrobacter freundii (2), E. aerogenes (3), E. cloacae (3), E. coli (4), Hafnia alvei (1) and Morganella morganii (1), production of plasmid-mediated AmpC beta-lactamase in K. pneumoniae (3) and E. coli (3) or hyperproduction of K1 enzyme in K. oxytoca (6). The MicroScan MIC-based clavulanate synergy correctly classified 50 of 57 ESBL strains as ESBL-positive and 23 of 30 non-ESBL strains as ESBL-negative (yielding a sensitivity of 88% and a specificity of 76.7%, respectively). False negatives among ESBL producers were highest with Enterobacter spp. due to masking interactions between ESBL and AmpC beta-lactamases. False-positive classifications occurred in two Acinetobacter spp., one E. coli producing plasmid-mediated AmpC beta-lactamase and two K. oxytoca hyperproducing their chromosomal K1 beta-lactamase. The MicroScan clavulanate synergy test proved to be a valuable tool for ESBL confirmation. However, this test has limitations in detecting ESBLs in Enterobacter spp. and in discriminating ESBL-related resistance from the K1 enzyme and from inherent clavulanate susceptibility in Acinetobacter spp.

Kinetics of Sulbactam Hydrolysis by β-Lactamases, and Kinetics of β-Lactamase Inhibition by Sulbactam

PubMed Central

2017-01-01

ABSTRACT Sulbactam is one of four β-lactamase inhibitors in current clinical use to counteract drug resistance caused by degradation of β-lactam antibiotics by these bacterial enzymes. As a β-lactam itself, sulbactam is susceptible to degradation by β-lactamases. I investigated the Michaelis-Menten kinetics of sulbactam hydrolysis by 14 β-lactamases, representing clinically widespread groups within all four Ambler classes, i.e., CTX-M-15, KPC-2, SHV-5, and TEM-1 for class A; IMP-1, NDM-1, and VIM-1 for class B; Acinetobacter baumannii ADC-7, Pseudomonas aeruginosa AmpC, and Enterobacter cloacae P99 for class C; and OXA-10, OXA-23, OXA-24, and OXA-48 for class D. All of the β-lactamases were able to hydrolyze sulbactam, although they varied widely in their kinetic constants for the reaction, even within each class. I also investigated the inactivation kinetics of the inhibition of these enzymes by sulbactam. The class A β-lactamases varied widely in their susceptibility to inhibition, the class C and D enzymes were very weakly inhibited, and the class B enzymes were essentially or completely unaffected. In addition, we measured the sulbactam turnover number, the sulbactam/enzyme molar ratio required for complete inhibition of each enzyme. Class C enzymes had the lowest turnover numbers, class A enzymes varied widely, and class D enzymes had very high turnover numbers. These results are valuable for understanding which β-lactamases ought to be well inhibited by sulbactam. Moreover, since sulbactam has intrinsic antibacterial activity against Acinetobacter species pathogens, these results contribute to understanding β-lactamase-mediated sulbactam resistance in Acinetobacter, especially due to the action of the widespread class D enzymes. PMID:28971872

Antimicrobial-resistant Pseudomonas aeruginosa and Acinetobacter baumannii From Patients With Hospital-acquired or Ventilator-associated Pneumonia in Vietnam.

PubMed

Biedenbach, Douglas J; Giao, Phan Trong; Hung Van, Pham; Su Minh Tuyet, Nguyen; Thi Thanh Nga, Tran; Phuong, Doan Mai; Vu Trung, Nguyen; Badal, Robert E

2016-09-01

Multidrug-resistant bacterial pathogens are becoming a significant problem worldwide. Acinetobacter baumannii and Pseudomonas aeruginosa are problematic multidrug-resistant pathogens. This multicenter study in Vietnam determined the level of resistance to antimicrobial agents used to treat A baumannii and P aeruginosa infections in this country. Five medical centers in Vietnam provided 529 P aeruginosa and 971 Acinetobacter species (904 A baumannii) isolates from patients with hospital-acquired or ventilator-associated pneumonia from 2012 to 2014. A central laboratory verified identification of the isolates and performed susceptibility testing using Clinical and Laboratory Standards Institute methods. Resistance to cephalosporins, β-lactam/β-lactamase inhibitors, carbapenems, and fluoroquinolones was >90% against A baumannii. Aminoglycosides had only slightly better activity, with amikacin resistance >80%. Only colistin (MIC90, ≤0.25 mg/L) and tigecycline (MIC90, 4 mg/L) had appreciable activity against A baumannii. Similar activity was observed among the β-lactams tested against P aeruginosa. Cefepime demonstrated the highest activity (60.1% susceptible), which was similar to doripenem (58.6% susceptible), the most active carbapenem tested. Amikacin was the most active aminoglycoside tested against P aeruginosa, with susceptibility of 81.7% compared with tobramycin (58.0%) and gentamicin (56.5%). Fluoroquinolones had limited activity against P aeruginosa with susceptibility to ciprofloxacin (55.0%). All P aeruginosa isolates had colistin MIC values ≤2 mg/L. The data from this 3-year longitudinal study in Vietnam demonstrate that 2 of the most common nonfermentative gram-negative pathogens associated with hospital-acquired and ventilator-associated pneumonia are significantly resistant to most of the available treatment options and require combination therapies unless new antimicrobial agents become available. Copyright © 2016. Published by Elsevier Inc.

Hymenoptera Genome Database: integrating genome annotations in HymenopteraMine

PubMed Central

Elsik, Christine G.; Tayal, Aditi; Diesh, Colin M.; Unni, Deepak R.; Emery, Marianne L.; Nguyen, Hung N.; Hagen, Darren E.

2016-01-01

We report an update of the Hymenoptera Genome Database (HGD) (http://HymenopteraGenome.org), a model organism database for insect species of the order Hymenoptera (ants, bees and wasps). HGD maintains genomic data for 9 bee species, 10 ant species and 1 wasp, including the versions of genome and annotation data sets published by the genome sequencing consortiums and those provided by NCBI. A new data-mining warehouse, HymenopteraMine, based on the InterMine data warehousing system, integrates the genome data with data from external sources and facilitates cross-species analyses based on orthology. New genome browsers and annotation tools based on JBrowse/WebApollo provide easy genome navigation, and viewing of high throughput sequence data sets and can be used for collaborative genome annotation. All of the genomes and annotation data sets are combined into a single BLAST server that allows users to select and combine sequence data sets to search. PMID:26578564

COMPUTATIONAL RESOURCES FOR BIOFUEL FEEDSTOCK SPECIES

DOE Office of Scientific and Technical Information (OSTI.GOV)

Buell, Carol Robin; Childs, Kevin L

2013-05-07

While current production of ethanol as a biofuel relies on starch and sugar inputs, it is anticipated that sustainable production of ethanol for biofuel use will utilize lignocellulosic feedstocks. Candidate plant species to be used for lignocellulosic ethanol production include a large number of species within the Grass, Pine and Birch plant families. For these biofuel feedstock species, there are variable amounts of genome sequence resources available, ranging from complete genome sequences (e.g. sorghum, poplar) to transcriptome data sets (e.g. switchgrass, pine). These data sets are not only dispersed in location but also disparate in content. It will be essentialmore » to leverage and improve these genomic data sets for the improvement of biofuel feedstock production. The objectives of this project were to provide computational tools and resources for data-mining genome sequence/annotation and large-scale functional genomic datasets available for biofuel feedstock species. We have created a Bioenergy Feedstock Genomics Resource that provides a web-based portal or clearing house for genomic data for plant species relevant to biofuel feedstock production. Sequence data from a total of 54 plant species are included in the Bioenergy Feedstock Genomics Resource including model plant species that permit leveraging of knowledge across taxa to biofuel feedstock species.We have generated additional computational analyses of these data, including uniform annotation, to facilitate genomic approaches to improved biofuel feedstock production. These data have been centralized in the publicly available Bioenergy Feedstock Genomics Resource (http://bfgr.plantbiology.msu.edu/).« less

Comparative genomics of the marine bacterial genus Glaciecola reveals the high degree of genomic diversity and genomic characteristic for cold adaptation.

PubMed

Qin, Qi-Long; Xie, Bin-Bin; Yu, Yong; Shu, Yan-Li; Rong, Jin-Cheng; Zhang, Yan-Jiao; Zhao, Dian-Li; Chen, Xiu-Lan; Zhang, Xi-Ying; Chen, Bo; Zhou, Bai-Cheng; Zhang, Yu-Zhong

2014-06-01

To what extent the genomes of different species belonging to one genus can be diverse and the relationship between genomic differentiation and environmental factor remain unclear for oceanic bacteria. With many new bacterial genera and species being isolated from marine environments, this question warrants attention. In this study, we sequenced all the type strains of the published species of Glaciecola, a recently defined cold-adapted genus with species from diverse marine locations, to study the genomic diversity and cold-adaptation strategy in this genus.The genome size diverged widely from 3.08 to 5.96 Mb, which can be explained by massive gene gain and loss events. Horizontal gene transfer and new gene emergence contributed substantially to the genome size expansion. The genus Glaciecola had an open pan-genome. Comparative genomic research indicated that species of the genus Glaciecola had high diversity in genome size, gene content and genetic relatedness. This may be prevalent in marine bacterial genera considering the dynamic and complex environments of the ocean. Species of Glaciecola had some common genomic features related to cold adaptation, which enable them to thrive and play a role in biogeochemical cycle in the cold marine environments.

In-silico Taxonomic Classification of 373 Genomes Reveals Species Misidentification and New Genospecies within the Genus Pseudomonas

PubMed Central

Tran, Phuong N.; Savka, Michael A.; Gan, Han Ming

2017-01-01

The genus Pseudomonas has one of the largest diversity of species within the Bacteria kingdom. To date, its taxonomy is still being revised and updated. Due to the non-standardized procedure and ambiguous thresholds at species level, largely based on 16S rRNA gene or conventional biochemical assay, species identification of publicly available Pseudomonas genomes remains questionable. In this study, we performed a large-scale analysis of all Pseudomonas genomes with species designation (excluding the well-defined P. aeruginosa) and re-evaluated their taxonomic assignment via in silico genome-genome hybridization and/or genetic comparison with valid type species. Three-hundred and seventy-three pseudomonad genomes were analyzed and subsequently clustered into 145 distinct genospecies. We detected 207 erroneous labels and corrected 43 to the proper species based on Average Nucleotide Identity Multilocus Sequence Typing (MLST) sequence similarity to the type strain. Surprisingly, more than half of the genomes initially designated as Pseudomonas syringae and Pseudomonas fluorescens should be classified either to a previously described species or to a new genospecies. Notably, high pairwise average nucleotide identity (>95%) indicating species-level similarity was observed between P. synxantha-P. libanensis, P. psychrotolerans–P. oryzihabitans, and P. kilonensis- P. brassicacearum, that were previously differentiated based on conventional biochemical tests and/or genome-genome hybridization techniques. PMID:28747902

Serendipitous discovery of Wolbachia genomes in multiple Drosophila species.

PubMed

Salzberg, Steven L; Dunning Hotopp, Julie C; Delcher, Arthur L; Pop, Mihai; Smith, Douglas R; Eisen, Michael B; Nelson, William C

2005-01-01

The Trace Archive is a repository for the raw, unanalyzed data generated by large-scale genome sequencing projects. The existence of this data offers scientists the possibility of discovering additional genomic sequences beyond those originally sequenced. In particular, if the source DNA for a sequencing project came from a species that was colonized by another organism, then the project may yield substantial amounts of genomic DNA, including near-complete genomes, from the symbiotic or parasitic organism. By searching the publicly available repository of DNA sequencing trace data, we discovered three new species of the bacterial endosymbiont Wolbachia pipientis in three different species of fruit fly: Drosophila ananassae, D. simulans, and D. mojavensis. We extracted all sequences with partial matches to a previously sequenced Wolbachia strain and assembled those sequences using customized software. For one of the three new species, the data recovered were sufficient to produce an assembly that covers more than 95% of the genome; for a second species the data produce the equivalent of a 'light shotgun' sampling of the genome, covering an estimated 75-80% of the genome; and for the third species the data cover approximately 6-7% of the genome. The results of this study reveal an unexpected benefit of depositing raw data in a central genome sequence repository: new species can be discovered within this data. The differences between these three new Wolbachia genomes and the previously sequenced strain revealed numerous rearrangements and insertions within each lineage and hundreds of novel genes. The three new genomes, with annotation, have been deposited in GenBank.

Transformation of Acinetobacter sp. Strain BD413(pFG4ΔnptII) with Transgenic Plant DNA in Soil Microcosms and Effects of Kanamycin on Selection of Transformants

PubMed Central

Nielsen, Kaare M.; van Elsas, Jan D.; Smalla, Kornelia

2000-01-01

Here we show that horizontal transfer of DNA, extracted from transgenic sugar beets, to bacteria, based on homologous recombination, can occur in soil. Restoration of a 317-bp-deleted nptII gene in Acinetobacter sp. strain BD413(pFG4) cells incubated in sterile soil microcosms was detected after addition of nutrients and transgenic plant DNA encoding a functional nptII gene conferring bacterial kanamycin resistance. Selective effects of the addition of kanamycin on the population dynamics of Acinetobacter sp. cells in soil were found, and high concentrations of kanamycin reduced the CFU of Acinetobacter sp. cells from 109 CFU/g of soil to below detection. In contrast to a chromosomal nptII-encoded kanamycin resistance, the pFG4-generated resistance was found to be unstable over a 31-day incubation period in vitro. PMID:10698801

Patterns of genome size variation in snapping shrimp.

PubMed

Jeffery, Nicholas W; Hultgren, Kristin; Chak, Solomon Tin Chi; Gregory, T Ryan; Rubenstein, Dustin R

2016-06-01

Although crustaceans vary extensively in genome size, little is known about how genome size may affect the ecology and evolution of species in this diverse group, in part due to the lack of large genome size datasets. Here we investigate interspecific, intraspecific, and intracolony variation in genome size in 39 species of Synalpheus shrimps, representing one of the largest genome size datasets for a single genus within crustaceans. We find that genome size ranges approximately 4-fold across Synalpheus with little phylogenetic signal, and is not related to body size. In a subset of these species, genome size is related to chromosome size, but not to chromosome number, suggesting that despite large genomes, these species are not polyploid. Interestingly, there appears to be 35% intraspecific genome size variation in Synalpheus idios among geographic regions, and up to 30% variation in Synalpheus duffyi genome size within the same colony.

Characterization of genome in tetraploid StY species of Elymus (Triticeae: Poaceae) using sequential FISH and GISH.

PubMed

Liu, Ruijuan; Wang, Richard R-C; Yu, Feng; Lu, Xingwang; Dou, Quanwen

2017-08-01

Genomes of ten species of Elymus, either presumed or known as tetraploid StY, were characterized using fluorescence in situ hybridization (FISH) and genomic in situ hybridization (GISH). These tetraploid species could be grouped into three categories. Type I included StY genome reported species-Roegneria pendulina, R. nutans, R. glaberrima, R. ciliaris, and Elymus nevskii, and StY genome presumed species-R. sinica, R. breviglumis, and R. dura, whose genome could be separated into two sets based on different GISH intensities. Type I genome constitution was deemed as putative StY. The St genome were mainly characterized with intense hybridization with pAs1, fewer AAG sites, and linked distribution of 5S rDNA and 18S-26S rDNA, while the Y genome with less intense hybridization with pAs1, more varied AAG sites, and isolated distribution of 5S rDNA and 18S-26S rDNA. Nevertheless, further genomic variations were detected among the different StY species. Type II included E. alashanicus, whose genome could be easily separated based on GISH pattern. FISH and GISH patterns suggested that E. alashanicus comprised a modified St genome and an unknown genome. Type III included E. longearistatus, whose genome could not be separated by GISH and was designated as St l Y l . Notably, a close relationship between S l and Y l genomes was observed.

Perspectives from the Avian Phylogenomics Project: Questions that Can Be Answered with Sequencing All Genomes of a Vertebrate Class.

PubMed

Jarvis, Erich D

2016-01-01

The rapid pace of advances in genome technology, with concomitant reductions in cost, makes it feasible that one day in our lifetime we will have available extant genomes of entire classes of species, including vertebrates. I recently helped cocoordinate the large-scale Avian Phylogenomics Project, which collected and sequenced genomes of 48 bird species representing most currently classified orders to address a range of questions in phylogenomics and comparative genomics. The consortium was able to answer questions not previously possible with just a few genomes. This success spurred on the creation of a project to sequence the genomes of at least one individual of all extant ∼10,500 bird species. The initiation of this project has led us to consider what questions now impossible to answer could be answered with all genomes, and could drive new questions now unimaginable. These include the generation of a highly resolved family tree of extant species, genome-wide association studies across species to identify genetic substrates of many complex traits, redefinition of species and the species concept, reconstruction of the genomes of common ancestors, and generation of new computational tools to address these questions. Here I present visions for the future by posing and answering questions regarding what scientists could potentially do with available genomes of an entire vertebrate class.

Comparative phenotypic analysis of Gossypium raimondii with Upland cotton

USDA-ARS?s Scientific Manuscript database

Gossypium raimondii Ulbr., a wild species with a diploid genome, has been sequenced due to its small genome size and sequence similarity with the polyploidy cultivated Gossypium species. Accessibility of the G. raimondii genome has made the species a reference used extensively in cotton genomic and...

Survival of Acinetobacter baumannii on dry surfaces.

PubMed Central

Wendt, C; Dietze, B; Dietz, E; Rüden, H

1997-01-01

Acinetobacter spp. have frequently been reported to be the causative agents of hospital outbreaks. The circumstances of some outbreaks demonstrated the long survival of Acinetobacter in a dry, inanimate environment. In laboratory experiments, we compared the abilities of five Acinetobacter baumannii strains, three Acinetobacter sp. strains from the American Type Culture Collection (ATCC), one Escherichia coli ATCC strain, and one Enterococcus faecium ATCC strain to survive under dry conditions. Bacterial solutions of the 10 strains were inoculated onto four different material samples (ceramic, polyvinyl chloride, rubber, and stainless steel) and stored under defined conditions. We investigated the bacterial counts of the material samples immediately after inoculation, after drying, and after 4 h, 1 day, and 1, 2, 4, 8, and 16 weeks of storage. A statistical model was used to distribute the 40 resulting curves among four types of survival curves. The type of survival curve was significantly associated with the bacterial strain but not with the material. The ability of the A. baumannii strains to survive under dry conditions varied greatly and correlated well with the source of the strain. Strains isolated from dry sources survived better than those isolated from wet sources. An outbreak strain that had caused hospital-acquired respiratory tract infections survived better than the strains from wet sources, but not as well as strains from dry sources. Resistance to dry conditions may promote the transmissibility of a strain, but it is not sufficient to make a strain an epidemic one. However, in the case of an outbreak, sources of Acinetobacter must be expected in the dry environment. PMID:9163451

A simple screening test for the detection of metallo-β-lactamase-producing Pseudomonas aeruginosa and Acinetobacter in a tertiary care hospital.

PubMed

Wan Nor Amilah, W A W; Noor Izani, N J; Ng, W K; Ashraful Haq, J

2012-12-01

Clinical utilization of carbapenems remains under threat with the emergence of acquired carbapenemase-producing bacteria, particularly metallo-β-lactamases (MBL). Rapid detection of MBL-producing Gram-negative bacilli is essential to prevent their widespread dissemination. However, no standardized detection method is available for routine laboratory use. The purpose of the study was to evaluate a chelating-agent based double disk synergic test and disk potentiation test for MBL-producing strain detection and to determine the isolation rate of MBL-producing Pseudomonas aeruginosa and Acinetobacter from clinical samples in our tertiary teaching hospital. A total of 22 and 66 imipenem-resistant P. aeruginosa and Acinetobacter isolates respectively were tested with ceftazidime (CAZ) disk by modified double disk synergic test and disk potentiation test using ethylenediaminetetraacetic acid (EDTA) and 2-mercaptopropionic acid (as chelating agents) to detect MBL production. The tests were compared with EDTA-phenanthroline-imipenem (EPI) microdilution MIC test as gold standard. MBL positive strains were detected in 17 (77.3%) P. aeruginosa and 2 (3.5%) Acinetobacter isolates. The disk potentiation test with 2-mercaptopropionic acid (2-MPA) dilution of 1:12 provided the most acceptable sensitivities and specificities (88.2% sensitivity and 100% specificity in P. aeruginosa; 100% sensitivity and specificity in Acinetobacter) compared to other screening methods used in this study. This study provided useful information on the local prevalence of MBL-producing P. aeruginosa and Acinetobacter in our hospital. Disc potentiation test with CAZ/2-MPA disc appears to be reliable and convenient MBL detection method in the routine clinical laboratory.

Biosystematics and evolutionary relationships of perennial Triticeae species revealed by genomic analyses

USDA-ARS?s Scientific Manuscript database

Literature published after 1984 were reviewed to address: (1) genome relationships among monogenomic diploid species, (2) progenitors of the unknown Y genome in Elymus polyploids, X in Thinopyrum intermedium, and Xm in Leymus, and (3) genome constitutions of some perennial Triticeae species that wer...

Characterization of the microbial flora in disinfecting footbaths with hypochlorite.

PubMed

Langsrud, Solveig; Seifert, Linn; Møretrø, Trond

2006-09-01

Change or disinfection of footwear are measures to prevent cross contamination between areas with low and high hygienic levels in the food industry. The efficacy of disinfecting footwear is not well documented. Samples of used disinfectant and from swabbing of corners after draining were taken from disinfecting footbaths containing chlorine in four Norwegian cheese factories. Bacteria were present in 9 of 12 footbaths and more positive samples were found from swab samples than from used disinfectant. The microbial flora in footbaths varied between the dairies. In two dairies, the flora was dominated by Pseudomonas spp. and Acinetobacter spp., respectively. In the third dairy, both Bacillus spp. and Staphylococcus spp. were present and in the fourth dairy, the flora was diverse (Acinetobacter sp., Enterococcus faecalis, Klebsiella pneumoniae, and Bacillus sp.). The strains were not resistant to the recommended user concentration of chlorine in bactericidal suspension or surface tests. The degree of attachment to plastic varied between strains and species and bacteria attached to surfaces were in general more resistant than suspended bacteria. The results of the survey indicated that disinfecting footbaths containing chlorine may act as contamination sources in food factories and should not be used without regular hygienic monitoring.

The lytic transglycosylase MltB connects membrane homeostasis and in vivo fitness of Acinetobacter baumannii.

PubMed

Crépin, Sébastien; Ottosen, Elizabeth N; Peters, Katharina; Smith, Sara N; Himpsl, Stephanie D; Vollmer, Waldemar; Mobley, Harry L T

2018-06-08

Acinetobacter baumannii has emerged as a leading nosocomial pathogen, infecting a wide range of anatomic sites including the respiratory tract and the bloodstream. In addition to being multi-drug resistant, little is known about the molecular basis of A. baumannii pathogenesis. To better understand A. baumannii virulence, a combination of a transposon-sequencing (TraDIS) screen and the neutropenic mouse model of bacteremia was used to identify the full set of fitness genes required during bloodstream infection. The lytic transglycosylase MltB was identified as a critical fitness factor. MltB cleaves the MurNAc-GlcNAc bond of peptidoglycan, which leads to cell wall remodeling. Here we show that MltB is part of a complex network connecting resistance to stresses, membrane homeostasis, biogenesis of pili and in vivo fitness. Indeed, inactivation of mltB not only impaired resistance to serum complement, cationic antimicrobial peptides and oxygen species, but also altered the cell envelope integrity, activated the envelope stress response, drastically reduced the number of pili at the cell surface and finally, significantly decreased colonization of both the bloodstream and the respiratory tract. This article is protected by copyright. All rights reserved. © 2018 John Wiley & Sons Ltd.

[Phylogenetic relationships and intraspecific variation of D-genome Aegilops L. as revealed by RAPD analysis].

PubMed

Goriunova, S V; Kochieva, E Z; Chikida, N N; Pukhal'skiĭ, V A

2004-05-01

RAPD analysis was carried out to study the genetic variation and phylogenetic relationships of polyploid Aegilops species, which contain the D genome as a component of the alloploid genome, and diploid Aegilops tauschii, which is a putative donor of the D genome for common wheat. In total, 74 accessions of six D-genome Aegilops species were examined. The highest intraspecific variation (0.03-0.21) was observed for Ae. tauschii. Intraspecific distances between accessions ranged 0.007-0.067 in Ae. cylindrica, 0.017-0.047 in Ae. vavilovii, and 0.00-0.053 in Ae. juvenalis. Likewise, Ae. ventricosa and Ae. crassa showed low intraspecific polymorphism. The among-accession difference in alloploid Ae. ventricosa (genome DvNv) was similar to that of one parental species, Ae. uniaristata (N), and substantially lower than in the other parent, Ae. tauschii (D). The among-accession difference in Ae. cylindrica (CcDc) was considerably lower than in either parent, Ae. tauschii (D) or Ae. caudata (C). With the exception of Ae. cylindrica, all D-genome species--Ae. tauschii (D), Ae. ventricosa (DvNv), Ae. crassa (XcrDcrl and XcrDcrlDcr2), Ae. juvenalis (XjDjUj), and Ae. vavilovii (XvaDvaSva)--formed a single polymorphic cluster, which was distinct from clusters of other species. The only exception, Ae. cylindrica, did not group with the other D-genome species, but clustered with Ae. caudata (C), a donor of the C genome. The cluster of these two species was clearly distinct from the cluster of the other D-genome species and close to a cluster of Ae. umbellulata (genome U) and Ae. ovata (genome UgMg). Thus, RAPD analysis for the first time was used to estimate and to compare the interpopulation polymorphism and to establish the phylogenetic relationships of all diploid and alloploid D-genome Aegilops species.

Performance and Scalability of Discriminative Metrics for Comparative Gene Identification in 12 Drosophila Genomes

PubMed Central

Lin, Michael F.; Deoras, Ameya N.; Rasmussen, Matthew D.; Kellis, Manolis

2008-01-01

Comparative genomics of multiple related species is a powerful methodology for the discovery of functional genomic elements, and its power should increase with the number of species compared. Here, we use 12 Drosophila genomes to study the power of comparative genomics metrics to distinguish between protein-coding and non-coding regions. First, we study the relative power of different comparative metrics and their relationship to single-species metrics. We find that even relatively simple multi-species metrics robustly outperform advanced single-species metrics, especially for shorter exons (≤240 nt), which are common in animal genomes. Moreover, the two capture largely independent features of protein-coding genes, with different sensitivity/specificity trade-offs, such that their combinations lead to even greater discriminatory power. In addition, we study how discovery power scales with the number and phylogenetic distance of the genomes compared. We find that species at a broad range of distances are comparably effective informants for pairwise comparative gene identification, but that these are surpassed by multi-species comparisons at similar evolutionary divergence. In particular, while pairwise discovery power plateaued at larger distances and never outperformed the most advanced single-species metrics, multi-species comparisons continued to benefit even from the most distant species with no apparent saturation. Last, we find that genes in functional categories typically considered fast-evolving can nonetheless be recovered at very high rates using comparative methods. Our results have implications for comparative genomics analyses in any species, including the human. PMID:18421375

Hymenoptera Genome Database: integrating genome annotations in HymenopteraMine.

PubMed

Elsik, Christine G; Tayal, Aditi; Diesh, Colin M; Unni, Deepak R; Emery, Marianne L; Nguyen, Hung N; Hagen, Darren E

2016-01-04

We report an update of the Hymenoptera Genome Database (HGD) (http://HymenopteraGenome.org), a model organism database for insect species of the order Hymenoptera (ants, bees and wasps). HGD maintains genomic data for 9 bee species, 10 ant species and 1 wasp, including the versions of genome and annotation data sets published by the genome sequencing consortiums and those provided by NCBI. A new data-mining warehouse, HymenopteraMine, based on the InterMine data warehousing system, integrates the genome data with data from external sources and facilitates cross-species analyses based on orthology. New genome browsers and annotation tools based on JBrowse/WebApollo provide easy genome navigation, and viewing of high throughput sequence data sets and can be used for collaborative genome annotation. All of the genomes and annotation data sets are combined into a single BLAST server that allows users to select and combine sequence data sets to search. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

Genomic patterns of species diversity and divergence in Eucalyptus.

PubMed

Hudson, Corey J; Freeman, Jules S; Myburg, Alexander A; Potts, Brad M; Vaillancourt, René E

2015-06-01

We examined genome-wide patterns of DNA sequence diversity and divergence among six species of the important tree genus Eucalyptus and investigated their relationship with genomic architecture. Using c. 90 range-wide individuals of each Eucalyptus species (E. grandis, E. urophylla, E. globulus, E. nitens, E. dunnii and E. camaldulensis), genetic diversity and divergence were estimated from 2840 polymorphic diversity arrays technology markers covering the 11 chromosomes. Species differentiating markers (SDMs) identified in each of 15 pairwise species comparisons, along with species diversity (HHW ) and divergence (FST ), were projected onto the E. grandis reference genome. Across all species comparisons, SDMs totalled 1.1-5.3% of markers and were widely distributed throughout the genome. Marker divergence (FST and SDMs) and diversity differed among and within chromosomes. Patterns of diversity and divergence were broadly conserved across species and significantly associated with genomic features, including the proximity of markers to genes, the relative number of clusters of tandem duplications, and gene density within or among chromosomes. These results suggest that genomic architecture influences patterns of species diversity and divergence in the genus. This influence is evident across the six species, encompassing diverse phylogenetic lineages, geography and ecology. © 2015 University of Tasmania New Phytologist © 2015 New Phytologist Trust.

Elevated Rate of Genome Rearrangements in Radiation-Resistant Bacteria.

PubMed

Repar, Jelena; Supek, Fran; Klanjscek, Tin; Warnecke, Tobias; Zahradka, Ksenija; Zahradka, Davor

2017-04-01

A number of bacterial, archaeal, and eukaryotic species are known for their resistance to ionizing radiation. One of the challenges these species face is a potent environmental source of DNA double-strand breaks, potential drivers of genome structure evolution. Efficient and accurate DNA double-strand break repair systems have been demonstrated in several unrelated radiation-resistant species and are putative adaptations to the DNA damaging environment. Such adaptations are expected to compensate for the genome-destabilizing effect of environmental DNA damage and may be expected to result in a more conserved gene order in radiation-resistant species. However, here we show that rates of genome rearrangements, measured as loss of gene order conservation with time, are higher in radiation-resistant species in multiple, phylogenetically independent groups of bacteria. Comparison of indicators of selection for genome organization between radiation-resistant and phylogenetically matched, nonresistant species argues against tolerance to disruption of genome structure as a strategy for radiation resistance. Interestingly, an important mechanism affecting genome rearrangements in prokaryotes, the symmetrical inversions around the origin of DNA replication, shapes genome structure of both radiation-resistant and nonresistant species. In conclusion, the opposing effects of environmental DNA damage and DNA repair result in elevated rates of genome rearrangements in radiation-resistant bacteria. Copyright © 2017 Repar et al.

AmphiBase: A new genomic resource for non-model amphibian species.

PubMed

Kwon, Taejoon

2017-01-01

More than five thousand genes annotated in the recently published Xenopus laevis and Xenopus tropicalis genomes do not have a candidate orthologous counterpart in other vertebrate species. To determine whether these sequences represent genuine amphibian-specific genes or annotation errors, it is necessary to analyze them alongside sequences from other amphibian species. However, due to large genome sizes and an abundance of repeat sequences, there are limited numbers of gene sequences available from amphibian species other than Xenopus. AmphiBase is a new genomic resource covering non-model amphibian species, based on public domain transcriptome data and computational methods developed during the X. laevis genome project. Here, I review the current status of AmphiBase, including amphibian species with available transcriptome data or biological samples, and describe the challenges of building a comprehensive amphibian genomic resource in the absence of genomes. This mini-review will be informative for researchers interested in functional genomic experiments using amphibian model organisms, such as Xenopus and axolotl, and will assist in interpretation of results implicating "orphan genes." Additionally, this study highlights an opportunity for researchers working on non-model amphibian species to collaborate in their future efforts and develop amphibian genomic resources as a community. © 2017 Wiley Periodicals, Inc.

Comparative Genome Structure, Secondary Metabolite, and Effector Coding Capacity across Cochliobolus Pathogens

PubMed Central

Bushley, Kathryn E.; Ohm, Robin A.; Otillar, Robert; Martin, Joel; Schackwitz, Wendy; Grimwood, Jane; MohdZainudin, NurAinIzzati; Xue, Chunsheng; Wang, Rui; Manning, Viola A.; Dhillon, Braham; Tu, Zheng Jin; Steffenson, Brian J.; Salamov, Asaf; Sun, Hui; Lowry, Steve; LaButti, Kurt; Han, James; Copeland, Alex; Lindquist, Erika; Barry, Kerrie; Schmutz, Jeremy; Baker, Scott E.; Ciuffetti, Lynda M.; Grigoriev, Igor V.; Zhong, Shaobin; Turgeon, B. Gillian

2013-01-01

The genomes of five Cochliobolus heterostrophus strains, two Cochliobolus sativus strains, three additional Cochliobolus species (Cochliobolus victoriae, Cochliobolus carbonum, Cochliobolus miyabeanus), and closely related Setosphaeria turcica were sequenced at the Joint Genome Institute (JGI). The datasets were used to identify SNPs between strains and species, unique genomic regions, core secondary metabolism genes, and small secreted protein (SSP) candidate effector encoding genes with a view towards pinpointing structural elements and gene content associated with specificity of these closely related fungi to different cereal hosts. Whole-genome alignment shows that three to five percent of each genome differs between strains of the same species, while a quarter of each genome differs between species. On average, SNP counts among field isolates of the same C. heterostrophus species are more than 25× higher than those between inbred lines and 50× lower than SNPs between Cochliobolus species. The suites of nonribosomal peptide synthetase (NRPS), polyketide synthase (PKS), and SSP–encoding genes are astoundingly diverse among species but remarkably conserved among isolates of the same species, whether inbred or field strains, except for defining examples that map to unique genomic regions. Functional analysis of several strain-unique PKSs and NRPSs reveal a strong correlation with a role in virulence. PMID:23357949

Comparative Genome Structure, Secondary Metabolite, and Effector Coding Capacity across Cochliobolus Pathogens

DOE Office of Scientific and Technical Information (OSTI.GOV)

Condon, Bradford J.; Leng, Yueqiang; Wu, Dongliang

The genomes of five Cochliobolus heterostrophus strains, two Cochliobolus sativus strains, three additional Cochliobolus species (Cochliobolus victoriae, Cochliobolus carbonum, Cochliobolus miyabeanus), and closely related Setosphaeria turcica were sequenced at the Joint Genome Institute (JGI). The datasets were used to identify SNPs between strains and species, unique genomic regions, core secondary metabolism genes, and small secreted protein (SSP) candidate effector encoding genes with a view towards pinpointing structural elements and gene content associated with specificity of these closely related fungi to different cereal hosts. Whole-genome alignment shows that three to five of each genome differs between strains of the same species,more » while a quarter of each genome differs between species. On average, SNP counts among field isolates of the same C. heterostrophus species are more than 25 higher than those between inbred lines and 50 lower than SNPs between Cochliobolus species. The suites of nonribosomal peptide synthetase (NRPS), polyketide synthase (PKS), and SSP encoding genes are astoundingly diverse among species but remarkably conserved among isolates of the same species, whether inbred or field strains, except for defining examples that map to unique genomic regions. Functional analysis of several strain-unique PKSs and NRPSs reveal a strong correlation with a role in virulence.« less

Genome Editing in the Cricket, Gryllus bimaculatus.

PubMed

Watanabe, Takahito; Noji, Sumihare; Mito, Taro

2017-01-01

Hemimetabolous, or incompletely metamorphosing, insects are phylogenetically basal and include many beneficial and deleterious species. The cricket, Gryllus bimaculatus, is an emerging model for hemimetabolous insects, based on the success of RNA interference (RNAi)-based gene-functional analyses and transgenic technology. Taking advantage of genome editing technologies in this species would greatly promote functional genomics studies. Genome editing has proven to be an effective method for site-specific genome manipulation in various species. Here, we describe a protocol for genome editing including gene knockout and gene knockin in G. bimaculatus for functional genomics studies.

Environmental colonization and onward clonal transmission of carbapenem-resistant Acinetobacter baumannii (CRAB) in a medical intensive care unit: the case for environmental hygiene.

PubMed

Ng, Deborah H L; Marimuthu, Kalisvar; Lee, Jia Jun; Khong, Wei Xin; Ng, Oon Tek; Zhang, Wei; Poh, Bee Fong; Rao, Pooja; Raj, Maya Devi Rajinder; Ang, Brenda; De, Partha Pratim

2018-01-01

In May 2015, we noticed an increase in carbapenem-resistant Acinetobacter baumannii (CRAB) infections in the Medical Intensive Care Unit (MICU). To investigate this, we studied the extent of environmental contamination and subsequent onward clonal transmission of CRAB. We conducted a one-day point prevalence screening (PPS) of the patients and environment in the MICU. We screened patients using endotracheal tube aspirates and swabs from nares, axillae, groin, rectum, wounds, and exit sites of drains. We collected environmental samples from patients' rooms and environment outside the patients' rooms. CRAB isolates from the PPS and clinical samples over the subsequent one month were studied for genetic relatedness by whole genome sequencing (WGS). We collected 34 samples from seven patients and 244 samples from the environment. On the day of PPS, we identified 8 CRAB carriers: 3 who screened positive and 5 previously known clinical infections. We detected environmental contamination in nearly two-thirds of the rooms housing patients with CRAB. WGS demonstrated genetic clustering of isolates within rooms but not across rooms. We analysed 4 CRAB isolates from clinical samples following the PPS. One genetically-related CRAB was identified in the respiratory sample of a patient with nosocomial pneumonia, who was admitted to the MICU five days after the PPS. The extensive environmental colonization of CRAB by patients highlights the importance of environmental hygiene. The transmission dynamics of CRAB needs further investigation.

Genomic taxonomy of vibrios

PubMed Central

Thompson, Cristiane C; Vicente, Ana Carolina P; Souza, Rangel C; Vasconcelos, Ana Tereza R; Vesth, Tammi; Alves, Nelson; Ussery, David W; Iida, Tetsuya; Thompson, Fabiano L

2009-01-01

Background Vibrio taxonomy has been based on a polyphasic approach. In this study, we retrieve useful taxonomic information (i.e. data that can be used to distinguish different taxonomic levels, such as species and genera) from 32 genome sequences of different vibrio species. We use a variety of tools to explore the taxonomic relationship between the sequenced genomes, including Multilocus Sequence Analysis (MLSA), supertrees, Average Amino Acid Identity (AAI), genomic signatures, and Genome BLAST atlases. Our aim is to analyse the usefulness of these tools for species identification in vibrios. Results We have generated four new genome sequences of three Vibrio species, i.e., V. alginolyticus 40B, V. harveyi-like 1DA3, and V. mimicus strains VM573 and VM603, and present a broad analyses of these genomes along with other sequenced Vibrio species. The genome atlas and pangenome plots provide a tantalizing image of the genomic differences that occur between closely related sister species, e.g. V. cholerae and V. mimicus. The vibrio pangenome contains around 26504 genes. The V. cholerae core genome and pangenome consist of 1520 and 6923 genes, respectively. Pangenomes might allow different strains of V. cholerae to occupy different niches. MLSA and supertree analyses resulted in a similar phylogenetic picture, with a clear distinction of four groups (Vibrio core group, V. cholerae-V. mimicus, Aliivibrio spp., and Photobacterium spp.). A Vibrio species is defined as a group of strains that share > 95% DNA identity in MLSA and supertree analysis, > 96% AAI, ≤ 10 genome signature dissimilarity, and > 61% proteome identity. Strains of the same species and species of the same genus will form monophyletic groups on the basis of MLSA and supertree. Conclusion The combination of different analytical and bioinformatics tools will enable the most accurate species identification through genomic computational analysis. This endeavour will culminate in the birth of the online genomic taxonomy whereby researchers and end-users of taxonomy will be able to identify their isolates through a web-based server. This novel approach to microbial systematics will result in a tremendous advance concerning biodiversity discovery, description, and understanding. PMID:19860885

Phylogenomic Analysis and Dynamic Evolution of Chloroplast Genomes in Salicaceae

PubMed Central

Huang, Yuan; Wang, Jun; Yang, Yongping; Fan, Chuanzhu; Chen, Jiahui

2017-01-01

Chloroplast genomes of plants are highly conserved in both gene order and gene content. Analysis of the whole chloroplast genome is known to provide much more informative DNA sites and thus generates high resolution for plant phylogenies. Here, we report the complete chloroplast genomes of three Salix species in family Salicaceae. Phylogeny of Salicaceae inferred from complete chloroplast genomes is generally consistent with previous studies but resolved with higher statistical support. Incongruences of phylogeny, however, are observed in genus Populus, which most likely results from homoplasy. By comparing three Salix chloroplast genomes with the published chloroplast genomes of other Salicaceae species, we demonstrate that the synteny and length of chloroplast genomes in Salicaceae are highly conserved but experienced dynamic evolution among species. We identify seven positively selected chloroplast genes in Salicaceae, which might be related to the adaptive evolution of Salicaceae species. Comparative chloroplast genome analysis within the family also indicates that some chloroplast genes are lost or became pseudogenes, infer that the chloroplast genes horizontally transferred to the nucleus genome. Based on the complete nucleus genome sequences from two Salicaceae species, we remarkably identify that the entire chloroplast genome is indeed transferred and integrated to the nucleus genome in the individual of the reference genome of P. trichocarpa at least once. This observation, along with presence of the large nuclear plastid DNA (NUPTs) and NUPTs-containing multiple chloroplast genes in their original order in the chloroplast genome, favors the DNA-mediated hypothesis of organelle to nucleus DNA transfer. Overall, the phylogenomic analysis using chloroplast complete genomes clearly elucidates the phylogeny of Salicaceae. The identification of positively selected chloroplast genes and dynamic chloroplast-to-nucleus gene transfers in Salicaceae provide resources to better understand the successful adaptation of Salicaceae species. PMID:28676809

The draft genome of the pest tephritid fruit fly Bactrocera tryoni: resources for the genomic analysis of hybridising species.

PubMed

Gilchrist, Anthony Stuart; Shearman, Deborah C A; Frommer, Marianne; Raphael, Kathryn A; Deshpande, Nandan P; Wilkins, Marc R; Sherwin, William B; Sved, John A

2014-12-20

The tephritid fruit flies include a number of economically important pests of horticulture, with a large accumulated body of research on their biology and control. Amongst the Tephritidae, the genus Bactrocera, containing over 400 species, presents various species groups of potential utility for genetic studies of speciation, behaviour or pest control. In Australia, there exists a triad of closely-related, sympatric Bactrocera species which do not mate in the wild but which, despite distinct morphologies and behaviours, can be force-mated in the laboratory to produce fertile hybrid offspring. To exploit the opportunities offered by genomics, such as the efficient identification of genetic loci central to pest behaviour and to the earliest stages of speciation, investigators require genomic resources for future investigations. We produced a draft de novo genome assembly of Australia's major tephritid pest species, Bactrocera tryoni. The male genome (650-700 Mbp) includes approximately 150 Mb of interspersed repetitive DNA sequences and 60 Mb of satellite DNA. Assessment using conserved core eukaryotic sequences indicated 98% completeness. Over 16,000 MAKER-derived gene models showed a large degree of overlap with other Dipteran reference genomes. The sequence of the ribosomal RNA transcribed unit was also determined. Unscaffolded assemblies of B. neohumeralis and B. jarvisi were then produced; comparison with B. tryoni showed that the species are more closely related than any Drosophila species pair. The similarity of the genomes was exploited to identify 4924 potentially diagnostic indels between the species, all of which occur in non-coding regions. This first draft B. tryoni genome resembles other dipteran genomes in terms of size and putative coding sequences. For all three species included in this study, we have identified a comprehensive set of non-redundant repetitive sequences, including the ribosomal RNA unit, and have quantified the major satellite DNA families. These genetic resources will facilitate the further investigations of genetic mechanisms responsible for the behavioural and morphological differences between these three species and other tephritids. We have also shown how whole genome sequence data can be used to generate simple diagnostic tests between very closely-related species where only one of the species is scaffolded.

