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Sample records for baculatum type strain

  1. Complete genome sequence of Desulfomicrobium baculatum type strain (XT)

    SciTech Connect

    Copeland, Alex; Spring, Stefan; Goker, Markus; Schneider, Susanne; Lapidus, Alla; Glavina Del Rio, Tijana; Tice, Hope; Cheng, Jan-Fang; Lucas, Susan; Chen, Feng; Nolan, Matt; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Ivanova, Natalia; Mavrommatis, Konstantinos; Ovchinnikova, Galina; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jefferies, Cynthia C; Meincke, Linda; Sims, David; Brettin, Thomas; Detter, John C; Han, Cliff; Chain, Patrick; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Klenk, Hans-Peter; Kyrpides, Nikos C; Lucas, Susan

    2009-05-20

    Desulfomicrobium baculatum is the type species of the genus Desulfomicrobium, which is the type genus of the family Desulfomicrobiaceae. It is of phylogenetic interest because of the isolated location of the family Desulfomicrobiaceae within the order Desulfovibrionales. D. baculatum strain XT is a Gram-negative, motile, sulfate-reducing bacterium isolated from water-saturated manganese carbonate ore. It is strictly anaerobic and does not require NaCl for growth, although NaCl concentrations up to 6percent (w/v) are tolerated. The metabolism is respiratory or fermentative. In the presence of sulfate, pyruvate and lactate are incompletely oxidized to acetate and CO2. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of a member of the deltaproteobacterial family Desulfomicrobiaceae, and this 3,942,657 bp long single replicon genome with its 3494 protein-coding and 72 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

  2. Complete genome sequence of Desulfomicrobium baculatum type strain (XT)

    SciTech Connect

    Copeland, A; Spring, Stefan; Goker, Markus; Schneider, Susan; Lapidus, Alla L.; Glavina Del Rio, Tijana; Tice, Hope; Cheng, Jan-Fang; Chen, Feng; Nolan, Matt; Bruce, David; Goodwin, Lynne A.; Pitluck, Sam; Ivanova, N; Mavromatis, K; Ovchinnikova, Galina; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam L; Hauser, Loren John; Chang, Yun-Juan; Jeffries, Cynthia; Meincke, Linda; Sims, David; Brettin, Tom; Detter, J. Chris; Han, Cliff; Chain, Patrick S. G.; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter

    2009-01-01

    Desulfomicrobium baculatum is the type species of the genus Desulfomicrobium, which is the type genus of the family Desulfomicrobiaceae. It is of phylogenetic interest because of the isolated location of the family Desulfomicrobiaceae within the order Desulfovibrionales. D. baculatum strain XT is a Gram-negative, motile, sulfate-reducing bacterium isolated from wa-ter-saturated manganese carbonate ore. It is strictly anaerobic and does not require NaCl for growth, although NaCl concentrations up to 6% (w/v) are tolerated. The metabolism is respi-ratory or fermentative. In the presence of sulfate, pyruvate and lactate are incompletely oxi-dized to acetate and CO2. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of a member of the deltaproteobacterial family Desulfomicrobiaceae, and this 3,942,657 bp long single replicon genome with its 3494 protein-coding and 72 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

  3. SNIT: SNP identification for strain typing

    PubMed Central

    2011-01-01

    With ever-increasing numbers of microbial genomes being sequenced, efficient tools are needed to perform strain-level identification of any newly sequenced genome. Here, we present the SNP identification for strain typing (SNIT) pipeline, a fast and accurate software system that compares a newly sequenced bacterial genome with other genomes of the same species to identify single nucleotide polymorphisms (SNPs) and small insertions/deletions (indels). Based on this information, the pipeline analyzes the polymorphic loci present in all input genomes to identify the genome that has the fewest differences with the newly sequenced genome. Similarly, for each of the other genomes, SNIT identifies the input genome with the fewest differences. Results from five bacterial species show that the SNIT pipeline identifies the correct closest neighbor with 75% to 100% accuracy. The SNIT pipeline is available for download at http://www.bhsai.org/snit.html PMID:21902825

  4. Typing of Proteus strains by proticine production and sensitivity.

    PubMed

    Senior, B W

    1977-02-01

    A simple, reliable and highly discriminating scheme for the bacteriocine typing of Proteus has been developed. Strains are typed on MacConkey's agar according to their ability to produce a proticine active against one of 14 indicator strains having a single and specific proticine sensitivity and also according to their sensitivity to the different proticines of 13 proticine-producing strains. This new scheme of combined production and sensitivity typing was formulated after 250 strains of Proteus from clinical material had been examined for the production of proticines active against the 24 indicator strains of Cradock-Watson's proticine typing scheme and for proticine activity and sensitivity towards each other. Three new types of proticinogenic strains were discovered and defined. Strains producing proticines of types 1, 2 and 3 were isolated frequently. These common proticines could be subtyped by their different actions on newly characterised indicator strains. By means of this production/sensitivity (P/S) typing scheme, 250 Proteus strains were differentiated into 90 distinct types, whereas typing by sensitivity alone distinguished only 40 types and typing by production alone distinguished only 20 types (including subtypes).

  5. SNIT: SNP Identification for Strain Typing

    DTIC Science & Technology

    2011-01-01

    Durkin S, Schneewind O, Nierman WC: Genome sequencing and analysis of Yersina pestis KIM D27, an avirulent strain exempt from select agent regulation. PLoS...gener- ated from next-generation sequencing (NGS) data, we selected the recently published Yersinia pestis KIM D27 genome [12]. The Y. pestis D27 strain...is a deriva- tive of Y. pestis KIM 10 strain (accession no. NC_004088). The Y. pestis KIM D27 draft genome (accession no. ADDC00000000) was generated

  6. Competitive inhibition between different Clostridium botulinum types and strains.

    PubMed

    Eklund, M W; Poysky, F T; Peterson, M E; Paranjpye, R N; Pelroy, G A

    2004-12-01

    Mixtures of proteolytic and nonproteolytic strains of toxigenic Clostridium botulinum types A, B, and F; nonproteolytic types B, E, and F; Clostridium sporogenes; and nontoxic E-like organisms resembling nonproteolytic C. botulinum were tested against each other for the purpose of selecting a mixture of compatible C. botulinum strains for inoculated pack studies on the basis of their sensitivity to bacteriophages and bacteriocin-like agents. All of the proteolytic strains produced bacteriocin-like agents that were inhibitory to three or more of the other proteolytic types and C. sporogenes. When selected strains of proteolytic types A and B were grown together, type A cultures produced neurotoxin, but type B toxin production was inhibited. Nonproteolytic strains of C. botulinum also produced bacteriocin-like agents against each other. Of these, type E strain EF4 produced bacteriocin-like agents against both proteolytic and nonproteolytic types of C. botulinum and C. sporogenes. EF4, however, was not inhibitory to the nontoxigenic E-like strains. When EF4 was grown with type A strain 62A, it had an inhibitory effect on type A toxin production. Strain 62A inactivated the type E toxin of EF4 after 7 to 21 days at 30 degrees C. On the basis of the production of these bacteriocin-like agents by different strains of C. botulinum and their potential effect on neurotoxin production, it is very important that compatible strains are used in mixtures for inoculated pack studies to determine the safety of a food process or product.

  7. Draft Genome Assembly of Neisseria lactamica Type Strain A7515.

    PubMed

    Minogue, T D; Daligault, H A; Davenport, K W; Bishop-Lilly, K A; Bruce, D C; Chain, P S; Chertkov, O; Coyne, S R; Freitas, T; Frey, K G; Jaissle, J; Koroleva, G I; Ladner, J T; Palacios, G F; Redden, C L; Xu, Y; Johnson, S L

    2014-09-25

    We present the scaffolded genome assembly of Neisseria lactamica type strain A7515 (ATCC 23970) as submitted to NCBI under accession no. JOVI00000000. This type strain of the lactose-fermenting Neisseria species is often used in quality control testing and intra-genus phylogenetic analyses. The assembly includes four contigs placed into a single scaffold.

  8. Prior Inoculation with Type B Strains of Francisella tularensis Provides Partial Protection against Virulent Type A Strains in Cottontail Rabbits

    PubMed Central

    Brown, Vienna R.; Adney, Danielle R.; Olea-Popelka, Francisco; Bowen, Richard A.

    2015-01-01

    Francisella tularensis is a highly virulent bacterium that is capable of causing severe disease (tularemia) in a wide range of species. This organism is characterized into two distinct subspecies: tularensis (type A) and holarctica (type B) which vary in several crucial ways, with some type A strains having been found to be considerably more virulent in humans and laboratory animals. Cottontail rabbits have been widely implicated as a reservoir species for this subspecies; however, experimental inoculation in our laboratory revealed type A organisms to be highly virulent, resulting in 100% mortality following challenge with 50–100 organisms. Inoculation of cottontail rabbits with the same number of organisms from type B strains of bacteria was found to be rarely lethal and to result in a robust humoral immune response. The objective of this study was to characterize the protection afforded by a prior challenge with type B strains against a later inoculation with a type A strain in North American cottontail rabbits (Sylvilagus spp). Previous infection with a type B strain of organism was found to lengthen survival time and in some cases prevent death following inoculation with a type A2 strain of F. tularensis. In contrast, inoculation of a type A1b strain was uniformly lethal in cottontail rabbits irrespective of a prior type B inoculation. These findings provide important insight about the role cottontail rabbits may play in environmental maintenance and transmission of this organism. PMID:26474413

  9. Diphthericin types, bacteriophage types and serotypes of Corynebacterium diphtheriae strains isolated in Australia

    PubMed Central

    Gibson, L. F.; Colman, G.

    1973-01-01

    A dipthericin typing scheme has been constructed using 441 strains of Corynebacterium diptheriae isolated in eastern Australia from 1962 to 1971. Ten types have been distinguished using seven strains of C. diphtheriae and two strains of C. belfanti as indicators of the diphthericins produced by the newly isolated strains. Strains grouped into types L2, L3 and L3a were found only in Melbourne and types L1 and L4 were predominant in Sydney. Type L5 strains were isolated intermittently throughout the period of study and were found in all eastern states. Numerical analysis of the characteristics of the strains suggests that associations exist between, on the one hand, diphthericin type and, on the other hand, bacteriophage type, serotype and biochemical activity. PMID:4203597

  10. Comparison of four molecular methods to type Salmonella Enteritidis strains.

    PubMed

    Campioni, Fábio; Pitondo-Silva, André; Bergamini, Alzira M M; Falcão, Juliana P

    2015-05-01

    This study compared the pulsed-field gel electrophoresis (PFGE), enterobacterial repetitive intergenic consensus-PCR (ERIC-PCR), multilocus variable-number of tanden-repeat analysis (MLVA), and multilocus sequence typing (MLST) methods for typing 188 Salmonella Enteritidis strains from different sources isolated over a 24-year period in Brazil. PFGE and ERIC-PCR were more efficient than MLVA for subtyping the strains. However, MLVA provided additional epidemiological information for those strains. In addition, MLST showed the Brazilian strains as belonging to the main clonal complex of S. Enteritidis, CC11, and provided the first report of two new STs in the S. enterica database but could not properly subtype the strains. Our results showed that the use of PFGE or ERIC-PCR together with MLVA is suitable to efficiently subtype S. Enteritidis strains and provide important epidemiological information.

  11. Draft Genome Sequence of Mycobacterium chimaera Type Strain Fl-0169

    PubMed Central

    Tokarev, Vasily; Kessler, Collin; McLimans, Christopher; Gomez-Alvarez, Vicente; Wright, Justin; King, Dawn; Lamendella, Regina

    2017-01-01

    ABSTRACT We report here the draft genome sequence of the type strain Mycobacterium chimaera Fl-0169, a member of the Mycobacterium avium complex (MAC). M. chimaera Fl-0169T was isolated from a patient in Italy and is highly similar to strains of M. chimaera isolated in Ireland, although Fl-0169T possesses unique virulence genes. PMID:28232435

  12. Draft Genome Sequence of Mycobacterium chimaera Type Strain Fl-0169.

    PubMed

    Pfaller, Stacy; Tokarev, Vasily; Kessler, Collin; McLimans, Christopher; Gomez-Alvarez, Vicente; Wright, Justin; King, Dawn; Lamendella, Regina

    2017-02-23

    We report here the draft genome sequence of the type strain Mycobacterium chimaera Fl-0169, a member of the Mycobacterium avium complex (MAC). M. chimaera Fl-0169(T) was isolated from a patient in Italy and is highly similar to strains of M. chimaera isolated in Ireland, although Fl-0169(T) possesses unique virulence genes.

  13. [Multilocus sequence-typing for characterization of Moscow strains of Haemophilus influenzae type b].

    PubMed

    Platonov, A E; Mironov, K O; Iatsyshina, S B; Koroleva, I S; Platonova, O V; Gushchin, A E; Shipulin, G A

    2003-01-01

    Haemophilius influenzae, type b (Hib) bacteria, were genotyped by multilocus sequence typing (MLST) using 5 loci (adk, fucK, mdh, pgi, recA). 42 Moscow Hib strains (including 38 isolates form cerebrospinal fluid of children, who had purulent meningitis in 1999-2001, and 4 strains isolated from healthy carriers of Hib), as well as 2 strains from Yekaterinburg were studied. In MLST a strain is characterized, by alleles and their combinations (an allele profile) referred to also as sequence-type (ST). 9 Sts were identified within the Russian Hib bacteria: ST-1 was found in 25 strains (57%), ST-12 was found in 8 strains (18%), ST-11 was found in 4 strains (9%) and ST-15 was found in 2 strains (4.5%); all other STs strains (13, 14, 16, 17, 51) were found in isolated cases (2.3%). A comparison of allelic profiles and of nucleotide sequences showed that 93% of Russian isolates, i.e. strain with ST-1, 11, 12, 13, 15 and 17, belong to one and the same clonal complex. 2 isolates from Norway and Sweden from among 7 foreign Hib strains studied up to now can be described as belonging to the same clonal complex; 5 Hib strains were different from the Russian ones.

  14. Multilocus sequence typing of oenological Saccharomyces cerevisiae strains.

    PubMed

    Muñoz, Rosario; Gómez, Alicia; Robles, Virginia; Rodríguez, Patricia; Cebollero, Eduardo; Tabera, Laura; Carrascosa, Alfonso V; Gonzalez, Ramon

    2009-12-01

    This study describes the application of a multilocus sequence typing (MLST) analysis for molecular discrimination at the strain level of Spanish wine yeast strains. The discrimination power of MLST is compared to mitochondrial RFLP analysis. Fragments of the ADP1, ACC1, RPN2, GLN4, and ALA1 genes were amplified by PCR from chromosomal DNA of 18 wine Saccharomyces cerevisiae strains. Ten polymorphic sites were found in the five loci analyzed showing 13 different genotypes, with 11 of them represented by only one strain. RFLP analysis of the same 18 wine yeast strains showed seventeen different mitochondrial patterns. Phylogenetic relationships among the strains analyzed, inferred by MLST data, showed wine isolates of S. cerevisiae as a rather homogeneous group. The discrimination potential of mitochondrial RFLP analysis was superior to the MLST scheme used in this work. However, MLST analysis allowed an easy construction of reliable phylogenetic trees. MLST analysis offers the possibility of typing wine S. cerevisiae strains simultaneously to the study of the genetic relationship among them.

  15. Revision of the taxonomic status of type strains of Mesorhizobium loti and reclassification of strain USDA 3471T as the type strain of Mesorhizobiumerdmanii sp. nov. and ATCC 33669T as the type strain of Mesorhizobiumjarvisii sp. nov.

    PubMed

    Martínez-Hidalgo, Pilar; Ramírez-Bahena, Martha Helena; Flores-Félix, José David; Rivas, Raúl; Igual, José M; Mateos, Pedro F; Martínez-Molina, Eustoquio; León-Barrios, Milagros; Peix, Álvaro; Velázquez, Encarna

    2015-06-01

    The species Mesorhizobim loti was isolated from nodules of Lotus corniculatus and its type strain deposited in several collections. Some of these type strains, such as those deposited in the USDA and ATCC collections before 1990, are not coincident with the original strain, NZP 2213T, deposited in the NZP culture collection. The analysis of the 16S rRNA gene showed that strains USDA 3471T and ATCC 33669T formed independent branches from that occupied by Mesorhizobium loti NZP 2213T and related to those occupied by Mesorhizobium opportunistum WSM2075T and Mesorhizobium huakuii IFO 15243T, respectively, with 99.9 % similarity in both cases. However, the analysis of concatenated recA, atpD and glnII genes with similarities lower than 96, 98 and 94 %, respectively, between strains USDA 3471T and M. opportunistum WSM2075T and between strains ATCC 33669T and M. huakuii IFO 15243T, indicated that the strains USDA 3471T and ATCC 33669T represent different species of the genus Mesorhizobium. These results were confirmed by DNA-DNA hybridization experiments and phenotypic characterization. Therefore, the two strains were reclassified as representatives of the two species Mesorhizobium erdmanii sp. nov. (type strain USDA 3471T = CECT 8631T = LMG 17826t2T) and Mesorhizobium jarvisii sp. nov. (type strain ATCC 33669T = CECT 8632T = LMG 28313T).

  16. Brunenders: a partially attenuated historic poliovirus type I vaccine strain.

    PubMed

    Sanders, Barbara P; Liu, Ying; Brandjes, Alies; van Hoek, Vladimir; de Los Rios Oakes, Isabel; Lewis, John; Wimmer, Eckard; Custers, Jerome H H V; Schuitemaker, Hanneke; Cello, Jeronimo; Edo-Matas, Diana

    2015-09-01

    Brunenders, a type I poliovirus (PV) strain, was developed in 1952 by J. F. Enders and colleagues through serial in vitro passaging of the parental Brunhilde strain, and was reported to display partial neuroattenuation in monkeys. This phenotype of attenuation encouraged two vaccine manufacturers to adopt Brunenders as the type I component for their inactivated poliovirus vaccines (IPVs) in the 1950s, although today no licensed IPV vaccine contains Brunenders. Here we confirmed, in a transgenic mouse model, the report of Enders on the reduced neurovirulence of Brunenders. Although dramatically neuroattenuated relative to WT PV strains, Brunenders remains more virulent than the attenuated oral vaccine strain, Sabin 1. Importantly, the neuroattenuation of Brunenders does not affect in vitro growth kinetics and in vitro antigenicity, which were similar to those of Mahoney, the conventional type I IPV vaccine strain. We showed, by full nucleotide sequencing, that Brunhilde and Brunenders differ at 31 nucleotides, eight of which lead to amino acid changes, all located in the capsid. Upon exchanging the Brunenders capsid sequence with that of the Mahoney capsid, WT neurovirulence was regained in vivo, suggesting a role for the capsid mutations in Brunenders attenuation. To date, as polio eradication draws closer, the switch to using attenuated strains for IPV is actively being pursued. Brunenders preceded this novel strategy as a partially attenuated IPV strain, accompanied by decades of successful use in the field. Providing data on the attenuation of Brunenders may be of value in the further construction of attenuated PV strains to support the grand pursuit of the global eradication of poliomyelitis.

  17. Complete genome sequence of Methanoculleus marisnigri type strain JR1

    SciTech Connect

    Anderson, Iain; Sieprawska-Lupa, Magdalena; Goltsman, Eugene; Lapidus, Alla L.; Copeland, A; Glavina Del Rio, Tijana; Tice, Hope; Dalin, Eileen; Barry, Kerrie; Saunders, Elizabeth H; Han, Cliff; Brettin, Tom; Detter, J. Chris; Bruce, David; Mikhailova, Natalia; Pitluck, Sam; Hauser, Loren John; Land, Miriam L; Lucas, Susan; Richardson, P M; Whitman, W. B.; Kyrpides, Nikos C

    2009-01-01

    Methanoculleus marisnigri Romesser et al. 1981 is a methanogen belonging to the order Methanomicrobiales within the archaeal phylum Euryarchaeota. The type strain, JR1, was isolated from anoxic sediments of the Black Sea. M. marisnigri is of phylogenetic interest because at the time the sequencing project began only one genome had previously been sequenced from the order Methanomicrobiales. We report here the complete genome sequence of M. marisnigri type strain JR1 and its annotation. This is part of a Joint Genome Institute 2006 Community Sequencing Program to sequence genomes of diverse Archaea.

  18. Complete genome sequence of Methanocorpusculum labreanum type strain Z

    SciTech Connect

    Anderson, Iain; Sieprawska-Lupa, Magdalena; Goltsman, Eugene; Lapidus, Alla L.; Copeland, A; Glavina Del Rio, Tijana; Tice, Hope; Dalin, Eileen; Barry, Kerrie; Pitluck, Sam; Hauser, Loren John; Land, Miriam L; Lucas, Susan; Richardson, P M; Whitman, W. B.; Kyrpides, Nikos C

    2009-01-01

    Methanocorpusculum labreanum is a methanogen belonging to the order Methanomicrobiales within the archaeal phylum Euryarchaeota. The type strain Z was isolated from surface sediments of Tar Pit Lake in the La Brea Tar Pits in Los Angeles, California. M. labreanum is of phylogenetic interest because at the time the sequencing project began only one genome had previously been sequenced from the order Methanomicrobiales. We report here the complete genome sequence of M. labreanum type strain Z and its annotation. This is part of a 2006 Joint Genome Institute Community Sequencing Program project to sequence genomes of diverse Archaea.

  19. Molecular methods for strain typing of Candida albicans: a review.

    PubMed

    Saghrouni, F; Ben Abdeljelil, J; Boukadida, J; Ben Said, M

    2013-06-01

    Candida albicans is one of the most medically important fungi because of its high frequency as a commensal and pathogenic microorganism causing superficial as well as invasive infections. Strain typing and delineation of the species are essential for understanding its biology, epidemiology and population structure. A wide range of molecular techniques have been used for this purpose including non-DNA-based methods (multi-locus enzyme electrophoresis), conventional DNA-based methods (electrophoretic karyotyping, random amplified polymorphic DNA, amplified fragment length polymorphism, restriction enzyme analysis with and without hybridization, rep-PCR) and DNA-based methods called exact typing methods because they generate unambiguous and highly reproducible typing data (including microsatellite length polymorphism and multi-locus sequence typing). In this review, the main molecular methods used for C. albicans strain typing are summarized, and their advantages and limitations are discussed with regard to their discriminatory power, reproducibility, cost and ease of performance.

  20. MLVA typing of Mycoplasma hyopneumoniae bacterins and field strains

    PubMed Central

    Tamiozzo, P.; Zamora, R.; Lucchesi, P. M. A.; Estanguet, A.; Parada, J.; Carranza, A.; Camacho, P.; Ambrogi, A.

    2015-01-01

    Because of the lack of information about both the genetic characteristics of Mycoplasma hyopneumoniae commercial vaccines and their relationship with field strains, the authors attempted to identify genetic subtypes of some M hyopneumoniae bacterins, and to compare them with M. hyopneumoniae field strains. Six commercial M hyopneumoniae bacterins and 28 bronchoalveolar lavages from pigs at slaughter from three herds were analysed by Multiple-Locus Variable number tandem repeat Analysis (MLVA) on p146R1, p146R3, H4, H5 and p95 loci. The results obtained showed the presence of more than one M hyopneumoniae genotype in some pigs and also in one of the bacterins analysed. It is also worth noting that MLVA typing allowed the distinction among circulating field strains and also when comparing them with vaccine strains, which, knowing the relatedness among them, could be useful in the research of the efficacy of the vaccines. PMID:26495127

  1. Characterization of six type A strains of Clostridium botulinum that contain type B toxin gene sequences.

    PubMed

    Kirma, Nameer; Ferreira, Joseph L; Baumstark, Barbara R

    2004-02-16

    Six Clostridium botulinum isolates exhibiting type A toxicity as measured by the mouse bioassay were found to contain both type A and type B neurotoxin DNA sequences. The six strains were divided into three groups based on the DNA sequence of the type B neurotoxin gene. Members of each group exhibited 100% sequence identity over the 3876 bp type B toxin open reading frame. The type B toxin sequence of all groups differed at more than 60 positions when compared to the BGB control strain.

  2. Complete Genome Sequence of Staphylococcus pseudintermedius Type Strain LMG 22219

    PubMed Central

    Abouelkhair, Mohamed A.; Riley, Matthew C.; Bemis, David A.

    2017-01-01

    ABSTRACT We report the first complete genome sequence of LMG 22219 (=ON 86T = CCUG 49543T), the Staphylococcus pseudintermedius type strain isolated from feline lung tissue. This sequence information will facilitate phylogenetic comparisons of staphylococcal species and other bacteria at the genome level. PMID:28209834

  3. Complete Genome Sequence of Staphylococcus pseudintermedius Type Strain LMG 22219.

    PubMed

    Abouelkhair, Mohamed A; Riley, Matthew C; Bemis, David A; Kania, Stephen A

    2017-02-16

    We report the first complete genome sequence of LMG 22219 (=ON 86(T) = CCUG 49543(T)), the Staphylococcus pseudintermedius type strain isolated from feline lung tissue. This sequence information will facilitate phylogenetic comparisons of staphylococcal species and other bacteria at the genome level.

  4. Genome Sequence of Type Strains of Genus Stenotrophomonas

    PubMed Central

    Patil, Prashant P.; Midha, Samriti; Kumar, Sanjeet; Patil, Prabhu B.

    2016-01-01

    Genomic resource of type strains and historically important strains of genus Stenotrophomonas allowed us to reveal the existence of 18 distinct species by applying modern phylogenomic criterions. Apart from Stenotrophomonas maltophilia, S. africana represents another species of clinical importance. Interestingly, Pseudomonas hibsicola, P. beteli, and S. pavani that are of plant origin are closer to S. maltophilia than the majority of the environmental isolates. The genus has an open pan-genome. By providing the case study on genes encoding metallo-β-lactamase and Clustered Regularly Interspaced Short Palindrome Repeats (CRISPR) regions, we have tried to show the importance of this genomic dataset in understanding its ecology. PMID:27014232

  5. Complete genome sequence of Rhodospirillum rubrum type strain (S1).

    PubMed

    Munk, A Christine; Copeland, Alex; Lucas, Susan; Lapidus, Alla; Del Rio, Tijana Glavina; Barry, Kerrie; Detter, John C; Hammon, Nancy; Israni, Sanjay; Pitluck, Sam; Brettin, Thomas; Bruce, David; Han, Cliff; Tapia, Roxanne; Gilna, Paul; Schmutz, Jeremy; Larimer, Frank; Land, Miriam; Kyrpides, Nikos C; Mavromatis, Konstantinos; Richardson, Paul; Rohde, Manfred; Göker, Markus; Klenk, Hans-Peter; Zhang, Yaoping; Roberts, Gary P; Reslewic, Susan; Schwartz, David C

    2011-07-01

    Rhodospirillum rubrum (Esmarch 1887) Molisch 1907 is the type species of the genus Rhodospirillum, which is the type genus of the family Rhodospirillaceae in the class Alphaproteobacteria. The species is of special interest because it is an anoxygenic phototroph that produces extracellular elemental sulfur (instead of oxygen) while harvesting light. It contains one of the most simple photosynthetic systems currently known, lacking light harvesting complex 2. Strain S1(T) can grow on carbon monoxide as sole energy source. With currently over 1,750 PubMed entries, R. rubrum is one of the most intensively studied microbial species, in particular for physiological and genetic studies. Next to R. centenum strain SW, the genome sequence of strain S1(T) is only the second genome of a member of the genus Rhodospirillum to be published, but the first type strain genome from the genus. The 4,352,825 bp long chromosome and 53,732 bp plasmid with a total of 3,850 protein-coding and 83 RNA genes were sequenced as part of the DOE Joint Genome Institute Program DOEM 2002.

  6. Complete genome sequence of Sebaldella termitidis type strain (NCTC 11300).

    PubMed

    Harmon-Smith, Miranda; Celia, Laura; Chertkov, Olga; Lapidus, Alla; Copeland, Alex; Glavina Del Rio, Tijana; Nolan, Matt; Lucas, Susan; Tice, Hope; Cheng, Jan-Fang; Han, Cliff; Detter, John C; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Pati, Amrita; Liolios, Konstantinos; Ivanova, Natalia; Mavromatis, Konstantinos; Mikhailova, Natalia; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D; Brettin, Thomas; Göker, Markus; Beck, Brian; Bristow, James; Eisen, Jonathan A; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter; Chen, Feng

    2010-03-30

    Sebaldella termitidis (Sebald 1962) Collins and Shah 1986, is the only species in the genus Sebaldella within the fusobacterial family 'Leptotrichiaceae'. The sole and type strain of the species was first isolated about 50 years ago from intestinal content of Mediterranean termites. The species is of interest for its very isolated phylogenetic position within the phylum Fusobacteria in the tree of life, with no other species sharing more than 90% 16S rRNA sequence similarity. The 4,486,650 bp long genome with its 4,210 protein-coding and 54 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

  7. Type II strained layer superlattice: A potential future IR solution

    NASA Astrophysics Data System (ADS)

    Tidrow, Meimei Z.

    2009-11-01

    Type II strained layer superlattice (SLS) has been making tremendous progress in the past few years funded by the Missile Defense Agency Advanced Technology Directorate (MDA/DV) under the Passive EO/IR Program. SLS has shown great potential as a future solution for infrared military systems. In this presentation, the most recent progress in SLS development will be presented. The presentation will also discuss the comparison of SLS with mercury-cadmium-telluride (HgCdTe) using Rule 07, SLS minority carrier lifetime issues, and future directions.

  8. [Capsular types, virulence factors and DNA types of Klebsiella oxytoca strains isolated from blood and bile].

    PubMed

    Ishihara, Yuka; Yagi, Tetsuya; Mochizuki, Mariko; Ohta, Michio

    2012-03-01

    Klebsiella oxytoca is an opportunistic pathogen and is isolated at the second highest frequency among genus Klebsiella from hospitalized patients. According to previous reports, the major virulence factors of K. pneumoniae include capsules and several kinds of pill, whereas the virulence factors of K. oxytoca have not been well investigated. We noticed an increased frequency of K. oxytoca isolates from patients who had undergone a biliary tract operation in a general hospital from May through November, 2009. We then performed a PCR analysis of the virulence factors and an epidemiological analysis with capsular typing (serotyping) and pulsed field gel electrophoresis (PFGE) for K. oxytoca of 11 blood isolates and 10 bile isolates. As a result, serotypes of K9, K15, K26, K31, K43, K47, K55, K70, and K79 were identified in these strains, and K1 and K2 which are frequent serotypes in K. pneumoniae strains were not observed. Two blood isolates of the K55 serotype showed almost the same PFGE pattern, suggesting that these isolates were very closely related and caused cross-infection in a hospital ward. Strains of the K43 serotype were three blood isolates and 1 bile isolate, all of which showed different PFGE patterns. There were no common isolates among the blood and bile isolates. A PCR search revealed that fimH and mrkD genes which are relevant to type 1 and type 2 pili, respectively, were present in all strains, whereas kfuBC, an iron uptake gene, and cf29a were detected in only a few strains. Neither of the mucoid phenotype-related genes magA and rmpA was present in any strains. These results strongly suggest that type 1 and/or type 3 pili would have important roles in the pathogenesis of blood infection and bile infection caused by K. oxytoca.

  9. Complete genome sequence of Chitinophaga pinensis type strain (UQM 2034).

    PubMed

    Glavina Del Rio, Tijana; Abt, Birte; Spring, Stefan; Lapidus, Alla; Nolan, Matt; Tice, Hope; Copeland, Alex; Cheng, Jan-Fang; Chen, Feng; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Ivanova, Natalia; Mavromatis, Konstantinos; Mikhailova, Natalia; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D; Chain, Patrick; Saunders, Elizabeth; Detter, John C; Brettin, Thomas; Rohde, Manfred; Göker, Markus; Bristow, Jim; Eisen, Jonathan A; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter; Lucas, Susan

    2010-02-28

    Chitinophaga pinensis Sangkhobol and Skerman 1981 is the type strain of the species which is the type species of the rapidly growing genus Chitinophaga in the sphingobacterial family 'Chitinophagaceae'. Members of the genus Chitinophaga vary in shape between filaments and spherical bodies without the production of a fruiting body, produce myxospores, and are of special interest for their ability to degrade chitin. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of a member of the family 'Chitinophagaceae', and the 9,127,347 bp long single replicon genome with its 7,397 protein-coding and 95 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

  10. Complete genome sequence of Desulfohalobium retbaense type strain (HR(100)).

    PubMed

    Spring, Stefan; Nolan, Matt; Lapidus, Alla; Glavina Del Rio, Tijana; Copeland, Alex; Tice, Hope; Cheng, Jan-Fang; Lucas, Susan; Land, Miriam; Chen, Feng; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Ivanova, Natalia; Mavromatis, Konstantinos; Mikhailova, Natalia; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D; Munk, Christine; Kiss, Hajnalka; Chain, Patrick; Han, Cliff; Brettin, Thomas; Detter, John C; Schüler, Esther; Göker, Markus; Rohde, Manfred; Bristow, Jim; Eisen, Jonathan A; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter

    2010-01-28

    Desulfohalobium retbaense (Ollivier et al. 1991) is the type species of the polyphyletic genus Desulfohalobium, which comprises, at the time of writing, two species and represents the family Desulfohalobiaceae within the Deltaproteobacteria. D. retbaense is a moderately halophilic sulfate-reducing bacterium, which can utilize H(2) and a limited range of organic substrates, which are incompletely oxidized to acetate and CO(2), for growth. The type strain HR(100) (T) was isolated from sediments of the hypersaline Retba Lake in Senegal. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of a member of the family Desulfohalobiaceae. The 2,909,567 bp genome (one chromosome and a 45,263 bp plasmid) with its 2,552 protein-coding and 57 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  11. Comparative metabolic flux analysis of an Ashbya gossypii wild type strain and a high riboflavin-producing mutant strain.

    PubMed

    Jeong, Bo-Young; Wittmann, Christoph; Kato, Tatsuya; Park, Enoch Y

    2015-01-01

    In the present study, we analyzed the central metabolic pathway of an Ashbya gossypii wild type strain and a riboflavin over-producing mutant strain developed in a previous study in order to characterize the riboflavin over-production pathway. (13)C-Metabolic flux analysis ((13)C-MFA) was carried out in both strains, and the resulting data were fit to a steady-state flux isotopomer model using OpenFLUX. Flux to pentose-5-phosphate (P5P) via the pentose phosphate pathway (PPP) was 9% higher in the mutant strain compared to the wild type strain. The flux from purine synthesis to riboflavin in the mutant strain was 1.6%, while that of the wild type strain was only 0.1%, a 16-fold difference. In addition, the flux from the cytoplasmic pyruvate pool to the extracellular metabolites, pyruvate, lactate, and alanine, was 2-fold higher in the mutant strain compared to the wild type strain. This result demonstrates that increased guanosine triphosphate (GTP) flux through the PPP and purine synthesis pathway (PSP) increased riboflavin production in the mutant strain. The present study provides the first insight into metabolic flux through the central carbon pathway in A. gossypii and sets the foundation for development of a quantitative and functional model of the A. gossypii metabolic network.

  12. Development of a duplex PCR for rapid detection and differentiation of Erysipelothrix rhusiopathiae vaccine strains and wild type strains.

    PubMed

    Zhu, Weifeng; Wu, Chao; Kang, Chao; Cai, Chengzhi; Jin, Meilin

    2017-02-01

    The differentiation of vaccine strains from wild type strains is important for disease control. A duplex PCR for rapid detection and differentiation of Erysipelothrix rhusiopathiae vaccine strains and wild type strains was developed based on the DNA polymerase IV gene. This duplex PCR was sensitive and specific. The detection results were coincident with that of a single nucleotide polymorphisms based PCR but the detection process was more rapid. In conclusion, this duplex PCR was a useful tool for Erysipelothrix rhusiopathiae infections' differential diagnosis in China.

  13. EPIDEMIOLOGY AND MOLECULAR TYPING OF BRUCELLA STRAINS CIRCULATING IN GEORGIA.

    PubMed

    Sidamonidze, K; Ramishvili, M; Kalandadze, I; Tsereteli, D; Nikolich, M P

    2015-10-01

    In 2009-2013, 851 cases of brucellosis were registered in Georgia. Most cases of brucellosis were found in eastern Georgia (91.3% of cases). Mainly men were infected with brucellosis (81.0%).The age group with the most frequent cases of brucellosis is 30-59 years (48.5%). Brucellosis is rarely found among children(0-4 years - 2.0%, 5-14 years - 8.0%). Brucellosis cases were linked to professional activity; mainly by farmers (33.0% of those infected) and shepherds (27.0%). Biotyping Brucella by microbiological methods alone has limitations, so molecular typing was implemented in this study to confirm species. Isolates from human blood and ruminant milk or blood were identified by a bacteriological algorithm and confirmed by real-time PCR (Brucella T1, Idaho Technology). Species identity was confirmed using the AMOS conventional PCR assay, which differentiates four human pathogenic species but cannot recognize certain biovars within them. This gap was addressed by using more universal species-specific Single Nucleotide Polymorphism (SNP) assays. Real-time PCR was used to confirm 86 Brucella strains (48 human, 38 animal isolates) obtained 2009-2011. AMOS PCR supported the biochemical test results for 53 B. melitensis and four B. abortus strains, but not for 29 suspected B. abortus human and animal isolates. SNP typing of all 86 isolates supported the AMOS PCR results but also confirmed the species of the 29 strains not amplified by AMOS PCR. In 2009-2013 years the prevalence of brucellosis was still high. Nowadays cases of brucellosis are higher in the western part of Georgia than in the 1991-2005 period by a factor of 2.62. Brucellosis continues to be mainly an infection in males, because men are mostly engaged in sheep and cattle care. Combined AMOS PCR and SNP typing in this study provided the first genetic confirmation that both B. abortus and B. melitensis are actively circulating in humans and animals in Georgia.

  14. Complete genome sequence of Treponema succinifaciens type strain (6091T)

    SciTech Connect

    Han, Cliff; Gronow, Sabine; Teshima, Hazuki; Lapidus, Alla L.; Nolan, Matt; Lucas, Susan; Hammon, Nancy; Deshpande, Shweta; Cheng, Jan-Fang; Zeytun, Ahmet; Tapia, Roxanne; Goodwin, Lynne A.; Pitluck, Sam; Liolios, Konstantinos; Pagani, Ioanna; Ivanova, N; Mavromatis, K; Mikhailova, Natalia; Huntemann, Marcel; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam L; Hauser, Loren John; Brambilla, Evelyne-Marie; Rohde, Manfred; Goker, Markus; Woyke, Tanja; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter; Detter, J. Chris

    2011-01-01

    Treponema succinifaciens Cwyk and Canale-Parola 1981 is of interest because this strictly anaerobic, apathogenic member of the genus Treponema oxidizes carbohydrates and couples the Embden-Meyerhof pathway via activity of a pyruvate-formate lyase to the production of acetyl-coenzyme A and formate. This feature separates this species from most other anaerob- ic spirochetes. The genome of T. succinifaciens 6091T is only the second completed and pub- lished type strain genome from the genus Treponema in the family Spirochaetaceae. The 2,897,425 bp long genome with one plasmid harbors 2,723 protein-coding and 63 RNA genes and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  15. Proposal for strained type II superlattice infrared detectors

    NASA Astrophysics Data System (ADS)

    Smith, D. L.; Mailhiot, C.

    1987-09-01

    It is shown that strained type II superlattices made of InAs-Ga(1-x)In(x)Sb(x) about 0.4 have favorable optical properties for infrared detection. By adjusting the layer thicknesses and the alloy composition, a wide range of wavelengths can be reached. Optical absorption calculations for a case where the cutoff wavelength is about 10 microns show that, near threshold, the absorption is as good as for the HgCdTe alloy with the same band gap. The electron effective mass is nearly isotropic and equal to 0.04 m. This effective mass should give favorable electrical properties, such as small diode tunneling currents and good mobilities, and diffusion lengths.

  16. Complete genome sequence of Pirellula staleyi type strain (ATCC 27377).

    PubMed

    Clum, Alicia; Tindall, Brian J; Sikorski, Johannes; Ivanova, Natalia; Mavrommatis, Konstantinos; Lucas, Susan; Glavina, Tijana; Del Rio; Nolan, Matt; Chen, Feng; Tice, Hope; Pitluck, Sam; Cheng, Jan-Fang; Chertkov, Olga; Brettin, Thomas; Han, Cliff; Detter, John C; Kuske, Cheryl; Bruce, David; Goodwin, Lynne; Ovchinikova, Galina; Pati, Amrita; Mikhailova, Natalia; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D; Chain, Patrick; Rohde, Manfred; Göker, Markus; Bristow, Jim; Eisen, Jonathan A; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter; Lapidus, Alla

    2009-12-30

    Pirellula staleyi Schlesner and Hirsch 1987 is the type species of the genus Pirellula of the family Planctomycetaceae. Members of this pear- or teardrop-shaped bacterium show a clearly visible pointed attachment pole and can be distinguished from other Planctomycetes by a lack of true stalks. Strains closely related to the species have been isolated from fresh and brackish water, as well as from hypersaline lakes. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of the order Planctomyces and only the second sequence from the phylum Planctobacteria/Planctomycetes. The 6,196,199 bp long genome with its 4773 protein-coding and 49 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  17. Complete genome sequence of Nakamurella multipartita type strain (Y-104).

    PubMed

    Tice, Hope; Mayilraj, Shanmugam; Sims, David; Lapidus, Alla; Nolan, Matt; Lucas, Susan; Glavina Del Rio, Tijana; Copeland, Alex; Cheng, Jan-Fang; Meincke, Linda; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Ivanova, Natalia; Mavromatis, Konstantinos; Ovchinnikova, Galina; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D; Detter, John C; Brettin, Thomas; Rohde, Manfred; Göker, Markus; Bristow, Jim; Eisen, Jonathan A; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter; Chen, Feng

    2010-03-30

    Nakamurella multipartita (Yoshimi et al. 1996) Tao et al. 2004 is the type species of the monospecific genus Nakamurella in the actinobacterial suborder Frankineae. The nonmotile, coccus-shaped strain was isolated from activated sludge acclimated with sugar-containing synthetic wastewater, and is capable of accumulating large amounts of polysaccharides in its cells. Here we describe the features of the organism, together with the complete genome sequence and annotation. This is the first complete genome sequence of a member of the family Nakamurellaceae. The 6,060,298 bp long single replicon genome with its 5415 protein-coding and 56 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

  18. Electrophoretic Mobilities of Escherichia coli O157:H7 and Wild-Type Escherichia coli Strains

    PubMed Central

    Lytle, Darren A.; Rice, Eugene W.; Johnson, Clifford H.; Fox, Kim R.

    1999-01-01

    The electrophoretic mobilities (EPMs) of a number of Escherichia coli O157:H7 and wild-type E. coli strains were measured. The effects of pH and ionic strength on the EPMs were investigated. The EPMs of E. coli O157:H7 strains differed from those of wild-type strains. As the suspension pH decreased, the EPMs of both types of strains increased. PMID:10388724

  19. Complete genome sequence of Kytococcus sedentarius type strain (strain 541T)

    SciTech Connect

    Sims, David; Brettin, Thomas; Detter, John C.; Han, Cliff; Lapidus, Alla; Copeland, Alex; Glavina Del Rio, Tijana; Nolan, Matt; Chen, Feng; Lucas, Susan; Tice, Hope; Cheng, Jan-Fang; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Ovchinnikova, Galina; Pati, Amrita; Ivanova, Natalia; Mavrommatis, Konstantinos; Chen, Amy; Palaniappan, Krishna; D'haeseleer, Patrick; Chain, Patrick; Bristow, James; Eisen, Jonathan A.; Markowitz, Victor; Hugenholtz, Philip; Schneider, Susanne; Goker, Markus; Pukall, Rudiger; Kyrpides, Nikos C.; Klenk, Hans-Peter

    2009-05-20

    Kytococcus sedentarius (ZoBell and Upham 1944) Stackebrandt et al. 1995 is the type strain of the species, and is of phylogenetic interest because of its location in the Dermacoccaceae, a poorly studied family within the actinobacterial suborder Micrococcineae. K. sedentarius is known for the production of oligoketide antibiotics as well as for its role as an opportunistic pathogen causing valve endocarditis, hemorrhagic pneumonia, and pitted keratolysis. It is strictly aerobic and can only grow when several amino acids are provided in the medium. The strain described in this report is a free-living, nonmotile, Gram-positive bacterium, originally isolated from a marine environment. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of a member of the family Dermacoccaceae and the 2,785,024 bp long single replicon genome with its 2639 protein-coding and 64 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

  20. Draft Genome Sequences of Type Strain Sediminibacterium salmoneum NJ-44 and Sediminibacterium sp. Strain C3, a Novel Strain Isolated from Activated Sludge

    PubMed Central

    Ayarza, Joaquín M.; Figuerola, Eva L. M.

    2014-01-01

    The genus Sediminibacterium comprises species present in diverse natural and engineered environments. Here, we report for the first time the genome sequences of the type strain Sediminibacterium salmoneum NJ-44 (NBRC 103935) and Sediminibacterium sp. strain C3 (BNM541), isolated from activated sludge, a valuable model for the study of substrate-dependent autoaggregation. PMID:24435857

  1. Complete genome sequence of Actinosynnema mirum type strain (101T)

    SciTech Connect

    Land, Miriam; Lapidus, Alla; Mayilraj, Shanmugam; Chen, Feng; Copeland, Alex; Glavina Del Rio, Tijana; Nolan, Matt; Lucas, Susan; Tice, Hope; Cheng, Jan-Fang; Chertkov, Olga; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Rohde, Manfred; Goker, Markus; Pati, Amrita; Ivanova, Natalia; Mavrommatis, Konstantinos; Chen, Amy; Palaniappan, Krishna; Hauser, Loren; Chang, Yun-Juan; Jefferies, Cynthia; Brettin, Thomas; Detter, John C.; Han, Cliff; Chain, Patrick; Tindall, Brian; Bristow, James; Eisen, Jonathan A.; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C.; Klenk, Hans-Peter

    2009-05-20

    Actinosynnema mirum Hasegawa et al. 1978 is the type species of the genus, and is of phylogenetic interest because of its central phylogenetic location in the Actino-synnemataceae, a rapidly growing family within the actinobacterial suborder Pseudo-nocardineae. A. mirum is characterized by its motile spores borne on synnemata and as a producer of nocardicin antibiotics. It is capable of growing aerobically and under a moderate CO2 atmosphere. The strain is a Gram-positive, aerial and substrate mycelium producing bacterium, originally isolated from a grass blade collected from the Raritan River, New Jersey. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first complete genome sequence of a member of the family Actinosynnemataceae, and only the second sequence from the actinobacterial suborder Pseudonocardineae. The 8,248,144 bp long single replicon genome with its 7100 protein-coding and 77 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

  2. Complete genome sequence of Halomicrobium mukohataei type strain (arg-2).

    PubMed

    Tindall, Brian J; Schneider, Susanne; Lapidus, Alla; Copeland, Alex; Glavina Del Rio, Tijana; Nolan, Matt; Lucas, Susan; Chen, Feng; Tice, Hope; Cheng, Jan-Fang; Saunders, Elizabeth; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Mikhailova, Natalia; Pati, Amrita; Ivanova, Natalia; Mavrommatis, Konstantinos; Chen, Amy; Palaniappan, Krishna; Chain, Patrick; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D; Brettin, Thomas; Han, Cliff; Rohde, Manfred; Göker, Markus; Bristow, Jim; Eisen, Jonathan A; Markowitz, Victor; Hugenholtz, Philip; Klenk, Hans-Peter; Kyrpides, Nikos C; Detter, John C

    2009-11-22

    Halomicrobium mukohataei (Ihara et al. 1997) Oren et al. 2002 is the type species of the genus Halomicrobium. It is of phylogenetic interest because of its isolated location within the large euryarchaeal family Halobacteriaceae. H. mukohataei is an extreme halophile that grows essentially aerobically, but can also grow anaerobically under a change of morphology and with nitrate as electron acceptor. The strain, whose genome is described in this report, is a free-living, motile, Gram-negative euryarchaeon, originally isolated from Salinas Grandes in Jujuy, Andes highlands, Argentina. Its genome contains three genes for the 16S rRNA that differ from each other by up to 9%. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence from the poorly populated genus Halomicrobium, and the 3,332,349 bp long genome (chromosome and one plasmid) with its 3416 protein-coding and 56 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

  3. Complete genome sequence of Actinosynnema mirum type strain (101T)

    SciTech Connect

    Land, Miriam L; Lapidus, Alla L.; Mayilraj, Shanmugam; Chen, Feng; Copeland, A; Glavina Del Rio, Tijana; Nolan, Matt; Lucas, Susan; Tice, Hope; Cheng, Jan-Fang; Chertkov, Olga; Bruce, David; Goodwin, Lynne A.; Pitluck, Sam; Rohde, Manfred; Goker, Markus; Pati, Amrita; Ivanova, N; Mavromatis, K; Chen, Amy; Palaniappan, Krishna; Hauser, Loren John; Chang, Yun-Juan; Jeffries, Cynthia; Brettin, Thomas S; Detter, J. Chris; Han, Cliff; Chain, Patrick S. G.; Tindall, Brian; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter

    2009-01-01

    Actinosynnema mirum Hasegawa et al. 1978 is the type species of the genus, and is of phylogenetic interest because of its central phylogenetic location in the Actino-synnemataceae, a rapidly growing family within the actinobacterial suborder Pseudo-nocardineae. A. mirum is characterized by its motile spores borne on synnemata and as a producer of nocardicin antibiotics. It is capable of growing aerobically and under a moderate CO2 atmosphere. The strain is a Gram-positive, aerial and substrate mycelium producing bacterium, originally isolated from a grass blade collected from the Raritan River, New Jersey. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first complete genome sequence of a member of the family Actinosynnemataceae, and only the second sequence from the actinobacterial suborder Pseudonocardineae. The 8,248,144 bp long single replicon genome with its 7100 protein-coding and 77 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

  4. Draft Genome Sequence of Tannerella forsythia Type Strain ATCC 43037.

    PubMed

    Friedrich, Valentin; Pabinger, Stephan; Chen, Tsute; Messner, Paul; Dewhirst, Floyd E; Schäffer, Christina

    2015-06-11

    Tannerella forsythia is an oral pathogen implicated in the development of periodontitis. Here, we report the draft genome sequence of the Tannerella forsythia strain ATCC 43037. The previously available genome of this designation (NCBI reference sequence NC_016610.1) was discovered to be derived from a different strain, FDC 92A2 (= ATCC BAA-2717).

  5. Molecular typing of Brucella melitensis endemic strains and differentiation from the vaccine strain Rev-1.

    PubMed

    Noutsios, Georgios T; Papi, Rigini M; Ekateriniadou, Loukia V; Minas, Anastasios; Kyriakidis, Dimitrios A

    2012-03-01

    In the present study forty-four Greek endemic strains of Br. melitensis and three reference strains were genotyped by Multi locus Variable Number Tandem Repeat (ML-VNTR) analysis based on an eight-base pair tandem repeat sequence that was revealed in eight loci of Br. melitensis genome. The forty-four strains were discriminated from the vaccine strain Rev-1 by Restriction Fragment Length Polymorphism (RFLP) and Denaturant Gradient Gel Electrophoresis (DGGE). The ML-VNTR analysis revealed that endemic, reference and vaccine strains are genetically closely related, while most of the loci tested (1, 2, 4, 5 and 7) are highly polymorphic with Hunter-Gaston Genetic Diversity Index (HGDI) values in the range of 0.939 to 0.775. Analysis of ML-VNTRs loci stability through in vitro passages proved that loci 1 and 5 are non stable. Therefore, vaccine strain can be discriminated from endemic strains by allele's clusters of loci 2, 4, 6 and 7. RFLP and DGGE were also employed to analyse omp2 gene and reveled different patterns among Rev-1 and endemic strains. In RFLP, Rev-1 revealed three fragments (282, 238 and 44 bp), while endemic strains two fragments (238 and 44 bp). As for DGGE, the electrophoretic mobility of Rev-1 is different from the endemic strains due to heterologous binding of DNA chains of omp2a and omp2b gene. Overall, our data show clearly that it is feasible to genotype endemic strains of Br. melitensis and differentiate them from vaccine strain Rev-1 with ML-VNTR, RFLP and DGGE techniques. These tools can be used for conventional investigations in brucellosis outbreaks.

  6. Complete genome sequence of Mycoplasma pneumoniae type 2a strain 309, isolated in Japan.

    PubMed

    Kenri, Tsuyoshi; Horino, Atsuko; Matsui, Mari; Sasaki, Yuko; Suzuki, Satowa; Narita, Mitsuo; Ohya, Hitomi; Okazaki, Norio; Shibayama, Keigo

    2012-03-01

    Mycoplasma pneumoniae strain 309, a type 2a (subtype 2 variant) strain of this bacterium, has variations in the P1 protein, which is responsible for attachment of the bacterium to host cells. Here, we report the complete genome sequence of M. pneumoniae strain 309 isolated from a pneumonia patient in Japan.

  7. Genome Sequence of the Thermophile Bacillus coagulans Hammer, the Type Strain of the Species

    PubMed Central

    Su, Fei; Tao, Fei; Tang, Hongzhi

    2012-01-01

    Here we announce a 3.0-Mb assembly of the Bacillus coagulans Hammer strain, which is the type strain of the species within the genus Bacillus. Genomic analyses based on the sequence may provide insights into the phylogeny of the species and help to elucidate characteristics of the poorly studied strains of Bacillus coagulans. PMID:23105047

  8. Monoclonal antibody typing of Chlamydia psittaci strains derived from avian and mammalian species.

    PubMed Central

    Fukushi, H; Nojiri, K; Hirai, K

    1987-01-01

    A total of 77 Chlamydia psittaci strains of avian, human, and mammalian origin were grouped into four serovars with 11 monoclonal antibodies recognizing the lipopolysaccharide and the major outer membrane protein antigens. The avian and human strains, which were closely related to each other, were distinct from the mammalian strains. Immunological typing of C. psittaci with monoclonal antibodies seems practical. PMID:3667918

  9. Genome sequence of the thermophile Bacillus coagulans Hammer, the type strain of the species.

    PubMed

    Su, Fei; Tao, Fei; Tang, Hongzhi; Xu, Ping

    2012-11-01

    Here we announce a 3.0-Mb assembly of the Bacillus coagulans Hammer strain, which is the type strain of the species within the genus Bacillus. Genomic analyses based on the sequence may provide insights into the phylogeny of the species and help to elucidate characteristics of the poorly studied strains of Bacillus coagulans.

  10. Multilocus sequence typing reveals that Bacillus cereus strains isolated from clinical infections have distinct phylogenetic origins.

    PubMed

    Barker, Margaret; Thakker, Bishan; Priest, Fergus G

    2005-04-01

    Eight strains of Bacillus cereus isolated from bacteremia and soft tissue infections were assigned to seven sequence types (STs) by multilocus sequence typing (MLST). Two strains from different locations had identical STs. The concatenated sequences of the seven STs were aligned with 65 concatenated sequences from reference STs and a neighbor-joining tree was constructed. Two strains were distantly related to all reference STs. Three strains were recovered in a clade that included Bacillus anthracis, B. cereus and rare Bacillus thuringiensis strains while the other three strains were assigned to two STs that were more closely affiliated to most of the B. thuringiensis STs. We conclude that invasive B. cereus strains do not form a single clone or clonal complex of highly virulent strains.

  11. Strain typing of acetic acid bacteria responsible for vinegar production by the submerged elaboration method.

    PubMed

    Fernández-Pérez, Rocío; Torres, Carmen; Sanz, Susana; Ruiz-Larrea, Fernanda

    2010-12-01

    Strain typing of 103 acetic acid bacteria isolates from vinegars elaborated by the submerged method from ciders, wines and spirit ethanol, was carried on in this study. Two different molecular methods were utilised: pulsed field gel electrophoresis (PFGE) of total DNA digests with a number of restriction enzymes, and enterobacterial repetitive intergenic consensus (ERIC) - PCR analysis. The comparative study of both methods showed that restriction fragment PFGE of SpeI digests of total DNA was a suitable method for strain typing and for determining which strains were present in vinegar fermentations. Results showed that strains of the species Gluconacetobacter europaeus were the most frequent leader strains of fermentations by the submerged method in the studied vinegars, and among them strain R1 was the predominant one. Results showed as well that mixed populations (at least two different strains) occurred in vinegars from cider and wine, whereas unique strains were found in spirit vinegars, which offered the most stressing conditions for bacterial growth.

  12. Discriminatory Indices of Typing Methods for Epidemiologic Analysis of Contemporary Staphylococcus aureus Strains.

    PubMed

    Rodriguez, Marcela; Hogan, Patrick G; Satola, Sarah W; Crispell, Emily; Wylie, Todd; Gao, Hongyu; Sodergren, Erica; Weinstock, George M; Burnham, Carey-Ann D; Fritz, Stephanie A

    2015-09-01

    Historically, a number of typing methods have been evaluated for Staphylococcus aureus strain characterization. The emergence of contemporary strains of community-associated S. aureus, and the ensuing epidemic with a predominant strain type (USA300), necessitates re-evaluation of the discriminatory power of these typing methods for discerning molecular epidemiology and transmission dynamics, essential to investigations of hospital and community outbreaks. We compared the discriminatory index of 5 typing methods for contemporary S. aureus strain characterization. Children presenting to St. Louis Children's Hospital and community pediatric practices in St. Louis, Missouri (MO), with community-associated S. aureus infections were enrolled. Repetitive sequence-based PCR (repPCR), pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), staphylococcal protein A (spa), and staphylococcal cassette chromosome (SCC) mec typing were performed on 200 S. aureus isolates. The discriminatory index of each method was calculated using the standard formula for this metric, where a value of 1 is highly discriminatory and a value of 0 is not discriminatory. Overall, we identified 26 distinct strain types by repPCR, 17 strain types by PFGE, 30 strain types by MLST, 68 strain types by spa typing, and 5 strain types by SCCmec typing. RepPCR had the highest discriminatory index (D) of all methods (D = 0.88), followed by spa typing (D = 0.87), MLST (D = 0.84), PFGE (D = 0.76), and SCCmec typing (D = 0.60). The method with the highest D among MRSA isolates was repPCR (D = 0.64) followed by spa typing (D = 0.45) and MLST (D = 0.44). The method with the highest D among MSSA isolates was spa typing (D = 0.98), followed by MLST (D = 0.93), repPCR (D = 0.92), and PFGE (D = 0.89). Among isolates designated USA300 by PFGE, repPCR was most discriminatory, with 10 distinct strain types identified (D = 0.63). We identified 45

  13. Discriminatory Indices of Typing Methods for Epidemiologic Analysis of Contemporary Staphylococcus aureus Strains

    PubMed Central

    Rodriguez, Marcela; Hogan, Patrick G.; Satola, Sarah W.; Crispell, Emily; Wylie, Todd; Gao, Hongyu; Sodergren, Erica; Weinstock, George M.; Burnham, Carey-Ann D.; Fritz, Stephanie A.