Head Lice of Pygmies Reveal the Presence of Relapsing Fever Borreliae in the Republic of Congo.

PubMed

Amanzougaghene, Nadia; Akiana, Jean; Mongo Ndombe, Géor; Davoust, Bernard; Nsana, Nardiouf Sjelin; Parra, Henri-Joseph; Fenollar, Florence; Raoult, Didier; Mediannikov, Oleg

2016-12-01

Head lice, Pediculus humanus capitis, occur in four divergent mitochondrial clades (A, B, C and D), each having particular geographical distributions. Recent studies suggest that head lice, as is the case of body lice, can act as a vector for louse-borne diseases. Therefore, understanding the genetic diversity of lice worldwide is of critical importance to our understanding of the risk of louse-borne diseases. Here, we report the results of the first molecular screening of pygmies' head lice in the Republic of Congo for seven pathogens and an analysis of lice mitochondrial clades. We developed two duplex clade-specific real-time PCRs and identified three major mitochondrial clades: A, C, and D indicating high diversity among the head lice studied. We identified the presence of a dangerous human pathogen, Borrelia recurrentis, the causative agent of relapsing fever, in ten clade A head lice, which was not reported in the Republic of Congo, and B. theileri in one head louse. The results also show widespread infection among head lice with several species of Acinetobacter. A. junii was the most prevalent, followed by A. ursingii, A. baumannii, A. johnsonii, A. schindleri, A. lwoffii, A. nosocomialis and A. towneri. Our study is the first to show the presence of B. recurrentis in African pygmies' head lice in the Republic of Congo. This study is also the first to report the presence of DNAs of B. theileri and several species of Acinetobacter in human head lice. Further studies are needed to determine whether the head lice can transmit these pathogenic bacteria from person to another.

High-resolution mapping reveals hundreds of genetic incompatibilities in hybridizing fish species.

PubMed

Schumer, Molly; Cui, Rongfeng; Powell, Daniel L; Dresner, Rebecca; Rosenthal, Gil G; Andolfatto, Peter

2014-06-04

Hybridization is increasingly being recognized as a common process in both animal and plant species. Negative epistatic interactions between genes from different parental genomes decrease the fitness of hybrids and can limit gene flow between species. However, little is known about the number and genome-wide distribution of genetic incompatibilities separating species. To detect interacting genes, we perform a high-resolution genome scan for linkage disequilibrium between unlinked genomic regions in naturally occurring hybrid populations of swordtail fish. We estimate that hundreds of pairs of genomic regions contribute to reproductive isolation between these species, despite them being recently diverged. Many of these incompatibilities are likely the result of natural or sexual selection on hybrids, since intrinsic isolation is known to be weak. Patterns of genomic divergence at these regions imply that genetic incompatibilities play a significant role in limiting gene flow even in young species.

Quantifying Temporal Genomic Erosion in Endangered Species.

PubMed

Díez-Del-Molino, David; Sánchez-Barreiro, Fatima; Barnes, Ian; Gilbert, M Thomas P; Dalén, Love

2018-03-01

Many species have undergone dramatic population size declines over the past centuries. Although stochastic genetic processes during and after such declines are thought to elevate the risk of extinction, comparative analyses of genomic data from several endangered species suggest little concordance between genome-wide diversity and current population sizes. This is likely because species-specific life-history traits and ancient bottlenecks overshadow the genetic effect of recent demographic declines. Therefore, we advocate that temporal sampling of genomic data provides a more accurate approach to quantify genetic threats in endangered species. Specifically, genomic data from predecline museum specimens will provide valuable baseline data that enable accurate estimation of recent decreases in genome-wide diversity, increases in inbreeding levels, and accumulation of deleterious genetic variation. Copyright © 2017 Elsevier Ltd. All rights reserved.

Diverse Responses to UV-B Radiation and Repair Mechanisms of Bacteria Isolated from High-Altitude Aquatic Environments▿

PubMed Central

Fernández Zenoff, V.; Siñeriz, F.; Farías, M. E.

2006-01-01

Acinetobacter johnsonii A2 isolated from the natural community of Laguna Azul (Andean Mountains at 4,560 m above sea level), Serratia marcescens MF42, Pseudomonas sp. strain MF8 isolated from the planktonic community, and Cytophaga sp. strain MF7 isolated from the benthic community from Laguna Pozuelos (Andean Puna at 3,600 m above sea level) were subjected to UV-B (3,931 J m−2) irradiation. In addition, a marine Pseudomonas putida strain, 2IDINH, and a second Acinetobacter johnsonii strain, ATCC 17909, were used as external controls. Resistance to UV-B and kinetic rates of light-dependent (UV-A [315 to 400 nm] and cool white light [400 to 700 nm]) and -independent reactivation following exposure were determined by measuring the survival (expressed as CFU) and accumulation of cyclobutane pyrimidine dimers (CPD). Significant differences in survival after UV-B irradiation were observed: Acinetobacter johnsonii A2, 48%; Acinetobacter johnsonii ATCC 17909, 20%; Pseudomonas sp. strain MF8, 40%; marine Pseudomonas putida strain 2IDINH, 12%; Cytophaga sp. strain MF7, 20%; and Serratia marcescens, 21%. Most bacteria exhibited little DNA damage (between 40 and 80 CPD/Mb), except for the benthic isolate Cytophaga sp. strain MF7 (400 CPD/Mb) and Acinetobacter johnsonii ATCC 17909 (160 CPD/Mb). The recovery strategies through dark and light repair were different in all strains. The most efficient in recovering were both Acinetobacter johnsonii A2 and Cytophaga sp. strain MF7; Serratia marcescens MF42 showed intermediate recovery, and in both Pseudomonas strains, recovery was essentially zero. The UV-B responses and recovery abilities of the different bacteria were consistent with the irradiation levels in their native environment. PMID:17056692

Phenotypic characterization and colistin susceptibilities of carbapenem-resistant of Pseudomonas aeruginosa and Acinetobacter spp.

PubMed

Mohanty, Srujana; Maurya, Vijeta; Gaind, Rajni; Deb, Monorama

2013-11-15

Pseudomonas aeruginosa and Acinetobcter spp. are important nosocomial pathogens and carbapenem resistance is an emerging threat. Therapeutic options for infections with these isolates include colistin. This study was conducted to determine the prevalence of carbapenem resistance in P. aeruginosa and Acinetobacter spp. bloodstream isolates, phenotypically characterize the resistance mechanisms and evaluate the in vitro activity of colistin. Consecutive 145 (95 P.aeruginosa and 50 Acinetobacter spp.) non-repeat isolates were included. Antibiotic susceptibility testing was performed per CLSI guidelines. MIC for carbapenems and colistin was performed using Etest. Isolates showing reduced susceptibility or resistance to the carbapenems were tested for metallo-β-lactamase (MBL) production using imipenem-EDTA combined disk and MBL Etest. Carbapenem resistance was observed in 40% P. aeruginosa and 66.0% Acinetobacter spp. Carbapenem-resistant (CA-R) isolates were significantly (p <0.05) more frequently resistant to the other antibiotics than carbapenem-susceptible isolates. Approximately half of the CA-R strains were multidrug-resistant, and 3.1-5.5% were resistant to all antibiotics tested. MBL was found in 76.3% and 69.7% of the P. aeruginosa and Acinetobacter spp., respectively. Colistin resistance was observed in three (6.0%) Acinetobacter isolates and eight (8.4%) P. aeruginosa. MIC50 for carbapenems were two to four times higher for MBL-positive compared to MBL-negative isolates, but no difference was seen in MIC for colistin. Carbapenem resistance was observed to be mediated by MBL in a considerable number of isolates. Colistin is an alternative for infections caused by CA-R isolates; however, MIC testing should be performed whenever clinical use of colistin is considered.

Interactions of rice (Oryza sativa L.) and PAH-degrading bacteria (Acinetobacter sp.) on enhanced dissipation of spiked phenanthrene and pyrene in waterlogged soil.

PubMed

Gao, Y; Yu, X Z; Wu, S C; Cheung, K C; Tam, N F Y; Qian, P Y; Wong, M H

2006-12-15

The effects of cultivation of rice (Oryza sativa L.) and PAH-degrading bacteria (Acinetobacter sp.) separately, and in combination, on the dissipation of spiked phenanthrene and pyrene (0, 50+50, 100+100, 200+200 mg kg(-1)) in waterlogged soil were studied using pot trials. The population of introduced PAH-degrading bacteria remained at 10(5) CFU g(-1) dry soil after 20 days of treatment with Acinetobacter sp. only, but increased to 10(6) when planted with rice simultaneously. Shoot and root biomass of rice when grown alone was adversely affected by spiked PAHs, but significantly increased by 2-55% and 8-409%, respectively, when inoculated with Acinetobacter sp.. Phenanthrene and pyrene concentrations in roots ranged from 1-27 and 20-98 mg kg(-1), respectively, while their concentrations in shoots were generally lower than 0.2 mg kg(-1). The dissipation of phenanthrene was mainly due to abiotic loss as 70-78% phenanthrene was lost from the control soil at the end of 80 days, while removal of 86-87% phenanthrene had been achieved after 40 days in the treatment co-cultivated with Acinetobacter sp. and rice. Compared with the control where only 6-15% of pyrene was removed from soil, a much higher dissipation of pyrene (43-62%) was attained for the treatments co-cultivated with Acinetobacter sp. and rice at the end of 80 days. The results demonstrated that co-cultivation of rice and PAH-degrading bacteria may have a great potential to accelerate the bioremediation process of PAH-contaminated soil under waterlogged conditions.

Whole genome sequencing and comparative genomics of closely related Fusarium Head Blight fungi: Fusarium graminearum, F. meridionale and F. asiaticum.

PubMed

Walkowiak, Sean; Rowland, Owen; Rodrigue, Nicolas; Subramaniam, Rajagopal

2016-12-09

The Fusarium graminearum species complex is composed of many distinct fungal species that cause several diseases in economically important crops, including Fusarium Head Blight of wheat. Despite being closely related, these species and individuals within species have distinct phenotypic differences in toxin production and pathogenicity, with some isolates reported as non-pathogenic on certain hosts. In this report, we compare genomes and gene content of six new isolates from the species complex, including the first available genomes of F. asiaticum and F. meridionale, with four other genomes reported in previous studies. A comparison of genome structure and gene content revealed a 93-99% overlap across all ten genomes. We identified more than 700 k base pairs (kb) of single nucleotide polymorphisms (SNPs), insertions, and deletions (indels) within common regions of the genome, which validated the species and genetic populations reported within species. We constructed a non-redundant pan gene list containing 15,297 genes from the ten genomes and among them 1827 genes or 12% were absent in at least one genome. These genes were co-localized in telomeric regions and select regions within chromosomes with a corresponding increase in SNPs and indels. Many are also predicted to encode for proteins involved in secondary metabolism and other functions associated with disease. Genes that were common between isolates contained high levels of nucleotide variation and may be pseudogenes, allelic, or under diversifying selection. The genomic resources we have contributed will be useful for the identification of genes that contribute to the phenotypic variation and niche specialization that have been reported among members of the F. graminearum species complex.

Pan-genome analysis of Aeromonas hydrophila, Aeromonas veronii and Aeromonas caviae indicates phylogenomic diversity and greater pathogenic potential for Aeromonas hydrophila.

PubMed

Ghatak, Sandeep; Blom, Jochen; Das, Samir; Sanjukta, Rajkumari; Puro, Kekungu; Mawlong, Michael; Shakuntala, Ingudam; Sen, Arnab; Goesmann, Alexander; Kumar, Ashok; Ngachan, S V

2016-07-01

Aeromonas species are important pathogens of fishes and aquatic animals capable of infecting humans and other animals via food. Due to the paucity of pan-genomic studies on aeromonads, the present study was undertaken to analyse the pan-genome of three clinically important Aeromonas species (A. hydrophila, A. veronii, A. caviae). Results of pan-genome analysis revealed an open pan-genome for all three species with pan-genome sizes of 9181, 7214 and 6884 genes for A. hydrophila, A. veronii and A. caviae, respectively. Core-genome: pan-genome ratio (RCP) indicated greater genomic diversity for A. hydrophila and interestingly RCP emerged as an effective indicator to gauge genomic diversity which could possibly be extended to other organisms too. Phylogenomic network analysis highlighted the influence of homologous recombination and lateral gene transfer in the evolution of Aeromonas spp. Prediction of virulence factors indicated no significant difference among the three species though analysis of pathogenic potential and acquired antimicrobial resistance genes revealed greater hazards from A. hydrophila. In conclusion, the present study highlighted the usefulness of whole genome analyses to infer evolutionary cues for Aeromonas species which indicated considerable phylogenomic diversity for A. hydrophila and hitherto unknown genomic evidence for pathogenic potential of A. hydrophila compared to A. veronii and A. caviae.

Genomic signatures of near-extinction and rebirth of the crested ibis and other endangered bird species.

PubMed

Li, Shengbin; Li, Bo; Cheng, Cheng; Xiong, Zijun; Liu, Qingbo; Lai, Jianghua; Carey, Hannah V; Zhang, Qiong; Zheng, Haibo; Wei, Shuguang; Zhang, Hongbo; Chang, Liao; Liu, Shiping; Zhang, Shanxin; Yu, Bing; Zeng, Xiaofan; Hou, Yong; Nie, Wenhui; Guo, Youmin; Chen, Teng; Han, Jiuqiang; Wang, Jian; Wang, Jun; Chen, Chen; Liu, Jiankang; Stambrook, Peter J; Xu, Ming; Zhang, Guojie; Gilbert, M Thomas P; Yang, Huanming; Jarvis, Erich D; Yu, Jun; Yan, Jianqun

2014-01-01

Nearly one-quarter of all avian species is either threatened or nearly threatened. Of these, 73 species are currently being rescued from going extinct in wildlife sanctuaries. One of the previously most critically-endangered is the crested ibis, Nipponia nippon. Once widespread across North-East Asia, by 1981 only seven individuals from two breeding pairs remained in the wild. The recovering crested ibis populations thus provide an excellent example for conservation genomics since every individual bird has been recruited for genomic and demographic studies. Using high-quality genome sequences of multiple crested ibis individuals, its thriving co-habitant, the little egret, Egretta garzetta, and the recently sequenced genomes of 41 other avian species that are under various degrees of survival threats, including the bald eagle, we carry out comparative analyses for genomic signatures of near extinction events in association with environmental and behavioral attributes of species. We confirm that both loss of genetic diversity and enrichment of deleterious mutations of protein-coding genes contribute to the major genetic defects of the endangered species. We further identify that genetic inbreeding and loss-of-function genes in the crested ibis may all constitute genetic susceptibility to other factors including long-term climate change, over-hunting, and agrochemical overuse. We also establish a genome-wide DNA identification platform for molecular breeding and conservation practices, to facilitate sustainable recovery of endangered species. These findings demonstrate common genomic signatures of population decline across avian species and pave a way for further effort in saving endangered species and enhancing conservation genomic efforts.

Contrasting evolutionary patterns of multiple loci uncover new aspects in the genome origin and evolutionary history of Leymus (Triticeae; Poaceae).

PubMed

Sha, Li-Na; Fan, Xing; Li, Jun; Liao, Jin-Qiu; Zeng, Jian; Wang, Yi; Kang, Hou-Yang; Zhang, Hai-Qin; Zheng, You-Liang; Zhou, Yong-Hong

2017-09-01

Leymus Hochst. (Triticeae: Poaceae), a group of allopolyploid species with the NsXm genomes, is a perennial genus with diversity in morphology, cytology, ecology, and distribution in the Triticeae. To investigate the genome origin and evolutionary history of Leymus, three unlinked low-copy nuclear genes (Acc1, Pgk1, and GBSSI) and three chloroplast regions (trnL-F, matK, and rbcL) of 32 Leymus species were analyzed with those of 36 diploid species representing 18 basic genomes in the Triticeae. The phylogenetic relationships were reconstructed using Bayesian inference, Maximum parsimony, and NeighborNet methods. A time-calibrated phylogeny was generated to estimate the evolutionary history of Leymus. The results suggest that reticulate evolution has occurred in Leymus species, with several distinct progenitors contributing to the Leymus. The molecular data in resolution of the Xm-genome lineage resulted in two apparently contradictory results, with one placing the Xm-genome lineage as closely related to the P/F genome and the other splitting the Xm-genome lineage as sister to the Ns-genome donor. Our results suggested that (1) the Ns genome of Leymus was donated by Psathyrostachys, and additional Ns-containing alleles may be introgressed into some Leymus polyploids by recurrent hybridization; (2) The phylogenetic incongruence regarding the resolution of the Xm-genome lineage suggested that the Xm genome of Leymus was closely related to the P genome of Agropyron; (3) Both Ns- and Xm-genome lineages served as the maternal donor during the speciation of Leymus species; (4) The Pseudoroegneria, Lophopyrum and Australopyrum genomes contributed to some Leymus species. Copyright © 2017 Elsevier Inc. All rights reserved.

Risk factors and outcomes of imipenem-resistant Acinetobacter bloodstream infection in North-eastern Malaysia

PubMed Central

Deris, Zakuan Zainy; Shafei, Mohd Nazri; Harun, Azian

2011-01-01

Objective To determine the risk factors and outcomes of imipenem-resistant Acinetobacter baumannii (IRAB) bloodstream infection (BSI) cases, since there is very little publication on Acinetobacter baumannii infections from Malaysia. Methods A cross sectional study of 41 cases (73.2%) of imipenem-sensitive Acinetobacter baumanii (ISAB) and 15 cases (26.8%) of IRAB was conducted in a teaching hospital which was located at North-Eastern state of Malaysia. Results There was no independent risk factor for IRAB BSI identified but IRAB BSI was significantly associated with longer bacteraemic days [OR 1.23 (95% CI 1.01, 1.50)]. Although prior use of carbepenems and cephalosporin were higher among IRAB than ISAB group, statistically they were not significant. There was no significant difference in term of outcomes between the two groups. Conclusions Although statistically not significant, this analysis compliments previous publication highlighting the importance of appropriate empiric antibiotic usage in hospital especially carbepenems and need further evaluation with bigger subjects. PMID:23569782

Genome size variation among sex types in dioecious and triecious Caricaceae species

USDA-ARS?s Scientific Manuscript database

Caricaceae is a small family consisting of 35 species of varying sexual systems and includes economically important fruit crop, Carica papaya, and other species of “highland papayas”. Flow cytometry was used to obtain genome sizes for 11 species in three genera of Caricaceae to determine if genome s...

The Genome 10K Project: a way forward.

PubMed

Koepfli, Klaus-Peter; Paten, Benedict; O'Brien, Stephen J

2015-01-01

The Genome 10K Project was established in 2009 by a consortium of biologists and genome scientists determined to facilitate the sequencing and analysis of the complete genomes of 10,000 vertebrate species. Since then the number of selected and initiated species has risen from ∼26 to 277 sequenced or ongoing with funding, an approximately tenfold increase in five years. Here we summarize the advances and commitments that have occurred by mid-2014 and outline the achievements and present challenges of reaching the 10,000-species goal. We summarize the status of known vertebrate genome projects, recommend standards for pronouncing a genome as sequenced or completed, and provide our present and future vision of the landscape of Genome 10K. The endeavor is ambitious, bold, expensive, and uncertain, but together the Genome 10K Consortium of Scientists and the worldwide genomics community are moving toward their goal of delivering to the coming generation the gift of genome empowerment for many vertebrate species.

The Genome 10K Project: A Way Forward

PubMed Central

Koepfli, Klaus-Peter; Paten, Benedict; O’Brien, Stephen J.

2017-01-01

The Genome 10K Project was established in 2009 by a consortium of biologists and genome scientists determined to facilitate the sequencing and analysis of the complete genomes of 10,000 vertebrate species. Since then the number of selected and initiated species has risen from ~26 to 277 sequenced or ongoing with funding, an approximately tenfold increase in five years. Here we summarize the advances and commitments that have occurred by mid-2014 and outline the achievements and present challenges of reaching the 10,000-species goal. We summarize the status of known vertebrate genome projects, recommend standards for pronouncing a genome as sequenced or completed, and provide our present and future vision of the landscape of Genome 10K. The endeavor is ambitious, bold, expensive, and uncertain, but together the Genome 10K Consortium of Scientists and the worldwide genomics community are moving toward their goal of delivering to the coming generation the gift of genome empowerment for many vertebrate species. PMID:25689317

The dynamic evolutionary history of genome size in North American woodland salamanders.

PubMed

Newman, Catherine E; Gregory, T Ryan; Austin, Christopher C

2017-04-01

The genus Plethodon is the most species-rich salamander genus in North America, and nearly half of its species face an uncertain future. It is also one of the most diverse families in terms of genome sizes, which range from 1C = 18.2 to 69.3 pg, or 5-20 times larger than the human genome. Large genome size in salamanders results in part from accumulation of transposable elements and is associated with various developmental and physiological traits. However, genome sizes have been reported for only 25% of the species of Plethodon (14 of 55). We collected genome size data for Plethodon serratus to supplement an ongoing phylogeographic study, reconstructed the evolutionary history of genome size in Plethodontidae, and inferred probable genome sizes for the 41 species missing empirical data. Results revealed multiple genome size changes in Plethodon: genomes of western Plethodon increased, whereas genomes of eastern Plethodon decreased, followed by additional decreases or subsequent increases. The estimated genome size of P. serratus was 21 pg. New understanding of variation in genome size evolution, along with genome size inferences for previously unstudied taxa, provide a foundation for future studies on the biology of plethodontid salamanders.

Comparative Transcriptomics of Strawberries (Fragaria spp.) Provides Insights into Evolutionary Patterns.

PubMed

Qiao, Qin; Xue, Li; Wang, Qia; Sun, Hang; Zhong, Yang; Huang, Jinling; Lei, Jiajun; Zhang, Ticao

2016-01-01

Multiple closely related species with genomic sequences provide an ideal system for studies on comparative and evolutionary genomics, as well as the mechanism of speciation. The whole genome sequences of six strawberry species ( Fragaria spp.) have been released, which provide one of the richest genomic resources of any plant genus. In this study, we first generated seven transcriptome sequences of Fragaria species de novo , with a total of 48,557-82,537 unigenes per species. Combined with 13 other species genomes in Rosales, we reconstructed a phylogenetic tree at the genomic level. The phylogenic tree shows that Fragaria closed grouped with Rubus and the Fragaria clade is divided into three subclades. East Asian species appeared in every subclade, suggesting that the genus originated in this area at ∼7.99 Mya. Four species found in mountains of Southwest China originated at ∼3.98 Mya, suggesting that rapid speciation occurred to adapt to changing environments following the uplift of the Qinghai-Tibet Plateau. Moreover, we identified 510 very significantly positively selected genes in the cultivated species F . × ananassa genome. This set of genes was enriched in functions related to specific agronomic traits, such as carbon metabolism and plant hormone signal transduction processes, which are directly related to fruit quality and flavor. These findings illustrate comprehensive evolutionary patterns in Fragaria and the genetic basis of fruit domestication of cultivated strawberry at the genomic/transcriptomic level.

The perennial ryegrass GenomeZipper: targeted use of genome resources for comparative grass genomics.

PubMed

Pfeifer, Matthias; Martis, Mihaela; Asp, Torben; Mayer, Klaus F X; Lübberstedt, Thomas; Byrne, Stephen; Frei, Ursula; Studer, Bruno

2013-02-01

Whole-genome sequences established for model and major crop species constitute a key resource for advanced genomic research. For outbreeding forage and turf grass species like ryegrasses (Lolium spp.), such resources have yet to be developed. Here, we present a model of the perennial ryegrass (Lolium perenne) genome on the basis of conserved synteny to barley (Hordeum vulgare) and the model grass genome Brachypodium (Brachypodium distachyon) as well as rice (Oryza sativa) and sorghum (Sorghum bicolor). A transcriptome-based genetic linkage map of perennial ryegrass served as a scaffold to establish the chromosomal arrangement of syntenic genes from model grass species. This scaffold revealed a high degree of synteny and macrocollinearity and was then utilized to anchor a collection of perennial ryegrass genes in silico to their predicted genome positions. This resulted in the unambiguous assignment of 3,315 out of 8,876 previously unmapped genes to the respective chromosomes. In total, the GenomeZipper incorporates 4,035 conserved grass gene loci, which were used for the first genome-wide sequence divergence analysis between perennial ryegrass, barley, Brachypodium, rice, and sorghum. The perennial ryegrass GenomeZipper is an ordered, information-rich genome scaffold, facilitating map-based cloning and genome assembly in perennial ryegrass and closely related Poaceae species. It also represents a milestone in describing synteny between perennial ryegrass and fully sequenced model grass genomes, thereby increasing our understanding of genome organization and evolution in the most important temperate forage and turf grass species.

The Perennial Ryegrass GenomeZipper: Targeted Use of Genome Resources for Comparative Grass Genomics1[C][W

PubMed Central

Pfeifer, Matthias; Martis, Mihaela; Asp, Torben; Mayer, Klaus F.X.; Lübberstedt, Thomas; Byrne, Stephen; Frei, Ursula; Studer, Bruno

2013-01-01

Whole-genome sequences established for model and major crop species constitute a key resource for advanced genomic research. For outbreeding forage and turf grass species like ryegrasses (Lolium spp.), such resources have yet to be developed. Here, we present a model of the perennial ryegrass (Lolium perenne) genome on the basis of conserved synteny to barley (Hordeum vulgare) and the model grass genome Brachypodium (Brachypodium distachyon) as well as rice (Oryza sativa) and sorghum (Sorghum bicolor). A transcriptome-based genetic linkage map of perennial ryegrass served as a scaffold to establish the chromosomal arrangement of syntenic genes from model grass species. This scaffold revealed a high degree of synteny and macrocollinearity and was then utilized to anchor a collection of perennial ryegrass genes in silico to their predicted genome positions. This resulted in the unambiguous assignment of 3,315 out of 8,876 previously unmapped genes to the respective chromosomes. In total, the GenomeZipper incorporates 4,035 conserved grass gene loci, which were used for the first genome-wide sequence divergence analysis between perennial ryegrass, barley, Brachypodium, rice, and sorghum. The perennial ryegrass GenomeZipper is an ordered, information-rich genome scaffold, facilitating map-based cloning and genome assembly in perennial ryegrass and closely related Poaceae species. It also represents a milestone in describing synteny between perennial ryegrass and fully sequenced model grass genomes, thereby increasing our understanding of genome organization and evolution in the most important temperate forage and turf grass species. PMID:23184232

Comparative genomics of the bacterial genus Streptococcus illuminates evolutionary implications of species groups.

PubMed

Gao, Xiao-Yang; Zhi, Xiao-Yang; Li, Hong-Wei; Klenk, Hans-Peter; Li, Wen-Jun

2014-01-01

Members of the genus Streptococcus within the phylum Firmicutes are among the most diverse and significant zoonotic pathogens. This genus has gone through considerable taxonomic revision due to increasing improvements of chemotaxonomic approaches, DNA hybridization and 16S rRNA gene sequencing. It is proposed to place the majority of streptococci into "species groups". However, the evolutionary implications of species groups are not clear presently. We use comparative genomic approaches to yield a better understanding of the evolution of Streptococcus through genome dynamics, population structure, phylogenies and virulence factor distribution of species groups. Genome dynamics analyses indicate that the pan-genome size increases with the addition of newly sequenced strains, while the core genome size decreases with sequential addition at the genus level and species group level. Population structure analysis reveals two distinct lineages, one including Pyogenic, Bovis, Mutans and Salivarius groups, and the other including Mitis, Anginosus and Unknown groups. Phylogenetic dendrograms show that species within the same species group cluster together, and infer two main clades in accordance with population structure analysis. Distribution of streptococcal virulence factors has no obvious patterns among the species groups; however, the evolution of some common virulence factors is congruous with the evolution of species groups, according to phylogenetic inference. We suggest that the proposed streptococcal species groups are reasonable from the viewpoints of comparative genomics; evolution of the genus is congruent with the individual evolutionary trajectories of different species groups.

Comparative Genomics of the Bacterial Genus Streptococcus Illuminates Evolutionary Implications of Species Groups

PubMed Central

Gao, Xiao-Yang; Zhi, Xiao-Yang; Li, Hong-Wei; Klenk, Hans-Peter; Li, Wen-Jun

2014-01-01

Members of the genus Streptococcus within the phylum Firmicutes are among the most diverse and significant zoonotic pathogens. This genus has gone through considerable taxonomic revision due to increasing improvements of chemotaxonomic approaches, DNA hybridization and 16S rRNA gene sequencing. It is proposed to place the majority of streptococci into “species groups”. However, the evolutionary implications of species groups are not clear presently. We use comparative genomic approaches to yield a better understanding of the evolution of Streptococcus through genome dynamics, population structure, phylogenies and virulence factor distribution of species groups. Genome dynamics analyses indicate that the pan-genome size increases with the addition of newly sequenced strains, while the core genome size decreases with sequential addition at the genus level and species group level. Population structure analysis reveals two distinct lineages, one including Pyogenic, Bovis, Mutans and Salivarius groups, and the other including Mitis, Anginosus and Unknown groups. Phylogenetic dendrograms show that species within the same species group cluster together, and infer two main clades in accordance with population structure analysis. Distribution of streptococcal virulence factors has no obvious patterns among the species groups; however, the evolution of some common virulence factors is congruous with the evolution of species groups, according to phylogenetic inference. We suggest that the proposed streptococcal species groups are reasonable from the viewpoints of comparative genomics; evolution of the genus is congruent with the individual evolutionary trajectories of different species groups. PMID:24977706

Contrasting growth phenology of native and invasive forest shrubs mediated by genome size.

PubMed

Fridley, Jason D; Craddock, Alaä

2015-08-01

Examination of the significance of genome size to plant invasions has been largely restricted to its association with growth rate. We investigated the novel hypothesis that genome size is related to forest invasions through its association with growth phenology, as a result of the ability of large-genome species to grow more effectively through cell expansion at cool temperatures. We monitored the spring leaf phenology of 54 species of eastern USA deciduous forests, including native and invasive shrubs of six common genera. We used new measurements of genome size to evaluate its association with spring budbreak, cell size, summer leaf production rate, and photosynthetic capacity. In a phylogenetic hierarchical model that differentiated native and invasive species as a function of summer growth rate and spring budbreak timing, species with smaller genomes exhibited both faster growth and delayed budbreak compared with those with larger nuclear DNA content. Growth rate, but not budbreak timing, was associated with whether a species was native or invasive. Our results support genome size as a broad indicator of the growth behavior of woody species. Surprisingly, invaders of deciduous forests show the same small-genome tendencies of invaders of more open habitats, supporting genome size as a robust indicator of invasiveness. © 2015 The Authors. New Phytologist © 2015 New Phytologist Trust.

21 CFR 866.3010 - Acinetobacter calcoaceticus serological reagents.

Code of Federal Regulations, 2012 CFR

2012-04-01

... 21 Food and Drugs 8 2012-04-01 2012-04-01 false Acinetobacter calcoaceticus serological reagents. 866.3010 Section 866.3010 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Serological Reagents § 866.3010...

21 CFR 866.3010 - Acinetobacter calcoaceticus serological reagents.

Code of Federal Regulations, 2014 CFR

2014-04-01

... 21 Food and Drugs 8 2014-04-01 2014-04-01 false Acinetobacter calcoaceticus serological reagents. 866.3010 Section 866.3010 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Serological Reagents § 866.3010...

21 CFR 866.3010 - Acinetobacter calcoaceticus serological reagents.

Code of Federal Regulations, 2013 CFR

2013-04-01

... 21 Food and Drugs 8 2013-04-01 2013-04-01 false Acinetobacter calcoaceticus serological reagents. 866.3010 Section 866.3010 Food and Drugs FOOD AND DRUG ADMINISTRATION, DEPARTMENT OF HEALTH AND HUMAN SERVICES (CONTINUED) MEDICAL DEVICES IMMUNOLOGY AND MICROBIOLOGY DEVICES Serological Reagents § 866.3010...

Susceptibility of Acinetobacter Strains Isolated from Deployed U.S. Military Personnel▿

PubMed Central

Hawley, Joshua S.; Murray, Clinton K.; Griffith, Matthew E.; McElmeel, M. Leticia; Fulcher, Letitia C.; Hospenthal, Duane R.; Jorgensen, James H.

2007-01-01

The susceptibilities of 142 Acinetobacter baumannii-calcoaceticus complex isolates (95 from wounded U.S. soldiers deployed overseas) to 13 antimicrobial agents were determined by broth microdilution. The most active antimicrobial agents (≥95% of isolates susceptible) were colistin, polymyxin B, and minocycline. PMID:17043112

Transcriptionally active LTR retrotransposons in Eucalyptus genus are differentially expressed and insertionally polymorphic.

PubMed

Marcon, Helena Sanches; Domingues, Douglas Silva; Silva, Juliana Costa; Borges, Rafael Junqueira; Matioli, Fábio Filippi; Fontes, Marcos Roberto de Mattos; Marino, Celso Luis

2015-08-14

In Eucalyptus genus, studies on genome composition and transposable elements (TEs) are particularly scarce. Nearly half of the recently released Eucalyptus grandis genome is composed by retrotransposons and this data provides an important opportunity to understand TE dynamics in Eucalyptus genome and transcriptome. We characterized nine families of transcriptionally active LTR retrotransposons from Copia and Gypsy superfamilies in Eucalyptus grandis genome and we depicted genomic distribution and copy number in two Eucalyptus species. We also evaluated genomic polymorphism and transcriptional profile in three organs of five Eucalyptus species. We observed contrasting genomic and transcriptional behavior in the same family among different species. RLC_egMax_1 was the most prevalent family and RLC_egAngela_1 was the family with the lowest copy number. Most families of both superfamilies have their insertions occurring <3 million years, except one Copia family, RLC_egBianca_1. Protein theoretical models suggest different properties between Copia and Gypsy domains. IRAP and REMAP markers suggested genomic polymorphisms among Eucalyptus species. Using EST analysis and qRT-PCRs, we observed transcriptional activity in several tissues and in all evaluated species. In some families, osmotic stress increases transcript values. Our strategy was successful in isolating transcriptionally active retrotransposons in Eucalyptus, and each family has a particular genomic and transcriptional pattern. Overall, our results show that retrotransposon activity have differentially affected genome and transcriptome among Eucalyptus species.

Whole-genome sequencing of staphylococcus haemolyticus uncovers the extreme plasticity of its genome and the evolution of human-colonizing staphylococcal species.

PubMed

Takeuchi, Fumihiko; Watanabe, Shinya; Baba, Tadashi; Yuzawa, Harumi; Ito, Teruyo; Morimoto, Yuh; Kuroda, Makoto; Cui, Longzhu; Takahashi, Mikio; Ankai, Akiho; Baba, Shin-ichi; Fukui, Shigehiro; Lee, Jean C; Hiramatsu, Keiichi

2005-11-01

Staphylococcus haemolyticus is an opportunistic bacterial pathogen that colonizes human skin and is remarkable for its highly antibiotic-resistant phenotype. We determined the complete genome sequence of S.haemolyticus to better understand its pathogenicity and evolutionary relatedness to the other staphylococcal species. A large proportion of the open reading frames in the genomes of S.haemolyticus, Staphylococcus aureus, and Staphylococcus epidermidis were conserved in their sequence and order on the chromosome. We identified a region of the bacterial chromosome just downstream of the origin of replication that showed little homology among the species but was conserved among strains within a species. This novel region, designated the "oriC environ," likely contributes to the evolution and differentiation of the staphylococcal species, since it was enriched for species-specific nonessential genes that contribute to the biological features of each staphylococcal species. A comparative analysis of the genomes of S.haemolyticus, S.aureus, and S.epidermidis elucidated differences in their biological and genetic characteristics and pathogenic potentials. We identified as many as 82 insertion sequences in the S.haemolyticus chromosome that probably mediated frequent genomic rearrangements, resulting in phenotypic diversification of the strain. Such rearrangements could have brought genomic plasticity to this species and contributed to its acquisition of antibiotic resistance.

Transposable element junctions in marker development and genomic characterization of barley

USDA-ARS?s Scientific Manuscript database

Barley is a model plant in genomic studies of Triticeae species. A complete barley genome sequence will facilitate not only barley breeding programs, but also those for related species. However, the large genome size and high repetitive sequence content complicate the barley genome assembly. The ma...

Multiplex Polymerase Chain Reaction for Identification of Shigellae and Four Shigella Species Using Novel Genetic Markers Screened by Comparative Genomics.

PubMed

Kim, Hyun-Joong; Ryu, Ji-Oh; Song, Ji-Yeon; Kim, Hae-Yeong

2017-07-01

In the detection of Shigella species using molecular biological methods, previously known genetic markers for Shigella species were not sufficient to discriminate between Shigella species and diarrheagenic Escherichia coli. The purposes of this study were to screen for genetic markers of the Shigella genus and four Shigella species through comparative genomics and develop a multiplex polymerase chain reaction (PCR) for the detection of shigellae and Shigella species. A total of seven genomic DNA sequences from Shigella species were subjected to comparative genomics for the screening of genetic markers of shigellae and each Shigella species. The primer sets were designed from the screened genetic markers and evaluated using PCR with genomic DNAs from Shigella and other bacterial strains in Enterobacteriaceae. A novel Shigella quintuplex PCR, designed for the detection of Shigella genus, S. dysenteriae, S. boydii, S. flexneri, and S. sonnei, was developed from the evaluated primer sets, and its performance was demonstrated with specifically amplified results from each Shigella species. This Shigella multiplex PCR is the first to be reported with novel genetic markers developed through comparative genomics and may be a useful tool for the accurate detection of the Shigella genus and species from closely related bacteria in clinical microbiology and food safety.

Comparative genome-wide analysis reveals that Burkholderia contaminans MS14 possesses multiple antimicrobial biosynthesis genes but not major genetic loci required for pathogenesis.

PubMed

Deng, Peng; Wang, Xiaoqiang; Baird, Sonya M; Showmaker, Kurt C; Smith, Leif; Peterson, Daniel G; Lu, Shien

2016-06-01

Burkholderia contaminans MS14 shows significant antimicrobial activities against plant and animal pathogenic fungi and bacteria. The antifungal agent occidiofungin produced by MS14 has great potential for development of biopesticides and pharmaceutical drugs. However, the use of Burkholderia species as biocontrol agent in agriculture is restricted due to the difficulties in distinguishing between plant growth-promoting bacteria and the pathogenic bacteria. The complete MS14 genome was sequenced and analyzed to find what beneficial and virulence-related genes it harbors. The phylogenetic relatedness of B. contaminans MS14 and other 17 Burkholderia species was also analyzed. To research MS14's potential virulence, the gene regions related to the antibiotic production, antibiotic resistance, and virulence were compared between MS14 and other Burkholderia genomes. The genome of B. contaminans MS14 was sequenced and annotated. The genomic analyses reveal the presence of multiple gene sets for antimicrobial biosynthesis, which contribute to its antimicrobial activities. BLAST results indicate that the MS14 genome harbors a large number of unique regions. MS14 is closely related to another plant growth-promoting Burkholderia strain B. lata 383 according to the average nucleotide identity data. Moreover, according to the phylogenetic analysis, plant growth-promoting species isolated from soils and mammalian pathogenic species are clustered together, respectively. MS14 has multiple antimicrobial activity-related genes identified from the genome, but it lacks key virulence-related gene loci found in the pathogenic strains. Additionally, plant growth-promoting Burkholderia species have one or more antimicrobial biosynthesis genes in their genomes as compared with nonplant growth-promoting soil-isolated Burkholderia species. On the other hand, pathogenic species harbor multiple virulence-associated gene loci that are not present in nonpathogenic Burkholderia species. The MS14 genome as well as Burkholderia species genome show considerable diversity. Multiple antimicrobial agent biosynthesis genes were identified in the genome of plant growth-promoting species of Burkholderia. In addition, by comparing to nonpathogenic Burkholderia species, pathogenic Burkholderia species have more characterized homologs of the gene loci known to contribute to pathogenicity and virulence to plant and animals. © 2016 The Authors. MicrobiologyOpen published by John Wiley & Sons Ltd.

Nutritional Requirements of Acinetobacter Strains Isolated from Soil, Water, and Sewage

PubMed Central

Warskow, Alice L.; Juni, Elliot

1972-01-01

One hundred five strains of Acinetobacter were isolated from water, soil, and sewage on nonselective complex media, and their nutritional properties were studied. Only one of these strains requires growth factors in order to grow in a mineral medium containing a single carbon source. PMID:4563966

Novel Strategy to Control the Warfighter’s Exposure to Polymicrobial Environments

DTIC Science & Technology

2015-09-30

RELEASE 13. SUPPLEMENTARY NOTES 14. ABSTRACT Bacteriocins active against clinically-relevant Pseudomonas aeruginosa, Staphylococcus aureus ...SUBJECT TERMS Bacteriocins, Antimicrobials, Pseudomonas aeruginosa, Staphylococcus aureus , Acinetobacter baumanii, Bacillus cereus 16. SECURITY...Pseudomonas aeruginosa, Staphylococcus aureus , Acinetobacter baumanni and Bacillus cereus (target pathogens for the proposed research). Summary

Kisameet Clay Exhibits Potent Antibacterial Activity against the ESKAPE Pathogens

PubMed Central

Behroozian, Shekooh; Svensson, Sarah L.

2016-01-01

ABSTRACT The ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) pathogens cause an increasing number of nosocomial infections worldwide since they escape the inhibitory effect of the available antibiotics and the immune response. Here, we report the broad-spectrum and potent antibacterial activity of Kisameet clay, a natural clay mineral from British Columbia, Canada, against a group of multidrug-resistant ESKAPE strains. The results suggest that this natural clay might be developed as a therapeutic option for the treatment of serious infections caused by these important pathogens. PMID:26814180

Novel Insights into Tree Biology and Genome Evolution as Revealed Through Genomics.

PubMed

Neale, David B; Martínez-García, Pedro J; De La Torre, Amanda R; Montanari, Sara; Wei, Xiao-Xin

2017-04-28

Reference genome sequences are the key to the discovery of genes and gene families that determine traits of interest. Recent progress in sequencing technologies has enabled a rapid increase in genome sequencing of tree species, allowing the dissection of complex characters of economic importance, such as fruit and wood quality and resistance to biotic and abiotic stresses. Although the number of reference genome sequences for trees lags behind those for other plant species, it is not too early to gain insight into the unique features that distinguish trees from nontree plants. Our review of the published data suggests that, although many gene families are conserved among herbaceous and tree species, some gene families, such as those involved in resistance to biotic and abiotic stresses and in the synthesis and transport of sugars, are often expanded in tree genomes. As the genomes of more tree species are sequenced, comparative genomics will further elucidate the complexity of tree genomes and how this relates to traits unique to trees.

Entire nucleotide sequences of Gossypium raimondii and G. arboreum mitochondrial genomes revealed A-genome species as cytoplasmic donor of the allotetraploid species.

PubMed

Chen, Z; Nie, H; Grover, C E; Wang, Y; Li, P; Wang, M; Pei, H; Zhao, Y; Li, S; Wendel, J F; Hua, J

2017-05-01

Cotton (Gossypium spp.) is commonly grouped into eight diploid genomic groups, designated A-G and K, and an allotetraploid genomic group, AD. Gossypium raimondii (D 5 ) and G. arboreum (A 2 ) are the putative contributors to the progenitor of G. hirsutum (AD 1 ), the economically important fibre-producing cotton species. Mitochondrial DNA from week-old etiolated seedlings was extracted from isolated organelles using discontinuous sucrose density gradient method. Mitochondrial genomes were sequenced, assembled, annotated and analysed in orderly. Gossypium raimondii (D 5 ) and G. arboreum (A 2 ) mitochondrial genomes were provided in this study. The mitochondrial genomes of two diploid species harboured circular genome of 643,914 bp (D 5 ) and 687,482 bp (A 2 ), respectively. They differ in size and number of repeat sequences, both contain illuminating triplicate sequences with 7317 and 10,246 bp, respectively, demonstrating dynamic difference and rearranged genome organisations. Comparing the D 5 and A 2 mitogenomes with mitogenomes of tetraploid Gossypium species (AD 1 , G. hirsutum; AD 2 , G. barbadense), a shared 11 kbp fragment loss was detected in allotetraploid species, three regions shared by G. arboreum (A 2 ), G. hirsutum (AD 1 ) and G. barbadense (AD 2 ), while eight regions were specific to G. raimondii (D 5 ). The presence/absence variations and gene-based phylogeny supported that A-genome is a cytoplasmic donor to the progenitor of allotetraploid species G. hirsutum and G. barbadense. The results present structure variations and phylogeny of Gossypium mitochondrial genome evolution. © 2017 The Authors. Plant Biology published by John Wiley & Sons Ltd on behalf of German Botanical Society, Royal Dutch Botanical Society.

Complete mitochondrial genome of the aluminum-tolerant fungus Rhodotorula taiwanensis RS1 and comparative analysis of Basidiomycota mitochondrial genomes

PubMed Central

Zhao, Xue Qiang; Aizawa, Tomoko; Schneider, Jessica; Wang, Chao; Shen, Ren Fang; Sunairi, Michio

2013-01-01

The complete mitochondrial genome of Rhodotorula taiwanensis RS1, an aluminum-tolerant Basidiomycota fungus, was determined and compared with the known mitochondrial genomes of 12 Basidiomycota species. The mitochondrial genome of R. taiwanensis RS1 is a circular DNA molecule of 40,392 bp and encodes the typical 15 mitochondrial proteins, 23 tRNAs, and small and large rRNAs as well as 10 intronic open reading frames. These genes are apparently transcribed in two directions and do not show syntenies in gene order with other investigated Basidiomycota species. The average G+C content (41%) of the mitochondrial genome of R. taiwanensis RS1 is the highest among the Basidiomycota species. Two introns were detected in the sequence of the atp9 gene of R. taiwanensis RS1, but not in that of other Basidiomycota species. Rhodotorula taiwanensis is the first species of the genus Rhodotorula whose full mitochondrial genome has been sequenced; and the data presented here supply valuable information for understanding the evolution of fungal mitochondrial genomes and researching the mechanism of aluminum tolerance in microorganisms. PMID:23427135

High-density marker profiling confirms ancestral genomes of Avena species and identifies D-genome chromosomes of hexaploid oat.

PubMed

Yan, Honghai; Bekele, Wubishet A; Wight, Charlene P; Peng, Yuanying; Langdon, Tim; Latta, Robert G; Fu, Yong-Bi; Diederichsen, Axel; Howarth, Catherine J; Jellen, Eric N; Boyle, Brian; Wei, Yuming; Tinker, Nicholas A

2016-11-01

Genome analysis of 27 oat species identifies ancestral groups, delineates the D genome, and identifies ancestral origin of 21 mapped chromosomes in hexaploid oat. We investigated genomic relationships among 27 species of the genus Avena using high-density genetic markers revealed by genotyping-by-sequencing (GBS). Two methods of GBS analysis were used: one based on tag-level haplotypes that were previously mapped in cultivated hexaploid oat (A. sativa), and one intended to sample and enumerate tag-level haplotypes originating from all species under investigation. Qualitatively, both methods gave similar predictions regarding the clustering of species and shared ancestral genomes. Furthermore, results were consistent with previous phylogenies of the genus obtained with conventional approaches, supporting the robustness of whole genome GBS analysis. Evidence is presented to justify the final and definitive classification of the tetraploids A. insularis, A. maroccana (=A. magna), and A. murphyi as containing D-plus-C genomes, and not A-plus-C genomes, as is most often specified in past literature. Through electronic painting of the 21 chromosome representations in the hexaploid oat consensus map, we show how the relative frequency of matches between mapped hexaploid-derived haplotypes and AC (DC)-genome tetraploids vs. A- and C-genome diploids can accurately reveal the genome origin of all hexaploid chromosomes, including the approximate positions of inter-genome translocations. Evidence is provided that supports the continued classification of a diverged B genome in AB tetraploids, and it is confirmed that no extant A-genome diploids, including A. canariensis, are similar enough to the D genome of tetraploid and hexaploid oat to warrant consideration as a D-genome diploid.

The complete chloroplast genome sequence of Aconitum coreanum and Aconitum carmichaelii and comparative analysis with other Aconitum species

PubMed Central

Park, Inkyu; Kim, Wook-jin; Yang, Sungyu; Yeo, Sang-Min; Li, Hulin

2017-01-01

Aconitum species (belonging to the Ranunculaceae) are well known herbaceous medicinal ingredients and have great economic value in Asian countries. However, there are still limited genomic resources available for Aconitum species. In this study, we sequenced the chloroplast (cp) genomes of two Aconitum species, A. coreanum and A. carmichaelii, using the MiSeq platform. The two Aconitum chloroplast genomes were 155,880 and 157,040 bp in length, respectively, and exhibited LSC and SSC regions separated by a pair of inverted repeat regions. Both cp genomes had 38% GC content and contained 131 unique functional genes including 86 protein-coding genes, eight ribosomal RNA genes, and 37 transfer RNA genes. The gene order, content, and orientation of the two Aconitum cp genomes exhibited the general structure of angiosperms, and were similar to those of other Aconitum species. Comparison of the cp genome structure and gene order with that of other Aconitum species revealed general contraction and expansion of the inverted repeat regions and single copy boundary regions. Divergent regions were also identified. In phylogenetic analysis, Aconitum species positon among the Ranunculaceae was determined with other family cp genomes in the Ranunculales. We obtained a barcoding target sequence in a divergent region, ndhC–trnV, and successfully developed a SCAR (sequence characterized amplified region) marker for discrimination of A. coreanum. Our results provide useful genetic information and a specific barcode for discrimination of Aconitum species. PMID:28863163

The complete chloroplast genome sequence of Aconitum coreanum and Aconitum carmichaelii and comparative analysis with other Aconitum species.

PubMed

Park, Inkyu; Kim, Wook-Jin; Yang, Sungyu; Yeo, Sang-Min; Li, Hulin; Moon, Byeong Cheol

2017-01-01

Aconitum species (belonging to the Ranunculaceae) are well known herbaceous medicinal ingredients and have great economic value in Asian countries. However, there are still limited genomic resources available for Aconitum species. In this study, we sequenced the chloroplast (cp) genomes of two Aconitum species, A. coreanum and A. carmichaelii, using the MiSeq platform. The two Aconitum chloroplast genomes were 155,880 and 157,040 bp in length, respectively, and exhibited LSC and SSC regions separated by a pair of inverted repeat regions. Both cp genomes had 38% GC content and contained 131 unique functional genes including 86 protein-coding genes, eight ribosomal RNA genes, and 37 transfer RNA genes. The gene order, content, and orientation of the two Aconitum cp genomes exhibited the general structure of angiosperms, and were similar to those of other Aconitum species. Comparison of the cp genome structure and gene order with that of other Aconitum species revealed general contraction and expansion of the inverted repeat regions and single copy boundary regions. Divergent regions were also identified. In phylogenetic analysis, Aconitum species positon among the Ranunculaceae was determined with other family cp genomes in the Ranunculales. We obtained a barcoding target sequence in a divergent region, ndhC-trnV, and successfully developed a SCAR (sequence characterized amplified region) marker for discrimination of A. coreanum. Our results provide useful genetic information and a specific barcode for discrimination of Aconitum species.

Sequencing Needs for Viral Diagnostics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gardner, S N; Lam, M; Mulakken, N J

2004-01-26

We built a system to guide decisions regarding the amount of genomic sequencing required to develop diagnostic DNA signatures, which are short sequences that are sufficient to uniquely identify a viral species. We used our existing DNA diagnostic signature prediction pipeline, which selects regions of a target species genome that are conserved among strains of the target (for reliability, to prevent false negatives) and unique relative to other species (for specificity, to avoid false positives). We performed simulations, based on existing sequence data, to assess the number of genome sequences of a target species and of close phylogenetic relatives (''nearmore » neighbors'') that are required to predict diagnostic signature regions that are conserved among strains of the target species and unique relative to other bacterial and viral species. For DNA viruses such as variola (smallpox), three target genomes provide sufficient guidance for selecting species-wide signatures. Three near neighbor genomes are critical for species specificity. In contrast, most RNA viruses require four target genomes and no near neighbor genomes, since lack of conservation among strains is more limiting than uniqueness. SARS and Ebola Zaire are exceptional, as additional target genomes currently do not improve predictions, but near neighbor sequences are urgently needed. Our results also indicate that double stranded DNA viruses are more conserved among strains than are RNA viruses, since in most cases there was at least one conserved signature candidate for the DNA viruses and zero conserved signature candidates for the RNA viruses.« less

Comparative Transcriptomics of Strawberries (Fragaria spp.) Provides Insights into Evolutionary Patterns

PubMed Central

Qiao, Qin; Xue, Li; Wang, Qia; Sun, Hang; Zhong, Yang; Huang, Jinling; Lei, Jiajun; Zhang, Ticao

2016-01-01

Multiple closely related species with genomic sequences provide an ideal system for studies on comparative and evolutionary genomics, as well as the mechanism of speciation. The whole genome sequences of six strawberry species (Fragaria spp.) have been released, which provide one of the richest genomic resources of any plant genus. In this study, we first generated seven transcriptome sequences of Fragaria species de novo, with a total of 48,557–82,537 unigenes per species. Combined with 13 other species genomes in Rosales, we reconstructed a phylogenetic tree at the genomic level. The phylogenic tree shows that Fragaria closed grouped with Rubus and the Fragaria clade is divided into three subclades. East Asian species appeared in every subclade, suggesting that the genus originated in this area at ∼7.99 Mya. Four species found in mountains of Southwest China originated at ∼3.98 Mya, suggesting that rapid speciation occurred to adapt to changing environments following the uplift of the Qinghai–Tibet Plateau. Moreover, we identified 510 very significantly positively selected genes in the cultivated species F. × ananassa genome. This set of genes was enriched in functions related to specific agronomic traits, such as carbon metabolism and plant hormone signal transduction processes, which are directly related to fruit quality and flavor. These findings illustrate comprehensive evolutionary patterns in Fragaria and the genetic basis of fruit domestication of cultivated strawberry at the genomic/transcriptomic level. PMID:28018379

Genome size and chromosome number in velvet worms (Onychophora).

PubMed

Jeffery, Nicholas W; Oliveira, Ivo S; Gregory, T Ryan; Rowell, David M; Mayer, Georg

2012-12-01

The Onychophora (velvet worms) represents a small group of invertebrates (~180 valid species), which is commonly united with Tardigrada and Arthropoda in a clade called Panarthropoda. As with the majority of invertebrate taxa, genome size data are very limited for the Onychophora, with only one previously published estimate. Here we use both flow cytometry and Feulgen image analysis densitometry to provide genome size estimates for seven species of velvet worms from both major subgroups, Peripatidae and Peripatopsidae, along with karyotype data for each species. Genome sizes in these species range from roughly 5-19 pg, with densitometric estimates being slightly larger than those obtained by flow cytometry for all species. Chromosome numbers range from 2n = 8 to 2n = 54. No relationship is evident between genome size, chromosome number, or reproductive mode. Various avenues for future genomic research are presented based on these results.

Complete nucleotide sequence of the Cryptomeria japonica D. Don. chloroplast genome and comparative chloroplast genomics: diversified genomic structure of coniferous species.

PubMed

Hirao, Tomonori; Watanabe, Atsushi; Kurita, Manabu; Kondo, Teiji; Takata, Katsuhiko

2008-06-23

The recent determination of complete chloroplast (cp) genomic sequences of various plant species has enabled numerous comparative analyses as well as advances in plant and genome evolutionary studies. In angiosperms, the complete cp genome sequences of about 70 species have been determined, whereas those of only three gymnosperm species, Cycas taitungensis, Pinus thunbergii, and Pinus koraiensis have been established. The lack of information regarding the gene content and genomic structure of gymnosperm cp genomes may severely hamper further progress of plant and cp genome evolutionary studies. To address this need, we report here the complete nucleotide sequence of the cp genome of Cryptomeria japonica, the first in the Cupressaceae sensu lato of gymnosperms, and provide a comparative analysis of their gene content and genomic structure that illustrates the unique genomic features of gymnosperms. The C. japonica cp genome is 131,810 bp in length, with 112 single copy genes and two duplicated (trnI-CAU, trnQ-UUG) genes that give a total of 116 genes. Compared to other land plant cp genomes, the C. japonica cp has lost one of the relevant large inverted repeats (IRs) found in angiosperms, fern, liverwort, and gymnosperms, such as Cycas and Gingko, and additionally has completely lost its trnR-CCG, partially lost its trnT-GGU, and shows diversification of accD. The genomic structure of the C. japonica cp genome also differs significantly from those of other plant species. For example, we estimate that a minimum of 15 inversions would be required to transform the gene organization of the Pinus thunbergii cp genome into that of C. japonica. In the C. japonica cp genome, direct repeat and inverted repeat sequences are observed at the inversion and translocation endpoints, and these sequences may be associated with the genomic rearrangements. The observed differences in genomic structure between C. japonica and other land plants, including pines, strongly support the theory that the large IRs stabilize the cp genome. Furthermore, the deleted large IR and the numerous genomic rearrangements that have occurred in the C. japonica cp genome provide new insights into both the evolutionary lineage of coniferous species in gymnosperm and the evolution of the cp genome.

Preliminary Genomic Characterization of Ten Hardwood Tree Species from Multiplexed Low Coverage Whole Genome Sequencing

PubMed Central

Staton, Margaret; Best, Teodora; Khodwekar, Sudhir; Owusu, Sandra; Xu, Tao; Xu, Yi; Jennings, Tara; Cronn, Richard; Arumuganathan, A. Kathiravetpilla; Coggeshall, Mark; Gailing, Oliver; Liang, Haiying; Romero-Severson, Jeanne; Schlarbaum, Scott; Carlson, John E.

2015-01-01

Forest health issues are on the rise in the United States, resulting from introduction of alien pests and diseases, coupled with abiotic stresses related to climate change. Increasingly, forest scientists are finding genetic/genomic resources valuable in addressing forest health issues. For a set of ten ecologically and economically important native hardwood tree species representing a broad phylogenetic spectrum, we used low coverage whole genome sequencing from multiplex Illumina paired ends to economically profile their genomic content. For six species, the genome content was further analyzed by flow cytometry in order to determine the nuclear genome size. Sequencing yielded a depth of 0.8X to 7.5X, from which in silico analysis yielded preliminary estimates of gene and repetitive sequence content in the genome for each species. Thousands of genomic SSRs were identified, with a clear predisposition toward dinucleotide repeats and AT-rich repeat motifs. Flanking primers were designed for SSR loci for all ten species, ranging from 891 loci in sugar maple to 18,167 in redbay. In summary, we have demonstrated that useful preliminary genome information including repeat content, gene content and useful SSR markers can be obtained at low cost and time input from a single lane of Illumina multiplex sequence. PMID:26698853

Genome differentiation in a species pair of coregonine fishes: an extremely rapid speciation driven by stress-activated retrotransposons mediating extensive ribosomal DNA multiplications

PubMed Central

2013-01-01

Background Sympatric species pairs are particularly common in freshwater fishes associated with postglacial lakes in northern temperate environments. The nature of divergences between co-occurring sympatric species, factors contributing to reproductive isolation and modes of genome evolution is a much debated topic in evolutionary biology addressed by various experimental tools. To the best of our knowledge, nobody approached this field using molecular cytogenetics. We examined chromosomes and genomes of one postglacial species pair, sympatric European winter-spawning Coregonus albula and the local endemic dwarf-sized spring-spawning C. fontanae, both originating in Lake Stechlin. We have employed molecular cytogenetic tools to identify the genomic differences between the two species of the sympatric pair on the sub-chromosomal level of resolution. Results Fluorescence in situ hybridization (FISH) experiments consistently revealed a distinct variation in the copy number of loci of the major ribosomal DNA (the 45S unit) between C. albula and C. fontanae genomes. In C. fontanae, up to 40 chromosomes were identified to bear a part of the major ribosomal DNA, while in C. albula only 8–10 chromosomes possessed these genes. To determine mechanisms how such extensive genome alternation might have arisen, a PCR screening for retrotransposons from genomic DNA of both species was performed. The amplified retrotransposon Rex1 was used as a probe for FISH mapping onto chromosomes of both species. These experiments showed a clear co-localization of the ribosomal DNA and the retrotransposon Rex1 in a pericentromeric region of one or two acrocentric chromosomes in both species. Conclusion We demonstrated genomic consequences of a rapid ecological speciation on the level undetectable by neither sequence nor karyotype analysis. We provide indirect evidence that ribosomal DNA probably utilized the spreading mechanism of retrotransposons subsequently affecting recombination rates in both genomes, thus, leading to a rapid genome divergence. We attribute these extensive genome re-arrangements associated with speciation event to stress-induced retrotransposons (re)activation. Such causal interplay between genome differentiation, retrotransposons (re)activation and environmental conditions may become a topic to be explored in a broader genomic context in future evolutionary studies. PMID:23410024

Construction and sequence sampling of deep-coverage, large-insert BAC libraries for three model lepidopteran species

PubMed Central

Wu, Chengcang; Proestou, Dina; Carter, Dorothy; Nicholson, Erica; Santos, Filippe; Zhao, Shaying; Zhang, Hong-Bin; Goldsmith, Marian R

2009-01-01

Background Manduca sexta, Heliothis virescens, and Heliconius erato represent three widely-used insect model species for genomic and fundamental studies in Lepidoptera. Large-insert BAC libraries of these insects are critical resources for many molecular studies, including physical mapping and genome sequencing, but not available to date. Results We report the construction and characterization of six large-insert BAC libraries for the three species and sampling sequence analysis of the genomes. The six BAC libraries were constructed with two restriction enzymes, two libraries for each species, and each has an average clone insert size ranging from 152–175 kb. We estimated that the genome coverage of each library ranged from 6–9 ×, with the two combined libraries of each species being equivalent to 13.0–16.3 × haploid genomes. The genome coverage, quality and utility of the libraries were further confirmed by library screening using 6~8 putative single-copy probes. To provide a first glimpse into these genomes, we sequenced and analyzed the BAC ends of ~200 clones randomly selected from the libraries of each species. The data revealed that the genomes are AT-rich, contain relatively small fractions of repeat elements with a majority belonging to the category of low complexity repeats, and are more abundant in retro-elements than DNA transposons. Among the species, the H. erato genome is somewhat more abundant in repeat elements and simple repeats than those of M. sexta and H. virescens. The BLAST analysis of the BAC end sequences suggested that the evolution of the three genomes is widely varied, with the genome of H. virescens being the most conserved as a typical lepidopteran, whereas both genomes of H. erato and M. sexta appear to have evolved significantly, resulting in a higher level of species- or evolutionary lineage-specific sequences. Conclusion The high-quality and large-insert BAC libraries of the insects, together with the identified BACs containing genes of interest, provide valuable information, resources and tools for comprehensive understanding and studies of the insect genomes and for addressing many fundamental questions in Lepidoptera. The sample of the genomic sequences provides the first insight into the constitution and evolution of the insect genomes. PMID:19558662

Comparative Chloroplast Genomics of Gossypium Species: Insights Into Repeat Sequence Variations and Phylogeny

PubMed Central

Wu, Ying; Liu, Fang; Yang, Dai-Gang; Li, Wei; Zhou, Xiao-Jian; Pei, Xiao-Yu; Liu, Yan-Gai; He, Kun-Lun; Zhang, Wen-Sheng; Ren, Zhong-Ying; Zhou, Ke-Hai; Ma, Xiong-Feng; Li, Zhong-Hu

2018-01-01

Cotton is one of the most economically important fiber crop plants worldwide. The genus Gossypium contains a single allotetraploid group (AD) and eight diploid genome groups (A–G and K). However, the evolution of repeat sequences in the chloroplast genomes and the phylogenetic relationships of Gossypium species are unclear. Thus, we determined the variations in the repeat sequences and the evolutionary relationships of 40 cotton chloroplast genomes, which represented the most diverse in the genus, including five newly sequenced diploid species, i.e., G. nandewarense (C1-n), G. armourianum (D2-1), G. lobatum (D7), G. trilobum (D8), and G. schwendimanii (D11), and an important semi-wild race of upland cotton, G. hirsutum race latifolium (AD1). The genome structure, gene order, and GC content of cotton species were similar to those of other higher plant plastid genomes. In total, 2860 long sequence repeats (>10 bp in length) were identified, where the F-genome species had the largest number of repeats (G. longicalyx F1: 108) and E-genome species had the lowest (G. stocksii E1: 53). Large-scale repeat sequences possibly enrich the genetic information and maintain genome stability in cotton species. We also identified 10 divergence hotspot regions, i.e., rpl33-rps18, psbZ-trnG (GCC), rps4-trnT (UGU), trnL (UAG)-rpl32, trnE (UUC)-trnT (GGU), atpE, ndhI, rps2, ycf1, and ndhF, which could be useful molecular genetic markers for future population genetics and phylogenetic studies. Site-specific selection analysis showed that some of the coding sites of 10 chloroplast genes (atpB, atpE, rps2, rps3, petB, petD, ccsA, cemA, ycf1, and rbcL) were under protein sequence evolution. Phylogenetic analysis based on the whole plastomes suggested that the Gossypium species grouped into six previously identified genetic clades. Interestingly, all 13 D-genome species clustered into a strong monophyletic clade. Unexpectedly, the cotton species with C, G, and K-genomes were admixed and nested in a large clade, which could have been due to their recent radiation, incomplete lineage sorting, and introgression hybridization among different cotton lineages. In conclusion, the results of this study provide new insights into the evolution of repeat sequences in chloroplast genomes and interspecific relationships in the genus Gossypium. PMID:29619041

Clustering of Pan- and Core-genome of Lactobacillus provides Novel Evolutionary Insights for Differentiation.

PubMed

Inglin, Raffael C; Meile, Leo; Stevens, Marc J A

2018-04-24

Bacterial taxonomy aims to classify bacteria based on true evolutionary events and relies on a polyphasic approach that includes phenotypic, genotypic and chemotaxonomic analyses. Until now, complete genomes are largely ignored in taxonomy. The genus Lactobacillus consists of 173 species and many genomes are available to study taxonomy and evolutionary events. We analyzed and clustered 98 completely sequenced genomes of the genus Lactobacillus and 234 draft genomes of 5 different Lactobacillus species, i.e. L. reuteri, L. delbrueckii, L. plantarum, L. rhamnosus and L. helveticus. The core-genome of the genus Lactobacillus contains 266 genes and the pan-genome 20'800 genes. Clustering of the Lactobacillus pan- and core-genome resulted in two highly similar trees. This shows that evolutionary history is traceable in the core-genome and that clustering of the core-genome is sufficient to explore relationships. Clustering of core- and pan-genomes at species' level resulted in similar trees as well. Detailed analyses of the core-genomes showed that the functional class "genetic information processing" is conserved in the core-genome but that "signaling and cellular processes" is not. The latter class encodes functions that are involved in environmental interactions. Evolution of lactobacilli seems therefore directed by the environment. The type species L. delbrueckii was analyzed in detail and its pan-genome based tree contained two major clades whose members contained different genes yet identical functions. In addition, evidence for horizontal gene transfer between strains of L. delbrueckii, L. plantarum, and L. rhamnosus, and between species of the genus Lactobacillus is presented. Our data provide evidence for evolution of some lactobacilli according to a parapatric-like model for species differentiation. Core-genome trees are useful to detect evolutionary relationships in lactobacilli and might be useful in taxonomic analyses. Lactobacillus' evolution is directed by the environment and HGT.

Integrating Genomic Data Sets for Knowledge Discovery: An Informed Approach to Management of Captive Endangered Species.

PubMed

Irizarry, Kristopher J L; Bryant, Doug; Kalish, Jordan; Eng, Curtis; Schmidt, Peggy L; Barrett, Gini; Barr, Margaret C

2016-01-01

Many endangered captive populations exhibit reduced genetic diversity resulting in health issues that impact reproductive fitness and quality of life. Numerous cost effective genomic sequencing and genotyping technologies provide unparalleled opportunity for incorporating genomics knowledge in management of endangered species. Genomic data, such as sequence data, transcriptome data, and genotyping data, provide critical information about a captive population that, when leveraged correctly, can be utilized to maximize population genetic variation while simultaneously reducing unintended introduction or propagation of undesirable phenotypes. Current approaches aimed at managing endangered captive populations utilize species survival plans (SSPs) that rely upon mean kinship estimates to maximize genetic diversity while simultaneously avoiding artificial selection in the breeding program. However, as genomic resources increase for each endangered species, the potential knowledge available for management also increases. Unlike model organisms in which considerable scientific resources are used to experimentally validate genotype-phenotype relationships, endangered species typically lack the necessary sample sizes and economic resources required for such studies. Even so, in the absence of experimentally verified genetic discoveries, genomics data still provides value. In fact, bioinformatics and comparative genomics approaches offer mechanisms for translating these raw genomics data sets into integrated knowledge that enable an informed approach to endangered species management.

Integrating Genomic Data Sets for Knowledge Discovery: An Informed Approach to Management of Captive Endangered Species

PubMed Central

Irizarry, Kristopher J. L.; Bryant, Doug; Kalish, Jordan; Eng, Curtis; Schmidt, Peggy L.; Barrett, Gini; Barr, Margaret C.

2016-01-01

Many endangered captive populations exhibit reduced genetic diversity resulting in health issues that impact reproductive fitness and quality of life. Numerous cost effective genomic sequencing and genotyping technologies provide unparalleled opportunity for incorporating genomics knowledge in management of endangered species. Genomic data, such as sequence data, transcriptome data, and genotyping data, provide critical information about a captive population that, when leveraged correctly, can be utilized to maximize population genetic variation while simultaneously reducing unintended introduction or propagation of undesirable phenotypes. Current approaches aimed at managing endangered captive populations utilize species survival plans (SSPs) that rely upon mean kinship estimates to maximize genetic diversity while simultaneously avoiding artificial selection in the breeding program. However, as genomic resources increase for each endangered species, the potential knowledge available for management also increases. Unlike model organisms in which considerable scientific resources are used to experimentally validate genotype-phenotype relationships, endangered species typically lack the necessary sample sizes and economic resources required for such studies. Even so, in the absence of experimentally verified genetic discoveries, genomics data still provides value. In fact, bioinformatics and comparative genomics approaches offer mechanisms for translating these raw genomics data sets into integrated knowledge that enable an informed approach to endangered species management. PMID:27376076

Mycobacterial species as case-study of comparative genome analysis.

PubMed

Zakham, F; Belayachi, L; Ussery, D; Akrim, M; Benjouad, A; El Aouad, R; Ennaji, M M

2011-02-08

The genus Mycobacterium represents more than 120 species including important pathogens of human and cause major public health problems and illnesses. Further, with more than 100 genome sequences from this genus, comparative genome analysis can provide new insights for better understanding the evolutionary events of these species and improving drugs, vaccines, and diagnostics tools for controlling Mycobacterial diseases. In this present study we aim to outline a comparative genome analysis of fourteen Mycobacterial genomes: M. avium subsp. paratuberculosis K—10, M. bovis AF2122/97, M. bovis BCG str. Pasteur 1173P2, M. leprae Br4923, M. marinum M, M. sp. KMS, M. sp. MCS, M. tuberculosis CDC1551, M. tuberculosis F11, M. tuberculosis H37Ra, M. tuberculosis H37Rv, M. tuberculosis KZN 1435 , M. ulcerans Agy99,and M. vanbaalenii PYR—1, For this purpose a comparison has been done based on their length of genomes, GC content, number of genes in different data bases (Genbank, Refseq, and Prodigal). The BLAST matrix of these genomes has been figured to give a lot of information about the similarity between species in a simple scheme. As a result of multiple genome analysis, the pan and core genome have been defined for twelve Mycobacterial species. We have also introduced the genome atlas of the reference strain M. tuberculosis H37Rv which can give a good overview of this genome. And for examining the phylogenetic relationships among these bacteria, a phylogenic tree has been constructed from 16S rRNA gene for tuberculosis and non tuberculosis Mycobacteria to understand the evolutionary events of these species.

Genome-wide analysis of LTR-retrotransposon diversity and its impact on the evolution of the genus Helianthus (L.).

PubMed

Mascagni, Flavia; Giordani, Tommaso; Ceccarelli, Marilena; Cavallini, Andrea; Natali, Lucia

2017-08-18

Genome divergence by mobile elements activity and recombination is a continuous process that plays a key role in the evolution of species. Nevertheless, knowledge on retrotransposon-related variability among species belonging to the same genus is still limited. Considering the importance of the genus Helianthus, a model system for studying the ecological genetics of speciation and adaptation, we performed a comparative analysis of the repetitive genome fraction across ten species and one subspecies of sunflower, focusing on long terminal repeat retrotransposons at superfamily, lineage and sublineage levels. After determining the relative genome size of each species, genomic DNA was isolated and subjected to Illumina sequencing. Then, different assembling and clustering approaches allowed exploring the repetitive component of all genomes. On average, repetitive DNA in Helianthus species represented more than 75% of the genome, being composed mostly by long terminal repeat retrotransposons. Also, the prevalence of Gypsy over Copia superfamily was observed and, among lineages, Chromovirus was by far the most represented. Although nearly all the same sublineages are present in all species, we found considerable variability in the abundance of diverse retrotransposon lineages and sublineages, especially between annual and perennial species. This large variability should indicate that different events of amplification or loss related to these elements occurred following species separation and should have been involved in species differentiation. Our data allowed us inferring on the extent of interspecific repetitive DNA variation related to LTR-RE abundance, investigating the relationship between changes of LTR-RE abundance and the evolution of the genus, and determining the degree of coevolution of different LTR-RE lineages or sublineages between and within species. Moreover, the data suggested that LTR-RE abundance in a species was affected by the annual or perennial habit of that species.

The complete mitochondrial genomes of two band-winged grasshoppers, Gastrimargus marmoratus and Oedaleus asiaticus

PubMed Central

Ma, Chuan; Liu, Chunxiang; Yang, Pengcheng; Kang, Le

2009-01-01

Background The two closely related species of band-winged grasshoppers, Gastrimargus marmoratus and Oedaleus asiaticus, display significant differences in distribution, biological characteristics and habitat preferences. They are so similar to their respective congeneric species that it is difficult to differentiate them from other species within each genus. Hoppers of the two species have quite similar morphologies to that of Locusta migratoria, hence causing confusion in species identification. Thus we determined and compared the mitochondrial genomes of G. marmoratus and O. asiaticus to address these questions. Results The complete mitochondrial genomes of G. marmoratus and O. asiaticus are 15,924 bp and 16,259 bp in size, respectively, with O. asiaticus being the largest among all known mitochondrial genomes in Orthoptera. Both mitochondrial genomes contain a standard set of 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes and an A+T-rich region in the same order as those of the other analysed caeliferan species, but different from those of the ensiferan species by the rearrangement of trnD and trnK. The putative initiation codon for the cox1 gene in the two species is ATC. The presence of different sized tandem repeats in the A+T-rich region leads to size variation between their mitochondrial genomes. Except for nad2, nad4L, and nad6, most of the caeliferan mtDNA genes exhibit low levels of divergence. In phylogenetic analyses, the species from the suborder Caelifera form a monophyletic group, as is the case for the Ensifera. Furthermore, the two suborders cluster as sister groups, supporting the monophyly of Orthoptera. Conclusion The mitochondrial genomes of both G. marmoratus and O. asiaticus harbor the typical 37 genes and an A+T-rich region, exhibiting similar characters to those of other grasshopper species. Characterization of the two mitochondrial genomes has enriched our knowledge on mitochondrial genomes of Orthoptera. PMID:19361334

A de Bruijn graph approach to the quantification of closely-related genomes in a microbial community.

PubMed

Wang, Mingjie; Ye, Yuzhen; Tang, Haixu

2012-06-01

The wide applications of next-generation sequencing (NGS) technologies in metagenomics have raised many computational challenges. One of the essential problems in metagenomics is to estimate the taxonomic composition of a microbial community, which can be approached by mapping shotgun reads acquired from the community to previously characterized microbial genomes followed by quantity profiling of these species based on the number of mapped reads. This procedure, however, is not as trivial as it appears at first glance. A shotgun metagenomic dataset often contains DNA sequences from many closely-related microbial species (e.g., within the same genus) or strains (e.g., within the same species), thus it is often difficult to determine which species/strain a specific read is sampled from when it can be mapped to a common region shared by multiple genomes at high similarity. Furthermore, high genomic variations are observed among individual genomes within the same species, which are difficult to be differentiated from the inter-species variations during reads mapping. To address these issues, a commonly used approach is to quantify taxonomic distribution only at the genus level, based on the reads mapped to all species belonging to the same genus; alternatively, reads are mapped to a set of representative genomes, each selected to represent a different genus. Here, we introduce a novel approach to the quantity estimation of closely-related species within the same genus by mapping the reads to their genomes represented by a de Bruijn graph, in which the common genomic regions among them are collapsed. Using simulated and real metagenomic datasets, we show the de Bruijn graph approach has several advantages over existing methods, including (1) it avoids redundant mapping of shotgun reads to multiple copies of the common regions in different genomes, and (2) it leads to more accurate quantification for the closely-related species (and even for strains within the same species).

Microarray Genomic Systems Development

DTIC Science & Technology

2008-06-01

11 species), Escherichia coli TOP10 (7 strains), and Geobacillus stearothermophilus . Using standard molecular biology methods, we isolated genomic...comparisons. Results: Different species of bacteria, including Escherichia coli, Bacillus bacteria, and Geobacillus stearothermophilus produce qualitatively...oligonucleotides to labelled genomic DNA from a set of test samples, including eleven Bacillus species, Geobacillus stearothermophilus , and seven Escherichia

Genome analysis of 7 Kengyilia (Triticeae Poaceae) species with FISH and GISH

USDA-ARS?s Scientific Manuscript database

Genome composition of and genetic relationships among seven Kengyilia species were assessed using a technique of sequential FISH (fluorescence in situ hybridization) and GISH (genomic in situ hybridization). Five of these 7 species, K. kokonorica, K. rigidula, K. hirsula, K. grandiglumis, and K. th...

Whole-Genome Sequencing of Staphylococcus haemolyticus Uncovers the Extreme Plasticity of Its Genome and the Evolution of Human-Colonizing Staphylococcal Species

PubMed Central

Takeuchi, Fumihiko; Watanabe, Shinya; Baba, Tadashi; Yuzawa, Harumi; Ito, Teruyo; Morimoto, Yuh; Kuroda, Makoto; Cui, Longzhu; Takahashi, Mikio; Ankai, Akiho; Baba, Shin-ichi; Fukui, Shigehiro; Lee, Jean C.; Hiramatsu, Keiichi

2005-01-01

Staphylococcus haemolyticus is an opportunistic bacterial pathogen that colonizes human skin and is remarkable for its highly antibiotic-resistant phenotype. We determined the complete genome sequence of S.haemolyticus to better understand its pathogenicity and evolutionary relatedness to the other staphylococcal species. A large proportion of the open reading frames in the genomes of S.haemolyticus, Staphylococcus aureus, and Staphylococcus epidermidis were conserved in their sequence and order on the chromosome. We identified a region of the bacterial chromosome just downstream of the origin of replication that showed little homology among the species but was conserved among strains within a species. This novel region, designated the “oriC environ,” likely contributes to the evolution and differentiation of the staphylococcal species, since it was enriched for species-specific nonessential genes that contribute to the biological features of each staphylococcal species. A comparative analysis of the genomes of S.haemolyticus, S.aureus, and S.epidermidis elucidated differences in their biological and genetic characteristics and pathogenic potentials. We identified as many as 82 insertion sequences in the S.haemolyticus chromosome that probably mediated frequent genomic rearrangements, resulting in phenotypic diversification of the strain. Such rearrangements could have brought genomic plasticity to this species and contributed to its acquisition of antibiotic resistance. PMID:16237012

Long Terminal Repeat Retrotransposon Content in Eight Diploid Sunflower Species Inferred from Next-Generation Sequence Data

PubMed Central

Tetreault, Hannah M.; Ungerer, Mark C.

2016-01-01

The most abundant transposable elements (TEs) in plant genomes are Class I long terminal repeat (LTR) retrotransposons represented by superfamilies gypsy and copia. Amplification of these superfamilies directly impacts genome structure and contributes to differential patterns of genome size evolution among plant lineages. Utilizing short-read Illumina data and sequence information from a panel of Helianthus annuus (sunflower) full-length gypsy and copia elements, we explore the contribution of these sequences to genome size variation among eight diploid Helianthus species and an outgroup taxon, Phoebanthus tenuifolius. We also explore transcriptional dynamics of these elements in both leaf and bud tissue via RT-PCR. We demonstrate that most LTR retrotransposon sublineages (i.e., families) display patterns of similar genomic abundance across species. A small number of LTR retrotransposon sublineages exhibit lineage-specific amplification, particularly in the genomes of species with larger estimated nuclear DNA content. RT-PCR assays reveal that some LTR retrotransposon sublineages are transcriptionally active across all species and tissue types, whereas others display species-specific and tissue-specific expression. The species with the largest estimated genome size, H. agrestis, has experienced amplification of LTR retrotransposon sublineages, some of which have proliferated independently in other lineages in the Helianthus phylogeny. PMID:27233667

The genomic landscape at a late stage of stickleback speciation: High genomic divergence interspersed by small localized regions of introgression.

PubMed

Ravinet, Mark; Yoshida, Kohta; Shigenobu, Shuji; Toyoda, Atsushi; Fujiyama, Asao; Kitano, Jun

2018-05-01

Speciation is a continuous process and analysis of species pairs at different stages of divergence provides insight into how it unfolds. Previous genomic studies on young species pairs have revealed peaks of divergence and heterogeneous genomic differentiation. Yet less known is how localised peaks of differentiation progress to genome-wide divergence during the later stages of speciation in the presence of persistent gene flow. Spanning the speciation continuum, stickleback species pairs are ideal for investigating how genomic divergence builds up during speciation. However, attention has largely focused on young postglacial species pairs, with little knowledge of the genomic signatures of divergence and introgression in older stickleback systems. The Japanese stickleback species pair, composed of the Pacific Ocean three-spined stickleback (Gasterosteus aculeatus) and the Japan Sea stickleback (G. nipponicus), which co-occur in the Japanese islands, is at a late stage of speciation. Divergence likely started well before the end of the last glacial period and crosses between Japan Sea females and Pacific Ocean males result in hybrid male sterility. Here we use coalescent analyses and Approximate Bayesian Computation to show that the two species split approximately 0.68-1 million years ago but that they have continued to exchange genes at a low rate throughout divergence. Population genomic data revealed that, despite gene flow, a high level of genomic differentiation is maintained across the majority of the genome. However, we identified multiple, small regions of introgression, occurring mainly in areas of low recombination rate. Our results demonstrate that a high level of genome-wide divergence can establish in the face of persistent introgression and that gene flow can be localized to small genomic regions at the later stages of speciation with gene flow.

Pan-genome analysis of the emerging foodborne pathogen Cronobacter spp. suggests a species-level bidirectional divergence driven by niche adaptation

PubMed Central

2013-01-01

Background Members of the genus Cronobacter are causes of rare but severe illness in neonates and preterm infants following the ingestion of contaminated infant formula. Seven species have been described and two of the species genomes were subsequently published. In this study, we performed comparative genomics on eight strains of Cronobacter, including six that we sequenced (representing six of the seven species) and two previously published, closed genomes. Results We identified and characterized the features associated with the core and pan genome of the genus Cronobacter in an attempt to understand the evolution of these bacteria and the genetic content of each species. We identified 84 genomic regions that are present in two or more Cronobacter genomes, along with 45 unique genomic regions. Many potentially horizontally transferred genes, such as lysogenic prophages, were also identified. Most notable among these were several type six secretion system gene clusters, transposons that carried tellurium, copper and/or silver resistance genes, and a novel integrative conjugative element. Conclusions Cronobacter have diverged into two clusters, one consisting of C. dublinensis and C. muytjensii (Cdub-Cmuy) and the other comprised of C. sakazakii, C. malonaticus, C. universalis, and C. turicensis, (Csak-Cmal-Cuni-Ctur) from the most recent common ancestral species. While several genetic determinants for plant-association and human virulence could be found in the core genome of Cronobacter, the four Cdub-Cmuy clade genomes contained several accessory genomic regions important for survival in a plant-associated environmental niche, while the Csak-Cmal-Cuni-Ctur clade genomes harbored numerous virulence-related genetic traits. PMID:23724777

Selective significance of genome size in a plant community with heavy metal pollution.

PubMed

Vidic, T; Greilhuber, J; Vilhar, B; Dermastia, M

2009-09-01

In eukaryotes, nuclear genome sizes vary by more than five orders of magnitude. This variation is not related to organismal complexity, and its origin and biological significance are still disputed. One of the open questions is whether genome size has an adaptive role. We tested the hypothesis that genome size has selective significance, using five grassland communities occurring on a gradient of metal pollution of the soil as a model. We detected a negative correlation between the concentration of contaminating metals in the soil and the number of vascular plant species. Analysis of genome sizes of 70 herbaceous dicot perennial species occurring on the investigated plots revealed a negative correlation between the concentration of contaminating metals in the soil and the proportion of species with large genomes in plant communities. Consistent with the hypothesis, these results show that species with large genomes are at selective disadvantage in extreme environmental conditions.

Comparative genomics of Eucalyptus and Corymbia reveals low rates of genome structural rearrangement.

PubMed

Butler, J B; Vaillancourt, R E; Potts, B M; Lee, D J; King, G J; Baten, A; Shepherd, M; Freeman, J S

2017-05-22

Previous studies suggest genome structure is largely conserved between Eucalyptus species. However, it is unknown if this conservation extends to more divergent eucalypt taxa. We performed comparative genomics between the eucalypt genera Eucalyptus and Corymbia. Our results will facilitate transfer of genomic information between these important taxa and provide further insights into the rate of structural change in tree genomes. We constructed three high density linkage maps for two Corymbia species (Corymbia citriodora subsp. variegata and Corymbia torelliana) which were used to compare genome structure between both species and Eucalyptus grandis. Genome structure was highly conserved between the Corymbia species. However, the comparison of Corymbia and E. grandis suggests large (from 1-13 MB) intra-chromosomal rearrangements have occurred on seven of the 11 chromosomes. Most rearrangements were supported through comparisons of the three independent Corymbia maps to the E. grandis genome sequence, and to other independently constructed Eucalyptus linkage maps. These are the first large scale chromosomal rearrangements discovered between eucalypts. Nonetheless, in the general context of plants, the genomic structure of the two genera was remarkably conserved; adding to a growing body of evidence that conservation of genome structure is common amongst woody angiosperms.

Natural Selection and Recombination Rate Variation Shape Nucleotide Polymorphism Across the Genomes of Three Related Populus Species

PubMed Central

Wang, Jing; Street, Nathaniel R.; Scofield, Douglas G.; Ingvarsson, Pär K.

2016-01-01

A central aim of evolutionary genomics is to identify the relative roles that various evolutionary forces have played in generating and shaping genetic variation within and among species. Here we use whole-genome resequencing data to characterize and compare genome-wide patterns of nucleotide polymorphism, site frequency spectrum, and population-scaled recombination rates in three species of Populus: Populus tremula, P. tremuloides, and P. trichocarpa. We find that P. tremuloides has the highest level of genome-wide variation, skewed allele frequencies, and population-scaled recombination rates, whereas P. trichocarpa harbors the lowest. Our findings highlight multiple lines of evidence suggesting that natural selection, due to both purifying and positive selection, has widely shaped patterns of nucleotide polymorphism at linked neutral sites in all three species. Differences in effective population sizes and rates of recombination largely explain the disparate magnitudes and signatures of linked selection that we observe among species. The present work provides the first phylogenetic comparative study on a genome-wide scale in forest trees. This information will also improve our ability to understand how various evolutionary forces have interacted to influence genome evolution among related species. PMID:26721855

Natural Selection and Recombination Rate Variation Shape Nucleotide Polymorphism Across the Genomes of Three Related Populus Species.