    2015-01-01

    Abstract Historically, a number of typing methods have been evaluated for Staphylococcus aureus strain characterization. The emergence of contemporary strains of community-associated S. aureus, and the ensuing epidemic with a predominant strain type (USA300), necessitates re-evaluation of the discriminatory power of these typing methods for discerning molecular epidemiology and transmission dynamics, essential to investigations of hospital and community outbreaks. We compared the discriminatory index of 5 typing methods for contemporary S. aureus strain characterization. Children presenting to St. Louis Children's Hospital and community pediatric practices in St. Louis, Missouri (MO), with community-associated S. aureus infections were enrolled. Repetitive sequence-based PCR (repPCR), pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), staphylococcal protein A (spa), and staphylococcal cassette chromosome (SCC) mec typing were performed on 200 S. aureus isolates. The discriminatory index of each method was calculated using the standard formula for this metric, where a value of 1 is highly discriminatory and a value of 0 is not discriminatory. Overall, we identified 26 distinct strain types by repPCR, 17 strain types by PFGE, 30 strain types by MLST, 68 strain types by spa typing, and 5 strain types by SCCmec typing. RepPCR had the highest discriminatory index (D) of all methods (D = 0.88), followed by spa typing (D = 0.87), MLST (D = 0.84), PFGE (D = 0.76), and SCCmec typing (D = 0.60). The method with the highest D among MRSA isolates was repPCR (D = 0.64) followed by spa typing (D = 0.45) and MLST (D = 0.44). The method with the highest D among MSSA isolates was spa typing (D = 0.98), followed by MLST (D = 0.93), repPCR (D = 0.92), and PFGE (D = 0.89). Among isolates designated USA300 by PFGE, repPCR was most discriminatory, with 10 distinct strain types identified (D = 0.63). We

  14. Complete Genome Sequence of the Mycobacterium immunogenum Type Strain CCUG 47286

    PubMed Central

    Jaén-Luchoro, Daniel; Seguí, Carolina; Aliaga-Lozano, Francisco; Salvà-Serra, Francisco; Busquets, Antonio; Gomila, Margarita; Ramírez, Antonio; Ruiz, Mikel; Lalucat, Jorge

    2016-01-01

    Here, we report the complete genome sequence of Mycobacterium immunogenum type strain CCUG 47286, a nontuberculous mycobacterium. The whole genome has 5,573,781 bp and covers as many as 5,484 predicted genes. This genome contributes to the task of closing the still-existing gap of genomes of rapidly growing mycobacterial type strains. PMID:27231356

  15. ELECTROPHORETIC MOBILITIES OF ESCHERICHIA COLI 0157:H7 AND WILD-TYPE ESCHERICHIA COLI STRAINS

    EPA Science Inventory

    The electrophoretic mobility (EPM) of a number of human-virulent and "wild-type" Escherichia coli strains in phosphate buffered water was measured. The impact of pH, ionic strength, cation type (valence) and concentration, and bacterial strain on the EPM was investigated. Resul...

  16. Association of Ocular Toxoplasmosis with Type I Toxoplasma gondii Strains: Direct Genotyping from Peripheral Blood Samples▿

    PubMed Central

    Switaj, Karolina; Master, Adam; Borkowski, Piotr Karol; Skrzypczak, Magdalena; Wojciechowicz, Jacek; Zaborowski, Piotr

    2006-01-01

    Toxoplasma gondii strains were genotyped directly from blood samples of patients with ocular toxoplasmosis. Analysis of nontranscribed spacer 2 revealed that all detected strains belonged to type I, suggesting an association of ocular toxoplasmosis with this type. The method shows the usefulness of blood samples for genotyping in ocular toxoplasmosis. PMID:17005742

  17. Phylogeny and identification of Pantoea species and typing of Pantoea agglomerans strains by multilocus gene sequencing.

    PubMed

    Delétoile, Alexis; Decré, Dominique; Courant, Stéphanie; Passet, Virginie; Audo, Jennifer; Grimont, Patrick; Arlet, Guillaume; Brisse, Sylvain

    2009-02-01

    Pantoea agglomerans and other Pantoea species cause infections in humans and are also pathogenic to plants, but the diversity of Pantoea strains and their possible association with hosts and disease remain poorly known, and identification of Pantoea species is difficult. We characterized 36 Pantoea strains, including 28 strains of diverse origins initially identified as P. agglomerans, by multilocus gene sequencing based on six protein-coding genes, by biochemical tests, and by antimicrobial susceptibility testing. Phylogenetic analysis and comparison with other species of Enterobacteriaceae revealed that the genus Pantoea is highly diverse. Most strains initially identified as P. agglomerans by use of API 20E strips belonged to a compact sequence cluster together with the type strain, but other strains belonged to diverse phylogenetic branches corresponding to other species of Pantoea or Enterobacteriaceae and to probable novel species. Biochemical characteristics such as fosfomycin resistance and utilization of d-tartrate could differentiate P. agglomerans from other Pantoea species. All 20 strains of P. agglomerans could be distinguished by multilocus sequence typing, revealing the very high discrimination power of this method for strain typing and population structure in this species, which is subdivided into two phylogenetic groups. PCR detection of the repA gene, associated with pathogenicity in plants, was positive in all clinical strains of P. agglomerans, suggesting that clinical and plant-associated strains do not form distinct populations. We provide a multilocus gene sequencing method that is a powerful tool for Pantoea species delineation and identification and for strain tracking.

  18. Production of toxin by Clostridium botulinum type A strains cured by plasmids.

    PubMed Central

    Weickert, M J; Chambliss, G H; Sugiyama, H

    1986-01-01

    Twelve strains of Clostridium botulinum type A and seven strains of Clostridium sporogenes were screened for plasmids by agarose gel electrophoresis of cleared lysates of cells from 5 ml of mid-log-phase culture. Nine type A strains had one or more plasmids of 4.3, 6.8, or 36 megadaltons (MDa); several strains showed a large plasmid of 61 MDa, but it was not consistently recovered. Four C. sporogenes strains had one or more plasmids of 4.3, 5.6 or 36 MDa. Isolates obtained from cultures of plasmid-containing C. botulinum type A strains grown in ionic detergent broth and from spontaneously arising variants were screened both for toxin production and for plasmid content. Toxigenicity of C. botulinum could not be correlated with the presence of any one plasmid. Images PMID:3082278

  19. Vibrio pelagius: differences of the type strain deposited at various culture collections.

    PubMed

    Macián, M C; Ludwig, W; Schleifer, K H; Garay, E; Pujalte, M J

    2000-10-01

    A critical evaluation of published and own taxonomic and phylogenetic studies on Vibrio pelagius showed substantial diversity of strains received as type strains from various Culture Collections. The comparison of data based upon 16S rRNA sequence analyses, earlier genomic DNA-DNA similarity studies as well as physiological investigations and the original description indicate that Vibrio pelagius strains CECT 4202T and ATCC 25916T really represent the originally described type species whereas strains NCIMB 1900T and CIP 102762T highly likely are representatives of Vibrio natriegens.

  20. Complete genome sequence of Mesorhizobium opportunistum type strain WSM2075

    SciTech Connect

    Reeve, Wayne; Nandesena, Kemanthi; YatesIII, John R.; Tiwari, Ravi; O'Hara, Graham; Ninawi, Mohamed; Chertkov, Olga; Goodwin, Lynne A.; Bruce, David; Detter, J. Chris; Tapia, Roxanne; Han, Cliff; Woyke, Tanja; Pitluck, Sam; Nolan, Matt; Land, Miriam L; Copeland, A; Liolios, Konstantinos; Pati, Amrita; Mavromatis, K; Markowitz, Victor; Kyrpides, Nikos C; Ivanova, N; Meenakshi, Uma; Howieson, John

    2013-01-01

    Mesorhizobium opportunistum strain WSM2075T was isolated inWestern Australia in 2000 from root nodules of the pasture legume Biserrula pelecinus that had beeninoculated with M. ciceri bv. biserrulae WSM1271. WSM2075T is an aerobic, motile, Gram negative, non-spore-forming rod that has gained the ability to nodulate B. pelecinus but is completely ineffective in N2 fixation with this host. This report reveals thegenome of M. opportunistum strain WSM2075T contains a chromosome ofsize 6,884,444 bp which encodes 6,685 protein-coding genes and 62 RNA-onlyencoding genes. This genome does not contain any plasmids but has a 455.7 kbgenomic island from Mesorhizobium ciceri bv. biserrulae WSM1271 that has been integrated into a phenylalanine-tRNA gene.

  1. Genomic Encyclopedia of Bacterial and Archaeal Type Strains, Phase III: the genomes of soil and plant-associated and newly described type strains.

    PubMed

    Whitman, William B; Woyke, Tanja; Klenk, Hans-Peter; Zhou, Yuguang; Lilburn, Timothy G; Beck, Brian J; De Vos, Paul; Vandamme, Peter; Eisen, Jonathan A; Garrity, George; Hugenholtz, Philip; Kyrpides, Nikos C

    2015-01-01

    The Genomic Encyclopedia of Bacteria and Archaea (GEBA) project was launched by the JGI in 2007 as a pilot project to sequence about 250 bacterial and archaeal genomes of elevated phylogenetic diversity. Herein, we propose to extend this approach to type strains of prokaryotes associated with soil or plants and their close relatives as well as type strains from newly described species. Understanding the microbiology of soil and plants is critical to many DOE mission areas, such as biofuel production from biomass, biogeochemistry, and carbon cycling. We are also targeting type strains of novel species while they are being described. Since 2006, about 630 new species have been described per year, many of which are closely aligned to DOE areas of interest in soil, agriculture, degradation of pollutants, biofuel production, biogeochemical transformation, and biodiversity.

  2. Draft Genome Sequences for Two Metal-Reducing Pelosinus fermentans Strains Isolated from a Cr(VI) Contaminated Site and for Type Strain R7

    SciTech Connect

    Brown, Steven D; Podar, Mircea; Klingeman, Dawn Marie; Johnson, Courtney M; Yang, Zamin Koo; Utturkar, Sagar M; Land, Miriam L; Mosher, Jennifer J; Hurt, Jr., Richard Ashley; Phelps, Tommy Joe; Palumbo, Anthony Vito; Arkin, Adam; Hazen, Terry C; Elias, Dwayne A

    2012-01-01

    Pelosinus fermentans 16S rRNA gene sequences have been reported from diverse geographical sites since the recent isolation of the type strain. We present the genome sequence of the P. fermentans type strain R7 (DSM 17108) and genome sequences for two new strains with different abilities to reduce iron, chromate, and uranium.

  3. The Houghton strain of Eimeria tenella: a review of the type strain selected for genome sequencing.

    PubMed

    Chapman, H D; Shirley, M W

    2003-04-01

    A landmark decision was taken in 2002 by the Biotechnology and Biological Sciences Research Council (BBSRC) in the UK to fund the genome sequencing of an eimerian (apicomplexan) parasite from the fowl. The project is a joint collaboration between the Institute for Animal Health (IAH) at Compton, UK and the Wellcome Trust Sanger Institute, Cambridge, UK (see http://www.sanger.ac.uk/Projects/E_tenella/ and http://www.iah.bbsrc.ac.uk/eimeria/). The species chosen, Eimeria tenella, is the best known member of the genus and the Houghton (H) strain is one of the most widely studied. The H strain was isolated in 1949 in the UK. It was maintained initially at the Houghton Poultry Research Station (HPRS), Houghton, and, following closure of that laboratory in 1992, thereafter at the IAH in Compton. At various times the parasite has been provided to other institutions and research groups carrying out coccidiosis research in the fowl. The H strain has been utilised in many fundamental studies on the eimerian life cycle and its relationship with the host. It has also been used to investigate the nature of drug resistance, and to derive attenuated lines-one of which, a "precocious line", is a component of a multivalent live attenuated coccidiosis vaccine (Paracox vaccine, Schering-Plough Animal Health). In this article, some immunological, epidemiological, genetic, and chemotherapeutic investigations with the H strain are reviewed, a summary is provided of the biological characteristics of the parasite and some of the core methods used to prepare purified extracellular life cycle stages for experimental studies or passage are given.

  4. Complete genome sequence of Methanospirillum hungatei type strain JF1

    DOE PAGES

    Gunsalus, Robert; Cook, Lauren E.; Crable, Bryan R.; ...

    2016-01-06

    Methanospirillum hungatei strain JF1 is a hydrogenotrophic methanogen that belongs to the order Methanomicrobiales. Members of the genus Methanospirillum are commonly encountered in syntrophic association with fermenting microorganisms. M. hungatei serves as the model partner organism in laboratory cocultures that syntrophically oxidize fatty and aromatic acids. Furthermore, when grown syntrophically, M. hungatei rapidly uses the hydrogen or formate produced by its syntrophic partner and maintains the concentration of these metabolites at very low levels so that the degradation of the syntrophic substrate is thermodynamically favorable.

  5. Interfacial strain effect on type-I and type-II core/shell quantum dots

    NASA Astrophysics Data System (ADS)

    Gheshlaghi, Negar; Pisheh, Hadi Sedaghat; Karim, M. Rezaul; Malkoc, Derya; Ünlü, Hilmi

    2016-09-01

    A comparative experimental and theoretical study on the calculation of capped core diameter in ZnSe/ZnS, CdSe/Cd(Zn)S type-I and ZnSe/CdS type-II core/shell nanocrystals is presented. The lattice mismatch induced interface strain between core and shell was calculated from continuum elastic theory and applied in effective mass approximation method to obtain the corresponding capped core diameter. The calculated results were compared with diameter of bare cores (CdSe and ZnSe) from transmission electron microscopy images to obtain the amount of the stretched or squeezed core after deposition of tensile or compressive shells. The result of the study showed that the core is squeezed in ZnSe/ZnS and CdSe/Cd(Zn)S after compressive shell and stretched in ZnSe/CdS after tensile shell deposition. The stretched and squeezed amount of the capped core found to be in proportion with lattice mismatch amount in the core/shell structure.

  6. Complete genome sequence of Staphylothermus marinus Stetter and Fiala 1986 type strain F1

    SciTech Connect

    Anderson, Iain; Sun, Hui; Lapidus, Alla L.; Copeland, A; Glavina Del Rio, Tijana; Tice, Hope; Dalin, Eileen; Lucas, Susan; Barry, Kerrie; Land, Miriam L; Richardson, P M; Huber, Harald; Kyrpides, Nikos C

    2009-01-01

    Staphylothermus marinus Fiala and Stetter 1986 belongs to the order Desulfurococcales within the archaeal phylum Crenarchaeota. S. marinus is a hyperthermophilic, sulfur-dependent, anaerobic heterotroph. Strain F1 was isolated from geothermally heated sediments at Vulcano, Italy, but S. marinus has also been isolated from a hydrothermal vent on the East Pacific Rise. We report the complete genome of S. marinus strain F1, the type strain of the species. This is the fifth reported complete genome sequence from the order Desulfurococcales.

  7. Experimental infection of specific pathogen free piglets with French strains of Streptococcus suis capsular type 2.

    PubMed Central

    Berthelot-Hérault, F; Cariolet, R; Labbé, A; Gottschalk, M; Cardinal, J Y; Kobisch, M

    2001-01-01

    A standardized model of Streptococcus suis type 2 infection in specific-pathogen-free piglets, housed in high-security barns, was used to compare the virulence of 3 French field strains of S. suis serotype 2 isolated from tonsils of a healthy pig (strain 65) or from diseased pigs (meningitis, strain 166', or septicemia, strain 24). In one of the 2 trials, 7-week-old pigs, in 3 groups of 8, were inoculated intravenously with 2 x 10(8) colony-forming units of S. suis type 2. In each group, 1 uninfected animal was a sentinel. Eight animals were also used as negative control group. The experiment was repeated under similar conditions with strains 65 and 166'. Virulence differed markedly among these S. suis strains when clinical signs, zootechnical performances, lesions, and bacteriological data were analyzed. Strain 65 did not induce clinical signs in inoculated pigs. In contrast, pigs infected with the other 2 strains exhibited clinical signs and typical lesions of S. suis type 2 infections. Differences in virulence were also observed between the 2 virulent strains. Sentinel animals exhibited the same manifestations as those recorded in inoculated piglets. Results were similar in the second trial, indicating that under the present experimental conditions, results were reproducible. The standardized conditions described in this study could be a useful tool to further study about the S. suis infection. PMID:11480526

  8. Draft Genome Sequences of Mycobacterium setense Type Strain DSM-45070 and the Nonpathogenic Strain Manresensis, Isolated from the Bank of the Cardener River in Manresa, Catalonia, Spain

    PubMed Central

    Vilaplana, Cristina; Velasco, Juan; Pluvinet, Raquel; Santín, Sheila; Prat, Cristina; Julián, Esther; Alcaide, Fernando; Comas, Iñaki; Sumoy, Lauro; Cardona, Pere-Joan

    2015-01-01

    We present here the draft genome sequences of two Mycobacterium setense strains. One of them corresponds to the M. setense type strain DSM-45070, originally isolated from a patient with a posttraumatic chronic skin abscess. The other one corresponds to the nonpathogenic M. setense strain Manresensis, isolated from the Cardener River crossing Manresa, Catalonia, Spain. A comparative genomic analysis shows a smaller genome size and fewer genes in M. setense strain Manresensis relative to those of the type strain, and it shows the genome segments unique to each strain. PMID:25657273

  9. High-resolution typing reveals distinct Chlamydia trachomatis strains in an at-risk population in Nanjing, China.

    PubMed

    Bom, Reinier J M; van den Hoek, Anneke; Wang, Qianqiu; Long, Fuquan; de Vries, Henry J C; Bruisten, Sylvia M

    2013-08-01

    We investigated Chlamydia trachomatis strains from Nanjing, China, and whether these strains differed from Amsterdam, the Netherlands. C. trachomatis type was determined with multilocus sequence typing. Most strains were specific to Nanjing, but some clustered with strains from Amsterdam. This demonstrates a geographical variation in C. trachomatis previously left undetected.

  10. Typing of Streptococcus mutans strains isolated from caries free and susceptible subjects by multilocus enzyme electrophoresis.

    PubMed

    Tahmourespour, Arezoo; Nabinejad, Abdolreza; Shirian, Hannaneh; Rosa, Edvaldo Antonio Ribeiro; Tahmourespour, Sanaz

    2013-01-01

    This study was evaluated the clonal diversity of Streptococcus mutans in caries-free and caries-active subjects using MLEE. Strains from caries-free subjects were grouped in a single taxon. Unrooted dendrogram showed that different strains clustered in four different clades, also showed that more than one clonal type can be found in a same individual.

  11. Draft Whole-Genome Sequence of the Type Strain Bacillus horikoshii DSM 8719.

    PubMed

    Hernández-González, Ismael L; Olmedo-Álvarez, Gabriela

    2016-07-14

    Members of the Bacillus genus have been extensively studied because of their ability to produce enzymes with high biotechnological value. Here, we report the draft of the whole-genome sequence of the type strain Bacillus horikoshii DSM 8719, an alkali-tolerant strain.

  12. Draft Genome Sequence of a Klebsiella pneumoniae Strain (New Sequence Type 2357) Carrying Tn3926

    PubMed Central

    Mi, Zu-huang; Wang, Chun-xin; Zhu, Jian-ming

    2016-01-01

    We present the draft genome sequence of a Klebsiella pneumoniae carbapenemase–producing sequence type 2357 (ST2357) strain, NB60, which contains drug-resistant genes encoding resistance to beta-lactams, fluoroquinolones, aminoglycosides, trimethoprim-sulfamethoxazole, colistin, macrolides, and tetracycline. Strain NB60 was isolated from human blood, making it an important tool for studying K. pneumoniae pathogenesis. PMID:27660779

  13. Draft Whole-Genome Sequence of the Type Strain Bacillus horikoshii DSM 8719

    PubMed Central

    Hernández-González, Ismael L.

    2016-01-01

    Members of the Bacillus genus have been extensively studied because of their ability to produce enzymes with high biotechnological value. Here, we report the draft of the whole-genome sequence of the type strain Bacillus horikoshii DSM 8719, an alkali-tolerant strain. PMID:27417833

  14. Genome sequence of Brucella melitensis strain 128, an isolate of biovar 3 of sequence type 8.

    PubMed

    Li, Tiefeng; Yuan, Xitong; Ding, Jiabo; Zhen, Qing; Ke, Yuehua; Wang, Yufei; Huang, Liuyu; Mao, Kairong; Chen, Zeliang; Wang, Dali

    2012-12-01

    Brucella melitensis is the most common Brucella species causing human brucellosis. B. melitensis is divided into 3 biovars. Here, we report the complete genome sequence of B. melitensis strain 128, a strain of biovar 3 of sequence type 8, which is prevalent in China.

  15. Complete genome sequence of Desulfotomaculum acetoxidans type strain (5575).

    PubMed

    Spring, Stefan; Lapidus, Alla; Schröder, Maren; Gleim, Dorothea; Sims, David; Meincke, Linda; Glavina Del Rio, Tijana; Tice, Hope; Copeland, Alex; Cheng, Jan-Fang; Lucas, Susan; Chen, Feng; Nolan, Matt; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Ivanova, Natalia; Mavromatis, Konstantinos; Mikhailova, Natalia; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D; Chain, Patrick; Saunders, Elizabeth; Brettin, Thomas; Detter, John C; Göker, Markus; Bristow, Jim; Eisen, Jonathan A; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter; Han, Cliff

    2009-11-22

    Desulfotomaculum acetoxidans Widdel and Pfennig 1977 was one of the first sulfate-reducing bacteria known to grow with acetate as sole energy and carbon source. It is able to oxidize substrates completely to carbon dioxide with sulfate as the electron acceptor, which is reduced to hydrogen sulfide. All available data about this species are based on strain 5575(T), isolated from piggery waste in Germany. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of a Desulfotomaculum species with validly published name. The 4,545,624 bp long single replicon genome with its 4370 protein-coding and 100 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  16. Complete genome sequence of Desulfotomaculum acetoxidans type strain (5575T)

    SciTech Connect

    Spring, Stefan; Lapidus, Alla L.; Schroder, Maren; Gleim, Dorothea; Sims, David; Meincke, Linda; Glavina Del Rio, Tijana; Tice, Hope; Copeland, A; Cheng, Jan-Fang; Chen, Feng; Lucas, Susan; Nolan, Matt; Bruce, David; Goodwin, Lynne A.; Pitluck, Sam; Ivanova, N; Mavromatis, K; Mikhailova, Natalia; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam L; Hauser, Loren John; Chang, Yun-Juan; Jeffries, Cynthia; Chain, Patrick S. G.; Saunders, Elizabeth H; Brettin, Tom; Detter, J. Chris; Goker, Markus; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter; Han, Cliff

    2009-01-01

    Desulfotomaculum acetoxidans Widdel and Pfennig 1977 was one of the first sulfate-reducing bacteria known to grow with acetate as sole energy and carbon source. It is able to oxidize substrates completely to carbon dioxide with sulfate as the electron acceptor, which is reduced to hydrogen sulfide. All available data about this species are based on strain 5575T, isolated from piggery waste in Germany. Here we describe the features of this organ-ism, together with the complete genome sequence and annotation. This is the first completed genome sequence of a Desulfotomaculum species with validly published name. The 4,545,624 bp long single replicon genome with its 4370 protein-coding and 100 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  17. Complete Genome Sequence of Type Strain Campylobacter fetus subsp. fetus ATCC 27374

    PubMed Central

    Oliveira, Luciana M.; Resende, Daniela M.; Dorneles, Elaine M. S.; Horácio, Elvira C. A.; Alves, Fernanda L.; Gonçalves, Leilane O.; Tavares, Grace S.; Stynen, Ana Paula R.; Lage, Andrey P.

    2016-01-01

    Campylobacter fetus subsp. fetus is a zoonotic bacterium important for animal and public health. The complete sequencing and annotation of the genome of the type strain C. fetus subsp. fetus ATCC 27374 are reported here. PMID:27979934

  18. Complete Genome Sequence of Type Strain Campylobacter fetus subsp. fetus ATCC 27374.

    PubMed

    Oliveira, Luciana M; Resende, Daniela M; Dorneles, Elaine M S; Horácio, Elvira C A; Alves, Fernanda L; Gonçalves, Leilane O; Tavares, Grace S; Stynen, Ana Paula R; Lage, Andrey P; Ruiz, Jeronimo C

    2016-12-15

    Campylobacter fetus subsp. fetus is a zoonotic bacterium important for animal and public health. The complete sequencing and annotation of the genome of the type strain C. fetus subsp. fetus ATCC 27374 are reported here.

  19. Whole genome sequence of Enterobacter ludwigii type strain EN-119T, isolated from clinical specimens.

    PubMed

    Li, Gengmi; Hu, Zonghai; Zeng, Ping; Zhu, Bing; Wu, Lijuan

    2015-04-01

    Enterobacter ludwigii strain EN-119(T) is the type strain of E. ludwigii, which belongs to the E. cloacae complex (Ecc). This strain was first reported and nominated in 2005 and later been found in many hospitals. In this paper, the whole genome sequencing of this strain was carried out. The total genome size of EN-119(T) is 4952,770 bp with 4578 coding sequences, 88 tRNAs and 10 rRNAs. The genome sequence of EN-119(T) is the first whole genome sequence of E. ludwigii, which will further our understanding of Ecc.

  20. Diffusion and persistence of multidrug resistant Salmonella Typhimurium strains phage type DT120 in southern Italy.

    PubMed

    De Vito, Danila; Monno, Rosa; Nuccio, Federica; Legretto, Marilisa; Oliva, Marta; Coscia, Maria Franca; Dionisi, Anna Maria; Calia, Carla; Capolongo, Carmen; Pazzani, Carlo

    2015-01-01

    Sixty-two multidrug resistant Salmonella enterica serovar Typhimurium strains isolated from 255 clinical strains collected in Southern Italy in 2006-2008 were characterised for antimicrobial resistance genes, pulsotype, and phage type. Most strains (83.9%) were resistant to ampicillin, chloramphenicol, streptomycin, sulfamethoxazole, and tetracycline (ACSSuT) encoded in 88.5% by the Salmonella genomic island (SGI1) and in 11.5% by the InH-like integron (bla OXA-30-aadA1) and catA1, sul1, and tet(B) genes. STYMXB.0061 (75%) and DT120 (84.6%) were the prevalent pulsotype and phage type identified in these strains, respectively. Five other resistance patterns were found either in single or in a low number of isolates. The pandemic clone DT104 (ACSSuT encoded by SGI1) has been identified in Italy since 1992, while strains DT120 (ACSSuT encoded by SGI1) have never been previously reported in Italy. In Europe, clinical strains DT120 have been reported from sporadic outbreaks linked to the consumption of pork products. However, none of these strains were STYMXB.0061 and SGI1 positive. The prevalent identification and persistence of DT120 isolates would suggest, in Southern Italy, a phage type shifting of the pandemic DT104 clone pulsotype STYMXB.0061. Additionally, these findings raise epidemiological concern about the potential diffusion of these emerging multidrug resistant (SGI linked) DT120 strains.

  1. Analysis of chromosome-sized DNA and genome typing of isolated strains of Taylorella equigenitalis.

    PubMed

    Matsuda, M; Asami, Y; Miyazawa, T; Samata, T; Isayama, Y; Honda, M; Ide, Y

    1994-01-01

    Analysis of chromosome-sized DNA and genome typing of Taylorella equigenitalis NCTC11184, Kentucky 188, and five strains of T. equigenitalis isolated in Japan were carried out. The three restriction enzymes used, ApaI, NaeI and NotI, cleaved the genomic DNAs of five Japanese strains of T. equigenitalis into relatively limited numbers of restriction fragments, which were well resolved on crossed-field gel electrophoresis (CFGE). The respective profiles after CFGE of the restriction fragments from all five strains were essentially identical to each other after digestion by ApaI, NaeI or NotI. Hence it appears that these strains have a common genome type with respect to these three restriction enzymes. It was also shown that the respective profiles from these strains were essentially different from those of T. equigenitalis NCTC11184 and those of Kentucky 188 after digestion with ApaI, NaeI or NotI.

  2. Regulation of oxygen vacancy types on SnO2 (110) surface by external strain

    NASA Astrophysics Data System (ADS)

    Zhou, Z. H.; Min, Y. M.; Liu, X. X.; Ding, J. Q.; Guo, J. H.; Hu, F. R.; Liu, L. Z.

    2016-05-01

    In tin dioxide nanostructures, oxygen vacancies (OVs) play an important role in their optical properties and thus regulation of both OV concentration and type via external strain is crucial to exploration of more applications. First-principle calculations of SnO2 (110) surface disclose that asymmetric deformations induced by external strain not only lead to its intrinsic surface elastic changes, but also result in different OV formation energy. In the absence of external strain, the energetically favorable oxygen vacancies(EFOV) appear in the bridging site of second layer. When -3.5% external strain is applied along y direction, the EFOV moves into plane site. This can be ascribed that the compressed deformation gives rise to redistribution of electronic wave function near OVs, therefore, formation of newly bond structures. Our results suggest that different type OVs in SnO2 surface can be controlled by strain engineering.

  3. Dual toxin-producing strain of Clostridium botulinum type Bf isolated from a California patient with infant botulism.

    PubMed

    Barash, Jason R; Arnon, Stephen S

    2004-04-01

    A retrospective study of Clostridium botulinum strains isolated from patients from California with infant botulism identified the fourth known C. botulinum strain that produces both type B and type F botulinum toxins. This unique strain represented 0.12% of the California infant botulism case isolates from 1976 to 2003. The relative concentrations of type B and F toxins produced were temperature dependent.

  4. Complete genome sequence of Nocardiopsis dassonvillei type strain (IMRU 509).

    PubMed

    Sun, Hui; Lapidus, Alla; Nolan, Matt; Lucas, Susan; Del Rio, Tijana Glavina; Tice, Hope; Cheng, Jan-Fang; Tapia, Roxane; Han, Cliff; Goodwin, Lynne; Pitluck, Sam; Pagani, Ioanna; Ivanova, Natalia; Mavromatis, Konstantinos; Mikhailova, Natalia; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D; Djao, Olivier Duplex Ngatchou; Rohde, Manfred; Sikorski, Johannes; Göker, Markus; Woyke, Tanja; Bristow, James; Eisen, Jonathan A; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter

    2010-11-30

    Nocardiopsis dassonvillei (Brocq-Rousseau 1904) Meyer 1976 is the type species of the genus Nocardiopsis, which in turn is the type genus of the family Nocardiopsaceae. This species is of interest because of its ecological versatility. Members of N. dassonvillei have been isolated from a large variety of natural habitats such as soil and marine sediments, from different plant and animal materials as well as from human patients. Moreover, representatives of the genus Nocardiopsis participate actively in biopolymer degradation. This is the first complete genome sequence in the family Nocardiopsaceae. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 6,543,312 bp long genome consist of a 5.77 Mbp chromosome and a 0.78 Mbp plasmid and with its 5,570 protein-coding and 77 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  5. Draft Genome Sequences for Clostridium thermocellum Wild-Type Strain YS and Derived Cellulose Adhesion-Defective Mutant Strain AD2

    SciTech Connect

    Brown, Steven D; Lamed, Raphael; Morag, Ely; Borovok, Ilya; Shoham, Yuval; Klingeman, Dawn Marie; Johnson, Courtney M; Yang, Zamin; Land, Miriam L; Utturkar, Sagar M; Keller, Martin; Bayer, Edward A

    2012-01-01

    Clostridium thermocellum wild-type strain YS is an anaerobic, thermophilic, cellulolytic bacterium capable of directly converting cellulosic substrates into ethanol. Strain YS and a derived cellulose adhesion-defective mutant strain AD2 played pivotal roles in describing the original cellulosome concept. We present their draft genome sequences.

  6. A qPCR method to characterize the sex type of the cell strains from rats.

    PubMed

    Xiang, Junbei; Li, Zhilin; Wan, Qian; Chen, Qiang; Liu, Mianxue; Jiang, Xiaohui; Xie, Linfeng

    2016-10-01

    A simple and fast method was established to identify the sex types of the rat-derived cell strains. The single copy X-chromosome-linked gene AR and the single copy Y-chromosome-linked gene Sry were both detected with qPCR for the rat genomic DNA sample and the AR/Sry ratio was calculated. According to the law of the AR/Sry ratio, a new method to identify the sex types of the rat-derived cell strains was developed. The new assay was proved effective. The new assay showed advantages over the traditional sex type identification PCR methods, which detected only the Sry gene. Moreover, the new method was used to identify the sex types of two rat-derived cell strains unknown for the sex types and the results were confirmed with the in situ hybridization. Finally, the problem of the cross contamination between the female and the male samples was addressed and discussed extensively.

  7. Complete genome sequence of Gordonia bronchialis type strain (3410T)

    SciTech Connect

    Ivanova, N; Sikorski, Johannes; Jando, Marlen; Lapidus, Alla L.; Nolan, Matt; Glavina Del Rio, Tijana; Tice, Hope; Copeland, A; Cheng, Jan-Fang; Chen, Feng; Bruce, David; Goodwin, Lynne A.; Pitluck, Sam; Mavromatis, K; Ovchinnikova, Galina; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam L; Hauser, Loren John; Chang, Yun-Juan; Jeffries, Cynthia; Chain, Patrick S. G.; Saunders, Elizabeth H; Han, Cliff; Detter, J C; Brettin, Thomas S; Rohde, Manfred; Goker, Markus; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Klenk, Hans-Peter; Kyrpides, Nikos C

    2010-01-01

    Gordonia bronchialis Tsukamura 1971 is the type species of the genus. G. bronchialis is a human-pathogenic organism that has been isolated from a large variety of human tissues. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of the family Gordoniaceae. The 5,290,012 bp long genome with its 4,944 protein-coding and 55 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

  8. Complete genome sequence of Acidimicrobium ferrooxidans type strain (ICPT)

    SciTech Connect

    Clum, Alicia; Nolan, Matt; Lang, Elke; Glavina Del Rio, Tijana; Tice, Hope; Copeland, Alex; Cheng, Jan-Fang; Lucas, Susan; Chen, Feng; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Ivanova, Natalia; Mavrommatis, Konstantinos; Mikhailova, Natalia; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Goker, Markus; Spring, Stefan; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jefferies, Cynthia C.; Chain, Patrick; Bristow, James; Eisen, Jonathan A.; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C.; Klenk, Hans-Peter; Lapidus, Alla

    2009-05-20

    Acidimicrobium ferrooxidans (Clark and Norris 1996) is the sole and type species of the genus, which until recently was the only genus within the actinobacterial family Acidimicrobiaceae and in the order Acidomicrobiales. Rapid oxidation of iron pyrite during autotrophic growth in the absence of an enhanced CO2 concentration is characteristic for A. ferrooxidans. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of the order Acidomicrobiales, and the 2,158,157 bp long single replicon genome with its 2038 protein coding and 54 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

  9. Complete genome sequence of Gordonia bronchialis type strain (3410T)

    PubMed Central

    Ivanova, Natalia; Sikorski, Johannes; Jando, Marlen; Lapidus, Alla; Nolan, Matt; Lucas, Susan; Del Rio, Tijana Glavina; Tice, Hope; Copeland, Alex; Cheng, Jan-Fang; Chen, Feng; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Mavromatis, Konstantinos; Ovchinnikova, Galina; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Chain, Patrick; Saunders, Elizabeth; Han, Cliff; Detter, John C.; Brettin, Thomas; Rohde, Manfred; Göker, Markus; Bristow, Jim; Eisen, Jonathan A.; Markowitz, Victor; Hugenholtz, Philip; Klenk, Hans-Peter; Kyrpides, Nikos C.

    2010-01-01

    Gordonia bronchialis Tsukamura 1971 is the type species of the genus. G. bronchialis is a human-pathogenic organism that has been isolated from a large variety of human tissues. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of the family Gordoniaceae. The 5,290,012 bp long genome with its 4,944 protein-coding and 55 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project. PMID:21304674

  10. Complete genome sequence of Thermomonospora curvata type strain (B9)

    SciTech Connect

    Chertkov, Olga; Sikorski, Johannes; Nolan, Matt; Lapidus, Alla L.; Lucas, Susan; Glavina Del Rio, Tijana; Tice, Hope; Cheng, Jan-Fang; Goodwin, Lynne A.; Pitluck, Sam; Liolios, Konstantinos; Ivanova, N; Mavromatis, K; Mikhailova, Natalia; Ovchinnikova, Galina; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Ngatchou, Olivier Duplex; Land, Miriam L; Hauser, Loren John; Chang, Yun-Juan; Jeffries, Cynthia; Brettin, Thomas S; Han, Cliff; Detter, J. Chris; Rohde, Manfred; Goker, Markus; Woyke, Tanja; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Klenk, Hans-Peter; Kyrpides, Nikos C

    2011-01-01

    Thermomonospora curvata Henssen 1957 is the type species of the genus Thermomonospora. This genus is of interest because members of this clade are sources of new antibiotics, enzymes, and products with pharmacological activity. In addition, members of this genus participate in the active degradation of cellulose. This is the first complete genome sequence of a member of the family Thermomonosporaceae. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 5,639,016 bp long genome with its 4,985 protein-coding and 76 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  11. Complete genome sequence of Sulfurospirillum deleyianum type strain (5175T)

    PubMed Central

    Sikorski, Johannes; Lapidus, Alla; Copeland, Alex; Glavina Del Rio, Tijana; Nolan, Matt; Lucas, Susan; Chen, Feng; Tice, Hope; Cheng, Jan-Fang; Saunders, Elizabeth; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Ovchinnikova, Galina; Pati, Amrita; Ivanova, Natalia; Mavromatis, Konstantinos; Chen, Amy; Palaniappan, Krishna; Chain, Patrick; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Brettin, Thomas; Detter, John C.; Han, Cliff; Rohde, Manfred; Lang, Elke; Spring, Stefan; Göker, Markus; Bristow, Jim; Eisen, Jonathan A.; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C.; Klenk, Hans-Peter

    2010-01-01

    Sulfurospirillum deleyianum Schumacher et al. 1993 is the type species of the genus Sulfurospirillum. S. deleyianum is a model organism for studying sulfur reduction and dissimilatory nitrate reduction as an energy source for growth. Also, it is a prominent model organism for studying the structural and functional characteristics of cytochrome c nitrite reductase. Here, we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of the genus Sulfurospirillum. The 2,306,351 bp long genome with its 2,291 protein-coding and 52 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project. PMID:21304697

  12. Phylogeny of Flabellulidae (Amoebozoa: Leptomyxida) inferred from SSU rDNA sequences of the type strain of Flabellula citata Schaeffer, 1926 and newly isolated strains of marine amoebae.

    PubMed

    Dyková, Iva; Fiala, Ivan; Pecková, Hana; Dvoráková, Helena

    2008-12-01

    New strains of non-vannellid flattened amoebae isolated from fish, an invertebrate and the marine environment were studied together with Flabellula citata Schaeffer, 1926 selected by morphology as a reference strain. The study revealed a paucity of features distinguishing individual strains at the generic level, but clearly evidenced mutual phylogenetic relationships within the assemblage of strains as well as their affiliation to the Leptomyxida. In this study, the SSU rDNA dataset of leptomyxids was expanded and a new branching pattern was presented within this lineage of Amoebozoa. Sequences of three newly introduced strains clustered in close relationship with the type strain of F. citata, the type species of the genus. Three strains, including one resembling Flamella sp., were positioned within a sister-group containing Paraflabellula spp. Results of phylogenetic analysis confirmed doubts of previous authors regarding generic assignment of several Rhizanmoeba and Ripidomnyxa strains.

  13. Molecular Typing of Environmental and Clinical Strains of Vibrio vulnificus Isolated in the Northeastern USA

    PubMed Central

    Reynaud, Yann; Pitchford, Steven; De Decker, Sophie; Wikfors, Gary H.; Brown, Christopher L.

    2013-01-01

    Vibrio vulnificus is a ubiquitous marine bacterium that is responsible for infections and some seafood-related illnesses and deaths in the United States, mainly in individuals with compromised health status in the Gulf of Mexico region. Most phylogenetic studies focus on V. vulnificus strains isolated in the southern United States, but almost no genetic data are available on northeastern bacterial isolates of clinical or environmental origin. Our goal in this study was to examine the genetic diversity of environmental strains isolated from commercially-produced oysters and in clinical strains of known pathogenicity in northeastern United States. We conducted analyses of a total of eighty-three strains of V. vulnificus, including 18 clinical strains known to be pathogenic. A polyphasic, molecular-typing approach was carried out, based upon established biotypes, vcg, CPS, 16S rRNA types and three other genes possibly associated with virulence (arylsulfatase A, mtlABC, and nanA). An established Multi Locus Sequence Typing (MLST) method was also performed. Phylogenetic analyses of these markers and MLST results produced similar patterns of clustering of strains into two main lineages (we categorized as ‘LI’ and ‘LII’), with clinical and environmental strains clustering together in both lineages. Lineage LII was comprised primarily but not entirely of clinical bacterial isolates. Putative virulence markers were present in both clinical and environmental strains. These results suggest that some northeastern environmental strains of V. vulnificus are phylogenetically close to clinical strains and probably are capable of virulence. Further studies are necessary to assess the risk of human illness from consuming raw oysters harvested in the northeastern US. PMID:24386187

  14. Molecular typing of environmental and clinical strains of Vibrio vulnificus isolated in the northeastern USA.

    PubMed

    Reynaud, Yann; Pitchford, Steven; De Decker, Sophie; Wikfors, Gary H; Brown, Christopher L

    2013-01-01

    Vibrio vulnificus is a ubiquitous marine bacterium that is responsible for infections and some seafood-related illnesses and deaths in the United States, mainly in individuals with compromised health status in the Gulf of Mexico region. Most phylogenetic studies focus on V. vulnificus strains isolated in the southern United States, but almost no genetic data are available on northeastern bacterial isolates of clinical or environmental origin. Our goal in this study was to examine the genetic diversity of environmental strains isolated from commercially-produced oysters and in clinical strains of known pathogenicity in northeastern United States. We conducted analyses of a total of eighty-three strains of V. vulnificus, including 18 clinical strains known to be pathogenic. A polyphasic, molecular-typing approach was carried out, based upon established biotypes, vcg, CPS, 16S rRNA types and three other genes possibly associated with virulence (arylsulfatase A, mtlABC, and nanA). An established Multi Locus Sequence Typing (MLST) method was also performed. Phylogenetic analyses of these markers and MLST results produced similar patterns of clustering of strains into two main lineages (we categorized as 'LI' and 'LII'), with clinical and environmental strains clustering together in both lineages. Lineage LII was comprised primarily but not entirely of clinical bacterial isolates. Putative virulence markers were present in both clinical and environmental strains. These results suggest that some northeastern environmental strains of V. vulnificus are phylogenetically close to clinical strains and probably are capable of virulence. Further studies are necessary to assess the risk of human illness from consuming raw oysters harvested in the northeastern US.

  15. Thermal Output of WK-Type Strain Gauges on Various Materials at Cryogenic and Elevated Temperatures

    NASA Technical Reports Server (NTRS)

    Kowalkowski, Matthew K.; Rivers, H. Kevin; Smith, Russell W.

    1998-01-01

    Strain gage apparent strain (thermal output) is one of the largest sources of error associated with the measurement of strain when temperatures and mechanical loads are varied. In this paper, experimentally determined apparent strains of WK-type strain gages, installed on both metallic and composite-laminate materials of various lay-ups and resin systems for temperatures ranging from -450 F to 230 F are presented. For the composite materials apparent strain in both the 0 ply orientation angle and the 90 ply orientation angle were measured. Metal specimens tested included: aluminum-lithium alloy (Al-LI 2195-T87), aluminum alloy (Al 2219-T87), and titanium alloy. Composite materials tested include: graphite-toughened-epoxy (IM7/997- 2), graphite-bismaleimide (IM7/5260), and graphite-K3 (IM7/K3B). The experimentally determined apparent strain data are curve fit with a fourth-order polynomial for each of the materials studied. The apparent strain data and the polynomials that are fit to the data are compared with those produced by the strain gage manufacturer, and the results and comparisons are presented. Unacceptably high errors between the manufacture's data and the experimentally determined data were observed (especially at temperatures below - 270-F).

  16. Complete genome sequence of Cellulomonas flavigena type strain (134T)

    SciTech Connect

    Abt, Birte; Foster, Brian; Lapidus, Alla L.; Clum, Alicia; Sun, Hui; Pukall, Rudiger; Lucas, Susan; Glavina Del Rio, Tijana; Nolan, Matt; Tice, Hope; Cheng, Jan-Fang; Pitluck, Sam; Liolios, Konstantinos; Ivanova, N; Mavromatis, K; Ovchinnikova, Galina; Pati, Amrita; Goodwin, Lynne A.; Chen, Amy; Palaniappan, Krishna; Land, Miriam L; Hauser, Loren John; Chang, Yun-Juan; Jeffries, Cynthia; Rohde, Manfred; Goker, Markus; Woyke, Tanja; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter

    2010-01-01

    Cellulomonas flavigena (Kellerman and McBeth 1912) Bergey et al. 1923 is the type species of the genus Cellulomonas of the actinobacterial family Cellulomonadaceae. Members of the genus Cellulomonas are of special interest for their ability to degrade cellulose and hemicellulose, particularly with regard to the use of biomass as an alternative energy source. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of a member of the genus Cellulomonas, and next to the human pathogen Tropheryma whipplei the second complete genome sequence within the actinobacterial family Cellulomonadaceae. The 4,123,179 bp long single replicon genome with its 3,735 protein-coding and 53 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

  17. Complete genome sequence of Alicyclobacillus acidocaldarius type strain (104-IAT)

    SciTech Connect

    Mavromatis, K; Sikorski, Johannes; Lapidus, Alla L.; Glavina Del Rio, Tijana; Copeland, A; Tice, Hope; Cheng, Jan-Fang; Lucas, Susan; Chen, Feng; Nolan, Matt; Bruce, David; Goodwin, Lynne A.; Pitluck, Sam; Ivanova, N; Ovchinnikova, Galina; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam L; Hauser, Loren John; Chang, Yun-Juan; Jeffries, Cynthia; Chain, Patrick S. G.; Meincke, Linda; Sims, David; Chertkov, Olga; Han, Cliff; Brettin, Tom; Detter, J C; Wahrenburg, Claudia; Rohde, Manfred; Pukall, Rudiger; Goker, Markus; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Klenk, Hans-Peter; Kyrpides, Nikos C

    2010-01-01

    Alicyclobacillus acidocaldarius (Darland and Brock 1971) is the type species of the larger of the two genera in the bacillal family Alicyclobacillaceae . A. acidocaldarius is a free-living and non-pathogenic organism, but may also be associated with food and fruit spoilage. Due to its acidophilic nature, several enzymes from this species have since long been subjected to detailed molecular and biochemical studies. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of the family Alicyclobacillaceae . The 3,205,686 bp long genome (chromosome and three plasmids) with its 3,153 protein-coding and 82 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

  18. Complete genome sequence of Weeksella virosa type strain (9751T)

    SciTech Connect

    Lang, Elke; Teshima, Hazuki; Lucas, Susan; Lapidus, Alla L.; Hammon, Nancy; Deshpande, Shweta; Nolan, Matt; Cheng, Jan-Fang; Pitluck, Sam; Liolios, Konstantinos; Pagani, Ioanna; Mikhailova, Natalia; Ivanova, N; Mavromatis, K; Pati, Amrita; Tapia, Roxanne; Han, Cliff; Goodwin, Lynne A.; Chen, Amy; Palaniappan, Krishna; Land, Miriam L; Hauser, Loren John; Chang, Yun-Juan; Jeffries, Cynthia; Brambilla, Evelyne-Marie; Kopitz, marcus; Rohde, Manfred; Goker, Markus; Tindall, Brian; Detter, J. Chris; Woyke, Tanja; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Klenk, Hans-Peter; Kyrpides, Nikos C

    2011-01-01

    Weeksella virosa Holmes et al. 1987 is the sole member and type species of the genus Weeksella which belongs to the family Flavobacteriaceae of the phylum Bacteroidetes. Twenty-nine isolates, collected from clinical specimens provided the basis for the taxon description. While the species seems to be a saprophyte of the mucous membranes of healthy man and warm-blooded animals a causal relationship with disease has been reported in a few instances. Except for the ability to produce indole and to hydrolyze Tween and proteins such as casein and gelatin, this aerobic, non-motile, non-pigmented bacterial species is metabolically inert in most traditional biochemical tests. The 2,272,954 bp long genome with its 2,105 protein-coding and 76 RNA genes consists of one circular chromosome and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  19. Complete genome sequence of Haliscomenobacter hydrossis type strain (OT)

    SciTech Connect

    Daligault, Hajnalka E.; Lapidus, Alla L.; Zeytun, Ahmet; Nolan, Matt; Lucas, Susan; Glavina Del Rio, Tijana; Tice, Hope; Cheng, Jan-Fang; Tapia, Roxanne; Han, Cliff; Goodwin, Lynne A.; Pitluck, Sam; Liolios, Konstantinos; Pagani, Ioanna; Ivanova, N; Huntemann, Marcel; Mavromatis, K; Mikhailova, Natalia; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam L; Hauser, Loren John; Brambilla, Evelyne-Marie; Rohde, Manfred; Verbarg, Susanne; Goker, Markus; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter; Woyke, Tanja

    2011-01-01

    Haliscomenobacter hydrossis van Veen et al. 1973 is the type species of the genus Halisco- menobacter, which belongs to order 'Sphingobacteriales'. The species is of interest because of its isolated phylogenetic location in the tree of life, especially the so far genomically un- charted part of it, and because the organism grows in a thin, hardly visible hyaline sheath. Members of the species were isolated from fresh water of lakes and from ditch water. The genome of H. hydrossis is the first completed genome sequence reported from a member of the family 'Saprospiraceae'. The 8,771,651 bp long genome with its three plasmids of 92 kbp, 144 kbp and 164 kbp length contains 6,848 protein-coding and 60 RNA genes, and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  20. Complete genome sequence of Cellulomonas flavigena type strain (134).

    PubMed

    Abt, Birte; Foster, Brian; Lapidus, Alla; Clum, Alicia; Sun, Hui; Pukall, Rüdiger; Lucas, Susan; Glavina Del Rio, Tijana; Nolan, Matt; Tice, Hope; Cheng, Jan-Fang; Pitluck, Sam; Liolios, Konstantinos; Ivanova, Natalia; Mavromatis, Konstantinos; Ovchinnikova, Galina; Pati, Amrita; Goodwin, Lynne; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D; Rohde, Manfred; Göker, Markus; Woyke, Tanja; Bristow, James; Eisen, Jonathan A; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter

    2010-07-29

    Cellulomonas flavigena (Kellerman and McBeth 1912) Bergey et al. 1923 is the type species of the genus Cellulomonas of the actinobacterial family Cellulomonadaceae. Members of the genus Cellulomonas are of special interest for their ability to degrade cellulose and hemicellulose, particularly with regard to the use of biomass as an alternative energy source. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of a member of the genus Cellulomonas, and next to the human pathogen Tropheryma whipplei the second complete genome sequence within the actinobacterial family Cellulomonadaceae. The 4,123,179 bp long single replicon genome with its 3,735 protein-coding and 53 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

  1. Complete genome sequence of Kangiella koreensis type strain (SW-125).

    PubMed

    Han, Cliff; Sikorski, Johannes; Lapidus, Alla; Nolan, Matt; Glavina Del Rio, Tijana; Tice, Hope; Cheng, Jan-Fang; Lucas, Susan; Chen, Feng; Copeland, Alex; Ivanova, Natalia; Mavromatis, Konstantinos; Ovchinnikova, Galina; Pati, Amrita; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D; Chain, Patrick; Saunders, Elizabeth; Brettin, Thomas; Göker, Markus; Tindall, Brian J; Bristow, Jim; Eisen, Jonathan A; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter; Detter, John C

    2009-11-22

    Kangiella koreensis (Yoon et al. 2004) is the type species of the genus and is of phylogenetic interest because of the very isolated location of the genus Kangiella in the gammaproteobacterial order Oceanospirillales. K. koreensis SW-125(T) is a Gram-negative, non-motile, non-spore-forming bacterium isolated from tidal flat sediments at Daepo Beach, Yellow Sea, Korea. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first completed genome sequence from the genus Kangiella and only the fourth genome from the order Oceanospirillales. This 2,852,073 bp long single replicon genome with its 2647 protein-coding and 48 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

  2. Complete genome sequence of Haliangium ochraceum type strain (SMP-2).

    PubMed

    Ivanova, Natalia; Daum, Chris; Lang, Elke; Abt, Birte; Kopitz, Markus; Saunders, Elizabeth; Lapidus, Alla; Lucas, Susan; Glavina Del Rio, Tijana; Nolan, Matt; Tice, Hope; Copeland, Alex; Cheng, Jan-Fang; Chen, Feng; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Mavromatis, Konstantinos; Pati, Amrita; Mikhailova, Natalia; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D; Detter, John C; Brettin, Thomas; Rohde, Manfred; Göker, Markus; Bristow, Jim; Markowitz, Victor; Eisen, Jonathan A; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter

    2010-01-28

    Haliangium ochraceum Fudou et al. 2002 is the type species of the genus Haliangium in the myxococcal family 'Haliangiaceae'. Members of the genus Haliangium are the first halophilic myxobacterial taxa described. The cells of the species follow a multicellular lifestyle in highly organized biofilms, called swarms, they decompose bacterial and yeast cells as most myxobacteria do. The fruiting bodies contain particularly small coccoid myxospores. H. ochraceum encodes the first actin homologue identified in a bacterial genome. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of a member of the myxococcal suborder Nannocystineae, and the 9,446,314 bp long single replicon genome with its 6,898 protein-coding and 53 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

  3. Complete genome sequence of Alicyclobacillus acidocaldarius type strain (104-IAT)

    PubMed Central

    Mavromatis, Konstantinos; Sikorski, Johannes; Lapidus, Alla; Glavina Del Rio, Tijana; Copeland, Alex; Tice, Hope; Cheng, Jan-Fang; Lucas, Susan; Chen, Feng; Nolan, Matt; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Ivanova, Natalia; Ovchinnikova, Galina; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Chain, Patrick; Meincke, Linda; Sims, David; Chertkov, Olga; Han, Cliff; Brettin, Thomas; Detter, John C.; Wahrenburg, Claudia; Rohde, Manfred; Pukall, Rüdiger; Göker, Markus; Bristow, Jim; Eisen, Jonathan A.; Markowitz, Victor; Hugenholtz, Philip; Klenk, Hans-Peter; Kyrpides, Nikos C.

    2010-01-01

    Alicyclobacillus acidocaldarius (Darland and Brock 1971) is the type species of the larger of the two genera in the bacillal family ‘Alicyclobacillaceae’. A. acidocaldarius is a free-living and non-pathogenic organism, but may also be associated with food and fruit spoilage. Due to its acidophilic nature, several enzymes from this species have since long been subjected to detailed molecular and biochemical studies. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of the family ‘Alicyclobacillaceae’. The 3,205,686 bp long genome (chromosome and three plasmids) with its 3,153 protein-coding and 82 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project. PMID:21304673

  4. Complete genome sequence of Cellulomonas flavigena type strain (134T)

    PubMed Central

    Abt, Birte; Foster, Brian; Lapidus, Alla; Clum, Alicia; Sun, Hui; Pukall, Rüdiger; Lucas, Susan; Glavina Del Rio, Tijana; Nolan, Matt; Tice, Hope; Cheng, Jan-Fang; Pitluck, Sam; Liolios, Konstantinos; Ivanova, Natalia; Mavromatis, Konstantinos; Ovchinnikova, Galina; Pati, Amrita; Goodwin, Lynne; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Rohde, Manfred; Göker, Markus; Woyke, Tanja; Bristow, James; Eisen, Jonathan A.; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C.; Klenk, Hans-Peter

    2010-01-01

    Cellulomonas flavigena (Kellerman and McBeth 1912) Bergey et al. 1923 is the type species of the genus Cellulomonas of the actinobacterial family Cellulomonadaceae. Members of the genus Cellulomonas are of special interest for their ability to degrade cellulose and hemicellulose, particularly with regard to the use of biomass as an alternative energy source. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of a member of the genus Cellulomonas, and next to the human pathogen Tropheryma whipplei the second complete genome sequence within the actinobacterial family Cellulomonadaceae. The 4,123,179 bp long single replicon genome with its 3,735 protein-coding and 53 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project. PMID:21304688

  5. [MLST types of vancomycin-resistant Enterococcus faecium strains isolated from blood cultures].

    PubMed

    Arslan, Uğur; Demir, Esra; Oryaşin, Erman; Türk Dağı, Hatice; Tuncer, Inci; Fındık, Duygu; Bozdoğan, Bülent

    2013-07-01

    Enterococci, particularly vancomycin-resistant enterococci (VRE), are important nosocomial pathogens with limited treatment options. Enterococci have low-level resistance to penicillins and aminoglycosides and are intrinsically resistant to cephalosporins. In addition, they can acquire high-level resistance to beta-lactam antibiotics, aminoglycosides and glycopeptides. The aim of this study was to determine glycopeptide resistance mechanisms and genetic relationships of vancomycin-resistant E.faecium strains isolated from blood cultures between 2003-2009 years by molecular epidemiologic methods. A total of 38 VRE strains isolated from blood cultures were included in this study. The isolates were identified by conventional methods and Phoenix 100 BD automated system (Becton Dickinson Diagnostic Systems, USA) and confirmed by sequence analysis of 16S rRNA amplicons. Antibiotic susceptibility tests were performed by the Kirby-Bauer disk diffusion method accor-ding to the CLSI standards. MIC values of vancomycin were determined in vancomycin resistant strains by E-test (AB Biodisk, Sweden) method. Vancomycin resistance genes included vanA, vanB, vanC, and vanD were investigated by polymerase chain reaction (PCR) method. Clonal relationship between strains was determined by pulsed-field gel electrophoresis (PFGE). Sequence analysis was performed for examples selected for multilocus sequence typing (MLST) of each pulsotype and subtype. Thirty eight strains of enterococci isolated from blood cultures were defined as E.faecium by phenotypic methods and confirmed by 16S rRNA sequence analysis. Vancomycin MIC values of strains were determined as > 256 µg/ml by E test. The vanA gene was detected in all isolates. Clonal relationship of 38 isolates E.faecium carrying the vanA gene was determined by PFGE and MLST methods. PFGE detected four pulsotypes (A-D) and one sporadic isolate. Twenty nine strains belonged to A pulsotype, three strains belonged to B pulsotype, two strains

  6. Complete genome sequence of the larval shellfish pathogen Vibrio Tubiashii type strain ATCC 19109

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Vibrio tubiashii is a larval shellfish pathogen. Here we report the first closed genome sequence for this species (American Type Culture Collection type strain 19109), which has two chromosomes (3,294,490 and 1,766,582 bp), two megaplasmids (251,408 and 122,808 bp) and two plasmids (57,076 and 47,9...

  7. Complete genome sequence of Pyrolobus fumarii type strain (1AT)

    SciTech Connect

    Anderson, Iain; Goker, Markus; Nolan, Matt; Lucas, Susan; Hammon, Nancy; Deshpande, Shweta; Cheng, Jan-Fang; Tapia, Roxanne; Han, Cliff; Goodwin, Lynne A.; Pitluck, Sam; Huntemann, Marcel; Liolios, Konstantinos; Ivanova, N; Pagani, Ioanna; Mavromatis, K; Ovchinnikova, Galina; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam L; Hauser, Loren John; Brambilla, Evelyne-Marie; Huber, Harald; Yasawong, Montri; Rohde, Manfred; Spring, Stefan; Abt, Birte; Sikorski, Johannes; Wirth, Reinhard; Detter, J. Chris; Woyke, Tanja; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter; Lapidus, Alla L.

    2011-01-01

    Pyrolobus fumarii Bl chl et al. 1997 is the type species of the genus Pyrolobus, which be- longs to the crenarchaeal family Pyrodictiaceae. The species is a facultatively microaerophilic non-motile crenarchaeon. It is of interest because of its isolated phylogenetic location in the tree of life and because it is a hyperthermophilic chemolithoautotroph known as the primary producer of organic matter at deep-sea hydrothermal vents. P. fumarii exhibits currently the highest optimal growth temperature of all life forms on earth (106 C). This is the first com- pleted genome sequence of a member of the genus Pyrolobus to be published and only the second genome sequence from a member of the family Pyrodictiaceae. Although Diversa Corporation announced the completion of sequencing of the P. fumarii genome on Septem- ber 25, 2001, this sequence was never released to the public. The 1,843,267 bp long genome with its 1,986 protein-coding and 52 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  8. Complete genome sequence of Denitrovibrio acetiphilus type strain (N2460).