PubMed

Wang, Jing; Street, Nathaniel R; Scofield, Douglas G; Ingvarsson, Pär K

2016-03-01

A central aim of evolutionary genomics is to identify the relative roles that various evolutionary forces have played in generating and shaping genetic variation within and among species. Here we use whole-genome resequencing data to characterize and compare genome-wide patterns of nucleotide polymorphism, site frequency spectrum, and population-scaled recombination rates in three species of Populus: Populus tremula, P. tremuloides, and P. trichocarpa. We find that P. tremuloides has the highest level of genome-wide variation, skewed allele frequencies, and population-scaled recombination rates, whereas P. trichocarpa harbors the lowest. Our findings highlight multiple lines of evidence suggesting that natural selection, due to both purifying and positive selection, has widely shaped patterns of nucleotide polymorphism at linked neutral sites in all three species. Differences in effective population sizes and rates of recombination largely explain the disparate magnitudes and signatures of linked selection that we observe among species. The present work provides the first phylogenetic comparative study on a genome-wide scale in forest trees. This information will also improve our ability to understand how various evolutionary forces have interacted to influence genome evolution among related species. Copyright © 2016 by the Genetics Society of America.

Decoding the similarities and differences among mycobacterial species

PubMed Central

Vedithi, Sundeep Chaitanya; Blundell, Tom L.

2017-01-01

Mycobacteriaceae comprises pathogenic species such as Mycobacterium tuberculosis, M. leprae and M. abscessus, as well as non-pathogenic species, for example, M. smegmatis and M. thermoresistibile. Genome comparison and annotation studies provide insights into genome evolutionary relatedness, identify unique and pathogenicity-related genes in each species, and explore new targets that could be used for developing new diagnostics and therapeutics. Here, we present a comparative analysis of ten-mycobacterial genomes with the objective of identifying similarities and differences between pathogenic and non-pathogenic species. We identified 1080 core orthologous clusters that were enriched in proteins involved in amino acid and purine/pyrimidine biosynthetic pathways, DNA-related processes (replication, transcription, recombination and repair), RNA-methylation and modification, and cell-wall polysaccharide biosynthetic pathways. For their pathogenicity and survival in the host cell, pathogenic species have gained specific sets of genes involved in repair and protection of their genomic DNA. M. leprae is of special interest owing to its smallest genome (1600 genes and ~1300 psuedogenes), yet poor genome annotation. More than 75% of the pseudogenes were found to have a functional ortholog in the other mycobacterial genomes and belong to protein families such as transferases, oxidoreductases and hydrolases. PMID:28854187

Acinetobacter baumannii in Human Body Louse

PubMed Central

Raoult, Didier

2004-01-01

While we were isolating Bartonella quintana from body lice, 40 Acinetobacter baumannii strains were also isolated and genotyped. One clone was unique and the other was ampicillin susceptible. A. baumannii DNA was later detected in 21% of 622 lice collected worldwide. These findings show an A. baumannii epidemic in human body lice. PMID:15498175

Longitudinal Characterization of Acinetobacter baumannii-calcoaceticus Complex, Klebsiella pneumoniae, and Methicillin-Resistant Staphylococcus aureus Colonizing and Infecting Combat Casualties

DTIC Science & Technology

2012-01-01

Afghanistan.1-3 Multidrug-resistant (MDR) Acinetobacter baumannii-calcoaceticus complex (ABC), extended-spectrum b-lactamase ( ESBL )-producing Klebsiella...September 2008 were screened (nares for MRSA, axillae and groin for gram-negative organisms) for the presence of ABC, ESBL -producing K pneumoniae, and

Characterization of the chromosomal cephalosporinases produced by Acinetobacter lwoffii and Acinetobacter baumannii clinical isolates.

PubMed Central

Perilli, M; Felici, A; Oratore, A; Cornaglia, G; Bonfiglio, G; Rossolini, G M; Amicosante, G

1996-01-01

The beta-lactamases produced by Acinetobacter lwoffii ULA-501, Acinetobacter baumannii ULA-187, and A. baumannii AC-14 strains were purified and characterized, and their kinetic interactions with several beta-lactam molecules, including substrates and inhibitors, were studied in detail. The three enzymes appeared to be cephalosporinases with different acylation efficiencies (kcat/Km ratio values), and their hydrolytic activities were inhibited by benzylpenicillin, piperacillin, and cefotaxime, which did not behave as substrates. Carbenicillin was a substrate for the beta-lactamase from A. lwoffii ULA-501, whereas it acted as a transient inactivator of the enzymes produced by the two A. baumannii strains. Clavulanic acid was unable to inactivate the three beta-lactamases, whereas sulbactam behaved as an inactivator only at a high concentration (1 mM) which is difficult to achieve during antibiotic therapy. Analysis of the interaction with 6-beta-iodopenicillanic acid also allowed us to better discriminate the three beta-lactamases analyzed in the present study, which can be included in the group 1 functional class (5). PMID:8851599

Acinetobacter community-acquired pneumonia in a healthy child.

PubMed

Moreira Silva, G; Morais, L; Marques, L; Senra, V

2012-01-01

Acinetobacter is involved in a variety of infectious diseases primarily associated with healthcare. Recently there has been increasing evidence of the important role these pathogens play in community acquired infections. We report on the case of a previously healthy child, aged 28 months, admitted for fever, cough and pain on the left side of the chest, which on radiographic examination corresponded to a lower lobe necrotizing pneumonia. After detailed diagnostic work-up, community acquired Acinetobacter lwoffii pneumonia was diagnosed. The child had frequently shared respiratory equipment with elderly relatives with chronic obstructive pulmonary disease. As there were no other apparent risk factors, it could be assumed that the sharing of the equipment was the source of infection. The authors wish to draw attention to this possibility, that a necrotising community-acquired pneumonia due to Acinetobacter lwoffii can occur in a previously healthy child and to the dangers of inappropriate use and poor sterilisation of nebulisers. This case is a warning of the dangers that these bacteria may pose in the future in a community setting. Copyright © 2011 Sociedade Portuguesa de Pneumologia. Published by Elsevier España. All rights reserved.

Signature Motifs Identify an Acinetobacter Cif Virulence Factor with Epoxide Hydrolase Activity*

PubMed Central

Bahl, Christopher D.; Hvorecny, Kelli L.; Bridges, Andrew A.; Ballok, Alicia E.; Bomberger, Jennifer M.; Cady, Kyle C.; O'Toole, George A.; Madden, Dean R.

2014-01-01

Endocytic recycling of the cystic fibrosis transmembrane conductance regulator (CFTR) is blocked by the CFTR inhibitory factor (Cif). Originally discovered in Pseudomonas aeruginosa, Cif is a secreted epoxide hydrolase that is transcriptionally regulated by CifR, an epoxide-sensitive repressor. In this report, we investigate a homologous protein found in strains of the emerging nosocomial pathogens Acinetobacter nosocomialis and Acinetobacter baumannii (“aCif”). Like Cif, aCif is an epoxide hydrolase that carries an N-terminal secretion signal and can be purified from culture supernatants. When applied directly to polarized airway epithelial cells, mature aCif triggers a reduction in CFTR abundance at the apical membrane. Biochemical and crystallographic studies reveal a dimeric assembly with a stereochemically conserved active site, confirming our motif-based identification of candidate Cif-like pathogenic EH sequences. Furthermore, cif expression is transcriptionally repressed by a CifR homolog (“aCifR”) and is induced in the presence of epoxides. Overall, this Acinetobacter protein recapitulates the essential attributes of the Pseudomonas Cif system and thus may facilitate airway colonization in nosocomial lung infections. PMID:24474692

Detection of VIM- and IMP-type Metallo-Beta-Lactamase Genes in Acinetobacter baumannii Isolates from Patients in Two Hospitals in Tehran

PubMed Central

Davoodi, Saba; Boroumand, Mohammad Ali; Sepehriseresht, Saeed; Pourgholi, Leila

2015-01-01

Background Acinetobacter baumannii, is an opportunistic pathogen and is responsible for numerous nosocomial infections. In recent years, this microorganism has been resistant to a wide range of antibiotics. One of the most important mechanisms of resistance in this microorganism is production of metallo-beta-lactamases (MBLs). Objectives The aim of this study was to detect VIM- and IMP-type metallo-beta-lactamase genes in Acinetobacter baumanniiisolates from patients in two Hospitals in Tehran. Materials and Methods 104 isolates were tested using the PCR method for the identification of VIM- and IMP-type genes. Results vim1, vim2, imp1 and imp2 genes were detected in 6.7%, 41.7%, 50% and 1.7% of the isolates from Tehran Heart Center, and in 29.5%, 38.6%, 4.5% and 4.5% of the isolates from Shahid Mutahhari Hospital respectively. Discussions Our analysis revealed that the majority of the isolates had at least one of these genes, indicating that MBLs production is an important resistance mechanism in Acinetobacter baumannii. PMID:28959283

Clarification of Taxonomic Status within the Pseudomonas syringae Species Group Based on a Phylogenomic Analysis.

PubMed

Gomila, Margarita; Busquets, Antonio; Mulet, Magdalena; García-Valdés, Elena; Lalucat, Jorge

2017-01-01

The Pseudomonas syringae phylogenetic group comprises 15 recognized bacterial species and more than 60 pathovars. The classification and identification of strains is relevant for practical reasons but also for understanding the epidemiology and ecology of this group of plant pathogenic bacteria. Genome-based taxonomic analyses have been introduced recently to clarify the taxonomy of the whole genus. A set of 139 draft and complete genome sequences of strains belonging to all species of the P. syringae group available in public databases were analyzed, together with the genomes of closely related species used as outgroups. Comparative genomics based on the genome sequences of the species type strains in the group allowed the delineation of phylogenomic species and demonstrated that a high proportion of strains included in the study are misclassified. Furthermore, representatives of at least 7 putative novel species were detected. It was also confirmed that P. ficuserectae, P. meliae , and P. savastanoi are later synonyms of P. amygdali and that " P. coronafaciens " should be revived as a nomenspecies.

Molecular Markers of Pesticide Resistance and Pathogens in Human Head Lice (Phthiraptera: Pediculidae) From Rural Georgia, USA.

PubMed

Eremeeva, Marina E; Capps, Danielle; Winful, Emmanuel B; Warang, Shamta S; Braswell, Sarah E; Tokarevich, Nikolay K; Bonilla, Denise L; Durden, Lance A

2017-07-01

Although the head louse, Pediculus humanus capitis De Geer, and body louse, Pediculus humanus humanus L., both have a worldwide distribution, the occurrence of head louse pediculosis appears to be more prevalent in modern societies despite systematic use of various pediculicides. This study tested head lice collected in rural Georgia and body lice collected in Russia for the prevalence of a kdr-biomarker that is associated with permethrin resistance. This study also screened lice for the presence of DNA from Bartonella quintana and Acinetobacter species. The kdr-permethrin resistance biomarker for the T917I mutation was detected by RFLP and PCR in 99.9% of head lice tested from Georgia, whereas only 2.9% of body lice from Russia tested positive for this kdr biomarker. DNA of B. quintana was detected in 10.3% of head lice from Georgia, whereas 84.8% of body lice from Russia tested positive. Acinetobacter DNA was detected in 80.8% (95% CI, 68-89%) of head lice from Georgia and all body lice from Russia tested. © The Authors 2017. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Pyrosequencing Reveals a Core Community of Anodic Bacterial Biofilms in Bioelectrochemical Systems from China

PubMed Central

Xiao, Yong; Zheng, Yue; Wu, Song; Zhang, En-Hua; Chen, Zheng; Liang, Peng; Huang, Xia; Yang, Zhao-Hui; Ng, I-Son; Chen, Bor-Yann; Zhao, Feng

2015-01-01

Bioelectrochemical systems (BESs) are promising technologies for energy and product recovery coupled with wastewater treatment, and the core microbial community in electrochemically active biofilm in BESs remains controversy. In the present study, 7 anodic communities from 6 bioelectrochemical systems in 4 labs in southeast, north and south-central of China are explored by 454 pyrosequencing. A total of 251,225 effective sequences are obtained for 7 electrochemically active biofilm samples at 3% cutoff level. While Alpha-, Beta-, and Gamma-proteobacteria are the most abundant classes (averaging 16.0–17.7%), Bacteroidia and Clostridia are the two sub-dominant and commonly shared classes. Six commonly shared genera i.e., Azospira, Azospirillum, Acinetobacter, Bacteroides, Geobacter, Pseudomonas, and Rhodopseudomonas dominate the electrochemically active communities and are defined as core genera. A total of 25 OTUs with average relative abundance >0.5% were selected and designated as core OTUs, and some species relating to these OTUs have been reported electrochemically active. Furthermore, cyclic voltammetry and chronoamperometry tests show that two strains from Acinetobacter guillouiae and Stappia indica, bacteria relate to two core OTUs, are electrochemically active. Using randomly selected bioelectrochemical systems, the study has presented extremely diverse bacterial communities in anodic biofilms, though, we still can suggest some potentially microbes for investigating the electrochemical mechanisms in bioelectrochemical systems. PMID:26733958

Genome analysis of medicinal Ganoderma spp. with plant-pathogenic and saprotrophic life-styles.

PubMed

Kües, Ursula; Nelson, David R; Liu, Chang; Yu, Guo-Jun; Zhang, Jianhui; Li, Jianqin; Wang, Xin-Cun; Sun, Hui

2015-06-01

Ganoderma is a fungal genus belonging to the Ganodermataceae family and Polyporales order. Plant-pathogenic species in this genus can cause severe diseases (stem, butt, and root rot) in economically important trees and perennial crops, especially in tropical countries. Ganoderma species are white rot fungi and have ecological importance in the breakdown of woody plants for nutrient mobilization. They possess effective machineries of lignocellulose-decomposing enzymes useful for bioenergy production and bioremediation. In addition, the genus contains many important species that produce pharmacologically active compounds used in health food and medicine. With the rapid adoption of next-generation DNA sequencing technologies, whole genome sequencing and systematic transcriptome analyses become affordable approaches to identify an organism's genes. In the last few years, numerous projects have been initiated to identify the genetic contents of several Ganoderma species, particularly in different strains of Ganoderma lucidum. In November 2013, eleven whole genome sequencing projects for Ganoderma species were registered in international databases, three of which were already completed with genomes being assembled to high quality. In addition to the nuclear genome, two mitochondrial genomes for Ganoderma species have also been reported. Complementing genome analysis, four transcriptome studies on various developmental stages of Ganoderma species have been performed. Information obtained from these studies has laid the foundation for the identification of genes involved in biological pathways that are critical for understanding the biology of Ganoderma, such as the mechanism of pathogenesis, the biosynthesis of active components, life cycle and cellular development, etc. With abundant genetic information becoming available, a few centralized resources have been established to disseminate the knowledge and integrate relevant data to support comparative genomic analyses of Ganoderma species. The current review carries out a detailed comparison of the nuclear genomes, mitochondrial genomes and transcriptomes from several Ganoderma species. Genes involved in biosynthetic pathways such as CYP450 genes and in cellular development such as matA and matB genes are characterized and compared in detail, as examples to demonstrate the usefulness of comparative genomic analyses for the identification of critical genes. Resources needed for future data integration and exploitation are also discussed. Copyright © 2014 Elsevier Ltd. All rights reserved.

Visualization of genome signatures of eukaryote genomes by batch-learning self-organizing map with a special emphasis on Drosophila genomes.

PubMed

Abe, Takashi; Hamano, Yuta; Ikemura, Toshimichi

2014-01-01

A strategy of evolutionary studies that can compare vast numbers of genome sequences is becoming increasingly important with the remarkable progress of high-throughput DNA sequencing methods. We previously established a sequence alignment-free clustering method "BLSOM" for di-, tri-, and tetranucleotide compositions in genome sequences, which can characterize sequence characteristics (genome signatures) of a wide range of species. In the present study, we generated BLSOMs for tetra- and pentanucleotide compositions in approximately one million sequence fragments derived from 101 eukaryotes, for which almost complete genome sequences were available. BLSOM recognized phylotype-specific characteristics (e.g., key combinations of oligonucleotide frequencies) in the genome sequences, permitting phylotype-specific clustering of the sequences without any information regarding the species. In our detailed examination of 12 Drosophila species, the correlation between their phylogenetic classification and the classification on the BLSOMs was observed to visualize oligonucleotides diagnostic for species-specific clustering.

Bolbase: a comprehensive genomics database for Brassica oleracea.

PubMed

Yu, Jingyin; Zhao, Meixia; Wang, Xiaowu; Tong, Chaobo; Huang, Shunmou; Tehrim, Sadia; Liu, Yumei; Hua, Wei; Liu, Shengyi

2013-09-30

Brassica oleracea is a morphologically diverse species in the family Brassicaceae and contains a group of nutrition-rich vegetable crops, including common heading cabbage, cauliflower, broccoli, kohlrabi, kale, Brussels sprouts. This diversity along with its phylogenetic membership in a group of three diploid and three tetraploid species, and the recent availability of genome sequences within Brassica provide an unprecedented opportunity to study intra- and inter-species divergence and evolution in this species and its close relatives. We have developed a comprehensive database, Bolbase, which provides access to the B. oleracea genome data and comparative genomics information. The whole genome of B. oleracea is available, including nine fully assembled chromosomes and 1,848 scaffolds, with 45,758 predicted genes, 13,382 transposable elements, and 3,581 non-coding RNAs. Comparative genomics information is available, including syntenic regions among B. oleracea, Brassica rapa and Arabidopsis thaliana, synonymous (Ks) and non-synonymous (Ka) substitution rates between orthologous gene pairs, gene families or clusters, and differences in quantity, category, and distribution of transposable elements on chromosomes. Bolbase provides useful search and data mining tools, including a keyword search, a local BLAST server, and a customized GBrowse tool, which can be used to extract annotations of genome components, identify similar sequences and visualize syntenic regions among species. Users can download all genomic data and explore comparative genomics in a highly visual setting. Bolbase is the first resource platform for the B. oleracea genome and for genomic comparisons with its relatives, and thus it will help the research community to better study the function and evolution of Brassica genomes as well as enhance molecular breeding research. This database will be updated regularly with new features, improvements to genome annotation, and new genomic sequences as they become available. Bolbase is freely available at http://ocri-genomics.org/bolbase.

When COI barcodes deceive: complete genomes reveal introgression in hairstreaks

PubMed Central

Shen, Jinhui; Borek, Dominika; Robbins, Robert K.; Opler, Paul A.; Otwinowski, Zbyszek; Grishin, Nick V.

2017-01-01

Two species of hairstreak butterflies from the genus Calycopis are known in the United States: C. cecrops and C. isobeon. Analysis of mitochondrial COI barcodes of Calycopis revealed cecrops-like specimens from the eastern US with atypical barcodes that were 2.6% different from either USA species, but similar to Central American Calycopis species. To address the possibility that the specimens with atypical barcodes represent an undescribed cryptic species, we sequenced complete genomes of 27 Calycopis specimens of four species: C. cecrops, C. isobeon, C. quintana and C. bactra. Some of these specimens were collected up to 60 years ago and preserved dry in museum collections, but nonetheless produced genomes as complete as fresh samples. Phylogenetic trees reconstructed using the whole mitochondrial and nuclear genomes were incongruent. While USA Calycopis with atypical barcodes grouped with Central American species C. quintana by mitochondria, nuclear genome trees placed them within typical USA C. cecrops in agreement with morphology, suggesting mitochondrial introgression. Nuclear genomes also show introgression, especially between C. cecrops and C. isobeon. About 2.3% of each C. cecrops genome has probably (p-value < 0.01, FDR < 0.1) introgressed from C. isobeon and about 3.4% of each C. isobeon genome may have come from C. cecrops. The introgressed regions are enriched in genes encoding transmembrane proteins, mitochondria-targeting proteins and components of the larval cuticle. This study provides the first example of mitochondrial introgression in Lepidoptera supported by complete genome sequencing. Our results caution about relying solely on COI barcodes and mitochondrial DNA for species identification or discovery. PMID:28179510

The first complete organellar genomes of an Antarctic red alga, Pyropia endiviifolia: insights into its genome architecture and phylogenetic position within genus Pyropia (Bangiales, Rhodophyta)

NASA Astrophysics Data System (ADS)

Xu, Kuipeng; Tang, Xianghai; Bi, Guiqi; Cao, Min; Wang, Lu; Mao, Yunxiang

2017-08-01

Pyropia species grow in the intertidal zone and are cold-water adapted. To date, most of the information about the whole plastid and mitochondrial genomes (ptDNA and mtDNA) of this genus is limited to Northern Hemisphere species. Here, we report the sequencing of the ptDNA and mtDNA of the Antarctic red alga Pyropia endiviifolia using the Illumina platform. The plastid genome (195 784 bp, 33.28% GC content) contains 210 protein-coding genes, 37 tRNA genes and 6 rRNA genes. The mitochondrial genome (34 603 bp, 30.5% GC content) contains 26 protein-coding genes, 25 tRNA genes and 2 rRNA genes. Our results suggest that the organellar genomes of Py. endiviifolia have a compact organization. Although the collinearity of these genomes is conserved compared with other Pyropia species, the genome sizes show significant differences, mainly because of the different copy numbers of rDNA operons in the ptDNA and group II introns in the mtDNA. The other Pyropia species have 2u20133 distinct intronic ORFs in their cox 1 genes, but Py. endiviifolia has no introns in its cox 1 gene. This has led to a smaller mtDNA than in other Pyropia species. The phylogenetic relationships within Pyropia were examined using concatenated gene sets from most of the available organellar genomes with both the maximum likelihood and Bayesian methods. The analysis revealed a sister taxa affiliation between the Antarctic species Py. endiviifolia and the North American species Py. kanakaensis.

Biodegradation of 4-nitroaniline by plant-growth promoting Acinetobacter sp. AVLB2 and toxicological analysis of its biodegradation metabolites.

PubMed

Silambarasan, Sivagnanam; Vangnai, Alisa S

2016-01-25

4-nitroaniline (4-NA) is one of the major priority pollutants generated from industrial productions and pesticide transformation; however very limited biodegradation details have been reported. This work is the first to report 4-NA biodegradation kinetics and toxicity reduction using a newly isolated plant-growth promoting bacterium, Acinetobacter sp. AVLB2. The 4-NA-dependent growth kinetics parameters: μmax, Ks and Ki, were determined to be 0.039 h(-1), 6.623 mg L(-1) and 25.57 mg L(-1), respectively using Haldane inhibition model, while the maximum biodegradation rate (Vmax) of 4-NA was at 0.541 mg L(-1) h(-1) and 0.551 mg L(-1) h(-1), following Michaelis-Menten and Hanes-Woolf models, respectively. Biodegradation pathway of 4-NA by Acinetobacter sp. AVLB2 was proposed, and successfully led to the reduction of 4-NA toxicity according to the following toxicity assessments: microbial toxicity using Escherichia coli DH5α, phytotoxicity with Vigna radiata and Crotalaria juncea, and cytogenotoxicity with Allium cepa root-tip cells. In addition, Acinetobacter sp. AVLB2 possess important plant-growth promoting traits, both in the presence and absence of 4-NA. This study has provided a new insight into 4-NA biodegradation ability and concurrent plant-growth promoting activities of Acinetobacter sp. AVLB2, which may indicate its potential role for rhizoremediation, while sustaining crop production even under 4-NA stressed environment. Copyright © 2015 Elsevier B.V. All rights reserved.

Molecular characterization of Ambler class A to D β-lactamases, ISAba1, and integrons reveals multidrug-resistant Acinetobacter spp. isolates in northeastern China.

PubMed

Sun, Xiaoyu; Liu, Bin; Chen, Yan; Huang, Honglan; Wang, Guoqing; Li, Fan; Ni, Zhaohui

2016-12-01

The prevalence of various Ambler class A to D β-lactamases, ISAba1, and class 1 and 2 integrons as well as the clonal relatedness in 105 Acinetobacter spp. isolates found in northeastern China was investigated. All 105 Acinetobacter spp. isolates were determined to be multidrug resistant (MDR), and the resistance rates to carbapenem agents were approximately 50%. PER, IMP, AmpC, and OXA-23 were found to be dominant β-lactamases belonging to different classes, respectively. This is the first report of the coexistence of bla PER , bla IMP , bla AmpC , and bla OXA-23-like genes in Acinetobacter spp. isolates from northeastern China. ISAba1 was found upstream of the bla OXA-23-like gene in 87.8% (36/41) strains and upstream of the bla OXA-51-like gene in 26.5% (13/49) strains. ISAba3-like element was found upstream of the bla OXA-58-like gene in one bla OXA-58-like -positive strain. The presence of IntI1 was detected in 63.8% (67/105) of the isolates and the most prevalent gene cassettes were aacA4, aadA1, and catB8. The highly prevalent isolates belong to international clonal lineage (ICL)-II. These results indicate that the wide horizontal and clonal spread of MDR Acinetobacter spp. isolates harbouring multiple β-lactamase genes has become a serious problem in northeastern China.

Effect of multipurpose solutions against Acinetobacter carrying QAC genes.

PubMed

Boost, Maureen V; Chan, Jessica; Shi, Guang-sen; Cho, Pauline

2014-03-01

Acinetobacter has low virulence but causes infections in subjects with reduced immunity. It has been reported in ocular infections including those of patients using contact lenses. Treatment is difficult because Acinetobacter is frequently multidrug resistant. Antibiotic-resistant strains frequently also harbor genes for antiseptic resistance (quaternary ammonium compound [QAC]) genes. Because Acinetobacter is part of the normal flora, it may contaminate contact lens and accessories. This study aims to investigate carriage rates of QAC genes in household and clinical isolates of Acinetobacter and to determine the effectiveness of two multipurpose solutions (MPSs) for soft lenses against organisms carrying QAC genes. DNA was extracted from 11 bathroom isolates and 15 clinical isolates and amplified by polymerase chain reaction to determine the presence of qacEΔ1. Gene-positive and gene-negative control strains were used to challenge the two MPSs, and minimum inhibitory concentrations (MICs) of these organisms to benzalkonium chloride and chlorhexidine gluconate were determined. More than 90% of isolates carried qacEΔ1. The MICs of clinical isolates were higher than those of isolates of bathrooms. Both MPSs were able to produce a 3-log reduction in the numbers of all isolates. Although most isolates carried qacEΔ1 and elevated MICs to benzalkonium chloride and chlorhexidine gluconate were observed, all were susceptible to both MPSs tested. However, if there were to be poor compliance with care procedures, it is probable that such organisms could survive in the presence of diluted or expired solutions.

Phylogenetic relationship and virulence inference of Streptococcus Anginosus Group: curated annotation and whole-genome comparative analysis support distinct species designation

PubMed Central

2013-01-01

Background The Streptococcus Anginosus Group (SAG) represents three closely related species of the viridans group streptococci recognized as commensal bacteria of the oral, gastrointestinal and urogenital tracts. The SAG also cause severe invasive infections, and are pathogens during cystic fibrosis (CF) pulmonary exacerbation. Little genomic information or description of virulence mechanisms is currently available for SAG. We conducted intra and inter species whole-genome comparative analyses with 59 publically available Streptococcus genomes and seven in-house closed high quality finished SAG genomes; S. constellatus (3), S. intermedius (2), and S. anginosus (2). For each SAG species, we sequenced at least one numerically dominant strain from CF airways recovered during acute exacerbation and an invasive, non-lung isolate. We also evaluated microevolution that occurred within two isolates that were cultured from one individual one year apart. Results The SAG genomes were most closely related to S. gordonii and S. sanguinis, based on shared orthologs and harbor a similar number of proteins within each COG category as other Streptococcus species. Numerous characterized streptococcus virulence factor homologs were identified within the SAG genomes including; adherence, invasion, spreading factors, LPxTG cell wall proteins, and two component histidine kinases known to be involved in virulence gene regulation. Mobile elements, primarily integrative conjugative elements and bacteriophage, account for greater than 10% of the SAG genomes. S. anginosus was the most variable species sequenced in this study, yielding both the smallest and the largest SAG genomes containing multiple genomic rearrangements, insertions and deletions. In contrast, within the S. constellatus and S. intermedius species, there was extensive continuous synteny, with only slight differences in genome size between strains. Within S. constellatus we were able to determine important SNPs and changes in VNTR numbers that occurred over the course of one year. Conclusions The comparative genomic analysis of the SAG clarifies the phylogenetics of these bacteria and supports the distinct species classification. Numerous potential virulence determinants were identified and provide a foundation for further studies into SAG pathogenesis. Furthermore, the data may be used to enable the development of rapid diagnostic assays and therapeutics for these pathogens. PMID:24341328

Digestion of rice straw and oil palm fronds by microflora from rumen and termite bacteria, in vitro.

PubMed

Ramin, M; Alimon, A R; Panandam, J M; Sijam, K; Javanmard, A; Abdullah, N

2008-02-15

The digestion and Volatile Fatty Acid (VFA) production from rice straw and oil palm fronds by cellulolytic bacteria isolated from the termite Coptotermes curvignathus were investigated. The bacteria were Acinetobacter strain Raminalimon, Enterobacter aerogenes strain Razmin C, Enterobacter cloacae strain Razmin B, Bacillus cereus strain Razmin A and Chryseobacterium kwangyangense strain Cb. Acinetobacter strain Raminalimon is an aerobic bacterium, while the other species are facultative anaerobes. There were significant differences (p<0.05) among the bacteria for Dry Matter (DM) lost and acetic acid production from rice straw and Acinetobacter strain Raminalimon showed the highest activity. The facultative bacteria C. kwangyangense strain Cb (cfu mL(-1) 231 x 10(-6), OD: 0.5), E. cloacae (cfu mL(-1) 68 x 10(-7), OD: 0.5) and E. aerogenes (cfu mL(-1) 33 x 10(-7), OD: 0.5) were used for digestion study with the rumen fluid microflora. The in vitro gas production technique was applied for the comparative study and the parameters measured were pH, gas (volume), dry matter lost, acetic acid, propionic acid and butyric acid concentrations. pH was not significantly (p<0.05) different among the five treatments. The bacterium C. kwangyangense strain Cb showed the highest activity (p<0.05) for DM lost, acetic acid, propionic acid and butyric acid production from rice straw when compared to the other bacterial activities. There was no significance (p<0.05) difference between the three bacteria for the dry matter lost of oil palm fronds but the production of Volatile Fatty Acids (VFA) was significantly (p<0.05) high in the treatment which was inoculated with C. kwangyangense strain Cb. The Gen Bank NCBI/EMBL accession numbers for the bacterial strains are EU332791, EU305608, EU305609, EU294508 and EU169201.

Antibacterial activity of BMS-180680, a new catechol-containing monobactam.

PubMed Central

Fung-Tomc, J; Bush, K; Minassian, B; Kolek, B; Flamm, R; Gradelski, E; Bonner, D

1997-01-01

The in vitro activities of a new catechol-containing monobactam, BMS-180680 (SQ 84,100), were compared to those of aztreonam, ceftazidime, imipenem, piperacillin-tazobactam, ciprofloxacin, amikacin, and trimethoprim-sulfamethoxazole. BMS-180680 was often the most active compound against many species of the family Enterobacteriaceae, with MICs at which 90% of the isolates were inhibited (MIC90s) of < or = 0.5 microg/ml for Escherichia coli, Klebsiella spp., Citrobacter diversus, Enterobacter aerogenes, Serratia marcescens, Proteus spp., and Providencia spp. BMS-180680 had moderate activities (MIC90s of 2 to 8 microg/ml) against Citrobacter freundii, Morganella morganii, Shigella spp., and non-E. aerogenes Enterobacter spp. BMS-180680 was the only antibiotic evaluated that was active against >90% of the Pseudomonas aeruginosa (MIC90, 0.25 microg/ml), Burkholderia cepacia, and Stenotrophomonas maltophilia (MIC90s, 1 microg/ml) strains tested. BMS-180680 was inactive against most strains of Pseudomonas fluorescens, Pseudomonas stutzeri, Pseudomonas diminuta, and Burkholderia pickettii. BMS-180680 was moderately active (MIC90s of 4 to 8 microg/ml) against Alcaligenes spp. and Acinetobacter lwoffii and less active (MIC90, 16 microg/ml) against Acinetobacter calcoaceticus-Acinetobacter baumanii complex. BMS-180680 lacked activity against gram-positive bacteria and anaerobic bacteria. Both tonB and cir fiu double mutants of E. coli had greatly decreased susceptibility to BMS-180680. Of the TEM, PSE, and chromosomal-encoded beta-lactamases tested, only the K1 enzyme hydrolyzed BMS-180680 to any measurable extent. Like aztreonam, BMS-180680 bound preferentially to penicillin-binding protein 3. The MICs of BMS-180680 were not influenced by the presence of hematin or 5% sheep blood in the test medium or with incubation in an atmosphere containing 5% CO2. BMS-180680 MICs obtained under strict anaerobic conditions were significantly higher than those obtained in ambient air. PMID:9145861

Positive Selection Driving Cytoplasmic Genome Evolution of the Medicinally Important Ginseng Plant Genus Panax

PubMed Central

Jiang, Peng; Shi, Feng-Xue; Li, Ming-Rui; Liu, Bao; Wen, Jun; Xiao, Hong-Xing; Li, Lin-Feng

2018-01-01

Panax L. (the ginseng genus) is a shade-demanding group within the family Araliaceae and all of its species are of crucial significance in traditional Chinese medicine. Phylogenetic and biogeographic analyses demonstrated that two rounds of whole genome duplications accompanying with geographic and ecological isolations promoted the diversification of Panax species. However, contributions of the cytoplasmic genomes to the adaptive evolution of Panax species remained largely uninvestigated. In this study, we sequenced the chloroplast and mitochondrial genomes of 11 accessions belonging to seven Panax species. Our results show that heterogeneity in nucleotide substitution rate is abundant in both of the two cytoplasmic genomes, with the mitochondrial genome possessing more variants at the total level but the chloroplast showing higher sequence polymorphisms at the genic regions. Genome-wide scanning of positive selection identified five and 12 genes from the chloroplast and mitochondrial genomes, respectively. Functional analyses further revealed that these selected genes play important roles in plant development, cellular metabolism and adaptation. We therefore conclude that positive selection might be one of the potential evolutionary forces that shaped nucleotide variation pattern of these Panax species. In particular, the mitochondrial genes evolved under stronger selective pressure compared to the chloroplast genes. PMID:29670636

Positive Selection Driving Cytoplasmic Genome Evolution of the Medicinally Important Ginseng Plant Genus Panax.

PubMed

Jiang, Peng; Shi, Feng-Xue; Li, Ming-Rui; Liu, Bao; Wen, Jun; Xiao, Hong-Xing; Li, Lin-Feng

2018-01-01

Panax L. (the ginseng genus) is a shade-demanding group within the family Araliaceae and all of its species are of crucial significance in traditional Chinese medicine. Phylogenetic and biogeographic analyses demonstrated that two rounds of whole genome duplications accompanying with geographic and ecological isolations promoted the diversification of Panax species. However, contributions of the cytoplasmic genomes to the adaptive evolution of Panax species remained largely uninvestigated. In this study, we sequenced the chloroplast and mitochondrial genomes of 11 accessions belonging to seven Panax species. Our results show that heterogeneity in nucleotide substitution rate is abundant in both of the two cytoplasmic genomes, with the mitochondrial genome possessing more variants at the total level but the chloroplast showing higher sequence polymorphisms at the genic regions. Genome-wide scanning of positive selection identified five and 12 genes from the chloroplast and mitochondrial genomes, respectively. Functional analyses further revealed that these selected genes play important roles in plant development, cellular metabolism and adaptation. We therefore conclude that positive selection might be one of the potential evolutionary forces that shaped nucleotide variation pattern of these Panax species. In particular, the mitochondrial genes evolved under stronger selective pressure compared to the chloroplast genes.

Complete mitochondrial genome of the aluminum-tolerant fungus Rhodotorula taiwanensis RS1 and comparative analysis of Basidiomycota mitochondrial genomes.

PubMed

Zhao, Xue Qiang; Aizawa, Tomoko; Schneider, Jessica; Wang, Chao; Shen, Ren Fang; Sunairi, Michio

2013-04-01

The complete mitochondrial genome of Rhodotorula taiwanensis RS1, an aluminum-tolerant Basidiomycota fungus, was determined and compared with the known mitochondrial genomes of 12 Basidiomycota species. The mitochondrial genome of R. taiwanensis RS1 is a circular DNA molecule of 40,392 bp and encodes the typical 15 mitochondrial proteins, 23 tRNAs, and small and large rRNAs as well as 10 intronic open reading frames. These genes are apparently transcribed in two directions and do not show syntenies in gene order with other investigated Basidiomycota species. The average G+C content (41%) of the mitochondrial genome of R. taiwanensis RS1 is the highest among the Basidiomycota species. Two introns were detected in the sequence of the atp9 gene of R. taiwanensis RS1, but not in that of other Basidiomycota species. Rhodotorula taiwanensis is the first species of the genus Rhodotorula whose full mitochondrial genome has been sequenced; and the data presented here supply valuable information for understanding the evolution of fungal mitochondrial genomes and researching the mechanism of aluminum tolerance in microorganisms. © 2013 The Authors. Published by Blackwell Publishing Ltd.

Complete genomes of Hairstreak butterflies, their speciation, and nucleo-mitochondrial incongruence

PubMed Central

Cong, Qian; Shen, Jinhui; Borek, Dominika; Robbins, Robert K.; Otwinowski, Zbyszek; Grishin, Nick V.

2016-01-01

Comparison of complete genomes of closely related species enables research on speciation and how phenotype is determined by genotype. Lepidoptera, an insect order of 150,000 species with diverse phenotypes, is well-suited for such comparative genomics studies if new genomes, which cover additional Lepidoptera families are acquired. We report a 729 Mbp genome assembly of the Calycopis cecrops, the first genome from the family Lycaenidae and the largest available Lepidoptera genome. As detritivore, Calycopis shows expansion in detoxification and digestion enzymes. We further obtained complete genomes of 8 Calycopis specimens: 3 C. cecrops and 5 C. isobeon, including a dry specimen stored in the museum for 30 years. The two species differ subtly in phenotype and cannot be differentiated by mitochondrial DNA. However, nuclear genomes revealed a deep split between them. Genes that can clearly separate the two species (speciation hotspots) mostly pertain to circadian clock, mating behavior, transcription regulation, development and cytoskeleton. The speciation hotspots and their function significantly overlap with those we previously found in Pterourus, suggesting common speciation mechanisms in these butterflies. PMID:27120974

Complete genomes of Hairstreak butterflies, their speciation, and nucleo-mitochondrial incongruence.

PubMed

Cong, Qian; Shen, Jinhui; Borek, Dominika; Robbins, Robert K; Otwinowski, Zbyszek; Grishin, Nick V

2016-04-28

Comparison of complete genomes of closely related species enables research on speciation and how phenotype is determined by genotype. Lepidoptera, an insect order of 150,000 species with diverse phenotypes, is well-suited for such comparative genomics studies if new genomes, which cover additional Lepidoptera families are acquired. We report a 729 Mbp genome assembly of the Calycopis cecrops, the first genome from the family Lycaenidae and the largest available Lepidoptera genome. As detritivore, Calycopis shows expansion in detoxification and digestion enzymes. We further obtained complete genomes of 8 Calycopis specimens: 3 C. cecrops and 5 C. isobeon, including a dry specimen stored in the museum for 30 years. The two species differ subtly in phenotype and cannot be differentiated by mitochondrial DNA. However, nuclear genomes revealed a deep split between them. Genes that can clearly separate the two species (speciation hotspots) mostly pertain to circadian clock, mating behavior, transcription regulation, development and cytoskeleton. The speciation hotspots and their function significantly overlap with those we previously found in Pterourus, suggesting common speciation mechanisms in these butterflies.

Binucleation to breed new plant species adaptable to their environments

PubMed Central

Moustafa, Khaled

2015-01-01

Classical plant breeding approaches may fall short to breed new plant species of high environmental and ecological interests. Biotechnological and genetic manipulations, on the other hand, may hold more effective capabilities to circumvent the limitations of sexual incompatibility and conventional breeding programs. Given that plant cells encompass multiple copies of organellar genomes (mitochondrial and plastidial genomes), an important question could be raised about whether an artificial attempt to duplicate the nuclear genome might also be conceivable through a binucleation approach (generating plant cells with 2 nuclei from 2 different plant species) for potential production of new polyploidies that would characterize new plant species. Since the complexities of plant genomes are the result of multiple genome duplications, an artificial binucleation approach would thus be of some interest to eventually varying plant genomes and producing new polyploidy from related or distal plant species. Here, I discuss the potentiality of such an approach to engineer binucleated plant cells as a germ of new plant species to fulfill some environmental applications such as increasing the biodiversity and breeding new species adaptable to harsh environmental stresses and increasing green surfaces to reduce atmospheric pollutions in arid lands with poor vegetation. PMID:26322577

MICROBIAL PROFILE AND ANTIBIOTIC SUSCEPTIBILITY PATTERNS OF PATHOGENS CAUSING VENTILATOR- ASSOCIATED PNEUMONIA AT INTENSIVE CARE UNIT, SESTRE MILOSRDNICE UNIVERSITY HOSPITAL CENTER, ZAGREB, CROATIA.

PubMed

Turković, Tihana Magdić; Grginić, Ana Gverić; Cucujić, Branka Đuras; Gašpar, Božena; Širanović, Mladen; Perić, Mladen

2015-06-01

Ventilator-associated pneumonia (VAP) is very common in many intensive care Units, but there are still many uncertainties about VAP, especially about the choice of initial empiric antibiotics. The incidence of specific pathogens with different susceptibility patterns causing VAP varies from hospital to hospital. This is the reason why empiric initial antibiotic treatment for VAP should be based not only on general guidelines (that recommend therapy according to the presence of risk factors for multidrug-resistant bacteria), but also on up-to-date information on local epidemiology. The aim of this study was to determine the microbial profile of pathogens causing VAP and their antibiotic susceptibility patterns. The study was conducted in the 15-bed surgical and neurosurgical Intensive Care Unit, Department of Anesthesiology and Intensive Care, Sestre milosrdnice University Hospital Center, Zagreb, Croatia. Retrospective data were collected from September 2009 to March 2013. All patients that developed VAP during the study period were eligible for the study. According to study results, the incidence of VAP was 29.4%. The most commonly isolated bacterium was Staphylococcus aureus (21.1%), followed by Pseudomonas aeruginosa (19.0%) and Acinetobacter species (13.6%). All Staphylococcus aureus isolates were susceptible to vancomycin and linezolid. Pseudomonas aeruginosa showed 100% susceptibility to cefepime and very high susceptibility to pip'eracillin-tazobactam (96%), ceftazidime (93%) and ciprofloxacin (89%). Ampicillin-sulbactam was highly effective for Acinetobacter species, showing resistance in only 8% of isolates. In conclusion, according to study data, appropriate empiric antibiotic therapy for patients with VAP without risk factors for multidrug-resistant bacteria is ceftriaxone and for patients with risk factors for multidrug-resistant bacteria ampicillin-sulbactam plus cefepime plus vancomycin or linezolid.

Uterine bacterial flora in postpartum Danish Holstein dairy cows determined using DNA-based fingerprinting: correlation to uterine condition and calving management.

PubMed

Elkjær, K; Ancker, M-L; Gustafsson, H; Friggens, N C; Waldmann, A; Mølbak, L; Callesen, H

2013-04-01

The overall aim of this study was to describe uterine bacterial flora during the postpartum period in Danish Holstein cows using the Terminal Restriction Fragment Length Polymorphism (T-RFLP) method. This method produces a pattern of nucleic acid fragments from the microorganisms present, reflecting the "fingerprint" of the actual microbial flora. As well as characterizing changes in flora with time from calving and between herds, data were examined for strong relations between uterine bacterial flora, calving management and uterine condition. In total 125 Holstein cows from five herds were included, and for each cow calving management was recorded. Cows were clinically examined on average 8 (range 0-19) and 28 (range 22-38) days after calving, and a uterine sample was taken for bacterial identification using T-RFLP. Milk samples were taken weekly for progesterone analysis. Bacteria were found in all cows at both examinations, and the flora was composed of many species, including species not traditionally reported to be present in the bovine uterus. The bacterial composition differed according to days from calving and herd. In all five herds Fusobacterium necrophorum, Pseudomonas/Acinetobacter and Bacteroides/Sphingobacterium/Prevotellaceae were among the most common at both examinations. In four herds there was a percentage decrease of F. necrophorum from first to second examination, and in all herds there was a percentage increase of Pseudomonas/Acinetobacter from first to second examination. No differences in bacterial flora were found between cows with different uterine scores, which were influenced by herd, calving difficulty and retained placenta. Copyright © 2013 Elsevier B.V. All rights reserved.

Inactivation of Gram-negative and Gram-positive bacteria in red cell concentrates using INACTINE PEN110 chemistry.

PubMed

Zavizion, B; Serebryanik, D; Chapman, J; Alford, B; Purmal, A

2004-10-01

The risk of transfusion-transmitted bacterial infections as a result of the presence of bacteria in blood is one of the major concerns in transfusion medicine. The purpose of this study was to investigate whether bacteria inoculated into red blood cell concentrates can be inactivated by the INACTINE PEN110 pathogen-reduction process. Four bacterial species were chosen for the study: anaerobic Gram-positive Clostridium perfringens and Propionibacterium acnes, known to be transfusion-transmitted; and two Gram-negative species, Acinetobacter johnsonii and Acinetobacter lwoffii, recently reported to be a common cause of transfusion-associated infections in Europe. Identical units of leucoreduced red cell concentrates were inoculated with A. johnsonii, A. lwoffii, C. perfringens, or P. acnes. The 4 degrees C control units were put on storage immediately after receiving the spike. The test units were subjected to PEN110 treatment and then stored. The bacterial titre in all units was monitored during a 6-week storage period. The PEN110 inactivation of all tested bacterial strains was time- and titre-dependent. For A. johnsonii and A. lwoffii, no viable bacteria were detected in the units spiked with up to 10(4) colony-forming units (CFU)/ml and treated with PEN110. For red cell units spiked with 10(4)-10(5) CFU/ml of C. perfringens and P. acnes, no viable bacteria were detected in the units treated with PEN110. In control units, there was a gradual decrease in A. johnsonii, A. lwoffii and C. perfringens titres during cold storage, while P. acnes titres remained stable. The PEN110 pathogen-reduction process was demonstrated to inactivate high titres of A. johnsonii, A. lwoffii, C. perfringens and P. acnes in red cell concentrates.

Head Lice of Pygmies Reveal the Presence of Relapsing Fever Borreliae in the Republic of Congo

PubMed Central

Amanzougaghene, Nadia; Akiana, Jean; Mongo Ndombe, Géor; Davoust, Bernard; Nsana, Nardiouf Sjelin; Parra, Henri-Joseph; Fenollar, Florence; Raoult, Didier; Mediannikov, Oleg

2016-01-01

Background Head lice, Pediculus humanus capitis, occur in four divergent mitochondrial clades (A, B, C and D), each having particular geographical distributions. Recent studies suggest that head lice, as is the case of body lice, can act as a vector for louse-borne diseases. Therefore, understanding the genetic diversity of lice worldwide is of critical importance to our understanding of the risk of louse-borne diseases. Methodology/Principal Findings Here, we report the results of the first molecular screening of pygmies’ head lice in the Republic of Congo for seven pathogens and an analysis of lice mitochondrial clades. We developed two duplex clade-specific real-time PCRs and identified three major mitochondrial clades: A, C, and D indicating high diversity among the head lice studied. We identified the presence of a dangerous human pathogen, Borrelia recurrentis, the causative agent of relapsing fever, in ten clade A head lice, which was not reported in the Republic of Congo, and B. theileri in one head louse. The results also show widespread infection among head lice with several species of Acinetobacter. A. junii was the most prevalent, followed by A. ursingii, A. baumannii, A. johnsonii, A. schindleri, A. lwoffii, A. nosocomialis and A. towneri. Conclusions/Significance Our study is the first to show the presence of B. recurrentis in African pygmies’ head lice in the Republic of Congo. This study is also the first to report the presence of DNAs of B. theileri and several species of Acinetobacter in human head lice. Further studies are needed to determine whether the head lice can transmit these pathogenic bacteria from person to another. PMID:27911894

Development and cross-species/genera transferability of microsatellite markers discovered using 454 genome sequencing in chokecherry (Prunus virginiana L.).

PubMed

Wang, Hongxia; Walla, James A; Zhong, Shaobin; Huang, Danqiong; Dai, Wenhao

2012-11-01

Chokecherry (Prunus virginiana L.) (2n = 4x = 32) is a unique Prunus species for both genetics and disease-resistance research due to its tetraploid nature and X-disease resistance. However, no genetic and genomic information on chokecherry is available. A partial chokecherry genome was sequenced using Roche 454 sequencing technology. A total of 145,094 reads covering 4.8 Mbp of the chokecherry genome were generated and 15,113 contigs were assembled, of which 11,675 contigs were larger than 100 bp in size. A total of 481 SSR loci were identified from 234 (out of 11,675) contigs and 246 polymerase chain reaction (PCR) primer pairs were designed. Of 246 primers, 212 (86.2 %) effectively produced amplification from the genomic DNA of chokecherry. All 212 amplifiable chokecherry primers were used to amplify genomic DNA from 11 other rosaceous species (sour cherry, sweet cherry, black cherry, peach, apricot, plum, apple, crabapple, pear, juneberry, and raspberry). Thus, chokecherry SSR primers can be transferable across Prunus species and other rosaceous species. An average of 63.2 and 58.7 % of amplifiable chokecherry primers amplified DNA from cherry and other Prunus species, respectively, while 47.2 % of amplifiable chokecherry primers amplified DNA from other rosaceous species. Using random genome sequence data generated from next-generation sequencing technology to identify microsatellite loci appears to be rapid and cost-efficient, particularly for species with no sequence information available. Sequence information and confirmed transferability of the identified chokecherry SSRs among species will be valuable for genetic research in Prunus and other rosaceous species. Key message A total of 246 SSR primers were identified from chokecherry genome sequences. Of which, 212 were confirmed amplifiable both in chokecherry and other 11 other rosaceous species.

Development and characterization of microsatellite markers for Morus spp. and assessment of their transferability to other closely related species

PubMed Central

2013-01-01

Background Adoption of genomics based breeding has emerged as a promising approach for achieving comprehensive crop improvement. Such an approach is more relevant in the case of perennial species like mulberry. However, unavailability of genomic resources of co-dominant marker systems has been the major constraint for adopting molecular breeding to achieve genetic enhancement of Mulberry. The goal of this study was to develop and characterize a large number of locus specific genic and genomic SSR markers which can be effectively used for molecular characterization of mulberry species/genotypes. Result We analyzed a total of 3485 DNA sequences including genomic and expressed sequences (ESTs) of mulberry (Morus alba L.) genome. We identified 358 sequences to develop appropriate microsatellite primer pairs representing 222 genomic and 136 EST regions. Primers amplifying locus specific regions of Dudia white (a genotype of Morus alba L), were identified and 137 genomic and 51 genic SSR markers were standardized. A two pronged strategy was adopted to assess the applicability of these SSR markers using mulberry species and genotypes along with a few closely related species belonging to the family Moraceae viz., Ficus, Fig and Jackfruit. While 100% of these markers amplified specific loci on the mulberry genome, 79% were transferable to other related species indicating the robustness of these markers and the potential they hold in analyzing the molecular and genetic diversity among mulberry germplasm as well as other related species. The inherent ability of these markers in detecting heterozygosity combined with a high average polymorphic information content (PIC) of 0.559 ranging between 0.076 and 0.943 clearly demonstrates their potential as genomic resources in diversity analysis. The dissimilarity coefficient determined based on Neighbor joining method, revealed that the markers were successful in segregating the mulberry species, genotypes and other related species into distinct clusters. Conclusion We report a total of 188 genomic and genic SSR markers in Morus alba L. A large proportion of these markers (164) were polymorphic both among mulberry species and genotypes. A substantial number of these markers (149) were also transferable to other related species like Ficus, Fig and Jackfruit. The extent of polymorphism revealed and the ability to detect heterozygosity among the cross pollinated mulberry species and genotypes render these markers an invaluable genomic resource that can be utilized in assessing molecular diversity as well as in QTL mapping and subsequently mulberry crop improvement through MAS. PMID:24289047

The Complete Chloroplast Genome of Wild Rice (Oryza minuta) and Its Comparison to Related Species.

PubMed

Asaf, Sajjad; Waqas, Muhammad; Khan, Abdul L; Khan, Muhammad A; Kang, Sang-Mo; Imran, Qari M; Shahzad, Raheem; Bilal, Saqib; Yun, Byung-Wook; Lee, In-Jung

2017-01-01

Oryza minuta , a tetraploid wild relative of cultivated rice (family Poaceae), possesses a BBCC genome and contains genes that confer resistance to bacterial blight (BB) and white-backed (WBPH) and brown (BPH) plant hoppers. Based on the importance of this wild species, this study aimed to understand the phylogenetic relationships of O. minuta with other Oryza species through an in-depth analysis of the composition and diversity of the chloroplast (cp) genome. The analysis revealed a cp genome size of 135,094 bp with a typical quadripartite structure and consisting of a pair of inverted repeats separated by small and large single copies, 139 representative genes, and 419 randomly distributed microsatellites. The genomic organization, gene order, GC content and codon usage are similar to those of typical angiosperm cp genomes. Approximately 30 forward, 28 tandem and 20 palindromic repeats were detected in the O . minuta cp genome. Comparison of the complete O. minuta cp genome with another eleven Oryza species showed a high degree of sequence similarity and relatively high divergence of intergenic spacers. Phylogenetic analyses were conducted based on the complete genome sequence, 65 shared genes and matK gene showed same topologies and O. minuta forms a single clade with parental O. punctata . Thus, the complete O . minuta cp genome provides interesting insights and valuable information that can be used to identify related species and reconstruct its phylogeny.

Small genomes and large seeds: chromosome numbers, genome size and seed mass in diploid Aesculus species (Sapindaceae)

PubMed Central

Krahulcová, Anna; Trávníček, Pavel; Rejmánek, Marcel

2017-01-01

Background and Aims Aesculus L. (horse chestnut, buckeye) is a genus of 12–19 extant woody species native to the temperate Northern Hemisphere. This genus is known for unusually large seeds among angiosperms. While chromosome counts are available for many Aesculus species, only one has had its genome size measured. The aim of this study is to provide more genome size data and analyse the relationship between genome size and seed mass in this genus. Methods Chromosome numbers in root tip cuttings were confirmed for four species and reported for the first time for three additional species. Flow cytometric measurements of 2C nuclear DNA values were conducted on eight species, and mean seed mass values were estimated for the same taxa. Key Results The same chromosome number, 2n = 40, was determined in all investigated taxa. Original measurements of 2C values for seven Aesculus species (eight taxa), added to just one reliable datum for A. hippocastanum, confirmed the notion that the genome size in this genus with relatively large seeds is surprisingly low, ranging from 0·955 pg 2C–1 in A. parviflora to 1·275 pg 2C–1 in A. glabra var. glabra. Conclusions The chromosome number of 2n = 40 seems to be conclusively the universal 2n number for non-hybrid species in this genus. Aesculus genome sizes are relatively small, not only within its own family, Sapindaceae, but also within woody angiosperms. The genome sizes seem to be distinct and non-overlapping among the four major Aesculus clades. These results provide an extra support for the most recent reconstruction of Aesculus phylogeny. The correlation between the 2C values and seed masses in examined Aesculus species is slightly negative and not significant. However, when the four major clades are treated separately, there is consistent positive association between larger genome size and larger seed mass within individual lineages. PMID:28065925

Comparative Genomics of Bacillus species and its Relevance in Industrial Microbiology.

PubMed

Sharma, Archana; Satyanarayana, T

2013-01-01

With the advent of high throughput sequencing platforms and relevant analytical tools, the rate of microbial genome sequencing has accelerated which has in turn led to better understanding of microbial molecular biology and genetics. The complete genome sequences of important industrial organisms provide opportunities for human health, industry, and the environment. Bacillus species are the dominant workhorses in industrial fermentations. Today, genome sequences of several Bacillus species are available, and comparative genomics of this genus helps in understanding their physiology, biochemistry, and genetics. The genomes of these bacterial species are the sources of many industrially important enzymes and antibiotics and, therefore, provide an opportunity to tailor enzymes with desired properties to suit a wide range of applications. A comparative account of strengths and weaknesses of the different sequencing platforms are also highlighted in the review.

Divergence with gene flow across a speciation continuum of Heliconius butterflies.

PubMed

Supple, Megan A; Papa, Riccardo; Hines, Heather M; McMillan, W Owen; Counterman, Brian A

2015-09-24

A key to understanding the origins of species is determining the evolutionary processes that drive the patterns of genomic divergence during speciation. New genomic technologies enable the study of high-resolution genomic patterns of divergence across natural speciation continua, where taxa pairs with different levels of reproductive isolation can be used as proxies for different stages of speciation. Empirical studies of these speciation continua can provide valuable insights into how genomes diverge during speciation. We examine variation across a handful of genomic regions in parapatric and allopatric populations of Heliconius butterflies with varying levels of reproductive isolation. Genome sequences were mapped to 2.2-Mb of the H. erato genome, including 1-Mb across the red color pattern locus and multiple regions unlinked to color pattern variation. Phylogenetic analyses reveal a speciation continuum of pairs of hybridizing races and incipient species in the Heliconius erato clade. Comparisons of hybridizing pairs of divergently colored races and incipient species reveal that genomic divergence increases with ecological and reproductive isolation, not only across the locus responsible for adaptive variation in red wing coloration, but also at genomic regions unlinked to color pattern. We observe high levels of divergence between the incipient species H. erato and H. himera, suggesting that divergence may accumulate early in the speciation process. Comparisons of genomic divergence between the incipient species and allopatric races suggest that limited gene flow cannot account for the observed high levels of divergence between the incipient species. Our results provide a reconstruction of the speciation continuum across the H. erato clade and provide insights into the processes that drive genomic divergence during speciation, establishing the H. erato clade as a powerful framework for the study of speciation.

Comparative genomics reveals high biological diversity and specific adaptations in the industrially and medically important fungal genus Aspergillus.

PubMed

de Vries, Ronald P; Riley, Robert; Wiebenga, Ad; Aguilar-Osorio, Guillermo; Amillis, Sotiris; Uchima, Cristiane Akemi; Anderluh, Gregor; Asadollahi, Mojtaba; Askin, Marion; Barry, Kerrie; Battaglia, Evy; Bayram, Özgür; Benocci, Tiziano; Braus-Stromeyer, Susanna A; Caldana, Camila; Cánovas, David; Cerqueira, Gustavo C; Chen, Fusheng; Chen, Wanping; Choi, Cindy; Clum, Alicia; Dos Santos, Renato Augusto Corrêa; Damásio, André Ricardo de Lima; Diallinas, George; Emri, Tamás; Fekete, Erzsébet; Flipphi, Michel; Freyberg, Susanne; Gallo, Antonia; Gournas, Christos; Habgood, Rob; Hainaut, Matthieu; Harispe, María Laura; Henrissat, Bernard; Hildén, Kristiina S; Hope, Ryan; Hossain, Abeer; Karabika, Eugenia; Karaffa, Levente; Karányi, Zsolt; Kraševec, Nada; Kuo, Alan; Kusch, Harald; LaButti, Kurt; Lagendijk, Ellen L; Lapidus, Alla; Levasseur, Anthony; Lindquist, Erika; Lipzen, Anna; Logrieco, Antonio F; MacCabe, Andrew; Mäkelä, Miia R; Malavazi, Iran; Melin, Petter; Meyer, Vera; Mielnichuk, Natalia; Miskei, Márton; Molnár, Ákos P; Mulé, Giuseppina; Ngan, Chew Yee; Orejas, Margarita; Orosz, Erzsébet; Ouedraogo, Jean Paul; Overkamp, Karin M; Park, Hee-Soo; Perrone, Giancarlo; Piumi, Francois; Punt, Peter J; Ram, Arthur F J; Ramón, Ana; Rauscher, Stefan; Record, Eric; Riaño-Pachón, Diego Mauricio; Robert, Vincent; Röhrig, Julian; Ruller, Roberto; Salamov, Asaf; Salih, Nadhira S; Samson, Rob A; Sándor, Erzsébet; Sanguinetti, Manuel; Schütze, Tabea; Sepčić, Kristina; Shelest, Ekaterina; Sherlock, Gavin; Sophianopoulou, Vicky; Squina, Fabio M; Sun, Hui; Susca, Antonia; Todd, Richard B; Tsang, Adrian; Unkles, Shiela E; van de Wiele, Nathalie; van Rossen-Uffink, Diana; Oliveira, Juliana Velasco de Castro; Vesth, Tammi C; Visser, Jaap; Yu, Jae-Hyuk; Zhou, Miaomiao; Andersen, Mikael R; Archer, David B; Baker, Scott E; Benoit, Isabelle; Brakhage, Axel A; Braus, Gerhard H; Fischer, Reinhard; Frisvad, Jens C; Goldman, Gustavo H; Houbraken, Jos; Oakley, Berl; Pócsi, István; Scazzocchio, Claudio; Seiboth, Bernhard; vanKuyk, Patricia A; Wortman, Jennifer; Dyer, Paul S; Grigoriev, Igor V

2017-02-14

The fungal genus Aspergillus is of critical importance to humankind. Species include those with industrial applications, important pathogens of humans, animals and crops, a source of potent carcinogenic contaminants of food, and an important genetic model. The genome sequences of eight aspergilli have already been explored to investigate aspects of fungal biology, raising questions about evolution and specialization within this genus. We have generated genome sequences for ten novel, highly diverse Aspergillus species and compared these in detail to sister and more distant genera. Comparative studies of key aspects of fungal biology, including primary and secondary metabolism, stress response, biomass degradation, and signal transduction, revealed both conservation and diversity among the species. Observed genomic differences were validated with experimental studies. This revealed several highlights, such as the potential for sex in asexual species, organic acid production genes being a key feature of black aspergilli, alternative approaches for degrading plant biomass, and indications for the genetic basis of stress response. A genome-wide phylogenetic analysis demonstrated in detail the relationship of the newly genome sequenced species with other aspergilli. Many aspects of biological differences between fungal species cannot be explained by current knowledge obtained from genome sequences. The comparative genomics and experimental study, presented here, allows for the first time a genus-wide view of the biological diversity of the aspergilli and in many, but not all, cases linked genome differences to phenotype. Insights gained could be exploited for biotechnological and medical applications of fungi.

Origin of the Y genome in Elymus and its relationship to other genomes in Triticeae based on evidence from elongation factor G (EF-G) gene sequences.

PubMed

Sun, Genlou; Komatsuda, Takao

2010-08-01

It is well known that Elymus arose through hybridization between representatives of different genera. Cytogenetic analyses show that all its members include the St genome in combination with one or more of four other genomes, the H, Y, P, and W genomes. The origins of the H, P, and W genomes are known, but not for the Y genome. We analyzed the single copy nuclear gene coding for elongation factor G (EF-G) from 28 accessions of polyploid Elymus species and 45 accessions of diploid Triticeae species in order to investigate origin of the Y genome and its relationship to other genomes in the tribe Triticeae. Sequence comparisons among the St, H, Y, P, W, and E genomes detected genome-specific polymorphisms at 66 nucleotide positions. The St and Y genomes are relatively dissimilar. The phylogeny of the Y genome sequences was investigated for the first time. They were most similar to the W genome sequences. The Y genome sequences were placed in two different groups. These two groups were included in an unresolved clade that included the W and E sequences as well as sequences from many annual species. The H genomes sequences were in a clade with the F, P, and Ns genome sequences as sister groups. These two clades were more closely related to each other and to the L and Xp genomes than they were to the St genome sequences. These data support the hypothesis that the Y genome evolved in a diploid species and has a different origin from the St genome. Copyright 2010 Elsevier Inc. All rights reserved.

Benefits of Genomic Insights and CRISPR-Cas Signatures to Monitor Potential Pathogens across Drinking Water Production and Distribution Systems

PubMed Central

Zhang, Ya; Kitajima, Masaaki; Whittle, Andrew J.; Liu, Wen-Tso

2017-01-01

The occurrence of pathogenic bacteria in drinking water distribution systems (DWDSs) is a major health concern, and our current understanding is mostly related to pathogenic species such as Legionella pneumophila and Mycobacterium avium but not to bacterial species closely related to them. In this study, genomic-based approaches were used to characterize pathogen-related species in relation to their abundance, diversity, potential pathogenicity, genetic exchange, and distribution across an urban drinking water system. Nine draft genomes recovered from 10 metagenomes were identified as Legionella (4 draft genomes), Mycobacterium (3 draft genomes), Parachlamydia (1 draft genome), and Leptospira (1 draft genome). The pathogenicity potential of these genomes was examined by the presence/absence of virulence machinery, including genes belonging to Type III, IV, and VII secretion systems and their effectors. Several virulence factors known to pathogenic species were detected with these retrieved draft genomes except the Leptospira-related genome. Identical clustered regularly interspaced short palindromic repeats-CRISPR-associated proteins (CRISPR-Cas) genetic signatures were observed in two draft genomes recovered at different stages of the studied system, suggesting that the spacers in CRISPR-Cas could potentially be used as a biomarker in the monitoring of Legionella related strains at an evolutionary scale of several years across different drinking water production and distribution systems. Overall, metagenomics approach was an effective and complementary tool of culturing techniques to gain insights into the pathogenic characteristics and the CRISPR-Cas signatures of pathogen-related species in DWDSs. PMID:29097994

Mammalian Comparative Genomics Reveals Genetic and Epigenetic Features Associated with Genome Reshuffling in Rodentia

PubMed Central

Capilla, Laia; Sánchez-Guillén, Rosa Ana; Farré, Marta; Paytuví-Gallart, Andreu; Malinverni, Roberto; Ventura, Jacint; Larkin, Denis M.

2016-01-01

Abstract Understanding how mammalian genomes have been reshuffled through structural changes is fundamental to the dynamics of its composition, evolutionary relationships between species and, in the long run, speciation. In this work, we reveal the evolutionary genomic landscape in Rodentia, the most diverse and speciose mammalian order, by whole-genome comparisons of six rodent species and six representative outgroup mammalian species. The reconstruction of the evolutionary breakpoint regions across rodent phylogeny shows an increased rate of genome reshuffling that is approximately two orders of magnitude greater than in other mammalian species here considered. We identified novel lineage and clade-specific breakpoint regions within Rodentia and analyzed their gene content, recombination rates and their relationship with constitutive lamina genomic associated domains, DNase I hypersensitivity sites and chromatin modifications. We detected an accumulation of protein-coding genes in evolutionary breakpoint regions, especially genes implicated in reproduction and pheromone detection and mating. Moreover, we found an association of the evolutionary breakpoint regions with active chromatin state landscapes, most probably related to gene enrichment. Our results have two important implications for understanding the mechanisms that govern and constrain mammalian genome evolution. The first is that the presence of genes related to species-specific phenotypes in evolutionary breakpoint regions reinforces the adaptive value of genome reshuffling. Second, that chromatin conformation, an aspect that has been often overlooked in comparative genomic studies, might play a role in modeling the genomic distribution of evolutionary breakpoints. PMID:28175287

Mammalian Comparative Genomics Reveals Genetic and Epigenetic Features Associated with Genome Reshuffling in Rodentia.

PubMed

Capilla, Laia; Sánchez-Guillén, Rosa Ana; Farré, Marta; Paytuví-Gallart, Andreu; Malinverni, Roberto; Ventura, Jacint; Larkin, Denis M; Ruiz-Herrera, Aurora

2016-12-01

Understanding how mammalian genomes have been reshuffled through structural changes is fundamental to the dynamics of its composition, evolutionary relationships between species and, in the long run, speciation. In this work, we reveal the evolutionary genomic landscape in Rodentia, the most diverse and speciose mammalian order, by whole-genome comparisons of six rodent species and six representative outgroup mammalian species. The reconstruction of the evolutionary breakpoint regions across rodent phylogeny shows an increased rate of genome reshuffling that is approximately two orders of magnitude greater than in other mammalian species here considered. We identified novel lineage and clade-specific breakpoint regions within Rodentia and analyzed their gene content, recombination rates and their relationship with constitutive lamina genomic associated domains, DNase I hypersensitivity sites and chromatin modifications. We detected an accumulation of protein-coding genes in evolutionary breakpoint regions, especially genes implicated in reproduction and pheromone detection and mating. Moreover, we found an association of the evolutionary breakpoint regions with active chromatin state landscapes, most probably related to gene enrichment. Our results have two important implications for understanding the mechanisms that govern and constrain mammalian genome evolution. The first is that the presence of genes related to species-specific phenotypes in evolutionary breakpoint regions reinforces the adaptive value of genome reshuffling. Second, that chromatin conformation, an aspect that has been often overlooked in comparative genomic studies, might play a role in modeling the genomic distribution of evolutionary breakpoints.

Comparative Genomics of Erwinia amylovora and Related Erwinia Species—What do We Learn?

PubMed Central

Zhao, Youfu; Qi, Mingsheng

2011-01-01

Erwinia amylovora, the causal agent of fire blight disease of apples and pears, is one of the most important plant bacterial pathogens with worldwide economic significance. Recent reports on the complete or draft genome sequences of four species in the genus Erwinia, including E. amylovora, E. pyrifoliae, E. tasmaniensis, and E. billingiae, have provided us near complete genetic information about this pathogen and its closely-related species. This review describes in silico subtractive hybridization-based comparative genomic analyses of eight genomes currently available, and highlights what we have learned from these comparative analyses, as well as genetic and functional genomic studies. Sequence analyses reinforce the assumption that E. amylovora is a relatively homogeneous species and support the current classification scheme of E. amylovora and its related species. The potential evolutionary origin of these Erwinia species is also proposed. The current understanding of the pathogen, its virulence mechanism and host specificity from genome sequencing data is summarized. Future research directions are also suggested. PMID:24710213

The complete mitochondrial genome of a stonefly species, Togoperla sp. (Plecoptera: Perlidae).

PubMed

Wang, Kai; Wang, Yuyu; Yang, Ding

2016-05-01

The complete mitochondrial (mt) genome of a stonefly species, Togoperla sp. (Plecoptera: Perlidae), was sequenced. The 15,723 bp long genome has the standard metazoan complement of 37 genes and an A+T-rich region, which is the same as the insect ancestral genome arrangement.

Development of a Custom-Designed, Pan Genomic DNA Microarray to Characterize Strain-Level Diversity among Cronobacter spp.

PubMed Central

Tall, Ben Davies; Gangiredla, Jayanthi; Gopinath, Gopal R.; Yan, Qiongqiong; Chase, Hannah R.; Lee, Boram; Hwang, Seongeun; Trach, Larisa; Park, Eunbi; Yoo, YeonJoo; Chung, TaeJung; Jackson, Scott A.; Patel, Isha R.; Sathyamoorthy, Venugopal; Pava-Ripoll, Monica; Kotewicz, Michael L.; Carter, Laurenda; Iversen, Carol; Pagotto, Franco; Stephan, Roger; Lehner, Angelika; Fanning, Séamus; Grim, Christopher J.

2015-01-01

Cronobacter species cause infections in all age groups; however neonates are at highest risk and remain the most susceptible age group for life-threatening invasive disease. The genus contains seven species:Cronobacter sakazakii, Cronobacter malonaticus, Cronobacter turicensis, Cronobacter muytjensii, Cronobacter dublinensis, Cronobacter universalis, and Cronobacter condimenti. Despite an abundance of published genomes of these species, genomics-based epidemiology of the genus is not well established. The gene content of a diverse group of 126 unique Cronobacter and taxonomically related isolates was determined using a pan genomic-based DNA microarray as a genotyping tool and as a means to identify outbreak isolates for food safety, environmental, and clinical surveillance purposes. The microarray constitutes 19,287 independent genes representing 15 Cronobacter genomes and 18 plasmids and 2,371 virulence factor genes of phylogenetically related Gram-negative bacteria. The Cronobacter microarray was able to distinguish the seven Cronobacter species from one another and from non-Cronobacter species; and within each species, strains grouped into distinct clusters based on their genomic diversity. These results also support the phylogenic divergence of the genus and clearly highlight the genomic diversity among each member of the genus. The current study establishes a powerful platform for further genomics research of this diverse genus, an important prerequisite toward the development of future countermeasures against this foodborne pathogen in the food safety and clinical arenas. PMID:25984509

Genotypic and Phenotypic Correlations of Multidrug-Resistant Acinetobacter baumannii-A. calcoaceticus Complex Strains Isolated from Patients at the National Naval Medical Center

USDA-ARS?s Scientific Manuscript database

Acinetobacter baumannii-calcoaceticus complex (ABC) infections have complicated the care of U.S. combat casualties. In this study, 102 ABC isolates from wounded soldiers treated at National Naval Medical Center (NNMC) were characterized by phenotype and genotype to identify clones in this population...

Infrequent air contamination with Acinetobacter baumannii of air surrounding known colonized or infected patients.

PubMed

Rock, Clare; Harris, Anthony D; Johnson, J Kristie; Bischoff, Werner E; Thom, Kerri A

2015-07-01

Using a validated air sampling method we found Acinetobacter baumannii in the air surrounding only 1 of 12 patients known to be colonized or infected with A. baumannii. Patients' closed-circuit ventilator status, frequent air exchanges in patient rooms, and short sampling time may have contributed to this low burden.

The spectrum of genomic signatures: from dinucleotides to chaos game representation.

PubMed

Wang, Yingwei; Hill, Kathleen; Singh, Shiva; Kari, Lila

2005-02-14

In the post genomic era, access to complete genome sequence data for numerous diverse species has opened multiple avenues for examining and comparing primary DNA sequence organization of entire genomes. Previously, the concept of a genomic signature was introduced with the observation of species-type specific Dinucleotide Relative Abundance Profiles (DRAPs); dinucleotides were identified as the subsequences with the greatest bias in representation in a majority of genomes. Herein, we demonstrate that DRAP is one particular genomic signature contained within a broader spectrum of signatures. Within this spectrum, an alternative genomic signature, Chaos Game Representation (CGR), provides a unique visualization of patterns in sequence organization. A genomic signature is associated with a particular integer order or subsequence length that represents a measure of the resolution or granularity in the analysis of primary DNA sequence organization. We quantitatively explore the organizational information provided by genomic signatures of different orders through different distance measures, including a novel Image Distance. The Image Distance and other existing distance measures are evaluated by comparing the phylogenetic trees they generate for 26 complete mitochondrial genomes from a diversity of species. The phylogenetic tree generated by the Image Distance is compatible with the known relatedness of species. Quantitative evaluation of the spectrum of genomic signatures may be used to ultimately gain insight into the determinants and biological relevance of the genome signatures.

Nucleic Acid Homologies Among Oxidase-Negative Moraxella Species

PubMed Central

Johnson, John L.; Anderson, Robert S.; Ordal, Erling J.

1970-01-01

The deoxyribonucleic acid (DNA) base composition and DNA homologies of more than 40 strains of oxidase-negative Moraxella species were determined. These bacteria have also been identified as belonging to the Mima-Herellea-Acinetobacter group and the Bacterium anitratum group, as well as to several other genera including Achromobacter and Alcaligenes. The DNA base content of these strains ranged from 40 to 46% guanine plus cytosine. DNA–DNA competition experiments distinguished five groups whose members were determined by showing 50% or more homology to one of the reference strains: B. anitratum type B5W, Achromobacter haemolyticus var. haemolyticus, Alcaligenes haemolysans, Achromobacter metalcaligenes, and Moraxella lwoffi. A sixth group comprised those strains showing less than 50% homology to any of the reference strains. Negligible homology was found between strains of oxidase-negative and oxidase-positive Moraxella species in DNA–DNA competition experiments. However, evidence of a distant relationship between the two groups was obtained in competition experiments by using ribosomal ribonucleic acid. PMID:5413826

Variability among Cucurbitaceae species (melon, cucumber and watermelon) in a genomic region containing a cluster of NBS-LRR genes.

PubMed

Morata, Jordi; Puigdomènech, Pere

2017-02-08

Cucurbitaceae species contain a significantly lower number of genes coding for proteins with similarity to plant resistance genes belonging to the NBS-LRR family than other plant species of similar genome size. A large proportion of these genes are organized in clusters that appear to be hotspots of variability. The genomes of the Cucurbitaceae species measured until now are intermediate in size (between 350 and 450 Mb) and they apparently have not undergone any genome duplications beside those at the origin of eudicots. The cluster containing the largest number of NBS-LRR genes has previously been analyzed in melon and related species and showed a high degree of interspecific and intraspecific variability. It was of interest to study whether similar behavior occurred in other cluster of the same family of genes. The cluster of NBS-LRR genes located in melon chromosome 9 was analyzed and compared with the syntenic regions in other cucurbit genomes. This is the second cluster in number within this species and it contains nine sequences with a NBS-LRR annotation including two genes, Fom1 and Prv, providing resistance against Fusarium and Ppapaya ring-spot virus (PRSV). The variability within the melon species appears to consist essentially of single nucleotide polymorphisms. Clusters of similar genes are present in the syntenic regions of the two species of Cucurbitaceae that were sequenced, cucumber and watermelon. Most of the genes in the syntenic clusters can be aligned between species and a hypothesis of generation of the cluster is proposed. The number of genes in the watermelon cluster is similar to that in melon while a higher number of genes (12) is present in cucumber, a species with a smaller genome than melon. After comparing genome resequencing data of 115 cucumber varieties, deletion of a group of genes is observed in a group of varieties of Indian origin. Clusters of genes coding for NBS-LRR proteins in cucurbits appear to have specific variability in different regions of the genome and between different species. This observation is in favour of considering that the adaptation of plant species to changing environments is based upon the variability that may occur at any location in the genome and that has been produced by specific mechanisms of sequence variation acting on plant genomes. This information could be useful both to understand the evolution of species and for plant breeding.

In vitro activity and beta-lactamase stability of a new difluoro oxacephem, 6315-S.

PubMed Central

Neu, H C; Chin, N X

1986-01-01

6315-S, a novel difluoromethyl thioacetamido oxacephem, had in vitro activity comparable to that of cefotaxime and moxalactam against Escherichia coli, Klebsiella pneumoniae, Proteus mirabilis, Klebsiella oxytoca, Citrobacter diversus, Salmonella spp., and Shigella spp., inhibiting 90% at less than or equal to 0.25 microgram/ml. It inhibited piperacillin- and cefoperazone-resistant isolates in these species. 6315-S did not inhibit cefotaxime- or moxalactam-resistant Citrobacter freundii, Enterobacter aerogenes, or Enterobacter cloacae (MICs for 90% of the strains tested were greater than or equal to 16 micrograms/ml). Proteus vulgaris resistant to cefotaxime was inhibited. Pseudomonas species and Acinetobacter species were resistant (MICs greater than 64 micrograms/ml). MICs for 90% of the Staphylococcus aureus and S. epidermidis isolates were 4 micrograms/ml. 6315-S was highly active against anaerobic species of Clostridium, Fusobacterium, Bacteroides, and peptostreptococci and was superior to other agents against these organisms. 6315-S was not hydrolyzed by the major plasmid and chromosomal beta-lactamases, but it induced chromosomal beta-lactamases in Enterobacter cloacae and Pseudomonas aeruginosa. PMID:3492172

GENOMIC APPROACHES FOR CROSS-SPECIES EXTRAPOLATION IN TOXICOLOGY

EPA Science Inventory

The latest tools for investigating stress in organisms, genomic technologies provide great insight into how different organisms respond to environmental conditions. However, their usefulness needs testing, verification, and codification. Genomic Approaches for Cross-Species Extra...

Genomics of Parallel Ecological Speciation in Lake Victoria Cichlids.

PubMed

Meier, Joana Isabel; Marques, David Alexander; Wagner, Catherine Elise; Excoffier, Laurent; Seehausen, Ole

2018-06-01

The genetic basis of parallel evolution of similar species is of great interest in evolutionary biology. In the adaptive radiation of Lake Victoria cichlid fishes, sister species with either blue or red-back male nuptial coloration have evolved repeatedly, often associated with shallower and deeper water, respectively. One such case is blue and red-backed Pundamilia species, for which we recently showed that a young species pair may have evolved through "hybrid parallel speciation". Coalescent simulations suggested that the older species P. pundamilia (blue) and P. nyererei (red-back) admixed in the Mwanza Gulf and that new "nyererei-like" and "pundamilia-like" species evolved from the admixed population. Here, we use genome scans to study the genomic architecture of differentiation, and assess the influence of hybridization on the evolution of the younger species pair. For each of the two species pairs, we find over 300 genomic regions, widespread across the genome, which are highly differentiated. A subset of the most strongly differentiated regions of the older pair are also differentiated in the younger pair. These shared differentiated regions often show parallel allele frequency differences, consistent with the hypothesis that admixture-derived alleles were targeted by divergent selection in the hybrid population. However, two-thirds of the genomic regions that are highly differentiated between the younger species are not highly differentiated between the older species, suggesting independent evolutionary responses to selection pressures. Our analyses reveal how divergent selection on admixture-derived genetic variation can facilitate new speciation events.

The Echinococcus canadensis (G7) genome: a key knowledge of parasitic platyhelminth human diseases.

PubMed

Maldonado, Lucas L; Assis, Juliana; Araújo, Flávio M Gomes; Salim, Anna C M; Macchiaroli, Natalia; Cucher, Marcela; Camicia, Federico; Fox, Adolfo; Rosenzvit, Mara; Oliveira, Guilherme; Kamenetzky, Laura

2017-02-27

The parasite Echinococcus canadensis (G7) (phylum Platyhelminthes, class Cestoda) is one of the causative agents of echinococcosis. Echinococcosis is a worldwide chronic zoonosis affecting humans as well as domestic and wild mammals, which has been reported as a prioritized neglected disease by the World Health Organisation. No genomic data, comparative genomic analyses or efficient therapeutic and diagnostic tools are available for this severe disease. The information presented in this study will help to understand the peculiar biological characters and to design species-specific control tools. We sequenced, assembled and annotated the 115-Mb genome of E. canadensis (G7). Comparative genomic analyses using whole genome data of three Echinococcus species not only confirmed the status of E. canadensis (G7) as a separate species but also demonstrated a high nucleotide sequences divergence in relation to E. granulosus (G1). The E. canadensis (G7) genome contains 11,449 genes with a core set of 881 orthologs shared among five cestode species. Comparative genomics revealed that there are more single nucleotide polymorphisms (SNPs) between E. canadensis (G7) and E. granulosus (G1) than between E. canadensis (G7) and E. multilocularis. This result was unexpected since E. canadensis (G7) and E. granulosus (G1) were considered to belong to the species complex E. granulosus sensu lato. We described SNPs in known drug targets and metabolism genes in the E. canadensis (G7) genome. Regarding gene regulation, we analysed three particular features: CpG island distribution along the three Echinococcus genomes, DNA methylation system and small RNA pathway. The results suggest the occurrence of yet unknown gene regulation mechanisms in Echinococcus. This is the first work that addresses Echinococcus comparative genomics. The resources presented here will promote the study of mechanisms of parasite development as well as new tools for drug discovery. The availability of a high-quality genome assembly is critical for fully exploring the biology of a pathogenic organism. The E. canadensis (G7) genome presented in this study provides a unique opportunity to address the genetic diversity among the genus Echinococcus and its particular developmental features. At present, there is no unequivocal taxonomic classification of Echinococcus species; however, the genome-wide SNPs analysis performed here revealed the phylogenetic distance among these three Echinococcus species. Additional cestode genomes need to be sequenced to be able to resolve their phylogeny.

Ecology and genomics of Bacillus subtilis.

PubMed

Earl, Ashlee M; Losick, Richard; Kolter, Roberto

2008-06-01

Bacillus subtilis is a remarkably diverse bacterial species that is capable of growth within many environments. Recent microarray-based comparative genomic analyses have revealed that members of this species also exhibit considerable genomic diversity. The identification of strain-specific genes might explain how B. subtilis has become so broadly adapted. The goal of identifying ecologically adaptive genes could soon be realized with the imminent release of several new B. subtilis genome sequences. As we embark upon this exciting new era of B. subtilis comparative genomics we review what is currently known about the ecology and evolution of this species.

Dissection of the Octoploid Strawberry Genome by Deep Sequencing of the Genomes of Fragaria Species

PubMed Central

Hirakawa, Hideki; Shirasawa, Kenta; Kosugi, Shunichi; Tashiro, Kosuke; Nakayama, Shinobu; Yamada, Manabu; Kohara, Mistuyo; Watanabe, Akiko; Kishida, Yoshie; Fujishiro, Tsunakazu; Tsuruoka, Hisano; Minami, Chiharu; Sasamoto, Shigemi; Kato, Midori; Nanri, Keiko; Komaki, Akiko; Yanagi, Tomohiro; Guoxin, Qin; Maeda, Fumi; Ishikawa, Masami; Kuhara, Satoru; Sato, Shusei; Tabata, Satoshi; Isobe, Sachiko N.

2014-01-01

Cultivated strawberry (Fragaria x ananassa) is octoploid and shows allogamous behaviour. The present study aims at dissecting this octoploid genome through comparison with its wild relatives, F. iinumae, F. nipponica, F. nubicola, and F. orientalis by de novo whole-genome sequencing on an Illumina and Roche 454 platforms. The total length of the assembled Illumina genome sequences obtained was 698 Mb for F. x ananassa, and ∼200 Mb each for the four wild species. Subsequently, a virtual reference genome termed FANhybrid_r1.2 was constructed by integrating the sequences of the four homoeologous subgenomes of F. x ananassa, from which heterozygous regions in the Roche 454 and Illumina genome sequences were eliminated. The total length of FANhybrid_r1.2 thus created was 173.2 Mb with the N50 length of 5137 bp. The Illumina-assembled genome sequences of F. x ananassa and the four wild species were then mapped onto the reference genome, along with the previously published F. vesca genome sequence to establish the subgenomic structure of F. x ananassa. The strategy adopted in this study has turned out to be successful in dissecting the genome of octoploid F. x ananassa and appears promising when applied to the analysis of other polyploid plant species. PMID:24282021

Comparative chloroplast genomes of eleven Schima (Theaceae) species: Insights into DNA barcoding and phylogeny.

PubMed

Yu, Xiang-Qin; Drew, Bryan T; Yang, Jun-Bo; Gao, Lian-Ming; Li, De-Zhu

2017-01-01

Schima is an ecologically and economically important woody genus in tea family (Theaceae). Unresolved species delimitations and phylogenetic relationships within Schima limit our understanding of the genus and hinder utilization of the genus for economic purposes. In the present study, we conducted comparative analysis among the complete chloroplast (cp) genomes of 11 Schima species. Our results indicate that Schima cp genomes possess a typical quadripartite structure, with conserved genomic structure and gene order. The size of the Schima cp genome is about 157 kilo base pairs (kb). They consistently encode 114 unique genes, including 80 protein-coding genes, 30 tRNAs, and 4 rRNAs, with 17 duplicated in the inverted repeat (IR). These cp genomes are highly conserved and do not show obvious expansion or contraction of the IR region. The percent variability of the 68 coding and 93 noncoding (>150 bp) fragments is consistently less than 3%. The seven most widely touted DNA barcode regions as well as one promising barcode candidate showed low sequence divergence. Eight mutational hotspots were identified from the 11 cp genomes. These hotspots may potentially be useful as specific DNA barcodes for species identification of Schima. The 58 cpSSR loci reported here are complementary to the microsatellite markers identified from the nuclear genome, and will be leveraged for further population-level studies. Phylogenetic relationships among the 11 Schima species were resolved with strong support based on the cp genome data set, which corresponds well with the species distribution pattern. The data presented here will serve as a foundation to facilitate species identification, DNA barcoding and phylogenetic reconstructions for future exploration of Schima.