    PubMed

    Kiss, Hajnalka; Lang, Elke; Lapidus, Alla; Copeland, Alex; Nolan, Matt; Glavina Del Rio, Tijana; Chen, Feng; Lucas, Susan; Tice, Hope; Cheng, Jan-Fang; Han, Cliff; Goodwin, Lynne; Pitluck, Sam; Liolios, Konstantinos; Pati, Amrita; Ivanova, Natalia; Mavromatis, Konstantinos; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D; Detter, John C; Brettin, Thomas; Spring, Stefan; Rohde, Manfred; Göker, Markus; Woyke, Tanja; Bristow, James; Eisen, Jonathan A; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter

    2010-06-15

    Denitrovibrio acetiphilus Myhr and Torsvik 2000 is the type species of the genus Denitrovibrio in the bacterial family Deferribacteraceae. It is of phylogenetic interest because there are only six genera described in the family Deferribacteraceae. D. acetiphilus was isolated as a representative of a population reducing nitrate to ammonia in a laboratory column simulating the conditions in off-shore oil recovery fields. When nitrate was added to this column undesirable hydrogen sulfide production was stopped because the sulfate reducing populations were superseded by these nitrate reducing bacteria. Here we describe the features of this marine, mesophilic, obligately anaerobic organism respiring by nitrate reduction, together with the complete genome sequence, and annotation. This is the second complete genome sequence of the order Deferribacterales and the class Deferribacteres, which is the sole class in the phylum Deferribacteres. The 3,222,077 bp genome with its 3,034 protein-coding and 51 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

  9. In vitro permissivity of bovine cells for wild-type and vaccinal myxoma virus strains.

    PubMed

    Pignolet, Béatrice; Duteyrat, Jean-Luc; Allemandou, Aude; Gelfi, Jacqueline; Foucras, Gilles; Bertagnoli, Stéphane

    2007-09-27

    Myxoma virus (MYXV), a leporide-specific poxvirus, represents an attractive candidate for the generation of safe, non-replicative vaccine vector for non-host species. However, there is very little information concerning infection of non-laboratory animals species cells with MYXV. In this study, we investigated interactions between bovine cells and respectively a wild type strain (T1) and a vaccinal strain (SG33) of MYXV. We showed that bovine KOP-R, BT and MDBK cell lines do not support MYXV production. Electron microscopy observations of BT-infected cells revealed the low efficiency of viral entry and the production of defective virions. In addition, infection of bovine peripheral blood mononuclear cells (PBMC) occurred at a very low level, even following non-specific activation, and was always abortive. We did not observe significant differences between the wild type strain and the vaccinal strain of MYXV, indicating that SG33 could be used for new bovine vaccination strategies.

  10. Multiplex PCR for Identification of Two Capsular Types in Epidemic KPC-Producing Klebsiella pneumoniae Sequence Type 258 Strains

    PubMed Central

    Chen, Liang; Chavda, Kalyan D.; Findlay, Jacqueline; Peirano, Gisele; Hopkins, Katie; Pitout, Johann D. D.; Bonomo, Robert A.; Woodford, Neil; DeLeo, Frank R.

    2014-01-01

    We developed a multiplex PCR assay capable of identifying two capsular polysaccharide synthesis sequence types (sequence type 258 [ST258] cps-1 and cps-2) in epidemic Klebsiella pneumoniae ST258 strains. The assay performed with excellent sensitivity (100%) and specificity (100%) for identifying cps types in 60 ST258 K. pneumoniae sequenced isolates. The screening of 419 ST258 clonal isolates revealed a significant association between cps type and K. pneumoniae carbapenemase (KPC) variant: cps-1 is largely associated with KPC-2, while cps-2 is primarily associated with KPC-3. PMID:24733470

  11. Draft Genome Sequence of Burkholderia cordobensis Type Strain LMG 27620, Isolated from Agricultural Soils in Argentina

    PubMed Central

    Draghi, Walter Omar; Mancini Villagra, Ulises M.; Wall, Luis Gabriel

    2015-01-01

    Bacteria of the genus Burkholderia are commonly found in diverse ecological niches in nature. We report here the draft genome sequence of Burkholderia cordobensis type strain LMG 27620, isolated from agricultural soil in Córdoba, Argentina. This strain harbors several genes involved in chitin utilization and phenol degradation, which make it an interesting candidate for biocontrol purposes and xenobiotic degradation in polluted environments. PMID:26494680

  12. Draft Genome Sequence of JVAP01T, the Type Strain of the Novel Species Acinetobacter dijkshoorniae

    PubMed Central

    Fernández-Orth, Dietmar; Cosgaya, Clara; Telli, Murat; Mosqueda, Noraida; Marí-Almirall, Marta

    2017-01-01

    ABSTRACT Here, we report the draft genome sequence of the type strain of Acinetobacter dijkshoorniae, a novel human pathogen within the Acinetobacter calcoaceticus–Acinetobacter baumannii (ACB) complex. Strain JVAP01T has an estimated genome size of 3.9 Mb, exhibits a 38.8% G+C content, and carries a plasmid with the blaNDM-1 carbapenemase gene. PMID:28082506

  13. Phylogeny and virulence of naturally occurring type III secretion system-deficient Pectobacterium strains.

    PubMed

    Kim, Hye-Sook; Ma, Bing; Perna, Nicole T; Charkowski, Amy O

    2009-07-01

    Pectobacterium species are enterobacterial plant-pathogenic bacteria that cause soft rot disease in diverse plant species. Previous epidemiological studies of Pectobacterium species have suffered from an inability to identify most isolates to the species or subspecies level. We used three previously described DNA-based methods, 16S-23S intergenic transcribed spacer PCR-restriction fragment length polymorphism analysis, multilocus sequence analysis (MLSA), and pulsed-field gel electrophoresis, to examine isolates from diseased stems and tubers and found that MLSA provided the most reliable classification of isolates. We found that strains belonging to at least two Pectobacterium clades were present in each field examined, although representatives of only three of five Pectobacterium clades were isolated. Hypersensitive response and DNA hybridization assays revealed that strains of both Pectobacterium carotovorum and Pectobacterium wasabiae lack a type III secretion system (T3SS). Two of the T3SS-deficient strains assayed lack genes adjacent to the T3SS gene cluster, suggesting that multiple deletions occurred in Pectobacterium strains in this locus, and all strains appear to have only six rRNA operons instead of the seven operons typically found in Pectobacterium strains. The virulence of most of the T3SS-deficient strains was similar to that of T3SS-encoding strains in stems and tubers.

  14. Molecular typing of Candida albicans strains isolated from denture wearers by repetitive sequence-based PCR.

    PubMed

    Abaci, O; Haliki-Uztan, A; Ozturk, B; Toksavul, S; Ulusoy, M; Boyacioglu, H

    2011-02-01

    Long-term use of prosthesis is the most important risk factor for the colonization of Candida species on the mucosal surfaces, which can lead to the development of denture-related stomatitis (DRS). Some individuals wearing prosthesis develop DRS and others do not. C. albicans strains isolated from both groups were genotypically compared. The purpose of this study was to determine whether the strain causing prosthesis stomatitis was different from the other strains genotypically. The study included 90 individuals wearing different prostheses and 20 control individuals with natural teeth. In the study 109 C. albicans strains were used which were isolated from the saliva samples and the mucosal surfaces of the tongues and palates of 51 individuals and then defined phenotypically. Phenotypic diagnosis of the isolates was genotypically verified by using species-specific PCR. For molecular typing, repetitive extragenic palindromic sequence polymerase chain reaction (REP-PCR) was employed. The results of the study revealed that REP-PCR had the capability to separate 109 C. albicans strains and six reference strains into 44 genotypes. Whereas C. albicans strains showed heterogenic distribution, C. albicans strains isolated from the individuals suffering from prosthesis stomatitis showed no specific genotypes. REP-PCR is a simple, fast and low-cost method and helped work on a great number of samples.

  15. Mapping of attenuating sequences of an avirulent poliovirus type 2 strain.

    PubMed

    Moss, E G; O'Neill, R E; Racaniello, V R

    1989-05-01

    A mouse model for poliomyelitis was used to identify genomic sequences that attenuate neurovirulence of poliovirus strain P2/P712. This type 2 strain is avirulent in primates and mice yet grows as well as virulent strains in cell culture. The approach used was to exchange portions of the genome of the mouse-virulent P2/Lansing strain with the corresponding region from P2/P712 to identify sequences that could attenuate Lansing neurovirulence in mice. A full-length infectious cDNA of P2/P712 was assembled and used to construct recombinants between P2/P712 and P2/Lansing. The results of neurovirulence testing of 11 recombinants indicated that strong attenuating determinants are located in the 5' noncoding region of P2/P712 and a region encoding capsid protein VP1 and 2Apro, 2B, and part of 2C. An attenuating determinant was further localized to between nucleotides 456 and 628 of P2/P712. A third sequence from P2/P712, nucleotides 752 to 2268, encoding VP4, VP2, and part of VP3, was weakly attenuating. The sequence from nucleotide 4454, approximately halfway through the 2C-coding region, to the end of the P2/P712 genome did not contain attenuating determinants. Nucleotide sequence analysis revealed that P2/P712 differs from the type 2 Sabin vaccine strain by only 22 nucleotides. Six differences lead to amino acid changes in the coding region, and four differences are in the 5' noncoding region. These studies show that, like the type 1 and type 3 Sabin vaccine strains, the attenuated type 2 strain P712 contains multiple attenuating sequences, including strongly attenuating sequences in the 5' noncoding region of the genome.

  16. Damage type and strain mode associations in human compact bone bending fatigue.

    PubMed

    Boyce, T M; Fyhrie, D P; Glotkowski, M C; Radin, E L; Schaffler, M B

    1998-05-01

    When compact bone is subjected to fatigue loading, it develops matrix microdamage, which reduces the tissue's ability to resist fracture. The relative influence of different strain modes on damage and strength in compact bone has not been characterized, to our knowledge. In this study, the nonuniform strain field produced by four-point bending was used to introduce fatigue damage into tibial bending beam specimens from men 40-49 years old. The specimens were then bulk-stained with basic fuchsin to mark damage surfaces and were examined histologically and with confocal microscopy to describe damage morphologies and position relative to tension and compression-strained regions of the specimen. Histomorphometric methods were used to quantify the amounts of different types of bone microdamage. Three major types were observed. In regions subjected to tensile strains, the bone had focal regions of diffusely increased basic fuchsin staining (i.e., diffuse microdamage). Confocal microscopy of these regions showed them to be composed of extensive networks of fine, ultrastructural-level cracks. In compressive strain regions, the tissue developed linear microcracks in interstitial areas similar to those originally described by Frost. Fine, tearing-type (wispy-appearing) cracks were observed near and in the plane of the neutral axis. The paths of these fine cracks were not influenced by microstructural boundaries. Other minor damage morphologies (sector-stained osteons, delamination of regions of lamellae, and intraosteonal cracking) were observed, but their distribution was unrelated to local strain field. Thus. in fatigue of human compact bone, the principal mechanisms of matrix failure (i.e., linear microcrack, diffuse damage foci, and tearing-type damage) are strongly dependent on local strain type.

  17. MetaMLST: multi-locus strain-level bacterial typing from metagenomic samples

    PubMed Central

    Zolfo, Moreno; Tett, Adrian; Jousson, Olivier; Donati, Claudio; Segata, Nicola

    2017-01-01

    Metagenomic characterization of microbial communities has the potential to become a tool to identify pathogens in human samples. However, software tools able to extract strain-level typing information from metagenomic data are needed. Low-throughput molecular typing schema such as Multilocus Sequence Typing (MLST) are still widely used and provide a wealth of strain-level information that is currently not exploited by metagenomic methods. We introduce MetaMLST, a software tool that reconstructs the MLST loci of microorganisms present in microbial communities from metagenomic data. Tested on synthetic and spiked-in real metagenomes, the pipeline was able to reconstruct the MLST sequences with >98.5% accuracy at coverages as low as 1×. On real samples, the pipeline showed higher sensitivity than assembly-based approaches and it proved successful in identifying strains in epidemic outbreaks as well as in intestinal, skin and gastrointestinal microbiome samples. PMID:27651451

  18. Comparative genomics of wild type yeast strains unveils important genome diversity

    PubMed Central

    Carreto, Laura; Eiriz, Maria F; Gomes, Ana C; Pereira, Patrícia M; Schuller, Dorit; Santos, Manuel AS

    2008-01-01

    Background Genome variability generates phenotypic heterogeneity and is of relevance for adaptation to environmental change, but the extent of such variability in natural populations is still poorly understood. For example, selected Saccharomyces cerevisiae strains are variable at the ploidy level, have gene amplifications, changes in chromosome copy number, and gross chromosomal rearrangements. This suggests that genome plasticity provides important genetic diversity upon which natural selection mechanisms can operate. Results In this study, we have used wild-type S. cerevisiae (yeast) strains to investigate genome variation in natural and artificial environments. We have used comparative genome hybridization on array (aCGH) to characterize the genome variability of 16 yeast strains, of laboratory and commercial origin, isolated from vineyards and wine cellars, and from opportunistic human infections. Interestingly, sub-telomeric instability was associated with the clinical phenotype, while Ty element insertion regions determined genomic differences of natural wine fermentation strains. Copy number depletion of ASP3 and YRF1 genes was found in all wild-type strains. Other gene families involved in transmembrane transport, sugar and alcohol metabolism or drug resistance had copy number changes, which also distinguished wine from clinical isolates. Conclusion We have isolated and genotyped more than 1000 yeast strains from natural environments and carried out an aCGH analysis of 16 strains representative of distinct genotype clusters. Important genomic variability was identified between these strains, in particular in sub-telomeric regions and in Ty-element insertion sites, suggesting that this type of genome variability is the main source of genetic diversity in natural populations of yeast. The data highlights the usefulness of yeast as a model system to unravel intraspecific natural genome diversity and to elucidate how natural selection shapes the yeast genome

  19. R-type pyocin is required for competitive growth advantage between Pseudomonas aeruginosa strains.

    PubMed

    Heo, Yun-Jeong; Chung, In-Young; Choi, Kelly B; Cho, You-Hee

    2007-01-01

    R-type pyocin is a bacteriophage tail-shaped bacteriocin produced by Pseudomonas aeruginosa, but its physiological roles are relatively unknown. Here we describe a role of R-type pyocin in the competitive growth advantages between P. aeruginosa strains. Partial purification and gene disruption revealed that the major killing activity from the culture supernatant of PA14 is attributed to R-type pyocin, neither F-type nor S-type pyocins. These findings may provide insight into the forces governing P. aeruginosa population dynamics to promote and maintain its biodiversity.

  20. Primary isolation strain determines both phage type and receptors recognised by Campylobacter jejuni bacteriophages.

    PubMed

    Sørensen, Martine C Holst; Gencay, Yilmaz Emre; Birk, Tina; Baldvinsson, Signe Berg; Jäckel, Claudia; Hammerl, Jens A; Vegge, Christina S; Neve, Horst; Brøndsted, Lone

    2015-01-01

    In this study we isolated novel bacteriophages, infecting the zoonotic bacterium Campylobacter jejuni. These phages may be used in phage therapy of C. jejuni colonized poultry to prevent spreading of the bacteria to meat products causing disease in humans. Many C. jejuni phages have been isolated using NCTC12662 as the indicator strain, which may have biased the selection of phages. A large group of C. jejuni phages rely on the highly diverse capsular polysaccharide (CPS) for infection and recent work identified the O-methyl phosphoramidate modification (MeOPN) of CPS as a phage receptor. We therefore chose seven C. jejuni strains each expressing different CPS structures as indicator strains in a large screening for phages in samples collected from free-range poultry farms. Forty-three phages were isolated using C. jejuni NCTC12658, NCTC12662 and RM1221 as host strains and 20 distinct phages were identified based on host range analysis and genome restriction profiles. Most phages were isolated using C. jejuni strains NCTC12662 and RM1221 and interestingly phage genome size (140 kb vs. 190 kb), host range and morphological appearance correlated with the isolation strain. Thus, according to C. jejuni phage grouping, NCTC12662 and NCTC12658 selected for CP81-type phages, while RM1221 selected for CP220-type phages. Furthermore, using acapsular ∆kpsM mutants we demonstrated that phages isolated on NCTC12658 and NCTC12662 were dependent on the capsule for infection. In contrast, CP220-type phages isolated on RM1221 were unable to infect non-motile ∆motA mutants, hence requiring motility for successful infection. Hence, the primary phage isolation strain determines both phage type (CP81 or CP220) as well as receptors (CPS or flagella) recognised by the isolated phages.

  1. Complete Proteome of a Quinolone-Resistant Salmonella Typhimurium Phage Type DT104B Clinical Strain

    PubMed Central

    Correia, Susana; Nunes-Miranda, Júlio D.; Pinto, Luís; Santos, Hugo M.; de Toro, María; Sáenz, Yolanda; Torres, Carmen; Capelo, José Luis; Poeta, Patrícia; Igrejas, Gilberto

    2014-01-01

    Salmonellosis is one of the most common and widely distributed foodborne diseases. The emergence of Salmonella strains that are resistant to a variety of antimicrobials is a serious global public health concern. Salmonella enterica serovar Typhimurium definitive phage type 104 (DT104) is one of these emerging epidemic multidrug resistant strains. Here we collate information from the diverse and comprehensive range of experiments on Salmonella proteomes that have been published. We then present a new study of the proteome of the quinolone-resistant Se20 strain (phage type DT104B), recovered after ciprofloxacin treatment and compared it to the proteome of reference strain SL1344. A total of 186 and 219 protein spots were recovered from Se20 and SL1344 protein extracts, respectively, after two-dimensional gel electrophoresis. The signatures of 94% of the protein spots were successfully identified through matrix-assisted laser desorption/ionization mass spectrometry (MALDI-TOF MS). Three antimicrobial resistance related proteins, whose genes were previously detected by polymerase chain reaction (PCR), were identified in the clinical strain. The presence of these proteins, dihydropteroate synthase type-2 (sul2 gene), aminoglycoside resistance protein A (strA gene) and aminoglycoside 6'-N-acetyltransferase type Ib-cr4 (aac(6')-Ib-cr4 gene), was confirmed in the DT104B clinical strain. The aac(6')-Ib-cr4 gene is responsible for plasmid-mediated aminoglycoside and quinolone resistance. This is a preliminary analysis of the proteome of these two S. Typhimurium strains and further work is being developed to better understand how antimicrobial resistance is developing in this pathogen. PMID:25196519

  2. Complete genome sequence of Halopiger xanaduensis type strain (SH6T)

    SciTech Connect

    Anderson, Iain; Tindall, Brian; Rohde, Manfred; Lucas, Susan; Han, James; Lapidus, Alla L.; Cheng, Jan-Fang; Goodwin, Lynne A.; Pitluck, Sam; Peters, Lin; Pati, Amrita; Mikhailova, Natalia; Pagani, Ioanna; Teshima, Hazuki; Han, Cliff; Tapia, Roxanne; Land, Miriam L; Woyke, Tanja; Klenk, Hans-Peter; Kyrpides, Nikos C; Ivanova, N

    2012-01-01

    Halopiger xanaduensis is the type species of the genus Halopiger and belongs to the euryarchaeal family Halobacteriaceae. H. xanaduensis strain SH-6, which is designated as the type strain, was isolated from the sediment of a salt lake in Inner Mongolia, Lake Shangmatala. Like other members of the family Halobacteriaceae, it is an extreme halophile requiring at least 2.5 M salt for growth. We report here the sequencing and annotation of the 4,355,268 bp genome, which includes one chromosome and three plasmids. This genome is part of a Joint Genome Institute (JGI) Community Sequencing Program (CSP) project to sequence diverse haloarchaeal genomes.

  3. Complete genome sequence of the Antarctic Halorubrum lacusprofundi type strain ACAM 34

    DOE PAGES

    Anderson, Iain J.; DasSarma, Priya; Lucas, Susan; ...

    2016-09-10

    Halorubrum lacusprofundi is an extreme halophile within the archaeal phylum Euryarchaeota. The type strain ACAM 34 was isolated from Deep Lake, Antarctica. H. lacusprofundi is of phylogenetic interest because it is distantly related to the haloarchaea that have previously been sequenced. It is also of interest because of its psychrotolerance. We report here the complete genome sequence of H. lacusprofundi type strain ACAM 34 and its annotation. In conclusion, this genome is part of a 2006 Joint Genome Institute Community Sequencing Program project to sequence genomes of diverse Archaea.

  4. Complete genome sequence of the Antarctic Halorubrum lacusprofundi type strain ACAM 34

    SciTech Connect

    Anderson, Iain J.; DasSarma, Priya; Lucas, Susan; Copeland, Alex; Lapidus, Alla; Del Rio, Tijana Glavina; Tice, Hope; Dalin, Eileen; Bruce, David C.; Goodwin, Lynne; Pitluck, Sam; Sims, David; Brettin, Thomas S.; Detter, John C.; Han, Cliff S.; Larimer, Frank; Hauser, Loren; Land, Miriam; Ivanova, Natalia; Richardson, Paul; Cavicchioli, Ricardo; DasSarma, Shiladitya; Woese, Carl R.; Kyrpides, Nikos C.

    2016-09-10

    Halorubrum lacusprofundi is an extreme halophile within the archaeal phylum Euryarchaeota. The type strain ACAM 34 was isolated from Deep Lake, Antarctica. H. lacusprofundi is of phylogenetic interest because it is distantly related to the haloarchaea that have previously been sequenced. It is also of interest because of its psychrotolerance. We report here the complete genome sequence of H. lacusprofundi type strain ACAM 34 and its annotation. In conclusion, this genome is part of a 2006 Joint Genome Institute Community Sequencing Program project to sequence genomes of diverse Archaea.

  5. Discriminatory power and reproducibility of novel DNA typing methods for Mycobacterium tuberculosis complex strains.

    PubMed

    Kremer, Kristin; Arnold, Catherine; Cataldi, Angel; Gutiérrez, M Cristina; Haas, Walter H; Panaiotov, Stefan; Skuce, Robin A; Supply, Philip; van der Zanden, Adri G M; van Soolingen, Dick

    2005-11-01

    In recent years various novel DNA typing methods have been developed which are faster and easier to perform than the current internationally standardized IS6110 restriction fragment length polymorphism typing method. However, there has been no overview of the utility of these novel typing methods, and it is largely unknown how they compare to previously published methods. In this study, the discriminative power and reproducibility of nine recently described PCR-based typing methods for Mycobacterium tuberculosis were investigated using the strain collection of the interlaboratory study of Kremer et al. This strain collection contains 90 M. tuberculosis complex and 10 non-M. tuberculosis complex mycobacterial strains, as well as 31 duplicated DNA samples to assess reproducibility. The highest reproducibility was found with variable numbers of tandem repeat typing using mycobacterial interspersed repetitive units (MIRU VNTR) and fast ligation-mediated PCR (FLiP), followed by second-generation spoligotyping, ligation-mediated PCR (LM-PCR), VNTR typing using five repeat loci identified at the Queens University of Belfast (QUB VNTR), and the Amadio speciation PCR. Poor reproducibility was associated with fluorescent amplified fragment length polymorphism typing, which was performed in three different laboratories. The methods were ordered from highest discrimination to lowest by the Hunter-Gaston discriminative index as follows: QUB VNTR typing, MIRU VNTR typing, FLiP, LM-PCR, and spoligotyping. We conclude that both VNTR typing methods and FLiP typing are rapid, highly reliable, and discriminative epidemiological typing methods for M. tuberculosis and that VNTR typing is the epidemiological typing method of choice for the near future.

  6. Early Cardiac Dysfunction in the Type 1 Diabetic Heart Using Speckle-Tracking Based Strain Imaging

    PubMed Central

    Shepherd, Danielle L.; Nichols, Cody E.; Croston, Tara L.; McLaughlin, Sarah L.; Petrone, Ashley B.; Lewis, Sara E.; Thapa, Dharendra; Long, Dustin M.; Dick, Gregory M.; Hollander, John M.

    2016-01-01

    Enhanced sensitivity in echocardiographic analyses may allow for early detection of changes in cardiac function beyond the detection limits of conventional echocardiographic analyses, particularly in a small animal model. The goal of this study was to compare conventional echocardiographic measurements and speckle-tracking based strain imaging analyses in a small animal model of type 1 diabetes mellitus. Conventional analyses revealed differences in ejection fraction, fractional shortening, cardiac output, and stroke volume in diabetic animals relative to controls at 6-weeks post-diabetic onset. In contrast, when assessing short- and long-axis speckle-tracking based strain analyses, diabetic mice showed changes in average systolic radial strain, radial strain rate, radial displacement, and radial velocity, as well as decreased circumferential and longitudinal strain rate, as early as 1-week post-diabetic onset and persisting throughout the diabetic study. Further, we performed regional analyses for the LV and found that the free wall region was affected in both the short- and long-axis when assessing radial dimension parameters. These changes began 1-week post-diabetic onset and remained throughout the progression of the disease. These findings demonstrate the use of speckle-tracking based strain as an approach to elucidate cardiac dysfunction from a global perspective, identifying left ventricular cardiac regions affected during the progression of type 1 diabetes mellitus earlier than contractile changes detected by conventional echocardiographic measurements. PMID:26654913

  7. Population Structure and Antimicrobial Resistance Profiles of Streptococcus suis Serotype 2 Sequence Type 25 Strains

    PubMed Central

    Athey, Taryn B. T.; Teatero, Sarah; Takamatsu, Daisuke; Wasserscheid, Jessica; Dewar, Ken; Gottschalk, Marcelo; Fittipaldi, Nahuel

    2016-01-01

    Strains of serotype 2 Streptococcus suis are responsible for swine and human infections. Different serotype 2 genetic backgrounds have been defined using multilocus sequence typing (MLST). However, little is known about the genetic diversity within each MLST sequence type (ST). Here, we used whole-genome sequencing to test the hypothesis that S. suis serotype 2 strains of the ST25 lineage are genetically heterogeneous. We evaluated 51 serotype 2 ST25 S. suis strains isolated from diseased pigs and humans in Canada, the United States of America, and Thailand. Whole-genome sequencing revealed numerous large-scale rearrangements in the ST25 genome, compared to the genomes of ST1 and ST28 S. suis strains, which result, among other changes, in disruption of a pilus island locus. We report that recombination and lateral gene transfer contribute to ST25 genetic diversity. Phylogenetic analysis identified two main and distinct Thai and North American clades grouping most strains investigated. These clades also possessed distinct patterns of antimicrobial resistance genes, which correlated with acquisition of different integrative and conjugative elements (ICEs). Some of these ICEs were found to be integrated at a recombination hot spot, previously identified as the site of integration of the 89K pathogenicity island in serotype 2 ST7 S. suis strains. Our results highlight the limitations of MLST for phylogenetic analysis of S. suis, and the importance of lateral gene transfer and recombination as drivers of diversity in this swine pathogen and zoonotic agent. PMID:26954687

  8. Enrichment, Isolation, and Cultural Characteristics of Marine Strains of Clostridium botulinum Type C

    PubMed Central

    Segner, W. P.; Schmidt, C. F.; Boltz, J. K.

    1971-01-01

    Terrestrial strains of Clostridium botulinum type C, designated 468 and 571, were used to screen various media for growth and sporulation at 30 C. Of the various formulations tested, only egg meat medium fortified with 1% additions of yeast extract, ammonium sulfate, and glucose (FEM medium) gave good growth and satisfactory sporulation. FEM medium was used to recover four marine type C isolates from inshore sediments collected along the Atlantic, the Gulf of Mexico, and the Pacific coasts of the United States. The isolation techniques involved repeated transfer of cultures showing type C toxin in FEM medium and purification by a deep tube method. The medium used for purification was beef infusion-agar supplemented with 0.14% sodium bicarbonate and 0.1% l-cysteine hydrochloride. l-Cysteine was adopted in preference to sodium thioglycolate, because some lots of the latter were definitely inhibitory for growth. The addition of bicarbonate markedly increased viable spore counts of both the marine and terrestrial strains. Various cultural and biochemical characteristics of the marine and the terrestrial strains were compared. With the exception of some variations in their fermentation patterns, both groups showed similar characteristics. Of 23 fermentable compounds tested, the terrestrial strains attacked only glucose and mannose. The marine strains fermented glucose, mannose, galactose, and ribose actively; dextrin, inositol, maltose, and melibiose were weakly fermented. PMID:4944800

  9. SNP/RD typing of Mycobacterium tuberculosis Beijing strains reveals local and worldwide disseminated clonal complexes.

    PubMed

    Schürch, Anita C; Kremer, Kristin; Hendriks, Amber C A; Freyee, Benthe; McEvoy, Christopher R E; van Crevel, Reinout; Boeree, Martin J; van Helden, Paul; Warren, Robin M; Siezen, Roland J; van Soolingen, Dick

    2011-01-01

    The Beijing strain is one of the most successful genotypes of Mycobacterium tuberculosis worldwide and appears to be highly homogenous according to existing genotyping methods. To type Beijing strains reliably we developed a robust typing scheme using single nucleotide polymorphisms (SNPs) and regions of difference (RDs) derived from whole-genome sequencing data of eight Beijing strains. SNP/RD typing of 259 M. tuberculosis isolates originating from 45 countries worldwide discriminated 27 clonal complexes within the Beijing genotype family. A total of 16 Beijing clonal complexes contained more than one isolate of known origin, of which two clonal complexes were strongly associated with South African origin. The remaining 14 clonal complexes encompassed isolates from different countries. Even highly resolved clonal complexes comprised isolates from distinct geographical sites. Our results suggest that Beijing strains spread globally on multiple occasions and that the tuberculosis epidemic caused by the Beijing genotype is at least partially driven by modern migration patterns. The SNPs and RDs presented in this study will facilitate future molecular epidemiological and phylogenetic studies on Beijing strains.

  10. Usefulness of phage typing and "two-way ribotyping" to differentiate Salmonella enteritidis strains.

    PubMed

    Landeras, E; Usera, M A; Calderón, C; Mendoza, M C

    1997-12-01

    The capacity to differentiate Salmonella enteritidis strains by phage typing and "two-way ribotyping" performed with PstI and SphI was evaluated. The typeability was 96.8% in phage typing and 100% in ribotyping. The series was differentiated into 13 phage types, 19 combined ribotypes, and 39 subtypes or clonal lines by combining results from both methods (of which 11, 13, and 35, respectively, were represented by natural strains). Ribotyping differentiated strains ascribed to PTs 1, 4, 6a, 7, 8, RDNC and UPT. Conversely, some strains of PTs 1, 4, 5a, 6, 6a, 7, 34, RDNC and UPT fall into the most frequent combined ribotype. A dendrogram of genetic similarity generated from the combined ribotypes was traced, and, at a 0.82 similarity level, it showed a major cluster (including 17 combined ribotypes, 88.4% strains ascribed to all PTs tested except PT11), a minor cluster, and four additional lines more loosely related.

  11. Effect of wheelchair mass, tire type and tire pressure on physical strain and wheelchair propulsion technique.

    PubMed

    de Groot, Sonja; Vegter, Riemer J K; van der Woude, Lucas H V

    2013-10-01

    The purpose of this study was to evaluate the effect of wheelchair mass, solid vs. pneumatic tires and tire pressure on physical strain and wheelchair propulsion technique. 11 Able-bodied participants performed 14 submaximal exercise blocks on a treadmill with a fixed speed (1.11 m/s) within 3 weeks to determine the effect of tire pressure (100%, 75%, 50%, 25% of the recommended value), wheelchair mass (0 kg, 5 kg, or 10 kg extra) and tire type (pneumatic vs. solid). All test conditions (except pneumatic vs. solid) were performed with and without instrumented measurement wheels. Outcome measures were power output (PO), physical strain (heart rate (HR), oxygen uptake (VO2), gross mechanical efficiency (ME)) and propulsion technique (timing, force application). At 25% tire pressure PO and subsequently VO2 were higher compared to 100% tire pressure. Furthermore, a higher tire pressure led to a longer cycle time and contact angle and subsequently lower push frequency. Extra mass did not lead to an increase in PO, physical strain or propulsion technique. Solid tires led to a higher PO and physical strain. The solid tire effect was amplified by increased mass (tire × mass interaction). In contrast to extra mass, tire pressure and tire type have an effect on PO, physical strain or propulsion technique of steady-state wheelchair propulsion. As expected, it is important to optimize tire pressure and tire type.

  12. HYDROGEN EFFECTS ON STRAIN-INDUCED MARTENSITE FORMATION IN TYPE 304L STAINLESS STEEL

    SciTech Connect

    Morgan, M; Ps Lam, P

    2008-12-11

    Unstable austenitic stainless steels undergo a strain-induced martensite transformation. The effect of hydrogen on this transformation is not well understood. Some researchers believe that hydrogen makes the transformation to martensite more difficult because hydrogen is an austenite stabilizer. Others believe that hydrogen has little or no effect at all on the transformation and claim that the transformation is simply a function of strain and temperature. Still other researchers believe that hydrogen should increase the ability of the metal to transform due to hydrogen-enhanced dislocation mobility and slip planarity. While the role of hydrogen on the martensite transformation is still debated, it has been experimentally verified that this transformation does occur in hydrogen-charged materials. What is the effect of strain-induced martensite on hydrogen embrittlement? Martensite near crack-tips or other highly strained regions could provide much higher hydrogen diffusivity and allow for quicker hydrogen concentration. Martensite may be more intrinsically brittle than austenite and has been shown to be severely embrittled by hydrogen. However, it does not appear to be a necessary condition for embrittlement since Type 21-6-9 stainless steel is more stable than Type 304L stainless steel but susceptible to hydrogen embrittlement. In this study, the effect of hydrogen on strain-induced martensite formation in Type 304L stainless steel was investigated by monitoring the formation of martensite during tensile tests of as-received and hydrogen-charged samples and metallographically examining specimens from interrupted tensile tests after increasing levels of strain. The effect of hydrogen on the fracture mechanisms was also studied by examining the fracture features of as-received and hydrogen-charged specimens and relating them to the stress-strain behavior.

  13. Comparative genomics of type VI secretion systems in strains of Pantoea ananatis from different environments

    PubMed Central

    2014-01-01

    Background The Type VI secretion system (T6SS) has been identified in several different bacteria, including the plant pathogenPantoea ananatis. Previous in silico analyses described three different T6SS loci present in the pathogenic strain of P. ananatis LMG 20103. This initial investigation has been extended to include an additional seven sequenced strains of P. ananatis together with 39 strains from different ecological niches. Comparative and phylogenetic analyses were used to investigate the distribution, evolution, intra-strain variability and operon structure of the T6SS in the sequenced strains. Results Three different T6SS loci were identified in P. ananatis strain LMG 20103 and designated PA T6SS 1-3. PA T6SS-1 was present in all sequenced strains of P. ananatis and in all 39 additional strains examined in this study. In addition, PA T6SS-1 included all 13 core T6SS genes required for synthesis of a functional T6SS. The plasmid-borne PA T6SS-2 also included all 13 core T6SS genes but was restricted to only 33% (15/46) of the strains examined. In addition, PA T6SS-2 was restricted to strains of P. ananatis isolated from symptomatic plant material. This finding raises the possibility of an association between PA T6SS-2 and either pathogenicity or host specificity. The third cluster PA T6SS-3 was present in all strains analyzed in this study but lacked 11 of the 13 core T6SS genes suggesting it may not encoded a functional T6SS. Inter-strain variability was also associated with hcp and vgrG islands, which are associated with the T6SS and encode a variable number of proteins usually of unknown function. These proteins may play a role in the fitness of different strains in a variety of ecological niches or as candidate T6SS effectors. Phylogenetic analysis indicated that PA T6SS-1 and PA T6SS-2 are evolutionarily distinct. Conclusion Our analysis indicates that the three T6SSs of P. ananatis appear to have been independently acquired and may play different

  14. Genome Sequence of the Symbiotic Type Strain Rhizobium tibeticum CCBAU85039T

    PubMed Central

    Wibberg, Daniel; Winkler, Anika; Ormeño-Orrillo, Ernesto; Martínez-Romero, Esperanza; Niehaus, Karsten; Pühler, Alfred; Kalinowski, Jörn; Lagares, Antonio; Schlüter, Andreas; Pistorio, Mariano

    2017-01-01

    ABSTRACT Rhizobium tibeticum was originally isolated from root nodules of Trigonella archiducis-nicolai grown in Tibet, China. This species is also able to nodulate Medicago sativa and Phaseolus vulgaris. The whole-genome sequence of the type strain, R. tibeticum CCBAU85039T, is reported in this study. PMID:28126941

  15. Draft Whole-Genome Sequence of the Type Strain Bacillus aquimaris TF12T.

    PubMed

    Hernández-González, Ismael L; Olmedo-Álvarez, Gabriela

    2016-07-14

    Bacillus aquimaris TF12 is a Gram-positive bacteria isolated from a tidal flat of the Yellow Sea in South Korea. We report the draft whole-genome sequence of Bacillus aquimaris TF12, the type strain of a set of bacteria typically associated with marine habitats and with a potentially high biotechnology value.

  16. Complete genome sequence of Helicobacter cinaedi type strain ATCC BAA-847.

    PubMed

    Miyoshi-Akiyama, Tohru; Takeshita, Nozomi; Ohmagari, Norio; Kirikae, Teruo

    2012-10-01

    Here we report the completely annotated genome sequence of the Helicobacter cinaedi type strain (ATCC BAA-847), which is an emerging pathogen that causes cellulitis and bacteremia. The genome sequence will provide new insights into the diagnosis, pathogenic mechanisms, and drug resistance of H. cinaedi.

  17. Complete Genome Sequences for Three Chromosomes of the Burkholderia stabilis Type Strain (ATCC BAA-67).

    PubMed

    Bugrysheva, Julia V; Cherney, Blake; Sue, David; Conley, Andrew B; Rowe, Lori A; Knipe, Kristen M; Frace, Michael A; Loparev, Vladimir N; Avila, Julie R; Anderson, Kevin; Hodge, David R; Pillai, Segaran P; Weigel, Linda M

    2016-11-17

    We report here the complete annotated genome sequence of the Burkholderia stabilis type strain ATCC BAA-67. There were three circular chromosomes with a combined size of 8,527,947 bp and G+C composition of 66.4%. These characteristics closely resemble the genomes of other sequenced members of the Burkholderia cepacia complex.

  18. Draft Genome Sequence of Streptomyces specialis Type Strain GW41-1564 (DSM 41924)

    PubMed Central

    Loucif, Lotfi; Michelle, Caroline; Terras, Jérôme; Rolain, Jean-Marc; Raoult, Didier

    2017-01-01

    ABSTRACT Here, we report the draft genome sequence of Streptomyces specialis type strain GW41-1564, which was isolated from soil. This 5.87-Mb genome exhibits a high G+C content of 72.72% and contains 5,486 protein-coding genes. PMID:28360168

  19. Genome Sequence of the Symbiotic Type Strain Rhizobium tibeticum CCBAU85039T.

    PubMed

    Torres Tejerizo, Gonzalo; Wibberg, Daniel; Winkler, Anika; Ormeño-Orrillo, Ernesto; Martínez-Romero, Esperanza; Niehaus, Karsten; Pühler, Alfred; Kalinowski, Jörn; Lagares, Antonio; Schlüter, Andreas; Pistorio, Mariano

    2017-01-26

    Rhizobium tibeticum was originally isolated from root nodules of Trigonella archiducis-nicolai grown in Tibet, China. This species is also able to nodulate Medicago sativa and Phaseolus vulgaris The whole-genome sequence of the type strain, R. tibeticum CCBAU85039(T), is reported in this study.

  20. Genome sequencing of phomopsis longicolla type strain twh p74 causing phomopsis seed decay in soybean

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Phomopsis longicolla (syn. Diaporthe longicolla) is the primary cause of Phomopsis seed decay in soybean. We report the de novo assembled draft genome sequence of P. longicolla type strain TWH P74. The resulting draft genome was estimated to be approximately 64 Mb in size with an overall G+C content...

  1. Complete Genome Sequence of Type Strain Campylobacter fetus subsp. venerealis NCTC 10354T

    PubMed Central

    Stynen, Ana Paula Reinato; Lage, Andrey Pereira; Moore, Robert J.; Rezende, Antonio Mauro; de Resende, Vivian D'Afonseca da Silva; Ruy, Patricia de Cássia; Daher, Nesley; Resende, Daniela de Melo; de Almeida, Sintia Silva; Soares, Siomar de Castro; de Abreu, Vinicius Augusto Carvalho; Rocha, Aryane Aparecida C. Magalhães; dos Santos, Anderson Rodrigues; Barbosa, Eudes Guilherme Vieira; Costa, Danielle Fonseca; Dorella, Fernanda Alves; Miyoshi, Anderson; de Lima, Alex Ranieri Jerônimo; Campos, Frederico Davi da Silva; de Sá, Pablo Gomes; Lopes, Thiago Souza; Rodrigues, Ryan Mauricio Araujo; Carneiro, Adriana Ribeiro; Leão, Thiago; Cerdeira, Louise Teixeira; Ramos, Rommel Thiago Jucá; Silva, Artur; Azevedo, Vasco; Ruiz, Jerônimo C.

    2011-01-01

    Campylobacter fetus subsp. venerealis is the etiologic agent of bovine genital campylobacteriosis, a sexually transmitted disease of cattle that is of worldwide importance. The complete sequencing and annotation of the genome of the type strain C. fetus subsp. venerealis NCTC 10354T are reported. PMID:21952544

  2. Draft Whole-Genome Sequence of the Type Strain Bacillus aquimaris TF12T

    PubMed Central

    Hernández-González, Ismael L.

    2016-01-01

    Bacillus aquimaris TF12 is a Gram-positive bacteria isolated from a tidal flat of the Yellow Sea in South Korea. We report the draft whole-genome sequence of Bacillus aquimaris TF12, the type strain of a set of bacteria typically associated with marine habitats and with a potentially high biotechnology value. PMID:27417832

  3. Complete genome sequence of Mycobacterium fortuitum subsp. fortuitum type strain DSM46621.

    PubMed

    Ho, Yung S; Adroub, Sabir A; Aleisa, Fajr; Mahmood, Hanan; Othoum, Ghofran; Rashid, Fahad; Zaher, Manal; Ali, Shahjahan; Bitter, Wilbert; Pain, Arnab; Abdallah, Abdallah M

    2012-11-01

    Mycobacterium fortuitum is a member of the rapidly growing nontuberculous mycobacteria (NTM). It is ubiquitous in water and soil habitats, including hospital environments. M. fortuitum is increasingly recognized as an opportunistic nosocomial pathogen causing disseminated infection. Here we report the genome sequence of M. fortuitum subsp. fortuitum type strain DSM46621.

  4. Complete genome sequence of Dehalogenimonas lykanthroporepellens type strain (BL-DC-9T) and comparison to Dehalococcoides strains

    SciTech Connect

    Siddaramappa, Shivakumara; Delano, Susana; Green, Lance D.; Daligault, Hajnalka E.; Bruce, David; Detter, J. Chris; Tapia, Roxanne; Han, Cliff; Goodwin, Lynne A.; Han, James; Woyke, Tanja; Pitluck, Sam; Pennacchio, Len; Nolan, Matt; Land, Miriam L; Chang, Yun-Juan; Kyrpides, Nikos C; Ovchinnikova, Galina; Hauser, Loren John; Lapidus, Alla L.; Yan, Jun; Bowman, Kimberly; Da Costa, Milton S,; Rainey, Fred A.; Moe, William M.

    2012-01-01

    Dehalogenimonas lykanthroporepellens is the type species of the genus Dehalogenimonas, which belongs to a deeply branching lineage within the phylum Chloroflexi. This strictly anaerobic, mesophilic, non spore forming, Gram negative staining bacterium was first isolated from chlorinated solvent contaminated groundwater at a Superfund site located near Baton Rouge, Louisiana, USA. D. lykanthroporepellens was of interest for genome sequencing for two reasons: (a) its unusual ability to couple growth with reductive dechlorination of environmentally important polychlorinated aliphatic alkanes and (b) its phylogenetic position distant from previously sequenced bacteria. The 1,686,510 bp circular chromosome of strain BL-DC-9{sup T} contains 1,720 predicted protein coding genes, 47 tRNA genes, a single large subunit rRNA (23S-5S) locus, and a single, orphan, small unit rRNA (16S) locus.

  5. Mating Type Gene (MAT) and Itraconazole Susceptibility of Trichophyton tonsurans Strains Isolated in Japan.

    PubMed

    Hiruma, Junichiro; Okubo, Miki; Kano, Rui; Kumagawa, Mai; Hiruma, Masataro; Hasegawa, Atsuhiko; Kamata, Hiroshi; Tsuboi, Ryoji

    2016-06-01

    Infection by Trichophyton tonsurans is an emerging fungal epidemic in Japan. Itraconazole (ITZ) and terbinafine have been used for the treatment of this infection for 15 years. However, patients with T. tonsurans infections have been shown to remain uncured or to become reinfected, suggesting that subclinical infection or polyphyletic strains and/or antifungal drug-resistant strains might be occurring in Japan. In this study, PCR analysis was performed to confirm the presence of the mating type locus MAT in genomic DNA from 60 Japanese clinical isolates of T. tonsurans, and to assess the previously postulated clonal origin of clinical isolates of this species. Antifungal susceptibility testing on isolates also was performed to confirm the absence of strains resistant to ITZ. PCR analysis proved that all 60 strains contained the MAT1-1 allele, while none contained the MAT1-2 allele. As determined by E-test, the mean MIC of ITZ in the 60 strains was 0.023 mg/L (range 0.002-0.125 mg/L). All strains of T. tonsurans isolated in Japan were clonal and were not resistant to ITZ. Therefore, dermatophytosis due to T. tonsurans is expected to respond to ITZ, since clinical isolates of T. tonsurans tested to date have been susceptible to this antifungal. This infection is proliferating as a subclinical infection in Japan.

  6. Ribitol dehydrogenase of Klebsiella aerogenes. Sequence and properties of wild-type and mutant strains.

    PubMed Central

    Dothie, J M; Giglio, J R; Moore, C B; Taylor, S S; Hartley, B S

    1985-01-01

    Evidence is presented for the sequence of 249 amino acids in ribitol dehydrogenase-A from Klebsiella aerogenes. Continuous culture on xylitol yields strains that superproduce 'wild-type' enzyme but mutations appear to have arisen in this process. Other strains selected by such continuous culture produce enzymes with increased specific activity for xylitol but without loss of ribitol activity. One such enzyme, ribitol dehydrogenase-D, has Pro-196 for Gly-196. Another, ribitol dehydrogenase-B, has a different mutation. PMID:3904726

  7. Narrowing of antiferromagnetic domain wall in corundum-type Cr2O3 by lattice strain

    NASA Astrophysics Data System (ADS)

    Kota, Yohei; Imamura, Hiroshi

    2017-01-01

    The effect of lattice strain on single-ion magnetic anisotropy and antiferromagnetic domain wall width in corundum-type Cr2O3 is studied using first-principles calculations and micromagnetics simulations. Without lattice strain, the domain wall width L DW is about 80 nm. When the lattice constant a is increased by 1-2%, L DW is reduced to less than 20 nm due to the increase in the single-ion anisotropy constant K 1 to on the order of 106 erg/cm3.

  8. Complete genome sequence of Rhodospirillum rubrum type strain (S1T)

    SciTech Connect

    Munk, Christine; Copeland, A; Lucas, Susan; Lapidus, Alla L.; Glavina Del Rio, Tijana; Barry, Kerrie; Detter, J. Chris; Hammon, Nancy; Israni, Sanjay; Pitluck, Sam; Brettin, Thomas S; Bruce, David; Han, Cliff; Tapia, Roxanne; Gilna, Paul; Schmutz, Jeremy; Larimer, Frank W; Land, Miriam L; Kyrpides, Nikos C; Mavromatis, K; Richardson, P M; Rohde, Manfred; Goker, Markus; Klenk, Hans-Peter; Zhang, Yaoping; Roberts, Gary P.; Reslewic, Susan; Schwartz, David C.

    2011-01-01

    Rhodospirillum rubrum (Esmarch 1887) Molisch 1907 is the type species of the genus Rho- dospirillum, which is the type genus of the family Rhodospirillaceae in the class Alphaproteo- bacteria. The species is of special interest because it is an anoxygenic phototroph that pro- duces extracellular elemental sulfur (instead of oxygen) while harvesting light. It contains one of the most simple photosynthetic systems currently known, lacking light harvesting complex 2. Strain S1T can grow on carbon monoxide as sole energy source. With currently over 1,750 PubMed entries, R. rubrum is one of the most intensively studied microbial species, in partic- ular for physiological and genetic studies. Next to R. centenum strain SW, the genome se- quence of strain S1T is only the second genome of a member of the genus Rhodospirillum to be published, but the first type strain genome from the genus. The 4,352,825 bp long chro- mosome and 53,732 bp plasmid with a total of 3,850 protein-coding and 83 RNA genes were sequenced as part of the DOE Joint Genome Institute Program DOEM 2002.

  9. Molecular analysis of Acinetobacter baumannii strains isolated in Lebanon using four different typing methods.

    PubMed

    Rafei, Rayane; Dabboussi, Fouad; Hamze, Monzer; Eveillard, Matthieu; Lemarié, Carole; Gaultier, Marie-Pierre; Mallat, Hassan; Moghnieh, Rima; Husni-Samaha, Rola; Joly-Guillou, Marie-Laure; Kempf, Marie

    2014-01-01

    This study analyzed 42 Acinetobacter baumannii strains collected between 2009-2012 from different hospitals in Beyrouth and North Lebanon to better understand the epidemiology and carbapenem resistance mechanisms in our collection and to compare the robustness of pulsed field gel electrophoresis (PFGE), multilocus sequence typing (MLST), repetitive sequence-based PCR (rep-PCR) and blaOXA-51 sequence-based typing (SBT). Among 31 carbapenem resistant strains, we have detected three carbapenem resistance genes: 28 carried the blaOXA-23 gene, 1 the blaOXA-24 gene and 2 strains the blaOXA-58 gene. This is the first detection of blaOXA-23 and blaOXA-24 in Lebanon. PFGE identified 11 types and was the most discriminating technique followed by rep-PCR (9 types), blaOXA-51 SBT (8 types) and MLST (7 types). The PFGE type A'/ST2 was the dominant genotype in our collection present in Beyrouth and North Lebanon. The clustering agreement between all techniques was measured by adjust Wallace coefficient. An overall agreement has been demonstrated. High values of adjust Wallace coefficient were found with followed combinations: PFGE to predict MLST types  = 100%, PFGE to predict blaOXA-51 SBT = 100%, blaOXA-51 SBT to predict MLST = 100%, MLST to predict blaOXA-51 SBT = 84.7%, rep-PCR to predict MLST = 81.5%, PFGE to predict rep-PCR = 69% and rep-PCR to predict blaOXA-51 SBT = 67.2%. PFGE and MLST are gold standard methods for outbreaks investigation and population structure studies respectively. Otherwise, these two techniques are technically, time and cost demanding. We recommend the use of blaOXA-51 SBT as first typing method to screen isolates and assign them to their corresponding clonal lineages. Repetitive sequence-based PCR is a rapid tool to access outbreaks but careful interpretation of results must be always performed.

  10. Evaluation of chemotherapy with benznidazole and nifurtimox in mice infected with Trypanosoma cruzi strains of different types*

    PubMed Central

    Andrade, S. G.; Magalhães, J. B.; Pontes, A. L.

    1985-01-01

    A test was made of the susceptibility of 30 strains of Trypanosoma cruzi to chemotherapy with nifurtimox (Bay 2502) and benznidazole (Ro 7-1051). The strains had previously been classified as type I, II, or III according to their morphobiological and isoenzymic characteristics. Three type I strains, 14 type II strains, and 13 type III strains were studied. Mice were infected with 2 × 105 blood forms of these parasites and treated for 90 days with benznidazole or nifurtimox. All the surviving mice were submitted to parasitological tests (direct parasitaemia, xenodiagnosis, inoculation in new-born mice, and haemoculture) and serological tests (indirect immunofluorescence). As the latter remained positive in about 80% of the parasitologically negative animals, the cure rates were based on the more reliable parasitological tests. Type I strains displayed high susceptibility, type II strains showed medium to high susceptibility, and type III strains were highly resistant to both drugs. The fact that a particular strain type, with its own level of susceptibility, usually predominates in a given geographical area may explain the contradictory results after chemotherapy from different endemic areas. PMID:3936634

  11. Structure and genetic content of the megaplasmids of neurotoxigenic clostridium butyricum type E strains from Italy.

    PubMed

    Iacobino, Angelo; Scalfaro, Concetta; Franciosa, Giovanna

    2013-01-01

    We determined the genetic maps of the megaplasmids of six neutoroxigenic Clostridium butyricum type E strains from Italy using molecular and bioinformatics techniques. The megaplasmids are circular, not linear as we had previously proposed. The differently-sized megaplasmids share a genetic region that includes structural, metabolic and regulatory genes. In addition, we found that a 168 kb genetic region is present only in the larger megaplasmids of two tested strains, whereas it is absent from the smaller megaplasmids of the four remaining strains. The genetic region unique to the larger megaplasmids contains, among other features, a locus for clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR associated (cas) genes, i.e. a bacterial adaptive immune system providing sequence-specific protection from invading genetic elements. Some CRISPR spacer sequences of the neurotoxigenic C. butyricum type E strains showed homology to prophage, phage and plasmid sequences from closely related clostridia species or from distant species, all sharing the intestinal habitat, suggesting that the CRISPR locus might be involved in the microorganism adaptation to the human or animal intestinal environment. Besides, we report here that each of four distinct CRISPR spacers partially matched DNA sequences of different prophages and phages, at identical nucleotide locations. This suggests that, at least in neurotoxigenic C. butyricum type E, the CRISPR locus is potentially able to recognize the same conserved DNA sequence of different invading genetic elements, besides targeting sequences unique to previously encountered invading DNA, as currently predicted for a CRISPR locus. Thus, the results of this study introduce the possibility that CRISPR loci can provide resistance to a wider range of invading DNA elements than previously appreciated. Whether it is more advantageous for the peculiar neurotoxigenic C. butyricum type E strains to maintain or to lose the

  12. Structure and Genetic Content of the Megaplasmids of Neurotoxigenic Clostridium butyricum Type E Strains from Italy

    PubMed Central

    Iacobino, Angelo; Scalfaro, Concetta; Franciosa, Giovanna

    2013-01-01

    We determined the genetic maps of the megaplasmids of six neutoroxigenic Clostridium butyricum type E strains from Italy using molecular and bioinformatics techniques. The megaplasmids are circular, not linear as we had previously proposed. The differently-sized megaplasmids share a genetic region that includes structural, metabolic and regulatory genes. In addition, we found that a 168 kb genetic region is present only in the larger megaplasmids of two tested strains, whereas it is absent from the smaller megaplasmids of the four remaining strains. The genetic region unique to the larger megaplasmids contains, among other features, a locus for clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR associated (cas) genes, i.e. a bacterial adaptive immune system providing sequence-specific protection from invading genetic elements. Some CRISPR spacer sequences of the neurotoxigenic C. butyricum type E strains showed homology to prophage, phage and plasmid sequences from closely related clostridia species or from distant species, all sharing the intestinal habitat, suggesting that the CRISPR locus might be involved in the microorganism adaptation to the human or animal intestinal environment. Besides, we report here that each of four distinct CRISPR spacers partially matched DNA sequences of different prophages and phages, at identical nucleotide locations. This suggests that, at least in neurotoxigenic C. butyricum type E, the CRISPR locus is potentially able to recognize the same conserved DNA sequence of different invading genetic elements, besides targeting sequences unique to previously encountered invading DNA, as currently predicted for a CRISPR locus. Thus, the results of this study introduce the possibility that CRISPR loci can provide resistance to a wider range of invading DNA elements than previously appreciated. Whether it is more advantageous for the peculiar neurotoxigenic C. butyricum type E strains to maintain or to lose the

  13. Selective enrichment media bias the types of Salmonella enterica strains isolated from mixed strain cultures and complex enrichment broths.

    PubMed

    Gorski, Lisa

    2012-01-01

    For foodborne outbreak investigations it can be difficult to isolate the relevant strain from food and/or environmental sources. If the sample is contaminated by more than one strain of the pathogen the relevant strain might be missed. In this study mixed cultures of Salmonella enterica were grown in one set of standard enrichment media to see if culture bias patterns emerged. Nineteen strains representing four serogroups and ten serotypes were compared in four-strain mixtures in Salmonella-only and in cattle fecal culture enrichment backgrounds using Salmonella enrichment media. One or more strain(s) emerged as dominant in each mixture. No serotype was most fit, but strains of serogroups C2 and E were more likely to dominate enrichment culture mixtures than strains of serogroups B or C1. Different versions of Rappaport-Vassiliadis (RV) medium gave different patterns of strain dominance in both Salmonella-only and fecal enrichment culture backgrounds. The fittest strains belonged to serogroups C1, C2, and E, and included strains of S. Infantis, S. Thompson S. Newport, S. 6,8:d:-, and S. Give. Strains of serogroup B, which included serotypes often seen in outbreaks such as S. Typhimurium, S. Saintpaul, and S. Schwarzengrund were less likely to emerge as dominant strains in the mixtures when using standard RV as part of the enrichment. Using a more nutrient-rich version of RV as part of the protocol led to a different pattern of strains emerging, however some were still present in very low numbers in the resulting population. These results indicate that outbreak investigations of food and/or other environmental samples should include multiple enrichment protocols to ensure isolation of target strains of Salmonella.

  14. CC8 MRSA Strains Harboring SCCmec Type IVc are Predominant in Colombian Hospitals

    PubMed Central

    Jiménez, J. Natalia; Ocampo, Ana M.; Vanegas, Johanna M.; Rodriguez, Erika A.; Mediavilla, José R.; Chen, Liang; Muskus, Carlos E.; A. Vélez, Lázaro; Rojas, Carlos; Restrepo, Andrea V.; Ospina, Sigifredo; Garcés, Carlos; Franco, Liliana; Bifani, Pablo; Kreiswirth, Barry N.; Correa, Margarita M.

    2012-01-01

    Background Recent reports highlight the incursion of community-associated MRSA within healthcare settings. However, knowledge of this phenomenon remains limited in Latin America. The aim of this study was to evaluate the molecular epidemiology of MRSA in three tertiary-care hospitals in Medellín, Colombia. Methods An observational cross-sectional study was conducted from 2008–2010. MRSA infections were classified as either community-associated (CA-MRSA) or healthcare-associated (HA-MRSA), with HA-MRSA further classified as hospital-onset (HAHO-MRSA) or community-onset (HACO-MRSA) according to standard epidemiological definitions established by the U.S. Centers for Disease Control and Prevention (CDC). Genotypic analysis included SCCmec typing, spa typing, PFGE and MLST. Results Out of 538 total MRSA isolates, 68 (12.6%) were defined as CA-MRSA, 243 (45.2%) as HACO-MRSA and 227 (42.2%) as HAHO-MRSA. The majority harbored SCCmec type IVc (306, 58.7%), followed by SCCmec type I (174, 33.4%). The prevalence of type IVc among CA-, HACO- and HAHO-MRSA isolates was 92.4%, 65.1% and 43.6%, respectively. From 2008 to 2010, the prevalence of type IVc-bearing strains increased significantly, from 50.0% to 68.2% (p = 0.004). Strains harboring SCCmec IVc were mainly associated with spa types t1610, t008 and t024 (MLST clonal complex 8), while PFGE confirmed that the t008 and t1610 strains were closely related to the USA300-0114 CA-MRSA clone. Notably, strains belonging to these three spa types exhibited high levels of tetracycline resistance (45.9%). Conclusion CC8 MRSA strains harboring SCCmec type IVc are becoming predominant in Medellín hospitals, displacing previously reported CC5 HA-MRSA clones. Based on shared characteristics including SCCmec IVc, absence of the ACME element and tetracycline resistance, the USA300-related isolates in this study are most likely related to USA300-LV, the recently-described ‘Latin American variant’ of USA300. PMID:22745670

  15. IS200 and multilocus sequence typing for the identification of Salmonella enterica serovar Typhi strains from Indonesia.

    PubMed

    Martínez-Gamboa, Areli; Silva, Claudia; Fernández-Mora, Marcos; Wiesner, Magdalena; Ponce de León, Alfredo; Calva, Edmundo

    2015-06-01

    In this work, IS200 and multi-locus sequence typing (MLST) were used to analyze 19 strains previously serotyped as Salmonella enterica serovar Typhi and isolated in Indonesia (16 strains), Mexico (2 strains), and Switzerland (1 strain). Most of the strains showed the most common Typhi sequence types, ST1 and ST2, and a new Typhi genotype (ST1856) was described. However, one isolate from Mexico and another from Indonesia were of the ST365 and ST426 sequence types, indicating that they belonged to serovars Weltevreden and Aberdeen, respectively. These results were supported by the amplification of IS200 fragments, which rapidly distinguish Typhi from other serovars. Our results demonstrate the utility of IS200 and MLST in the classification of Salmonella strains into serovars. These methods provide information on the clonal relatedness of strains isolated worldwide.

  16. Selective enrichment media bias the types of salmonella enterica strains isolated from mixed strain cultures and complex enrichment broths

    Technology Transfer Automated Retrieval System (TEKTRAN)

    For foodborne outbreak investigations it can be difficult to isolate the relevant strain from food and/or environmental sources. If the sample is contaminated by more than one strain of the organism the relevant strain might be missed. In this study mixed cultures of Salmonella enterica were grown...

  17. Single-strand conformation polymorphism of microsatellite for rapid strain typing of Candida albicans.

    PubMed

    Li, Juan; Bai, Feng-Yan

    2007-11-01

    Single-strand conformation polymorphisms (SSCP) of Candida albicans' microsatellite CAI were characterized. Among the 76 clinical isolates recovered from different patients (independent strains), 60 distinct CAI SSCP patterns were recognized, resulting in a discriminatory power of 0.993. The multiple isolates recovered sequentially from the same or different body locations of the same patient showed exactly the same CAI SSCP pattern. The reliability of the SSCP analysis was confirmed by GeneScan and sequence analyses. From the same set of independent strains, 59 distinct CAI genotypes were identified by GeneScan analysis. Sequence comparison showed the advantage of SSCP over GeneSan analysis in the detection of point mutations in the microsatellite. The results indicated that PCR SSCP analysis of CAI microsatellite is a powerful and economical approach for rapid strain typing of C. albicans in clinical laboratories, especially in the detection of microevolutionary changes in microsatellites and in large-scale epidemiological investigation.

  18. Complete genome sequence of Tolumonas auensis type strain (TA 4T)

    SciTech Connect

    Chertkov, Olga; Copeland, Alex; Lucas1, Susa; Lapidus, Alla; Berry, KerrieW.; Detter, JohnC.; Glavina Del Rio, Tijana; Hammon, Nancy; Dalin, Eileen; Tice, Hope; Pitluck, Sam; Richardson, Paul; Bruce, David; Goodwin, Lynne; Han, Cliff; Tapia, Roxanne; Saunders, Elizabeth; Schmutz, Jeremy; Brettin, Thomas; Larimer, Frank; Land, Miriam; Hauser, Loren; Spring, Stefan; Rohde, Manfred; Kyrpides, NikosC.; Ivanova, Natalia; Göker, Markus; Beller, HarryR.; Klenk, Hans-Peter; Woyke, Tanja

    2011-10-04

    Tolumonas auensis (Fischer-Romero et al. 1996) is currently the only validly named species of the genus Tolumonas in the family Aeromonadaceae. The strain is of interest because of its ability to produce toluene from phenylalanine and other phenyl precursors, as well as phenol from tyrosine. This is of interest because toluene is normally considered to be a tracer of anthropogenic pollution in lakes, but T. auensis represents a biogenic source of toluene. Other than Aeromonas hydrophila subsp. hydrophila, T. auensis strain TA 4T is the only other member in the family Aeromonadaceae with a completely sequenced type-strain genome. The 3,471,292-bp chromosome with a total of 3,288 protein-coding and 116 RNA genes was sequenced as part of the DOE Joint Genome Institute Program JBEI 2008.

  19. Permissive growth of human adenovirus type 4 vaccine strain-based vector in porcine cell lines.

    PubMed

    Gao, Dong-sheng; Li, Xiao-jing; Wan, Wen-yan; Li, Hong-jie; Wang, Xiao-xue; Yang, Xia; Li, Yong-tao; Chang, Hong-tao; Chen, Lu; Wang, Chuan-qing; Zhao, Jun

    2016-02-01

    In recent years, there has been considerable interest in using adenoviruses as live vectors to develop recombinant vaccines. Previous studies have demonstrated the safety and effectiveness of HIV/SIV and influenza vaccine candidates based on human adenovirus type 4 (Ad4) replication-competent vectors in rhesus macaque and human model. To explore the possibility of human Ad4 vaccine strain used as a vector in developing porcine vaccines, the growth properties of replication-competent human Ad4 vaccine strain recombinant encoding EGFP in different porcine cell lines were investigated. All tested cell lines are permissive for Ad4 vaccine strain vector with varied replication efficiency. Thus, human Ad4 based vectors would be promising supplement to adenovirus vectors as a delivery vehicle for recombinant vaccines in swine industry.

  20. Development of Immunoassays for Burkholderia pseudomallei Typical and Atypical Lipopolysaccharide Strain Typing

    PubMed Central

    Nualnoi, Teerapat; Norris, Michael H.; Tuanyok, Apichai; Brett, Paul J.; Burtnick, Mary N.; Keim, Paul S.; Settles, Erik W.; Allender, Christopher J.; AuCoin, David P.

    2017-01-01

    Burkholderia pseudomallei is the causative agent of melioidosis, a severe infection endemic to many tropical regions. Lipopolysaccharide (LPS) is recognized as an important virulence factor used by B. pseudomallei. Isolates of B. pseudomallei have been shown to express one of four different types of LPS (typical LPS, atypical LPS types B and B2, and rough LPS) and in vitro studies have demonstrated that LPS types may impact disease severity. The association between LPS types and clinical manifestations, however, is still unknown, in part because an effective method for LPS type identification is not available. Thus, we developed antigen capture immunoassays capable of distinguishing between the LPS types. Mice were injected with B or B2 LPS for atypical LPS–specific monoclonal antibody (mAb) isolation; only two mAbs (3A2 and 5B4) were isolated from mice immunized with B2 LPS. Immunoblot analysis and surface plasmon resonance demonstrated that 3A2 and 5B4 are reactive with both B2 and B LPS where 3A2 was shown to possess higher affinity. Assays were then developed using capsular polysaccharide–specific mAb 4C4 for bacterial capture and 4C7 (previously shown to bind typical LPS) or 3A2 mAbs for typical or atypical LPS strain detection, respectively. The evaluations performed with 197 strains of Burkholderia and non-Burkholderia species showed that the assays are reactive to B. pseudomallei and Burkholderia mallei strains and have an accuracy of 98.8% (zero false positives and two false negatives) for LPS typing. The results suggest that the assays are effective and applicable for B. pseudomallei LPS typing. PMID:27994103

  1. Phylogeny and Strain Typing of Escherichia coli, Inferred from Variation at Mononucleotide Repeat Loci

    PubMed Central

    Diamant, Eran; Palti, Yniv; Gur-Arie, Riva; Cohen, Helit; Hallerman, Eric M.; Kashi, Yechezkel

    2004-01-01

    Multilocus sequencing of housekeeping genes has been used previously for bacterial strain typing and for inferring evolutionary relationships among strains of Escherichia coli. In this study, we used shorter intergenic sequences that contained simple sequence repeats (SSRs) of repeating mononucleotide motifs (mononucleotide repeats [MNRs]) to infer the phylogeny of pathogenic and commensal E. coli strains. Seven noncoding loci (four MNRs and three non-SSRs) were sequenced in 27 strains, including enterohemorrhagic (six isolates of O157:H7), enteropathogenic, enterotoxigenic, B, and K-12 strains. The four MNRs were also sequenced in 20 representative strains of the E. coli reference (ECOR) collection. Sequence polymorphism was significantly higher at the MNR loci, including the flanking sequences, indicating a higher mutation rate in the sequences flanking the MNR tracts. The four MNR loci were amplifiable by PCR in the standard ECOR A, B1, and D groups, but only one (yaiN) in the B2 group was amplified, which is consistent with previous studies that suggested that B2 is the most ancient group. High sequence compatibility was found between the four MNR loci, indicating that they are in the same clonal frame. The phylogenetic trees that were constructed from the sequence data were in good agreement with those of previous studies that used multilocus enzyme electrophoresis. The results demonstrate that MNR loci are useful for inferring phylogenetic relationships and provide much higher sequence variation than housekeeping genes. Therefore, the use of MNR loci for multilocus sequence typing should prove efficient for clinical diagnostics, epidemiology, and evolutionary study of bacteria. PMID:15066845

  2. Detection and Strain Typing of Ancient Mycobacterium leprae from a Medieval Leprosy Hospital

    PubMed Central

    Taylor, G. Michael; Tucker, Katie; Butler, Rachel; Pike, Alistair W. G.; Lewis, Jamie; Roffey, Simon; Marter, Philip; Lee, Oona Y-C; Wu, Houdini H. T.; Minnikin, David E.; Besra, Gurdyal S.; Singh, Pushpendra; Cole, Stewart T.; Stewart, Graham R.

    2013-01-01

    Nine burials excavated from the Magdalen Hill Archaeological Research Project (MHARP) in Winchester, UK, showing skeletal signs of lepromatous leprosy (LL) have been studied using a multidisciplinary approach including osteological, geochemical and biomolecular techniques. DNA from Mycobacterium leprae was amplified from all nine skeletons but not from control skeletons devoid of indicative pathology. In several specimens we corroborated the identification of M. leprae with detection of mycolic acids specific to the cell wall of M. leprae and persistent in the skeletal samples. In five cases, the preservation of the material allowed detailed genotyping using single-nucleotide polymorphism (SNP) and multiple locus variable number tandem repeat analysis (MLVA). Three of the five cases proved to be infected with SNP type 3I-1, ancestral to contemporary M. leprae isolates found in southern states of America and likely carried by European migrants. From the remaining two burials we identified, for the first time in the British Isles, the occurrence of SNP type 2F. Stable isotope analysis conducted on tooth enamel taken from two of the type 3I-1 and one of the type 2F remains revealed that all three individuals had probably spent their formative years in the Winchester area. Previously, type 2F has been implicated as the precursor strain that migrated from the Middle East to India and South-East Asia, subsequently evolving to type 1 strains. Thus we show that type 2F had also spread westwards to Britain by the early medieval period. PMID:23638071

  3. Detection and strain typing of ancient Mycobacterium leprae from a medieval leprosy hospital.

    PubMed

    Taylor, G Michael; Tucker, Katie; Butler, Rachel; Pike, Alistair W G; Lewis, Jamie; Roffey, Simon; Marter, Philip; Lee, Oona Y-C; Wu, Houdini H T; Minnikin, David E; Besra, Gurdyal S; Singh, Pushpendra; Cole, Stewart T; Stewart, Graham R

    2013-01-01

    Nine burials excavated from the Magdalen Hill Archaeological Research Project (MHARP) in Winchester, UK, showing skeletal signs of lepromatous leprosy (LL) have been studied using a multidisciplinary approach including osteological, geochemical and biomolecular techniques. DNA from Mycobacterium leprae was amplified from all nine skeletons but not from control skeletons devoid of indicative pathology. In several specimens we corroborated the identification of M. leprae with detection of mycolic acids specific to the cell wall of M. leprae and persistent in the skeletal samples. In five cases, the preservation of the material allowed detailed genotyping using single-nucleotide polymorphism (SNP) and multiple locus variable number tandem repeat analysis (MLVA). Three of the five cases proved to be infected with SNP type 3I-1, ancestral to contemporary M. leprae isolates found in southern states of America and likely carried by European migrants. From the remaining two burials we identified, for the first time in the British Isles, the occurrence of SNP type 2F. Stable isotope analysis conducted on tooth enamel taken from two of the type 3I-1 and one of the type 2F remains revealed that all three individuals had probably spent their formative years in the Winchester area. Previously, type 2F has been implicated as the precursor strain that migrated from the Middle East to India and South-East Asia, subsequently evolving to type 1 strains. Thus we show that type 2F had also spread westwards to Britain by the early medieval period.

  4. Molecular analysis of Porcine Circovirus Type 2 strains from Uruguay: evidence for natural occurring recombination.

    PubMed

    Ramos, Natalia; Mirazo, Santiago; Castro, Gustavo; Arbiza, Juan

    2013-10-01

    Porcine Circovirus Type 2 (PCV2) is a worldwide distributed virus and is considered an important emerging pathogen related to several distinct disease syndromes in pigs. Genomic structure consists of three major open reading frames (ORFs). ORF1 (rep gene) encodes replication-related proteins, ORF2 (cap gene) encodes the capsid protein and ORF3 encodes a protein putatively involved in virus-induced apoptosis. Based on cap gene sequences, PCV2 strains are classified into two main genotypes, PCV2a with five clusters (2A-2E) and PCV2b with three clusters (1A-1C). According to previous theoretical studies, PCV2 strains can eventually undergo intra and inter-genotype recombination, mainly within the rep gene. Ever since, several evidences of recombination in the field have been reported and confirmed this hypothesis. In South America, data regarding molecular characterization of PCV2 strains is still scant. Genotyping studies in the region have concluded that PCV2b is the predominant circulating genotype in the region and till now, no recombinant strains have ever been reported. In this work we thoroughly characterized at the molecular level Uruguayan PCV2 strains by extensive sequence data analysis. Moreover, recombination software tools were applied to explore and characterize eventual occurrence of natural recombination events. Two recombinant PCV2 strains were detected in this study, as a consequence of an inter-genotype recombination event between PCV2b-1A and PCV2a-2D, as the major and minor parent, respectively. According to recombination software analysis, in both cases the event occurred within the ORF1. Herein, extensive viral sequence dataset is provided, including the characterization of the first PCV2 recombinant strains ever reported in South America. Additionally, our results suggested a multi-centered source of PCV2 infection in Uruguay, which probably involved Brazilian and European origins.

  5. Genomic Encyclopedia of Type Strains, Phase I: The one thousand microbial genomes (KMG-I) project.

    PubMed

    Kyrpides, Nikos C; Woyke, Tanja; Eisen, Jonathan A; Garrity, George; Lilburn, Timothy G; Beck, Brian J; Whitman, William B; Hugenholtz, Phil; Klenk, Hans-Peter

    2014-06-15

    The Genomic Encyclopedia of Bacteria and Archaea (GEBA) project was launched by the JGI in 2007 as a pilot project with the objective of sequencing 250 bacterial and archaeal genomes. The two major goals of that project were (a) to test the hypothesis that there are many benefits to the use the phylogenetic diversity of organisms in the tree of life as a primary criterion for generating their genome sequence and (b) to develop the necessary framework, technology and organization for large-scale sequencing of microbial isolate genomes. While the GEBA pilot project has not yet been entirely completed, both of the original goals have already been successfully accomplished, leading the way for the next phase of the project. Here we propose taking the GEBA project to the next level, by generating high quality draft genomes for 1,000 bacterial and archaeal strains. This represents a combined 16-fold increase in both scale and speed as compared to the GEBA pilot project (250 isolate genomes in 4+ years). We will follow a similar approach for organism selection and sequencing prioritization as was done for the GEBA pilot project (i.e. phylogenetic novelty, availability and growth of cultures of type strains and DNA extraction capability), focusing on type strains as this ensures reproducibility of our results and provides the strongest linkage between genome sequences and other knowledge about each strain. In turn, this project will constitute a pilot phase of a larger effort that will target the genome sequences of all available type strains of the Bacteria and Archaea.

  6. Helicobacter pylori with East Asian-type cagPAI genes is more virulent than strains with Western-type in some cagPAI genes.

    PubMed

    Yuan, Xiao-Yan; Yan, Jin-Jun; Yang, Ya-Chao; Wu, Chun-Mei; Hu, Yan; Geng, Jian-Li

    2016-12-22

    The severity of Helicobacter pylori-related disease is correlated with the presence and integrity of a cag pathogenicity island (cagPAI). cagPAI genotype may have a modifying effect on the pathogenic potential of the infecting strain. After analyzing the sequences of cagPAI genes, some strains with the East Asian-type cagPAI genes were selected for further analysis to examine the association between the diversity of the cagPAI genes and the virulence of H. pylori. The results showed that gastric mucosal inflammatory cell infiltration was significantly higher in patients with East Asian-type cagPAI genes H. pylori strain compared with mosaicism cagPAI genes H. pylori strain (p<0.05). H. pylori strains with the East Asian-type cagPAI genes were closely associated with IL-8 secretion in vitro and in vivo compared with H. pylori strains with the mosaicism cagPAI genes (p<0.01). H. pylori strains with East Asian-type cagPAI genes are able to strongly translocate CagA to host cells. These results suggest that H. pylori strains with East Asian-type cagPAI genes are more virulent than the strains of cagPAI gene/genes that are Western type.

  7. Filamentous sulfur bacteria of activated sludge: characterization of Thiothrix, Beggiatoa, and Eikelboom type 021N strains.

    PubMed Central

    Williams, T M; Unz, R F

    1985-01-01

    Seventeen strains of filamentous sulfur bacteria were isolated in axenic culture from activated sludge mixed liquor samples and sulfide-gradient enrichment cultures. Isolation procedures involved plating a concentrated inoculum of washed filaments onto media containing sulfide or thiosulfate. The isolates were identified as Thiothrix spp., Beggiatoa spp., and an organism of uncertain taxonomic status, designated type 021N. All bacteria were gram negative, reduced nitrate, and formed long, multicellular trichomes with internal reserves of sulfur, volutin, and sudanophilic material. Thiothrix spp. formed rosettes and gonidia, and four of six strains were ensheathed. Type 021N organisms utilized glucose, lacked a sheath, and differed from Thiothrix spp. in several aspects of cellular and cultural morphology. Beggiatoa spp. lacked catalase and oxidase, and filaments were motile. Biochemical and physiological characterization of the isolates revealed important distinguishing features between the three groups of bacteria. Strain differences were most evident among the Thiothrix cultures. A comparison of the filamentous sulfur bacteria with freshwater strains of Leucothrix was made also. Images PMID:4004221

  8. Use of variations in staphylococcal interspersed repeat units for molecular typing of methicillin-resistant Staphylococcus aureus strains.

    PubMed

    Hardy, Katherine J; Oppenheim, Beryl A; Gossain, Savita; Gao, Fang; Hawkey, Peter M

    2006-01-01

    Staphylococcal interspersed repeat unit typing has previously been shown to have the ability to discriminate between epidemic methicillin-resistant Staphylococcus aureus strains in the United Kingdom. The current study illustrates its ability to distinguish between strains within an endemic setting thereby providing a rapid transportable typing method for the identification of transmission events.

  9. Complete genome sequence of the thermophilic sulfur-reducer Hippea maritima type strain (MH(2)).

    PubMed

    Huntemann, Marcel; Lu, Megan; Nolan, Matt; Lapidus, Alla; Lucas, Susan; Hammon, Nancy; Deshpande, Shweta; Cheng, Jan-Fang; Tapia, Roxanne; Han, Cliff; Goodwin, Lynne; Pitluck, Sam; Liolios, Konstantinos; Pagani, Ioanna; Ivanova, Natalia; Ovchinikova, Galina; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Jeffries, Cynthia D; Detter, John C; Brambilla, Evelyne-Marie; Rohde, Manfred; Spring, Stefan; Göker, Markus; Woyke, Tanja; Bristow, James; Eisen, Jonathan A; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter; Mavromatis, Konstantinos

    2011-07-01

    Hippea maritima (Miroshnichenko et al. 1999) is the type species of the genus Hippea, which belongs to the family Desulfurellaceae within the class Deltaproteobacteria. The anaerobic, moderately thermophilic marine sulfur-reducer was first isolated from shallow-water hot vents in Matipur Harbor, Papua New Guinea. H. maritima was of interest for genome sequencing because of its isolated phylogenetic location, as a distant next neighbor of the genus Desulfurella. Strain MH(2) (T) is the first type strain from the order Desulfurellales with a completely sequenced genome. The 1,694,430 bp long linear genome with its 1,723 protein-coding and 57 RNA genes consists of one circular chromosome and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  10. Complete genome sequence of Hippea maritima type strain (MH2T)

    SciTech Connect

    Huntemann, Marcel; Lu, Megan; Nolan, Matt; Lapidus, Alla L.; Lucas, Susan; Hammon, Nancy; Deshpande, Shweta; Cheng, Jan-Fang; Tapia, Roxanne; Han, Cliff; Goodwin, Lynne A.; Pitluck, Sam; Liolios, Konstantinos; Pagani, Ioanna; Ivanova, N; Ovchinnikova, Galina; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam L; Hauser, Loren John; Jeffries, Cynthia; Detter, J. Chris; Brambilla, Evelyne-Marie; Rohde, Manfred; Spring, Stefan; Goker, Markus; Woyke, Tanja; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter; Mavromatis, K

    2011-01-01

    Hippea maritima (Miroshnichenko et al. 1999) is the type species of the genus Hippea, which belongs to the family Desulfurellaceae within the class Deltaproteobacteria. The anaerobic, moderately thermophilic marine sulfur-reducer was first isolated from shallow-water hot vents in Matipur Harbor, Papua New Guinea. H. maritima was of interest for genome se- quencing because of its isolated phylogenetic location, as a distant next neighbor of the ge- nus Desulfurella. Strain MH2T is the first type strain from the order Desulfurellales with a com- pletely sequenced genome. The 1,694,430 bp long linear genome with its 1,723 protein- coding and 57 RNA genes consists of one circular chromosome and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  11. Differentiation of Proteus mirabilis and Proteus vulgaris strains by means of proticine typing: a longitudinal epidemiological study.

    PubMed

    Sekaninová, G; Kolárová, M

    1996-05-01

    In the years 1979, 1980, 1982-83, 1986-87 and 1992-93, 673 strains of P. mirabilis and 25 strains of P. vulgaris were isolated from the urinary tracts of patients at a Teaching Hospital in Brno. In 1982-83 and 1992-93, strains of P. mirabilis and P. vulgaris were isolated from the urine and faeces of two groups of Brno population and used as controls. Using the P/S typing method, 94.7% of hospital isolates and 85.5% of control strains could be differentiated by their types. The strains that could not be typed (8.2%) were classified as PO/SO or N types; in the remaining strains, 182 various P/S types could be distinguished. The strains that could not be typed occurred more frequently in control groups (48 out of 337) than in hospital isolates (37 out of 698). Over the whole period, P5/S6, S7, S9 and P1/S2, S11 were the prevailing P/S types of hospital isolates and were placed, together with related types, in groups P5 and P1, respectively. In 1982-83, a significant shift (p < 0.01) from the initially prevailing P5/S6, S7, S9 type to the P1/S2, S11 type of P. mirabilis was recorded. Approximately one third of the hospital isolates in all the periods examined was found to be sporadic, with the exception of 1992-93 when the sporadic strains doubled in frequency (p < 0.01). In control strains, the frequency of sporadic types was twice that of the hospital isolates (p < 0.01) in 1982-83 and, 1992-93, it was equal to the frequency of hospital isolates. This implied a fall in the presence of hospital-acquired strains in the last period of study.

  12. Differentiation of the gene clusters encoding botulinum neurotoxin type A complexes in Clostridium botulinum type A, Ab, and A(B) strains.

    PubMed

    Franciosa, Giovanna; Floridi, Francesca; Maugliani, Antonella; Aureli, Paolo

    2004-12-01

    We describe a strategy to identify the clusters of genes encoding components of the botulinum toxin type A (boNT/A) complexes in 57 strains of Clostridium botulinum types A, Ab, and A(B) isolated in Italy and in the United States from different sources. Specifically, we combined the results of PCR for detecting the ha33 and/or p47 genes with those of boNT/A PCR-restriction fragment length polymorphism analysis. Three different type A toxin gene clusters were revealed; type A1 was predominant among the strains from the United States, whereas type A2 predominated among the Italian strains, suggesting a geographic distinction between strains. By contrast, no relationship between the toxin gene clusters and the clinical or food source of strains was evident. In two C. botulinum type A isolates from the United States, we recognized a third type A toxin gene cluster (designated type A3) which was similar to that previously described only for C. botulinum type A(B) and Ab strains. Total genomic DNA from the strains was subjected to pulsed-filed gel electrophoresis and randomly amplified polymorphic DNA analyses, and the results were consistent with the boNT/A gene clusters obtained.

  13. Differentiation of the Gene Clusters Encoding Botulinum Neurotoxin Type A Complexes in Clostridium botulinum Type A, Ab, and A(B) Strains

    PubMed Central

    Franciosa, Giovanna; Floridi, Francesca; Maugliani, Antonella; Aureli, Paolo

    2004-01-01

    We describe a strategy to identify the clusters of genes encoding components of the botulinum toxin type A (boNT/A) complexes in 57 strains of Clostridium botulinum types A, Ab, and A(B) isolated in Italy and in the United States from different sources. Specifically, we combined the results of PCR for detecting the ha33 and/or p47 genes with those of boNT/A PCR-restriction fragment length polymorphism analysis. Three different type A toxin gene clusters were revealed; type A1 was predominant among the strains from the United States, whereas type A2 predominated among the Italian strains, suggesting a geographic distinction between strains. By contrast, no relationship between the toxin gene clusters and the clinical or food source of strains was evident. In two C. botulinum type A isolates from the United States, we recognized a third type A toxin gene cluster (designated type A3) which was similar to that previously described only for C. botulinum type A(B) and Ab strains. Total genomic DNA from the strains was subjected to pulsed-filed gel electrophoresis and randomly amplified polymorphic DNA analyses, and the results were consistent with the boNT/A gene clusters obtained. PMID:15574917

  14. Genome Sequence of Youngiibacter fragilis, the Type Strain of the Genus Youngiibacter.

    PubMed

    Wawrik, Colin B; Callaghan, Amy V; Stamps, Blake W; Wawrik, Boris

    2014-01-23

    The genome of Youngiibacter fragilis, the type strain of the newly described genus Youngiibacter, was sequenced. The genome consists of 3.996 Mb, with a G+C content of 46.6 mol%. Y. fragilis originates from coal-bed methane-produced water and may provide insight into the microbiological basis of biogas production in coal beds.

  15. Strain typing of Zygosaccharomyces yeast species using a single molecular method based on polymorphism of the intergenic spacer region (IGS).

    PubMed

    Wrent, Petra; Rivas, Eva-María; Peinado, José M; de Silóniz, María-Isabel

    2010-08-15

    Unlike previously reported methods that need a combination of several typing techniques, we have developed a single method for strain typing of the Zygosaccharomyces bailii, Z. mellis and Z. rouxii spoilage species. Strains belonging to other species have also been included for comparison. We have demonstrated that the IGS-PCR RFLP method has a high discriminative power. Considering the three endonucleases used in this work, we have obtained a variability of 100% for Z. mellis and Z. rouxii strains and up to 70% for Z. bailii. We have also detected two misidentified Z. mellis strains (CBS 711 and CBS 7412) which have RFLP patterns with a set of bands characteristic of Z. rouxii strains. Sequencing of 26S rDNA D1/D2 domains and the 5.8-ITS rDNA region confirmed these strains as Z. rouxii. The method also groups three certified hybrid strains of Zygosaccharomyces in a separate cluster.

  16. Mouse model of Sanfilippo syndrome type B: relation of phenotypic features to background strain.

    PubMed

    Gografe, Sylvia I; Garbuzova-Davis, Svitlana; Willing, Alison E; Haas, Ken; Chamizo, Wilfredo; Sanberg, Paul R

    2003-12-01

    Sanfilippo syndrome type B or mucopolysaccharidosis type III B (MPS IIIB) is a lysosomal storage disorder that is inherited in autosomal recessive manner. It is characterized by systemic heparan sulfate accumulation in lysosomes due to deficiency of the enzyme alpha-N-acetylglucosaminidase (Naglu). Devastating clinical abnormalities with severe central nervous system involvement and somatic disease lead to premature death. A mouse model of Sanfilippo syndrome type B was created by targeted disruption of the gene encoding Naglu, providing a powerful tool for understanding pathogenesis and developing novel therapeutic strategies. However, the JAX GEMM Strain B6.129S6-Naglutm1Efn mouse, although showing biochemical similarities to humans with Sanfilippo syndrome, exhibits aging and behavioral differences. We observed idiosyncrasies, such as skeletal dysmorphism, hydrocephalus, ocular abnormalities, organomegaly, growth retardation, and anomalies of the integument, in our breeding colony of Naglu mutant mice and determined that several of them were at least partially related to the background strain C57BL/6. These background strain abnormalities, therefore, potentially mimic or overlap signs of the induced syndrome in our mice. Our observations may prove useful in studies of Naglu mutant mice. The necessity for distinguishing background anomalies from signs of the modeled disease is apparent.

  17. Phylogeny and Identification of Pantoea Species and Typing of Pantoea agglomerans Strains by Multilocus Gene Sequencing ▿ †

    PubMed Central

    Delétoile, Alexis; Decré, Dominique; Courant, Stéphanie; Passet, Virginie; Audo, Jennifer; Grimont, Patrick; Arlet, Guillaume; Brisse, Sylvain

    2009-01-01

    Pantoea agglomerans and other Pantoea species cause infections in humans and are also pathogenic to plants, but the diversity of Pantoea strains and their possible association with hosts and disease remain poorly known, and identification of Pantoea species is difficult. We characterized 36 Pantoea strains, including 28 strains of diverse origins initially identified as P. agglomerans, by multilocus gene sequencing based on six protein-coding genes, by biochemical tests, and by antimicrobial susceptibility testing. Phylogenetic analysis and comparison with other species of Enterobacteriaceae revealed that the genus Pantoea is highly diverse. Most strains initially identified as P. agglomerans by use of API 20E strips belonged to a compact sequence cluster together with the type strain, but other strains belonged to diverse phylogenetic branches corresponding to other species of Pantoea or Enterobacteriaceae and to probable novel species. Biochemical characteristics such as fosfomycin resistance and utilization of d-tartrate could differentiate P. agglomerans from other Pantoea species. All 20 strains of P. agglomerans could be distinguished by multilocus sequence typing, revealing the very high discrimination power of this method for strain typing and population structure in this species, which is subdivided into two phylogenetic groups. PCR detection of the repA gene, associated with pathogenicity in plants, was positive in all clinical strains of P. agglomerans, suggesting that clinical and plant-associated strains do not form distinct populations. We provide a multilocus gene sequencing method that is a powerful tool for Pantoea species delineation and identification and for strain tracking. PMID:19052179

  18. Rapid identification of drug-type strains in Cannabis sativa using loop-mediated isothermal amplification assay.

    PubMed

    Kitamura, Masashi; Aragane, Masako; Nakamura, Kou; Watanabe, Kazuhito; Sasaki, Yohei

    2017-01-01

    In Cannabis sativa L., tetrahydrocannabinol (THC) is the primary psychoactive compound and exists as the carboxylated form, tetrahydrocannabinolic acid (THCA). C. sativa is divided into two strains based on THCA content-THCA-rich (drug-type) strains and THCA-poor (fiber-type) strains. Both strains are prohibited by law in many countries including Japan, whereas the drug-type strains are regulated in Canada and some European countries. As the two strains cannot be discriminated by morphological analysis, a simple method for identifying the drug-type strains is required for quality control in legal cultivation and forensic investigation. We have developed a novel loop-mediated isothermal amplification (LAMP) assay for identifying the drug-type strains of C. sativa. We designed two selective LAMP primer sets for on-site or laboratory use, which target the drug-type THCA synthase gene. The LAMP assay was accomplished within approximately 40 min. The assay showed high specificity for the drug-type strains and its sensitivity was the same as or higher than that of conventional polymerase chain reaction. We also showed the effectiveness of melting curve analysis that was conducted after the LAMP assay. The melting temperature values of the drug-type strains corresponded to those of the cloned drug-type THCA synthase gene, and were clearly different from those of the cloned fiber-type THCA synthase gene. Moreover, the LAMP assay with simple sample preparation could be accomplished within 1 h from sample treatment to identification without the need for special devices or techniques. Our rapid, sensitive, specific, and simple assay is expected to be applicable to laboratory and on-site detection.

  19. Genome sequence of the Antarctic rhodopsins- containing flavobacterium Gillisia limnaea type strain (R- 8282T)

    SciTech Connect

    Riedel, Thomas; Held, Brittany; Nolan, Matt; Lucas, Susan; Lapidus, Alla L.; Tice, Hope; Glavina Del Rio, Tijana; Cheng, Jan-Fang; Han, Cliff; Tapia, Roxanne; Goodwin, Lynne A.; Pitluck, Sam; Liolios, Konstantinos; Mavromatis, K; Pagani, Ioanna; Ivanova, N; Mikhailova, Natalia; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam L; Rohde, Manfred; Tindall, Brian; Detter, J. Chris; Goker, Markus; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter; Woyke, Tanja

    2012-01-01

    Gillisia limnaea Van Trappen et al. 2004 is the type species of the genus Gillisia, which is a mem- ber of the well characterized family Flavobacteriaceae. The genome of G. limnea R-8282T is the first sequenced genome (permanent draft) from a type strain of the genus Gillisia. Here we de- scribe the features of this organism, together with the permanent-draft genome sequence and an- notation. The 3,966,857 bp long chromosome (two scaffolds) with its 3,569 protein-coding and 51 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  20. Complete genome sequence of Thermosphaera aggregans type strain (M11TLT)

    SciTech Connect

    Spring, Stefan; Rachel, Dr. Reinhard; Lapidus, Alla L.; Davenport, Karen W.; Tice, Hope; Copeland, A; Cheng, Jan-Fang; Lucas, Susan; Nolan, Matt; Bruce, David; Goodwin, Lynne A.; Pitluck, Sam; Ivanova, N; Mavromatis, K; Ovchinnikova, Galina; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam L; Hauser, Loren John; Chang, Yun-Juan; Jeffries, Cynthia; Detter, J. Chris; Tapia, Roxanne; Han, Cliff; Heimerl, Dr. Thomas; Weikl, Fabian; Brambilla, Evelyne-Marie; Goker, Markus; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter

    2010-01-01

    Thermosphaera aggregans Huber et al. 1998 is the type species of the genus Thermosphaera, which comprises at the time of writing only one species. This species represents archaea with a hyperthermophilic, heterotrophic, strictly anaerobic and fermentative phenotype. The type strain M11TLT was isolated from a water-sediment sample of a hot terrestrial spring (Obsidian Pool, Yellowstone National Park, Wyoming). Here we describe the features of this organism, together with the complete genome sequence and annotation. The 1,316,595 bp long single replicon genome with its 1,410 protein-coding and 47 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  1. Complete genome sequence of Streptosporangium roseum type strain (NI 9100T)

    SciTech Connect

    Nolan, Matt; Sikorski, Johannes; Jando, Marlen; Lucas, Susan; Lapidus, Alla L.; Glavina Del Rio, Tijana; Chen, Feng; Tice, Hope; Pitluck, Sam; Cheng, Jan-Fang; Chertkov, Olga; Sims, David; Meincke, Linda; Brettin, Thomas S; Han, Cliff; Detter, J. Chris; Bruce, David; Goodwin, Lynne A.; Land, Miriam L; Hauser, Loren John; Chang, Yun-Juan; Jeffries, Cynthia; Ivanova, N; Mavromatis, K; Mikhailova, Natalia; Chen, Amy; Palaniappan, Krishna; Chain, Patrick S. G.; Rohde, Manfred; Goker, Markus; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter

    2010-01-01

    Streptosporangium roseum Crauch 1955 is the type strain of the species which is the type species of the genus Streptosporangium. The pinkish coiled Streptomyces-like organism with a spore case was isolated from vegetable garden soil in 1955. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of a member of the family Streptosporangiaceae, and the second largest microbial genome sequence ever deciphered. The 10,369,518 bp long genome with its 9421 protein-coding and 80 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  2. Highly strained Esaki tunnel diodes on InP substrate with type-III band alignment

    NASA Astrophysics Data System (ADS)

    Karl, S.; Sprengel, S.; Amann, M.-C.

    2016-12-01

    The first of a kind InP-based Esaki tunnel diodes with type-III (broken gap) band alignment are presented. This type is expected to have the highest tunneling current densities at equal doping concentration and structure geometry, compared to homo-, type-I or type-II junctions. The broken gap alignment is achieved by highly strained n-Ga0.2In0.8As/p-GaAs0.2Sb0.8 junction layers. Samples were fabricated by molecular beam epitaxy, the junction doping was varied between 2 × 1018 cm-3 and 2 × 1019 cm-3. Peak current densities up to 34.0 kA cm-2, for a doping of 2 × 1019 cm-3, are reached. The peak tunneling current shows a low dependence on the doping level for the type-III aligned junction layers. For example, highly strained diodes with a doping concentration of 2 × 1018 cm-3 can reach peak tunnel current densities of 3.6 A cm-2, whereas, with the lattice-matched junction, one order of magnitude higher doping is required.

  3. Comparison of activity to stimulate mucosal IgA production between Leuconostoc mesenteroides strain NTM048 and type strain JCM6124 in mice

    PubMed Central

    MATSUZAKI, Chiaki; MATSUMOTO, Kenji; KATOH, Toshihiko; YAMAMOTO, Kenji; HISA, Keiko

    2015-01-01

    The effects of Leuconostoc mesenteroides strain NTM048 and type strain JCM6124T on the murine immune system were characterized. Although the bacterial cells and exopolysaccharides of each strain induced immunoglobulin A production in Peyer’s patch cells, the effects of NTM048 were more potent than those of JCM6124T. Oral administration of the cells of each strain increased the fecal immunoglobulin A content in NTM048-treated mice, but not in JCM6124T-treated mice. A flow cytometric analysis showed that the CD4+ T-cell populations in the mouse spleens tended to increase in the NTM048 group. These results suggest that immunomodulating ability is characteristic of strain NTM048. PMID:26858930

  4. Whole Genome Sequencing-Based Molecular Epidemiologic Analysis of Autochthonous Dengue Virus Type 1 Strains Circulating in Japan in 2014.

    PubMed

    Tajima, Shigeru; Nakayama, Eri; Kotaki, Akira; Moi, Meng Ling; Ikeda, Makiko; Yagasaki, Kazumi; Saito, Yuka; Shibasaki, Ken-Ichi; Saijo, Masayuki; Takasaki, Tomohiko

    2017-01-24

    Cases of autochthonous infections of dengue virus type 1 (DENV-1) were detected in Japan after a 70-year period devoid of dengue outbreaks. We previously showed that E gene sequences are identical in 11 of the 12 DENV-1 strains autochthonous to Japan. However, the E sequence represents only 14% of the DENV-1 genome. In the present study, we have sequenced the entire genome of 6 autochthonous DENV-1 strains that were isolated from patients during the 2014 outbreak. Sequencing of 5 Yoyogi group strains with identical E sequences and 1 Shizuoka strain with a different E sequence revealed that the first Yoyogi group strain differed from the Shizuoka strain by 18 amino acid residues. Furthermore, 2 Yoyogi group strains had different genomic sequences while the other 3 had identical genomes. Phylogenetic analyses indicated that the Hyogo strain, a Yoyogi group strain, was the first to diverge from the other 4 Yoyogi group strains. The E gene sequence of the Yoyogi group strains exhibits the highest homology to those of the strains isolated in Malaysia and Singapore between 2013 and 2014. The patient infected with the Hyogo strain visited Malaysia before the onset of dengue fever, suggesting that this was a case of dengue infection imported from Malaysia.

  5. Microbiological diagnosis and molecular typing of Legionella strains during an outbreak of legionellosis in Southern Germany.

    PubMed

    Essig, Andreas; von Baum, Heike; Gonser, Theodor; Haerter, Georg; Lück, Christian

    2016-02-01

    An explosive outbreak of Legionnaires' disease with 64 reported cases occurred in Ulm/Neu-Ulm in the South of Germany in December 2009/January 2010 caused by Legionella (L.) pneumophila serogroup 1, monoclonal (mAb) subtype Knoxville, sequence type (ST) 62. Here we present the clinical microbiological results from 51 patients who were diagnosed at the University hospital of Ulm, the results of the environmental investigations and of molecular typing of patients and environmental strains. All 50 patients from whom urine specimens were available were positive for L. pneumophila antigen when an enzyme-linked immunosorbent assay (EIA) was used following concentration of those urine samples that tested initially negative. The sensitivity of the BinaxNow rapid immunographic assay (ICA), after 15 min reading and after 60 min reading were 70% and 84%, respectively. Direct typing confirmed the monoclonal subtype Knoxville in 5 out of 8 concentrated urine samples. Real time PCR testing of respiratory tract specimens for L. pneumophila was positive in 15 out of 25 (60%) patients. Direct nested sequence based typing (nSBT) in some of these samples allowed partial confirmation of ST62. L. pneumophila serogroup 1, monoclonal subtype Knoxville ST62, defined as the epidemic strain was isolated from 8 out of 31 outbreak patients (26%) and from one cooling tower confirming it as the most likely source of the outbreak. While rapid detection of Legionella antigenuria was crucial for the recognition and management of the outbreak, culture and molecular typing of the strains from patients and environmental specimens was the clue for the rapid identification of the source of infection.

  6. Development and application of a new scheme of phages for typing and differentiating Salmonella strains from different sources.

    PubMed Central

    Castro, D; Morińigo, M A; Martinez-Manzanares, E; Cornax, R; Balebona, M C; Luque, A; Borrego, J J

    1992-01-01

    A set of 25 phages for typing and differentiating Salmonella strains from different origins (food, water, and disease outbreaks) is described. All the strains were typeable by use of the phages, whereas by the serological method more than 5% of the strains could not be classified. By using the phage typing scheme, 75 phage types were established, and all the results were reproducible 1 and 6 months later. Some phages were serotype and serogroup specific, which may be useful in additional tests for the identification of strains of some Salmonella serotypes. In addition, the strains responsible for an outbreak possessed the same phage type, which implies the potential epidemiological use of these phages. PMID:1624557

  7. Novel strain properties distinguishing sporadic prion diseases sharing prion protein genotype and prion type

    PubMed Central

    Cracco, Laura; Notari, Silvio; Cali, Ignazio; Sy, Man-Sun; Chen, Shu G.; Cohen, Mark L.; Ghetti, Bernardino; Appleby, Brian S.; Zou, Wen-Quan; Caughey, Byron; Safar, Jiri G.; Gambetti, Pierluigi

    2017-01-01

    In most human sporadic prion diseases the phenotype is consistently associated with specific pairings of the genotype at codon 129 of the prion protein gene and conformational properties of the scrapie PrP (PrPSc) grossly identified types 1 and 2. This association suggests that the 129 genotype favours the selection of a distinct strain that in turn determines the phenotype. However, this mechanism cannot play a role in the phenotype determination of sporadic fatal insomnia (sFI) and a subtype of sporadic Creutzfeldt-Jakob disease (sCJD) identified as sCJDMM2, which share 129 MM genotype and PrPSc type 2 but are associated with quite distinct phenotypes. Our detailed comparative study of the PrPSc conformers has revealed major differences between the two diseases, which preferentially involve the PrPSc component that is sensitive to digestion with proteases (senPrPSc) and to a lesser extent the resistant component (resPrPSc). We conclude that these variations are consistent with two distinct strains in sFI and sCJDMM2, and that the rarer sFI is the result of a variant strain selection pathway that might be favoured by a different brain site of initial PrPSc formation in the two diseases. PMID:28091514

  8. Molecular Analysis of Acinetobacter baumannii Strains Isolated in Lebanon Using Four Different Typing Methods

    PubMed Central

    Rafei, Rayane; Dabboussi, Fouad; Hamze, Monzer; Eveillard, Matthieu; Lemarié, Carole; Gaultier, Marie-Pierre; Mallat, Hassan; Moghnieh, Rima; Husni-Samaha, Rola; Joly-Guillou, Marie-Laure; Kempf, Marie

    2014-01-01

    This study analyzed 42 Acinetobacter baumannii strains collected between 2009–2012 from different hospitals in Beyrouth and North Lebanon to better understand the epidemiology and carbapenem resistance mechanisms in our collection and to compare the robustness of pulsed field gel electrophoresis (PFGE), multilocus sequence typing (MLST), repetitive sequence-based PCR (rep-PCR) and blaOXA-51 sequence-based typing (SBT). Among 31 carbapenem resistant strains, we have detected three carbapenem resistance genes: 28 carried the blaOXA-23 gene, 1 the blaOXA-24 gene and 2 strains the blaOXA-58 gene. This is the first detection of blaOXA-23 and blaOXA-24 in Lebanon. PFGE identified 11 types and was the most discriminating technique followed by rep-PCR (9 types), blaOXA-51 SBT (8 types) and MLST (7 types). The PFGE type A'/ST2 was the dominant genotype in our collection present in Beyrouth and North Lebanon. The clustering agreement between all techniques was measured by adjust Wallace coefficient. An overall agreement has been demonstrated. High values of adjust Wallace coefficient were found with followed combinations: PFGE to predict MLST types  = 100%, PFGE to predict blaOXA-51 SBT = 100%, blaOXA-51 SBT to predict MLST = 100%, MLST to predict blaOXA-51 SBT = 84.7%, rep-PCR to predict MLST = 81.5%, PFGE to predict rep-PCR = 69% and rep-PCR to predict blaOXA-51 SBT = 67.2%. PFGE and MLST are gold standard methods for outbreaks investigation and population structure studies respectively. Otherwise, these two techniques are technically, time and cost demanding. We recommend the use of blaOXA-51 SBT as first typing method to screen isolates and assign them to their corresponding clonal lineages. Repetitive sequence-based PCR is a rapid tool to access outbreaks but careful interpretation of results must be always performed. PMID:25541711

  9. Effects of Megaplasmid Loss on Growth of Neurotoxigenic Clostridium butyricum Strains and Botulinum Neurotoxin Type E Expression.

    PubMed

    Scalfaro, Concetta; Iacobino, Angelo; Grande, Laura; Morabito, Stefano; Franciosa, Giovanna

    2016-01-01

    Clostridium butyricum strains that atypically produce the botulinum neurotoxin type E (BoNT/E) possess a megaplasmid of unknown functions in their genome. In this study, we cured two botulinum neurotoxigenic C. butyricum type E strains of their megaplasmids, and compared the obtained megaplasmid-cured strains to their respective wild-type parental strains. Our results showed that the megaplasmids do not confer beta-lactam resistance on the neurotoxigenic C. butyricum type E strains, although they carry several putative beta-lactamase genes. Instead, we found that the megaplasmids are essential for growth of the neurotoxigenic C. butyricum type E strains at the relatively low temperature of 15°C, and are also relevant for growth of strains under limiting pH and salinity conditions, as well as under favorable environmental conditions. Moreover, the presence of the megaplasmids was associated with increased transcript levels of the gene encoding BoNT/E in the C. butyricum type E strains, indicating that the megaplasmids likely contain transcriptional regulators. However, the levels of BoNT/E in the supernatants of the cured and uncured strains were similar after 24 and 48 h culture, suggesting that expression of BoNT/E in the C. butyricum type E strains is not ultimately controlled by the megaplasmids. Together, our results reveal that the C. butyricum type E megaplasmids exert pleiotropic effects on the growth of their microbial hosts under optimal and limiting environmental conditions, and also highlight the possibility of original regulatory mechanisms controlling the expression of BoNT/E.

  10. Effects of Megaplasmid Loss on Growth of Neurotoxigenic Clostridium butyricum Strains and Botulinum Neurotoxin Type E Expression

    PubMed Central

    Scalfaro, Concetta; Iacobino, Angelo; Grande, Laura; Morabito, Stefano; Franciosa, Giovanna

    2016-01-01

    Clostridium butyricum strains that atypically produce the botulinum neurotoxin type E (BoNT/E) possess a megaplasmid of unknown functions in their genome. In this study, we cured two botulinum neurotoxigenic C. butyricum type E strains of their megaplasmids, and compared the obtained megaplasmid-cured strains to their respective wild-type parental strains. Our results showed that the megaplasmids do not confer beta-lactam resistance on the neurotoxigenic C. butyricum type E strains, although they carry several putative beta-lactamase genes. Instead, we found that the megaplasmids are essential for growth of the neurotoxigenic C. butyricum type E strains at the relatively low temperature of 15°C, and are also relevant for growth of strains under limiting pH and salinity conditions, as well as under favorable environmental conditions. Moreover, the presence of the megaplasmids was associated with increased transcript levels of the gene encoding BoNT/E in the C. butyricum type E strains, indicating that the megaplasmids likely contain transcriptional regulators. However, the levels of BoNT/E in the supernatants of the cured and uncured strains were similar after 24 and 48 h culture, suggesting that expression of BoNT/E in the C. butyricum type E strains is not ultimately controlled by the megaplasmids. Together, our results reveal that the C. butyricum type E megaplasmids exert pleiotropic effects on the growth of their microbial hosts under optimal and limiting environmental conditions, and also highlight the possibility of original regulatory mechanisms controlling the expression of BoNT/E. PMID:26941734

  11. Complete genome sequence of Saccharomonospora viridis type strain (P101T)

    SciTech Connect

    Pati, Amrita; Sikorski, Johannes; Nolan, Matt; Lapidus, Alla; Copeland, Alex; Glavina Del Rio, Tijana; Lucas, Susan; Chen, Feng; Tice, Hope; Pitluck, Sam; Cheng, Jan-Fang; Chertkov, Olga; Brettin, Thomas; Han, Cliff; Detter, John C.; Kuske, Cheryl; Bruce, David; Goodwin, Lynne; Chain, Patrick; D'haeseleer, Patrik; Chen, Amy; Palaniappan, Krishna; Ivanova, Natalia; Mavromatis, Konstantinos; Mikhailova, Natalia; Rohde, Manfred; Tindall, Brian J.; Goker, Markus; Bristow, Jim; Eisen, Jonathan A.; Markowitz, Victor; Hugenholtz, Philip; Kyrpides1, Nikos C.; Klenk, Hans-Peter

    2009-05-20

    Saccharomonospora viridis (Schuurmans et al. 1956) Nonomurea and Ohara 1971 is the type species of the genus Saccharomonospora which belongs to the family Pseudonocardiaceae. S. viridis is of interest because it is a Gram-negative organism classified amongst the usually Gram-positive actinomycetes. Members of the species are frequently found in hot compost and hay, and its spores can cause farmer?s lung disease, bagassosis, and humidifier fever. Strains of the species S. viridis have been found to metabolize the xenobiotic pentachlorophenol (PCP). The strain described in this study has been isolated from peat-bog in Ireland. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of the family Pseudonocardiaceae, and the 4,308,349 bp long single replicon genome with its 3906 protein-coding and 64 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

  12. Strain-balanced Si/SiGe type-II superlattices for near-infrared photodetection

    SciTech Connect

    Ali, Dyan; Richardson, Christopher J. K.

    2014-07-21

    Strain balanced silicon-silicon germanium type-II superlattice p-i-n photodetectors grown on a silicon germanium relaxed buffer layer are shown to exhibit an absorption band that extends beyond 0.7 eV (λ = 1.77 μm) with dark current densities of 27 μA cm{sup −2}. Simulations of the absorption edge, which are based on x-ray diffraction characterization, low observed dark current densities, and low dislocation densities, are consistent with fully strained heterostructures. Potential applications for devices made from this heterostructure design could include integrated silicon detectors, or low-noise absorption regions for infrared-extended silicon based avalanche photodiodes.

  13. Complete genome sequence of Anaerococcus prevotii type strain (PC1T)

    SciTech Connect

    LaButti, Kurt; Pukall, Rudiger; Steenblock, Katja; Glavina Del Rio, Tijana; Tice, Hope; Copeland, A; Cheng, Jan-Fang; Lucas, Susan; Chen, Feng; Nolan, Matt; Bruce, David; Goodwin, Lynne A.; Pitluck, Sam; Ivanova, N; Mavromatis, K; Ovchinnikova, Galina; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam L; Hauser, Loren John; Chang, Yun-Juan; Jeffries, Cynthia; Chain, Patrick S. G.; Saunders, Elizabeth H; Brettin, Tom; Detter, J. Chris; Han, Cliff; Barry, Kerrie; Goker, Markus; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter; Lapidus, Alla L.

    2009-01-01

    Anaerococcus prevotii (Foubert and Douglas 1948) Ezaki et al. 2001 is the type species of the genus, and is of phylogenetic interest because of its arguable assignment to the provisionally arranged family Peptostreptococcaceae . A. prevotii is an obligate anaerobic coccus, usually arranged in clumps or tetrads. The strain, whose genome is described here, was originally isolated from human plasma; other strains of the species were also isolated from clinical specimen. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of a member of the genus. Next to Finegoldia magna, A. prevotii is only the second species from the family Peptostreptococcaceae for which a complete genome sequence is described. The 1,998,633 bp long genome (chromosome and one plasmid) with its 1852 protein-coding and 61 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  14. Complete genome sequence of Stackebrandtia nassauensis type strain (LLR-40K-21T)

    SciTech Connect

    Munk, Chris; Lapidus, Alla; Copeland, Alex; Jando, Marlen; Mayilraj, Shanmugam; Glavina Del Rio, Tijana; Nolan, Matt; Chen, Feng; Lucas, Susan; Tice, Hope; Cheng, Jan-Fang; Han, Cliff; Detter, John C.; Bruce, David; Goodwin, Lynne; Chain, Patrick; Pitluck, Sam; Göker, Markus; Ovchinikova, Galina; Pati, Amrita; Ivanova, Natalia; Mavromatis, Konstantinos; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Bristow, Jim; Eisen, Jonathan A.; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C.; Klenk, Hans-Peter

    2009-12-30

    Stackebrandtia nassauensis Labeda and Kroppenstedt (2005) is the type species of the genus Stackebrandtia, and a member of the actinobacterial family Glycomycetaceae. Stackebrandtia currently contains two species, which are differentiated from Glycomyces spp. by cellular fatty acid and menaquinone composition. Strain LLR-40K-21T is Gram-positive, aerobic, and nonmotile, with a branched substrate mycelium and on some media an aerial mycelium. The strain was originally isolated from a soil sample collected from a road side in Nassau, Bahamas. We describe the features of this organism, together with the complete genome sequence and annotation. Lastly, this is the first complete genome sequence of the actinobacterial suborder Glycomycineae. The 6,841,557 bp long single replicon genome with its 6487 protein-coding and 53 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

  15. Complete genome sequence of Pedobacter heparinus type strain (HIM 762-3T)

    SciTech Connect

    Han, Cliff; Spring, Stefan; Lapidus, Alla L.; Glavina Del Rio, Tijana; Tice, Hope; Copeland, A; Cheng, Jan-Fang; Lucas, Susan; Chen, Feng; Nolan, Matt; Bruce, David; Goodwin, Lynne A.; Pitluck, Sam; Ivanova, N; Mavromatis, K; Mikhailova, Natalia; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam L; Hauser, Loren John; Chang, Yun-Juan; Jeffries, Cynthia; Saunders, Elizabeth H; Chertkov, Olga; Brettin, Tom; Goker, Markus; Rohde, Manfred; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter; Detter, J. Chris

    2009-01-01

    Pedobacter heparinus (Payza and Korn 1956) Steyn et al. 1998 comb. nov. is the type species of the rapidly growing genus Pedobacter within the family Sphingobacteriaceae of the phy-lum Bacteroidetes . P. heparinus is of interest, because it was the first isolated strain shown to grow with heparin as sole carbon and nitrogen source and because it produces several en-zymes involved in the degradation of mucopolysaccharides. All available data about this species are based on a sole strain that was isolated from dry soil. Here we describe the fea-tures of this organism, together with the complete genome sequence, and annotation. This is the first report on a complete genome sequence of a member of the genus Pedobacter, and the 5,167,383 bp long single replicon genome with its 4287 protein-coding and 54 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

  16. Complete genome sequence of Thermobaculum terrenum type strain (YNP1T)

    SciTech Connect

    Kiss, Hajnalka; Cleland, David M; Lapidus, Alla L.; Lucas, Susan; Glavina Del Rio, Tijana; Nolan, Matt; Tice, Hope; Han, Cliff; Goodwin, Lynne A.; Pitluck, Sam; Liolios, Konstantinos; Ivanova, N; Mavromatis, K; Ovchinnikova, Galina; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam L; Hauser, Loren John; Chang, Yun-Juan; Jeffries, Cynthia; Lu, Megan; Brettin, Thomas S; Detter, J. Chris; Goker, Markus; Tindall, Brian; Beck, Brian; McDermott, Timothy; Woyke, Tanja; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter; Cheng, Jan-Fang

    2010-01-01

    Thermobaculum terrenum (Botero et al. 2004) is the only species within the proposed genus Thermobaculum . Strain YNP1T represents the only cultivated member of an environmental clone group within the phylum Chloroflexi. Nonconformance to Rule 30(3a) of the Bacteriological Code prevents prevents valid publication of either the species and genus name for this phylogentically isolated bacterium that was cultivated from slightly acidic extreme thermal soil in Yellowstone National Park, Wyoming (USA). Depending on its final taxonomic allocation, this is probably the third completed genome sequence of a member of the class Thermomicrobia and the seventh type strain genome from the phylum Cloroflexi. The 3,101,581 bp long genome with its 2,872 protein-coding and 58 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  17. Complete genome sequence of Pedobacter heparinus type strain (HIM 762-3T)

    PubMed Central

    Han, Cliff; Spring, Stefan; Lapidus, Alla; Del Rio, Tijana Glavina; Tice, Hope; Copeland, Alex; Cheng, Jan-Fang; Lucas, Susan; Chen, Feng; Nolan, Matt; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Ivanova, Natalia; Mavromatis, Konstantinos; Mikhailova, Natalia; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia C.; Saunders, Elizabeth; Chertkov, Olga; Brettin, Thomas; Göker, Markus; Rohde, Manfred; Bristow, Jim; Eisen, Jonathan A.; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C.; Klenk, Hans-Peter; Detter, John C.

    2009-01-01

    Pedobacter heparinus (Payza and Korn 1956) Steyn et al. 1998 comb. nov. is the type species of the rapidly growing genus Pedobacter within the family Sphingobacteriaceae of the phylum ‘Bacteroidetes’. P. heparinus is of interest, because it was the first isolated strain shown to grow with heparin as sole carbon and nitrogen source and because it produces several enzymes involved in the degradation of mucopolysaccharides. All available data about this species are based on a sole strain that was isolated from dry soil. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first report on a complete genome sequence of a member of the genus Pedobacter, and the 5,167,383 bp long single replicon genome with its 4287 protein-coding and 54 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project. PMID:21304637

  18. Complete genome sequence of Pedobacter heparinus type strain (HIM 762-3T)

    SciTech Connect

    Han, Cliff; Spring, Stefan; Lapidus, Alla; Glavina Del Rio, Tijana; Tice, Hope; Copeland, Alex; Cheng, Jan-Fang; Lucas, Susan; Chen, Feng; Nolan, Matt; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Ivanova, Natalia; Mavrommatis, Konstantinos; Mikhailova, Natalia; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jefferies, Cynthia C.; Saunders, Elizabeth; Chertkov, Olga; Brettin, Thomas; Goker, Markus; Rohde, Manfred; Bristow, James; Eisen, Jonathan A.; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C.; Klenk, Hans-Peter; Detter, John C.

    2009-05-20

    Pedobacter heparinus (Payza and Korn 1956) Steyn et al. 1998 comb. nov. is the type species of the rapidly growing genus Pedobacter within the family Sphingobacteriaceae of the phylum 'Bacteroidetes'. P. heparinus is of interest, because it was the first isolated strain shown to grow with heparin as sole carbon and nitrogen source and because it produces several enzymes involved in the degradation of mucopolysaccharides. All available data about this species are based on a sole strain that was isolated from dry soil. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first report on a complete genome sequence of a member of the genus Pedobacter, and the 5,167,383 bp long single replicon genome with its 4287 protein-coding and 54 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

  19. Complete genome sequence of the gliding, heparinolytic Pedobacter saltans type strain (113T)

    PubMed Central

    Liolios, Konstantinos; Sikorski, Johannes; Lu, Meagan; Nolan, Matt; Lapidus, Alla; Lucas, Susan; Hammon, Nancy; Deshpande, Shweta; Cheng, Jan-Fang; Tapia, Roxanne; Han, Cliff; Goodwin, Lynne; Pitluck, Sam; Huntemann, Marcel; Ivanova, Natalia; Pagani, Ioanna; Mavromatis, Konstantinos; Ovchinikova, Galina; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Brambilla, Evelyne-Marie; Kotsyurbenko, Oleg; Rohde, Manfred; Tindall, Brian J.; Abt, Birte; Göker, Markus; Detter, John C.; Woyke, Tanja; Bristow, James; Eisen, Jonathan A.; Markowitz, Victor; Hugenholtz, Philip; Klenk, Hans-Peter; Kyrpides, Nikos C.