Genomic diversity within the haloalkaliphilic genus Thioalkalivibrio

DOE PAGES

Ahn, Anne-Catherine; Meier-Kolthoff, Jan P.; Overmars, Lex; ...

2017-03-10

Thioalkalivibrio is a genus of obligate chemolithoautotrophic haloalkaliphilic sulfur-oxidizing bacteria. Their habitat are soda lakes which are dual extreme environments with a pH range from 9.5 to 11 and salt concentrations up to saturation. More than 100 strains of this genus have been isolated from various soda lakes all over the world, but only ten species have been effectively described yet. Therefore, the assignment of the remaining strains to either existing or novel species is important and will further elucidate their genomic diversity as well as give a better general understanding of this genus. Recently, the genomes of 76 Thioalkalivibriomore » strains were sequenced. On these, we applied different methods including (i) 16S rRNA gene sequence analysis, (ii) Multilocus Sequence Analysis (MLSA) based on eight housekeeping genes, (iii) Average Nucleotide Identity based on BLAST (ANI b) and MUMmer (ANI m ), (iv) Tetranucleotide frequency correlation coefficients (TETRA), (v) digital DNA:DNA hybridization (dDDH) as well as (vi) nucleotide- and amino acid-based Genome BLAST Distance Phylogeny (GBDP) analyses. We detected a high genomic diversity by revealing 15 new "genomic" species and 16 new "genomic" subspecies in addition to the ten already described species. Phylogenetic and phylogenomic analyses showed that the genus is not monophyletic, because four strains were clearly separated from the other Thioalkalivibrio by type strains from other genera. Therefore, it is recommended to classify the latter group as a novel genus. The biogeographic distribution of Thioalkalivibrio suggested that the different "genomic" species can be classified as candidate disjunct or candidate endemic species. This study is a detailed genome-based classification and identification of members within the genus Thioalkalivibrio. However, future phenotypical and chemotaxonomical studies will be needed for a full species description of this genus.« less

Comparative primate genomics: emerging patterns of genome content and dynamics.

PubMed

Rogers, Jeffrey; Gibbs, Richard A

2014-05-01

Advances in genome sequencing technologies have created new opportunities for comparative primate genomics. Genome assemblies have been published for various primate species, and analyses of several others are underway. Whole-genome assemblies for the great apes provide remarkable new information about the evolutionary origins of the human genome and the processes involved. Genomic data for macaques and other non-human primates offer valuable insights into genetic similarities and differences among species that are used as models for disease-related research. This Review summarizes current knowledge regarding primate genome content and dynamics, and proposes a series of goals for the near future.

The complete chloroplast genomes of two Wisteria species, W. floribunda and W. sinensis (Fabaceae).

PubMed

Kim, Na-Rae; Kim, Kyunghee; Lee, Sang-Choon; Lee, Jung-Hoon; Cho, Seong-Hyun; Yu, Yeisoo; Kim, Young-Dong; Yang, Tae-Jin

2016-11-01

Wisteria floribunda and Wisteria sinensis are ornamental woody vines in the Fabaceae. The complete chloroplast genome sequences of the two species were generated by de novo assembly using whole genome next generation sequences. The chloroplast genomes of W. floribunda and W. sinensis were 130 960 bp and 130 561 bp long, respectively, and showed inverted repeat (IR)-lacking structures as those reported in IRLC in the Fabaceae. The chloroplast genomes of both species contained same number of protein-coding sequences (77), tRNA genes (30), and rRNA genes (4). The phylogenetic analysis with the reported chloroplast genomes confirmed close taxonomical relationship of W. floribunda and W. sinensis.

Full genome sequence analysis of a novel adenovirus of rhesus macaque origin indicates a new simian adenovirus type and species.

PubMed

Malouli, Daniel; Howell, Grant L; Legasse, Alfred W; Kahl, Christoph; Axthelm, Michael K; Hansen, Scott G; Früh, Klaus

2014-09-01

Multiple novel simian adenoviruses have been isolated over the past years and their potential to cross the species barrier and infect the human population is an ever present threat. Here we describe the isolation and full genome sequencing of a novel simian adenovirus (SAdV) isolated from the urine of two independent, never co-housed, late stage simian immunodeficiency virus (SIV)-infected rhesus macaques. The viral genome sequences revealed a novel type with a unique genome length, GC content, E3 region and DNA polymerase amino acid sequence that is sufficiently distinct from all currently known human- or simian adenovirus species to warrant classifying these isolates as a novel species of simian adenovirus. This new species, termed Simian mastadenovirus D (SAdV-D), displays the standard genome organization for the genus Mastadenovirus containing only one copy of the fiber gene which sets it apart from the old world monkey adenovirus species HAdV-G, SAdV-B and SAdV-C.

The oryza map alignment project: the golden path to unlocking the genetic potential of wild rice species.

PubMed

Wing, Rod A; Ammiraju, Jetty S S; Luo, Meizhong; Kim, Hyeran; Yu, Yeisoo; Kudrna, Dave; Goicoechea, Jose L; Wang, Wenming; Nelson, Will; Rao, Kiran; Brar, Darshan; Mackill, Dave J; Han, Bin; Soderlund, Cari; Stein, Lincoln; SanMiguel, Phillip; Jackson, Scott

2005-09-01

The wild species of the genus Oryza offer enormous potential to make a significant impact on agricultural productivity of the cultivated rice species Oryza sativa and Oryza glaberrima. To unlock the genetic potential of wild rice we have initiated a project entitled the 'Oryza Map Alignment Project' (OMAP) with the ultimate goal of constructing and aligning BAC/STC based physical maps of 11 wild and one cultivated rice species to the International Rice Genome Sequencing Project's finished reference genome--O. sativa ssp. japonica c. v. Nipponbare. The 11 wild rice species comprise nine different genome types and include six diploid genomes (AA, BB, CC, EE, FF and GG) and four tetrapliod genomes (BBCC, CCDD, HHKK and HHJJ) with broad geographical distribution and ecological adaptation. In this paper we describe our strategy to construct robust physical maps of all 12 rice species with an emphasis on the AA diploid O. nivara--thought to be the progenitor of modern cultivated rice.

Analysis of Acinetobacter baumannii resistance patterns in patients with chronic obstructive pulmonary disease (COPD) in terms of choice of effective empiric antibiotic therapy.

PubMed

Grochowalska, Aneta; Kozioł-Montewka, Maria; Sobieszczańska, Anna

2017-06-12

Introduction. Multi-resistant Acinetobacter baumannii isolated from patients has become one of the most hazardous pathogens in health care settings. The aim of the study was to analyze pneumonia caused by Acinetobacter baumannii in patients hospitalized because of exacerbation of chronic obstructive pulmonary diseases (COPD), who were admitted to the Pulmonology Ward of the Masovian Specialistic Hospital in Radom (MSS). The incidence and drug sensitivity of these non-fermenting rods were evaluated, and compliance with antimicrobial procedure with the algorithm of the guidelines in applicable recommendations, was estimated. This should result in determining the local patterns of resistance and verifying therapeutic procedures in accordance with the assumptions of hospital antibiotic policy. In addition, the study examined the effectiveness of empiric and targeted therapy according to the clinical condition of the patient, and the eradication of A. baumannii, in comparison with the aggravating factors of the patient. Materials and Method. The retrospective study included 90 patients with exacerbation of COPD whose etiological factor of infection was A. baumannii, hospitalized in the Department of Pulmonology (MSS) in 2012-2016. Results. Studies were conducted on 90 patients with COPD exacerbation from which A. baumannii was isolated. Co-infections with other bacterial species among 41 patients were additionally noted. The majority of A. baumannii strains showed a high resistance (90%) to fluoroquinolones, ceftazidime, piperacillin/tazobactam. For strains causing a co-infection, drug resistance was successively 44-56%, 44%, 44%. All of patients received empirical therapy. The most commonly used drug was amoxicillin with a clavulanic acid, often combined with fluoroquinolone. This type of therapy was effective among 10% of patients. The mortality in this group was determined at 29%. Among 79% of patients with COPD, a targeted therapy was performed which proved to be effective in 58% of treated cases by susceptibility testing. The highest efficacy was observer after the use of colistin and carbapenems. Conclusion. In the performed study, the infections caused by multi-resistant Acinetobacter baumannii, were observed in COPD, which should be taken into consideration in choosing empirical antibiotic therapy. Simultaneously, the local resistance patterns of multi-drug-resistant (MDR) Gram-negative strains co-infecting COPD should be considered in empirical treatment. Moreover, both additional clinical complication and co-infections contribute to a more severe course of diseases. In this study, the mortality percent exceeded 29%.

Draft genome of Haloarcula rubripromontorii strain SL3, a novel halophilic archaeon isolated from the solar salterns of Cabo Rojo, Puerto Rico.

PubMed

Sánchez-Nieves, Rubén; Facciotti, Marc; Saavedra-Collado, Sofía; Dávila-Santiago, Lizbeth; Rodríguez-Carrero, Roy; Montalvo-Rodríguez, Rafael

2016-03-01

The genus Haloarcula belongs to the family Halobacteriaceae which currently has 10 valid species. Here we report the draft genome sequence of strain SL3, a new species within this genus, isolated from the Solar Salterns of Cabo Rojo, Puerto Rico. Genome assembly performed using NGEN Assembler resulted in 18 contigs (N50 = 601,911 bp), the largest of which contains 1,023,775 bp. The genome consists of 3.97 MB and has a GC content of 61.97%. Like all species of Haloarcula, the genome encodes heterogeneous copies of the small subunit ribosomal RNA. In addition, the genome includes 6 rRNAs, 48 tRNAs, and 3797 protein coding sequences. Several carbohydrate-active enzymes genes were found, as well as enzymes involved in the dihydroxyacetone processing pathway which are not found in other Haloarcula species. The NCBI accession number for this genome is LIUF00000000 and the strain deposit number is CECT9001.

Genome Microscale Heterogeneity among Wild Potatoes Revealed by Diversity Arrays Technology Marker Sequences.

PubMed

Traini, Alessandra; Iorizzo, Massimo; Mann, Harpartap; Bradeen, James M; Carputo, Domenico; Frusciante, Luigi; Chiusano, Maria Luisa

2013-01-01

Tuber-bearing potato species possess several genes that can be exploited to improve the genetic background of the cultivated potato Solanum tuberosum. Among them, S. bulbocastanum and S. commersonii are well known for their strong resistance to environmental stresses. However, scant information is available for these species in terms of genome organization, gene function, and regulatory networks. Consequently, genomic tools to assist breeding are meager, and efficient exploitation of these species has been limited so far. In this paper, we employed the reference genome sequences from cultivated potato and tomato and a collection of sequences of 1,423 potato Diversity Arrays Technology (DArT) markers that show polymorphic representation across the genomes of S. bulbocastanum and/or S. commersonii genotypes. Our results highlighted microscale genome sequence heterogeneity that may play a significant role in functional and structural divergence between related species. Our analytical approach provides knowledge of genome structural and sequence variability that could not be detected by transcriptome and proteome approaches.

Harnessing Whole Genome Sequencing in Medical Mycology.

PubMed

Cuomo, Christina A

2017-01-01

Comparative genome sequencing studies of human fungal pathogens enable identification of genes and variants associated with virulence and drug resistance. This review describes current approaches, resources, and advances in applying whole genome sequencing to study clinically important fungal pathogens. Genomes for some important fungal pathogens were only recently assembled, revealing gene family expansions in many species and extreme gene loss in one obligate species. The scale and scope of species sequenced is rapidly expanding, leveraging technological advances to assemble and annotate genomes with higher precision. By using iteratively improved reference assemblies or those generated de novo for new species, recent studies have compared the sequence of isolates representing populations or clinical cohorts. Whole genome approaches provide the resolution necessary for comparison of closely related isolates, for example, in the analysis of outbreaks or sampled across time within a single host. Genomic analysis of fungal pathogens has enabled both basic research and diagnostic studies. The increased scale of sequencing can be applied across populations, and new metagenomic methods allow direct analysis of complex samples.

Clarification of Taxonomic Status within the Pseudomonas syringae Species Group Based on a Phylogenomic Analysis

PubMed Central

Gomila, Margarita; Busquets, Antonio; Mulet, Magdalena; García-Valdés, Elena; Lalucat, Jorge

2017-01-01

The Pseudomonas syringae phylogenetic group comprises 15 recognized bacterial species and more than 60 pathovars. The classification and identification of strains is relevant for practical reasons but also for understanding the epidemiology and ecology of this group of plant pathogenic bacteria. Genome-based taxonomic analyses have been introduced recently to clarify the taxonomy of the whole genus. A set of 139 draft and complete genome sequences of strains belonging to all species of the P. syringae group available in public databases were analyzed, together with the genomes of closely related species used as outgroups. Comparative genomics based on the genome sequences of the species type strains in the group allowed the delineation of phylogenomic species and demonstrated that a high proportion of strains included in the study are misclassified. Furthermore, representatives of at least 7 putative novel species were detected. It was also confirmed that P. ficuserectae, P. meliae, and P. savastanoi are later synonyms of P. amygdali and that “P. coronafaciens” should be revived as a nomenspecies. PMID:29270162

LTR Retrotransposons Contribute to Genomic Gigantism in Plethodontid Salamanders

PubMed Central

Sun, Cheng; Shepard, Donald B.; Chong, Rebecca A.; López Arriaza, José; Hall, Kathryn; Castoe, Todd A.; Feschotte, Cédric; Pollock, David D.; Mueller, Rachel Lockridge

2012-01-01

Among vertebrates, most of the largest genomes are found within the salamanders, a clade of amphibians that includes 613 species. Salamander genome sizes range from ∼14 to ∼120 Gb. Because genome size is correlated with nucleus and cell sizes, as well as other traits, morphological evolution in salamanders has been profoundly affected by genomic gigantism. However, the molecular mechanisms driving genomic expansion in this clade remain largely unknown. Here, we present the first comparative analysis of transposable element (TE) content in salamanders. Using high-throughput sequencing, we generated genomic shotgun data for six species from the Plethodontidae, the largest family of salamanders. We then developed a pipeline to mine TE sequences from shotgun data in taxa with limited genomic resources, such as salamanders. Our summaries of overall TE abundance and diversity for each species demonstrate that TEs make up a substantial portion of salamander genomes, and that all of the major known types of TEs are represented in salamanders. The most abundant TE superfamilies found in the genomes of our six focal species are similar, despite substantial variation in genome size. However, our results demonstrate a major difference between salamanders and other vertebrates: salamander genomes contain much larger amounts of long terminal repeat (LTR) retrotransposons, primarily Ty3/gypsy elements. Thus, the extreme increase in genome size that occurred in salamanders was likely accompanied by a shift in TE landscape. These results suggest that increased proliferation of LTR retrotransposons was a major molecular mechanism contributing to genomic expansion in salamanders. PMID:22200636

High-throughput SNP genotyping in the highly heterozygous genome of Eucalyptus: assay success, polymorphism and transferability across species

PubMed Central

2011-01-01

Background High-throughput SNP genotyping has become an essential requirement for molecular breeding and population genomics studies in plant species. Large scale SNP developments have been reported for several mainstream crops. A growing interest now exists to expand the speed and resolution of genetic analysis to outbred species with highly heterozygous genomes. When nucleotide diversity is high, a refined diagnosis of the target SNP sequence context is needed to convert queried SNPs into high-quality genotypes using the Golden Gate Genotyping Technology (GGGT). This issue becomes exacerbated when attempting to transfer SNPs across species, a scarcely explored topic in plants, and likely to become significant for population genomics and inter specific breeding applications in less domesticated and less funded plant genera. Results We have successfully developed the first set of 768 SNPs assayed by the GGGT for the highly heterozygous genome of Eucalyptus from a mixed Sanger/454 database with 1,164,695 ESTs and the preliminary 4.5X draft genome sequence for E. grandis. A systematic assessment of in silico SNP filtering requirements showed that stringent constraints on the SNP surrounding sequences have a significant impact on SNP genotyping performance and polymorphism. SNP assay success was high for the 288 SNPs selected with more rigorous in silico constraints; 93% of them provided high quality genotype calls and 71% of them were polymorphic in a diverse panel of 96 individuals of five different species. SNP reliability was high across nine Eucalyptus species belonging to three sections within subgenus Symphomyrtus and still satisfactory across species of two additional subgenera, although polymorphism declined as phylogenetic distance increased. Conclusions This study indicates that the GGGT performs well both within and across species of Eucalyptus notwithstanding its nucleotide diversity ≥2%. The development of a much larger array of informative SNPs across multiple Eucalyptus species is feasible, although strongly dependent on having a representative and sufficiently deep collection of sequences from many individuals of each target species. A higher density SNP platform will be instrumental to undertake genome-wide phylogenetic and population genomics studies and to implement molecular breeding by Genomic Selection in Eucalyptus. PMID:21492434

Draft Nuclear Genome, Complete Chloroplast Genome, and Complete Mitochondrial Genome for the Biofuel/Bioproduct Feedstock Species Scenedesmus obliquus Strain DOE0152z

DOE Office of Scientific and Technical Information (OSTI.GOV)

Starkenburg, S. R.; Polle, J. E. W.; Hovde, B.

ABSTRACT The green alga Scenedesmus obliquus is an emerging platform species for the industrial production of biofuels. Here, we report the draft assembly and annotation for the nuclear, plastid, and mitochondrial genomes of S. obliquus strain DOE0152z.

Genomic structural differences between cattle and river buffalo identified through a combination and genomic and transcriptomic analysis

USDA-ARS?s Scientific Manuscript database

Water buffalo (Bubalus bubalis L.) is an important livestock species worldwide. Like many other livestock species, water buffalo lacks high quality and continuous reference genome assembly required for fine-scale comparative genomics studies. In this work, we present a dataset, which characterizes g...

Characterization of the complete chloroplast genome of the endangered species Carya sinensis (Juglandaceae)

Treesearch

Yiheng Hu; Xi Chen; Xiaojia Feng; Keith E. Woeste; Peng Zhao

2016-01-01

Carya sinensis (Chinese Hickory, beaked walnut, or beaked hickory) is an endangered species that needs urgent conservation action. Here, we reported the complete chloroplast (cp) genome sequence and the genomic features of the C. sinensis cp, which is the first complete cp genome of any member of Carya. The...

Draft Nuclear Genome, Complete Chloroplast Genome, and Complete Mitochondrial Genome for the Biofuel/Bioproduct Feedstock Species Scenedesmus obliquus Strain DOE0152z

DOE PAGES

Starkenburg, S. R.; Polle, J. E. W.; Hovde, B.; ...

2017-08-10

ABSTRACT The green alga Scenedesmus obliquus is an emerging platform species for the industrial production of biofuels. Here, we report the draft assembly and annotation for the nuclear, plastid, and mitochondrial genomes of S. obliquus strain DOE0152z.

Initiation of a pan-genomic research project for Xylella fastidiosa

USDA-ARS?s Scientific Manuscript database

Differences in genomic structure and nucleotide polymorphism among strains form the genetic basis for adaptability of a bacterial species. This can be described by a bacterial pan-genome, which is defined as the full complement of genes in all strains of a species. The pan-genome is composed of a "c...

From Agrobacterium to viral vectors: genome modification of plant cells by rare cutting restriction enzymes.

PubMed

Marton, Ira; Honig, Arik; Omid, Ayelet; De Costa, Noam; Marhevka, Elena; Cohen, Barry; Zuker, Amir; Vainstein, Alexander

2013-01-01

Researchers and biotechnologists require methods to accurately modify the genome of higher eukaryotic cells. Such modifications include, but are not limited to, site-specific mutagenesis, site-specific insertion of foreign DNA, and replacement and deletion of native sequences. Accurate genome modifications in plant species have been rather limited, with only a handful of plant species and genes being modified through the use of early genome-editing techniques. The development of rare-cutting restriction enzymes as a tool for the induction of site-specific genomic double-strand breaks and their introduction as a reliable tool for genome modification in animals, animal cells and human cell lines have paved the way for the adaptation of rare-cutting restriction enzymes to genome editing in plant cells. Indeed, the number of plant species and genes which have been successfully edited using zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) and engineered homing endonucleases is on the rise. In our review, we discuss the basics of rare-cutting restriction enzyme-mediated genome-editing technology with an emphasis on its application in plant species.

Hybridization Reveals the Evolving Genomic Architecture of Speciation

PubMed Central

Kronforst, Marcus R.; Hansen, Matthew E.B.; Crawford, Nicholas G.; Gallant, Jason R.; Zhang, Wei; Kulathinal, Rob J.; Kapan, Durrell D.; Mullen, Sean P.

2014-01-01

SUMMARY The rate at which genomes diverge during speciation is unknown, as are the physical dynamics of the process. Here, we compare full genome sequences of 32 butterflies, representing five species from a hybridizing Heliconius butterfly community, to examine genome-wide patterns of introgression and infer how divergence evolves during the speciation process. Our analyses reveal that initial divergence is restricted to a small fraction of the genome, largely clustered around known wing-patterning genes. Over time, divergence evolves rapidly, due primarily to the origin of new divergent regions. Furthermore, divergent genomic regions display signatures of both selection and adaptive introgression, demonstrating the link between microevolutionary processes acting within species and the origin of species across macroevolutionary timescales. Our results provide a uniquely comprehensive portrait of the evolving species boundary due to the role that hybridization plays in reducing the background accumulation of divergence at neutral sites. PMID:24183670

Conservation genomics of threatened animal species.

PubMed

Steiner, Cynthia C; Putnam, Andrea S; Hoeck, Paquita E A; Ryder, Oliver A

2013-01-01

The genomics era has opened up exciting possibilities in the field of conservation biology by enabling genomic analyses of threatened species that previously were limited to model organisms. Next-generation sequencing (NGS) and the collection of genome-wide data allow for more robust studies of the demographic history of populations and adaptive variation associated with fitness and local adaptation. Genomic analyses can also advance management efforts for threatened wild and captive populations by identifying loci contributing to inbreeding depression and disease susceptibility, and predicting fitness consequences of introgression. However, the development of genomic tools in wild species still carries multiple challenges, particularly those associated with computational and sampling constraints. This review provides an overview of the most significant applications of NGS and the implications and limitations of genomic studies in conservation.

Comparative Genomics in Homo sapiens.

PubMed

Oti, Martin; Sammeth, Michael

2018-01-01

Genomes can be compared at different levels of divergence, either between species or within species. Within species genomes can be compared between different subpopulations, such as human subpopulations from different continents. Investigating the genomic differences between different human subpopulations is important when studying complex diseases that are affected by many genetic variants, as the variants involved can differ between populations. The 1000 Genomes Project collected genome-scale variation data for 2504 human individuals from 26 different populations, enabling a systematic comparison of variation between human subpopulations. In this chapter, we present step-by-step a basic protocol for the identification of population-specific variants employing the 1000 Genomes data. These variants are subsequently further investigated for those that affect the proteome or RNA splice sites, to investigate potentially biologically relevant differences between the populations.

Characterization and Comparative Analysis of the Complete Chloroplast Genome of the Critically Endangered Species Streptocarpus teitensis (Gesneriaceae).

PubMed

Kyalo, Cornelius M; Gichira, Andrew W; Li, Zhi-Zhong; Saina, Josphat K; Malombe, Itambo; Hu, Guang-Wan; Wang, Qing-Feng

2018-01-01

Streptocarpus teitensis (Gesneriaceae) is an endemic species listed as critically endangered in the International Union for Conservation of Nature (IUCN) red list of threatened species. However, the sequence and genome information of this species remains to be limited. In this article, we present the complete chloroplast genome structure of Streptocarpus teitensis and its evolution inferred through comparative studies with other related species. S. teitensis displayed a chloroplast genome size of 153,207 bp, sheltering a pair of inverted repeats (IR) of 25,402 bp each split by small and large single-copy (SSC and LSC) regions of 18,300 and 84,103 bp, respectively. The chloroplast genome was observed to contain 116 unique genes, of which 80 are protein-coding, 32 are transfer RNAs, and four are ribosomal RNAs. In addition, a total of 196 SSR markers were detected in the chloroplast genome of Streptocarpus teitensis with mononucleotides (57.1%) being the majority, followed by trinucleotides (33.2%) and dinucleotides and tetranucleotides (both 4.1%), and pentanucleotides being the least (1.5%). Genome alignment indicated that this genome was comparable to other sequenced members of order Lamiales. The phylogenetic analysis suggested that Streptocarpus teitensis is closely related to Lysionotus pauciflorus and Dorcoceras hygrometricum .

Genome-wide sequence variations between wild and cultivated tomato species revisited by whole genome sequence mapping.

PubMed

Sahu, Kamlesh Kumar; Chattopadhyay, Debasis

2017-06-02

Cultivated tomato (Solanum lycopersicum L.) is the second most important vegetable crop after potato and a member of thirteen interfertile species of Solanum genus. Domestication and continuous selection for desirable traits made cultivated tomato species susceptible to many stresses as compared to the wild species. In this study, we analyzed and compared the genomes of wild and cultivated tomato accessions to identify the genomic regions that encountered changes during domestication. Analysis was based on SNP and InDel mining of twentynine accessions of twelve wild tomato species and forty accessions of cultivated tomato. Percentage of common SNPs among the accessions within a species corresponded with the reproductive behavior of the species. SNP profiles of the wild tomato species within a phylogenetic subsection varied with their geographical distribution. Interestingly, the ratio of genic SNP to total SNPs increased with phylogenetic distance of the wild tomato species from the domesticated species, suggesting that variations in gene-coding region play a major role in speciation. We retrieved 2439 physical positions in 1594 genes including 32 resistance related genes where all the wild accessions possessed a common wild variant allele different from all the cultivated accessions studied. Tajima's D analysis predicted a very strong purifying selection associated with domestication in nearly 1% of its genome, half of which is contributed by chromosome 11. This genomic region with a low Tajima's D value hosts a variety of genes associated with important agronomic trait such as, fruit size, tiller number and wax deposition. Our analysis revealed a broad-spectrum genetic base in wild tomato species and erosion of that in cultivated tomato due to recurrent selection for agronomically important traits. Identification of the common wild variant alleles and the genomic regions undergoing purifying selection during cultivation would facilitate future breeding program by introgression from wild species.

Complete DNA sequences of the plastid genomes of two parasitic flowering plant species, Cuscuta reflexa and Cuscuta gronovii.

PubMed

Funk, Helena T; Berg, Sabine; Krupinska, Karin; Maier, Uwe G; Krause, Kirsten

2007-08-22

The holoparasitic plant genus Cuscuta comprises species with photosynthetic capacity and functional chloroplasts as well as achlorophyllous and intermediate forms with restricted photosynthetic activity and degenerated chloroplasts. Previous data indicated significant differences with respect to the plastid genome coding capacity in different Cuscuta species that could correlate with their photosynthetic activity. In order to shed light on the molecular changes accompanying the parasitic lifestyle, we sequenced the plastid chromosomes of the two species Cuscuta reflexa and Cuscuta gronovii. Both species are capable of performing photosynthesis, albeit with varying efficiencies. Together with the plastid genome of Epifagus virginiana, an achlorophyllous parasitic plant whose plastid genome has been sequenced, these species represent a series of progression towards total dependency on the host plant, ranging from reduced levels of photosynthesis in C. reflexa to a restricted photosynthetic activity and degenerated chloroplasts in C. gronovii to an achlorophyllous state in E. virginiana. The newly sequenced plastid genomes of C. reflexa and C. gronovii reveal that the chromosome structures are generally very similar to that of non-parasitic plants, although a number of species-specific insertions, deletions (indels) and sequence inversions were identified. However, we observed a gradual adaptation of the plastid genome to the different degrees of parasitism. The changes are particularly evident in C. gronovii and include (a) the parallel losses of genes for the subunits of the plastid-encoded RNA polymerase and the corresponding promoters from the plastid genome, (b) the first documented loss of the gene for a putative splicing factor, MatK, from the plastid genome and (c) a significant reduction of RNA editing. Overall, the comparative genomic analysis of plastid DNA from parasitic plants indicates a bias towards a simplification of the plastid gene expression machinery as a consequence of an increasing dependency on the host plant. A tentative assignment of the successive events in the adaptation of the plastid genomes to parasitism can be inferred from the current data set. This includes (1) a loss of non-coding regions in photosynthetic Cuscuta species that has resulted in a condensation of the plastid genome, (2) the simplification of plastid gene expression in species with largely impaired photosynthetic capacity and (3) the deletion of a significant part of the genetic information, including the information for the photosynthetic apparatus, in non-photosynthetic parasitic plants.

Complete DNA sequences of the plastid genomes of two parasitic flowering plant species, Cuscuta reflexa and Cuscuta gronovii

PubMed Central

Funk, Helena T; Berg, Sabine; Krupinska, Karin; Maier, Uwe G; Krause, Kirsten

2007-01-01

Background The holoparasitic plant genus Cuscuta comprises species with photosynthetic capacity and functional chloroplasts as well as achlorophyllous and intermediate forms with restricted photosynthetic activity and degenerated chloroplasts. Previous data indicated significant differences with respect to the plastid genome coding capacity in different Cuscuta species that could correlate with their photosynthetic activity. In order to shed light on the molecular changes accompanying the parasitic lifestyle, we sequenced the plastid chromosomes of the two species Cuscuta reflexa and Cuscuta gronovii. Both species are capable of performing photosynthesis, albeit with varying efficiencies. Together with the plastid genome of Epifagus virginiana, an achlorophyllous parasitic plant whose plastid genome has been sequenced, these species represent a series of progression towards total dependency on the host plant, ranging from reduced levels of photosynthesis in C. reflexa to a restricted photosynthetic activity and degenerated chloroplasts in C. gronovii to an achlorophyllous state in E. virginiana. Results The newly sequenced plastid genomes of C. reflexa and C. gronovii reveal that the chromosome structures are generally very similar to that of non-parasitic plants, although a number of species-specific insertions, deletions (indels) and sequence inversions were identified. However, we observed a gradual adaptation of the plastid genome to the different degrees of parasitism. The changes are particularly evident in C. gronovii and include (a) the parallel losses of genes for the subunits of the plastid-encoded RNA polymerase and the corresponding promoters from the plastid genome, (b) the first documented loss of the gene for a putative splicing factor, MatK, from the plastid genome and (c) a significant reduction of RNA editing. Conclusion Overall, the comparative genomic analysis of plastid DNA from parasitic plants indicates a bias towards a simplification of the plastid gene expression machinery as a consequence of an increasing dependency on the host plant. A tentative assignment of the successive events in the adaptation of the plastid genomes to parasitism can be inferred from the current data set. This includes (1) a loss of non-coding regions in photosynthetic Cuscuta species that has resulted in a condensation of the plastid genome, (2) the simplification of plastid gene expression in species with largely impaired photosynthetic capacity and (3) the deletion of a significant part of the genetic information, including the information for the photosynthetic apparatus, in non-photosynthetic parasitic plants. PMID:17714582

Total centromere size and genome size are strongly correlated in ten grass species.

PubMed

Zhang, Han; Dawe, R Kelly

2012-05-01

It has been known for decades that centromere size varies across species, but the factors involved in setting centromere boundaries are unknown. As a means to address this question, we estimated centromere sizes in ten species of the grass family including rice, maize, and wheat, which diverged 60~80 million years ago and vary by 40-fold in genome size. Measurements were made using a broadly reactive antibody to rice centromeric histone H3 (CENH3). In species-wide comparisons, we found a clear linear relationship between total centromere size and genome size. Species with large genomes and few chromosomes tend to have the largest centromeres (e.g., rye) while species with small genomes and many chromosomes have the smallest centromeres (e.g., rice). However, within a species, centromere size is surprisingly uniform. We present evidence from three oat-maize addition lines that support this claim, indicating that each of three maize centromeres propagated in oat are not measurably different from each other. In the context of previously published data, our results suggest that the apparent correlation between chromosome and centromere size is incidental to a larger trend that reflects genome size. Centromere size may be determined by a limiting component mechanism similar to that described for Caenorhabditis elegans centrosomes.

Genome size of 14 species of fireflies (Insecta, Coleoptera, Lampyridae)

PubMed Central

Liu, Gui-Chun; Dong, Zhi-Wei; He, Jin-Wu; Zhao, Ruo-Ping; Wang, Wen; Li, Xue-Yan

2017-01-01

Eukaryotic genome size data are important both as the basis for comparative research into genome evolution and as estimators of the cost and difficulty of genome sequencing programs for non-model organisms. In this study, the genome size of 14 species of fireflies (Lampyridae) (two genera in Lampyrinae, three genera in Luciolinae, and one genus in subfamily incertae sedis) were estimated by propidium iodide (PI)-based flow cytometry. The haploid genome sizes of Lampyridae ranged from 0. 42 to 1. 31 pg, a 3. 1-fold span. Genome sizes of the fireflies varied within the tested subfamilies and genera. Lamprigera and Pyrocoelia species had large and small genome sizes, respectively. No correlation was found between genome size and morphological traits such as body length, body width, eye width, and antennal length. Our data provide additional information on genome size estimation of the firefly family Lampyridae. Furthermore, this study will help clarify the cost and difficulty of genome sequencing programs for non-model organisms and will help promote studies on firefly genome evolution. PMID:29280364

Informing Antibiotic Treatment Decisions: Evaluating Rapid Molecular Diagnostics To Identify Susceptibility and Resistance to Carbapenems against Acinetobacter spp. in PRIMERS III.

PubMed

Evans, Scott R; Hujer, Andrea M; Jiang, Hongyu; Hill, Carol B; Hujer, Kristine M; Mediavilla, Jose R; Manca, Claudia; Tran, Thuy Tien T; Domitrovic, T Nicholas; Higgins, Paul G; Seifert, Harald; Kreiswirth, Barry N; Patel, Robin; Jacobs, Michael R; Chen, Liang; Sampath, Rangarajan; Hall, Thomas; Marzan, Christine; Fowler, Vance G; Chambers, Henry F; Bonomo, Robert A

2017-01-01

The widespread dissemination of carbapenem-resistant Acinetobacter spp. has created significant therapeutic challenges. At present, rapid molecular diagnostics (RMDs) that can identify this phenotype are not commercially available. Two RMD platforms, PCR combined with electrospray ionization mass spectrometry (PCR/ESI-MS) and molecular beacons (MB), for detecting genes conferring resistance/susceptibility to carbapenems in Acinetobacter spp. were evaluated. An archived collection of 200 clinical Acinetobacter sp. isolates was tested. Predictive values for susceptibility and resistance were estimated as a function of susceptibility prevalence and were based on the absence or presence of beta-lactamase (bla) NDM, VIM, IMP, KPC, and OXA carbapenemase genes (e.g., bla OXA-23 , bla OXA-24/40 , and bla OXA-58 found in this study) against the reference standard of MIC determinations. According to the interpretation of MICs, 49% (n = 98) of the isolates were carbapenem resistant (as defined by either resistance or intermediate resistance to imipenem). The susceptibility sensitivities (95% confidence interval [CI]) for imipenem were 82% (74%, 89%) and 92% (85%, 97%) for PCR/ESI-MS and MB, respectively. Resistance sensitivities (95% CI) for imipenem were 95% (88%, 98%) and 88% (80%, 94%) for PCR/ESI-MS and MB, respectively. PRIMERS III establishes that RMDs can discriminate between carbapenem resistance and susceptibility in Acinetobacter spp. In the context of a known prevalence of resistance, SPVs and RPVs can inform clinicians regarding the best choice for empiric antimicrobial therapy against this multidrug-resistant pathogen. Copyright © 2016 American Society for Microbiology.

The Sequenced Angiosperm Genomes and Genome Databases.

PubMed

Chen, Fei; Dong, Wei; Zhang, Jiawei; Guo, Xinyue; Chen, Junhao; Wang, Zhengjia; Lin, Zhenguo; Tang, Haibao; Zhang, Liangsheng

2018-01-01

Angiosperms, the flowering plants, provide the essential resources for human life, such as food, energy, oxygen, and materials. They also promoted the evolution of human, animals, and the planet earth. Despite the numerous advances in genome reports or sequencing technologies, no review covers all the released angiosperm genomes and the genome databases for data sharing. Based on the rapid advances and innovations in the database reconstruction in the last few years, here we provide a comprehensive review for three major types of angiosperm genome databases, including databases for a single species, for a specific angiosperm clade, and for multiple angiosperm species. The scope, tools, and data of each type of databases and their features are concisely discussed. The genome databases for a single species or a clade of species are especially popular for specific group of researchers, while a timely-updated comprehensive database is more powerful for address of major scientific mysteries at the genome scale. Considering the low coverage of flowering plants in any available database, we propose construction of a comprehensive database to facilitate large-scale comparative studies of angiosperm genomes and to promote the collaborative studies of important questions in plant biology.

Draft genome sequence of Halomonas lutea strain YIM 91125 T (DSM 23508 T) isolated from the alkaline Lake Ebinur in Northwest China

DOE Office of Scientific and Technical Information (OSTI.GOV)

Gao, Xiao-Yang; Zhi, Xiao-Yang; Li, Hong-Wei

Species of the genus Halomonas are halophilic and their flexible adaption to changes of salinity and temperature brings considerable potential biotechnology applications, such as degradation of organic pollutants and enzyme production. The type strain Halomonas lutea YIM 91125 T was isolated from a hypersaline lake in China. The genome of strain YIM 91125 T becomes the twelfth species sequenced in Halomonas, and the thirteenth species sequenced in Halomonadaceae. We described the features of H. lutea YIM 91125 T, together with the high quality draft genome sequence and annotation of its type strain. The 4,533,090 bp long genome of strain YIMmore » 91125 T with its 4,284 protein-coding and 84 RNA genes is a part of Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes (KMG-I) project. From the viewpoint of comparative genomics, H. lutea has a larger genome size and more specific genes, which indicated acquisition of function bringing better adaption to its environment. Finally, DDH analysis demonstrated that H. lutea is a distinctive species, and halophilic features and nitrogen metabolism related genes were discovered in its genome.« less

The Sequenced Angiosperm Genomes and Genome Databases

PubMed Central

Chen, Fei; Dong, Wei; Zhang, Jiawei; Guo, Xinyue; Chen, Junhao; Wang, Zhengjia; Lin, Zhenguo; Tang, Haibao; Zhang, Liangsheng

2018-01-01

Angiosperms, the flowering plants, provide the essential resources for human life, such as food, energy, oxygen, and materials. They also promoted the evolution of human, animals, and the planet earth. Despite the numerous advances in genome reports or sequencing technologies, no review covers all the released angiosperm genomes and the genome databases for data sharing. Based on the rapid advances and innovations in the database reconstruction in the last few years, here we provide a comprehensive review for three major types of angiosperm genome databases, including databases for a single species, for a specific angiosperm clade, and for multiple angiosperm species. The scope, tools, and data of each type of databases and their features are concisely discussed. The genome databases for a single species or a clade of species are especially popular for specific group of researchers, while a timely-updated comprehensive database is more powerful for address of major scientific mysteries at the genome scale. Considering the low coverage of flowering plants in any available database, we propose construction of a comprehensive database to facilitate large-scale comparative studies of angiosperm genomes and to promote the collaborative studies of important questions in plant biology. PMID:29706973

Draft genome sequence of Halomonas lutea strain YIM 91125 T (DSM 23508 T) isolated from the alkaline Lake Ebinur in Northwest China

DOE PAGES

Gao, Xiao-Yang; Zhi, Xiao-Yang; Li, Hong-Wei; ...

2015-01-20

Species of the genus Halomonas are halophilic and their flexible adaption to changes of salinity and temperature brings considerable potential biotechnology applications, such as degradation of organic pollutants and enzyme production. The type strain Halomonas lutea YIM 91125 T was isolated from a hypersaline lake in China. The genome of strain YIM 91125 T becomes the twelfth species sequenced in Halomonas, and the thirteenth species sequenced in Halomonadaceae. We described the features of H. lutea YIM 91125 T, together with the high quality draft genome sequence and annotation of its type strain. The 4,533,090 bp long genome of strain YIMmore » 91125 T with its 4,284 protein-coding and 84 RNA genes is a part of Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes (KMG-I) project. From the viewpoint of comparative genomics, H. lutea has a larger genome size and more specific genes, which indicated acquisition of function bringing better adaption to its environment. Finally, DDH analysis demonstrated that H. lutea is a distinctive species, and halophilic features and nitrogen metabolism related genes were discovered in its genome.« less

Genome Variation Map: a data repository of genome variations in BIG Data Center

PubMed Central

Tian, Dongmei; Li, Cuiping; Tang, Bixia; Dong, Lili; Xiao, Jingfa; Bao, Yiming; Zhao, Wenming; He, Hang

2018-01-01

Abstract The Genome Variation Map (GVM; http://bigd.big.ac.cn/gvm/) is a public data repository of genome variations. As a core resource in the BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, GVM dedicates to collect, integrate and visualize genome variations for a wide range of species, accepts submissions of different types of genome variations from all over the world and provides free open access to all publicly available data in support of worldwide research activities. Unlike existing related databases, GVM features integration of a large number of genome variations for a broad diversity of species including human, cultivated plants and domesticated animals. Specifically, the current implementation of GVM not only houses a total of ∼4.9 billion variants for 19 species including chicken, dog, goat, human, poplar, rice and tomato, but also incorporates 8669 individual genotypes and 13 262 manually curated high-quality genotype-to-phenotype associations for non-human species. In addition, GVM provides friendly intuitive web interfaces for data submission, browse, search and visualization. Collectively, GVM serves as an important resource for archiving genomic variation data, helpful for better understanding population genetic diversity and deciphering complex mechanisms associated with different phenotypes. PMID:29069473

Antimicrobial Resistance in Hospital-Acquired Gram-Negative Bacterial Infections

PubMed Central

Mehrad, Borna; Clark, Nina M.; Zhanel, George G.

2015-01-01

Aerobic gram-negative bacilli, including the family of Enterobacteriaceae and non-lactose fermenting bacteria such as Pseudomonas and Acinetobacter species, are major causes of hospital-acquired infections. The rate of antibiotic resistance among these pathogens has accelerated dramatically in recent years and has reached pandemic scale. It is no longer uncommon to encounter gram-negative infections that are untreatable using conventional antibiotics in hospitalized patients. In this review, we provide a summary of the major classes of gram-negative bacilli and their key mechanisms of antimicrobial resistance, discuss approaches to the treatment of these difficult infections, and outline methods to slow the further spread of resistance mechanisms. PMID:25940252

The First Mitochondrial Genome for Caddisfly (Insecta: Trichoptera) with Phylogenetic Implications

PubMed Central

Wang, Yuyu; Liu, Xingyue; Yang, Ding

2014-01-01

The Trichoptera (caddisflies) is a holometabolous insect order with 14,300 described species forming the second most species-rich monophyletic group of animals in freshwater. Hitherto, there is no mitochondrial genome reported of this order. Herein, we describe the complete mitochondrial (mt) genome of a caddisfly species, Eubasilissa regina (McLachlan, 1871). A phylogenomic analysis was carried out based on the mt genomic sequences of 13 mt protein coding genes (PCGs) and two rRNA genes of 24 species belonging to eight holometabolous orders. Both maximum likelihood and Bayesian inference analyses highly support the sister relationship between Trichoptera and Lepidoptera. PMID:24391451

The complex hybrid origins of the root knot nematodes revealed through comparative genomics

PubMed Central

Kumar, Sujai; Koutsovoulos, Georgios; Blaxter, Mark L.