    2011-01-01

    Pedobacter saltans Steyn et al. 1998 is one of currently 32 species in the genus Pedobacter within the family Sphingobacteriaceae. The species is of interest for its isolated location in the tree of life. Like other members of the genus P. saltans is heparinolytic. Cells of P. saltans show a peculiar gliding, dancing motility and can be distinguished from other Pedobacter strains by their ability to utilize glycerol and the inability to assimilate D-cellobiose. The genome presented here is only the second completed genome sequence of a type strain from a member of the family Sphingobacteriaceae to be published. The 4,635,236 bp long genome with its 3,854 protein-coding and 67 RNA genes consists of one chromosome, and is a part of the Genomic Encyclopedia of Bacteria and Archaea project. PMID:22180808

  20. Susceptibility to antimicrobial agents of Streptococcus suis capsular type 2 strains isolated from pigs.

    PubMed

    Seol, B; Kelneric, Z; Hajsig, D; Madic, J; Naglic, T

    1996-03-01

    The minimal inhibitory concentrations (MICs) for thirty-three epidemiologicaly unrelated clinical isolates of Streptococcus suis capsular type 2 were determined in relation to ampicillin, ampicillin-sulbactam, amoxicillin, clavulanate-amoxicillin, penicillin G, cephalexin, gentamicin, streptomycin, erythromycin, tylosin and doxycycline, using the microtitre broth dilution procedure described by the U.S. National Committee for Clinical Laboratory Standards (NCCLS). Gentamicin was the most active compound tested, with an MIC for 90% of the strains tested (MIC(90)) of 0.4 mg/L. Overall, 70% of strains were resistant to doxycycline (MIC(90) > or = 100.0 mg/L), followed by penicillin G (51% of strains) (MIC(90) + or = 100.0 mg/L). Resistance to amoxicillin and ampicillin was 36.4% (MIC(90) 12.5 mg/L) and 33.3% (MIC(90) 50.0 mg/L), respectively. 15.2% of S. suis strains were resistant to streptomycin, tylosin and cephalexin with MIC90 values of 25.0 mg/L, 12.5 mg/L and 25.0 mg/L, respectively. A combination of ampicillin and sulbactam (MIC(90) 6.3 mg/L) and a combination of amoxicillin and clavulanate (MIC(90) 3.1 mg/L) as well as erythromycin (1.6 mg/L) were of the same efficacy, with a total of 9.1% resistant S. suis strains. This high percentage of resistance to doxycycline and penicillin G precludes the use of these antibiotics as empiric therapy of swine diseases.

  1. Complex Population Structure and Virulence Differences among Serotype 2 Streptococcus suis Strains Belonging to Sequence Type 28

    PubMed Central

    Athey, Taryn B. T.; Auger, Jean-Philippe; Teatero, Sarah; Dumesnil, Audrey; Takamatsu, Daisuke; Wasserscheid, Jessica; Dewar, Ken; Gottschalk, Marcelo; Fittipaldi, Nahuel

    2015-01-01

    Streptococcus suis is a major swine pathogen and a zoonotic agent. Serotype 2 strains are the most frequently associated with disease. However, not all serotype 2 lineages are considered virulent. Indeed, sequence type (ST) 28 serotype 2 S. suis strains have been described as a homogeneous group of low virulence. However, ST28 strains are often isolated from diseased swine in some countries, and at least four human ST28 cases have been reported. Here, we used whole-genome sequencing and animal infection models to test the hypothesis that the ST28 lineage comprises strains of different genetic backgrounds and different virulence. We used 50 S. suis ST28 strains isolated in Canada, the United States and Japan from diseased pigs, and one ST28 strain from a human case isolated in Thailand. We report a complex population structure among the 51 ST28 strains. Diversity resulted from variable gene content, recombination events and numerous genome-wide polymorphisms not attributable to recombination. Phylogenetic analysis using core genome single-nucleotide polymorphisms revealed four discrete clades with strong geographic structure, and a fifth clade formed by US, Thai and Japanese strains. When tested in experimental animal models, strains from this latter clade were significantly more virulent than a Canadian ST28 reference strain, and a closely related Canadian strain. Our results highlight the limitations of MLST for both phylogenetic analysis and virulence prediction and raise concerns about the possible emergence of ST28 strains in human clinical cases. PMID:26375680

  2. Use of AFLP, plasmid typing and phenotyping in a comparative study to assess genetic diversity of Shigella flexneri strains.

    PubMed Central

    Herrera, S.; Cabrera, R.; Ramirez, M. M.; Usera, M. A.; Echeita, M. A.

    2002-01-01

    Shigella flexneri infections are one of the main causes of acute diarrhoea in Cuba. Twenty strains isolated from sporadic cases in nine different Cuban provinces were characterized. Serotyping, antibiotic-resistance typing, plasmid-typing and AFLP-typing were used to determine their suitability for use in epidemiological studies of S. flexneri. The predominant serotypes were serotype 6 (35%) and serotype 2 (35%). Eleven different plasmid profiles were detected (Diversity Index = 0.92). AFLP-typing discriminated 12 different patterns (DI = 0.95), these patterns were not coincident with plasmid-typing patterns. Both techniques combined distinguished 14 patterns among the 20 studied strains (DI = 0.99). There was no consistent relationship between plasmid-typing and AFLP-typing patterns or antibiotic-resistance typing patterns. Ninety-five percent of S. flexneri strains were multiresistant. PMID:12558326

  3. Effect of strain on electronic and magnetic properties of n-type Cr-doped WSe2 monolayer

    NASA Astrophysics Data System (ADS)

    Liu, Xiaomeng; Zhao, Xu; Ma, Xu; Wu, Ninghua; Xin, Qianqian; Wang, Tianxing

    2017-03-01

    Using first-principles calculations based on the density functional theory, we study the effect of strain on the electronic and magnetic properties of Cr-doped WSe2 monolayer. The results show that no magnetic moment is induced in the Cr-doped WSe2 monolayer without strain. For the Cr substitutions, the impurity states are close to the conduction bands, which indicate n-type doping occurs in this case. Then we applied strain (from -10% to 10%) to the doped system, and find that a little magnetic moment is induced with tensile strain from 6% to 9% and negligible. We find that the influence of strain on the magnetic properties is inappreciable in Cr-doped WSe2. Moreover, the tensile strain appears to be more effective in reducing the band gap of Cr-doped WSe2 monolayer than the compressive strain.

  4. Two Novel Toxin Variants Revealed by Whole-Genome Sequencing of 175 Clostridium botulinum Type E Strains

    PubMed Central

    Weedmark, K. A.; Lambert, D. L.; Mabon, P.; Hayden, K. L.; Urfano, C. J.; Leclair, D.; Van Domselaar, G.; Austin, J. W.

    2014-01-01

    We sequenced 175 Clostridium botulinum type E strains isolated from food, clinical, and environmental sources from northern Canada and analyzed their botulinum neurotoxin (bont) coding sequences (CDSs). In addition to bont/E1 and bont/E3 variant types, neurotoxin sequence analysis identified two novel BoNT type E variants termed E10 and E11. Strains producing type E10 were found along the eastern coastlines of Hudson Bay and the shores of Ungava Bay, while strains producing type E11 were only found in the Koksoak River region of Nunavik. Strains producing BoNT/E3 were widespread throughout northern Canada, with the exception of the coast of eastern Hudson Bay. PMID:25107978

  5. Molecular typing of Legionella pneumophila serogroup 1 clinical strains isolated in Italy.

    PubMed

    Fontana, Stefano; Scaturro, Maria; Rota, Maria Cristina; Caporali, Maria Grazia; Ricci, Maria Luisa

    2014-07-01

    Molecular typing methods for discriminating different bacterial isolates are essential epidemiological tools in prevention and control of Legionella infections and outbreaks. A selection of 56 out of 184 Legionella pneumophila serogroup 1 (Lp1) clinical isolates, collected from different Italian regions between 1987 and 2012, and stored at the National Reference Laboratory for Legionella, were typed by monoclonal antibody (MAb) subgrouping, amplified fragment length polymorphism (AFLP) and sequence based typing (SBT). These strains were isolated from 39 community (69.6%), 14 nosocomial (25%) and 3 travel associated (5.4%) Legionnaires'disease cases. MAb typing results showed a prevalence of MAb 3/1 positive isolates (75%) with the Philadelphia subgroup representing 35.7%, followed by Knoxville (23.2%), Benidorm (12.5%), Allentown/France (1.8%), Allentown/France-Philadelphia (1.8%). The remaining 25% were MAb 3/1 negative, namely 11 Olda (19.6%), 2 Oxford (3.6%) and 1 Bellingham (1.8%) subgroups. AFLP analysis detected 20 different genomic profiles. SBT analysis revealed 32 different sequence types (STs) with high diversity of STs (IODSTs=0.952) 12 of which were never described before. ST1 and ST23 were most frequently isolated as observed worldwide. A helpful analysis of data from SBT, MAb subgrouping and AFLP is provided, as well as a comparison to the Lp1 types investigated from other countries. This study describes the first Italian Lp1 strains database, providing molecular epidemiology data useful for future epidemiological investigations, especially of travel associated Legionnaires' diseases (TALD) cases, Italy being the country associated with the highest number of clusters.

  6. A MAT1–2 wild-type strain from Penicillium chrysogenum: functional mating-type locus characterization, genome sequencing and mating with an industrial penicillin-producing strain

    PubMed Central

    Böhm, Julia; Dahlmann, Tim A; Gümüşer, Hendrik; Kück, Ulrich

    2015-01-01

    In heterothallic ascomycetes, mating is controlled by two nonallelic idiomorphs that determine the ‘sex’ of the corresponding strains. We recently discovered mating-type loci and a sexual life cycle in the penicillin-producing fungus, Penicillium chrysogenum. All industrial penicillin production strains worldwide are derived from a MAT1-1 isolate. No MAT1-2 strain has been investigated in detail until now. Here, we provide the first functional analysis of a MAT1-2 locus from a wild-type strain. Similar to MAT1-1, the MAT1-2 locus has functions beyond sexual development. Unlike MAT1-1, the MAT1-2 locus affects germination and surface properties of conidiospores and controls light-dependent asexual sporulation. Mating of the MAT1-2 wild type with a MAT1-1 high penicillin producer generated sexual spores. We determined the genomic sequences of parental and progeny strains using next-generation sequencing and found evidence for genome-wide recombination. SNP calling showed that derived industrial strains had an uneven distribution of point mutations compared with the wild type. We found evidence for meiotic recombination in all chromosomes. Our results point to a strategy combining the use of mating-type genes, genetics, and next-generation sequencing to optimize conventional strain improvement methods. PMID:25521009

  7. Multi-locus sequence typing of Salmonella enterica subsp. enterica serovar Enteritidis strains in Japan between 1973 and 2004.

    PubMed

    Noda, Tamie; Murakami, Koichi; Asai, Tetsuo; Etoh, Yoshiki; Ishihara, Tomoe; Kuroki, Toshiro; Horikawa, Kazumi; Fujimoto, Shuji

    2011-06-15

    Salmonella enterica subsp. enterica serovar Enteritidis (S. Enteritidis) was responsible for a worldwide pandemic during the 1980s and 1990s; however, changes in the dominant lineage before and after this event remain unknown. This study determined S. Enteritidis lineages before and after this pandemic event in Japan using multilocus sequence typing (MLST). Thirty S. Enteritidis strains were collected in Japan between 1973 and 2004, consisting of 27 human strains from individual episodes, a bovine strain, a liquid egg strain and an eggshell strain. Strains showed nine phage types and 17 pulsed-field profiles with pulsed-field gel electrophoresis. All strains had homologous type 11 sequences without any nucleotide differences in seven housekeeping genes. These MLST results suggest that S. Enteritidis with the diversities revealed by phage typing and pulsed-field profiling has a highly clonal population. Although type 11 S. Enteritidis may exhibit both pleiotropic surface structure and pulsed-field type variation, it is likely to be a stable lineage derived from an ancestor before the 1980s and/or 1990s pandemic in Japan.

  8. The Draft Genome Sequence of the Yersinia entomophaga Entomopathogenic Type Strain MH96T

    PubMed Central

    Hurst, Mark R. H.; Beattie, Amy; Altermann, Eric; Moraga, Roger M.; Harper, Lincoln A.; Calder, Joanne; Laugraud, Aurelie

    2016-01-01

    Here we report the draft genome of Yersinia entomophaga type strain MH96T. The genome shows 93.8% nucleotide sequence identity to that of Yersinia nurmii type strain APN3a-cT, and comprises a single chromosome of approximately 4,275,531 bp. In silico analysis identified that, in addition to the previously documented Y. entomophaga Yen-TC gene cluster, the genome encodes a diverse array of toxins, including two type III secretion systems, and five rhs-associated gene clusters. As well as these multicomponent systems, several orthologs of known insect toxins, such as VIP2 toxin and the binary toxin PirAB, and distant orthologs of some mammalian toxins, including repeats-in-toxin, a cytolethal distending toxin, hemolysin-like genes and an adenylate cyclase were identified. The genome also contains a large number of hypothetical proteins and orthologs of known effector proteins, such as LopT, as well as genes encoding a wide range of proteolytic determinants, including metalloproteases and pathogen fitness determinants, such as genes involved in iron metabolism. The bioinformatic data derived from the current in silico analysis, along with previous information on the pathobiology of Y. entomophaga against its insect hosts, suggests that a number of these virulence systems are required for survival in the hemocoel and incapacitation of the insect host. PMID:27187466

  9. The Draft Genome Sequence of the Yersinia entomophaga Entomopathogenic Type Strain MH96T.

    PubMed

    Hurst, Mark R H; Beattie, Amy; Altermann, Eric; Moraga, Roger M; Harper, Lincoln A; Calder, Joanne; Laugraud, Aurelie

    2016-05-11

    Here we report the draft genome of Yersinia entomophaga type strain MH96T. The genome shows 93.8% nucleotide sequence identity to that of Yersinia nurmii type strain APN3a-cT, and comprises a single chromosome of approximately 4,275,531 bp. In silico analysis identified that, in addition to the previously documented Y. entomophaga Yen-TC gene cluster, the genome encodes a diverse array of toxins, including two type III secretion systems, and five rhs-associated gene clusters. As well as these multicomponent systems, several orthologs of known insect toxins, such as VIP2 toxin and the binary toxin PirAB, and distant orthologs of some mammalian toxins, including repeats-in-toxin, a cytolethal distending toxin, hemolysin-like genes and an adenylate cyclase were identified. The genome also contains a large number of hypothetical proteins and orthologs of known effector proteins, such as LopT, as well as genes encoding a wide range of proteolytic determinants, including metalloproteases and pathogen fitness determinants, such as genes involved in iron metabolism. The bioinformatic data derived from the current in silico analysis, along with previous information on the pathobiology of Y. entomophaga against its insect hosts, suggests that a number of these virulence systems are required for survival in the hemocoel and incapacitation of the insect host.

  10. Comparative sensitivities of Sabin and Mahoney poliovirus type 1 prototype strains and two recent isolates to low concentrations of glutaraldehyde.

    PubMed Central

    Chambon, M; Jallat-Archimbaud, C; Bailly, J L; Gourgand, J M; Charbonne, F; Henquell, C; Fuchs, F; Peigue-Lafeuille, H

    1997-01-01

    Significant intratypic differences in the glutaraldehyde (GTA) sensitivity of echovirus isolates have been shown. While exploring ways to optimize the study of GTA sensitivity of enteroviruses, we also observed intratypic differences in poliovirus type 1 isolates collected in France. A suspension procedure was used for assessing the virucidal effect of GTA at low concentrations (< or = 0.10%) against purified viruses. Two recent isolates of poliovirus type 1 tested were first fully characterized by the PCR restriction fragment length polymorphism (RFLP) test. The RFLP pattern of clinical isolate 5617 was similar to that of poliovirus type 1 LS-c, 2ab (Sabin strain), confirming the vaccine origin of strain 5617. The RFLP pattern of strain 5915 recovered from sewage was different from that of the Mahoney strain, suggesting a genetic variation in this wild isolate. We then analyzed under the same controlled conditions the GTA sensitivities of both isolates and their respective prototype strains. The wild Mahoney and 5915 strains exhibited significantly lower sensitivities to GTA than did the vaccine Sabin and 5617 strains. The inactivation rates of clinical isolates 5617 and 5915 were very similar to those of their corresponding reference Sabin and Mahoney strains. Both the conformational structure of the capsid of each strain and the amino acid constitution of structural polypeptides could be involved in the variations observed. The relevance of our comparative sensitivity studies to standardization of virucidal tests is discussed. PMID:9251206

  11. Characterization of Microbulbifer strain CMC-5, a new biochemical variant of Microbulbifer elongatus type strain DSM6810T isolated from decomposing seaweeds.

    PubMed

    Jonnadula, RaviChand; Verma, Pankaj; Shouche, Yogesh S; Ghadi, Sanjeev C

    2009-12-01

    A Gram-negative, rod-shaped, non-spore forming, non-motile and moderate halophilic bacteria designated as strain CMC-5 was isolated from decomposing seaweeds by enrichment culture. The growth of strain CMC-5 was assessed in synthetic seawater-based medium containing polysaccharide. The bacterium degraded and utilized agar, alginate, carrageenan, xylan, carboxymethyl cellulose and chitin. The strain was characterized using a polyphasic approach for taxonomic identification. Cellular fatty acid analysis showed the presence of iso-C(15:0) as major fatty acid and significant amounts of iso-C(17:1x9c) and C(18:1x7c). Phylogenetic analysis based on 16S rDNA sequence indicated that strain CMC-5 is phylogenetically related to Microbulbifer genus and 99% similar to type strain Microbulbifer elongatus DSM6810T. However in contrast to Microbulbifer elongatus DSM6810T, strain CMC-5 is non-motile, utilizes glucose, galactose, inositol and xylan, does not utilize fructose and succinate nor does it produce H2S. Further growth of bacterial strain CMC-5 was observed when inoculated in seawater-based medium containing sterile pieces of Gracilaria corticata thalli. The bacterial growth was associated with release of reducing sugar in the broth suggesting its role in carbon recycling of polysaccharides from seaweeds in marine ecosystem.

  12. Complete genome sequence of Sebaldella termitidis type strain (NCTC 11300T)

    SciTech Connect

    Harmon-Smith, Miranda; Celia, Laura; Chertkov, Olga; Lapidus, Alla L.; Copeland, A; Glavina Del Rio, Tijana; Nolan, Matt; Lucas, Susan; Tice, Hope; Cheng, Jan-Fang; Han, Cliff; Detter, J. Chris; Bruce, David; Goodwin, Lynne A.; Pitluck, Sam; Pati, Amrita; Liolios, Konstantinos; Ivanova, N; Mavromatis, K; Mikhailova, Natalia; Chen, Amy; Palaniappan, Krishna; Land, Miriam L; Hauser, Loren John; Chang, Yun-Juan; Jeffries, Cynthia; Goker, Markus; Beck, Brian; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter; Chen, Feng

    2010-01-01

    Sebaldella termitidis (Sebald 1962) Collins and Shah 1986, is the only species in the genus Sebaldella within the fusobacterial family Leptotrichiaceae . The sole and type strain of the species was first isolated about 50 years ago from intestinal content of Mediterranean ter-mites. The species is of interest for its very isolated phylogenetic position within the phylum Fusobacteria in the tree of life, with no other species sharing more than 90% 16S rRNA se-quence similarity. The 4,486,650 bp long genome with its 4,210 protein-coding and 54 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

  13. Complete genome sequence of Sebaldella termitidis type strain (NCTC 11300T)

    PubMed Central

    Harmon-Smith, Miranda; Celia, Laura; Chertkov, Olga; Lapidus, Alla; Copeland, Alex; Glavina Del Rio, Tijana; Nolan, Matt; Lucas, Susan; Tice, Hope; Cheng, Jan-Fang; Han, Cliff; Detter, John C.; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Pati, Amrita; Liolios, Konstantinos; Ivanova, Natalia; Mavromatis, Konstantinos; Mikhailova, Natalia; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Brettin, Thomas; Göker, Markus; Beck, Brian; Bristow, James; Eisen, Jonathan A.; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C.; Klenk, Hans-Peter; Chen, Feng

    2010-01-01

    Sebaldella termitidis (Sebald 1962) Collins and Shah 1986, is the only species in the genus Sebaldella within the fusobacterial family ‘Leptotrichiaceae’. The sole and type strain of the species was first isolated about 50 years ago from intestinal content of Mediterranean termites. The species is of interest for its very isolated phylogenetic position within the phylum Fusobacteria in the tree of life, with no other species sharing more than 90% 16S rRNA sequence similarity. The 4,486,650 bp long genome with its 4,210 protein-coding and 54 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project. PMID:21304705

  14. Complete genome sequence of Sanguibacter keddieii type strain (ST-74T)

    SciTech Connect

    Ivanova, Natalia; Sikorski, Johannes; Sims, David; Brettin, Thomas; Detter, John C.; Han, Cliff; Lapidus, Alla; Copeland, Alex; Glavina Del Rio, Tijana; Nolan, Matt; Chen, Feng; Lucas, Susan; Tice, Hope; Cheng, Jan-Fang; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Pati, Amrita; Mavromatis, Konstantinos; Chen, Amy; Palaniappan, Krishna; D'haeseleer, Patrik; Chain, Patrick; Bristow, Jim; Eisen, Jonathan A.; Markowitz, Victor; Hugenholtz, Philip; Goker, Markus; Pukall, Rudiger; Klenk, Hans-Peter; Kyrpides, Nikos

    2009-05-20

    Sanguibacter keddieii is the type species of the genus Sanguibacter, the only described genus within the family of Sanguibacteraceae. Phylogenetically, this family is located in the neighbourhood of the genus Oerskovia and the family Cellulomonadaceae within the actinobacterial suborder Micrococcineae. The strain described in this report was isolated from blood of apparently healthy cows. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of the family Sanguibacteraceae, and the 4,253,413 bp long single replicon genome with its 3735 protein-coding and 70 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

  15. Genetic diversity of Mycobacterium avium subspecies paratuberculosis and the influence of strain type on infection and pathogenesis: a review.

    PubMed

    Stevenson, Karen

    2015-06-19

    Mycobacterium avium subspecies paratuberculosis (Map) is an important pathogen that causes a chronic, progressive granulomatous enteritis known as Johne's disease or paratuberculosis. The disease is endemic in many parts of the world and responsible for considerable losses to the livestock and associated industries. Diagnosis and control are problematic, due mostly to the long incubation period of the disease when infected animals show no clinical signs and are difficult to detect, and the ability of the organism to survive and persist in the environment. The existence of phenotypically distinct strains of Map has been known since the 1930s but the genetic differentiation of Map strain types has been challenging and only recent technologies have proven sufficiently discriminative for strain comparisons, tracing the sources of infection and epidemiological studies. It is important to understand the differences that exist between Map strains and how they influence both development and transmission of disease. This information is required to develop improved diagnostics and effective vaccines for controlling Johne's disease. Here I review the current classification of Map strain types, the sources of the genetic variability within strains, growth characteristics and epidemiological traits associated with strain type and the influence of strain type on infection and pathogenicity.

  16. Recombinant herpes simplex virus type 1 strains with targeted mutations relevant for aciclovir susceptibility

    PubMed Central

    Brunnemann, Anne-Kathrin; Liermann, Kristin; Deinhardt-Emmer, Stefanie; Maschkowitz, Gregor; Pohlmann, Anja; Sodeik, Beate; Fickenscher, Helmut; Sauerbrei, Andreas; Krumbholz, Andi

    2016-01-01

    Here, we describe a novel reliable method to assess the significance of individual mutations within the thymidine kinase (TK) gene of herpes simplex virus type 1 (HSV-1) to nucleoside analogue resistance. Eleven defined single nucleotide polymorphisms that occur in the TK gene of clinical HSV-1 isolates and a fluorescence reporter were introduced into the HSV-1 strain 17+ that had been cloned into a bacterial artificial chromosome. The susceptibility of these different strains to aciclovir, penciclovir, brivudin, and foscarnet was determined with a modified cytopathic effect reduction assay. The strains were also tested for their aciclovir susceptibility by measuring the relative fluorescence intensity as an indicator for HSV-1 replication and by quantifying the virus yield. Our data indicate that the amino acid substitutions R41H, R106H, A118V, L139V, K219T, S276R, L298R, S345P, and V348I represent natural polymorphisms of the TK protein, whereas G61A and P84L mediate broad cross-resistance against aciclovir, penciclovir, brivudin, and susceptibility to foscarnet. This method allows the definition of the resistance genotype of otherwise unclear mutations in the TK gene of HSV-1. Thus, it provides a scientific basis for antiviral testing in clinical isolates of patients suffering from serious diseases and will facilitate testing of new antivirals against HSV-1. PMID:27426251

  17. Genome sequence of the Thermotoga thermarum type strain (LA3(T)) from an African solfataric spring.

    PubMed

    Göker, Markus; Spring, Stefan; Scheuner, Carmen; Anderson, Iain; Zeytun, Ahmet; Nolan, Matt; Lucas, Susan; Tice, Hope; Del Rio, Tijana Glavina; Cheng, Jan-Fang; Han, Cliff; Tapia, Roxanne; Goodwin, Lynne A; Pitluck, Sam; Liolios, Konstantinos; Mavromatis, Konstantinos; Pagani, Ioanna; Ivanova, Natalia; Mikhailova, Natalia; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D; Rohde, Manfred; Detter, John C; Woyke, Tanja; Bristow, James; Eisen, Jonathan A; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter; Lapidus, Alla

    2014-06-15

    Thermotoga thermarum Windberger et al. 1989 is a member to the genomically well characterized genus Thermotoga in the phylum 'Thermotogae'. T. thermarum is of interest for its origin from a continental solfataric spring vs. predominantly marine oil reservoirs of other members of the genus. The genome of strain LA3T also provides fresh data for the phylogenomic positioning of the (hyper-)thermophilic bacteria. T. thermarum strain LA3(T) is the fourth sequenced genome of a type strain from the genus Thermotoga, and the sixth in the family Thermotogaceae to be formally described in a publication. Phylogenetic analyses do not reveal significant discrepancies between the current classification of the group, 16S rRNA gene data and whole-genome sequences. Nevertheless, T. thermarum significantly differs from other Thermotoga species regarding its iron-sulfur cluster synthesis, as it contains only a minimal set of the necessary proteins. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,039,943 bp long chromosome with its 2,015 protein-coding and 51 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  18. Multilocus Microsatellite Typing as a New Tool for Discrimination of Leishmania infantum MON-1 Strains

    PubMed Central

    Ochsenreither, Sebastian; Kuhls, Katrin; Schaar, Matthias; Presber, Wolfgang; Schönian, Gabriele

    2006-01-01

    The Leishmania donovani complex, which consists of L. donovani, L. infantum-L. chagasi, and L. archibaldi, is responsible for visceral manifestations of leishmaniasis. Multilocus enzyme electrophoresis is the standard method for the characterization and identification of strains of Leishmania. For L. infantum, the predominance of zymodeme MON-1 significantly reduces the discriminative power of this approach. In the present study, we developed 17 independent polymorphic microsatellite markers for the typing of strains of L. infantum, with the main emphasis on zymodeme MON-1. The discriminative powers of 11 markers selected from among these markers were tested by using a panel of 63 isolates of the L. donovani complex. Unique multilocus genotypes were observed for the strains analyzed, with only three exceptions. Model-based and distance-based analyses of the data set showed comparable results. It was possible to discriminate between L. donovani sensu stricto, a non-MON-1 group of L. infantum isolates, and a MON-1 group of L. infantum isolates. Within MON-1, three clusters with geographical correlations became apparent. The frequency of heterozygosity in the alleles analyzed varied extremely between the different groups of isolates. The main clusters described are not consistent with species definitions based on isoenzyme analysis but confirm the results of former PCR-based investigations. PMID:16455904

  19. A staggered approach for the coupling of Cahn-Hilliard type diffusion and finite strain elasticity

    NASA Astrophysics Data System (ADS)

    Areias, P.; Samaniego, E.; Rabczuk, T.

    2016-02-01

    We develop an algorithm and computational implementation for simulation of problems that combine Cahn-Hilliard type diffusion with finite strain elasticity. We have in mind applications such as the electro-chemo-mechanics of lithium ion (Li-ion) batteries. We concentrate on basic computational aspects. A staggered algorithm is proposed for the coupled multi-field model. For the diffusion problem, the fourth order differential equation is replaced by a system of second order equations to deal with the issue of the regularity required for the approximation spaces. Low order finite elements are used for discretization in space of the involved fields (displacement, concentration, nonlocal concentration). Three (both 2D and 3D) extensively worked numerical examples show the capabilities of our approach for the representation of (i) phase separation, (ii) the effect of concentration in deformation and stress, (iii) the effect of strain in concentration, and (iv) lithiation. We analyze convergence with respect to spatial and time discretization and found that very good results are achievable using both a staggered scheme and approximated strain interpolation.

  20. Genome sequence of the Thermotoga thermarum type strain (LA3T) from an African solfataric spring

    PubMed Central

    Göker, Markus; Spring, Stefan; Scheuner, Carmen; Anderson, Iain; Zeytun, Ahmet; Nolan, Matt; Lucas, Susan; Tice, Hope; Del Rio, Tijana Glavina; Cheng, Jan-Fang; Han, Cliff; Tapia, Roxanne; Goodwin, Lynne A.; Pitluck, Sam; Liolios, Konstantinos; Mavromatis, Konstantinos; Pagani, Ioanna; Ivanova, Natalia; Mikhailova, Natalia; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Chang, Yun-juan; Jeffries, Cynthia D.; Rohde, Manfred; Detter, John C.; Woyke, Tanja; Bristow, James; Eisen, Jonathan A.; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C.; Klenk, Hans-Peter; Lapidus, Alla

    2014-01-01

    Thermotoga thermarum Windberger et al. 1989 is a member to the genomically well characterized genus Thermotoga in the phylum ‘Thermotogae’. T. thermarum is of interest for its origin from a continental solfataric spring vs. predominantly marine oil reservoirs of other members of the genus. The genome of strain LA3T also provides fresh data for the phylogenomic positioning of the (hyper-)thermophilic bacteria. T. thermarum strain LA3T is the fourth sequenced genome of a type strain from the genus Thermotoga, and the sixth in the family Thermotogaceae to be formally described in a publication. Phylogenetic analyses do not reveal significant discrepancies between the current classification of the group, 16S rRNA gene data and whole-genome sequences. Nevertheless, T. thermarum significantly differs from other Thermotoga species regarding its iron-sulfur cluster synthesis, as it contains only a minimal set of the necessary proteins. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,039,943 bp long chromosome with its 2,015 protein-coding and 51 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. PMID:25197486

  1. Complete genome sequence of the orange-red pigmented, radioresistant Deinococcus proteolyticus type strain (MRPT)

    SciTech Connect

    Copeland, A; Zeytun, Ahmet; Yasawong, Montri; Nolan, Matt; Lucas, Susan; Hammon, Nancy; Deshpande, Shweta; Cheng, Jan-Fang; Han, Cliff; Tapia, Roxanne; Goodwin, Lynne A.; Pitluck, Sam; Mavromatis, K; Liolios, Konstantinos; Pagani, Ioanna; Ivanova, N; Mikhailova, Natalia; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam L; Hauser, Loren John; Jeffries, Cynthia; Brambilla, Evelyne-Marie; Rohde, Manfred; Sikorski, Johannes; Pukall, Rudiger; Goker, Markus; Detter, J. Chris; Woyke, Tanja; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter; Lapidus, Alla L.

    2012-01-01

    Deinococcus proteolyticus (ex Kobatake et al. 1973) Brook and Murray 1981 is one of currently 47 species in the genus Deinococcus within the family Deinococcaceae. Strain MRPTT was isolated from faeces of Lama glama; it shares with various other species of the genus the extreme radiation resistance, with D. proteolyticus being resistant up to 1.5 Mrad of gamma radiation. Strain MRPT{sup T} is of further interest for its carotenoid pigment. The genome presented here is only the fifth completed genome sequence of a member of the genus Deinococcus (and the forth type strain) to be published, and will hopefully contribute to a better understanding of how members of this genus adapted to high gamma- or UV ionizing-radiation. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,886,836 bp long genome with its four large plasmids of 97 kbp, 132 kbp, 196 kbp and 315 kbp harbours 2,741 protein-coding and 58 RNA genes and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  2. Complete genome sequence of Hydrogenobacter thermophilus type strain (TK-6T)

    SciTech Connect

    Zeytun, Ahmet; Sikorski, Johannes; Nolan, Matt; Lapidus, Alla L.; Lucas, Susan; Han, James; Tice, Hope; Cheng, Jan-Fang; Tapia, Roxanne; Goodwin, Lynne A.; Pitluck, Sam; Liolios, Konstantinos; Ivanova, N; Mavromatis, K; Mikhailova, Natalia; Ovchinnikova, Galina; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Ngatchou, Olivier Duplex; Land, Miriam L; Hauser, Loren John; Chang, Yun-Juan; Jeffries, Cynthia; Han, Cliff; Detter, J. Chris; Ubler, Susanne; Rohde, Manfred; Tindall, Brian; Wirth, Reinhard; Woyke, Tanja; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Klenk, Hans-Peter; Kyrpides, Nikos C

    2011-01-01

    Hydrogenobacter thermophilus Kawasumi et al. 1984 is the type species of the genus Hydrogenobacter. H. thermophilus was the first obligate autotrophic organism reported among aerobic hydrogen-oxidizing bacteria. Strain TK-6T is of interest because of the unusually efficient hydrogen-oxidizing ability of this strain, which results in a faster generation time compared to other autotrophs. It is also able to grow anaerobically using nitrate as an electron acceptor when molecular hydrogen is used as the energy source, and able to aerobically fix CO2 via the reductive tricarboxylic acid cycle. This is the fifth completed genome sequence in the family Aquificaceae, and the second genome sequence determined from a strain derived from the original isolate. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 1,742,932 bp long genome with its 1,899 protein-coding and 49 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  3. Strain aging and load relaxation behavior of type 316 stainless steel at room temperature

    NASA Astrophysics Data System (ADS)

    Hannula, S. P.; Korhonen, M. A.; Li, C. Y.

    1986-10-01

    The strain aging and load relaxation behavior of type 316 stainless steel (SS) at room temperature were studied. It is shown that rapid aging occurs in 316 SS at room temperature to an extent that affects the load relaxation behavior of the material. Qualitatively, the aging behavior was found to agree with those reported earlier for Fe-Ni-C-alloys, and the observed aging characteristics could be explained by using an earlier proposed vacancy-interstitial mechanism. The load relaxation behavior is analyzed in terms of Hart’s state variable model. Effects of strain aging and strain hardening on the load relaxation behavior and the scaling of the relaxation curves are determined. It is shown that aging can be accounted for by a time-dependent change in a model parameter, which is dependent on the mobile dislocation density and the dislocation mobility. In addition, a dependency on plastic state of the same parameter previously held constant was found. It is concluded that this phenomenon, which in 316 SS could be rationalized in terms of increasing forest dislocation density, is likely to be more general, and a provision for it should be made in the state variable theory.

  4. [The presence of OXA type carbapenemases in Pseudomonas strains: first report from Turkey].

    PubMed

    Esenkaya Taşbent, Fatma; Özdemir, Mehmet

    2015-01-01

    from the samples of patients in intensive-care units, and bronchoalveolar lavage specimens were the most prevalent samples (85/184; 46.2%). This study determined the presence and frequency of OXA type carbapenemases among Pseudomonas strains for the first time in our region and Turkey. These resistance genes demonstrated in Acinetobacter spp. were also detected in this study in Pseudomonas spp. and they may cause carbapenem resistance directly or by affecting the other resistance mechanisms with a synergistic effect. This study is expected to provide a basis for further studies to elucidate resistance mechanisms.

  5. Pathogenic characterization of Erysipelothrix rhusiopathiae Met-203 type SpaA strains from chronic and subacute swine erysipelas in Japan.

    PubMed

    Uchiyama, Mariko; Shimazaki, Yohko; Isshiki, Yukari; Kojima, Akemi; Hirano, Fumiya; Yamamoto, Kinya; Kijima, Mayumi; Nagai, Hidetaka

    2017-01-20

    To characterize the Erysipelothrix rhusiopathiae Met-203 type surface protective antigen (Spa) A strains causing swine erysipelas in Japan, the nucleotide sequence of the hypervariable region of the spaA gene was determined in 80 E. rhusiopathiae (serotype 1a) isolates collected from pigs with chronic and subacute swine erysipelas in 14 prefectures in 2008-2014. In this study, 14 (17.5%) isolates were Met-203 type SpaA strains. We confirmed the pathogenicity of a Met-203 type SpaA strain in specific-pathogen-free pigs. In this experiment, the two challenged pigs displayed arthritis, urticaria and other clinical signs, but recovered within 10 days. Our results reveal the existence of the E. rhusiopathiae Met-203 type strains that have been causing chronic erysipelas in Japan.

  6. Pathogenic characterization of Erysipelothrix rhusiopathiae Met-203 type SpaA strains from chronic and subacute swine erysipelas in Japan

    PubMed Central

    UCHIYAMA, Mariko; SHIMAZAKI, Yohko; ISSHIKI, Yukari; KOJIMA, Akemi; HIRANO, Fumiya; YAMAMOTO, Kinya; KIJIMA, Mayumi; NAGAI, Hidetaka

    2016-01-01

    To characterize the Erysipelothrix rhusiopathiae Met-203 type surface protective antigen (Spa) A strains causing swine erysipelas in Japan, the nucleotide sequence of the hypervariable region of the spaA gene was determined in 80 E. rhusiopathiae (serotype 1a) isolates collected from pigs with chronic and subacute swine erysipelas in 14 prefectures in 2008–2014. In this study, 14 (17.5%) isolates were Met-203 type SpaA strains. We confirmed the pathogenicity of a Met-203 type SpaA strain in specific-pathogen-free pigs. In this experiment, the two challenged pigs displayed arthritis, urticaria and other clinical signs, but recovered within 10 days. Our results reveal the existence of the E. rhusiopathiae Met-203 type strains that have been causing chronic erysipelas in Japan. PMID:27773881

  7. Genome Sequence of Type Strain Fonsecaea multimorphosa CBS 980.96T, a Causal Agent of Feline Cerebral Phaeohyphomycosis

    PubMed Central

    Leao, Aniele C. Ribas; Weiss, Vinicius Almir; Vicente, Vania Aparecida; Costa, Flavia; Bombassaro, Amanda; Raittz, Roberto Tadeu; Steffens, Maria Berenice R.; Pedrosa, Fabio Oliveira; Gomes, Renata R.; Baura, Valter; Faoro, Helisson; Sfeir, Michelle Zibetti Tadra; Balsanelli, Eduardo; Moreno, Leandro F.; Najafzadeh, M. Javad

    2017-01-01

    ABSTRACT A draft genome sequence of type strain Fonsecaea multimorphosa CBS 980.96T was obtained. This species was first isolated from a cat with cerebral phaeohyphomycosis in Queensland, Australia. PMID:28209838

  8. Complete genome sequence of Chitinophaga pinensis type strain (UQM 2034T)

    SciTech Connect

    Glavina Del Rio, Tijana; Abt, Birte; Spring, Stefan; Lapidus, Alla L.; Nolan, Matt; Tice, Hope; Copeland, A; Cheng, Jan-Fang; Chen, Feng; Bruce, David; Goodwin, Lynne A.; Pitluck, Sam; Ivanova, N; Mavromatis, K; Mikhailova, Natalia; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam L; Hauser, Loren John; Chang, Yun-Juan; Jeffries, Cynthia; Chain, Patrick S. G.; Saunders, Elizabeth H; Detter, J C; Brettin, Thomas S; Rohde, Manfred; Goker, Markus; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter; Lucas, Susan

    2010-01-01

    Chitinophaga pinensis Sangkhobol and Skerman 1981 is the type strain of the species which is the type species of the rapidly growing genus Chitinophaga in the sphingobacterial family Chitinophagaceae . Members of the genus Chitinophaga vary in shape between filaments and spherical bodies without the production of a fruiting body, produce myxospores, and are of special interest for their ability to degrade chitin. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of a member of the family Chitinophagaceae , and the 9,127,347 bp long single replicon genome with its 7,397 protein-coding and 95 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

  9. Complete genome sequence of Conexibacter woesei type strain (ID131577T)

    SciTech Connect

    Pukall, Rudiger; Lapidus, Alla L.; Glavina Del Rio, Tijana; Copeland, A; Tice, Hope; Cheng, Jan-Fang; Lucas, Susan; Chen, Feng; Nolan, Matt; Bruce, David; Goodwin, Lynne A.; Pitluck, Sam; Mavromatis, K; Ivanova, N; Ovchinnikova, Galina; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam L; Hauser, Loren John; Chang, Yun-Juan; Jeffries, Cynthia; Chain, Patrick S. G.; Meincke, Linda; Sims, David; Detter, J. Chris; Rohde, Manfred; Goker, Markus; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Kyrpides, Nikos C; Klenk, Hans-Peter; Hugenholtz, Philip

    2010-01-01

    The genus Conexibacter (Monciardini et al. 2003) represents the type genus of the family Conexibacteraceae (Stackebrandt 2005, emend. Zhi et al. 2009) with Conexibacter woesei as the type species of the genus. C. woesei is a representative of a deep evolutionary line of des-cent within the class Actinobacteria. Strain ID131577T was originally isolated from temperate forest soil in Gerenzano (Italy). Cells are small, short rods that are motile by peritrichous fla-gella. They may form aggregates after a longer period of growth and, then as a typical charac-teristic, an undulate structure is formed by self-aggregation of flagella with entangled bacteri-al cells. Here we describe the features of the organism, together with the complete sequence and annotation. The 6,359,369 bp long genome of C. woesei contains 5,950 protein-coding and 48 RNA genes and is part of the Genomic Encyclopedia of Bacteria and Archaea project.

  10. Complete genome sequence of Tsukamurella paurometabola type strain (no. 33T)

    SciTech Connect

    Munk, Christine; Lapidus, Alla L.; Lucas, Susan; Nolan, Matt; Tice, Hope; Cheng, Jan-Fang; Glavina Del Rio, Tijana; Goodwin, Lynne A.; Pitluck, Sam; Liolios, Konstantinos; Huntemann, Marcel; Ivanova, N; Mavromatis, K; Mikhailova, Natalia; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Tapia, Roxanne; Han, Cliff; Land, Miriam L; Hauser, Loren John; Chang, Yun-Juan; Jeffries, Cynthia; Brettin, Thomas S; Yasawong, Montri; Brambilla, Evelyne-Marie; Rohde, Manfred; Sikorski, Johannes; Goker, Markus; Woyke, Tanja; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter

    2011-01-01

    Tsukamurella paurometabola corrig. (Steinhaus 1941) Collins et al. 1988 is the type species of the genus Tsukamurella, which is the type genus to the family Tsukamurellaceae. The spe- cies is not only of interest because of its isolated phylogenetic location, but also because it is a human opportunistic pathogen with some strains of the species reported to cause lung in- fection, lethal meningitis, and necrotizing tenosynovitis. This is the first completed genome sequence of a member of the genus Tsukamurella and the first genome sequence of a member of the family Tsukamurellaceae. The 4,479,724 bp long genome contains a 99,806 bp long plasmid and a total of 4,335 protein-coding and 56 RNA genes, and is a part of the Ge- nomic Encyclopedia of Bacteria and Archaea project.

  11. Complete genome sequence of Segniliparus rotundus type strain (CDC 1076T)

    SciTech Connect

    Sikorski, Johannes; Lapidus, Alla L.; Copeland, A; Misra, Monica; Glavina Del Rio, Tijana; Nolan, Matt; Lucas, Susan; Chen, Feng; Tice, Hope; Cheng, Jan-Fang; Jando, Marlen; Schneider, Susan; Bruce, David; Goodwin, Lynne A.; Pitluck, Sam; Liolios, Konstantinos; Mikhailova, Natalia; Pati, Amrita; Ivanova, N; Mavromatis, K; Chen, Amy; Palaniappan, Krishna; Chertkov, Olga; Land, Miriam L; Hauser, Loren John; Chang, Yun-Juan; Jeffries, Cynthia; Detter, J. Chris; Han, Cliff; Rohde, Manfred; Goker, Markus; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter

    2010-01-01

    Segniliparus rotundus Butler 2005 is the type species of the genus Segniliparus, which is cur-rently the only genus in the corynebacterial family Segniliparaceae. This family is of large in-terest because of a novel late-emerging genus-specific mycolate pattern. The type strain has been isolated from human sputum and is probably an opportunistic pathogen. Here we de-scribe the features of this organism, together with the complete genome sequence and anno-tation. This is the first completed genome sequence of the family Segniliparaceae. The 3,157,527 bp long genome with its 3,081 protein-coding and 52 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

  12. Complete genome sequence of Tsukamurella paurometabola type strain (no. 33T)

    PubMed Central

    Munk, A. Christine; Lapidus, Alla; Lucas, Susan; Nolan, Matt; Tice, Hope; Cheng, Jan-Fang; Del Rio, Tijana Glavina; Goodwin, Lynne; Pitluck, Sam; Liolios, Konstantinos; Huntemann, Marcel; Ivanova, Natalia; Mavromatis, Konstantinos; Mikhailova, Natalia; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Tapia, Roxanne; Han, Cliff; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Brettin, Thomas; Yasawong, Montri; Brambilla, Evelyne-Marie; Rohde, Manfred; Sikorski, Johannes; Göker, Markus; Detter, John C.; Woyke, Tanja; Bristow, James; Eisen, Jonathan A.; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C.; Klenk, Hans-Peter

    2011-01-01

    Tsukamurella paurometabola corrig. (Steinhaus 1941) Collins et al. 1988 is the type species of the genus Tsukamurella, which is the type genus to the family Tsukamurellaceae. The species is not only of interest because of its isolated phylogenetic location, but also because it is a human opportunistic pathogen with some strains of the species reported to cause lung infection, lethal meningitis, and necrotizing tenosynovitis. This is the first completed genome sequence of a member of the genus Tsukamurella and the first genome sequence of a member of the family Tsukamurellaceae. The 4,479,724 bp long genome contains a 99,806 bp long plasmid and a total of 4,335 protein-coding and 56 RNA genes, and is a part of the Genomic Encyclopedia of Bacteria and Archaea project. PMID:21886861

  13. Complete genome sequence of Sphaerobacter thermophilus type strain (S 6022T)

    SciTech Connect

    Pati, Amrita; LaButti, Kurt; Pukall, Rudiger; Nolan, Matt; Glavina Del Rio, Tijana; Tice, Hope; Cheng, Jan-Fang; Lucas, Susan; Chen, Feng; Copeland, A; Ivanova, N; Mavromatis, K; Mikhailova, Natalia; Pitluck, Sam; Bruce, David; Goodwin, Lynne A.; Land, Miriam L; Hauser, Loren John; Chang, Yun-Juan; Jeffries, Cynthia; Chen, Amy; Palaniappan, Krishna; Chain, Patrick S. G.; Brettin, Thomas S; Sikorski, Johannes; Rohde, Manfred; Goker, Markus; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter; Lapidus, Alla L.

    2010-01-01

    Sphaerobacter thermophilus Demharter et al. 1989 is the sole and type species of the genus Sphaerobacter, which is the type genus of the family Sphaerobacteraceae, the order Sphaerobacterales and the subclass Sphaerobacteridae. Phylogenetically, it belongs to the genomically little studied class of the Thermomicrobia in the bacterial phylum Chloroflexi. Here, the genome of strain S 6022T is described which is an obligate aerobe that was originally isolated from an aerated laboratory-scale fermentor that was pulse fed with municipal sewage sludge. We describe the features of this organism, together with the complete genome and annotation. This is the first complete genome sequence of the thermomicrobial subclass Sphaerobacteridae, and the second sequence from the chloroflexal class Thermomicrobia. The 3,993,764 bp genome with its 3,525 protein-coding and 57 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  14. Complete genome sequence of Sphaerobacter thermophilus type strain (S 6022T)

    PubMed Central

    Pati, Amrita; LaButti, Kurt; Pukall, Rüdiger; Nolan, Matt; Glavina Del Rio, Tijana; Tice, Hope; Cheng, Jan-Fang; Lucas, Susan; Chen, Feng; Copeland, Alex; Ivanova, Natalia; Mavromatis, Konstantinos; Mikhailova, Natalia; Pitluck, Sam; Bruce, David; Goodwin, Lynne; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Chen, Amy; Palaniappan, Krishna; Chain, Patrick; Brettin, Thomas; Sikorski, Johannes; Rohde, Manfred; Göker, Markus; Bristow, Jim; Eisen, Jonathan A.; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C.; Klenk, Hans-Peter; Lapidus, Alla

    2010-01-01

    Sphaerobacter thermophilus Demharter et al. 1989 is the sole and type species of the genus Sphaerobacter, which is the type genus of the family Sphaerobacteraceae, the order Sphaerobacterales and the subclass Sphaerobacteridae. Phylogenetically, it belongs to the genomically little studied class of the Thermomicrobia in the bacterial phylum Chloroflexi. Here, the genome of strain S 6022T is described which is an obligate aerobe that was originally isolated from an aerated laboratory-scale fermentor that was pulse fed with municipal sewage sludge. We describe the features of this organism, together with the complete genome and annotation. This is the first complete genome sequence of the thermomicrobial subclass Sphaerobacteridae, and the second sequence from the chloroflexal class Thermomicrobia. The 3,993,764 bp genome with its 3,525 protein-coding and 57 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. PMID:21304677

  15. Complete genome sequence of Desulfohalobium retbaense type strain (HR100T)

    PubMed Central

    Spring, Stefan; Nolan, Matt; Lapidus, Alla; Glavina Del Rio, Tijana; Copeland, Alex; Tice, Hope; Cheng, Jan-Fang; Lucas, Susan; Land, Miriam; Chen, Feng; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Ivanova, Natalia; Mavromatis, Konstantinos; Mikhailova, Natalia; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Munk, Christine; Kiss, Hajnalka; Chain, Patrick; Han, Cliff; Brettin, Thomas; Detter, John C.; Schüler, Esther; Göker, Markus; Rohde, Manfred; Bristow, Jim; Eisen, Jonathan A.; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C.; Klenk, Hans-Peter

    2010-01-01

    Desulfohalobium retbaense (Ollivier et al. 1991) is the type species of the polyphyletic genus Desulfohalobium, which comprises, at the time of writing, two species and represents the family Desulfohalobiaceae within the Deltaproteobacteria. D. retbaense is a moderately halophilic sulfate-reducing bacterium, which can utilize H2 and a limited range of organic substrates, which are incompletely oxidized to acetate and CO2, for growth. The type strain HR100T was isolated from sediments of the hypersaline Retba Lake in Senegal. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of a member of the family Desulfohalobiaceae. The 2,909,567 bp genome (one chromosome and a 45,263 bp plasmid) with its 2,552 protein-coding and 57 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. PMID:21304676

  16. Complete genome sequence of Desulfarculus baarsii type strain (2st14T)

    SciTech Connect

    Sun, Christine; Spring, Stefan; Lapidus, Alla L.; Davenport, Karen W.; Glavina Del Rio, Tijana; Tice, Hope; Nolan, Matt; Copeland, A; Cheng, Jan-Fang; Lucas, Susan; Tapia, Roxanne; Goodwin, Lynne A.; Pitluck, Sam; Ivanova, N; Pagani, Ioanna; Mavromatis, K; Ovchinnikova, Galina; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Hauser, Loren John; Chang, Yun-Juan; Jeffries, Cynthia; Detter, J. Chris; Han, Cliff; Rohde, Manfred; Brambilla, Evelyne-Marie; Goker, Markus; Woyke, Tanja; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter; Land, Miriam L

    2010-01-01

    Desulfarculus baarsii (Widdel 1981) Kuever et al. 2006 is the type and only species of the genus Desulfarculus, which represents the family Desulfarculaceae and the order Desulfarculales. This species is a mesophilic sulfate-reducing bacterium with the capability to oxidize acetate and fatty acids of up to 18 carbon atoms completely to CO2. The acetyl-CoA/CODH (Wood-Ljungdahl) pathway is used by this species for the complete oxidation of carbon sources and autotrophic growth on formate. The type strain 2st14T was isolated from a ditch sediment collected near the University of Konstanz, Germany. This is the first completed genome sequence of a member of the order Desulfarculales. The 3,655,731 bp long single replicon genome with its 3,303 protein-coding and 52 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  17. Complete genome sequence of Truepera radiovictrix type strain (RQ-24T)

    SciTech Connect

    Ivanova, N; Rohde, Christine; Munk, Christine; Nolan, Matt; Lucas, Susan; Glavina Del Rio, Tijana; Tice, Hope; Deshpande, Shweta; Cheng, Jan-Fang; Tapia, Roxanne; Han, Cliff; Goodwin, Lynne A.; Pitluck, Sam; Liolios, Konstantinos; Mavromatis, K; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam L; Hauser, Loren John; Chang, Yun-Juan; Jeffries, Cynthia; Brambilla, Evelyne-Marie; Rohde, Manfred; Goker, Markus; Tindall, Brian; Woyke, Tanja; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter; Lapidus, Alla L.

    2011-01-01

    Truepera radiovictrix Albuquerque et al. 2005 is the type species of the genus Truepera within the phylum Deinococcus/Thermus. T. radiovictrix is of special interest not only because of its isolated phylogenetic location in the order Deinococcales, but also because of its ability to grow under multiple extreme conditions in alkaline, moderately saline, and high temperature habitats. Of particular interest is the fact that, T. radiovictrix is also remarkably resistant to ionizing radiation, a feature it shares with members of the genus Deinococcus. This is the first completed genome sequence of a member of the family Trueperaceae and the fourth type strain genome sequence from a member of the order Deinococcales. The 3,260,398 bp long genome with its 2,994 protein-coding and 52 RNA genes consists of one circular chromosome and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  18. Complete genome sequence of Thermosphaera aggregans type strain (M11TL).

    PubMed

    Spring, Stefan; Rachel, Reinhard; Lapidus, Alla; Davenport, Karen; Tice, Hope; Copeland, Alex; Cheng, Jan-Fang; Lucas, Susan; Chen, Feng; Nolan, Matt; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Ivanova, Natalia; Mavromatis, Konstantinos; Ovchinnikova, Galina; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia C; Brettin, Thomas; Detter, John C; Tapia, Roxanne; Han, Cliff; Heimerl, Thomas; Weikl, Fabian; Brambilla, Evelyne; Göker, Markus; Bristow, James; Eisen, Jonathan A; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter

    2010-06-15

    Thermosphaera aggregans Huber et al. 1998 is the type species of the genus Thermosphaera, which comprises at the time of writing only one species. This species represents archaea with a hyperthermophilic, heterotrophic, strictly anaerobic and fermentative phenotype. The type strain M11TL(T) was isolated from a water-sediment sample of a hot terrestrial spring (Obsidian Pool, Yellowstone National Park, Wyoming). Here we describe the features of this organism, together with the complete genome sequence and annotation. The 1,316,595 bp long single replicon genome with its 1,410 protein-coding and 47 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  19. Complete genome sequence of Mahella australiensis type strain (50-1 BONT)

    SciTech Connect

    Sikorski, Johannes; Teshima, Hazuki; Nolan, Matt; Lucas, Susan; Hammon, Nancy; Deshpande, Shweta; Cheng, Jan-Fang; Pitluck, Sam; Liolios, Konstantinos; Pagani, Ioanna; Ivanova, N; Huntemann, Marcel; Mavromatis, K; Ovchinnikova, Galina; Pati, Amrita; Tapia, Roxanne; Han, Cliff; Goodwin, Lynne A.; Chen, Amy; Palaniappan, Krishna; Land, Miriam L; Hauser, Loren John; Ngatchou, Olivier Duplex; Rohde, Manfred; Pukall, Rudiger; Spring, Stefan; Abt, Birte; Goker, Markus; Detter, J. Chris; Woyke, Tanja; Bristow, James; Markowitz, Victor; Hugenholtz, Philip; Eisen, Jonathan; Kyrpides, Nikos C; Klenk, Hans-Peter; Lapidus, Alla L.

    2011-01-01

    Mahella australiensis Bonilla Salinas et al. 2004 is the type species of the genus Mahella, which belongs to the family Thermoanaerobacteraceae. The species is of interest because it differs from other known anaerobic spore-forming bacteria in its G+C content, and in certain phenotypic traits, such as carbon source utilization and relationship to temperature. Moreo- ver, it has been discussed that this species might be an indigenous member of petroleum and oil reservoirs. This is the first completed genome sequence of a member of the genus Mahella and the ninth completed type strain genome sequence from the family Thermoanaerobacte- raceae. The 3,135,972 bp long genome with its 2,974 protein-coding and 59 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  20. Complete genome sequence of Conexibacter woesei type strain (ID131577T)

    PubMed Central

    Pukall, Rüdiger; Lapidus, Alla; Glavina Del Rio, Tijana; Copeland, Alex; Tice, Hope; Cheng, Jan-Fang; Lucas, Susan; Chen, Feng; Nolan, Matt; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Mavromatis, Konstantinos; Ivanova, Natalia; Ovchinnikova, Galina; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Chain, Patrick; Meincke, Linda; Sims, David; Brettin, Thomas; Detter, John C.; Rohde, Manfred; Göker, Markus; Bristow, Jim; Eisen, Jonathan A.; Markowitz, Victor; Kyrpides, Nikos C.; Klenk, Hans-Peter; Hugenholtz, Philip

    2010-01-01

    The genus Conexibacter (Monciardini et al. 2003) represents the type genus of the family Conexibacteraceae (Stackebrandt 2005, emend. Zhi et al. 2009) with Conexibacter woesei as the type species of the genus. C. woesei is a representative of a deep evolutionary line of descent within the class Actinobacteria. Strain ID131577T was originally isolated from temperate forest soil in Gerenzano (Italy). Cells are small, short rods that are motile by peritrichous flagella. They may form aggregates after a longer period of growth and, then as a typical characteristic, an undulate structure is formed by self-aggregation of flagella with entangled bacterial cells. Here we describe the features of the organism, together with the complete sequence and annotation. The 6,359,369 bp long genome of C. woesei contains 5,950 protein-coding and 48 RNA genes and is part of the Genomic Encyclopedia of Bacteria and Archaea project. PMID:21304704

  1. Complete genome sequence of Desulfohalobium retbaense type strain (HR100T)

    SciTech Connect

    Spring, Stefan; Nolan, Matt; Lapidus, Alla L.; Glavina Del Rio, Tijana; Copeland, A; Tice, Hope; Cheng, Jan-Fang; Lucas, Susan; Land, Miriam L; Chen, Feng; Bruce, David; Goodwin, Lynne A.; Pitluck, Sam; Ivanova, N; Mavromatis, K; Mikhailova, Natalia; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Hauser, Loren John; Chang, Yun-Juan; Jeffries, Cynthia; Munk, Christine; Kiss, Hajnalka; Chain, Patrick S. G.; Han, Cliff; Brettin, Thomas S; Detter, J. Chris; Schuler, Esther; Goker, Markus; Rohde, Manfred; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter

    2010-01-01

    Desulfohalobium retbaense (Ollivier et al. 1991) is the type species of the polyphyletic genus Desulfohalobium, which comprises, at the time of writing, two species and represents the family Desulfohalobiaceae within the Deltaproteobacteria. D. retbaense is a moderately halophilic sulfate-reducing bacterium, which can utilize H2 and a limited range of organic substrates, which are incompletely oxidized to acetate and CO2, for growth. The type strain HR100T was isolated from sediments of the hypersaline Retba Lake in Senegal. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of a member of the family Desulfohalobiaceae. The 2,909,567 bp genome (one chromosome and a 45,263 bp plasmid) with its 2,552 protein-coding and 57 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  2. Complete genome sequence of Mahella australiensis type strain (50-1 BONT)

    PubMed Central

    Sikorski, Johannes; Teshima, Hazuki; Nolan, Matt; Lucas, Susan; Hammon, Nancy; Deshpande, Shweta; Cheng, Jan-Fang; Pitluck, Sam; Liolios, Konstantinos; Pagani, Ioanna; Ivanova, Natalia; Huntemann, Marcel; Mavromatis, Konstantinos; Ovchinikova, Galina; Pati, Amrita; Tapia, Roxanne; Han, Cliff; Goodwin, Lynne; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Ngatchou-Djao, Olivier D.; Rohde, Manfred; Pukall, Rüdiger; Spring, Stefan; Abt, Birte; Göker, Markus; Detter, John C.; Woyke, Tanja; Bristow, James; Markowitz, Victor; Hugenholtz, Philip; Eisen, Jonathan A.; Kyrpides, Nikos C.; Klenk, Hans-Peter; Lapidus, Alla

    2011-01-01

    Mahella australiensis Bonilla Salinas et al. 2004 is the type species of the genus Mahella, which belongs to the family Thermoanaerobacteraceae. The species is of interest because it differs from other known anaerobic spore-forming bacteria in its G+C content, and in certain phenotypic traits, such as carbon source utilization and relationship to temperature. Moreover, it has been discussed that this species might be an indigenous member of petroleum and oil reservoirs. This is the first completed genome sequence of a member of the genus Mahella and the ninth completed type strain genome sequence from the family Thermoanaerobacteraceae. The 3,135,972 bp long genome with its 2,974 protein-coding and 59 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. PMID:21886860

  3. Complete genome sequence of Chitinophaga pinensis type strain (UQM 2034T)

    PubMed Central

    Glavina Del Rio, Tijana; Abt, Birte; Spring, Stefan; Lapidus, Alla; Nolan, Matt; Tice, Hope; Copeland, Alex; Cheng, Jan-Fang; Chen, Feng; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Ivanova, Natalia; Mavromatis, Konstantinos; Mikhailova, Natalia; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Chain, Patrick; Saunders, Elizabeth; Detter, John C.; Brettin, Thomas; Rohde, Manfred; Göker, Markus; Bristow, Jim; Eisen, Jonathan A.; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C.; Klenk, Hans-Peter; Lucas, Susan

    2010-01-01

    Chitinophaga pinensis Sangkhobol and Skerman 1981 is the type strain of the species which is the type species of the rapidly growing genus Chitinophaga in the sphingobacterial family ‘Chitinophagaceae’. Members of the genus Chitinophaga vary in shape between filaments and spherical bodies without the production of a fruiting body, produce myxospores, and are of special interest for their ability to degrade chitin. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of a member of the family ‘Chitinophagaceae’, and the 9,127,347 bp long single replicon genome with its 7,397 protein-coding and 95 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project. PMID:21304681

  4. Job strain in different types of employment affects the immune response.

    PubMed

    Boscolo, Paolo; Forcella, Laura; Reale, Marcella; Vianale, Giovina; Battisti, Uliano; Bonfiglioli, Roberta; Cortini, Michela; Di Giampaolo, Luca; Di Donato, Angela; Salerno, Silvana

    2012-01-01

    The immune system, in cooperation with neuroendocrine functions, defends from cancer and infections mainly by the activity of blood natural killer (NK) cells. Blood NK activity may be influenced by the type of employment since work is the central part of life; moreover, job stress is a situation affecting both neuroendocrine and immune systems. This study examines anxiety (by STAI 1 and 2), job strain (by the Karasek's JCQ) and blood NK activity (by an in vitro radio-isotopic method) of 134 male workers. These men, over 38 years old with stable employment, were working in factories, in construction yards, in offices, as hospital attendants or as self-employed craftsmen. Workers in factories and in construction yards, with high job strain, showed lower NK activity, while office employees, with low job demand, and craftsmen with low anxiety and elevated decision latitude, showed higher NK activity; the level of NK activity of the hospital attendants was between the other groups. In conclusion, this study confirms that the type of employment, related to job stress, affects blood NK activity. Moreover, blood NK activity may be used in the bio-monitoring of workers at high risk.

  5. Complete genome sequence of Capnocytophaga ochracea type strain (VPI 2845T)

    SciTech Connect

    Mavromatis, Konstantinos; Gronow, Sabine; Saunders, Elizabeth; Land, Miriam; Lapidus, Alla; Copeland, Alex; Glavina Del Rio, Tijana; Nolan, Matt; Lucas, Susan; Chen, Feng; Tice1, Hope; Cheng, Jan-Fang; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Pati, Amrita; Ivanova, Natalia; Chen, Amy; Palaniappan, Krishna; Chain, Patrick; Hauser, Loren; Chang, Yun-Juan; Jefferies, Cynthia C.; Brettin, Thomas; Detter, John C.; Han, Cliff; Bristow, James; Goker, Markus; Rohde, Manfred; Eisen, Jonathan A.; Markowitz, Victor; Kyrpides, Nikos C.; Klenk, Hans-Peter; Hugenholtz, Philip

    2009-05-20

    Capnocytophaga ochracea (Prevot et al. 1956) Leadbetter et al. 1982 is the type species of the genus Capnocytophaga. It is of interest because of its location in the Flavobacteriaceae, a genomically yet uncharted family within the order Flavobacteriales. The species grows as fusiform to rod shaped cells which tend to form clumps and are able to move by gliding. C. ochracea is known as a capnophilic organism with the ability to grow under anaerobic as well as under aerobic conditions (oxygen concentration larger than 15percent), here only in the presence of 5percent CO2. Strain VPI 2845T, the type strain of the species, is portrayed in this report as a gliding, Gram-negative bacterium, originally isolated from a human oral cavity. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first completed genome sequence from the flavobacterial genus Capnocytophaga, and the 2,612,925 bp long single replicon genome with its 2193 protein-coding and 59 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  6. Construction and characterization of porcine circovirus type 2 carrying a genetic marker strain.

    PubMed

    Liu, Changming; Wei, Yanwu; Zhang, Caofan; Lu, Yueha; Kong, Xiangang

    2007-07-01

    Porcine circovirus type 2 (PCV2) is the primary causative agent of post-weaning multisystemic wasting syndrome in pigs. To generate a genetic marker strain of PCV2, the full-length genome of the virus was amplified using PCR, and two copies of the genome were ligated in tandem to construct an infectious molecular clone. A Sal I restriction enzyme site was inserted into the clone as a genetic marker, and the recombinant plasmid was transfected into porcine kidney cells to generate mutant virus. The antigenicity of the recovered virus was confirmed by immunoperoxidase monolayer assay. The viral antigen was visualized in the nucleus and cytoplasm of the virus-infected cells. The viral genome could be differentiated from the wild-type parent by PCR and restriction fragment length polymorphism (PCR-RFLP). The mutant virus was stable on multiplication through 60 passages in cell culture; the highest titer reached was 10(6.6)TCID(50)/ml. Four 35-day-old unvaccinated piglets were inoculated with the virus by the intranasal and intravenous routes. Two of the virus-infected pigs developed high temperatures, progressive weight loss, and swollen lymph nodes. The viral antigen and nucleic acid were detected in numerous tissues of the pigs. The results indicate that the genetic marker strain should be a useful tool in studies on pathogenesis, vaccination, and molecular diagnosis of PCV2.

  7. Complete genome sequence of Veillonella parvula type strain (Te3T)

    SciTech Connect

    Gronow, Sabine; Welnitz, Sabine; Lapidus, Alla L.; Nolan, Matt; Ivanova, N; Glavina Del Rio, Tijana; Copeland, A; Chen, Feng; Tice, Hope; Pitluck, Sam; Cheng, Jan-Fang; Saunders, Elizabeth H; Brettin, Thomas S; Han, Cliff; Detter, J. Chris; Bruce, David; Goodwin, Lynne A.; Land, Miriam L; Hauser, Loren John; Chang, Yun-Juan; Jeffries, Cynthia; Pati, Amrita; Mavromatis, K; Mikhailova, Natalia; Chen, Amy; Palaniappan, Krishna; Chain, Patrick S. G.; Rohde, Manfred; Goker, Markus; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter; Lucas, Susan

    2010-01-01

    Veillonella parvula (Veillon and Zuber 1898) Pr vot 1933 is the type species of the genus Veillonella in the family Veillonellaceae within the order Clostridiales. The species V. parvula is of interest because it is frequently isolated from dental plaque in the human oral cavity and can cause opportunistic infections. The species is strictly anaerobic and grows as small cocci which usually occur in pairs. Veillonellae are characterized by their unusual metabolism which is centered on the activity of the enzyme methylmalonyl-CoA decarboxylase. Strain Te3T, the type strain of the species, was isolated from the human intestinal tract. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of a member of the large clostridial family Veillonellaceae, and the 2,132,142 bp long single replicon genome with its 1859 protein-coding and 61 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

  8. Complete genome sequence of Capnocytophaga ochracea type strain (VPI 2845T)

    SciTech Connect

    Mavromatis, K; Gronow, Sabine; Saunders, Elizabeth H; Land, Miriam L; Lapidus, Alla L.; Copeland, A; Glavina Del Rio, Tijana; Nolan, Matt; Lucas, Susan; Chen, Feng; Bruce, David; Tice, Hope; Cheng, Jan-Fang; Goodwin, Lynne A.; Pitluck, Sam; Pati, Amrita; Ivanova, N; Chen, Amy; Palaniappan, Krishna; Chain, Patrick S. G.; Hauser, Loren John; Chang, Yun-Juan; Jeffries, Cynthia; Brettin, Thomas S; Detter, J. Chris; Han, Cliff; Bristow, James; Goker, Markus; Eisen, Jonathan; Markowitz, Victor; Kyrpides, Nikos C; Klenk, Hans-Peter; Hugenholtz, Philip

    2009-01-01

    Capnocytophaga ochracea (Pr vot et al. 1956) Leadbetter et al. 1982 is the type species of the genus Capnocytophaga. It is of interest because of its location in the Flavobacteriaceae, a genomically not yet charted family within the order Flavobacteriales. The species grows as fusiform to rod shaped cells which tend to form clumps and are able to move by gliding. C. ochracea is known as a capnophilic (CO2-requiring) organism with the ability to grow under anaerobic as well as aerobic conditions (oxygen concentration larger than 15%), here only in the presence of 5% CO2. Strain VPI 2845T, the type strain of the species, is portrayed in this report as a gliding, Gram-negative bacterium, originally isolated from a human oral cavity. Here we describe the features of this organism, together with the complete genome se-quence, and annotation. This is the first completed genome sequence from the flavobacterial genus Capnocytophaga, and the 2,612,925 bp long single replicon genome with its 2193 protein-coding and 59 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  9. Experimental infection of lambs with C and S-type strains of Mycobacterium avium subspecies paratuberculosis: immunological and pathological findings.

    PubMed

    Fernández, Miguel; Benavides, Julio; Sevilla, Iker A; Fuertes, Miguel; Castaño, Pablo; Delgado, Laetitia; García Marín, J Francisco; Garrido, Joseba M; Ferreras, M Carmen; Pérez, Valentín

    2014-01-16

    The two main genotypes of recognized isolates of Mycobacterium avium subsp. paratuberculosis (Map) are cattle (C) and sheep (S) strains. An experimental infection was conducted to establish the effect of Map strain on the pathogenesis of ovine paratuberculosis. Twenty-four out of thirty 1.5-month-old Assaf lambs were divided into 4 groups of 6 and infected orally with three low passage field isolates, two of S- (22G and the pigmented Ovicap49) and one of C- (764) type, and the reference K-10 strain (C type). The remaining six animals were unchallenged controls. Animals were euthanized at 150 and 390 days post-infection (dpi). Throughout the experiment, the peripheral immune response was assessed and histological and molecular (PCR) studies were conducted on samples of intestine and related lymphoid tissue. Specific antibody and IFN-γ production was significantly higher in animals infected with the C strains, while no consistent IFN- γ responses were observed in the S-type strain infected groups. A positive intradermal skin test response was detected in all infected groups. Lambs infected with S-type strains had granulomatous lesions restricted to the lymphoid tissue with no differences in the lesion intensity over time. In both C-type strain groups, lesions were more severe at 150 dpi while at 390 dpi lesions, characterized by well-demarcated granulomas with fibrosis, decreased in severity. Only infected lambs were positive to PCR. These results suggest that the strain of Map has a strong influence over the immune and pathological responses developed by the host. Lesions induced by C-type strains in lambs show a regressive character and tend to decrease as the infection progresses.

  10. Experimental infection of lambs with C and S-type strains of Mycobacterium avium subspecies paratuberculosis: immunological and pathological findings

    PubMed Central

    2014-01-01

    The two main genotypes of recognized isolates of Mycobacterium avium subsp. paratuberculosis (Map) are cattle (C) and sheep (S) strains. An experimental infection was conducted to establish the effect of Map strain on the pathogenesis of ovine paratuberculosis. Twenty-four out of thirty 1.5-month-old Assaf lambs were divided into 4 groups of 6 and infected orally with three low passage field isolates, two of S- (22G and the pigmented Ovicap49) and one of C– (764) type, and the reference K-10 strain (C type). The remaining six animals were unchallenged controls. Animals were euthanized at 150 and 390 days post-infection (dpi). Throughout the experiment, the peripheral immune response was assessed and histological and molecular (PCR) studies were conducted on samples of intestine and related lymphoid tissue. Specific antibody and IFN-γ production was significantly higher in animals infected with the C strains, while no consistent IFN- γ responses were observed in the S-type strain infected groups. A positive intradermal skin test response was detected in all infected groups. Lambs infected with S-type strains had granulomatous lesions restricted to the lymphoid tissue with no differences in the lesion intensity over time. In both C–type strain groups, lesions were more severe at 150 dpi while at 390 dpi lesions, characterized by well-demarcated granulomas with fibrosis, decreased in severity. Only infected lambs were positive to PCR. These results suggest that the strain of Map has a strong influence over the immune and pathological responses developed by the host. Lesions induced by C–type strains in lambs show a regressive character and tend to decrease as the infection progresses. PMID:24428881

  11. Difference in Degradation Patterns on Inulin-type Fructans among Strains of Lactobacillus delbrueckii and Lactobacillus paracasei.

    PubMed

    Tsujikawa, Yuji; Nomoto, Ryohei; Osawa, Ro

    2013-01-01

    Lactobacillus delbrueckii strains were assessed for their degradation patterns of various carbohydrates with specific reference to inulin-type fructans in comparison with those of Lactobacillus paracasei strains. Firstly, growth curves on glucose, fructose, sucrose and inulin-type fructans with increasing degrees of fructose polymerization (i.e., 1-kestose, fructo-oligosaccharides and inulin) of the strains were compared. L. paracasei DSM 20020 grew well on all these sugars, while the growth rates of the 4 L. delbrueckii strains were markedly higher on the fructans with a greater degree of polymerization than on fructose and sucrose. Secondly, sugar compositions of spent cultures of the strains of L. delbrueckii and L. paracasei grown in mMRS containing either the fructans or inulin were determined by thin layer chromatography, in which the spent cultures of L. paracasei DSM 20020 showed spots of short fructose and sucrose fractions, whereas those of the L. delbrueckii strains did not show such spots at all. These results suggest that, unlike the L. paracasei strains, the L. delbrueckii strains do not degrade the inulin-type fructans extracellularly, but transport the fructans capable of greater polymerization preferentially into their cells to be degraded intracellularly for their growth.

  12. Detection of multiple strains of Pasteurella multocida in fowl cholera outbreaks by polymerase chain reaction-based typing.

    PubMed

    Shivachandra, S B; Kumar, A A; Gautam, R; Saxena, M K; Chaudhuri, P; Srivastava, S K

    2005-12-01

    Applicability of molecular methods for the detection and differentiation of Pasteurella multocida strains involved in two separate fowl cholera outbreaks in a single poultry farm was investigated. A total of 12 and 18 strains of P. multocida obtained from two separate outbreaks were subjected to phenotypic and genotypic characterization. Phenotypically, all strains were similar; however, DNA-based techniques by employing polymerase chain reaction (PCR) assays were found to be highly specific and sensitive for rapid detection and differentiation of strains. All 30 strains gave amplicons of approximately 460 bp and approximately 1,044 bp specific for P. multocida and capsular serogroup A in the Multiplex Capsular PCR typing system. Molecular typing techniques such as repetitive extragenic palindromic PCR, enterobacterial repetitive intergenic consensus PCR and single primer PCR differentiated all 30 strains into different profiles. However, similar patterns of genome fragments were observed among all strains following restriction endonuclease analysis using the enzyme HpaII. The current investigation revealed involvement of the same and multiple strains of P. multocida in two outbreaks. The results also indicated that molecular methods of detection and typing are rapid in comparison with conventional methods for epidemiological investigations of fowl cholera outbreaks.

  13. Difference in Degradation Patterns on Inulin-type Fructans among Strains of Lactobacillus delbrueckii and Lactobacillus paracasei

    PubMed Central

    TSUJIKAWA, Yuji; NOMOTO, Ryohei; OSAWA, Ro

    2013-01-01

    Lactobacillus delbrueckii strains were assessed for their degradation patterns of various carbohydrates with specific reference to inulin-type fructans in comparison with those of Lactobacillus paracasei strains. Firstly, growth curves on glucose, fructose, sucrose and inulin-type fructans with increasing degrees of fructose polymerization (i.e., 1-kestose, fructo-oligosaccharides and inulin) of the strains were compared. L. paracasei DSM 20020 grew well on all these sugars, while the growth rates of the 4 L. delbrueckii strains were markedly higher on the fructans with a greater degree of polymerization than on fructose and sucrose. Secondly, sugar compositions of spent cultures of the strains of L. delbrueckii and L. paracasei grown in mMRS containing either the fructans or inulin were determined by thin layer chromatography, in which the spent cultures of L. paracasei DSM 20020 showed spots of short fructose and sucrose fractions, whereas those of the L. delbrueckii strains did not show such spots at all. These results suggest that, unlike the L. paracasei strains, the L. delbrueckii strains do not degrade the inulin-type fructans extracellularly, but transport the fructans capable of greater polymerization preferentially into their cells to be degraded intracellularly for their growth. PMID:24936375

  14. First Whole-Genome Sequence of a Haemophilus influenzae Type e Strain Isolated from a Patient with Invasive Disease in Italy

    PubMed Central

    Giufrè, Maria; Cardines, Rita

    2017-01-01

    ABSTRACT In the present era of conjugate vaccines against Haemophilus influenzae type b, non-vaccine-preventable strains are of concern. Here, we report the first whole-genome sequence of an invasive H. influenzae type e strain. This genomic information will enable further investigations on encapsulated non-type b H. influenzae strains. PMID:28360180

  15. Genome Analysis of Listeria monocytogenes Sequence Type 8 Strains Persisting in Salmon and Poultry Processing Environments and Comparison with Related Strains

    PubMed Central

    Fagerlund, Annette; Langsrud, Solveig; Schirmer, Bjørn C. T.; Møretrø, Trond; Heir, Even

    2016-01-01

    Listeria monocytogenes is an important foodborne pathogen responsible for the disease listeriosis, and can be found throughout the environment, in many foods and in food processing facilities. The main cause of listeriosis is consumption of food contaminated from sources in food processing environments. Persistence in food processing facilities has previously been shown for the L. monocytogenes sequence type (ST) 8 subtype. In the current study, five ST8 strains were subjected to whole-genome sequencing and compared with five additionally available ST8 genomes, allowing comparison of strains from salmon, poultry and cheese industry, in addition to a human clinical isolate. Genome-wide analysis of single-nucleotide polymorphisms (SNPs) confirmed that almost identical strains were detected in a Danish salmon processing plant in 1996 and in a Norwegian salmon processing plant in 2001 and 2011. Furthermore, we show that L. monocytogenes ST8 was likely to have been transferred between two poultry processing plants as a result of relocation of processing equipment. The SNP data were used to infer the phylogeny of the ST8 strains, separating them into two main genetic groups. Within each group, the plasmid and prophage content was almost entirely conserved, but between groups, these sequences showed strong divergence. The accessory genome of the ST8 strains harbored genetic elements which could be involved in rendering the ST8 strains resilient to incoming mobile genetic elements. These included two restriction-modification loci, one of which was predicted to show phase variable recognition sequence specificity through site-specific domain shuffling. Analysis indicated that the ST8 strains harbor all important known L. monocytogenes virulence factors, and ST8 strains are commonly identified as the causative agents of invasive listeriosis. Therefore, the persistence of this L. monocytogenes subtype in food processing facilities poses a significant concern for food safety

  16. Multilocus sequence typing of Mycoplasma hyorhinis strains identified by a real-time TaqMan PCR assay.

    PubMed

    Tocqueville, Véronique; Ferré, Séverine; Nguyen, Ngoc Hong Phuc; Kempf, Isabelle; Marois-Créhan, Corinne

    2014-05-01

    A real-time TaqMan PCR assay based on the gene encoding the protein p37 was developed to detect Mycoplasma hyorhinis. Its specificity was validated with 29 epidemiologically unrelated M. hyorhinis strains (28 field strains and one reference strain) and other mycoplasma species or with other microorganisms commonly found in pigs. The estimated detection limit of this qPCR assay was 125 microorganism equivalents/μl. The same 29 epidemiologically unrelated M. hyorhinis strains and four previously fully sequenced strains were typed by two portable typing methods, the sequencing of the p37 gene and a multilocus sequence typing (MLST) scheme. The first method revealed 18 distinct nucleotide sequences and insufficient discriminatory power (0.934). The MLST scheme was developed with the sequenced genomes of the M. hyorhinis strains HUB-1, GDL-1, MCLD, and SK76 and based on the genes dnaA, rpoB, gyrB, gltX, adk, and gmk. In total, 2,304 bp of sequence was analyzed for each strain. MLST was capable of subdividing the 33 strains into 29 distinct sequence types. The discriminatory power of the method was >0.95, which is the threshold value for interpreting typing results with confidence (D=0.989). Population analysis showed that recombination in M. hyorhinis occurs and that strains are diverse but with a certain clonality (one unique clonal complex was identified). The new qPCR assay and the robust MLST scheme are available for the acquisition of new knowledge on M. hyorhinis epidemiology. A web-accessible database has been set up for the M. hyorhinis MLST scheme at http://pubmlst.org/mhyorhinis/.

  17. Metal nanoparticle assisted polymerase chain reaction for strain typing of Salmonella Typhi.

    PubMed

    Rehman, Asma; Sarwar, Yasra; Raza, Zulfiqar Ali; Hussain, Syed Zajif; Mustafa, Tanveer; Khan, Waheed S; Ghauri, Muhammad Afzal; Haque, Abdul; Hussain, Irshad

    2015-11-07

    Salmonella enterica serotype Typhi (S. Typhi) is the causative agent of typhoid fever and remains a major health threat in most of the developing countries. The prompt diagnosis of typhoid directly from the patient's blood requires high level of sensitivity and specificity. Some of us were the first to report PCR based diagnosis of typhoid. This approach has since then been reported by many scientists using different genomic targets. Since the number of bacteria circulating in the blood of a patient can be as low as 0.3 cfu ml(-1), there is always a room for improvement in diagnostic PCR. In the present study, the role of different types of nanoparticles was investigated to improve the existing PCR based methods for diagnosis and strain typing of S. Typhi (targeting Variable Number of Tandem Repeats [VNTR]) by using optimized PCR systems. Three different types of nanoparticles were used i.e., citrate stabilized gold nanoparticles, rhamnolipid stabilized gold and silver nanoparticles, and magnetic iron oxide nanoparticles. The non-specific amplification was significantly reduced in VNTR typing when gold and silver nanoparticles were used in an appropriate concentration. More importantly, the addition of nanoparticles decreased the non-specificity to a significant level in the case of multiplex PCR thus further validating the reliability of PCR for the diagnosis of typhoid.

  18. Three cases of paralytic poliomyelitis associated with type 3 vaccine poliovirus strains in Bulgaria.

    PubMed

    Korsun, Neli; Kojouharova, Mira; Vladimirova, Nadezhda; Fiore, Lucia; Litvinenko, Ivan; Buttinelli, Gabriele; Fiore, Stefano; Voynova-Georgieva, Violeta; Mladenova, Zornitsa; Georgieva, Daniela

    2009-09-01

    Oral poliovirus vaccine (OPV) can cause, in extremely rare cases vaccine-associated paralytic poliomyelitis in recipients, or contacts of vaccinees. Three cases of vaccine-associated paralytic poliomyelitis (two contacts and one recipient) occurred in the Bourgas region of Bulgaria in the spring of 2006. The first two cases, notified as acute flaccid paralysis, were 55 days old unvaccinated twin brothers, having been in contact with vaccinees. The third case concerned a 4-month-old infant who had received the first OPV dose 37 days prior to the onset of illness. Complete clinical, epidemiological, virological, serological and molecular investigations of the children with paralysis and their contacts were undertaken. In all the three cases type 3 polioviruses were isolated from fecal samples and characterized as Sabin-like poliovirus strains. Type 3 polioviruses isolated from the twin brothers demonstrated by sequence analysis U-to-C back mutation at nt 472 of the 5' UTR, known to correlate with neurovirulence, and mutation in the VP1 region. Type 3 poliovirus isolated from the third child demonstrated in the 3D sequenced region a recombination with Sabin type 1 poliovirus. In the latter region, three silent mutations and one, resulting in amino acid substitution, were also observed. The clinical, epidemiological and virological data and the neurological sequelae observed 60 days following the onset of paralysis, confirmed the diagnosis of vaccine-associated paralytic poliomyelitis in all the three patients.

  19. Immunological inter-strain crossreactivity correlated to 18S rDNA sequence types in Acanthamoeba spp.

    PubMed

    Walochnik, J; Obwaller, A; Aspöck, H

    2001-02-01

    Various species of the genus Acanthamoeba have been described as potential pathogens; however, differentiation of acanthamoebae remains problematic. The genus has been divided into 12 18S rDNA sequence types, most keratitis causing strains exhibiting sequence type T4. We recently isolated a keratitis causing Acanthamoeba strain showing sequence type T6, but being morphologically identical to a T4 strain. The aim of our study was to find out, whether the 18S rDNA sequence based identification correlates to immunological differentiation. The protein and antigen profiles of the T6 isolate and three reference Acanthamoeba strains were investigated using two sera from Acanthamoeba keratitis patients and one serum from an asymptomatic individual. It was shown, that the T6 strain produces a distinctly different immunological pattern, while patterns within T4 were identical. Affinity purified antibodies were used to further explore immunological cross-reactivity between sequence types. Altogether, the results of our study support the Acanthamoeba 18S rDNA sequence type classification in the investigated strains.

  20. Decreased regional left ventricular myocardial strain in type 1 diabetic children: a first sign of diabetic cardiomyopathy?

    PubMed Central

    Hodzic, Amir; Ribault, Virginie; Maragnes, Pascale; Milliez, Paul; Saloux, Eric

    2016-01-01

    Abstract Background and Objectives Type 1 diabetes is a major cardiovascular risk factor associated with an excess of mortality in young adults due to premature cardiovascular events, which includes heart failure. The relation between type 1 diabetes and cardiac structure and function in children was poorly documented. Our study investigates (1) whether type 1 diabetic children have echocardiographic signs of subclinical cardiac dysfunction assessed by tissue Doppler strain and (2) whether state of metabolic control and diabetes duration have any influence on the cardiac event. Methods Standard echocardiography and tissue Doppler imaging were prospectively performed in type 1 diabetic children. Left ventricular dimensions, standard indices of systolic and diastolic function, and septal longitudinal strain were investigated. Results Thirty consecutive asymptomatic diabetic children (age: 12.4 [5–17] years; males: 53%) were compared to 30 age and sex-matched healthy control subjects. Left ventricular mass index and diastolic septal thickness were significantly increased in diabetic children. There was no difference between two groups as regards the left ventricular ejection fraction and conventional mitral Doppler parameters (E, A, Ea). The global longitudinal systolic strain and strain rate were found to be decreased in children with diabetes. The global longitudinal early diastolic strain rate (Esr) was negatively correlated with metabolic control. Longitudinal strain was not correlated with diabetes duration. Conclusion Children with Type 1 diabetes had subclinical alterations in left ventricular size and longitudinal myocardial deformation. PMID:28191526

  1. Profile of Cytokines and Chemokines Triggered by Wild-Type Strains of Rabies Virus in Mice

    PubMed Central

    Appolinário, Camila Michele; Allendorf, Susan Dora; Peres, Marina Gea; Ribeiro, Bruna Devidé; Fonseca, Clóvis R.; Vicente, Acácia Ferreira; de Paula Antunes, João Marcelo A.; Megid, Jane

    2016-01-01

    Rabies is a lethal infectious disease that causes 55,000 human deaths per year and is transmitted by various mammalian species, such as dogs and bats. The host immune response is essential for avoiding viral progression and promoting viral clearance. Cytokines and chemokines are crucial in the development of an immediate antiviral response; the rabies virus (RABV) attempts to evade this immune response. The virus's capacity for evasion is correlated with its pathogenicity and the host's inflammatory response, with highly pathogenic strains being the most efficient at hijacking the host's defense mechanisms and thereby decreasing inflammation. The purpose of this study was to evaluate the expression of a set of cytokine and chemokine genes that are related to the immune response in the brains of mice inoculated intramuscularly or intracerebrally with two wild-type strains of RABV, one from dog and the other from vampire bat. The results demonstrated that the gene expression profile is intrinsic to the specific rabies variant. The prompt production of cytokines and chemokines seems to be more important than their levels of expression for surviving a rabies infection. PMID:26711511

  2. Complete genome sequence of Kribbella flavida type strain (IFO 14399T)

    SciTech Connect

    Pukall, Rudiger; Lapidus, Alla L.; Glavina Del Rio, Tijana; Copeland, A; Tice, Hope; Cheng, Jan-Fang; Lucas, Susan; Chen, Feng; Nolan, Matt; LaButti, Kurt; Pati, Amrita; Ivanova, N; Mavromatis, K; Mikhailova, Natalia; Pitluck, Sam; Bruce, David; Goodwin, Lynne A.; Land, Miriam L; Hauser, Loren John; Chang, Yun-Juan; Jeffries, Cynthia; Chen, Amy; Palaniappan, Krishna; Chain, Patrick S. G.; Rohde, Manfred; Goker, Markus; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter

    2010-01-01

    The genus Kribbella consists of 15 species, with Kribbella flavida (Park et al. 1999) as the type species. The name Kribbella was formed from the acronym of the Korea Research Institute of Bioscience and Biotechnology, KRIBB. Strains of the various Kribbella species were originally isolated from soil, potato, alum slate mine, patinas of catacombs or from horse racecourses. Here we describe the features of K. flavida together with the complete genome sequence and annotation. In addition to the 5.3 Mbp genome of Nocardioides sp. JS614, this is only the second completed genome sequence of the family Nocardioidaceae. The 7,579,488 bp long genome with its 7,086 protein-coding and 60 RNA genes and is part of the Genomic Encyc-lopedia of Bacteria and Archaea project.

  3. Complete genome sequence of the sulfate-reducing firmicute Desulfotomaculum ruminis type strain (DLT)

    PubMed Central

    Spring, Stefan; Visser, Michael; Lu, Megan; Copeland, Alex; Lapidus, Alla; Lucas, Susan; Cheng, Jan-Fang; Han, Cliff; Tapia, Roxanne; Goodwin, Lynne A.; Pitluck, Sam; Ivanova, Natalia; Land, Miriam; Hauser, Loren; Larimer, Frank; Rohde, Manfred; Göker, Markus; Detter, John C.; Kyrpides, Nikos C.; Woyke, Tanja; Schaap, Peter J.; Plugge, Caroline M.; Muyzer, Gerard; Kuever, Jan; Pereira, Inês A. C.; Parshina, Sofiya N.; Bernier-Latmani, Rizlan; Stams, Alfons J.M.; Klenk, Hans-Peter

    2012-01-01

    Desulfotomaculum ruminis Campbell and Postgate 1965 is a member of the large genus Desulfotomaculum which contains 30 species and is contained in the family Peptococcaceae. This species is of interest because it represents one of the few sulfate-reducing bacteria that have been isolated from the rumen. Here we describe the features of D. ruminis together with the complete genome sequence and annotation. The 3,969,014 bp long chromosome with a total of 3,901 protein-coding and 85 RNA genes is the second completed genome sequence of a type strain of the genus Desulfotomaculum to be published, and was sequenced as part of the DOE Joint Genome Institute Community Sequencing Program 2009. PMID:23408247

  4. Genome sequence of the phage-gene rich marine Phaeobacter arcticus type strain DSM 23566T

    PubMed Central

    Freese, Heike M.; Dalingault, Hajnalka; Petersen, Jörn; Pradella, Silke; Davenport, Karen; Teshima, Hazuki; Chen, Amy; Pati, Amrita; Ivanova, Natalia; Goodwin, Lynne A.; Chain, Patrick; Detter, John C.; Rohde, Manfred; Gronow, Sabine; Kyrpides, Nikos C.; Woyke, Tanja; Brinkhoff, Thorsten; Göker, Markus; Overmann, Jörg; Klenk, Hans-Peter

    2013-01-01

    Phaeobacter arcticus Zhang et al. 2008 belongs to the marine Roseobacter clade whose members are phylogenetically and physiologically diverse. In contrast to the type species of this genus, Phaeobacter gallaeciensis, which is well characterized, relatively little is known about the characteristics of P. arcticus. Here, we describe the features of this organism including the annotated high-quality draft genome sequence and highlight some particular traits. The 5,049,232 bp long genome with its 4,828 protein-coding and 81 RNA genes consists of one chromosome and five extrachromosomal elements. Prophage sequences identified via PHAST constitute nearly 5% of the bacterial chromosome and included a potential Mu-like phage as well as a gene-transfer agent (GTA). In addition, the genome of strain DSM 23566T encodes all of the genes necessary for assimilatory nitrate reduction. Phylogenetic analysis and intergenomic distances indicate that the classification of the species might need to be reconsidered. PMID:24501630

  5. Complete genome sequence of Brachybacterium faecium type strain (Schefferle 6-10T)

    SciTech Connect

    Lapidus, Alla; Pukall, Rudiger; LaButti, Kurt; Copeland, Alex; Glavina Del Rio, Tijana; Nolan, Matt; Chen, Feng; Lucas, Susan; Tice, Hope; Cheng, Jan-Fang; Bruce, David; Goodwin, Lynne; Pitluck, Sam; Rohde, Manfred; Goker, Markus; Pati, Amrita; Ivanova, Natalia; Mavrommatis, Konstantinos; Chen, Amy; Palaniappan, Krishna; D'haeseleer, Patrik; Chain, Patrick; Bristow, Jim; Eisen, Johnathan A.; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C.; Klenk, Hans-Peter

    2009-05-20

    Brachybacterium faecium Collins et al. 1988 is the type species of the genus, and is of phylogenetic interest because of its location in the Dermabacteraceae, a rather isolated family within the actinobacterial suborder Micrococcineae. B. faecium is known for its rod-coccus growth cycle and the ability to degrade uric acid. It grows aerobically or weakly anaerobically. The strain described in this report is a free-living, nonmotile, Gram-positive bacterium, originally isolated from poultry deep litter. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of a member of the actinobacterial family Dermabacteraceae, and the 3,614,992 bp long single replicon genome with its 3129 protein-coding and 69 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

  6. Silica-induced malignant histiocytic lymphoma: incidence linked with strain of rat and type of silica.

    PubMed Central

    Wagner, M. M.; Wagner, J. C.; Davies, R.; Griffiths, D. M.

    1980-01-01

    It has already been established that a single intrapleural inoculation of crystalline silica (quartz) produces malignant lymphomas of histiocytic type (MLHT) in Wistar-derived rats. It has now been shown that after treatment with Min-U-Sil, rats of the Alderley Park strain have a tumour incidence of 35%, whereas the incidence in Agus rats is 5% and in PVG 8%. There was also a significant difference in the incidence of MLHT caused by injecting different samples of crystalline silica, particularly of tridymite. There was correlation between cytotoxicity to mouse peritoneal macrophages and tumour incidence, except for one dust (DQ12). Zeta potential, number of particles and their size range were considered, but the incidence does not show a clear correlation with these measurements. The results are discussed. Images Fig. 2 Fig. 3 Fig. 4 Fig. 5 Fig. 7 PMID:6252921

  7. Complete genome sequence of Parvibaculum lavamentivorans type strain (DS-1T)

    SciTech Connect

    Schleheck, David; Weiss, Michael; Pitluck, Sam; Bruce, David; Land, Miriam L; Han, Cliff; Saunders, Elizabeth H; Tapia, Roxanne; Detter, J. Chris; Brettin, Thomas S; Han, James; Woyke, Tanja; Goodwin, Lynne A.; Pennacchio, Len; Nolan, Matt; Cook, Alasdair M.; Kjelleberg, Staffan; Thomas, Torsten

    2011-01-01

    Parvibaculum lavamentivorans DS-1T is the type species of the novel genus Parvibaculum in the novel family Rhodobiaceae (formerly Phyllobacteriaceae) of the order Rhizobiales of Al- phaproteobacteria. Strain DS-1T is a non-pigmented, aerobic, heterotrophic bacterium and represents the first tier member of environmentally important bacterial communities that cata- lyze the complete degradation of synthetic laundry surfactants. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,914,745 bp long genome with its predicted 3,654 protein coding genes is the first com- pleted genome sequence of the genus Parvibaculum, and the first genome sequence of a rep- resentative of the family Rhodobiaceae.

  8. The Phenotypic Effects of Royal Jelly on Wild-Type D. melanogaster Are Strain-Specific

    PubMed Central

    Morgan, Stefanie L.; Seggio, Joseph A.; Hicks, Jasmin A.; Sharp, Katherine A.; Axelrod, Jeffrey D.; Wang, Kevin C.

    2016-01-01

    The role for royal jelly (RJ) in promoting caste differentiation of honeybee larvae into queens rather than workers is well characterized. A recent study demonstrated that this poorly understood complex nutrition drives strikingly similar phenotypic effects in Drosophila melanogaster, such as increased body size and reduced developmental time, making possible the use of D. melanogaster as a model system for the genetic analysis of the cellular mechanisms underlying RJ and caste differentiation. We demonstrate here that RJ increases the body size of some wild-type strains of D. melanogaster but not others, and report significant delays in developmental time in all flies reared on RJ. These findings suggest that cryptic genetic variation may be a factor in the D. melanogaster response to RJ, and should be considered when attempting to elucidate response mechanisms to environmental changes in non-honeybee species. PMID:27486863

  9. Complete genome sequence of the sulfate-reducing firmicute Desulfotomaculum ruminis type strain (DLT)

    SciTech Connect

    Spring, Stefan; Visser, Michael; Lu, Megan; Copeland, Alex; Lapidus, Alla; Lucas, Susan; Cheng, Jan-Fang; Han, Cliff; Tapia, Roxanne; Goodwin, Lynne A.; Pitluck, Sam; Ivanova, Natalia; Land, Miriam; Hauser, Loren; Larimer, Frank; Rohde, Manfred; Göker, Markus; Detter, John C.; Kyrpides, Nikos C.; Woyke, Tanja; Schaap, Peter J.; Plugge, Caroline M.; Muyzer, Gerard; Kuever, Jan; Pereira, Inês A. C.; Parshina, Sofiya N.; Bernier-Latmani, Rizlan; Stams, Alfons J. M.; Klenk, Hans-Peter

    2012-12-11

    Desulfotomaculum ruminis Campbell and Postgate 1965 is a member of the large genus Desulfotomaculum which contains 30 species and is contained in the family Peptococcaceae. This species is of interest because it represents one of the few sulfate- reducing bacteria that have been isolated from the rumen. Here we describe the features of D. ruminis together with the complete genome sequence and annotation. The 3,969,014 bp long chromosome with a total of 3,901 protein-coding and 85 RNA genes is the second completed genome sequence of a type strain of the genus Desulfotomaculum to be pub- lished, and was sequenced as part of the DOE Joint Genome Institute Community Sequencing Program 2009.

  10. Complete genome sequence of Olsenella uli type strain (VPI D76D-27CT)

    SciTech Connect

    Goker, Markus; Held, Brittany; Lucas, Susan; Nolan, Matt; Yasawong, Montri; Glavina Del Rio, Tijana; Tice, Hope; Cheng, Jan-Fang; Bruce, David; Detter, J. Chris; Tapia, Roxanne; Han, Cliff; Goodwin, Lynne A.; Pitluck, Sam; Liolios, Konstantinos; Ivanova, N; Mavromatis, K; Mikhailova, Natalia; Ovchinnikova, Galina; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam L; Hauser, Loren John; Chang, Yun-Juan; Jeffries, Cynthia; Rohde, Manfred; Sikorski, Johannes; Pukall, Rudiger; Woyke, Tanja; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter

    2010-01-01

    Olsenella uli (Olsen et al. 1991) Dewhirst et al. 2001 is the type species of the genus Olsenella, which belongs to the actinobacterial family Coriobacteriaceae. The species is of interest because it is frequently isolated from dental plaque in periodontitis patients and can cause primary endodontic infection. The species is a Gram-positive, non-motile and non-sporulating bacterium. The strain described in this study has been isolated from human gingival crevices in 1982. This is the first completed sequence of the genus Olsenella and the fifth sequence from the family Coriobacteriaceae. The 2,051,896 bp long genome with its 1,795 protein-coding and 55 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  11. Complete genome sequence of Eggerthella lenta type strain (IPP VPI 0255T)

    SciTech Connect

    Saunders, Elizabeth H; Pukall, Rudiger; Birte, Abt; Lapidus, Alla L.; Glavina Del Rio, Tijana; Copeland, A; Tice, Hope; Cheng, Jan-Fang; Lucas, Susan; Chen, Feng; Nolan, Matt; Bruce, David; Goodwin, Lynne A.; Pitluck, Sam; Ivanova, N; Mavromatis, K; Ovchinnikova, Galina; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam L; Hauser, Loren John; Chang, Yun-Juan; Jeffries, Cynthia; Chain, Patrick S. G.; Meincke, Linda; Sims, David; Brettin, Tom; Detter, J. Chris; Goker, Markus; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter; Han, Cliff

    2009-01-01

    Eggerthella lenta (Eggerth 1935) Wade et al. 1999, emended W rdemann et al. 2009 is the type species of the genus Eggerthella, which belongs to the actinobacterial family Coriobacteriaceae. E. lenta is a Gram-positive, non-motile, non-sporulating pathogenic bacterium that can cause severe bacteremia. The strain described in this study has been isolated from a rectal tumor in 1935. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of the genus Eggerthella, and the 3,632,260 bp long single replicon genome with its 3123 protein-coding and 58 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

  12. Complete genome sequence of Syntrophothermus lipocalidus type strain (TGB-C1T)

    SciTech Connect

    Ngatchou, Olivier Duplex; Zhang, Xiaojing; Lucas, Susan; Lapidus, Alla L.; Glavina Del Rio, Tijana; Nolan, Matt; Tice, Hope; Cheng, Jan-Fang; Han, Cliff; Tapia, Roxanne; Goodwin, Lynne A.; Pitluck, Sam; Liolios, Konstantinos; Ivanova, N; Mavromatis, K; Mikhailova, Natalia; Ovchinnikova, Galina; Pati, Amrita; Brambilla, Evelyne-Marie; Chen, Amy; Palaniappan, Krishna; Land, Miriam L; Hauser, Loren John; Chang, Yun-Juan; Jeffries, Cynthia; Rohde, Manfred; Sikorski, Johannes; Spring, Stefan; Goker, Markus; Detter, J. Chris; Woyke, Tanja; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Held, Brittany; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter

    2010-01-01

    Syntrophothermus lipocalidus Sekiguchi et al. 2000 is the type species of the genus Syntrophothermus. The species is of interest because of its strictly anaerobic lifestyle, its participation in the primary step of the degradation of organic maters, and for releasing products which serve as substrates for other microorganisms. It also contributes significantly to maintain a regular pH in its environment by removing the fatty acids through -oxidation. The strain is able to metabolize isobutyrate and butyrate, which are the substrate and the product of degradation of the substrate, respectively. This is the first complete genome sequence of a member of the genus Syntrophothermus and the second in the family Syntrophomonadaceae. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,405,559 bp long genome with its 2,385 protein-coding and 55 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  13. Complete genome sequence of Bacteroides helcogenes type strain (P 36-108T)

    SciTech Connect

    Pati, Amrita; Gronow, Sabine; Zeytun, Ahmet; Lapidus, Alla L.; Nolan, Matt; Hammon, Nancy; Deshpande, Shweta; Cheng, Jan-Fang; Tapia, Roxanne; Han, Cliff; Goodwin, Lynne A.; Pitluck, Sam; Liolios, Konstantinos; Pagani, Ioanna; Ivanova, N; Mavromatis, K; Chen, Amy; Palaniappan, Krishna; Land, Miriam L; Hauser, Loren John; Chang, Yun-Juan; Jeffries, Cynthia; Detter, J. Chris; Brambilla, Evelyne-Marie; Rohde, Manfred; Goker, Markus; Woyke, Tanja; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter; Lucas, Susan

    2011-01-01

    Bacteroides helcogenes Benno et al. 1983 is of interest because of its isolated phylogenetic location and, although it has been found in pig feces and is known to be pathogenic for pigs, occurrence of this bacterium is rare and it does not cause significant damage in intensive animal husbandry. The genome of B. helcogenes P 36-108T is already the fifth completed and published type strain genome from the genus Bacteroides in the family Bacteroidaceae. The 3,998,906 bp long genome with its 3,353 protein-coding and 83 RNA genes consists of one circular chromosome and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  14. Complete genome sequence of Marivirga tractuosa type strain (H-43T)

    SciTech Connect

    Pagani, Ioanna; Chertkov, Olga; Lapidus, Alla L.; Lucas, Susan; Glavina Del Rio, Tijana; Tice, Hope; Copeland, A; Cheng, Jan-Fang; Nolan, Matt; Saunders, Elizabeth H; Pitluck, Sam; Held, Brittany; Goodwin, Lynne A.; Liolios, Konstantinos; Ovchinnikova, Galina; Ivanova, N; Mavromatis, K; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam L; Hauser, Loren John; Jeffries, Cynthia; Detter, J. Chris; Han, Cliff; Tapia, Roxanne; Ngatchou, Olivier Duplex; Rohde, Manfred; Goker, Markus; Spring, Stefan; Sikorski, Johannes; Woyke, Tanja; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Klenk, Hans-Peter; Kyrpides, Nikos C

    2011-01-01

    Marivirga tractuosa (Lewin 1969) Nedashkovskaya et al. 2010 is the type species of the genus Marivirga, which belongs to the family Flammeovirgaceae. Members of this genus are of interest because of their gliding motility. The species is of interest because representative strains show resistance to several antibiotics, including gentamicin, kanamycin, neomycin, polymixin and streptomycin. This is the first complete genome sequence of a member of the family Flammeovirgaceae. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 4,511,574 bp long chromosome and the 4,916 bp plasmid with their 3,808 protein-coding and 49 RNA genes are a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  15. Non-contiguous finished genome sequence of Bacteroides coprosuis type strain (PC 139T)

    SciTech Connect

    Land, Miriam L; Held, Brittany; Gronow, Sabine; Abt, Birte; Lucas, Susan; Glavina Del Rio, Tijana; Nolan, Matt; Tice, Hope; Cheng, Jan-Fang; Pitluck, Sam; Liolios, Konstantinos; Pagani, Ioanna; Ivanova, N; Mavromatis, K; Pati, Amrita; Tapia, Roxanne; Han, Cliff; Goodwin, Lynne A.; Chen, Amy; Palaniappan, Krishna; Hauser, Loren John; Brambilla, Evelyne-Marie; Rohde, Manfred; Goker, Markus; Detter, J. Chris; Woyke, Tanja; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter; Lapidus, Alla L.

    2011-01-01

    Bacteroides coprosuis Whitehead et al. 2005 belongs to the genus Bacteroides, which is a member of the family Bacteroidaceae. Members of the genus Bacteroides in general are known as beneficial protectors of animal guts against pathogenic microorganisms, and as contributors to the degradation of complex molecules such as polysaccharides. B. coprosuis itself was isolated from a manure storage pit of a swine facility, but has not yet been found in an animal host. The species is of interest solely because of its isolated phylogenetic location. The genome of B. coprosuis is already the 5th sequenced type strain genome from the genus Bacteroides. The 2,991,798 bp long genome with its 2,461 protein-coding and 78 RNA genes and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  16. Complete genome sequence of Archaeoglobus profundus type strain (AV18T)

    PubMed Central

    von Jan, Mathias; Lapidus, Alla; Del Rio, Tijana Glavina; Copeland, Alex; Tice, Hope; Cheng, Jan-Fang; Lucas, Susan; Chen, Feng; Nolan, Matt; Goodwin, Lynne; Han, Cliff; Pitluck, Sam; Liolios, Konstantinos; Ivanova, Natalia; Mavromatis, Konstantinos; Ovchinnikova, Galina; Chertkov, Olga; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Chang, Yun-Juan; Jeffries, Cynthia D.; Saunders, Elizabeth; Brettin, Thomas; Detter, John C.; Chain, Patrick; Eichinger, Konrad; Huber, Harald; Spring, Stefan; Rohde, Manfred; Göker, Markus; Wirth, Reinhard; Woyke, Tanja; Bristow, Jim; Eisen, Jonathan A.; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter

    2010-01-01

    Archaeoglobus profundus (Burggraf et al. 1990) is a hyperthermophilic archaeon in the euryarchaeal class Archaeoglobi, which is currently represented by the single family Archaeoglobaceae, containing six validly named species and two strains ascribed to the genus 'Geoglobus' which is taxonomically challenged as the corresponding type species has no validly published name. All members were isolated from marine hydrothermal habitats and are obligate anaerobes. Here we describe the features of the organism, together with the complete genome sequence and annotation. This is the second completed genome sequence of a member of the class Archaeoglobi. The 1,563,423 bp genome with its 1,858 protein-coding and 52 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project. PMID:21304717

  17. Complete genome sequence of Nitratifractor salsuginis type strain (E9I37-1T)

    SciTech Connect

    Anderson, Iain; Sikorski, Johannes; Zeytun, Ahmet; Nolan, Matt; Lapidus, Alla L.; Lucas, Susan; Hammon, Nancy; Deshpande, Shweta; Cheng, Jan-Fang; Tapia, Roxanne; Han, Cliff; Goodwin, Lynne A.; Pitluck, Sam; Liolios, Konstantinos; Pagani, Ioanna; Ivanova, N; Huntemann, Marcel; Mavromatis, K; Ovchinnikova, Galina; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam L; Hauser, Loren John; Brambilla, Evelyne-Marie; Ngatchou, Olivier Duplex; Rohde, Manfred; Tindall, Brian; Goker, Markus; Detter, J. Chris; Woyke, Tanja; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Klenk, Hans-Peter; Kyrpides, Nikos C

    2011-01-01

    Nitratifractor salsuginis Nakagawa et al. 2005 is the type species of the genus Nitratifractor, a member of the family Nautiliaceae. The species is of interest because of its high capacity for nitrate reduction via conversion to N2 through respiration, which is a key compound in plant nutrition. The strain is also of interest because it represents the first mesophilic and faculta- tively anaerobic member of the Epsilonproteobacteria reported to grow on molecular hydro- gen. This is the first completed genome sequence of a member of the genus Nitratifractor and the second sequence from the family Nautiliaceae. The 2,101,285 bp long genome with its 2,121 protein-coding and 54 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  18. Complete genome sequence of Acidaminococcus fermentans type strain (VR4T)

    SciTech Connect

    Chang, Yun-Juan; Pukall, Rudiger; Saunders, Elizabeth H; Lapidus, Alla L.; Copeland, A; Nolan, Matt; Glavina Del Rio, Tijana; Lucas, Susan; Chen, Feng; Tice, Hope; Cheng, Jan-Fang; Han, Cliff; Detter, J. Chris; Bruce, David; Goodwin, Lynne A.; Pitluck, Sam; Mikhailova, Natalia; Liolios, Konstantinos; Pati, Amrita; Ivanova, N; Mavromatis, K; Chen, Amy; Palaniappan, Krishna; Land, Miriam L; Hauser, Loren John; Jeffries, Cynthia; Rohde, Manfred; Goker, Markus; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter

    2010-01-01

    Acidaminococcus fermentans (Rogosa 1969) is the type species of the genus Acidaminococcus, and is of phylogenetic interest because of its isolated placement in a genomically little characterized region of the clostridial family Veillonellaceae. A. fermentans is known for its gastrointestinal tract habitat and its ability to oxidize trans-aconitate. It grows strictly anaerobically and utilizes glutamate, citrate and trans-aconitate as sole energy sources for growth. The strain described in this report is a nonsporulating, nonmotile, Gram-negative coccus, originally isolated from a pig alimentary tract. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of a member of the genus Acidaminococcus, and the 2,329,769 bp long genome with its 2,101 protein-coding and 81 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

  19. Complete genome sequence of Pirellula staleyi type strain (ATCC 27377T)

    SciTech Connect

    Clum, Alicia; Tindall, Brian; Sikorski, Johannes; Ivanova, N; Mavromatis, K; Lucas, Susan; Glavina Del Rio, Tijana; Nolan, Matt; Chen, Feng; Tice, Hope; Pitluck, Sam; Cheng, Jan-Fang; Chertkov, Olga; Han, Cliff; Detter, J. Chris; Kuske, Cheryl R; Bruce, David; Goodwin, Lynne A.; Ovchinnikova, Galina; Pati, Amrita; Mikhailova, Natalia; Chen, Amy; Palaniappan, Krishna; Land, Miriam L; Hauser, Loren John; Chang, Yun-Juan; Jeffries, Cynthia; Chain, Patrick S. G.; Rohde, Manfred; Goker, Markus; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter; Lapidus, Alla L.

    2009-01-01

    Pirellula staleyi Schlesner and Hirsch 1987 is the type species of the genus Pirellula of the family Planctomycetaceae. Members of this pear- or teardrop-shaped bacterium show a clearly visible pointed attachment pole and can be distinguished from other Planctomycetes by a lack of true stalks. Strains closely related to the species have been isolated from fresh and brackish water, as well as from hypersaline lakes. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the first completed genome sequence of the order Planctomyces and only the second sequence from the phylum Planctomycetes. The 6,196,199 bp long genome with its 4773 protein-coding and 49 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  20. Non-contiguous finished genome sequence of Bacteroides coprosuis type strain (PC139T)

    PubMed Central

    Land, Miriam; Held, Brittany; Gronow, Sabine; Abt, Birte; Lucas, Susan; Del Rio, Tijana Glavina; Nolan, Matt; Tice, Hope; Cheng, Jan-Fang; Pitluck, Sam; Liolios, Konstantinos; Pagani, Ioanna; Ivanova, Natalia; Mavromatis, Konstantinos; Mikhailova, Natalia; Pati, Amrita; Tapia, Roxane; Han, Cliff; Goodwin, Lynne; Chen, Amy; Palaniappan, Krishna; Hauser, Loren; Brambilla, Evelyne-Marie; Rohde, Manfred; Göker, Markus; Detter, John C.; Woyke, Tanja; Bristow, James; Eisen, Jonathan A.; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C.; Klenk, Hans-Peter; Lapidus, Alla

    2011-01-01

    Bacteroides coprosuis Whitehead et al. 2005 belongs to the genus Bacteroides, which is a member of the family Bacteroidaceae. Members of the genus Bacteroides in general are known as beneficial protectors of animal guts against pathogenic microorganisms, and as contributors to the degradation of complex molecules such as polysaccharides. B. coprosuis itself was isolated from a manure storage pit of a swine facility, but has not yet been found in an animal host. The species is of interest solely because of its isolated phylogenetic location. The genome of B. coprosuis is already the 5th sequenced type strain genome from the genus Bacteroides. The 2,991,798 bp long genome with its 2,461 protein-coding and 78 RNA genes and is a part of the Genomic Encyclopedia of Bacteria and Archaea project. PMID:21677860

  1. DNA typing methods for differentiation of Debaryomyces hansenii strains and other yeasts related to surface ripened cheeses.

    PubMed

    Petersen, K M; Møller, P L; Jespersen, L

    2001-09-19

    The discriminative power of ITS-PCR, ITS-PCR RFLP and mitochondrial (mt)-DNA RFLP were evaluated for differentiation of yeasts of importance for surface ripened cheeses. In total 60 isolates were included. Of these, 40 strains of the following species, Debaryomyces hansenii var. hansenii, D. hansenii var. fabryi, Saccharomyces cerevisiae, Candida zeylanoides, Kluyveromyces lactis and Yarrowia lipolytica, were obtained from culture collections and 20 isolates of D. hansenii representing six different phenotypes were collected from seven Danish producers of surface ripened cheeses. ITS-PCR was evaluated for differentiation at species level on the 40 strains obtained from culture collections. Ten strains of each variety of D. hansenii and five strains of each of the above mentioned species were analysed. For each of the investigated species, a specific ITS1-5.8S rDNA-ITS2 region size was observed. Accordingly ITS-PCR was found valuable for differentiation at species level of yeasts of importance for surface ripened cheeses. ITS-PCR RFLP was investigated for the purpose of strain typing of D. hansenii. Ten CBS strains of each variety of D. hansenii were analysed. Only one enzyme (TaqI) out of several investigated (BamHI, DpnI, Fnu4HI, HaeIII, HindIII, HpaII, NlaII, Sau3AI, TaqI) demonstrated genetic diversity within the strains. This enzyme divided the 20 strains in three groups. Sequence analysis of the ITS1-5.8S rDNA-ITS2 region for the type strains of each variety of D. hansenii showed an identity of 99.84%, corresponding to a difference in one basepair. Based on these results, ITS-PCR RFLP was found ineffective for strain typing of D. hansenii. MtDNA RFLP using HaeIII and HpaII was evaluated for strain typing of D. hansenii on the 20 CBS strains of D. hansenii. The CBS strains were divided into 16 groups according to their restriction profiles, which proved the method useful for typing of D. hansenii at subspecies level. The 20 dairy isolates showed a lower genetic

  2. Genome sequence of Frateuria aurantia type strain (Kondo 67(T)), a xanthomonade isolated from Lilium auratium Lindl.

    SciTech Connect

    Anderson, Iain; Teshima, Hazuki; Nolan, Matt; Lapidus, Alla L.; Tice, Hope; Glavina Del Rio, Tijana; Cheng, Jan-Fang; Han, Cliff; Tapia, Roxanne; Goodwin, Lynne A.; Pitluck, Sam; Liolios, Konstantinos; Mavromatis, K; Pagani, Ioanna; Ivanova, N; Mikhailova, Natalia; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam L; Rohde, Manfred; Lang, Elke; Detter, J. Chris; Goker, Markus; Woyke, Tanja; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter

    2013-01-01

    rateuria aurantia (ex Kondo and Ameyama 1958) Swings et al. 1980 is a member of the bispecific genus Frateuria in the family Xanthomonadaceae, which is already heavily targeted for non-type strain genome sequencing. Strain Kondo 67(T) was initially (1958) identified as a member of 'Acetobacter aurantius', a name that was not considered for the approved list. Kondo 67(T) was therefore later designated as the type strain of the newly proposed acetogenic species Frateuria aurantia. The strain is of interest because of its triterpenoids (hopane family). F. aurantia Kondo 67(T) is the first member of the genus Frateura whose genome sequence has been deciphered, and here we describe the features of this organism, together with the complete genome sequence and annotation. The 3,603,458-bp long chromosome with its 3,200 protein-coding and 88 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  3. Meat quality and sensory attributes of a conventional and a Label Rouge-type broiler strain obtained at retail.

    PubMed

    Smith, D P; Northcutt, J K; Steinberg, E L

    2012-06-01

    Some consumers have reported preferences for meat from alternative broiler strains as compared with meat from conventional broiler strains relative to taste and texture, but relatively few objective measurements have been conducted on these particular strains. To directly compare meat quality from a Label Rouge-type alternative and a conventional broiler strain available at retail, 4 ready-to-cook conventional and 6 alternative strain carcasses were obtained from retail or a processing plant on each of 6 d. Boneless skinless breast fillets and boneless thighs were taken from each carcass and weighed. Raw meat was then assigned to different testing lots for cooking to evaluate yield, objective texture, meat color, sensory profile, and proximate composition (percentage protein, moisture, fat, and ash). Analyses of data revealed no significant difference (P < 0.05) due to broiler strain for percentage protein, moisture, fat, and ash, for either breast or thigh meat. Conventional breast (raw and cooked) weights were significantly higher than the alternative strain, but there was no difference in cooked yield. There were no differences between strain for thigh weights or yield. Both thigh and breast meat from the conventional broilers was more tender than meat from alternative broilers. Cooked conventional breast meat was darker and yellower, whereas cooked thigh was lighter, less red, and more yellow than alternative meat. Sensory analysis found no difference between strains for breast meat attributes. Conventional thigh meat scored higher than alternative for appearance, tenderness, juiciness, and how well the panelist liked the appearance, but there was no difference in aftertaste or overall liking. Although minimal differences were observed for cooked breast meat due to strain, conventional cooked thigh meat scored higher than the thigh meat from the Label Rouge-type alternative for most of the sensory attributes.