2014-01-01

Root knot nematodes (RKN) can infect most of the world’s agricultural crop species and are among the most important of all plant pathogens. As yet however we have little understanding of their origins or the genomic basis of their extreme polyphagy. The most damaging pathogens reproduce by obligatory mitotic parthenogenesis and it has been suggested that these species originated from interspecific hybridizations between unknown parental taxa. We have sequenced the genome of the diploid meiotic parthenogen Meloidogyne floridensis, and use a comparative genomic approach to test the hypothesis that this species was involved in the hybrid origin of the tropical mitotic parthenogen Meloidogyne incognita. Phylogenomic analysis of gene families from M. floridensis, M. incognita and an outgroup species Meloidogyne hapla was carried out to trace the evolutionary history of these species’ genomes, and we demonstrate that M. floridensis was one of the parental species in the hybrid origins of M. incognita. Analysis of the M. floridensis genome itself revealed many gene loci present in divergent copies, as they are in M. incognita, indicating that it too had a hybrid origin. The triploid M. incognita is shown to be a complex double-hybrid between M. floridensis and a third, unidentified, parent. The agriculturally important RKN have very complex origins involving the mixing of several parental genomes by hybridization and their extreme polyphagy and success in agricultural environments may be related to this hybridization, producing transgressive variation on which natural selection can act. It is now clear that studying RKN variation via individual marker loci may fail due to the species’ convoluted origins, and multi-species population genomics is essential to understand the hybrid diversity and adaptive variation of this important species complex. This comparative genomic analysis provides a compelling example of the importance and complexity of hybridization in generating animal species diversity more generally. PMID:24860695

Evidence for inter-specific recombination among the mitochondrial genomes of Fusarium species in the Gibberella fujikuroi complex.

PubMed

Fourie, Gerda; van der Merwe, Nicolaas A; Wingfield, Brenda D; Bogale, Mesfin; Tudzynski, Bettina; Wingfield, Michael J; Steenkamp, Emma T

2013-09-08

The availability of mitochondrial genomes has allowed for the resolution of numerous questions regarding the evolutionary history of fungi and other eukaryotes. In the Gibberella fujikuroi species complex, the exact relationships among the so-called "African", "Asian" and "American" Clades remain largely unresolved, irrespective of the markers employed. In this study, we considered the feasibility of using mitochondrial genes to infer the phylogenetic relationships among Fusarium species in this complex. The mitochondrial genomes of representatives of the three Clades (Fusarium circinatum, F. verticillioides and F. fujikuroi) were characterized and we determined whether or not the mitochondrial genomes of these fungi have value in resolving the higher level evolutionary relationships in the complex. Overall, the mitochondrial genomes of the three species displayed a high degree of synteny, with all the genes (protein coding genes, unique ORFs, ribosomal RNA and tRNA genes) in identical order and orientation, as well as introns that share similar positions within genes. The intergenic regions and introns generally contributed significantly to the size differences and diversity observed among these genomes. Phylogenetic analysis of the concatenated protein-coding dataset separated members of the Gibberella fujikuroi complex from other Fusarium species and suggested that F. fujikuroi ("Asian" Clade) is basal in the complex. However, individual mitochondrial gene trees were largely incongruent with one another and with the concatenated gene tree, because six distinct phylogenetic trees were recovered from the various single gene datasets. The mitochondrial genomes of Fusarium species in the Gibberella fujikuroi complex are remarkably similar to those of the previously characterized Fusarium species and Sordariomycetes. Despite apparently representing a single replicative unit, all of the genes encoded on the mitochondrial genomes of these fungi do not share the same evolutionary history. This incongruence could be due to biased selection on some genes or recombination among mitochondrial genomes. The results thus suggest that the use of individual mitochondrial genes for phylogenetic inference could mask the true relationships between species in this complex.

Genetic relationships among seven sections of genus Arachis studied by using SSR markers

PubMed Central

2010-01-01

Background The genus Arachis, originated in South America, is divided into nine taxonomical sections comprising of 80 species. Most of the Arachis species are diploids (2n = 2x = 20) and the tetraploid species (2n = 2x = 40) are found in sections Arachis, Extranervosae and Rhizomatosae. Diploid species have great potential to be used as resistance sources for agronomic traits like pests and diseases, drought related traits and different life cycle spans. Understanding of genetic relationships among wild species and between wild and cultivated species will be useful for enhanced utilization of wild species in improving cultivated germplasm. The present study was undertaken to evaluate genetic relationships among species (96 accessions) belonging to seven sections of Arachis by using simple sequence repeat (SSR) markers developed from Arachis hypogaea genomic library and gene sequences from related genera of Arachis. Results The average transferability rate of 101 SSR markers tested to section Arachis and six other sections was 81% and 59% respectively. Five markers (IPAHM 164, IPAHM 165, IPAHM 407a, IPAHM 409, and IPAHM 659) showed 100% transferability. Cluster analysis of allelic data from a subset of 32 SSR markers on 85 wild and 11 cultivated accessions grouped accessions according to their genome composition, sections and species to which they belong. A total of 109 species specific alleles were detected in different wild species, Arachis pusilla exhibited largest number of species specific alleles (15). Based on genetic distance analysis, the A-genome accession ICG 8200 (A. duranensis) and the B-genome accession ICG 8206 (A. ipaënsis) were found most closely related to A. hypogaea. Conclusion A set of cross species and cross section transferable SSR markers has been identified that will be useful for genetic studies of wild species of Arachis, including comparative genome mapping, germplasm analysis, population genetic structure and phylogenetic inferences among species. The present study provides strong support based on both genomic and genic markers, probably for the first time, on relationships of A. monticola and A. hypogaea as well as on the most probable donor of A and B-genomes of cultivated groundnut. PMID:20089171

Effectiveness of Halogen-Based Disinfectants Against Acinetobacter Baumannii: Wound Care and Environmental Decontamination

DTIC Science & Technology

2006-11-01

EFFECTIVENESS OF HALOGEN-BASED DISINFECTANTS AGAINST Acinetobacter baumannii: WOUND CARE AND ENVIROMENTAL DECONTAMINATION James...a standard E. coli comparator, in a novel bacterial culture system that incorporated a three log range of organic growth media concentrations. We...report the highest dilutions of stock disinfectant able to inhibit replication or kill the bacteria , denoted as the maximum inhibitory dilution

[Infection of chronic otitis media with Acinetobacter：6 cases report].

PubMed

Zhang, K; Qu, P; Jia, N; Fu, T

2016-12-01

Objective: To investigate the clinical characteristics, diagnostic methods and prognosis of patients with chronic otitis media with Acinetobacter infection. Method: Retrospective analysis of clinical data of 6 cases of chronic otitis media complicated with Acinetobacter infection. Including history, clinical manifestations, laboratory examination, audiology, inner ear, CT, MRI imaging characteristics, treatment and prognosis of etc. to summarize the clinical characteristics, diagnosis and treatment of chronic otitis media with Acinetobacter infection. Result: The age was between 17 years old and 61 years old (Median age 30 years) .Two of them was male and 4 were female. Four cases were had underlying diseases. Five cases with main symptom of cholesteatoma, 1 case with earache symptoms, and 1 case with facial paralysis symptoms. Four cases had vary degrees of physical decline and destruction of bone. After surgery treatment, five patients improved ear pus, among 3 cases was cured, 2 cases of recurrence. Conclusion: Chronic otitis media with Acinetobacter infection occurs in the patient with elderly, poor physical constitution. However, the recurrence rate of conventional treatment is higher. The disease has high misdiagnosis rate. Operation combined with sensitive antibiotic therapy is a radical cure method. Copyright© by the Editorial Department of Journal of Clinical Otorhinolaryngology Head and Neck Surgery.

Coaggregation between Rhodococcus and Acinetobacter strains isolated from the food industry.

PubMed

Møretrø, Trond; Sharifzadeh, Shahab; Langsrud, Solveig; Heir, Even; Rickard, Alexander H

2015-07-01

In this study, coaggregation interactions between Rhodococcus and Acinetobacter strains isolated from food-processing surfaces were characterized. Rhodococcus sp. strain MF3727 formed intrageneric coaggregates with Rhodococcus sp. strain MF3803 and intergeneric coaggregates with 2 strains of Acinetobacter calcoaceticus (MF3293, MF3627). Stronger coaggregation between A. calcoaceticus MF3727 and Rhodococcus sp. MF3293 was observed after growth in batch culture at 30 °C than at 20 °C, after growth in tryptic soy broth than in liquid R2A medium, and between cells in exponential and early stationary phases than cells in late stationary phase. The coaggregation ability of Rhodococcus sp. MF3727 was maintained even after heat and Proteinase K treatment, suggesting its ability to coaggregate was protein independent whereas the coaggregation determinants of the other strains involved proteinaceous cell-surface-associated polymers. Coaggregation was stable at pH 5-9. The mechanisms of coaggregation among Acinetobacter and Rhodococcus strains bare similarity to those displayed by coaggregating bacteria of oral and freshwater origin, with respect to binding between proteinaceous and nonproteinaceous determinants and the effect of environmental factors on coaggregation. Coaggregation may contribute to biofilm formation on industrial food surfaces, protecting bacteria against cleaning and disinfection.

New strains of oil-degrading microorganisms for treating contaminated soils and wastes

NASA Astrophysics Data System (ADS)

Muratova, A. Yu; Panchenko, L. V.; Semina, D. V.; Golubev, S. N.; Turkovskaya, O. V.

2018-01-01

Two new strains Achromobacter marplatensis101n and Acinetobacter sp. S-33, capable of degrading 49 and 46% of oil within 7 days were isolated, identified, and characterized. The application of A. marplatensis 101n in combination with ammonium nitrate (100 mg·kg-1) for 30 days of cultivation resulted in the degradation of 49% of the initial total petroleum hydrocarbon content (274 g·kg-1) in the original highly acid (pH 4.9) oil-contaminated waste. Up to 30% of oil sludge added to a liquid mineral medium at a concentration of 15% was degraded after 10 days of cultivation of A. marplatensis 101n. Application of yellow alfalfa (Medicago falcata L.) plants with Acinetobacter sp. S-33 for bioremediation of oil-sludge-contaminated soil improved the quality of cleanup in comparison with the bacterium- or plant-only treatment. Inoculation of Acinetobacter sp. S-33 increased the growth of both roots and shoots by more than 40%, and positively influenced the soil microflora. We conclude that the new oil-degrading strains, Acinetobacter sp. S-33 and A. marplatensis 101n, can serve as the basis for new bioremediation agents for the treatment of oil contaminated soils and waste.

Bolbase: a comprehensive genomics database for Brassica oleracea

PubMed Central

2013-01-01

Background Brassica oleracea is a morphologically diverse species in the family Brassicaceae and contains a group of nutrition-rich vegetable crops, including common heading cabbage, cauliflower, broccoli, kohlrabi, kale, Brussels sprouts. This diversity along with its phylogenetic membership in a group of three diploid and three tetraploid species, and the recent availability of genome sequences within Brassica provide an unprecedented opportunity to study intra- and inter-species divergence and evolution in this species and its close relatives. Description We have developed a comprehensive database, Bolbase, which provides access to the B. oleracea genome data and comparative genomics information. The whole genome of B. oleracea is available, including nine fully assembled chromosomes and 1,848 scaffolds, with 45,758 predicted genes, 13,382 transposable elements, and 3,581 non-coding RNAs. Comparative genomics information is available, including syntenic regions among B. oleracea, Brassica rapa and Arabidopsis thaliana, synonymous (Ks) and non-synonymous (Ka) substitution rates between orthologous gene pairs, gene families or clusters, and differences in quantity, category, and distribution of transposable elements on chromosomes. Bolbase provides useful search and data mining tools, including a keyword search, a local BLAST server, and a customized GBrowse tool, which can be used to extract annotations of genome components, identify similar sequences and visualize syntenic regions among species. Users can download all genomic data and explore comparative genomics in a highly visual setting. Conclusions Bolbase is the first resource platform for the B. oleracea genome and for genomic comparisons with its relatives, and thus it will help the research community to better study the function and evolution of Brassica genomes as well as enhance molecular breeding research. This database will be updated regularly with new features, improvements to genome annotation, and new genomic sequences as they become available. Bolbase is freely available at http://ocri-genomics.org/bolbase. PMID:24079801

Physiological and molecular characterization of Si uptake in wild rice species.

PubMed

Mitani-Ueno, Namiki; Ogai, Hisao; Yamaji, Naoki; Ma, Jian Feng

2014-07-01

Cultivated rice (Oryza sativa) accumulates high concentration of silicon (Si), which is required for its high and sustainable production. High Si accumulation in cultivated rice is achieved by a high expression of both influx (Lsi1) and efflux (Lsi2) Si transporters in roots. Herein, we physiologically investigated Si uptake, isolated and functionally characterized Si transporters in six wild rice species with different genome types. Si uptake by the roots was lower in Oryza rufipogon, Oryza barthii (AA genome), Oryza australiensis (EE genome) and Oryza punctata (BB genome), but similar in Oryza glumaepatula and Oryza meridionalis (AA genome) compared with the cultivated rice (cv. Nipponbare). However, all wild rice species and the cultivated rice showed similar concentration of Si in the shoots when grown in a field. All species with AA genome showed the same amino acid sequence of both Lsi1 and Lsi2 as O. sativa, whereas species with EE and BB genome showed several nucleotide differences in both Lsi1 and Lsi2. However, proteins encoded by these genes also showed transport activity for Si in Xenopus oocyte. The mRNA expression of Lsi1 in all wild rice species was lower than that in the cultivated rice, whereas the expression of Lsi2 was lower in O. rufipogon and O. barthii but similar in other species. Similar cellular localization of Lsi1 and Lsi2 was observed in all wild rice as the cultivated rice. These results indicate that superior Si uptake, the important trait for rice growth, is basically conserved in wild and cultivated rice species. © 2013 Scandinavian Plant Physiology Society.

Mitochondrial DNA Evidence Supports the Hypothesis that Triodontophorus Species Belong to Cyathostominae

PubMed Central

Gao, Yuan; Zhang, Yan; Yang, Xin; Qiu, Jian-Hua; Duan, Hong; Xu, Wen-Wen; Chang, Qiao-Cheng; Wang, Chun-Ren

2017-01-01

Equine strongyles, the significant nematode pathogens of horses, are characterized by high quantities and species abundance, but classification of this group of parasitic nematodes is debated. Mitochondrial (mt) genome DNA data are often used to address classification controversies. Thus, the objectives of this study were to determine the complete mt genomes of three Cyathostominae nematode species (Cyathostomum catinatum, Cylicostephanus minutus, and Poteriostomum imparidentatum) of horses and reconstruct the phylogenetic relationship of Strongylidae with other nematodes in Strongyloidea to test the hypothesis that Triodontophorus spp. belong to Cyathostominae using the mt genomes. The mt genomes of Cy. catinatum, Cs. minutus, and P. imparidentatum were 13,838, 13,826, and 13,817 bp in length, respectively. Complete mt nucleotide sequence comparison of all Strongylidae nematodes revealed that sequence identity ranged from 77.8 to 91.6%. The mt genome sequences of Triodontophorus species had relatively high identity with Cyathostominae nematodes, rather than Strongylus species of the same subfamily (Strongylinae). Comparative analyses of mt genome organization for Strongyloidea nematodes sequenced to date revealed that members of this superfamily possess identical gene arrangements. Phylogenetic analyses using mtDNA data indicated that the Triodontophorus species clustered with Cyathostominae species instead of Strongylus species. The present study first determined the complete mt genome sequences of Cy. catinatum, Cs. minutus, and P. imparidentatum, which will provide novel genetic markers for further studies of Strongylidae taxonomy, population genetics, and systematics. Importantly, sequence comparison and phylogenetic analyses based on mtDNA sequences supported the hypothesis that Triodontophorus belongs to Cyathostominae. PMID:28824575

Cleaning and Disinfection of Biofilms Composed of Listeria monocytogenes and Background Microbiota from Meat Processing Surfaces

PubMed Central

Møretrø, Trond; Heir, Even; Briandet, Romain; Langsrud, Solveig

2017-01-01

ABSTRACT Surfaces of food processing premises are exposed to regular cleaning and disinfection (C&D) regimes, using biocides that are highly effective against bacteria growing as planktonic cells. However, bacteria growing in surface-associated communities (biofilms) are typically more tolerant toward C&D than their individual free-cell counterparts, and survival of pathogens such as Listeria monocytogenes may be affected by interspecies interactions within biofilms. In this study, Pseudomonas and Acinetobacter were the most frequently isolated genera surviving on conveyor belts subjected to C&D in meat processing plants. In the laboratory, Pseudomonas, Acinetobacter, and L. monocytogenes dominated the community, both in suspensions and in biofilms formed on conveyor belts, when cultures were inoculated with eleven-genus cocktails of representative bacterial strains from the identified background flora. When biofilms were exposed to daily C&D cycles mimicking treatments used in food industry, the levels of Acinetobacter and Pseudomonas mandelii diminished, and biofilms were instead dominated by Pseudomonas putida (65 to 76%), Pseudomonas fluorescens (11 to 15%) and L. monocytogenes (3 to 11%). The dominance of certain species after daily C&D correlated with high planktonic growth rates at 12°C and tolerance to C&D. In single-species biofilms, L. monocytogenes developed higher tolerance to C&D over time, for both the peracetic acid and quaternary ammonium disinfectants, indicating that a broad-spectrum mechanism was involved. Survival after C&D appeared to be a common property of L. monocytogenes strains, as persistent and sporadic subtypes showed equal survival rates in complex biofilms. Biofilms established preferentially in surface irregularities of conveyor belts, potentially constituting harborage sites for persistent contamination. IMPORTANCE In the food industry, efficient production hygiene is a key measure to avoid the accumulation of spoilage bacteria and eliminate pathogens. However, the persistence of bacteria is an enduring problem in food processing environments. This study demonstrated that environmental bacteria can survive foam cleaning and disinfection (C&D) at concentrations used in the industrial environment. The phenomenon was replicated in laboratory experiments. Important characteristics of persisting bacteria were a high growth rate at low temperature, a tolerance to the cleaning agent, and the ability to form biofilms. This study also supports other recent research suggesting that strain-to-strain variation cannot explain why certain subtypes of Listeria monocytogenes persist in food processing environments while others are found only sporadically. The present investigation highlights the failure of regular C&D and a need for research on improved agents that efficiently detach the biofilm matrix. PMID:28667108

Cleaning and disinfection of biofilms composed of Listeria monocytogenes and background microbiota from meat processing surfaces.

PubMed

Fagerlund, Annette; Møretrø, Trond; Heir, Even; Briandet, Romain; Langsrud, Solveig

2017-06-30

Surfaces of food processing premises are exposed to regular cleaning and disinfection (C&D) regimes, using biocides that are highly effective against bacteria growing as planktonic cells. However, bacteria growing in surface associated communities (biofilms) are typically more tolerant towards C&D than their individual free cells counterparts, and survival of pathogens such as Listeria monocytogenes may be affected by interspecies interactions within biofilms. In this study, Pseudomonas and Acinetobacter were the most frequently isolated genera surviving on conveyor belts subjected to C&D in meat processing plants. In the laboratory, Pseudomonas , Acinetobacter and L. monocytogenes dominated the community both in suspensions and in biofilms formed on conveyor belts, when cultures were inoculated with eleven-genera cocktails of representative bacterial strains from the identified background flora. When biofilms were exposed to daily C&D cycles, mimicking treatments used in food industry, the levels of Acinetobacter and Pseudomonas mandelii diminished, and biofilms were instead dominated by Pseudomonas putida (65-76%), Pseudomonas fluorescens (11-15%) and L. monocytogenes (3-11%). The dominance of certain species after daily C&D correlated with high planktonic growth rates at 12°C and tolerance to C&D. In single-species biofilms, L. monocytogenes developed higher tolerance to C&D over time, both for the peracetic acid and quaternary ammonium disinfectant, indicating that a broad-spectrum mechanism was involved. Survival after C&D appeared to be a common property of L. monocytogenes strains, as both persistent and sporadic subtypes showed equal survival in complex biofilms. Biofilms established preferentially in surface irregularities of conveyor belts, potentially constituting harborage sites for persistent contamination. IMPORTANCE In food industry, efficient production hygiene is a key measure to avoid accumulation of spoilage bacteria and eliminate pathogens. Persistence of bacteria is however a withstanding problem in food processing environments. This study demonstrated that environmental bacteria can survive foam cleaning and disinfection (C&D) at user concentrations in the industrial environment. The phenomenon was replicated in laboratory experiments. Important characteristics of persisting bacteria were high growth rate at low temperature, tolerance to the cleaning agent and ability to form biofilm. This study also supports other recent research suggesting that strain-to-strain variation cannot explain why certain subtypes of Listeria monocytogenes persist in food processing environments while others are found only sporadically. The present investigation highlights the failure of regular C&D and a need for research on improved agents efficiently detaching the biofilm matrix. Copyright © 2017 American Society for Microbiology.

Genome resequencing in Populus: Revealing large-scale genome variation and implications on specialized-trait genomics

DOE Office of Scientific and Technical Information (OSTI.GOV)

Muchero, Wellington; Labbe, Jessy L; Priya, Ranjan

2014-01-01

To date, Populus ranks among a few plant species with a complete genome sequence and other highly developed genomic resources. With the first genome sequence among all tree species, Populus has been adopted as a suitable model organism for genomic studies in trees. However, far from being just a model species, Populus is a key renewable economic resource that plays a significant role in providing raw materials for the biofuel and pulp and paper industries. Therefore, aside from leading frontiers of basic tree molecular biology and ecological research, Populus leads frontiers in addressing global economic challenges related to fuel andmore » fiber production. The latter fact suggests that research aimed at improving quality and quantity of Populus as a raw material will likely drive the pursuit of more targeted and deeper research in order to unlock the economic potential tied in molecular biology processes that drive this tree species. Advances in genome sequence-driven technologies, such as resequencing individual genotypes, which in turn facilitates large scale SNP discovery and identification of large scale polymorphisms are key determinants of future success in these initiatives. In this treatise we discuss implications of genome sequence-enable technologies on Populus genomic and genetic studies of complex and specialized-traits.« less

Simultaneous gene finding in multiple genomes.

PubMed

König, Stefanie; Romoth, Lars W; Gerischer, Lizzy; Stanke, Mario

2016-11-15

As the tree of life is populated with sequenced genomes ever more densely, the new challenge is the accurate and consistent annotation of entire clades of genomes. We address this problem with a new approach to comparative gene finding that takes a multiple genome alignment of closely related species and simultaneously predicts the location and structure of protein-coding genes in all input genomes, thereby exploiting negative selection and sequence conservation. The model prefers potential gene structures in the different genomes that are in agreement with each other, or-if not-where the exon gains and losses are plausible given the species tree. We formulate the multi-species gene finding problem as a binary labeling problem on a graph. The resulting optimization problem is NP hard, but can be efficiently approximated using a subgradient-based dual decomposition approach. The proposed method was tested on whole-genome alignments of 12 vertebrate and 12 Drosophila species. The accuracy was evaluated for human, mouse and Drosophila melanogaster and compared to competing methods. Results suggest that our method is well-suited for annotation of (a large number of) genomes of closely related species within a clade, in particular, when RNA-Seq data are available for many of the genomes. The transfer of existing annotations from one genome to another via the genome alignment is more accurate than previous approaches that are based on protein-spliced alignments, when the genomes are at close to medium distances. The method is implemented in C ++ as part of Augustus and available open source at http://bioinf.uni-greifswald.de/augustus/ CONTACT: stefaniekoenig@ymail.com or mario.stanke@uni-greifswald.deSupplementary information: Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press. All rights reserved. For Permissions, please e-mail: journals.permissions@oup.com.

OryzaGenome: Genome Diversity Database of Wild Oryza Species.

PubMed

Ohyanagi, Hajime; Ebata, Toshinobu; Huang, Xuehui; Gong, Hao; Fujita, Masahiro; Mochizuki, Takako; Toyoda, Atsushi; Fujiyama, Asao; Kaminuma, Eli; Nakamura, Yasukazu; Feng, Qi; Wang, Zi-Xuan; Han, Bin; Kurata, Nori

2016-01-01

The species in the genus Oryza, encompassing nine genome types and 23 species, are a rich genetic resource and may have applications in deeper genomic analyses aiming to understand the evolution of plant genomes. With the advancement of next-generation sequencing (NGS) technology, a flood of Oryza species reference genomes and genomic variation information has become available in recent years. This genomic information, combined with the comprehensive phenotypic information that we are accumulating in our Oryzabase, can serve as an excellent genotype-phenotype association resource for analyzing rice functional and structural evolution, and the associated diversity of the Oryza genus. Here we integrate our previous and future phenotypic/habitat information and newly determined genotype information into a united repository, named OryzaGenome, providing the variant information with hyperlinks to Oryzabase. The current version of OryzaGenome includes genotype information of 446 O. rufipogon accessions derived by imputation and of 17 accessions derived by imputation-free deep sequencing. Two variant viewers are implemented: SNP Viewer as a conventional genome browser interface and Variant Table as a text-based browser for precise inspection of each variant one by one. Portable VCF (variant call format) file or tab-delimited file download is also available. Following these SNP (single nucleotide polymorphism) data, reference pseudomolecules/scaffolds/contigs and genome-wide variation information for almost all of the closely and distantly related wild Oryza species from the NIG Wild Rice Collection will be available in future releases. All of the resources can be accessed through http://viewer.shigen.info/oryzagenome/. © The Author 2015. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists.

A Deluge of Complex Repeats: The Solanum Genome

PubMed Central

Mehra, Mrigaya; Gangwar, Indu; Shankar, Ravi

2015-01-01

Repetitive elements have lately emerged as key components of genome, performing varieties of roles. It has now become necessary to have an account of repeats for every genome to understand its dynamics and state. Recently, genomes of two major Solanaceae species, Solanum tuberosum and Solanum lycopersicum, were sequenced. These species are important crops having high commercial significance as well as value as model species. However, there is a reasonable gap in information about repetitive elements and their possible roles in genome regulation for these species. The present study was aimed at detailed identification and characterization of complex repetitive elements in these genomes, along with study of their possible functional associations as well as to assess possible transcriptionally active repetitive elements. In this study, it was found that ~50–60% of genomes of S. tuberosum and S. lycopersicum were composed of repetitive elements. It was also found that complex repetitive elements were associated with >95% of genes in both species. These two genomes are mostly composed of LTR retrotransposons. Two novel repeat families very similar to LTR/ERV1 and LINE/RTE-BovB have been reported for the first time. Active existence of complex repeats was estimated by measuring their transcriptional abundance using Next Generation Sequencing read data and Microarray platforms. A reasonable amount of regulatory components like transcription factor binding sites and miRNAs appear to be under the influence of these complex repetitive elements in these species, while several genes appeared to possess exonized repeats. PMID:26241045

A linkage map for the B-genome of Arachis (Fabaceae) and its synteny to the A-genome

PubMed Central

Moretzsohn, Márcio C; Barbosa, Andrea VG; Alves-Freitas, Dione MT; Teixeira, Cristiane; Leal-Bertioli, Soraya CM; Guimarães, Patrícia M; Pereira, Rinaldo W; Lopes, Catalina R; Cavallari, Marcelo M; Valls, José FM; Bertioli, David J; Gimenes, Marcos A

2009-01-01

Background Arachis hypogaea (peanut) is an important crop worldwide, being mostly used for edible oil production, direct consumption and animal feed. Cultivated peanut is an allotetraploid species with two different genome components, A and B. Genetic linkage maps can greatly assist molecular breeding and genomic studies. However, the development of linkage maps for A. hypogaea is difficult because it has very low levels of polymorphism. This can be overcome by the utilization of wild species of Arachis, which present the A- and B-genomes in the diploid state, and show high levels of genetic variability. Results In this work, we constructed a B-genome linkage map, which will complement the previously published map for the A-genome of Arachis, and produced an entire framework for the tetraploid genome. This map is based on an F2 population of 93 individuals obtained from the cross between the diploid A. ipaënsis (K30076) and the closely related A. magna (K30097), the former species being the most probable B genome donor to cultivated peanut. In spite of being classified as different species, the parents showed high crossability and relatively low polymorphism (22.3%), compared to other interspecific crosses. The map has 10 linkage groups, with 149 loci spanning a total map distance of 1,294 cM. The microsatellite markers utilized, developed for other Arachis species, showed high transferability (81.7%). Segregation distortion was 21.5%. This B-genome map was compared to the A-genome map using 51 common markers, revealing a high degree of synteny between both genomes. Conclusion The development of genetic maps for Arachis diploid wild species with A- and B-genomes effectively provides a genetic map for the tetraploid cultivated peanut in two separate diploid components and is a significant advance towards the construction of a transferable reference map for Arachis. Additionally, we were able to identify affinities of some Arachis linkage groups with Medicago truncatula, which will allow the transfer of information from the nearly-complete genome sequences of this model legume to the peanut crop. PMID:19351409

Whole Genome Sequencing of Danish Staphylococcus argenteus Reveals a Genetically Diverse Collection with Clear Separation from Staphylococcus aureus.

PubMed

Hansen, Thomas A; Bartels, Mette D; Høgh, Silje V; Dons, Lone E; Pedersen, Michael; Jensen, Thøger G; Kemp, Michael; Skov, Marianne N; Gumpert, Heidi; Worning, Peder; Westh, Henrik

2017-01-01

Staphylococcus argenteus ( S. argenteus ) is a newly identified Staphylococcus species that has been misidentified as Staphylococcus aureus ( S. aureus ) and is clinically relevant. We identified 25 S. argenteus genomes in our collection of whole genome sequenced S. aureus . These genomes were compared to publicly available genomes and a phylogeny revealed seven clusters corresponding to seven clonal complexes. The genome of S. argenteus was found to be different from the genome of S. aureus and a core genome analysis showed that ~33% of the total gene pool was shared between the two species, at 90% homology level. An assessment of mobile elements shows flow of SCC mec cassettes, plasmids, phages, and pathogenicity islands, between S. argenteus and S. aureus . This dataset emphasizes that S. argenteus and S. aureus are two separate species that share genetic material.

Tapping the promise of genomics in species with complex, nonmodel genomes.

PubMed

Hirsch, Candice N; Buell, C Robin

2013-01-01

Genomics is enabling a renaissance in all disciplines of plant biology. However, many plant genomes are complex and remain recalcitrant to current genomic technologies. The complexities of these nonmodel plant genomes are attributable to gene and genome duplication, heterozygosity, ploidy, and/or repetitive sequences. Methods are available to simplify the genome and reduce these barriers, including inbreeding and genome reduction, making these species amenable to current sequencing and assembly methods. Some, but not all, of the complexities in nonmodel genomes can be bypassed by sequencing the transcriptome rather than the genome. Additionally, comparative genomics approaches, which leverage phylogenetic relatedness, can aid in the interpretation of complex genomes. Although there are limitations in accessing complex nonmodel plant genomes using current sequencing technologies, genome manipulation and resourceful analyses can allow access to even the most recalcitrant plant genomes.

Comparative functional genomics of salt stress in related model and cultivated plants identifies and overcomes limitations to translational genomics.

PubMed

Sanchez, Diego H; Pieckenstain, Fernando L; Szymanski, Jedrzey; Erban, Alexander; Bromke, Mariusz; Hannah, Matthew A; Kraemer, Ute; Kopka, Joachim; Udvardi, Michael K

2011-02-14

One of the objectives of plant translational genomics is to use knowledge and genes discovered in model species to improve crops. However, the value of translational genomics to plant breeding, especially for complex traits like abiotic stress tolerance, remains uncertain. Using comparative genomics (ionomics, transcriptomics and metabolomics) we analyzed the responses to salinity of three model and three cultivated species of the legume genus Lotus. At physiological and ionomic levels, models responded to salinity in a similar way to crop species, and changes in the concentration of shoot Cl(-) correlated well with tolerance. Metabolic changes were partially conserved, but divergence was observed amongst the genotypes. Transcriptome analysis showed that about 60% of expressed genes were responsive to salt treatment in one or more species, but less than 1% was responsive in all. Therefore, genotype-specific transcriptional and metabolic changes overshadowed conserved responses to salinity and represent an impediment to simple translational genomics. However, 'triangulation' from multiple genotypes enabled the identification of conserved and tolerant-specific responses that may provide durable tolerance across species.

Chromhome: A rich internet application for accessing comparative chromosome homology maps

PubMed Central

Nagarajan, Sridevi; Rens, Willem; Stalker, James; Cox, Tony; Ferguson-Smith, Malcolm A

2008-01-01

Background Comparative genomics has become a significant research area in recent years, following the availability of a number of sequenced genomes. The comparison of genomes is of great importance in the analysis of functionally important genome regions. It can also be used to understand the phylogenetic relationships of species and the mechanisms leading to rearrangement of karyotypes during evolution. Many species have been studied at the cytogenetic level by cross species chromosome painting. With the large amount of such information, it has become vital to computerize the data and make them accessible worldwide. Chromhome is a comprehensive web application that is designed to provide cytogenetic comparisons among species and to fulfil this need. Results The Chromhome application architecture is multi-tiered with an interactive client layer, business logic and database layers. Enterprise java platform with open source framework OpenLaszlo is used to implement the Rich Internet Chromhome Application. Cross species comparative mapping raw data are collected and the processed information is stored into MySQL Chromhome database. Chromhome Release 1.0 contains 109 homology maps from 51 species. The data cover species from 14 orders and 30 families. The homology map displays all the chromosomes of the compared species as one image, making comparisons among species easier. Inferred data also provides maps of homologous regions that could serve as a guideline for researchers involved in phylogenetic or evolution based studies. Conclusion Chromhome provides a useful resource for comparative genomics, holding graphical homology maps of a wide range of species. It brings together cytogenetic data of many genomes under one roof. Inferred painting can often determine the chromosomal homologous regions between two species, if each has been compared with a common third species. Inferred painting greatly reduces the need to map entire genomes and helps focus only on relevant regions of the chromosomes of the species under study. Future releases of Chromhome will accommodate more species and their respective gene and BAC maps, in addition to chromosome painting data. Chromhome application provides a single-page interface (SPI) with desktop style layout, delivering a better and richer user experience. PMID:18366796

A bicontinental origin of polyploid Australian/New Zealand Lepidium species (Brassicaceae)? Evidence from genomic in situ hybridization.

PubMed

Dierschke, Tom; Mandáková, Terezie; Lysak, Martin A; Mummenhoff, Klaus

2009-09-01

Incongruence between chloroplast and nuclear DNA phylogenies, and single additive nucleotide positions in internal transcribed spacer (ITS) sequences of polyploid Australian/New Zealand (NZ) Lepidium species have been used to suggest a bicontinental hybrid origin. This pattern was explained by two trans-oceanic dispersals of Lepidium species from California and Africa and subsequent hybridization followed by homogenization of the ribosomal DNA sequence either to the Californian (C-clade) or to the African ITS-type (A-clade) in two different ITS-lineages of Australian/NZ Lepidium polyploids. Genomic in situ hybridization (GISH) was used to unravel the genomic origin of polyploid Australian/NZ Lepidium species. Fluorescence in situ hybridization (FISH) with ribosomal DNA (rDNA) probes was applied to test the purported ITS evolution, and to facilitate chromosome counting in high-numbered polyploids. In Australian/NZ A-clade Lepidium polyploids, GISH identified African and Australian/NZ C-clade species as putative ancestral genomes. Neither the African nor the Californian genome were detected in Australian/NZ C-clade species and the Californian genome was not detected in Australian/NZ A-clade species. Five of the eight polyploid species (from 7x to 11x) displayed a diploid-like set of rDNA loci. Even the undecaploid species Lepidium muelleriferdinandi (2n = 11x = 88) showed only one pair of each rDNA repeat. In A-clade allopolyploids, in situ rDNA localization combined with GISH corroborated the presence of the African ITS-type. The nuclear genomes of African and Australian/NZ C-clade species were detected by GISH in allopolyploid Australian/NZ Lepidium species of the A-clade, supporting their hybrid origin. The presumed hybrid origin of Australian/NZ C-clade taxa could not be confirmed. Hence, it is assumed that Californian ancestral taxa experienced rapid radiation in Australia/NZ into extant C-clade polyploid taxa followed by hybridization with African species. As a result, A-clade allopolyploid Lepidium species share the Californian chloroplast type and the African ITS-type with the C-clade Australian/NZ polyploid and African diploid species, respectively.

Chromhome: a rich internet application for accessing comparative chromosome homology maps.

PubMed

Nagarajan, Sridevi; Rens, Willem; Stalker, James; Cox, Tony; Ferguson-Smith, Malcolm A

2008-03-26

Comparative genomics has become a significant research area in recent years, following the availability of a number of sequenced genomes. The comparison of genomes is of great importance in the analysis of functionally important genome regions. It can also be used to understand the phylogenetic relationships of species and the mechanisms leading to rearrangement of karyotypes during evolution. Many species have been studied at the cytogenetic level by cross species chromosome painting. With the large amount of such information, it has become vital to computerize the data and make them accessible worldwide. Chromhome http://www.chromhome.org is a comprehensive web application that is designed to provide cytogenetic comparisons among species and to fulfil this need. The Chromhome application architecture is multi-tiered with an interactive client layer, business logic and database layers. Enterprise java platform with open source framework OpenLaszlo is used to implement the Rich Internet Chromhome Application. Cross species comparative mapping raw data are collected and the processed information is stored into MySQL Chromhome database. Chromhome Release 1.0 contains 109 homology maps from 51 species. The data cover species from 14 orders and 30 families. The homology map displays all the chromosomes of the compared species as one image, making comparisons among species easier. Inferred data also provides maps of homologous regions that could serve as a guideline for researchers involved in phylogenetic or evolution based studies. Chromhome provides a useful resource for comparative genomics, holding graphical homology maps of a wide range of species. It brings together cytogenetic data of many genomes under one roof. Inferred painting can often determine the chromosomal homologous regions between two species, if each has been compared with a common third species. Inferred painting greatly reduces the need to map entire genomes and helps focus only on relevant regions of the chromosomes of the species under study. Future releases of Chromhome will accommodate more species and their respective gene and BAC maps, in addition to chromosome painting data. Chromhome application provides a single-page interface (SPI) with desktop style layout, delivering a better and richer user experience.

PanCoreGen - Profiling, detecting, annotating protein-coding genes in microbial genomes.

PubMed

Paul, Sandip; Bhardwaj, Archana; Bag, Sumit K; Sokurenko, Evgeni V; Chattopadhyay, Sujay

2015-12-01

A large amount of genomic data, especially from multiple isolates of a single species, has opened new vistas for microbial genomics analysis. Analyzing the pan-genome (i.e. the sum of genetic repertoire) of microbial species is crucial in understanding the dynamics of molecular evolution, where virulence evolution is of major interest. Here we present PanCoreGen - a standalone application for pan- and core-genomic profiling of microbial protein-coding genes. PanCoreGen overcomes key limitations of the existing pan-genomic analysis tools, and develops an integrated annotation-structure for a species-specific pan-genomic profile. It provides important new features for annotating draft genomes/contigs and detecting unidentified genes in annotated genomes. It also generates user-defined group-specific datasets within the pan-genome. Interestingly, analyzing an example-set of Salmonella genomes, we detect potential footprints of adaptive convergence of horizontally transferred genes in two human-restricted pathogenic serovars - Typhi and Paratyphi A. Overall, PanCoreGen represents a state-of-the-art tool for microbial phylogenomics and pathogenomics study. Copyright © 2015 Elsevier Inc. All rights reserved.

Comparative Analysis of Begonia Plastid Genomes and Their Utility for Species-Level Phylogenetics

PubMed Central

Harrison, Nicola; Harrison, Richard J.

2016-01-01

Recent, rapid radiations make species-level phylogenetics difficult to resolve. We used a multiplexed, high-throughput sequencing approach to identify informative genomic regions to resolve phylogenetic relationships at low taxonomic levels in Begonia from a survey of sixteen species. A long-range PCR method was used to generate draft plastid genomes to provide a strong phylogenetic backbone, identify fast evolving regions and provide informative molecular markers for species-level phylogenetic studies in Begonia. PMID:27058864

Sequencing and comparative analyses of the genomes of zoysiagrasses

PubMed Central

Tanaka, Hidenori; Hirakawa, Hideki; Kosugi, Shunichi; Nakayama, Shinobu; Ono, Akiko; Watanabe, Akiko; Hashiguchi, Masatsugu; Gondo, Takahiro; Ishigaki, Genki; Muguerza, Melody; Shimizu, Katsuya; Sawamura, Noriko; Inoue, Takayasu; Shigeki, Yuichi; Ohno, Naoki; Tabata, Satoshi; Akashi, Ryo; Sato, Shusei

2016-01-01

Zoysia is a warm-season turfgrass, which comprises 11 allotetraploid species (2n = 4x = 40), each possessing different morphological and physiological traits. To characterize the genetic systems of Zoysia plants and to analyse their structural and functional differences in individual species and accessions, we sequenced the genomes of Zoysia species using HiSeq and MiSeq platforms. As a reference sequence of Zoysia species, we generated a high-quality draft sequence of the genome of Z. japonica accession ‘Nagirizaki’ (334 Mb) in which 59,271 protein-coding genes were predicted. In parallel, draft genome sequences of Z. matrella ‘Wakaba’ and Z. pacifica ‘Zanpa’ were also generated for comparative analyses. To investigate the genetic diversity among the Zoysia species, genome sequence reads of three additional accessions, Z. japonica ‘Kyoto’, Z. japonica ‘Miyagi’ and Z. matrella ‘Chiba Fair Green’, were accumulated, and aligned against the reference genome of ‘Nagirizaki’ along with those from ‘Wakaba’ and ‘Zanpa’. As a result, we detected 7,424,163 single-nucleotide polymorphisms and 852,488 short indels among these species. The information obtained in this study will be valuable for basic studies on zoysiagrass evolution and genetics as well as for the breeding of zoysiagrasses, and is made available in the ‘Zoysia Genome Database’ at http://zoysia.kazusa.or.jp. PMID:26975196

The Agassiz’s desert tortoise genome provides a resource for the conservation of a threatened species

PubMed Central

Tollis, Marc; DeNardo, Dale F.; Cornelius, John A.; Dolby, Greer A.; Edwards, Taylor; Henen, Brian T.; Karl, Alice E.; Murphy, Robert W.

2017-01-01

Agassiz’s desert tortoise (Gopherus agassizii) is a long-lived species native to the Mojave Desert and is listed as threatened under the US Endangered Species Act. To aid conservation efforts for preserving the genetic diversity of this species, we generated a whole genome reference sequence with an annotation based on deep transcriptome sequences of adult skeletal muscle, lung, brain, and blood. The draft genome assembly for G. agassizii has a scaffold N50 length of 252 kbp and a total length of 2.4 Gbp. Genome annotation reveals 20,172 protein-coding genes in the G. agassizii assembly, and that gene structure is more similar to chicken than other turtles. We provide a series of comparative analyses demonstrating (1) that turtles are among the slowest-evolving genome-enabled reptiles, (2) amino acid changes in genes controlling desert tortoise traits such as shell development, longevity and osmoregulation, and (3) fixed variants across the Gopherus species complex in genes related to desert adaptations, including circadian rhythm and innate immune response. This G. agassizii genome reference and annotation is the first such resource for any tortoise, and will serve as a foundation for future analysis of the genetic basis of adaptations to the desert environment, allow for investigation into genomic factors affecting tortoise health, disease and longevity, and serve as a valuable resource for additional studies in this species complex. PMID:28562605

The Agassiz's desert tortoise genome provides a resource for the conservation of a threatened species.

PubMed

Tollis, Marc; DeNardo, Dale F; Cornelius, John A; Dolby, Greer A; Edwards, Taylor; Henen, Brian T; Karl, Alice E; Murphy, Robert W; Kusumi, Kenro

2017-01-01

Agassiz's desert tortoise (Gopherus agassizii) is a long-lived species native to the Mojave Desert and is listed as threatened under the US Endangered Species Act. To aid conservation efforts for preserving the genetic diversity of this species, we generated a whole genome reference sequence with an annotation based on deep transcriptome sequences of adult skeletal muscle, lung, brain, and blood. The draft genome assembly for G. agassizii has a scaffold N50 length of 252 kbp and a total length of 2.4 Gbp. Genome annotation reveals 20,172 protein-coding genes in the G. agassizii assembly, and that gene structure is more similar to chicken than other turtles. We provide a series of comparative analyses demonstrating (1) that turtles are among the slowest-evolving genome-enabled reptiles, (2) amino acid changes in genes controlling desert tortoise traits such as shell development, longevity and osmoregulation, and (3) fixed variants across the Gopherus species complex in genes related to desert adaptations, including circadian rhythm and innate immune response. This G. agassizii genome reference and annotation is the first such resource for any tortoise, and will serve as a foundation for future analysis of the genetic basis of adaptations to the desert environment, allow for investigation into genomic factors affecting tortoise health, disease and longevity, and serve as a valuable resource for additional studies in this species complex.