  4. Wild-Type Measles Virus with the Hemagglutinin Protein of the Edmonston Vaccine Strain Retains Wild-Type Tropism in Macaques

    PubMed Central

    Nagata, Noriyo; Kato, Sei-ich; Ami, Yasushi; Suzaki, Yuriko; Suzuki, Tadaki; Sato, Yuko; Tsunetsugu-Yokota, Yasuko; Mori, Kazuyasu; Van Nguyen, Nguyen; Kimura, Hideki; Nagata, Kyosuke

    2012-01-01

    A major difference between vaccine and wild-type strains of measles virus (MV) in vitro is the wider cell specificity of vaccine strains, resulting from the receptor usage of the hemagglutinin (H) protein. Wild-type H proteins recognize the signaling lymphocyte activation molecule (SLAM) (CD150), which is expressed on certain cells of the immune system, whereas vaccine H proteins recognize CD46, which is ubiquitously expressed on all nucleated human and monkey cells, in addition to SLAM. To examine the effect of the H protein on the tropism and attenuation of MV, we generated enhanced green fluorescent protein (EGFP)-expressing recombinant wild-type MV strains bearing the Edmonston vaccine H protein (MV-EdH) and compared them to EGFP-expressing wild-type MV strains. In vitro, MV-EdH replicated in SLAM+ as well as CD46+ cells, including primary cell cultures from cynomolgus monkey tissues, whereas the wild-type MV replicated only in SLAM+ cells. However, in macaques, both wild-type MV and MV-EdH strains infected lymphoid and respiratory organs, and widespread infection of MV-EdH was not observed. Flow cytometric analysis indicated that SLAM+ lymphocyte cells were infected preferentially with both strains. Interestingly, EGFP expression of MV-EdH in tissues and lymphocytes was significantly weaker than that of the wild-type MV. Taken together, these results indicate that the CD46-binding activity of the vaccine H protein is important for determining the cell specificity of MV in vitro but not the tropism in vivo. They also suggest that the vaccine H protein attenuates MV growth in vivo. PMID:22238320

  5. Enterotoxin production, phage typing and serotyping of Staphylococcus aureus strains isolated from clinical materials and food.

    PubMed Central

    Melconian, A. K.; Brun, Y.; Fleurette, J.

    1983-01-01

    The production of enterotoxins A, B, C and F by strains of Staphylococcus aureus isolated from various clinical sources and from isolates implicated in food poisoning was investigated. One hundred and ninety one of the 374 clinical strains (51.1%) were found to be enterotoxigenic; of these, 81 (27.7%) strains produced enterotoxin A, 57 (15.3%) strains produced enterotoxin B, 23 (6.2%) strains produced enterotoxin C, and 64 (17.1%) strains produced enterotoxin F. These enterotoxigenic strains were most frequently lysed by phages of group III (21.5%) or were not typable (22%). Eighteen of the 29 strains implicated in food poisoning were enterotoxigenic. The correlation of antigens and bacteriophage patterns with enterotoxigenicity was determined: enterotoxin A being related to a4 antigen, enterotoxin B to phages of 94/96 complex with c1, o antigens, and enterotoxin F to phages of group I with 2632, k1k2, m antigens. PMID:6227656

  6. Draft Genome Sequences of Eight Nontypeable Haemophilus influenzae Strains Previously Characterized Using an Electrophoretic Typing Scheme.

    PubMed

    Mussa, Huda J; VanWagoner, Timothy M; Morton, Daniel J; Seale, Thomas W; Whitby, Paul W; Stull, Terrence L

    2015-11-25

    Nontypeable Haemophilus influenzae is an important cause of human disease. Strains were selected for genome sequencing to represent the breadth of nontypeable strains within the species, as previously defined by the electrophoretic mobility of 16 metabolic enzymes.

  7. Draft Genome Sequences of Eight Nontypeable Haemophilus influenzae Strains Previously Characterized Using an Electrophoretic Typing Scheme

    PubMed Central

    Mussa, Huda J.; VanWagoner, Timothy M.; Seale, Thomas W.; Whitby, Paul W.; Stull, Terrence L.

    2015-01-01

    Nontypeable Haemophilus influenzae is an important cause of human disease. Strains were selected for genome sequencing to represent the breadth of nontypeable strains within the species, as previously defined by the electrophoretic mobility of 16 metabolic enzymes. PMID:26607889

  8. Computerized restriction endonuclease analysis compared with O-serotype and phage type in the epidemiologic fingerprinting of Pseudomonas aeruginosa strains.

    PubMed

    Garaizar, Javier; Latorre, Mikel; López-Molina, Nuria; Laconcha, Idoia; Alberdi, Leire; Rementeria, Aitor; Audicana, Ana; Uliarte, Rosario; Cisterna, Ramón

    1997-04-01

    OBJECTIVE: To assess restriction endonuclease analysis (REA) of chromosomal DNA using SalI enzyme, low-concentration (0.4%) agarose gels and digitalized data management of the REA patterns obtained for the typing of clinical Pseudomonas aeruginosa isolates. METHODS: A group of 67 clinical unrelated isolates from 10 Spanish hospitals was used to study the discriminatory power, reproducibility and typeability of REA typing. RESULTS: A SalI REA pattern consisted of a variety (1--10) of restriction bands in the range between 12.2 and 48.5 kb and an unresolvable smear of low-molecular-weight bands. Forty different SalI REA patterns with an index of discrimination of 0.979 were obtained. Low typeability (91.04%) was the major limitation of REA typing. Analysis of blinded subcultures of eight Pseudomonas aeruginosa strains showed the reproducibility of REA typing to be 87.5%. Combined phenotypic typing (O-serotyping and phage typing) performed on the same group of strains showed comparable discrimination but much lower reproducibility. Isolates selected from five clusters of nosocomial infections in hospitals in the UK were typed by REA typing, and the results show high agreement when compared with conventional phenotypic typing methods in distinguishing between strains. CONCLUSIONS: These data underline the usefulness of REA typing enhanced with digitalized data management for the epidemiologic subtyping of clinical Pseudomonas aeruginosa isolates.

  9. Identification of a Lactobacillus plantarum strain that ameliorates chronic inflammation and metabolic disorders in obese and type 2 diabetic mice.

    PubMed

    Toshimitsu, T; Mochizuki, J; Ikegami, S; Itou, H

    2016-02-01

    In this study, we identified a strain of lactic acid bacteria (LAB) that induces high levels of IL-10 production by immune cells, and evaluated the ability of the strain to suppress chronic inflammation and ameliorate metabolic disorders in in vitro and in vivo models. Among a collection of LAB strains, Lactobacillus plantarum strain OLL2712 (OLL2712) induced the highest levels of IL-10 production in mouse-derived dendritic cells and peritoneal macrophages. The anti-inflammatory effects of this strain were evaluated using a co-culture system comprising RAW 264.7 and 3T3-L1 cells. We also administered heat-killed OLL2712 to obese and type 2 diabetic KKAy mice for 3 wk to evaluate the in vivo effects of the strain. The OLL2712 significantly decreased the production of proinflammatory cytokines in vitro. Likewise, the administration of OLL2712 significantly suppressed proinflammatory cytokine levels in both the visceral adipose tissue and the serum of KKAy mice, and reduced serum triglyceride concentrations. The strain also alleviated oxidative stress and adrenaline levels in the serum of KKAy mice. On the other hand, Lactobacillus gasseri strain MEP222804 (a moderate IL-10 inducer) did not ameliorate the systemic inflammation and hyperlipidemia in KKAy mice. Our results suggest that treatment with strong IL-10-inducing LAB has the potential to ameliorate metabolic disorders by suppressing chronic inflammation in the host animal.

  10. Application of physico-chemical typing methods for the epidemiological analysis of Salmonella enteritidis strains of phage type 25/17.

    PubMed Central

    Seltmann, G.; Voigt, W.; Beer, W.

    1994-01-01

    Eighty-nine Salmonella enteritidis phage type 25/17 strains isolated from a localized outbreak in the German state Nordrhein-Westfalen (outbreak NWI) could not be further differentiated by biochemotyping and plasmid pattern analysis. They were submitted to a complex typing system consisting of modern physico-chemical analytical procedures. In lipopolysaccharide pattern analysis the strains proved to be homogeneous. In multilocus enzyme electrophoresis, outer membrane and whole cell protein pattern (WCPP) analysis, and Fourier-transform infrared (FT-IR) spectroscopy (increasing extent of differentiation in the given order) strains deviating from each basal pattern were found. The extent of correspondence in these deviations was satisfactory. Forty-six strains of the same sero- and phage type, however, obtained from different outbreaks, were additionally typed. The results obtained with them indicate that the data of the first group were not restricted to strains from outbreak NWI, but of general validity. It was found that both WCPP and FT-IR represent valuable methods for the sub-grouping of bacteria. Images Fig. 1 Fig. 2 Fig. 3 PMID:7995351

  11. Vaccination with a modified-live bovine viral diarrhea virus (BVDV) type 1a vaccine completely protected calves against challenge with BVDV type 1b strains.

    PubMed

    Xue, Wenzhi; Mattick, Debra; Smith, Linda; Umbaugh, Jerry; Trigo, Emilio

    2010-12-10

    Vaccination plays a significant role in the control of bovine viral diarrhea virus (BVDV) infection and spread. Recent studies revealed that type 1b is the predominant BVDV type 1 subgenotype, representing more than 75% of field isolates of BVDV-1. However, nearly all current, commercially available BVDV type 1 vaccines contain BVDV-1a strains. Previous studies have indicated that anti-BVDV sera, induced by BVDV-1a viruses, show less neutralization activity to BVDV-1b isolates than type 1a. Therefore, it is critically important to evaluate BVDV-1a vaccines in their ability to prevent BVDV-1b infection in calves. In current studies, calves were vaccinated subcutaneously, intradermally or intranasally with a single dose of a multivalent, modified-live viral vaccine containing a BVDV-1a strain, and were challenged with differing BVDV-1b strains to determine the efficacy and duration of immunity of the vaccine against these heterologous virus strains. Vaccinated calves, in all administration routes, were protected from respiratory disease caused by the BVDV-1b viruses, as indicated by significantly fewer clinical signs, lower rectal temperatures, reduced viral shedding and greater white blood cell counts than non-vaccinated control animals. The BVDV-1a vaccine elicited efficacious protection in calves against each BVDV-1b challenge strain, with a duration of immunity of at least 6 months.

  12. Comparative metabolic profiling of mce1 operon mutant vs wild-type Mycobacterium tuberculosis strains.

    PubMed

    Queiroz, Adriano; Medina-Cleghorn, Daniel; Marjanovic, Olivera; Nomura, Daniel K; Riley, Lee W

    2015-11-01

    Mycobacterium tuberculosis disrupted in a 13-gene operon (mce1) accumulates free mycolic acids (FM) in its cell wall and causes accelerated death in mice. Here, to more comprehensively analyze differences in their cell wall lipid composition, we used an untargeted metabolomics approach to compare the lipid profiles of wild-type and mce1 operon mutant strains. By liquid chromatography-mass spectrometry, we identified >400 distinct lipids significantly altered in the mce1 mutant compared to wild type. These lipids included decreased levels of saccharolipids and glycerophospholipids, and increased levels of alpha-, methoxy- and keto mycolic acids (MA), and hydroxyphthioceranic acid. The mutant showed reduced expression of mmpL8, mmpL10, stf0, pks2 and papA2 genes involved in transport and metabolism of lipids recognized to induce proinflammatory response; these lipids were found to be decreased in the mutant. In contrast, the transcripts of mmpL3, fasI, kasA, kasB, acpM and RV3451 involved in MA transport and metabolism increased; MA inhibits inflammatory response in macrophages. Since the mce1 operon is known to be regulated in intracellular M. tuberculosis, we speculate that the differences we observed in cell wall lipid metabolism and composition may affect host response to M. tuberculosis infection and determine the clinical outcome of such an infection.

  13. Genetic recombination of tick-borne flaviviruses among wild-type strains.

    PubMed

    Norberg, Peter; Roth, Anette; Bergström, Tomas

    2013-06-05

    Genetic recombination has been suggested to occur in mosquito-borne flaviviruses. In contrast, tick-borne flaviviruses have been thought to evolve in a clonal manner, although recent studies suggest that recombination occurs also for these viruses. We re-analyzed the data and found that previous conclusions on wild type recombination were probably falsely drawn due to misalignments of nucleotide sequences, ambiguities in GenBank sequences, or different laboratory culture histories suggestive of recombination events in laboratory. To evaluate if reliable predictions of wild type recombination of tick-borne flaviviruses can be made, we analyzed viral strains sequenced exclusively for this study, and other flavivirus sequences retrieved from GenBank. We detected genetic signals supporting recombination between viruses within the three clades of TBEV-Eu, TBEV-Sib and TBEV-Fe, respectively. Our results suggest that the tick-borne encephalitis viruses may undergo recombination under natural conditions, but that geographic barriers restrict most recombination events to involve only closely genetically related viruses.

  14. Eye-mediated immune tolerance to Type II collagen in arthritis-prone strains of mice.

    PubMed

    Farooq, Shukkur M; Kumar, Ashok; Ashour, Hossam M

    2014-12-01

    Type II collagen (CII) is a cartilage structural protein that plays important roles in joint function, arthritis and ageing. In studying the ability of CII to induce eye-mediated specific immune tolerance, we have recently proven that CII is capable of inducing anterior chamber-associated immune deviation (ACAID) in Balb/c mice. Here, we study the ability of CII to induce eye-mediated immune tolerance in strains of mice that are prone to the induction of rheumatoid arthritis. Thus, we hypothesized that CII induces ACAID in DBA/1 mice and in C57BL/6 mice through the AC route (direct injection) or the intravenous route (adoptive transfer of in vitro-generated CII-specific ACAID macrophages or of CII-specific in vitro-generated T regulatory cells). Specific immune tolerance induction was assessed using both delayed-type hypersensitivity (DTH) and local adoptive transfer (LAT) assays. Results indicated the ability of CII to generate CII-specific ACAID-mediated immune tolerance in vivo and in vitro in both DBA/1 mice and C57BL/6 mice. These findings could be beneficial in studies of immune tolerance induction using CII.

  15. Genome sequence of the phylogenetically isolated spirochete Leptonema illini type strain (3055T)

    PubMed Central

    Huntemann, Marcel; Stackebrandt, Erko; Held, Brittany; Nolan, Matt; Lucas, Susan; Hammon, Nancy; Deshpande, Shweta; Cheng, Jan-Fang; Tapia, Roxanne; Goodwin, Lynne A.; Pitluck, Sam; Liolios, Konstantinos; Pagani, Ioanna; Ivanova, Natalia; Mavromatis, Konstantinos; Mikhailova, Natalia; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Rohde, Manfred; Gronow, Sabine; Göker, Markus; Detter, John C.; Bristow, James; Eisen, Jonathan A.; Markowitz, Victor; Woyke, Tanja; Hugenholtz, Philip; Kyrpides, Nikos C.; Klenk, Hans-Peter; Lapidus, Alla

    2013-01-01

    Leptonema illini Hovind-Hougen 1979 is the type species of the genus Leptonema, family Leptospiraceae, phylum Spirochaetes. Organisms of this family have a Gram-negative-like cell envelope consisting of a cytoplasmic membrane and an outer membrane. The peptidoglycan layer is associated with the cytoplasmic rather than the outer membrane. The two flagella of members of Leptospiraceae extend from the cytoplasmic membrane at the ends of the bacteria into the periplasmic space and are necessary for their motility. Here we describe the features of the L. illini type strain, together with the complete genome sequence, and annotation. This is the first genome sequence (finished at the level of Improved High Quality Draft) to be reported from of a member of the genus Leptonema and a representative of the third genus of the family Leptospiraceae for which complete or draft genome sequences are now available. The three scaffolds of the 4,522,760 bp draft genome sequence reported here, and its 4,230 protein-coding and 47 RNA genes are part of the Genomic Encyclopedia of Bacteria and Archaea project. PMID:23991250

  16. Genome sequence of the phylogenetically isolated spirochete Leptonema illini type strain (3055(T)).

    PubMed

    Huntemann, Marcel; Stackebrandt, Erko; Held, Brittany; Nolan, Matt; Lucas, Susan; Hammon, Nancy; Deshpande, Shweta; Cheng, Jan-Fang; Tapia, Roxanne; Goodwin, Lynne A; Pitluck, Sam; Liolios, Konstantinos; Pagani, Ioanna; Ivanova, Natalia; Mavromatis, Konstantinos; Mikhailova, Natalia; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Rohde, Manfred; Gronow, Sabine; Göker, Markus; Detter, John C; Bristow, James; Eisen, Jonathan A; Markowitz, Victor; Woyke, Tanja; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter; Lapidus, Alla

    2013-01-01

    Leptonema illini Hovind-Hougen 1979 is the type species of the genus Leptonema, family Leptospiraceae, phylum Spirochaetes. Organisms of this family have a Gram-negative-like cell envelope consisting of a cytoplasmic membrane and an outer membrane. The peptidoglycan layer is associated with the cytoplasmic rather than the outer membrane. The two flagella of members of Leptospiraceae extend from the cytoplasmic membrane at the ends of the bacteria into the periplasmic space and are necessary for their motility. Here we describe the features of the L. illini type strain, together with the complete genome sequence, and annotation. This is the first genome sequence (finished at the level of Improved High Quality Draft) to be reported from of a member of the genus Leptonema and a representative of the third genus of the family Leptospiraceae for which complete or draft genome sequences are now available. The three scaffolds of the 4,522,760 bp draft genome sequence reported here, and its 4,230 protein-coding and 47 RNA genes are part of the G enomic E ncyclopedia of Bacteria and Archaea project.

  17. Genome sequence of the phylogenetically isolated spirochete Leptonema illini type strain (3055T)

    SciTech Connect

    Huntemann, Marcel; Stackebrandt, Erko; Held, Brittany; Nolan, Matt; Lucas, Susan; Hammon, Nancy; Deshpande, Shweta; Cheng, Jan-Fang; Tapia, Roxanne; Goodwin, Lynne A.; Pitluck, Sam; Liolios, Konstantinos; Pagani, Ioanna; Ivanova, N; Mavromatis, K; Mikhailova, Natalia; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam L; Rohde, Manfred; Gronow, Sabine; Goker, Markus; Detter, J. Chris; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Woyke, Tanja; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter; Lapidus, Alla L.

    2013-01-01

    Leptonema illini Hovind-Hougen 1979 is the type species of the genus Leptonema, family Leptospiraceae, phylum Spirochaetes. Organisms of this family have a Gram-negative-like cell enve- lope consisting of a cytoplasmic membrane and an outer membrane. The peptidoglycan layer is as- sociated with the cytoplasmic rather than the outer membrane. The two flagella of members of Leptospiraceae extend from the cytoplasmic membrane at the ends of the bacteria into the periplasmic space and are necessary for their motility. Here we describe the features of the L. illini type strain, together with the complete genome sequence, and annotation. This is the first genome sequence (finished at the level of Improved High Quality Draft) to be reported from of a member of the genus Leptonema and a representative of the third genus of the family Leptospiraceae for which complete or draft genome sequences are now available. The three scaffolds of the 4,522,760 bp draft genome sequence reported here, and its 4,230 protein-coding and 47 RNA genes are part of the Ge- nomic Encyclopedia of Bacteria and Archaea project.

  18. Contributions of NanI sialidase to Caco-2 cell adherence by Clostridium perfringens type A and C strains causing human intestinal disease.

    PubMed

    Li, Jihong; McClane, Bruce A

    2014-11-01

    Previous studies showed that Clostridium perfringens type D animal disease strain CN3718 uses NanI sialidase for adhering to enterocyte-like Caco-2 cells. The current study analyzed whether NanI is similarly important when type A and C human intestinal disease strains attach to Caco-2 cells. A PCR survey determined that the nanI gene was absent from typical type A food poisoning (FP) strains carrying a chromosomal enterotoxin (CPE) gene or the genetically related type C Darmbrand (Db) strains. However, the nanI gene was present in type A strains from healthy humans, type A strains causing CPE-associated antibiotic-associated diarrhea (AAD) or sporadic diarrhea (SD), and type C Pig-Bel strains. Consistent with NanI sialidase being the major C. perfringens sialidase when produced, FP and Db strains had little supernatant sialidase activity compared to other type A or C human intestinal strains. All type A and C human intestinal strains bound to Caco-2 cells, but NanI-producing strains had higher attachment levels. When produced, NanI can contribute to host cell attachment of human intestinal disease strains, since a nanI null mutant constructed in type A SD strain F4969 had lower Caco-2 cell adhesion than wild-type F4969 or a complemented strain. Further supporting a role for NanI in host cell attachment, sialidase inhibitors reduced F4969 adhesion to Caco-2 cells. Collectively, these results suggest that NanI may contribute to the intestinal attachment and colonization needed for the chronic diarrhea of CPE-associated AAD and SD, but this sialidase appears to be dispensable for the acute pathogenesis of type A FP or type C enteritis necroticans.

  19. Calomys callosus chronically infected by Toxoplasma gondii clonal type II strain and reinfected by Brazilian strains is not able to prevent vertical transmission

    PubMed Central

    Franco, Priscila S.; da Silva, Neide M.; de Freitas Barbosa, Bellisa; de Oliveira Gomes, Angelica; Ietta, Francesca; Shwab, E. K.; Su, Chunlei; Mineo, José R.; Ferro, Eloisa A. V.

    2015-01-01

    Considering that Toxoplasma gondii has shown high genetic diversity in Brazil, the aim of this study was to determine whether Calomys callosus chronically infected by the ME-49 strain might be susceptible to reinfection by these Brazilian strains, including vertical transmission of the parasite. Survival curves were analyzed in non-pregnant females chronically infected with ME-49 and reinfected with the TgChBrUD1 or TgChBrUD2 strain, and vertical transmission was analyzed after reinfection of pregnant females with these same strains. On the 19th day of pregnancy (dop), placentas, uteri, fetuses, liver, spleen, and lung were processed for detection of the parasite. Blood samples were collected for humoral and cellular immune response analyses. All non-pregnant females survived after reinfection and no changes were observed in body weight and morbidity scores. In pregnant females, parasites were detected in the placentas of ME-49 chronically infected females and reinfected females, but were only detected in the fetuses of reinfected females. TgChBrUD2 reinfected females showed more impaired pregnancy outcomes, presenting higher numbers of animals with fetal loss and a higher resorption rate, in parallel with higher levels of pro-inflammatory cytokines and IgG2a subclass antibodies. Vertical transmission resulting from chronic infection of immunocompetent C. callosus is considered a rare event, being attributed instead to either reactivation or reinfection. That is, the pregnancy may be responsible for reactivation of the latent infection or the reinfection may promote T. gondii vertical transmission. Our results clearly demonstrate that, during pregnancy, protection against T. gondii can be breached after reinfection with parasites belonging to different genotypes, particularly when non-clonal strains are involved in this process and in this case the reinfection promoted vertical transmission of both type II and Brazilian T. gondii strains. PMID:25806028

  20. Effects that different types of sports have on the hearts of children and adolescents and the value of two-dimensional strain-strain-rate echocardiography.

    PubMed

    Binnetoğlu, Fatih Köksal; Babaoğlu, Kadir; Altun, Gürkan; Kayabey, Özlem

    2014-01-01

    Whether the hypertrophy found in the hearts of athletes is physiologic or a risk factor for the progression of pathologic hypertrophy remains controversial. The diastolic and systolic functions of athletes with left ventricular (LV) hypertrophy usually are normal when measured by conventional methods. More precise assessment of global and regional myocardial function may be possible using a newly developed two-dimensional (2D) strain echocardiographic method. This study evaluated the effects that different types of sports have on the hearts of children and adolescents and compared the results of 2D strain and strain-rate echocardiographic techniques with conventional methods. Athletes from clubs for five different sports (basketball, swimming, football, wrestling, and tennis) who had practiced regularly at least 3 h per week during at least the previous 2 years were included in the study. The control group consisted of sedentary children and adolescents with no known cardiac or systemic diseases (n = 25). The athletes were grouped according to the type of exercise: dynamic (football, tennis), static (wrestling), or static and dynamic (basketball, swimming). Shortening fraction and ejection fraction values were within normal limits for the athletes in all the sports disciplines. Across all 140 athletes, LV geometry was normal in 58 athletes (41.4 %), whereas 22 athletes (15.7 %) had concentric remodeling, 20 (14.3 %) had concentric hypertrophy, and 40 (28.6 %) had eccentric hypertrophy. Global LV longitudinal strain values obtained from the average of apical four-, two-, and three-chamber global strain values were significantly lower for the basketball players than for all the other groups (p < 0.001).

  1. Pathogenesis of a Chinese strain of bovine adenovirus type 3 infection in albino guinea pigs.

    PubMed

    Shi, Hong-Fei; Zhu, Yuan-Mao; Yan, Hao; Ma, Lei; Wang, Xue-Zhi; Xue, Fei

    2014-12-01

    Bovine adenovirus type 3 (BAV-3) is considered one of the most important respiratory tract agents of cattle and is widespread among cattle around the world. A BAV-3 strain was isolated from a bovine nasal swab for the first time in China in 2009 and named HLJ0955. Subsequently, BAV-3 has frequently been isolated from calves with respiratory diseases in China. To date, only limited study on the pathogenesis of BAV-3 infection in cotton rats has been conducted, and the pathogenesis of BAV-3 infection in guinea pigs has not been reported. Therefore, sixteen albino guinea pigs were inoculated intranasally with HLJ0955. All of the infected guinea pigs had apparently elevated rectal temperatures (39.2 °C-39.9 °C) at 2-7 days post-inoculation (PI). Consolidation and petechial hemorrhage were also observed in guinea pigs experimentally infected with HLJ0955. Viral replication was detectable by virus isolation and titration and by immunohistochemistry in the lungs of guinea pigs as early as 24 h PI. Viral DNA was detectable in the lungs of infected guinea pigs during 11 days of observation by real-time PCR. Virus-neutralizing antibodies against BAV-3 were detectable from 11 days PI and reached a peak titer at 15 days PI. Histopathological changes mainly occurred in the lungs of infected guinea pigs and were characterized by thickening of alveolar septa, mononuclear cell infiltration, hemorrhage and alveolar epithelial necrosis. These results indicate that HLJ0955 can replicate in the lungs of guinea pigs and cause fever and gross and histological lesions. The guinea pig infection model of BAV-3 would serve as a useful system for monitoring the infection process and pathogenesis of the Chinese BAV-3 strain HLJ0955, as well as immune responses to BAV-3 vaccines.

  2. Assessing benzene-induced toxicity on wild type Euglena gracilis Z and its mutant strain SMZ.

    PubMed

    Peng, Cheng; Arthur, Dionne M; Sichani, Homa Teimouri; Xia, Qing; Ng, Jack C

    2013-11-01

    Benzene is a representative member of volatile organic compounds and has been widely used as an industrial solvent. Groundwater contamination of benzene may pose risks to human health and ecosystems. Detection of benzene in the groundwater using chemical analysis is expensive and time consuming. In addition, biological responses to environmental exposures are uninformative using such analysis. Therefore, the aim of this study was to employ a microorganism, Euglena gracilis (E. gracilis) as a putative model to monitor the contamination of benzene in groundwater. To this end, we examined the wild type of E. gracilis Z and its mutant form, SMZ in their growth rate, morphology, chlorophyll content, formation of reactive oxygen species (ROS) and DNA damage in response to benzene exposure. The results showed that benzene inhibited cell growth in a dose response manner up to 48 h of exposure. SMZ showed a greater sensitivity compared to Z in response to benzene exposure. The difference was more evident at lower concentrations of benzene (0.005-5 μM) where growth inhibition occurred in SMZ but not in Z cells. We found that benzene induced morphological changes, formation of lipofuscin, and decreased chlorophyll content in Z strain in a dose response manner. No significant differences were found between the two strains in ROS formation and DNA damage by benzene at concentrations affecting cell growth. Based on these results, we conclude that E. gracilis cells were sensitive to benzene-induced toxicities for certain endpoints such as cell growth rate, morphological change, depletion of chlorophyll. Therefore, it is a potentially suitable model for monitoring the contamination of benzene and its effects in the groundwater.

  3. Direct type II-indirect type I conversion of InP/GaAs/InP strained quantum wells induced by hydrostatic pressure

    NASA Astrophysics Data System (ADS)

    Gerling, M.; Pistol, M.-E.; Samuelson, L.; Seifert, W.; Fornell, J.-O.; Ledebo, L.

    1991-08-01

    Photoluminescence from thin strained layers of GaAs grown on InP has been studied under hydrostatic pressure. The structures are type II at atmospheric pressure. At higher pressures the structures change to type I with the lowest conduction band edge in the strained GaAs layer being the X minimum. This transformation is characterized by a drastic change in the pressure derivative of the emission energy and a rapid disappearance of the photoluminescence intensity at slightly higher pressures. A hydrostatic pressure derivative of less than one meV/kbar is measured for the valence band offset.

  4. Population Genetic Structure of Listeria monocytogenes Strains as Determined by Pulsed-Field Gel Electrophoresis and Multilocus Sequence Typing

    PubMed Central

    Henri, Clémentine; Félix, Benjamin; Guillier, Laurent; Leekitcharoenphon, Pimlapas; Michelon, Damien; Mariet, Jean-François; Aarestrup, Frank M.; Mistou, Michel-Yves; Hendriksen, René S.

    2016-01-01

    ABSTRACT Listeria monocytogenes is a ubiquitous bacterium that may cause the foodborne illness listeriosis. Only a small amount of data about the population genetic structure of strains isolated from food is available. This study aimed to provide an accurate view of the L. monocytogenes food strain population in France. From 1999 to 2014, 1,894 L. monocytogenes strains were isolated from food at the French National Reference Laboratory for L. monocytogenes and classified according to the five risk food matrices defined by the European Food Safety Authority (EFSA). A total of 396 strains were selected on the basis of different pulsed-field gel electrophoresis (PFGE) clusters, serotypes, and strain origins and typed by multilocus sequence typing (MLST), and the MLST results were supplemented with MLST data available from Institut Pasteur, representing human and additional food strains from France. The distribution of sequence types (STs) was compared between food and clinical strains on a panel of 675 strains. High congruence between PFGE and MLST was found. Out of 73 PFGE clusters, the two most prevalent corresponded to ST9 and ST121. Using original statistical analysis, we demonstrated that (i) there was not a clear association between ST9 and ST121 and the food matrices, (ii) serotype IIc, ST8, and ST4 were associated with meat products, and (iii) ST13 was associated with dairy products. Of the two major STs, ST121 was the ST that included the fewest clinical strains, which might indicate lower virulence. This observation may be directly relevant for refining risk analysis models for the better management of food safety. IMPORTANCE This study showed a very useful backward compatibility between PFGE and MLST for surveillance. The results enabled better understanding of the population structure of L. monocytogenes strains isolated from food and management of the health risks associated with L. monocytogenes food strains. Moreover, this work provided an accurate view

  5. Capsular Polysaccharide (CPS) Release by Serotype 3 Pneumococcal Strains Reduces the Protective Effect of Anti-Type 3 CPS Antibodies.

    PubMed

    Choi, Eun Hwa; Zhang, Fan; Lu, Ying-Jie; Malley, Richard

    2015-12-16

    The efficacy of the serotype 3 (ST3) pneumococcal conjugate vaccine (PCV) remains unclear. While the synthesis of capsular polysaccharide (CPS) of most serotypes is wzy dependent, the strains of two serotypes, 3 and 37, synthesize CPS by the synthase-dependent pathway, resulting in a polysaccharide that is not covalently linked to peptidoglycan and can be released during growth. We hypothesized that the release of CPS during growth reduces anti-type 3 CPS antibody-mediated protection and may explain the lower efficacy of the type 3 component of PCV than that of other PCVs. The in vitro-released CPS concentrations per 10(7) CFU of ST3 and ST37 strains were significantly higher than those for the ST1, ST4, ST6B, and ST14 strains. Following intraperitoneal (i.p.) injection in mice, blood concentrations of CPS were significantly higher for the ST3 than for the ST4/5 strains. The opsonophagocytic killing assay (OPKA) titer of anti-type 3 CPS antibody was significantly reduced by type 3 CPS, culture supernatant, or serum from Streptococcus pneumoniae ST3 strain WU2-infected mice. Mice were injected with capsule-specific antibodies and challenged i.p. with or without the addition of sterile culture supernatant containing type-specific CPS. The addition of 0.2 μl of culture supernatant from WU2 inhibited passive protection, whereas 100-fold-more culture supernatant from S. pneumoniae ST4 strain TIGR4 was required for the inhibition of protection. We conclude that released type 3 CPS interferes with antibody-mediated killing and protection by anti-CPS antibodies. The relative failure of ST3 PCV may be due to CPS release, suggesting that alternative immunization approaches for ST3 may be necessary.

  6. Capsular Polysaccharide (CPS) Release by Serotype 3 Pneumococcal Strains Reduces the Protective Effect of Anti-Type 3 CPS Antibodies

    PubMed Central

    Choi, Eun Hwa; Zhang, Fan; Lu, Ying-Jie

    2015-01-01

    The efficacy of the serotype 3 (ST3) pneumococcal conjugate vaccine (PCV) remains unclear. While the synthesis of capsular polysaccharide (CPS) of most serotypes is wzy dependent, the strains of two serotypes, 3 and 37, synthesize CPS by the synthase-dependent pathway, resulting in a polysaccharide that is not covalently linked to peptidoglycan and can be released during growth. We hypothesized that the release of CPS during growth reduces anti-type 3 CPS antibody-mediated protection and may explain the lower efficacy of the type 3 component of PCV than that of other PCVs. The in vitro-released CPS concentrations per 107 CFU of ST3 and ST37 strains were significantly higher than those for the ST1, ST4, ST6B, and ST14 strains. Following intraperitoneal (i.p.) injection in mice, blood concentrations of CPS were significantly higher for the ST3 than for the ST4/5 strains. The opsonophagocytic killing assay (OPKA) titer of anti-type 3 CPS antibody was significantly reduced by type 3 CPS, culture supernatant, or serum from Streptococcus pneumoniae ST3 strain WU2-infected mice. Mice were injected with capsule-specific antibodies and challenged i.p. with or without the addition of sterile culture supernatant containing type-specific CPS. The addition of 0.2 μl of culture supernatant from WU2 inhibited passive protection, whereas 100-fold-more culture supernatant from S. pneumoniae ST4 strain TIGR4 was required for the inhibition of protection. We conclude that released type 3 CPS interferes with antibody-mediated killing and protection by anti-CPS antibodies. The relative failure of ST3 PCV may be due to CPS release, suggesting that alternative immunization approaches for ST3 may be necessary. PMID:26677201

  7. Immunity status of adults and children against poliomyelitis virus type 1 strains CHAT and Sabin (LSc-2ab) in Germany

    PubMed Central

    2010-01-01

    Background In October 2007, the working group CEN/TC 216 of the European Committee for standardisation suggested that the Sabin oral poliovirus vaccine type 1 strain (LSc-2ab) presently used for virucidal tests should be replaced by another attenuated vaccine poliovirus type 1 strain, CHAT. Both strains were historically used as oral vaccines, but the Sabin type 1 strain was acknowledged to be more attenuated. In Germany, vaccination against poliomyelitis was introduced in 1962 using the oral polio vaccine (OPV) containing Sabin strain LSc-2ab. The vaccination schedule was changed from OPV to an inactivated polio vaccine (IPV) containing wild polio virus type 1 strain Mahoney in 1998. In the present study, we assessed potential differences in neutralising antibody titres to Sabin and CHAT in persons with a history of either OPV, IPV, or OPV with IPV booster. Methods Neutralisation poliovirus antibodies against CHAT and Sabin 1 were measured in sera of 41 adults vaccinated with OPV. Additionally, sera from 28 children less than 10 years of age and immunised with IPV only were analysed. The neutralisation assay against poliovirus was performed according to WHO guidelines. Results The neutralisation activity against CHAT in adults with OPV vaccination history was significantly lower than against Sabin poliovirus type 1 strains (Wilcoxon signed-rank test P < 0.025). In eight sera, the antibody titres measured against CHAT were less than 8, although the titre against Sabin 1 varied between 8 and 64. Following IPV booster, anti-CHAT antibodies increased rapidly in sera of CHAT-negative adults with OPV history. Sera from children with IPV history neutralised CHAT and Sabin 1 strains equally. Conclusion The lack of neutralising antibodies against the CHAT strain in persons vaccinated with OPV might be associated with an increased risk of reinfection with the CHAT polio virus type 1, and this implies a putative risk of transmission of the virus to polio-free communities. We

  8. Pulsed-field gel electrophoresis typing, antibiotic resistance, and plasmid profiles of Escherichia coli strains isolated from foods.

    PubMed

    Uysal, Ahmet; Durak, Yusuf

    2012-11-01

    Bacterial contamination in foods and antimicrobial resistance levels of common pathogenic strains causing food-borne disease are important in human health. Thus, typing technologies are important tools to determine primary sources of bacterial contamination. In this study, 40 Escherichia coli strains isolated from 85 food samples were evaluated in terms of genetic diversity, susceptibility to certain antibiotics, and plasmid profiles. Pulsed-field gel electrophoresis was used to identify the genetic relations of E. coli isolates. It was determined that the 40 E. coli strains revealed 32 different pulsotypes represented by 6 subtypes. Antibiotic susceptibility tests conducted by using a disc diffusion method against 15 antibiotics showed that although the isolates revealed 14 different types of resistance profiles, the strains showed the greatest resistance to ampicillin (77.5%), followed by ticarcillin-clavulanic acid (30%), tetracycline (22.5%), and cephalothin (14.5%). Plasmid isolations studies of the strains conducted by the method of alkaline lysis revealed that 18 (45%) of 40 E. coli strains contain 31 different plasmid bands ranging between 64.4 and 1 kb. The results showed that PFGE was a powerful method in tracking sources of food contamination and that the antibiotic resistance levels of food isolates were high and should be monitored.

  9. Early detection of cardiac dysfunction in the type 1 diabetic heart using speckle-tracking based strain imaging.

    PubMed

    Shepherd, Danielle L; Nichols, Cody E; Croston, Tara L; McLaughlin, Sarah L; Petrone, Ashley B; Lewis, Sara E; Thapa, Dharendra; Long, Dustin M; Dick, Gregory M; Hollander, John M

    2016-01-01

    Enhanced sensitivity in echocardiographic analyses may allow for early detection of changes in cardiac function beyond the detection limits of conventional echocardiographic analyses, particularly in a small animal model. The goal of this study was to compare conventional echocardiographic measurements and speckle-tracking based strain imaging analyses in a small animal model of type 1 diabetes mellitus. Conventional analyses revealed differences in ejection fraction, fractional shortening, cardiac output, and stroke volume in diabetic animals relative to controls at 6-weeks post-diabetic onset. In contrast, when assessing short- and long-axis speckle-tracking based strain analyses, diabetic mice showed changes in average systolic radial strain, radial strain rate, radial displacement, and radial velocity, as well as decreased circumferential and longitudinal strain rate, as early as 1-week post-diabetic onset and persisting throughout the diabetic study. Further, we performed regional analyses for the LV and found that the free wall region was affected in both the short- and long-axis when assessing radial dimension parameters. These changes began 1-week post-diabetic onset and remained throughout the progression of the disease. These findings demonstrate the use of speckle-tracking based strain as an approach to elucidate cardiac dysfunction from a global perspective, identifying left ventricular cardiac regions affected during the progression of type 1 diabetes mellitus earlier than contractile changes detected by conventional echocardiographic measurements.

  10. The effect of Clostridium perfringens type C strain CN3685 and its isogenic beta toxin null mutant in goats

    PubMed Central

    Garcia, J. P.; Beingesser, J.; Fisher, D. J.; Sayeed, S.; McClane, B. A.; Posthaus, H.; Uzal, F. A.

    2012-01-01

    Clostridium perfringens type C is an important cause of enteritis and/or enterocolitis in several animal species, including pigs, sheep, goats, horses and humans. The disease is a classic enterotoxemia and the enteric lesions and associated systemic effects are thought to be caused primarily by beta toxin (CPB), one of two typing toxins produced by C. perfringens type C. This has been demonstrated recently by fulfilling molecular Koch’s postulates in rabbits and mice. We present here an experimental study to fulfill these postulates in goats, a natural host of C. perfringens type C disease. Nine healthy male or female Anglo Nubian goat kids were inoculated with the virulent C. perfringens type C wild-type strain CN3685, an isogenic CPB null mutant or a strain where the cpb null mutation had been reversed. Three goats inoculated with the wild-type strain presented abdominal pain, hemorrhagic diarrhea, necrotizing enterocolitis, pulmonary edema, hydropericardium and death within 24 h of inoculation. Two goats inoculated with the CPB null mutant and two goats inoculated with sterile culture media (negative controls) remained clinically healthy during 24 h after inoculation and no gross or histological abnormalities were observed in the tissues of any of them. Reversal of the null mutation to partially restore CPB production also increased virulence; 2 goats inoculated with this reversed mutant presented clinical and pathological changes similar to those observed in goats inoculated with the wild-type strain, except that spontaneous death was not observed. These results indicate that CPB is required for C. perfringens type C to induce disease in goats, supporting a key role for this toxin in natural C. perfringens type C disease pathogenesis. PMID:22296994

  11. The effect of Clostridium perfringens type C strain CN3685 and its isogenic beta toxin null mutant in goats.

    PubMed

    Garcia, J P; Beingesser, J; Fisher, D J; Sayeed, S; McClane, B A; Posthaus, H; Uzal, F A

    2012-06-15

    Clostridium perfringens type C is an important cause of enteritis and/or enterocolitis in several animal species, including pigs, sheep, goats, horses and humans. The disease is a classic enterotoxemia and the enteric lesions and associated systemic effects are thought to be caused primarily by beta toxin (CPB), one of two typing toxins produced by C. perfringens type C. This has been demonstrated recently by fulfilling molecular Koch's postulates in rabbits and mice. We present here an experimental study to fulfill these postulates in goats, a natural host of C. perfringens type C disease. Nine healthy male or female Anglo Nubian goat kids were inoculated with the virulent C. perfringens type C wild-type strain CN3685, an isogenic CPB null mutant or a strain where the cpb null mutation had been reversed. Three goats inoculated with the wild-type strain presented abdominal pain, hemorrhagic diarrhea, necrotizing enterocolitis, pulmonary edema, hydropericardium and death within 24h of inoculation. Two goats inoculated with the CPB null mutant and two goats inoculated with sterile culture media (negative controls) remained clinically healthy during 24h after inoculation and no gross or histological abnormalities were observed in the tissues of any of them. Reversal of the null mutation to partially restore CPB production also increased virulence; 2 goats inoculated with this reversed mutant presented clinical and pathological changes similar to those observed in goats inoculated with the wild-type strain, except that spontaneous death was not observed. These results indicate that CPB is required for C. perfringens type C to induce disease in goats, supporting a key role for this toxin in natural C. perfringens type C disease pathogenesis.

  12. An ultra fast detection method reveals strain-induced Ca(2+) entry via TRPV2 in alveolar type II cells.

    PubMed

    Fois, Giorgio; Wittekindt, Oliver; Zheng, Xing; Felder, Erika Tatiana; Miklavc, Pika; Frick, Manfred; Dietl, Paul; Felder, Edward

    2012-09-01

    A commonly used technique to investigate strain-induced responses of adherent cells is culturing them on an elastic membrane and globally stretching the membrane. However, it is virtually impossible to acquire microscopic images immediately after the stretch with this method. Using a newly developed technique, we recorded the strain-induced increase of the cytoplasmic Ca(2+) concentration ([Ca(2+)](c)) in rat primary alveolar type II (ATII) cells at an acquisition rate of 30ms and without any temporal delay. We can show that the onset of the mechanically induced rise in [Ca(2+)](c) was very fast (<30 ms), and Ca(2+) entry was immediately abrogated when the stimulus was withdrawn. This points at a direct mechanical activation of an ion channel. RT-PCR revealed high expression of TRPV2 in ATII cells, and silencing TRPV2, as well as blocking TRPV channels with ruthenium red, significantly reduced the strain-induced Ca(2+) response. Moreover, the usually homogenous pattern of the strain-induced [Ca(2+)](c) increase was converted into a point-like response after both treatments. Also interfering with actin/myosin and integrin binding inhibited the strain-induced increase of [Ca(2)](c). We conclude that TRPV2 participates in strain-induced Ca(2+) entry in ATII cells and suggest a direct mechanical activation of the channel that depends on FAs and actin/myosin. Furthermore, our results underline the importance of cell strain systems that allow high temporal resolution.

  13. Complete genome sequence of Marinobacter adhaerens type strain (HP15), a diatom-interacting marine microorganism.

    PubMed

    Gärdes, Astrid; Kaeppel, Eva; Shehzad, Aamir; Seebah, Shalin; Teeling, Hanno; Yarza, Pablo; Glöckner, Frank Oliver; Grossart, Hans-Peter; Ullrich, Matthias S

    2010-09-28

    Marinobacter adhaerens HP15 is the type strain of a newly identified marine species, which is phylogenetically related to M. flavimaris, M. algicola, and M. aquaeolei. It is of special interest for research on marine aggregate formation because it showed specific attachment to diatom cells. In vitro it led to exopolymer formation and aggregation of these algal cells to form marine snow particles. M. adhaerens HP15 is a free-living, motile, rod-shaped, Gram-negative gammaproteobacterium, which was originally isolated from marine particles sampled in the German Wadden Sea. M. adhaerens HP15 grows heterotrophically on various media, is easy to access genetically, and serves as a model organism to investigate the cellular and molecular interactions with the diatom Thalassiosira weissflogii. Here we describe the complete and annotated genome sequence of M. adhaerens HP15 as well as some details on flagella-associated genes. M. adhaerens HP15 possesses three replicons; the chromosome comprises 4,422,725 bp and codes for 4,180 protein-coding genes, 51 tRNAs and three rRNA operons, while the two circular plasmids are ~187 kb and ~42 kb in size and contain 178 and 52 protein-coding genes, respectively.

  14. Genomic Encyclopedia of Bacteria and Archaea: Sequencing a Myriad of Type Strains

    PubMed Central

    Kyrpides, Nikos C.; Hugenholtz, Philip; Eisen, Jonathan A.; Woyke, Tanja; Göker, Markus; Parker, Charles T.; Amann, Rudolf; Beck, Brian J.; Chain, Patrick S. G.; Chun, Jongsik; Colwell, Rita R.; Danchin, Antoine; Dawyndt, Peter; Dedeurwaerdere, Tom; DeLong, Edward F.; Detter, John C.; De Vos, Paul; Donohue, Timothy J.; Dong, Xiu-Zhu; Ehrlich, Dusko S.; Fraser, Claire; Gibbs, Richard; Gilbert, Jack; Gilna, Paul; Glöckner, Frank Oliver; Jansson, Janet K.; Keasling, Jay D.; Knight, Rob; Labeda, David; Lapidus, Alla; Lee, Jung-Sook; Li, Wen-Jun; MA, Juncai; Markowitz, Victor; Moore, Edward R. B.; Morrison, Mark; Meyer, Folker; Nelson, Karen E.; Ohkuma, Moriya; Ouzounis, Christos A.; Pace, Norman; Parkhill, Julian; Qin, Nan; Rossello-Mora, Ramon; Sikorski, Johannes; Smith, David; Sogin, Mitch; Stevens, Rick; Stingl, Uli; Suzuki, Ken-ichiro; Taylor, Dorothea; Tiedje, Jim M.; Tindall, Brian; Wagner, Michael; Weinstock, George; Weissenbach, Jean; White, Owen; Wang, Jun; Zhang, Lixin; Zhou, Yu-Guang; Field, Dawn; Whitman, William B.; Garrity, George M.; Klenk, Hans-Peter

    2014-01-01

    Microbes hold the key to life. They hold the secrets to our past (as the descendants of the earliest forms of life) and the prospects for our future (as we mine their genes for solutions to some of the planet's most pressing problems, from global warming to antibiotic resistance). However, the piecemeal approach that has defined efforts to study microbial genetic diversity for over 20 years and in over 30,000 genome projects risks squandering that promise. These efforts have covered less than 20% of the diversity of the cultured archaeal and bacterial species, which represent just 15% of the overall known prokaryotic diversity. Here we call for the funding of a systematic effort to produce a comprehensive genomic catalog of all cultured Bacteria and Archaea by sequencing, where available, the type strain of each species with a validly published name (currently∼11,000). This effort will provide an unprecedented level of coverage of our planet's genetic diversity, allow for the large-scale discovery of novel genes and functions, and lead to an improved understanding of microbial evolution and function in the environment. PMID:25093819

  15. Genomic encyclopedia of bacteria and archaea: sequencing a myriad of type strains.

    PubMed

    Kyrpides, Nikos C; Hugenholtz, Philip; Eisen, Jonathan A; Woyke, Tanja; Göker, Markus; Parker, Charles T; Amann, Rudolf; Beck, Brian J; Chain, Patrick S G; Chun, Jongsik; Colwell, Rita R; Danchin, Antoine; Dawyndt, Peter; Dedeurwaerdere, Tom; DeLong, Edward F; Detter, John C; De Vos, Paul; Donohue, Timothy J; Dong, Xiu-Zhu; Ehrlich, Dusko S; Fraser, Claire; Gibbs, Richard; Gilbert, Jack; Gilna, Paul; Glöckner, Frank Oliver; Jansson, Janet K; Keasling, Jay D; Knight, Rob; Labeda, David; Lapidus, Alla; Lee, Jung-Sook; Li, Wen-Jun; Ma, Juncai; Markowitz, Victor; Moore, Edward R B; Morrison, Mark; Meyer, Folker; Nelson, Karen E; Ohkuma, Moriya; Ouzounis, Christos A; Pace, Norman; Parkhill, Julian; Qin, Nan; Rossello-Mora, Ramon; Sikorski, Johannes; Smith, David; Sogin, Mitch; Stevens, Rick; Stingl, Uli; Suzuki, Ken-Ichiro; Taylor, Dorothea; Tiedje, Jim M; Tindall, Brian; Wagner, Michael; Weinstock, George; Weissenbach, Jean; White, Owen; Wang, Jun; Zhang, Lixin; Zhou, Yu-Guang; Field, Dawn; Whitman, William B; Garrity, George M; Klenk, Hans-Peter

    2014-08-01

    Microbes hold the key to life. They hold the secrets to our past (as the descendants of the earliest forms of life) and the prospects for our future (as we mine their genes for solutions to some of the planet's most pressing problems, from global warming to antibiotic resistance). However, the piecemeal approach that has defined efforts to study microbial genetic diversity for over 20 years and in over 30,000 genome projects risks squandering that promise. These efforts have covered less than 20% of the diversity of the cultured archaeal and bacterial species, which represent just 15% of the overall known prokaryotic diversity. Here we call for the funding of a systematic effort to produce a comprehensive genomic catalog of all cultured Bacteria and Archaea by sequencing, where available, the type strain of each species with a validly published name (currently∼11,000). This effort will provide an unprecedented level of coverage of our planet's genetic diversity, allow for the large-scale discovery of novel genes and functions, and lead to an improved understanding of microbial evolution and function in the environment.

  16. Genome sequence of the chemoheterotrophic soil bacterium Saccharomonospora cyanea type strain (NA-134(T)).

    PubMed

    Meier-Kolthoff, Jan P; Lu, Megan; Huntemann, Marcel; Lucas, Susan; Lapidus, Alla; Copeland, Alex; Pitluck, Sam; Goodwin, Lynne A; Han, Cliff; Tapia, Roxanne; Pötter, Gabriele; Land, Miriam; Ivanova, Natalia; Rohde, Manfred; Göker, Markus; Detter, John C; Woyke, Tanja; Kyrpides, Nikos C; Klenk, Hans-Peter

    2013-10-16

    Saccharomonospora cyanea Runmao et al. 1988 is a member of the genus Saccharomonospora in the family Pseudonocardiaceae that is moderately well characterized at the genome level thus far. Members of the genus Saccharomonospora are of interest because they originate from diverse habitats, such as soil, leaf litter, manure, compost, surface of peat, moist, over-heated grain, and ocean sediment, where they probably play a role in the primary degradation of plant material by attacking hemicellulose. Species of the genus Saccharomonospora are usually Gram-positive, non-acid fast, and are classified among the actinomycetes. S. cyanea is characterized by a dark blue (= cyan blue) aerial mycelium. After S. viridis, S. azurea, and S. marina, S. cyanea is only the fourth member in the genus for which a completely sequenced (non-contiguous finished draft status) type strain genome will be published. Here we describe the features of this organism, together with the draft genome sequence, and annotation. The 5,408,301 bp long chromosome with its 5,139 protein-coding and 57 RNA genes was sequenced as part of the DOE funded Community Sequencing Program (CSP) 2010 at the Joint Genome Institute (JGI).

  17. Genome sequence of the chemoheterotrophic soil bacterium Saccharomonospora cyanea type strain (NA-134T)

    PubMed Central

    Meier-Kolthoff, Jan P.; Lu, Megan; Huntemann, Marcel; Lucas, Susan; Lapidus, Alla; Copeland, Alex; Pitluck, Sam; Goodwin, Lynne A.; Han, Cliff; Tapia, Roxanne; Pötter, Gabriele; Land, Miriam; Ivanova, Natalia; Rohde, Manfred; Göker, Markus; Detter, John C.; Woyke, Tanja; Kyrpides, Nikos C.; Klenk, Hans-Peter

    2013-01-01

    Saccharomonospora cyanea Runmao et al. 1988 is a member of the genus Saccharomonospora in the family Pseudonocardiaceae that is moderately well characterized at the genome level thus far. Members of the genus Saccharomonospora are of interest because they originate from diverse habitats, such as soil, leaf litter, manure, compost, surface of peat, moist, over-heated grain, and ocean sediment, where they probably play a role in the primary degradation of plant material by attacking hemicellulose. Species of the genus Saccharomonospora are usually Gram-positive, non-acid fast, and are classified among the actinomycetes. S. cyanea is characterized by a dark blue (= cyan blue) aerial mycelium. After S. viridis, S. azurea, and S. marina, S. cyanea is only the fourth member in the genus for which a completely sequenced (non-contiguous finished draft status) type strain genome will be published. Here we describe the features of this organism, together with the draft genome sequence, and annotation. The 5,408,301 bp long chromosome with its 5,139 protein-coding and 57 RNA genes was sequenced as part of the DOE funded Community Sequencing Program (CSP) 2010 at the Joint Genome Institute (JGI). PMID:24501643

  18. Molecular Typing of Mycobacterium Tuberculosis Strains: A Fundamental Tool for Tuberculosis Control and Elimination.

    PubMed

    Cannas, Angela; Mazzarelli, Antonio; Di Caro, Antonino; Delogu, Giovanni; Girardi, Enrico

    2016-06-24

    Tuberculosis (TB) is still an important cause of morbidity and mortality worldwide. An improvement of the strategies for disease control is necessary in both low- and high-incidence TB countries. Clinicians, epidemiologists, laboratory specialists, and public health players should work together in order to achieve a significant reduction in TB transmission and spread of drug-resistant strains. Effective TB surveillance relies on early diagnosis of new cases, appropriate therapy, and accurate detection of outbreaks in the community, in order to implement proper TB control strategies. To achieve this goal, information from classical and molecular epidemiology, together with patient clinical data need to be combined. In this review, we summarize the methodologies currently used in molecular epidemiology, namely molecular typing. We will discuss their efficiency to phylogenetically characterize Mycobacterium tuberculosis isolates, and their ability to provide information that can be useful for disease control. We will also introduce next generation sequencing as the methodology that potentially could provide in a short time both, detection of new outbreaks and identification of resistance patterns. This could envision a potential of next generation sequencing as an important tool for accurate patient management and disease control.

  19. Genome sequence of the chemoheterotrophic soil bacterium Saccharomonospora cyanea type strain (NA-134(T))

    SciTech Connect

    Meier-Kolthoff, Jan P.; Lu, Megan; Huntemann, Marcel; Lucas, Susan; Lapidus, Alla L.; Copeland, A; Pitluck, Sam; Goodwin, Lynne A.; Han, Cliff; Tapia, Roxanne; Potter, Gabriele; Land, Miriam L; Ivanova, N; Rohde, Manfred; Goker, Markus; Detter, J. Chris; Woyke, Tanja; Kyrpides, Nikos C; Klenk, Hans-Peter

    2013-01-01

    Saccharomonospora cyanea Runmao et al. 1988 is a member of the genus Saccharomonospora in the family Pseudonocardiaceae that is moderately well characterized at the genome level thus far. Members of the genus Saccharomonospora are of interest because they originate from diverse habitats, such as soil, leaf litter, manure, compost, surface of peat, moist, over-heated grain, and ocean sediment, where they probably play a role in the primary degradation of plant material by attacking hemicellulose. Species of the genus Saccharomonospora are usually Gram-positive, non-acid fast, and are classified among the actinomycetes. S. cyanea is characterized by a dark blue (= cyan blue) aerial mycelium. After S. viridis, S. azurea, and S. marina, S. cyanea is only the fourth member in the genus for which a completely sequenced (non-contiguous finished draft status) type strain genome will be published. Here we describe the features of this organism, together with the draft genome sequence, and annotation. The 5,408,301 bp long chromosome with its 5,139 protein-coding and 57 RNA genes was sequenced as part of the DOE funded Community Sequencing Program (CSP) 2010 at the Joint Genome Institute (JGI).

  20. Genome sequence of the soil bacterium Saccharomonospora azurea type strain (NA-128T)

    SciTech Connect

    Klenk, Hans-Peter; Held, Brittany; Lucas, Susan; Lapidus, Alla L.; Copeland, A; Hammon, Nancy; Pitluck, Sam; Goodwin, Lynne A.; Han, Cliff; Tapia, Roxanne; Brambilla, Evelyne-Marie; Potter, Gabriele; Land, Miriam L; Ivanova, N; Rohde, Manfred; Goker, Markus; Detter, J. Chris; Kyrpides, Nikos C; Woyke, Tanja

    2012-01-01

    Saccharomonospora azurea Runmao et al. 1987 is a member to the genomically so far poorly characterized genus Saccharomonospora in the family Pseudonocardiaceae. Members of the genus Sacharomonosoras are of interest because they originate from diverse habitats, such as leaf litter, manure, compost, surface of peat, moist and over-heated grain, where they might play a role in the primary degradation of plant material by attacking hemicellulose. They are Gram-negative staining organisms classified among the usually Gram-positive actinomycetes. Next to S. viridis, S. azurea is only the second member in the genus Saccharomonospora for with a completely sequenced type strain genome will be published. Here we describe the features of this organism, together with the complete genome sequence with project status 'permanent draft', and annotation. The 4,763,832 bp long chromosome with its 4,472 protein-coding and 58 RNA genes was sequenced as part of the DOE funded Community Sequencing Program (CSP) 2010 at the Joint Genome Institute (JGI).

  1. Genome sequence of the ocean sediment bacterium Saccharomonospora marina type strain (XMU15T)

    SciTech Connect

    Klenk, Hans-Peter; Lu, Megan; Lucas, Susan; Copeland, A; Pitluck, Sam; Goodwin, Lynne A.; Han, Cliff; Tapia, Roxanne; Brambilla, Evelyne-Marie; Potter, Gabriele; Land, Miriam L; Ivanova, N; Rohde, Manfred; Goker, Markus; Detter, J. Chris; Li, Wen-Jun; Kyrpides, Nikos C; Woyke, Tanja

    2012-01-01

    Saccharomonospora marina Liu et al. 2010 is a member to the genomically so far poorly characterized genus Saccharomonospora in the family Pseudonocardiaceae. Members of the genus Sacharomonospora are of interest because they originate from diverse habitats, such as leaf litter, manure, compost, surface of peat, moist, over-heated grain, and ocean sediment, where they might play a role in the primary degradation of plant material by attacking hemicellulose. Organisms belonging to the genus are usually Gram-positive staining, non-acid fast, and classify among the actinomycetes. Next to S. viridis and S. azurea, S. marina is the third member in the genus Saccharomonospora for with a completely sequenced (permanent draft status) type strain genome will be published. Here we describe the features of this organism, together with the complete genome sequence, and annotation. The 5,965,593 bp long chromosome with its 5,727 protein-coding and 57 RNA genes was sequenced as part of the DOE funded Community Sequencing Program (CSP) 2010 at the Joint Genome Institute (JGI).