Sequencing and comparative analyses of the genomes of zoysiagrasses.

PubMed

Tanaka, Hidenori; Hirakawa, Hideki; Kosugi, Shunichi; Nakayama, Shinobu; Ono, Akiko; Watanabe, Akiko; Hashiguchi, Masatsugu; Gondo, Takahiro; Ishigaki, Genki; Muguerza, Melody; Shimizu, Katsuya; Sawamura, Noriko; Inoue, Takayasu; Shigeki, Yuichi; Ohno, Naoki; Tabata, Satoshi; Akashi, Ryo; Sato, Shusei

2016-04-01

Zoysiais a warm-season turfgrass, which comprises 11 allotetraploid species (2n= 4x= 40), each possessing different morphological and physiological traits. To characterize the genetic systems of Zoysia plants and to analyse their structural and functional differences in individual species and accessions, we sequenced the genomes of Zoysia species using HiSeq and MiSeq platforms. As a reference sequence of Zoysia species, we generated a high-quality draft sequence of the genome of Z. japonica accession 'Nagirizaki' (334 Mb) in which 59,271 protein-coding genes were predicted. In parallel, draft genome sequences of Z. matrella 'Wakaba' and Z. pacifica 'Zanpa' were also generated for comparative analyses. To investigate the genetic diversity among the Zoysia species, genome sequence reads of three additional accessions, Z. japonica'Kyoto', Z. japonica'Miyagi' and Z. matrella'Chiba Fair Green', were accumulated, and aligned against the reference genome of 'Nagirizaki' along with those from 'Wakaba' and 'Zanpa'. As a result, we detected 7,424,163 single-nucleotide polymorphisms and 852,488 short indels among these species. The information obtained in this study will be valuable for basic studies on zoysiagrass evolution and genetics as well as for the breeding of zoysiagrasses, and is made available in the 'Zoysia Genome Database' at http://zoysia.kazusa.or.jp. © The Author 2016. Published by Oxford University Press on behalf of Kazusa DNA Research Institute.

Small genomes and large seeds: chromosome numbers, genome size and seed mass in diploid Aesculus species (Sapindaceae).

PubMed

Krahulcová, Anna; Trávnícek, Pavel; Krahulec, František; Rejmánek, Marcel

2017-04-01

Aesculus L. (horse chestnut, buckeye) is a genus of 12-19 extant woody species native to the temperate Northern Hemisphere. This genus is known for unusually large seeds among angiosperms. While chromosome counts are available for many Aesculus species, only one has had its genome size measured. The aim of this study is to provide more genome size data and analyse the relationship between genome size and seed mass in this genus. Chromosome numbers in root tip cuttings were confirmed for four species and reported for the first time for three additional species. Flow cytometric measurements of 2C nuclear DNA values were conducted on eight species, and mean seed mass values were estimated for the same taxa. The same chromosome number, 2 n = 40, was determined in all investigated taxa. Original measurements of 2C values for seven Aesculus species (eight taxa), added to just one reliable datum for A. hippocastanum , confirmed the notion that the genome size in this genus with relatively large seeds is surprisingly low, ranging from 0·955 pg 2C -1 in A. parviflora to 1·275 pg 2C -1 in A. glabra var. glabra. The chromosome number of 2 n = 40 seems to be conclusively the universal 2 n number for non-hybrid species in this genus. Aesculus genome sizes are relatively small, not only within its own family, Sapindaceae, but also within woody angiosperms. The genome sizes seem to be distinct and non-overlapping among the four major Aesculus clades. These results provide an extra support for the most recent reconstruction of Aesculus phylogeny. The correlation between the 2C values and seed masses in examined Aesculus species is slightly negative and not significant. However, when the four major clades are treated separately, there is consistent positive association between larger genome size and larger seed mass within individual lineages. © The Author 2017. Published by Oxford University Press on behalf of the Annals of Botany Company. All rights reserved. For Permissions, please email: journals.permissions@oup.com

Genome-wide comparative analysis of NBS-encoding genes between Brassica species and Arabidopsis thaliana.

PubMed

Yu, Jingyin; Tehrim, Sadia; Zhang, Fengqi; Tong, Chaobo; Huang, Junyan; Cheng, Xiaohui; Dong, Caihua; Zhou, Yanqiu; Qin, Rui; Hua, Wei; Liu, Shengyi

2014-01-03

Plant disease resistance (R) genes with the nucleotide binding site (NBS) play an important role in offering resistance to pathogens. The availability of complete genome sequences of Brassica oleracea and Brassica rapa provides an important opportunity for researchers to identify and characterize NBS-encoding R genes in Brassica species and to compare with analogues in Arabidopsis thaliana based on a comparative genomics approach. However, little is known about the evolutionary fate of NBS-encoding genes in the Brassica lineage after split from A. thaliana. Here we present genome-wide analysis of NBS-encoding genes in B. oleracea, B. rapa and A. thaliana. Through the employment of HMM search and manual curation, we identified 157, 206 and 167 NBS-encoding genes in B. oleracea, B. rapa and A. thaliana genomes, respectively. Phylogenetic analysis among 3 species classified NBS-encoding genes into 6 subgroups. Tandem duplication and whole genome triplication (WGT) analyses revealed that after WGT of the Brassica ancestor, NBS-encoding homologous gene pairs on triplicated regions in Brassica ancestor were deleted or lost quickly, but NBS-encoding genes in Brassica species experienced species-specific gene amplification by tandem duplication after divergence of B. rapa and B. oleracea. Expression profiling of NBS-encoding orthologous gene pairs indicated the differential expression pattern of retained orthologous gene copies in B. oleracea and B. rapa. Furthermore, evolutionary analysis of CNL type NBS-encoding orthologous gene pairs among 3 species suggested that orthologous genes in B. rapa species have undergone stronger negative selection than those in B .oleracea species. But for TNL type, there are no significant differences in the orthologous gene pairs between the two species. This study is first identification and characterization of NBS-encoding genes in B. rapa and B. oleracea based on whole genome sequences. Through tandem duplication and whole genome triplication analysis in B. oleracea, B. rapa and A. thaliana genomes, our study provides insight into the evolutionary history of NBS-encoding genes after divergence of A. thaliana and the Brassica lineage. These results together with expression pattern analysis of NBS-encoding orthologous genes provide useful resource for functional characterization of these genes and genetic improvement of relevant crops.

Comparative Functional Genomics of Lactobacillus spp. Reveals Possible Mechanisms for Specialization of Vaginal Lactobacilli to Their Environment

PubMed Central

Suzuki, Haruo; Hickey, Roxana J.; Forney, Larry J.

2014-01-01

Lactobacilli are found in a wide variety of habitats. Four species, Lactobacillus crispatus, L. gasseri, L. iners, and L. jensenii, are common and abundant in the human vagina and absent from other habitats. These may be adapted to the vagina and possess characteristics enabling them to thrive in that environment. Furthermore, stable codominance of multiple Lactobacillus species in a single community is infrequently observed. Thus, it is possible that individual vaginal Lactobacillus species possess unique characteristics that confer to them host-specific competitive advantages. We performed comparative functional genomic analyses of representatives of 25 species of Lactobacillus, searching for habitat-specific traits in the genomes of the vaginal lactobacilli. We found that the genomes of the vaginal species were significantly smaller and had significantly lower GC content than those of the nonvaginal species. No protein families were found to be specific to the vaginal species analyzed, but some were either over- or underrepresented relative to nonvaginal species. We also found that within the vaginal species, each genome coded for species-specific protein families. Our results suggest that even though the vaginal species show no general signatures of adaptation to the vaginal environment, each species has specific and perhaps unique ways of interacting with its environment, be it the host or other microbes in the community. These findings will serve as a foundation for further exploring the role of lactobacilli in the ecological dynamics of vaginal microbial communities and their ultimate impact on host health. PMID:24488312

The cotton centromere contains a Ty3-gypsy-like LTR retroelement.

PubMed

Luo, Song; Mach, Jennifer; Abramson, Bradley; Ramirez, Rolando; Schurr, Robert; Barone, Pierluigi; Copenhaver, Gregory; Folkerts, Otto

2012-01-01

The centromere is a repeat-rich structure essential for chromosome segregation; with the long-term aim of understanding centromere structure and function, we set out to identify cotton centromere sequences. To isolate centromere-associated sequences from cotton, (Gossypium hirsutum) we surveyed tandem and dispersed repetitive DNA in the genus. Centromere-associated elements in other plants include tandem repeats and, in some cases, centromere-specific retroelements. Examination of cotton genomic survey sequences for tandem repeats yielded sequences that did not localize to the centromere. However, among the repetitive sequences we also identified a gypsy-like LTR retrotransposon (Centromere Retroelement Gossypium, CRG) that localizes to the centromere region of all chromosomes in domestic upland cotton, Gossypium hirsutum, the major commercially grown cotton. The location of the functional centromere was confirmed by immunostaining with antiserum to the centromere-specific histone CENH3, which co-localizes with CRG hybridization on metaphase mitotic chromosomes. G. hirsutum is an allotetraploid composed of A and D genomes and CRG is also present in the centromere regions of other AD cotton species. Furthermore, FISH and genomic dot blot hybridization revealed that CRG is found in D-genome diploid cotton species, but not in A-genome diploid species, indicating that this retroelement may have invaded the A-genome centromeres during allopolyploid formation and amplified during evolutionary history. CRG is also found in other diploid Gossypium species, including B and E2 genome species, but not in the C, E1, F, and G genome species tested. Isolation of this centromere-specific retrotransposon from Gossypium provides a probe for further understanding of centromere structure, and a tool for future engineering of centromere mini-chromosomes in this important crop species.

The Cotton Centromere Contains a Ty3-gypsy-like LTR Retroelement

PubMed Central

Luo, Song; Mach, Jennifer; Abramson, Bradley; Ramirez, Rolando; Schurr, Robert; Barone, Pierluigi; Copenhaver, Gregory; Folkerts, Otto

2012-01-01

The centromere is a repeat-rich structure essential for chromosome segregation; with the long-term aim of understanding centromere structure and function, we set out to identify cotton centromere sequences. To isolate centromere-associated sequences from cotton, (Gossypium hirsutum) we surveyed tandem and dispersed repetitive DNA in the genus. Centromere-associated elements in other plants include tandem repeats and, in some cases, centromere-specific retroelements. Examination of cotton genomic survey sequences for tandem repeats yielded sequences that did not localize to the centromere. However, among the repetitive sequences we also identified a gypsy-like LTR retrotransposon (Centromere Retroelement Gossypium, CRG) that localizes to the centromere region of all chromosomes in domestic upland cotton, Gossypium hirsutum, the major commercially grown cotton. The location of the functional centromere was confirmed by immunostaining with antiserum to the centromere-specific histone CENH3, which co-localizes with CRG hybridization on metaphase mitotic chromosomes. G. hirsutum is an allotetraploid composed of A and D genomes and CRG is also present in the centromere regions of other AD cotton species. Furthermore, FISH and genomic dot blot hybridization revealed that CRG is found in D-genome diploid cotton species, but not in A-genome diploid species, indicating that this retroelement may have invaded the A-genome centromeres during allopolyploid formation and amplified during evolutionary history. CRG is also found in other diploid Gossypium species, including B and E2 genome species, but not in the C, E1, F, and G genome species tested. Isolation of this centromere-specific retrotransposon from Gossypium provides a probe for further understanding of centromere structure, and a tool for future engineering of centromere mini-chromosomes in this important crop species. PMID:22536361

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ahn, Anne-Catherine; Meier-Kolthoff, Jan P.; Overmars, Lex

Thioalkalivibrio is a genus of obligate chemolithoautotrophic haloalkaliphilic sulfur-oxidizing bacteria. Their habitat are soda lakes which are dual extreme environments with a pH range from 9.5 to 11 and salt concentrations up to saturation. More than 100 strains of this genus have been isolated from various soda lakes all over the world, but only ten species have been effectively described yet. Therefore, the assignment of the remaining strains to either existing or novel species is important and will further elucidate their genomic diversity as well as give a better general understanding of this genus. Recently, the genomes of 76 Thioalkalivibriomore » strains were sequenced. On these, we applied different methods including (i) 16S rRNA gene sequence analysis, (ii) Multilocus Sequence Analysis (MLSA) based on eight housekeeping genes, (iii) Average Nucleotide Identity based on BLAST (ANI b) and MUMmer (ANI m ), (iv) Tetranucleotide frequency correlation coefficients (TETRA), (v) digital DNA:DNA hybridization (dDDH) as well as (vi) nucleotide- and amino acid-based Genome BLAST Distance Phylogeny (GBDP) analyses. We detected a high genomic diversity by revealing 15 new "genomic" species and 16 new "genomic" subspecies in addition to the ten already described species. Phylogenetic and phylogenomic analyses showed that the genus is not monophyletic, because four strains were clearly separated from the other Thioalkalivibrio by type strains from other genera. Therefore, it is recommended to classify the latter group as a novel genus. The biogeographic distribution of Thioalkalivibrio suggested that the different "genomic" species can be classified as candidate disjunct or candidate endemic species. This study is a detailed genome-based classification and identification of members within the genus Thioalkalivibrio. However, future phenotypical and chemotaxonomical studies will be needed for a full species description of this genus.« less

Complete genome sequence of two tomato-infecting begomoviruses in Venezuela: evidence of a putative novel species and a novel recombinant strain.

PubMed

Romay, Gustavo; Chirinos, Dorys T; Geraud-Pouey, Francis; Gillis, Annika; Mahillon, Jacques; Bragard, Claude

2018-02-01

At least six begomovirus species have been reported infecting tomato in Venezuela. In this study the complete genomes of two tomato-infecting begomovirus isolates (referred to as Trujillo-427 and Zulia-1084) were cloned and sequenced. Both isolates showed the typical genome organization of New World bipartite begomoviruses, with DNA-A genomic components displaying 88.8% and 90.3% similarity with established begomoviruses, for isolates Trujillo-427 and Zulia-1084, respectively. In accordance to the guidelines for begomovirus species demarcation, the Trujillo-427 isolate represents a putative new species and the name "Tomato wrinkled mosaic virus" is proposed. Meanwhile, Zulia-1084 represents a putative new strain classifiable within species Tomato chlorotic leaf distortion virus, for which a recombinant origin is suggested.

Comparative genomic analysis of three Leishmania species that cause diverse human disease

PubMed Central

Peacock, Christopher S; Seeger, Kathy; Harris, David; Murphy, Lee; Ruiz, Jeronimo C; Quail, Michael A; Peters, Nick; Adlem, Ellen; Tivey, Adrian; Aslett, Martin; Kerhornou, Arnaud; Ivens, Alasdair; Fraser, Audrey; Rajandream, Marie-Adele; Carver, Tim; Norbertczak, Halina; Chillingworth, Tracey; Hance, Zahra; Jagels, Kay; Moule, Sharon; Ormond, Doug; Rutter, Simon; Squares, Rob; Whitehead, Sally; Rabbinowitsch, Ester; Arrowsmith, Claire; White, Brian; Thurston, Scott; Bringaud, Frédéric; Baldauf, Sandra L; Faulconbridge, Adam; Jeffares, Daniel; Depledge, Daniel P; Oyola, Samuel O; Hilley, James D; Brito, Loislene O; Tosi, Luiz R O; Barrell, Barclay; Cruz, Angela K; Mottram, Jeremy C; Smith, Deborah F; Berriman, Matthew

2008-01-01

Leishmania parasites cause a broad spectrum of clinical disease. Here we report the sequencing of the genomes of two species of Leishmania: Leishmania infantum and Leishmania braziliensis. The comparison of these sequences with the published genome of Leishmania major reveals marked conservation of synteny and identifies only ∼200 genes with a differential distribution between the three species. L. braziliensis, contrary to Leishmania species examined so far, possesses components of a putative RNA-mediated interference pathway, telomere-associated transposable elements and spliced leader–associated SLACS retrotransposons. We show that pseudogene formation and gene loss are the principal forces shaping the different genomes. Genes that are differentially distributed between the species encode proteins implicated in host-pathogen interactions and parasite survival in the macrophage. PMID:17572675

The genome sequence of the biocontrol fungus Metarhizium anisopliae and comparative genomics of Metarhizium species.

PubMed

Pattemore, Julie A; Hane, James K; Williams, Angela H; Wilson, Bree A L; Stodart, Ben J; Ash, Gavin J

2014-08-07

Metarhizium anisopliae is an important fungal biocontrol agent of insect pests of agricultural crops. Genomics can aid the successful commercialization of biopesticides by identification of key genes differentiating closely related species, selection of virulent microbial isolates which are amenable to industrial scale production and formulation and through the reduction of phenotypic variability. The genome of Metarhizium isolate ARSEF23 was recently published as a model for M. anisopliae, however phylogenetic analysis has since re-classified this isolate as M. robertsii. We present a new annotated genome sequence of M. anisopliae (isolate Ma69) and whole genome comparison to M. robertsii (ARSEF23) and M. acridum (CQMa 102). Whole genome analysis of M. anisopliae indicates significant macrosynteny with M. robertsii but with some large genomic inversions. In comparison to M. acridum, the genome of M. anisopliae shares lower sequence homology. While alignments overall are co-linear, the genome of M. acridum is not contiguous enough to conclusively observe macrosynteny. Mating type gene analysis revealed both MAT1-1 and MAT1-2 genes present in M. anisopliae suggesting putative homothallism, despite having no known teleomorph, in contrast with the putatively heterothallic M. acridum isolate CQMa 102 (MAT1-2) and M. robertsii isolate ARSEF23 (altered MAT1-1). Repetitive DNA and RIP analysis revealed M. acridum to have twice the repetitive content of the other two species and M. anisopliae to be five times more RIP affected than M. robertsii. We also present an initial bioinformatic survey of candidate pathogenicity genes in M. anisopliae. The annotated genome of M. anisopliae is an important resource for the identification of virulence genes specific to M. anisopliae and development of species- and strain- specific assays. New insight into the possibility of homothallism and RIP affectedness has important implications for the development of M. anisopliae as a biopesticide as it may indicate the potential for greater inherent diversity in this species than the other species. This could present opportunities to select isolates with unique combinations of pathogenicity factors, or it may point to instability in the species, a negative attribute in a biopesticide.

The Complete Chloroplast Genome Sequences of Five Epimedium Species: Lights into Phylogenetic and Taxonomic Analyses

PubMed Central

Zhang, Yanjun; Du, Liuwen; Liu, Ao; Chen, Jianjun; Wu, Li; Hu, Weiming; Zhang, Wei; Kim, Kyunghee; Lee, Sang-Choon; Yang, Tae-Jin; Wang, Ying

2016-01-01

Epimedium L. is a phylogenetically and economically important genus in the family Berberidaceae. We here sequenced the complete chloroplast (cp) genomes of four Epimedium species using Illumina sequencing technology via a combination of de novo and reference-guided assembly, which was also the first comprehensive cp genome analysis on Epimedium combining the cp genome sequence of E. koreanum previously reported. The five Epimedium cp genomes exhibited typical quadripartite and circular structure that was rather conserved in genomic structure and the synteny of gene order. However, these cp genomes presented obvious variations at the boundaries of the four regions because of the expansion and contraction of the inverted repeat (IR) region and the single-copy (SC) boundary regions. The trnQ-UUG duplication occurred in the five Epimedium cp genomes, which was not found in the other basal eudicotyledons. The rapidly evolving cp genome regions were detected among the five cp genomes, as well as the difference of simple sequence repeats (SSR) and repeat sequence were identified. Phylogenetic relationships among the five Epimedium species based on their cp genomes showed accordance with the updated system of the genus on the whole, but reminded that the evolutionary relationships and the divisions of the genus need further investigation applying more evidences. The availability of these cp genomes provided valuable genetic information for accurately identifying species, taxonomy and phylogenetic resolution and evolution of Epimedium, and assist in exploration and utilization of Epimedium plants. PMID:27014326

Phylogenomic Insights into Mouse Evolution Using a Pseudoreference Approach

PubMed Central

Sarver, Brice A.J.; Keeble, Sara; Cosart, Ted; Tucker, Priscilla K.; Dean, Matthew D.

2017-01-01

Comparative genomic studies are now possible across a broad range of evolutionary timescales, but the generation and analysis of genomic data across many different species still present a number of challenges. The most sophisticated genotyping and down-stream analytical frameworks are still predominantly based on comparisons to high-quality reference genomes. However, established genomic resources are often limited within a given group of species, necessitating comparisons to divergent reference genomes that could restrict or bias comparisons across a phylogenetic sample. Here, we develop a scalable pseudoreference approach to iteratively incorporate sample-specific variation into a genome reference and reduce the effects of systematic mapping bias in downstream analyses. To characterize this framework, we used targeted capture to sequence whole exomes (∼54 Mbp) in 12 lineages (ten species) of mice spanning the Mus radiation. We generated whole exome pseudoreferences for all species and show that this iterative reference-based approach improved basic genomic analyses that depend on mapping accuracy while preserving the associated annotations of the mouse reference genome. We then use these pseudoreferences to resolve evolutionary relationships among these lineages while accounting for phylogenetic discordance across the genome, contributing an important resource for comparative studies in the mouse system. We also describe patterns of genomic introgression among lineages and compare our results to previous studies. Our general approach can be applied to whole or partitioned genomic data and is easily portable to any system with sufficient genomic resources, providing a useful framework for phylogenomic studies in mice and other taxa. PMID:28338821

Transposable Elements versus the Fungal Genome: Impact on Whole-Genome Architecture and Transcriptional Profiles

DOE Office of Scientific and Technical Information (OSTI.GOV)

Castanera, Raul; Lopez-Varas, Leticia; Borgognone, Alessandra

Transposable elements (TEs) are exceptional contributors to eukaryotic genome diversity. Their ubiquitous presence impacts the genomes of nearly all species and mediates genome evolution by causing mutations and chromosomal rearrangements and by modulating gene expression. We performed an exhaustive analysis of the TE content in 18 fungal genomes, including strains of the same species and species of the same genera. Our results depicted a scenario of exceptional variability, with species having 0.02 to 29.8% of their genome consisting of transposable elements. A detailed analysis performed on two strains of Pleurotus ostreatus uncovered a genome that is populated mainly by Classmore » I elements, especially LTR-retrotransposons amplified in recent bursts from 0 to 2 million years (My) ago. The preferential accumulation of TEs in clusters led to the presence of genomic regions that lacked intra- and inter-specific conservation. In addition, we investigated the effect of TE insertions on the expression of their nearby upstream and downstream genes. Our results showed that an important number of genes under TE influence are significantly repressed, with stronger repression when genes are localized within transposon clusters. Our transcriptional analysis performed in four additional fungal models revealed that this TE-mediated silencing was present only in species with active cytosine methylation machinery. We hypothesize that this phenomenon is related to epigenetic defense mechanisms that are aimed to suppress TE expression and control their proliferation.« less

Transposable Elements versus the Fungal Genome: Impact on Whole-Genome Architecture and Transcriptional Profiles

DOE PAGES

Castanera, Raul; Lopez-Varas, Leticia; Borgognone, Alessandra; ...

2016-06-13

Transposable elements (TEs) are exceptional contributors to eukaryotic genome diversity. Their ubiquitous presence impacts the genomes of nearly all species and mediates genome evolution by causing mutations and chromosomal rearrangements and by modulating gene expression. We performed an exhaustive analysis of the TE content in 18 fungal genomes, including strains of the same species and species of the same genera. Our results depicted a scenario of exceptional variability, with species having 0.02 to 29.8% of their genome consisting of transposable elements. A detailed analysis performed on two strains of Pleurotus ostreatus uncovered a genome that is populated mainly by Classmore » I elements, especially LTR-retrotransposons amplified in recent bursts from 0 to 2 million years (My) ago. The preferential accumulation of TEs in clusters led to the presence of genomic regions that lacked intra- and inter-specific conservation. In addition, we investigated the effect of TE insertions on the expression of their nearby upstream and downstream genes. Our results showed that an important number of genes under TE influence are significantly repressed, with stronger repression when genes are localized within transposon clusters. Our transcriptional analysis performed in four additional fungal models revealed that this TE-mediated silencing was present only in species with active cytosine methylation machinery. We hypothesize that this phenomenon is related to epigenetic defense mechanisms that are aimed to suppress TE expression and control their proliferation.« less

Genome sequence of M6, a diploid inbred clone of the high-glycoalkaloid-producing tuber-bearing potato species Solanum chacoense, reveals residual heterozygosity.

PubMed

Leisner, Courtney P; Hamilton, John P; Crisovan, Emily; Manrique-Carpintero, Norma C; Marand, Alexandre P; Newton, Linsey; Pham, Gina M; Jiang, Jiming; Douches, David S; Jansky, Shelley H; Buell, C Robin

2018-05-01

Cultivated potato (Solanum tuberosum L.) is a highly heterozygous autotetraploid that presents challenges in genome analyses and breeding. Wild potato species serve as a resource for the introgression of important agronomic traits into cultivated potato. One key species is Solanum chacoense and the diploid, inbred clone M6, which is self-compatible and has desirable tuber market quality and disease resistance traits. Sequencing and assembly of the genome of the M6 clone of S. chacoense generated an assembly of 825 767 562 bp in 8260 scaffolds with an N50 scaffold size of 713 602 bp. Pseudomolecule construction anchored 508 Mb of the genome assembly into 12 chromosomes. Genome annotation yielded 49 124 high-confidence gene models representing 37 740 genes. Comparative analyses of the M6 genome with six other Solanaceae species revealed a core set of 158 367 Solanaceae genes and 1897 genes unique to three potato species. Analysis of single nucleotide polymorphisms across the M6 genome revealed enhanced residual heterozygosity on chromosomes 4, 8 and 9 relative to the other chromosomes. Access to the M6 genome provides a resource for identification of key genes for important agronomic traits and aids in genome-enabled development of inbred diploid potatoes with the potential to accelerate potato breeding. © 2018 The Authors The Plant Journal © 2018 John Wiley & Sons Ltd.

YersiniaBase: a genomic resource and analysis platform for comparative analysis of Yersinia.

PubMed

Tan, Shi Yang; Dutta, Avirup; Jakubovics, Nicholas S; Ang, Mia Yang; Siow, Cheuk Chuen; Mutha, Naresh Vr; Heydari, Hamed; Wee, Wei Yee; Wong, Guat Jah; Choo, Siew Woh

2015-01-16

Yersinia is a Gram-negative bacteria that includes serious pathogens such as the Yersinia pestis, which causes plague, Yersinia pseudotuberculosis, Yersinia enterocolitica. The remaining species are generally considered non-pathogenic to humans, although there is evidence that at least some of these species can cause occasional infections using distinct mechanisms from the more pathogenic species. With the advances in sequencing technologies, many genomes of Yersinia have been sequenced. However, there is currently no specialized platform to hold the rapidly-growing Yersinia genomic data and to provide analysis tools particularly for comparative analyses, which are required to provide improved insights into their biology, evolution and pathogenicity. To facilitate the ongoing and future research of Yersinia, especially those generally considered non-pathogenic species, a well-defined repository and analysis platform is needed to hold the Yersinia genomic data and analysis tools for the Yersinia research community. Hence, we have developed the YersiniaBase, a robust and user-friendly Yersinia resource and analysis platform for the analysis of Yersinia genomic data. YersiniaBase has a total of twelve species and 232 genome sequences, of which the majority are Yersinia pestis. In order to smooth the process of searching genomic data in a large database, we implemented an Asynchronous JavaScript and XML (AJAX)-based real-time searching system in YersiniaBase. Besides incorporating existing tools, which include JavaScript-based genome browser (JBrowse) and Basic Local Alignment Search Tool (BLAST), YersiniaBase also has in-house developed tools: (1) Pairwise Genome Comparison tool (PGC) for comparing two user-selected genomes; (2) Pathogenomics Profiling Tool (PathoProT) for comparative pathogenomics analysis of Yersinia genomes; (3) YersiniaTree for constructing phylogenetic tree of Yersinia. We ran analyses based on the tools and genomic data in YersiniaBase and the preliminary results showed differences in virulence genes found in Yersinia pestis and Yersinia pseudotuberculosis compared to other Yersinia species, and differences between Yersinia enterocolitica subsp. enterocolitica and Yersinia enterocolitica subsp. palearctica. YersiniaBase offers free access to wide range of genomic data and analysis tools for the analysis of Yersinia. YersiniaBase can be accessed at http://yersinia.um.edu.my .

Genome sequencing and comparative genomics of honey bee microsporidia, Nosema apis reveal novel insights into host-parasite interactions.

PubMed

Chen, Yan ping; Pettis, Jeffery S; Zhao, Yan; Liu, Xinyue; Tallon, Luke J; Sadzewicz, Lisa D; Li, Renhua; Zheng, Huoqing; Huang, Shaokang; Zhang, Xuan; Hamilton, Michele C; Pernal, Stephen F; Melathopoulos, Andony P; Yan, Xianghe; Evans, Jay D

2013-07-05

The microsporidia parasite Nosema contributes to the steep global decline of honey bees that are critical pollinators of food crops. There are two species of Nosema that have been found to infect honey bees, Nosema apis and N. ceranae. Genome sequencing of N. apis and comparative genome analysis with N. ceranae, a fully sequenced microsporidia species, reveal novel insights into host-parasite interactions underlying the parasite infections. We applied the whole-genome shotgun sequencing approach to sequence and assemble the genome of N. apis which has an estimated size of 8.5 Mbp. We predicted 2,771 protein- coding genes and predicted the function of each putative protein using the Gene Ontology. The comparative genomic analysis led to identification of 1,356 orthologs that are conserved between the two Nosema species and genes that are unique characteristics of the individual species, thereby providing a list of virulence factors and new genetic tools for studying host-parasite interactions. We also identified a highly abundant motif in the upstream promoter regions of N. apis genes. This motif is also conserved in N. ceranae and other microsporidia species and likely plays a role in gene regulation across the microsporidia. The availability of the N. apis genome sequence is a significant addition to the rapidly expanding body of microsprodian genomic data which has been improving our understanding of eukaryotic genome diversity and evolution in a broad sense. The predicted virulent genes and transcriptional regulatory elements are potential targets for innovative therapeutics to break down the life cycle of the parasite.

Once-Daily Amikacin Dosing in Burn Patients Treated with Continuous Venovenous Hemofiltration

DTIC Science & Technology

2011-10-01

previously documented inaccuracies with the Vitek 2 instrument (1), all Acinetobacter baumannii isolates reported as susceptible to amikacin were confirmed...to the analysis. Bacteriology. Amikacin MICs were determined for Gram-negative blood- stream isolates using the Vitek 2 instrument (bioMérieux...al. 2010. Aminoglycoside resistance and susceptibility testing errors in Acinetobacter baumannii-calcoaceticus complex. J. Clin. Microbiol. 48:1132

Novel Compounds From Shark And Stingray Epidermal Mucus With Antimicrobial Activity Against Wound Infection Pathogens

DTIC Science & Technology

2012-03-01

Staphylococcus epidermidis, Micrococcus sp., Enterococcus faecalis, Listeria monocytogenes, Shigella boydii, Shigella sonnei, Shigella flexneri...MSSA, VRE B. cereus, MSSA, MRSA, Micrococcus , E. faecalis, L. monocytogenes, Shigella, E. coli, S. enterica, Acinetobacter 505 G1 B. subtilis 505...subtilis B. cereus 506 B3 VRE B. cereus, MSSA, MRSA, Micrococcus , E. faecalis, L. monocytogenes, Shigella, E. coli, S. enterica, Acinetobacter

G-Anchor: a novel approach for whole-genome comparative mapping utilizing evolutionary conserved DNA sequences.

PubMed

Lenis, Vasileios Panagiotis E; Swain, Martin; Larkin, Denis M

2018-05-01

Cross-species whole-genome sequence alignment is a critical first step for genome comparative analyses, ranging from the detection of sequence variants to studies of chromosome evolution. Animal genomes are large and complex, and whole-genome alignment is a computationally intense process, requiring expensive high-performance computing systems due to the need to explore extensive local alignments. With hundreds of sequenced animal genomes available from multiple projects, there is an increasing demand for genome comparative analyses. Here, we introduce G-Anchor, a new, fast, and efficient pipeline that uses a strictly limited but highly effective set of local sequence alignments to anchor (or map) an animal genome to another species' reference genome. G-Anchor makes novel use of a databank of highly conserved DNA sequence elements. We demonstrate how these elements may be aligned to a pair of genomes, creating anchors. These anchors enable the rapid mapping of scaffolds from a de novo assembled genome to chromosome assemblies of a reference species. Our results demonstrate that G-Anchor can successfully anchor a vertebrate genome onto a phylogenetically related reference species genome using a desktop or laptop computer within a few hours and with comparable accuracy to that achieved by a highly accurate whole-genome alignment tool such as LASTZ. G-Anchor thus makes whole-genome comparisons accessible to researchers with limited computational resources. G-Anchor is a ready-to-use tool for anchoring a pair of vertebrate genomes. It may be used with large genomes that contain a significant fraction of evolutionally conserved DNA sequences and that are not highly repetitive, polypoid, or excessively fragmented. G-Anchor is not a substitute for whole-genome aligning software but can be used for fast and accurate initial genome comparisons. G-Anchor is freely available and a ready-to-use tool for the pairwise comparison of two genomes.

Exome-wide DNA capture and next generation sequencing in domestic and wild species.

PubMed

Cosart, Ted; Beja-Pereira, Albano; Chen, Shanyuan; Ng, Sarah B; Shendure, Jay; Luikart, Gordon

2011-07-05

Gene-targeted and genome-wide markers are crucial to advance evolutionary biology, agriculture, and biodiversity conservation by improving our understanding of genetic processes underlying adaptation and speciation. Unfortunately, for eukaryotic species with large genomes it remains costly to obtain genome sequences and to develop genome resources such as genome-wide SNPs. A method is needed to allow gene-targeted, next-generation sequencing that is flexible enough to include any gene or number of genes, unlike transcriptome sequencing. Such a method would allow sequencing of many individuals, avoiding ascertainment bias in subsequent population genetic analyses.We demonstrate the usefulness of a recent technology, exon capture, for genome-wide, gene-targeted marker discovery in species with no genome resources. We use coding gene sequences from the domestic cow genome sequence (Bos taurus) to capture (enrich for), and subsequently sequence, thousands of exons of B. taurus, B. indicus, and Bison bison (wild bison). Our capture array has probes for 16,131 exons in 2,570 genes, including 203 candidate genes with known function and of interest for their association with disease and other fitness traits. We successfully sequenced and mapped exon sequences from across the 29 autosomes and X chromosome in the B. taurus genome sequence. Exon capture and high-throughput sequencing identified thousands of putative SNPs spread evenly across all reference chromosomes, in all three individuals, including hundreds of SNPs in our targeted candidate genes. This study shows exon capture can be customized for SNP discovery in many individuals and for non-model species without genomic resources. Our captured exome subset was small enough for affordable next-generation sequencing, and successfully captured exons from a divergent wild species using the domestic cow genome as reference.

Whole genome sequencing of the fish pathogen Francisella noatunensis subsp. orientalis Toba04 gives novel insights into Francisella evolution and pathogenecity

PubMed Central

2012-01-01

Background Francisella is a genus of gram-negative bacterium highly virulent in fishes and human where F. tularensis is causing the serious disease tularaemia in human. Recently Francisella species have been reported to cause mortality in aquaculture species like Atlantic cod and tilapia. We have completed the sequencing and draft assembly of the Francisella noatunensis subsp. orientalisToba04 strain isolated from farmed Tilapia. Compared to other available Francisella genomes, it is most similar to the genome of Francisella philomiragia subsp. philomiragia, a free-living bacterium not virulent to human. Results The genome is rearranged compared to the available Francisella genomes even though we found no IS-elements in the genome. Nearly 16% percent of the predicted ORFs are pseudogenes. Computational pathway analysis indicates that a number of the metabolic pathways are disrupted due to pseudogenes. Comparing the novel genome with other available Francisella genomes, we found around 2.5% of unique genes present in Francisella noatunensis subsp. orientalis Toba04 and a list of genes uniquely present in the human-pathogenic Francisella subspecies. Most of these genes might have transferred from bacterial species through horizontal gene transfer. Comparative analysis between human and fish pathogen also provide insights into genes responsible for pathogenecity. Our analysis of pseudogenes indicates that the evolution of Francisella subspecies’s pseudogenes from Tilapia is old with large number of pseudogenes having more than one inactivating mutation. Conclusions The fish pathogen has lost non-essential genes some time ago. Evolutionary analysis of the Francisella genomes, strongly suggests that human and fish pathogenic Francisella species have evolved independently from free-living metabolically competent Francisella species. These findings will contribute to understanding the evolution of Francisella species and pathogenesis. PMID:23131096

PLAZA 3.0: an access point for plant comparative genomics

PubMed Central

Proost, Sebastian; Van Bel, Michiel; Vaneechoutte, Dries; Van de Peer, Yves; Inzé, Dirk; Mueller-Roeber, Bernd; Vandepoele, Klaas

2015-01-01

Comparative sequence analysis has significantly altered our view on the complexity of genome organization and gene functions in different kingdoms. PLAZA 3.0 is designed to make comparative genomics data for plants available through a user-friendly web interface. Structural and functional annotation, gene families, protein domains, phylogenetic trees and detailed information about genome organization can easily be queried and visualized. Compared with the first version released in 2009, which featured nine organisms, the number of integrated genomes is more than four times higher, and now covers 37 plant species. The new species provide a wider phylogenetic range as well as a more in-depth sampling of specific clades, and genomes of additional crop species are present. The functional annotation has been expanded and now comprises data from Gene Ontology, MapMan, UniProtKB/Swiss-Prot, PlnTFDB and PlantTFDB. Furthermore, we improved the algorithms to transfer functional annotation from well-characterized plant genomes to other species. The additional data and new features make PLAZA 3.0 (http://bioinformatics.psb.ugent.be/plaza/) a versatile and comprehensible resource for users wanting to explore genome information to study different aspects of plant biology, both in model and non-model organisms. PMID:25324309

DNA Extraction Protocols for Whole-Genome Sequencing in Marine Organisms.

PubMed

Panova, Marina; Aronsson, Henrik; Cameron, R Andrew; Dahl, Peter; Godhe, Anna; Lind, Ulrika; Ortega-Martinez, Olga; Pereyra, Ricardo; Tesson, Sylvie V M; Wrange, Anna-Lisa; Blomberg, Anders; Johannesson, Kerstin

2016-01-01

The marine environment harbors a large proportion of the total biodiversity on this planet, including the majority of the earths' different phyla and classes. Studying the genomes of marine organisms can bring interesting insights into genome evolution. Today, almost all marine organismal groups are understudied with respect to their genomes. One potential reason is that extraction of high-quality DNA in sufficient amounts is challenging for many marine species. This is due to high polysaccharide content, polyphenols and other secondary metabolites that will inhibit downstream DNA library preparations. Consequently, protocols developed for vertebrates and plants do not always perform well for invertebrates and algae. In addition, many marine species have large population sizes and, as a consequence, highly variable genomes. Thus, to facilitate the sequence read assembly process during genome sequencing, it is desirable to obtain enough DNA from a single individual, which is a challenge in many species of invertebrates and algae. Here, we present DNA extraction protocols for seven marine species (four invertebrates, two algae, and a marine yeast), optimized to provide sufficient DNA quality and yield for de novo genome sequencing projects.

Comparative mapping in intraspecific populations uncovers a high degree of macrosynteny between A- and B-genome diploid species of peanut

PubMed Central

2012-01-01

Background Cultivated peanut or groundnut (Arachis hypogaea L.) is an important oilseed crop with an allotetraploid genome (AABB, 2n = 4x = 40). Both the low level of genetic variation within the cultivated gene pool and its polyploid nature limit the utilization of molecular markers to explore genome structure and facilitate genetic improvement. Nevertheless, a wealth of genetic diversity exists in diploid Arachis species (2n = 2x = 20), which represent a valuable gene pool for cultivated peanut improvement. Interspecific populations have been used widely for genetic mapping in diploid species of Arachis. However, an intraspecific mapping strategy was essential to detect chromosomal rearrangements among species that could be obscured by mapping in interspecific populations. To develop intraspecific reference linkage maps and gain insights into karyotypic evolution within the genus, we comparatively mapped the A- and B-genome diploid species using intraspecific F2 populations. Exploring genome organization among diploid peanut species by comparative mapping will enhance our understanding of the cultivated tetraploid peanut genome. Moreover, new sources of molecular markers that are highly transferable between species and developed from expressed genes will be required to construct saturated genetic maps for peanut. Results A total of 2,138 EST-SSR (expressed sequence tag-simple sequence repeat) markers were developed by mining a tetraploid peanut EST assembly including 101,132 unigenes (37,916 contigs and 63,216 singletons) derived from 70,771 long-read (Sanger) and 270,957 short-read (454) sequences. A set of 97 SSR markers were also developed by mining 9,517 genomic survey sequences of Arachis. An SSR-based intraspecific linkage map was constructed using an F2 population derived from a cross between K 9484 (PI 298639) and GKBSPSc 30081 (PI 468327) in the B-genome species A. batizocoi. A high degree of macrosynteny was observed when comparing the homoeologous linkage groups between A (A. duranensis) and B (A. batizocoi) genomes. Comparison of the A- and B-genome genetic linkage maps also showed a total of five inversions and one major reciprocal translocation between two pairs of chromosomes under our current mapping resolution. Conclusions Our findings will contribute to understanding tetraploid peanut genome origin and evolution and eventually promote its genetic improvement. The newly developed EST-SSR markers will enrich current molecular marker resources in peanut. PMID:23140574

Ancient Antimicrobial Peptides Kill Antibiotic-Resistant Pathogens: Australian Mammals Provide New Options

PubMed Central

Wang, Jianghui; Wong, Emily S. W.; Whitley, Jane C.; Li, Jian; Stringer, Jessica M.; Short, Kirsty R.; Renfree, Marilyn B.

2011-01-01

Background To overcome the increasing resistance of pathogens to existing antibiotics the 10×'20 Initiative declared the urgent need for a global commitment to develop 10 new antimicrobial drugs by the year 2020. Naturally occurring animal antibiotics are an obvious place to start. The recently sequenced genomes of mammals that are divergent from human and mouse, including the tammar wallaby and the platypus, provide an opportunity to discover novel antimicrobials. Marsupials and monotremes are ideal potential sources of new antimicrobials because they give birth to underdeveloped immunologically naïve young that develop outside the sterile confines of a uterus in harsh pathogen-laden environments. While their adaptive immune system develops innate immune factors produced either by the mother or by the young must play a key role in protecting the immune-compromised young. In this study we focus on the cathelicidins, a key family of antimicrobial peptide genes. Principal Finding We identified 14 cathelicidin genes in the tammar wallaby genome and 8 in the platypus genome. The tammar genes were expressed in the mammary gland during early lactation before the adaptive immune system of the young develops, as well as in the skin of the pouch young. Both platypus and tammar peptides were effective in killing a broad range of bacterial pathogens. One potent peptide, expressed in the early stages of tammar lactation, effectively killed multidrug-resistant clinical isolates of Pseudomonas aeruginosa, Klebsiella pneumoniae and Acinetobacter baumannii. Conclusions and Significance Marsupial and monotreme young are protected by antimicrobial peptides that are potent, broad spectrum and salt resistant. The genomes of our distant relatives may hold the key for the development of novel drugs to combat multidrug-resistant pathogens. PMID:21912615