  2. Multilocus sequence typing (MLST) of leptospiral strains isolated from two geographic locations of Tamil Nadu, India.

    PubMed

    Kanagavel, Murugesan; Princy Margreat, Alphonse Asirvatham; Arunkumar, Manivel; Prabhakaran, Shanmugarajan Gnanasekaran; Shanmughapriya, Santhanam; Natarajaseenivasan, Kalimuthusamy

    2016-01-01

    Here the rodent carrier status for the transmission of human leptospirosis in Tiruchirappalli, district, Tamil Nadu, India was assessed. The predominantly circulating leptospiral STs were recognized by multilocus sequence typing (MLST). A total of 113 rodents were trapped from different provinces of the Tiruchirappalli district. The most prevalent rodent was Bandicota bengalensis (37.2%), and of the total, 52.2% (n=59) rodents were found to be positive for leptospiral 16S rRNA. These results were validated with a leptospiral culture positivity of 45.8% (n=27). Three isolates from Chennai (2 rodents and 1 human) and 1 human isolate from Tiruchirappalli were included to understand the spatial variations and to track the source of human leptospirosis. The serogroup, serovar, and species level identification of all 31 isolates identified 28 to be Leptospira borgpetersenii serovar Javanica and three as Leptospira interrogans serovar Autumnalis. MLST analysis defined all isolates to the existing ST profiles (ST145 and ST27) with the exception of 6 L. borgpetersenii (ST DR) isolates that showed variations in the sucA and pfkB loci. The DR ST was locally confined to Chatram province of Tiruchirappalli suggesting an epidemiological link. The predominant STs, ST145 and ST-DR form a group, indicating the presence of original strain that subsequently diverged evolutionarily into two STs. The variations between L. borgpetersenii in sucA and pfkB loci may be an indication that evolutionary changes transpired in Tiruchirappalli.

  3. Radiometric characterization of an LWIR, type-II strained layer superlattice pBiBn photodetector

    NASA Astrophysics Data System (ADS)

    Treider, L. A.; Morath, C. P.; Cowan, V. M.; Tian, Z. B.; Krishna, S.

    2015-05-01

    Type-II Strained Layer Superlattice (T2SLS) infrared photodetectors have been in development over the last decade. T2SLS offers a theoretically longer Auger recombination lifetime than traditional mercury cadmium telluride (MCT), which presumably translates to infrared detectors with lower dark-current and higher operating temperatures. However, these improvements did not materialize due to the presence of Shockley-Read-Hall (SRH) defects in T2SLSs, which limits the recombination lifetime well below the Auger-limit. With the recent introduction of the pBiBn, and other similar unipolar barrier detectors, T2SLS material has seen renewed interest since these designs ideally eliminate the SRH-generation and surface currents while retaining the other potential advantages of T2SLS: reduced manufacturing cost, better availability of a durable state-side manufacturing base, ability to tune the cutoff wavelength, and better uniformity. Here, an electrical and optical characterization of a long-wave, pBiBn detector with a T2SLS absorber is presented. Dark-current, spectral response and optical response were measured as functions of temperature and bias. Activation energy was then determined as a function of bias from the dark-current measurements. Quantum efficiency was also determined as a function of bias from the optical response measurements. Additionally, noise spectrum measurements were taken as a function of bias.

  4. [Response to antibiotics of Proteus strains isolated from different types of clinical material].

    PubMed

    Ovetchin, P V; Tsyganenko, A Ia

    1984-04-01

    The data on the study of the antibiotic response to 42 Proteus strains isolated from different sources in the hospitals of Kharkov are presented. The isolates belonged to P. mirabilis and P. vulgaris. Many strains were resistant to gentamicin, ampicillin and carbenicillin irrespective of the isolation source. 58.0 and 90.3 per cent of the strains isolated from patients with intestinal infections, 66.6 and 100 per cent of the strains isolated from patients with otitis, 33.3 and 66.6 per cent of the strains isolated from patients with bronchopulmonary affections and 100 and 100 per cent of the strains isolated from patients with urological diseases were resistant to gentamicin and carbenicillin, respectively. As for ampicillin, the respective figures were 74.2, 66.6, 66.6 and 100 per cent. All the strains of P. vulgaris isolated from patients with otitis, urological diseases and bronchopulmonary affections were resistant to ampicillin. The MIC of carbenicillin for all the strains except 4 indole-positive strains of P. vulgaris isolated from the faeces and bronchial excreta was much higher than the borderline values.

  5. An assessment of cold work effects on strain-controlled low-cycle fatigue behavior of type 304 stainless steel

    NASA Astrophysics Data System (ADS)

    Rao, K. Bhanu Sankara; Valsan, M.; Sandhya, R.; Mannan, S. L.; Rodriguez, P.

    1993-04-01

    The influence of prior cold work (PCW) on low-cycle fatigue (LCF) behavior of type 304 stainless steel has been studied at 300, 823, 923, and 1023 K by conducting total axial strain-controlled tests in solution annealed (SA, 0 pct PCW) condition and on specimens having three levels of PCW, namely, 10, 20, and 30 pct. A triangular waveform with a constant frequency of 0.1 Hz was employed for all of the tests performed over strain amplitudes in the range of ±0.25 to ± 1.25 pct. These studies have revealed that fatigue life is strongly dependent on PCW, temperature, and strain amplitude employed in testing. The SA material generally displayed better endurance in terms of total and plastic strain amplitudes than the material in 10, 20, and 30 pct PCW conditions at all of the temperatures. However, at 300 K at very low strain amplitudes, PCW material exhibited better total strain fatigue resistance. At 823 K, LCF life decreased with increasing PCW, whereas at 923 K, 10 pct PCW displayed the lowest life. An improvement in life occurred for prior deformations exceeding 10 pct at all strain amplitudes at 923 K. Fatigue life showed a noticeable decrease with increasing temperature up to 1023 K in PCW state. On the other hand, SA material displayed a minimum in fatigue life at 923 K. The fatigue life results of SA as well as all of the PCW conditions obeyed the Basquin and Coffin-Manson relationships at 300, 823, and 923 K. The constants and exponents in these equations were found to depend on the test temperature and prior metallurgical state of the material. A study is made of cyclic stress-strain behavior in SA and PCW states and the relationship between the cyclic strain-hardening exponent and fatigue behavior at different temperatures has been explored. The influence of environment on fatigue crack initiation and propagation behavior has been examined.

  6. An assessment of cold work effects on strain-controlled low-cycle fatigue behavior of type 304 stainless steel

    SciTech Connect

    Bhanu Sankara Rao, K.; Valsan, M.; Sandhya, R.; Mannan, S.L.; Rodriguez, P. )

    1993-04-01

    The influence of prior cold work (PCW) on low-cycle fatigue (LCF) behavior of type 304 stainless steel has been studied at 300, 823, 923, and 1,023 K by conducting total axial strain-controlled tests in solution annealed (SA, 0 pct PCW) condition and on specimens having three levels of PCW, namely, 10, 20, and 30 pct. A triangular waveform with a constant frequency of 0.1 Hz was employed for all of the tests performed over strain amplitudes in the range of [plus minus]0.25 to [plus minus]1.25%. These studies have revealed that fatigue life is strongly dependent on PCW, temperature, and strain amplitude employed in testing. The SA material generally displayed better endurance in terms of total and plastic strain amplitudes than the material in 10, 20, and 30% PCW conditions at all of the temperatures. However, at 300 K at very low strain amplitudes, PCW material exhibited better total strain fatigue resistance. At 823 K, LCF life decreased with increasing PCW, whereas at 923 K, 10% PCW displayed the lowest life. An improvement in life occurred for prior deformation exceeding 10% at all strain amplitudes at 923 K. Fatigue life showed a noticeable decrease with increasing temperature up to 1,023 K in PCW state. On the other hand, SA material displayed a minimum in fatigue life at 923 K. The fatigue life results of SA as well as all of the PCW conditions obeyed the Basquin and Coffin-Manson relationships at 300, 823, and 923 K. A study is made of cyclic stress-strain behavior in SA and PCW states and the relationship between the cyclic strain-hardening exponent and fatigue behavior at different temperatures has been explored. The influence of environment on fatigue crack initiation and propagation behavior has been examined.

  7. Typing and selection of wild strains of Trichoderma spp. producers of extracellular laccase.

    PubMed

    Cázares-García, Saila Viridiana; Arredondo-Santoyo, Marina; Vázquez-Marrufo, Gerardo; Soledad Vázquez-Garcidueñas, Ma; Robinson-Fuentes, Virginia A; Gómez-Reyes, Víctor Manuel

    2016-05-01

    Using the ITS region and the gene tef1, 23 strains of the genus Trichoderma were identified as belonging to the species T. harzianum (n = 14), T. olivascens (n = 1), T. trixiae (n = 1), T. viridialbum (n = 1), T. tomentosum (n = 2), T. koningii (n = 1), T. atroviride (n = 1), T. viride (n = 1), and T. gamsii (n = 1). Strains expressing extracellular laccase activity were selected by decolorization/oxidation assays in solid media, using azo, anthraquinone, indigoid, and triphenylmethane dyes, and the phenolic substances tannic acid and guaiacol. No strain decolorized Direct Blue 71 or Chicago Blue 6B, but all of them weakly oxidized guaiacol, decolorized Methyl Orange, and efficiently oxidized tannic acid. Based in decolorization/oxidation assays, strains CMU-1 (T. harzianum), CMU-8 (T. atroviride), CMU-218 (T. viride), and CMU-221 (T. tomentosum) were selected for evaluating their extracellular laccase activity in liquid media. Strain CMU-8 showed no basal laccase activity, while strains CMU-1, CMU-218, and CMU-221 had a basal laccase activity of 1,313.88 mU/mL, 763.88 mU/mL, and 799.53 mU/mL, respectively. Addition of sorghum straw inhibited laccase activity in strain CMU-1 by 34%, relative to the basal culture, while strains CMU-8, CMU-21, and CMU-221 increased their laccase activity by 1,321.5%, 64%, and 47%, respectively. These results show that assayed phenolic substrates are good tools for selecting laccase producer strains in Trichoderma. These same assays indicate the potential use of studied strains for bioremediation processes. Straw laccase induction suggests that analyzed strains have potential for straw delignification in biopulping and other biotechnological applications. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:787-798, 2016.

  8. Complete Genome Sequence of Rothia aeria Type Strain JCM 11412, Isolated from Air in the Russian Space Laboratory Mir.

    PubMed

    Nambu, Takayuki; Tsuzukibashi, Osamu; Uchibori, Satoshi; Yamane, Kazuyoshi; Yamanaka, Takeshi; Maruyama, Hugo; Wang, Pao-Li; Mugita, Naho; Morioka, Hiroki; Takahashi, Kazuya; Komasa, Yutaka; Mashimo, Chiho

    2016-12-29

    Here, we present the complete genome sequence of Rothia aeria type strain JCM 11412, isolated from air in the Russian space laboratory Mir. Recently, there has been an increasing number of reports on infections caused by R. aeria The genomic information will enable researchers to identify the pathogenicity of this organism.

  9. Pathogenicity of three type 2 Porcine Reproductive and Respiratory Syndrome virus strains in experimentally inoculated pregnant gilts

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Mechanisms of reproductive failure resulting from infection with porcine reproductive and respiratory syndrome virus (PRRSv) are still poorly understood. The present study, a side-by-side evaluation of the pathogenicity of three type 2 PRRSv strains in a reproductive model, was used as a pilot study...

  10. Whole-Genome Sequence and Annotation of Salmonella enterica subsp. enterica Serovar Enteritidis Phage Type 8 Strain EN1660

    PubMed Central

    Perry, Benjamin J.; Fitzgerald, Stephen F.; Kröger, Carsten

    2017-01-01

    ABSTRACT The genome of Salmonella enterica subspecies enterica serovar Enteritidis phage type 8 strain EN1660, isolated from an outbreak in Thunder Bay, Canada, was sequenced to 46-fold coverage using an Illumina MiSeq with 300-bp paired-end sequencing chemistry to produce 28 contigs with an N50 value of 490,721 bp. PMID:28126943

  11. Practical approaches for application of resistance type strain gages on high temperature composites

    NASA Technical Reports Server (NTRS)

    Moore, Thomas C., Sr.

    1991-01-01

    Four major areas of interest with respect to utilizing strain gages on carbon/carbon (with SiC surfaces) and titanium matrix composites are addressed. Strain gage and adhesive combinations on carbon/carbon (C/C) at temperatures from minus 190 C to to 540 C, half-bridge gaging for reducing apparent strain on C/C using Poisson's ratio and bending configurations, a review of the 'field installation' techniques developed for gaging a C/C hypersonic generic elevon, and results of initial strain gaging efforts on titanium matrix composites are discussed. Current research in developing techniques for increasing the maximum temperature for strain gages on carbon/carbon are reviewed.

  12. Strains of the Propionibacterium acnes type III lineage are associated with the skin condition progressive macular hypomelanosis

    PubMed Central

    Barnard, Emma; Liu, Jared; Yankova, Eliza; Cavalcanti, Silvana M.; Magalhães, Marcelo; Li, Huiying; Patrick, Sheila; McDowell, Andrew

    2016-01-01

    Progressive macular hypomelanosis (PMH) is a common skin disorder that causes hypopigmentation in a variety of skin types. Although the underlying aetiology of this condition is unclear, there is circumstantial evidence that links the skin bacterium Propionibacterium acnes to the condition. We now describe the first detailed population genetic analysis of P. acnes isolates recovered from paired lesional and non-lesional skin of PMH patients. Our results demonstrate a strong statistical association between strains from the type III phylogenetic lineage and PMH lesions (P = 0.0019), but not those representing other phylogroups, including those associated with acne (type IA1). We also demonstrate, based on in silico 16S rDNA analysis, that PMH isolates previously recovered from patients in Europe are also consistent with the type III lineage. Using comparative genome analysis, we identified multiple genomic regions that are specific for, or absent from, type III strains compared to other phylogroups. In the former case, these include open reading frames with putative functions in metabolism, transport and transcriptional regulation, as well as predicted proteins of unknown function. Further study of these genomic elements, along with transcriptional and functional analyses, may help to explain why type III strains are associated with PMH. PMID:27555369

  13. Molecular characterization of Brazilian equid herpesvirus type 1 strains based on neuropathogenicity markers

    PubMed Central

    Mori, Enio; Lara, Maria do Carmo C.S.H.; Cunha, Elenice M.S.; Villalobos, Eliana M.C.; Mori, Claudia M.C.; Soares, Rodrigo M.; Brandão, Paulo E.; Fernandes, Wilson R.; Richtzenhain, Leonardo J.

    2015-01-01

    Partial nucleotide sequences of ORF72 (glycoprotein D, gD), ORF64 (infected cell protein 4, ICP4) and ORF30 (DNA polymerase) genes were compared with corresponding sequences of EHV-1 reference strains to characterize the molecular variability of Brazilian strains. Virus isolation assays were applied to 74 samples including visceral tissue, total blood, cerebrospinal fluid (CSF) and nasal swabs of specimens from a total of 64 animals. Only one CSF sample (Iso07/05 strain) was positive by virus isolation in cell culture. EHV-1 Iso07/05 neurologic strain and two abortion visceral tissues samples (Iso11/06 and Iso33/06) were PCR-positive for ORF33 (glycoprotein B, gB) gene of EHV-1. A sequence analysis of the ORF72, ORF64 and ORF30 genes from three EHV-1 archival strains (A3/97, A4/72, A9/92) and three clinical samples (Iso07/05, Iso11/06 and Iso33/06) suggested that among Brazilian EHV-1 strains, the amplified region of the gD gene sequence is highly conserved. Additionally, the analysis of ICP4 gene showed high nucleotide and amino acid identities when compared with genotype P strains, suggesting that the EHV-1 Brazilian strains belonged to the same group. All the EHV-1 Brazilian strains were classified as non-neuropathogenic variants (N752) based on the ORF30 analysis. These findings indicate a high conservation of the gD-, ICP4- and ORF30-encoding sequences. Different pathotypes of the EHV-1 strain might share identical genes with no specific markers, and tissue tropism is not completely dependent on the gD envelope, immediate-early ICP4 and DNA polymerase proteins. PMID:26273275

  14. VanA-Type Staphylococcus aureus Strain VRSA-7 Is Partially Dependent on Vancomycin for Growth ▿

    PubMed Central

    Moubareck, Carole; Meziane-Cherif, Djalal; Courvalin, Patrice; Périchon, Bruno

    2009-01-01

    VanA-type Staphylococcus aureus strain VRSA-7 was partially dependent on glycopeptides for growth. The vanA gene cluster, together with the erm(A) and the ant(9)-Ia resistance genes, was carried by the ca. 35- to 40-kb conjugative plasmid pIP848 present at five copies per cell. The chromosomal ddl gene had a mutation that led to a N308K substitution in the d-Ala:d-Ala ligase that resulted in a 1,000-fold decrease in activity relative to that of strain VRSA-6. Strain VRSA-7 grown in the absence or in the presence of vancomycin mainly synthesized precursors ending in d-Ala-d-Lac, indicating that the strain relied on the vancomycin resistance pathway for peptidoglycan synthesis. Greatly enhanced growth in the presence of glycopeptides and the absence of mutations in the genes for VanR and VanS indicated the inducible expression of resistance. Thus, a combination of loose regulation of the vanA operon by the two-component system and a gene dosage effect accounts for the partial glycopeptide dependence of VRSA-7. Since peptidoglycan precursors ending in d-Ala-d-Lac are not processed by PBP 2′, the strain was fully susceptible to oxacillin, despite the production of a wild-type PBP 2′. PMID:19528271

  15. Two-component systems are involved in the regulation of botulinum neurotoxin synthesis in Clostridium botulinum type A strain Hall.

    PubMed

    Connan, Chloé; Brüggemann, Holger; Brueggemann, Holger; Mazuet, Christelle; Raffestin, Stéphanie; Cayet, Nadège; Popoff, Michel R

    2012-01-01

    Clostridium botulinum synthesizes a potent neurotoxin (BoNT) which associates with non-toxic proteins (ANTPs) to form complexes of various sizes. The bont and antp genes are clustered in two operons. In C. botulinum type A, bont/A and antp genes are expressed during the end of the exponential growth phase and the beginning of the stationary phase under the control of an alternative sigma factor encoded by botR/A, which is located between the two operons. In the genome of C. botulinum type A strain Hall, 30 gene pairs predicted to encode two-component systems (TCSs) and 9 orphan regulatory genes have been identified. Therefore, 34 Hall isogenic antisense strains on predicted regulatory genes (29 TCSs and 5 orphan regulatory genes) have been obtained by a mRNA antisense procedure. Two TCS isogenic antisense strains showed more rapid growth kinetics and reduced BoNT/A production than the control strain, as well as increased bacterial lysis and impairment of the bacterial cell wall structure. Three other TCS isogenic antisense strains induced a low level of BoNT/A and ANTP production. Interestingly, reduced expression of bont/A and antp genes was shown to be independent of botR/A. These results indicate that BoNT/A synthesis is under the control of a complex network of regulation including directly at least three TCSs.

  16. Two-Component Systems Are Involved in the Regulation of Botulinum Neurotoxin Synthesis in Clostridium botulinum Type A Strain Hall

    PubMed Central

    Connan, Chloé; Brueggemann, Holger; Mazuet, Christelle; Raffestin, Stéphanie; Cayet, Nadège; Popoff, Michel R.

    2012-01-01

    Clostridium botulinum synthesizes a potent neurotoxin (BoNT) which associates with non-toxic proteins (ANTPs) to form complexes of various sizes. The bont and antp genes are clustered in two operons. In C. botulinum type A, bont/A and antp genes are expressed during the end of the exponential growth phase and the beginning of the stationary phase under the control of an alternative sigma factor encoded by botR/A, which is located between the two operons. In the genome of C. botulinum type A strain Hall, 30 gene pairs predicted to encode two-component systems (TCSs) and 9 orphan regulatory genes have been identified. Therefore, 34 Hall isogenic antisense strains on predicted regulatory genes (29 TCSs and 5 orphan regulatory genes) have been obtained by a mRNA antisense procedure. Two TCS isogenic antisense strains showed more rapid growth kinetics and reduced BoNT/A production than the control strain, as well as increased bacterial lysis and impairment of the bacterial cell wall structure. Three other TCS isogenic antisense strains induced a low level of BoNT/A and ANTP production. Interestingly, reduced expression of bont/A and antp genes was shown to be independent of botR/A. These results indicate that BoNT/A synthesis is under the control of a complex network of regulation including directly at least three TCSs. PMID:22848632

  17. Recombination and Insertion Events Involving the Botulinum Neurotoxin Complex Genes in Clostridium botulinum Types A, B, E and F and Clostridium butyricum Type E Strains

    DTIC Science & Technology

    2009-10-05

    tetani CTC E88 C. tetani E88 AE015927 C. botulinum B192 C. botulinum CLD type-B1 Okra C. baratii AB240209 C. baratii AY341243 C. botulinum B257 C...B1 Okra I CLD CP000939/CP000940 HA-B1 plasmid C. botulinum Bf ----- I CBB ABDP01000001-70 HA-bvB, orfX-F plasmid C. botulinum prot F Langeland I CLI...Loch Maree, 657, Okra or Langeland strains. Panel 1b and 1c plots compare Hall and C. butyricum BL 5262 to the BoNT/E-producing Alaska E43 strain, where

  18. Molecular characterization of wild-type measles viruses in Tamil Nadu, India, during 2005-2006: relationship of genotype D8 strains from Tamil Nadu to global strains.

    PubMed

    Duraisamy, Raja; Rota, Paul A; Palani, Gunasekaran; Elango, Varalakshmi; Sambasivam, Mohana; Lowe, Luis; Lopareva, Elena; Ramamurty, Nalini

    2012-02-01

    Molecular characterization of measles viruses is a valuable tool for measuring the effectiveness of measles control and elimination programmes. WHO recommends that virological surveillance be conducted during all phases of measles control to document circulation of indigenous strains and trace future importation. This report describes the genetic characterization of wild type measles viruses from Tamil Nadu, India isolated between January 2005 and January 2006. In the study, 304 suspected measles cases (292 from 56 outbreaks and 12 sporadic cases) were investigated. Blood samples were collected from suspected measles outbreaks and 11 suspected sporadic cases and tested for the presence of measles and rubella specific IgM. Based on serological results, 53 outbreaks were confirmed as measles, 2 as a combination of measles and rubella, and 1 negative for both. Eight sporadic cases were confirmed as measles and one as rubella. Throat swab and urine samples were collected for virus isolation and 28 isolates were obtained. Sequencing and analysis showed that 3 isolates belonged to genotype D4 and 25 to genotype D8. Comparison of the genotype D8 sequences from Tamil Nadu with previously reported genotype D8 sequences from India and abroad showed six distinct clusters with Tamil Nadu strains forming two clusters. This study has established baseline molecular data and is the first report that describes genetic diversity of circulating measles strains in Tamil Nadu, a state in India. D8 has multiple lineages and this has been linked with importation of measles into the USA and UK.

  19. Characterization of transferrin binding proteins 1 and 2 in invasive type b and nontypeable strains of Haemophilus influenzae.

    PubMed Central

    Gray-Owen, S D; Schryvers, A B

    1995-01-01

    Haemophilus influenzae has the ability to obtain iron from human transferrin via two bacterial cell surface transferrin binding proteins, Tbp1 and Tbp2. Although a wide array of strains have been shown to express these receptor proteins, two studies have recently identified a series of isolates which appeared to lack the ability to bind transferrin. Included in this group were the members of a cryptic genospecies of nontypeable biotype IV strains which appear to possess a tropism for female urogenital tissues and are major etiologic agents of neonatal and postpartum bacteremia due to H. influenzae. The present study employed oligonucleotide primers specific for genes encoding the Tbp proteins of a type b biotype I strain of H. influenzae to probe the genomic DNAs of isolates from the previous studies. The tbpA and tbpB genes which encode Tbp1 and Tbp2, respectively, were detected in all of the strains tested either by PCR amplification directly or by Southern hybridization analysis. All of the strains displayed a transferrin binding phenotype, and affinity isolation of receptor proteins with transferrin-conjugated Sepharose recovered Tbp1 and/or Tbp2 from 11 of 14 strains, including 2 of the nontypeable biotype IV strains. In addition, all of the strains were capable of growing on human transferrin specifically, indicating that the mechanism of iron assimilation from transferrin is functional and is not siderophore mediated. These results confirm the presence of tbp genes in all of the invasive H. influenzae isolates characterized to date, suggesting that Tbp-mediated iron acquisition is important in disease which initiates from either the respiratory or urogenital mucosa. PMID:7558284

  20. Human Immunodeficiency Virus Type 1 Clade B Superinfection: Evidence for Differential Immune Containment of Distinct Clade B Strains

    PubMed Central

    Yang, Otto O.; Daar, Eric S.; Jamieson, Beth D.; Balamurugan, Arumugam; Smith, Davey M.; Pitt, Jacqueline A.; Petropoulos, Christos J.; Richman, Douglas D.; Little, Susan J.; Brown, Andrew J. Leigh

    2005-01-01

    Sequential infection with different strains of human immunodeficiency virus type 1 (HIV-1) is a rarely identified phenomenon with important implications for immunopathogenesis and vaccine development. Here, we identify an individual whose good initial control of viremia was lost in association with reduced containment of a superinfecting strain. Subject 2030 presented with acute symptoms of HIV-1 infection with high viremia and an incomplete seroconversion as shown by Western blotting. A low set point of viremia (∼1,000 HIV-1 copies/ml) was initially established without drug therapy, but a new higher set point (∼40,000 HIV-1 copies/ml) manifested about 5 months after infection. Drug susceptibility testing demonstrated a multidrug-resistant virus initially but a fully sensitive virus after 5 months, and an analysis of pol genotypes showed that these were two phylogenetically distinct strains of virus (strains A and B). Replication capacity assays suggested that the outgrowth of strain B was not due to higher fitness conferred by pol, and env sequences indicated that the two strains had the same R5 coreceptor phenotype. Delineation of CD8+-T-lymphocyte responses against HIV-1 showed a striking pattern of decay of the initial cellular immune responses after superinfection, followed by some adaptation of targeting to new epitopes. An examination of targeted sequences suggested that differences in the recognized epitopes contributed to the poor immune containment of strain B. In conclusion, the rapid overgrowth of a superinfecting strain of HIV-1 of the same subtype raises major concerns for effective vaccine development. PMID:15613314

  1. A STUDY OF PNEUMOCOCCI REACTING WITH ANTIPNEUMOCOCCUS SERA OF TYPES I, II, AND III, WITH AN OBSERVATION OF A MUTATION OF ONE OF THE STRAINS.

    PubMed

    Clough, M C

    1919-08-01

    In this paper are reported the results of a study of nine strains of pneumococci agglutinating with antipneumococcus sera of all three types (Nos. I, II, and III). Seven of the strains were the cause of serious or fatal infections in human beings. Morphologically they were typical pneumococci with characteristic growth on ordinary media. Most of the strains were soluble in bile, fermented inulin, and caused no precipitation on glucose ascitic fluid agar. Two of the strains, however, resembled streptococci in these three cultural characteristics, but have been regarded as pneumococci on account of their serological reactions. Variations in the cultural reactions occurred with several strains while they were under observation. The virulence of the strains varied greatly, some strains being almost non-pathogenic, and others killing mice in doses of 0.000001 cc. of a 24 hour broth culture. Antipneumococcus Sera I, II, and III agglutinated all the strains in fairly high dilution (1:8 to 1:64 or higher), while normal horse serum caused no agglutination. Antipneumococcus Sera I, II, and III stimulated active phagocytosis of all the strains, while no phagocytosis occurred in control preparations with normal horse serum. These strains elaborated a soluble substance in the body of inoculated mice which caused the formation of a precipitate when the peritoneal washings, cleared by centrifugalization, were added to the antipneumococcus sera of all three types. Antipneumococcus Sera I, II, and III protected mice equally well against 1,000 to 10,000 times the minimal lethal dose of the two strains with which protection tests could be carried out. Absorption of serum of Types I and II with the homologous pneumococcus removed the agglutinins and the bacteriotropins for all these strains. Absorption of these sera with Strains T and N removed the agglutinins and the bacteriotropins for the homologous strain only, and not for typical members of Type I or II, or for the other

  2. Membrane vesicles of Clostridium perfringens Type A strains induce innate and adaptive immunity

    PubMed Central

    Jiang, Yanlong; Kong, Qingke; Roland, Kenneth L.; Curtiss, Roy

    2014-01-01

    Vesicle shedding from bacteria is a universal process in most Gram-negative bacteria and a few Gram-positive bacteria. In this report, we isolate extracellular membrane vesicles (MVs) from the supernatants of Gram-positive pathogen Clostridium perfringens (C. perfringens). We demonstrated vesicle production in a variety of virulent and nonvirulent type A strains. MVs did not contain alpha-toxin and NetB toxin demonstrated by negative reaction to specific antibody and absence of specific proteins identified by LC-MS/MS. C. perfringens MVs contained DNA components such as 16S ribosomal RNA gene (16S rRNA), alpha-toxin gene (plc) and the perfringolysin O gene (pfoA) demonstrated by PCR. We also identified a total of 431 proteins in vesicles by 1-D gel separation and LC-MS/MS analysis. In vitro studies demonstrated that vesicles could be internalized into murine macrophage RAW264.7 cells without direct cytotoxicity effects, causing release of inflammation cytokines including granulocyte colony stimulating factor (G-CSF), tumor necrosis factor-alpha (TNF-α) and interleukin-1 (IL-1), which could also be detected in mice injected with MVs through intraperitoneal (i.p.) route. Mice immunized with C. perfringens MVs produced high titer IgG, especially IgG1, antibodies against C. perfringens membrane proteins. However, this kind of antibody could not provide protection in mice following challenge, though it could slightly postpone the time of death. Our results indicate that release of MVs from C. perfringens could provide a previously unknown mechanism to induce release of inflammatory cytokines, especially TNF-α, these findings may contribute to a better understanding of the pathogenesis of C. perfringens infection. PMID:24631214

  3. Microsatellite typing as a new tool for identification of Saccharomyces cerevisiae strains.

    PubMed

    Hennequin, C; Thierry, A; Richard, G F; Lecointre, G; Nguyen, H V; Gaillardin, C; Dujon, B

    2001-02-01

    Since Saccharomyces cerevisiae appears to be an emerging pathogen, there is a need for a valuable molecular marker able to distinguish among strains. In this work, we investigated the potential value of microsatellite length polymorphism with a panel of 91 isolates, including 41 clinical isolates, 14 laboratory strains, and 28 strains with industrial relevance. Testing seven polymorphic regions (five trinucleotide repeats and two dinucleotide repeats) in a subgroup of 58 unrelated strains identified a total of 69 alleles (6 to 13 per locus) giving 52 different patterns with a discriminatory power of 99.03%. We found a cluster of clinical isolates sharing their genotype with a bakery strain, suggesting a digestive colonization following ingestion of this strain with diet. With the exception of this cluster of isolates and isolates collected from the same patient or from patients treated with Saccharomyces boulardii, all clinical isolates gave different and unique patterns. The genotypes are stable, and the method is reproducible. The possibility to make the method portable is of great interest for further studies using this technique. This work shows the possibility to readily identify S. boulardii (a strain increasingly isolated from invasive infections) using a unique and specific microsatellite allele.

  4. Characterization of the antibody response in birds following infection with wild-type and attenuated strains of Eimeria tenella and Eimeria necatrix.

    PubMed

    Constantinoiu, C C; Molloy, J B; Jorgensen, W K; Coleman, G T

    2011-01-10

    Live vaccines containing attenuated parasite strains are increasingly used to control chicken coccidiosis. In this paper antibody responses elicited by infections with wild-type and attenuated strains of Eimeria tenella and Eimeria necatrix were characterized by immunoblotting and ELISA with homologous and heterologous antisera. Few differences between antisera from birds infected with wild and attenuated strains of E. tenella were evident in immunoblots conducted with merozoite antigen preparations from both E. tenella strains, however the reactivity of sera raised in birds infected with the wild-type strain was noticeably more intense. In ELISAs conducted with merozoite antigen preparations, antisera from birds infected with the wild-type strains of E. tenella and E. necatrix consistently produced a significantly higher (P<0.05) antibody response than antisera from birds infected with the attenuated strains. Likewise, avidity ELISAs conducted with the E. tenella strains demonstrated that antibodies in birds infected with the wild-type strain were of significantly higher avidity (P<0.05) than antibodies in birds infected with the attenuated strain. The differences in the antibody responses are probably due to changes in the attenuated strain as a result of selection for precocious development and the less severe tissue damage and inflammation of the intestine resulting from infection with the attenuated strain.

  5. High quality draft genome sequence of Bacteroides barnesiae type strain BL2T (DSM 18169T) from chicken caecum

    DOE PAGES

    Sakamoto, Mitsuo; Lapidus, Alla L.; Han, James; ...

    2015-08-02

    Bacteroides barnesiae Lan et al. 2006 is a species of the genus Bacteroides, which belongs to the family Bacteroidaceae. Strain BL2T is of interest because it was isolated from the gut of a chicken and the growing awareness that the anaerobic microbiota of the caecum is of benefit for the host and may impact poultry farming. We report that the 3,621,509 bp long genome with its 3,059 protein-coding and 97 RNA genes is a part of the Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes (KMG) project.

  6. High quality draft genome sequence of Bacteroides barnesiae type strain BL2(T) (DSM 18169(T)) from chicken caecum.

    PubMed

    Sakamoto, Mitsuo; Lapidus, Alla L; Han, James; Trong, Stephan; Haynes, Matthew; Reddy, T B K; Mikhailova, Natalia; Huntemann, Marcel; Pati, Amrita; Ivanova, Natalia N; Pukall, Rüdiger; Markowitz, Victor M; Woyke, Tanja; Klenk, Hans-Peter; Kyrpides, Nikos C; Ohkuma, Moriya

    2015-01-01

    Bacteroides barnesiae Lan et al. 2006 is a species of the genus Bacteroides, which belongs to the family Bacteroidaceae. Strain BL2(T) is of interest because it was isolated from the gut of a chicken and the growing awareness that the anaerobic microbiota of the caecum is of benefit for the host and may impact poultry farming. The 3,621,509 bp long genome with its 3,059 protein-coding and 97 RNA genes is a part of the Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes (KMG) project.

  7. High quality draft genome of Nakamurella lactea type strain, a rock actinobacterium, and emended description of Nakamurella lactea.

    PubMed

    Nouioui, Imen; Göker, Markus; Carro, Lorena; Montero-Calasanz, Maria Del Carmen; Rohde, Manfred; Woyke, Tanja; Kyrpides, Nikos C; Klenk, Hans-Peter

    2017-01-01

    Nakamurella lactea DLS-10(T), isolated from rock in Korea, is one of the four type strains of the genus Nakamurella. In this study, we describe the high quality draft genome of N. lactea DLS-10(T) and its annotation. A summary of phenotypic data collected from previously published studies was also included. The genome of strain DLS-10(T) presents a size of 5.82 Mpb, 5100 protein coding genes, and a C + G content of 68.9%. Based on the genome analysis, emended description of N. lactea in terms of G + C content was also proposed.

  8. Genotypic Diversity and Population Structure of Vibrio vulnificus Strains Isolated in Taiwan and Korea as Determined by Multilocus Sequence Typing.

    PubMed

    Kim, Hye-Jin; Cho, Jae-Chang

    2015-01-01

    The genetic diversity and population structure of Vibrio vulnificus isolates from Korea and Taiwan were investigated using PCR-based assays targeting putative virulence-related genes and multilocus sequence typing (MLST). BOX-PCR genomic fingerprinting identified 52 unique genotypes in 84 environmental and clinical V. vulnificus isolates. The majority (> 50%) of strains had pathogenic genotypes for all loci tested; moreover, many environmental strains had pathogenic genotypes. Although significant (p < 0.05) inter-relationships among the genotypes were observed, the association between genotype and strain source (environmental or clinical) was not significant, indicating that genotypic characteristics alone are not sufficient to predict the isolation source or the virulence of a given V. vulnificus strain and vice versa. MLST revealed 23-35 allelic types per locus analyzed, resulting in a total of 44 unique sequence types (STs). Two major monophyletic groups (lineages A and B) corresponding to the two known lineages of V. vulnificus were observed; lineage A had six STs that were exclusively environmental, whereas lineage B had STs from both environmental and clinical sources. Pathogenic and nonpathogenic genotypes predominated in MLST lineages B and A, respectively. In addition, V. vulnificus was shown to be in linkage disequilibrium (p < 0.05), although two different recombination tests (PHI and Sawyer's tests) detected significant evidence of recombination. Tajima's D test also indicated that V. vulnificus might be comprised of recently sub-divided lineages. These results suggested that the two lineages revealed by MLST correspond to two distinct ecotypes of V. vulnificus.

  9. Over Six Thousand Trypanosoma cruzi Strains Classified into Discrete Typing Units (DTUs): Attempt at an Inventory.

    PubMed

    Brenière, Simone Frédérique; Waleckx, Etienne; Barnabé, Christian

    2016-08-01

    Trypanosoma cruzi, the causative agent of Chagas disease, presents wide genetic diversity. Currently, six discrete typing units (DTUs), named TcI to TcVI, and a seventh one called TcBat are used for strain typing. Beyond the debate concerning this classification, this systematic review has attempted to provide an inventory by compiling the results of 137 articles that have used it. A total of 6,343 DTU identifications were analyzed according to the geographical and host origins. Ninety-one percent of the data available is linked to South America. This sample, although not free of potential bias, nevertheless provides today's picture of T. cruzi genetic diversity that is closest to reality. DTUs were genotyped from 158 species, including 42 vector species. Remarkably, TcI predominated in the overall sample (around 60%), in both sylvatic and domestic cycles. This DTU known to present a high genetic diversity, is very widely distributed geographically, compatible with a long-term evolution. The marsupial is thought to be its most ancestral host and the Gran Chaco region the place of its putative origin. TcII was rarely sampled (9.6%), absent, or extremely rare in North and Central America, and more frequently identified in domestic cycles than in sylvatic cycles. It has a low genetic diversity and has probably found refuge in some mammal species. It is thought to originate in the south-Amazon area. TcIII and TcIV were also rarely sampled. They showed substantial genetic diversity and are thought to be composed of possible polyphyletic subgroups. Even if they are mostly associated with sylvatic transmission cycles, a total of 150 human infections with these DTUs have been reported. TcV and TcVI are clearly associated with domestic transmission cycles. Less than 10% of these DTUs were identified together in sylvatic hosts. They are thought to originate in the Gran Chaco region, where they are predominant and where putative parents exist (TcII and TcIII). Trends in host

  10. Over Six Thousand Trypanosoma cruzi Strains Classified into Discrete Typing Units (DTUs): Attempt at an Inventory

    PubMed Central

    Brenière, Simone Frédérique; Waleckx, Etienne; Barnabé, Christian

    2016-01-01

    Trypanosoma cruzi, the causative agent of Chagas disease, presents wide genetic diversity. Currently, six discrete typing units (DTUs), named TcI to TcVI, and a seventh one called TcBat are used for strain typing. Beyond the debate concerning this classification, this systematic review has attempted to provide an inventory by compiling the results of 137 articles that have used it. A total of 6,343 DTU identifications were analyzed according to the geographical and host origins. Ninety-one percent of the data available is linked to South America. This sample, although not free of potential bias, nevertheless provides today’s picture of T. cruzi genetic diversity that is closest to reality. DTUs were genotyped from 158 species, including 42 vector species. Remarkably, TcI predominated in the overall sample (around 60%), in both sylvatic and domestic cycles. This DTU known to present a high genetic diversity, is very widely distributed geographically, compatible with a long-term evolution. The marsupial is thought to be its most ancestral host and the Gran Chaco region the place of its putative origin. TcII was rarely sampled (9.6%), absent, or extremely rare in North and Central America, and more frequently identified in domestic cycles than in sylvatic cycles. It has a low genetic diversity and has probably found refuge in some mammal species. It is thought to originate in the south-Amazon area. TcIII and TcIV were also rarely sampled. They showed substantial genetic diversity and are thought to be composed of possible polyphyletic subgroups. Even if they are mostly associated with sylvatic transmission cycles, a total of 150 human infections with these DTUs have been reported. TcV and TcVI are clearly associated with domestic transmission cycles. Less than 10% of these DTUs were identified together in sylvatic hosts. They are thought to originate in the Gran Chaco region, where they are predominant and where putative parents exist (TcII and TcIII). Trends in

  11. Trichoderma reesei xylanase 5 is defective in the reference strain QM6a but functional alleles are present in other wild-type strains.

    PubMed

    Ramoni, Jonas; Marchetti-Deschmann, Martina; Seidl-Seiboth, Verena; Seiboth, Bernhard

    2017-02-22

    Trichoderma reesei is a paradigm for the regulation and industrial production of plant cell wall-degrading enzymes. Among these, five xylanases, including the glycoside hydrolase (GH) family 11 XYN1 and XYN2, the GH10 XYN3, and the GH30 XYN4 and XYN6, were described. By genome mining and transcriptome analysis, a further putative xylanase, encoded by xyn5, was identified. Analysis of xyn5 from the genome-sequenced reference strain T. reesei QM6a shows that it encodes a non-functional, truncated form of XYN5. However, non-truncated orthologues are present in other genome sequenced Trichoderma spp., and sequencing of xyn5 in other T. reesei wild-type isolates shows that they harbor a putative functional xyn5 allele. In silico analysis and 3D modeling revealed that the encoded XYN5 has significant structural similarities to xylanases of the GH11 family, including a GH-typical substrate binding groove and a carboxylate pair in the active site. The xyn5 of wild-type strain TUCIM1282 was recombinantly expressed in a T. reesei strain with a (hemi)cellulase-free background and the corresponding protein purified to apparent homogeneity. The pH and temperature optima and the kinetic parameters of the purified XYN5 were pH 4, 50 °C, and V max = 2646 nkat/mg with a K m of 9.68 mg/ml. This functional xyn5 allele was used to replace the mutated version which led to an overall increase of the xylanolytic activity. These findings are of particular importance as GH11 xylanases are of high biotechnological relevance, and T. reesei is one of the main industrial producers of such lignocellulose-degrading enzymes.

  12. Typing of Canine Parvovirus Strains Circulating in North-East China.

    PubMed

    Zhao, H; Wang, J; Jiang, Y; Cheng, Y; Lin, P; Zhu, H; Han, G; Yi, L; Zhang, S; Guo, L; Cheng, S

    2017-04-01

    Canine parvovirus (CPV) is highly contagious and is a major cause of haemorrhagic enteritis and myocarditis in dogs. We investigated the genetic variation of emerging CPV strains by sequencing 64 CPV VP2 genes from 216 clinical samples of dogs from Heilongjiang, Jilin, Liaoning, Shandong and Hebei in 2014. Genetic analysis revealed that CPV-2b was predominant in Hebei and CPV-2a was predominant in the other four provinces. In addition, a CPV-2c strain has emerged in Shandong province. All samples had a Ser-Ala substitution at residue 297 and an Ile-Arg substitution at residue 324. Interestingly, in five separate canine samples, we found a mutation of Gln370 to Arg, until now detected only in isolates from pandas. The phylogenetic analysis showed clear distinctions between epidemic isolates and vaccine strains and between Chinese CPV-2c strains and CPV-2c strains found in other countries. Monitoring recent incidence of CPV strains enables evaluation and implementation of disease control strategies.

  13. Molecular typing of PPRV strains detected during an outbreak in sheep and goats in south-eastern Gabon in 2011

    PubMed Central

    2013-01-01

    Background Peste des petits ruminanats (PPR) is an economically important viral disease affecting goats and sheep. Four genetically distinct lineages of peste des petits ruminants virus (PPRV) have been identified. In Gabon, the virus has not so far been detected. Findings Epidemiological investigations of Aboumi PPR outbreak revealed a high case fatality rate in sheep (98.9%). We detected and characterized peste des petits ruminants virus (PPRV), in October 2011, during the suspected outbreak in sheep and goats in Aboumi village located in the south-eastern. PPRV RNA was detected in 10 of 14 samples from three sick animals. Phylogenetic analysis revealed that the PPRV strain belonged to lineage IV and was closely related to strain circulating in neighboring Cameroon. Conclusions This is the first molecular detection and typing of the PPRV strain associated with fatal PPR infection in these small ruminants and concrete evidence that PPRV is present and circulating in Gabon. PMID:23497402

  14. High-quality draft genome sequence of the Thermus amyloliquefaciens type strain YIM 77409(T) with an incomplete denitrification pathway.

    PubMed

    Zhou, En-Min; Murugapiran, Senthil K; Mefferd, Chrisabelle C; Liu, Lan; Xian, Wen-Dong; Yin, Yi-Rui; Ming, Hong; Yu, Tian-Tian; Huntemann, Marcel; Clum, Alicia; Pillay, Manoj; Palaniappan, Krishnaveni; Varghese, Neha; Mikhailova, Natalia; Stamatis, Dimitrios; Reddy, T B K; Ngan, Chew Yee; Daum, Chris; Shapiro, Nicole; Markowitz, Victor; Ivanova, Natalia; Spunde, Alexander; Kyrpides, Nikos; Woyke, Tanja; Li, Wen-Jun; Hedlund, Brian P

    2016-01-01

    Thermus amyloliquefaciens type strain YIM 77409(T) is a thermophilic, Gram-negative, non-motile and rod-shaped bacterium isolated from Niujie Hot Spring in Eryuan County, Yunnan Province, southwest China. In the present study we describe the features of strain YIM 77409(T) together with its genome sequence and annotation. The genome is 2,160,855 bp long and consists of 6 scaffolds with 67.4 % average GC content. A total of 2,313 genes were predicted, comprising 2,257 protein-coding and 56 RNA genes. The genome is predicted to encode a complete glycolysis, pentose phosphate pathway, and tricarboxylic acid cycle. Additionally, a large number of transporters and enzymes for heterotrophy highlight the broad heterotrophic lifestyle of this organism. A denitrification gene cluster included genes predicted to encode enzymes for the sequential reduction of nitrate to nitrous oxide, consistent with the incomplete denitrification phenotype of this strain.

  15. High quality draft genome sequence of Corynebacterium ulceribovis type strain IMMIB-L1395(T) (DSM 45146(T)).

    PubMed

    Yassin, Atteyet F; Lapidus, Alla; Han, James; Reddy, T B K; Huntemann, Marcel; Pati, Amrita; Ivanova, Natalia; Markowitz, Victor; Woyke, Tanja; Klenk, Hans-Peter; Kyrpides, Nikos C

    2015-01-01

    Corynebacterium ulceribovis strain IMMIB L-1395(T) (= DSM 45146(T)) is an aerobic to facultative anaerobic, Gram-positive, non-spore-forming, non-motile rod-shaped bacterium that was isolated from the skin of the udder of a cow, in Schleswig Holstein, Germany. The cell wall of C. ulceribovis contains corynemycolic acids. The cellular fatty acids are those described for the genus Corynebacterium, but tuberculostearic acid is not present. Here we describe the features of C. ulceribovis strain IMMIB L-1395(T), together with genome sequence information and its annotation. The 2,300,451 bp long genome containing 2,104 protein-coding genes and 54 RNA-encoding genes and is part of the Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes (KMG) project.

  16. Genome sequence of the flexirubin-pigmented soil bacterium Niabella soli type strain (JS13-8T)

    SciTech Connect

    Anderson, Iain; Munk, Christine; Lapidus, Alla L.; Nolan, Matt; Lucas, Susan; Tice, Hope; Glavina Del Rio, Tijana; Cheng, Jan-Fang; Han, Cliff; Tapia, Roxanne; Goodwin, Lynne A.; Pitluck, Sam; Liolios, Konstantinos; Mavromatis, K; Pagani, Ioanna; Mikhailova, Natalia; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam L; Rohde, Manfred; Tindall, Brian; Goker, Markus; Detter, J. Chris; Woyke, Tanja; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter; Ivanova, N

    2012-01-01

    Niabella soli Weon et al. 2008 is a member of the Chitinophagaceae, a family within the class Sphingobacteriia that is poorly characterized at the genome level, thus far. N. soli strain JS13-8T is of interest for its ability to produce a variety of glycosyl hydrolases. The ge- nome of N. soli strain JS13-8T is only the second genome sequence of a type strain from the family Chitinophagaceae to be published, and the first one from the genus Niabella. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 4,697,343 bp long chromosome with its 3,931 protein-coding and 49 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  17. High quality draft genome sequence of Corynebacterium ulceribovis type strain IMMIB-L1395T (DSM 45146T)

    SciTech Connect

    Yassin, Atteyet F.; Lapidus, Alla; Han, James; Reddy, T. B. K.; Huntemann, Marcel; Pati, Amrita; Ivanova, Natalia; Markowitz, Victor; Woyke, Tanja; Klenk, Hans-Peter; Kyrpides, Nikos C.

    2015-08-05

    We report that the Corynebacterium ulceribovis strain IMMIB L-1395T (= DSM 45146T) is an aerobic to facultative anaerobic, Gram-positive, non-spore-forming, non-motile rod-shaped bacterium that was isolated from the skin of the udder of a cow, in Schleswig Holstein, Germany. The cell wall of C. ulceribovis contains corynemycolic acids. The cellular fatty acids are those described for the genus Corynebacterium, but tuberculostearic acid is not present. Here we describe the features of C. ulceribovis strain IMMIB L-1395T, together with genome sequence information and its annotation. The 2,300,451 bp long genome containing 2,104 protein-coding genes and 54 RNA-encoding genes and is part of the Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes (KMG) project.

  18. High quality draft genome sequence of Corynebacterium ulceribovis type strain IMMIB-L1395T (DSM 45146T)

    DOE PAGES

    Yassin, Atteyet F.; Lapidus, Alla; Han, James; ...

    2015-08-05

    We report that the Corynebacterium ulceribovis strain IMMIB L-1395T (= DSM 45146T) is an aerobic to facultative anaerobic, Gram-positive, non-spore-forming, non-motile rod-shaped bacterium that was isolated from the skin of the udder of a cow, in Schleswig Holstein, Germany. The cell wall of C. ulceribovis contains corynemycolic acids. The cellular fatty acids are those described for the genus Corynebacterium, but tuberculostearic acid is not present. Here we describe the features of C. ulceribovis strain IMMIB L-1395T, together with genome sequence information and its annotation. The 2,300,451 bp long genome containing 2,104 protein-coding genes and 54 RNA-encoding genes and is partmore » of the Genomic Encyclopedia of Type Strains, Phase I: the one thousand microbial genomes (KMG) project.« less

  19. Transcriptomic analysis of Clostridium thermocellum Populus hydrolysate-tolerant mutant strain shows increased cellular efficiency in response to Populus hydrolysate compared to the wild type strain

    PubMed Central

    2014-01-01

    Background The thermophilic, anaerobic bacterium, Clostridium thermocellum is a model organism for consolidated processing due to its efficient fermentation of cellulose. Constituents of dilute acid pretreatment hydrolysate are known to inhibit C. thermocellum and other microorganisms. To evaluate the biological impact of this type of hydrolysate, a transcriptomic analysis of growth in hydrolysate-containing medium was conducted on 17.5% v/v Populus hydrolysate-tolerant mutant (PM) and wild type (WT) strains of C. thermocellum. Results In two levels of Populus hydrolysate medium (0% and 10% v/v), the PM showed both gene specific increases and decreases of gene expression compared to the wild-type strain. The PM had increased expression of genes in energy production and conversion, and amino acid transport and metabolism in both standard and 10% v/v Populus hydrolysate media. In particular, expression of the histidine metabolism increased up to 100 fold. In contrast, the PM decreased gene expression in cell division and sporulation (standard medium only), cell defense mechanisms, cell envelope, cell motility, and cellulosome in both media. The PM downregulated inorganic ion transport and metabolism in standard medium but upregulated it in the hydrolysate media when compared to the WT. The WT differentially expressed 1072 genes in response to the hydrolysate medium which included increased transcription of cell defense mechanisms, cell motility, and cellulosome, and decreased expression in cell envelope, amino acid transport and metabolism, inorganic ion transport and metabolism, and lipid metabolism, while the PM only differentially expressed 92 genes. The PM tolerates up to 17.5% v/v Populus hydrolysate and growth in it elicited 489 genes with differential expression, which included increased expression in energy production and conversion, cellulosome production, and inorganic ion transport and metabolism and decreased expression in transcription and cell

  20. First worldwide proficiency study on variable-number tandem-repeat typing of Mycobacterium tuberculosis complex strains.

    PubMed

    de Beer, Jessica L; Kremer, Kristin; Ködmön, Csaba; Supply, Philip; van Soolingen, Dick

    2012-03-01

    Although variable-number tandem-repeat (VNTR) typing has gained recognition as the new standard for the DNA fingerprinting of Mycobacterium tuberculosis complex (MTBC) isolates, external quality control programs have not yet been developed. Therefore, we organized the first multicenter proficiency study on 24-locus VNTR typing. Sets of 30 DNAs of MTBC strains, including 10 duplicate DNA samples, were distributed among 37 participating laboratories in 30 different countries worldwide. Twenty-four laboratories used an in-house-adapted method with fragment sizing by gel electrophoresis or an automated DNA analyzer, nine laboratories used a commercially available kit, and four laboratories used other methods. The intra- and interlaboratory reproducibilities of VNTR typing varied from 0% to 100%, with averages of 72% and 60%, respectively. Twenty of the 37 laboratories failed to amplify particular VNTR loci; if these missing results were ignored, the number of laboratories with 100% interlaboratory reproducibility increased from 1 to 5. The average interlaboratory reproducibility of VNTR typing using a commercial kit was better (88%) than that of in-house-adapted methods using a DNA analyzer (70%) or gel electrophoresis (50%). Eleven laboratories using in-house-adapted manual typing or automated typing scored inter- and intralaboratory reproducibilities of 80% or higher, which suggests that these approaches can be used in a reliable way. In conclusion, this first multicenter study has documented the worldwide quality of VNTR typing of MTBC strains and highlights the importance of international quality control to improve genotyping in the future.

  1. Ocular avirulence of a herpes simplex virus type 1 strain is associated with heightened sensitivity to alpha/beta interferon.

    PubMed Central

    Su, Y H; Oakes, J E; Lausch, R N

    1990-01-01

    BALB/c mice infected on the scarified cornea with herpes simplex virus type 1 strain 35 [HSV-1(35)] rarely developed ocular disease even at challenge doses as high as 10(7) PFU per eye. In contrast, HSV-1(RE) consistently induced stromal keratitis at an inoculum of 2 x 10(4) PFU. The goal of this study was to determine the reason for the difference in virulence between the two HSV strains. Both HSV-1 strains replicated to similar titers in excised corneal "buttons." However, after in vivo infection of the cornea, the growth of strain 35 was evident only during the first 24 h postinfection, whereas the replication of strain RE persisted for at least 4 days. In vitro tests revealed that HSV-1(35) was greater than 10 times more sensitive to alpha/beta interferon (IFN-alpha/beta) than HSV-1(RE). Both strains induced comparable serum levels of IFN after intraperitoneal inoculation. The kinetics of HSV-1(35) clearance from the eye was markedly altered by treatment with rabbit anti-IFN-alpha/beta. Virus titers exceeding 10(4) PFU per eye could be demonstrated 4 to 5 days postinfection in mice given a single inoculation of antiserum 1 h after infection. Furthermore, anti-IFN treatment in 3-week-old mice infected with HSV-1(35) led to the development of clinically apparent corneal disease which subsequently progressed to stromal keratitis in the majority of recipients. These results indicate that the striking difference in the capacity of HSV-1(35) and HSV-1(RE) to induce corneal disease was related to the inherently greater sensitivity of strain 35 to IFN-alpha/beta produced by the host in response to infection. PMID:2157880

  2. PFGE standard operating procedures for Listeria monocytogenes: harmonizing the typing of food and clinical strains in Europe.

    PubMed

    Michelon, Damien; Félix, Benjamin; Vingadassalon, Noemie; Mariet, Jean-François; Larsson, Jonas T; Møller-Nielsen, Eva; Roussel, Sophie

    2015-03-01

    Listeria monocytogenes is a foodborne pathogen responsible for a severe disease known as listeriosis. The European Centre for Disease Prevention and Control (ECDC) coordinates a network of national public health laboratories (NPHLs) in charge of typing clinical strains. In food, it is the European Union Reference Laboratory for L. monocytogenes (EURL Lm), which manages a network of National Reference Laboratories (NRLs). A pulsed-field gel electrophoresis (PFGE) standard operating procedure (EURL SOP) has been used routinely at the EURL Lm since 2007. The EURL Lm has recommended that NRLs use the EURL SOP, whereas the Statens Serum Institut (SSI), under contract for ECDC, requested that NPHLs use Halpins' SOP (HSOP) published in 2010 for the PulseNet USA network. An update of Halpins' SOP (uHSOP) was published in 2013. To facilitate the exchange of profiles among human and food European reference laboratories, it is crucial to ensure that the PFGE profiles obtained with these different SOPs are comparable. The aim here was to compare the EURL SOP with HSOP and uHSOP. The panel comprised 114 well-characterized SSI/EURL strains. All were characterized at the EURL using both the EURL SOP and uHSOP. Seventy of the 114 strains were also characterized at the SSI using HSOP. The EURL SOP and uHSOP produced indistinguishable combined (ApaI/AscI) profiles for the 114 strains tested. The EURL SOP and HSOP produced indistinguishable combined profiles for 69 of the 70 strains tested. One strain displayed for the AscI profile an additional low-intensity band at 184 kbp with HSOP. For this strain, SSI and EUR Lm had already observed the same profile from NPHLs and NRLs. However, this deviation is minor as it accounted for about 1% of all the 114 combined profiles. This study should facilitate the exchange of reproducible PFGE profiles among human and food reference laboratories.

  3. Multilocus sequence typing of bifidobacterial strains from infant's faeces and human milk: are bifidobacteria being sustainably shared during breastfeeding?

    PubMed

    Makino, H; Martin, R; Ishikawa, E; Gawad, A; Kubota, H; Sakai, T; Oishi, K; Tanaka, R; Ben-Amor, K; Knol, J; Kushiro, A

    2015-01-01

    Bifidobacteria are considered to be one of the most important beneficial intestinal bacteria for infants, contributing to the priming of the mucosal immune system. These microbes can also be detected in mother's milk, suggesting a potential role of human milk in the colonisation of infant's gut. However, little is known about the timing of bacteria appearance in human milk, and whether human milk is the first source of inoculation. Here, we investigated whether specific strains are shared sustainably between maternal milk and infant's gut. Faecal samples and human milk were collected from 102 healthy mother-infant pairs (infant's faeces: meconium, 7, 30 days of age; mother's milk: once before delivery, colostrum, 7, 30 days after delivery). Bifidobacterial strains were isolated from these samples, and were discriminated by means of multilocus sequencing typing. No bifidobacteria were detected from human milk collected before delivery, or colostrum. Strains were isolated only from human milk samples obtained 7 days after birth or later. On the other hand, bifidobacterial strains were obtained from infant's faeces throughout the study period, sometimes as early as the first day of life (meconium). We have found that bifidobacterial species belonging to Bifidobacterium bifidum, Bifidobacterium breve, and Bifidobacterium longum subsp. longum could be identified as monophyletic between infant's faeces and their mother's milk. These strains were confirmed to be sustainably shared between maternal milk and infant's gut. Moreover, monophyletic strains were isolated at the same time point or earlier from infant's faeces than from human milk, and none were isolated earlier from human milk than from infant's faeces. Although it remains unclear whether human milk is the first source of microbes for infants, our results confirm that human milk is a reservoir of bifidobacteria, and specific strains are shared between infant's intestine and human milk during breastfeeding.

  4. Virological and molecular characterization of a mammalian orthoreovirus type 3 strain isolated from a dog in Italy.

    PubMed

    Decaro, Nicola; Campolo, Marco; Desario, Costantina; Ricci, Dominga; Camero, Michele; Lorusso, Eleonora; Elia, Gabriella; Lavazza, Antonio; Martella, Vito; Buonavoglia, Canio

    2005-08-10

    A mammalian orthoreovirus (MRV) strain was isolated from a pup with fatal diarrhea, which had a concurrent infection by canine parvovirus type 2. The reovirus isolate showed an atypical hemagglutination pattern and a retarded electrophoretic mobility of the S1 segment, which is characteristic of MRV type 3 (MRV-3). Assignment of the isolated virus to MRV-3 was confirmed by type-specific RT-PCR assays, targeting the S1 gene, and by subsequent sequence analysis of the PCR product. By phylogeny based on the S1 gene of several MRVs, the isolate fell into lineage E, along with the murine strain T3C9/61 and the bovine strains T3C18/61 and T3C31/59. Conversely, L1 sequences were found to segregate regardless of the viral type. A total of 110 fecal samples, 56 nasal and 31 ocular swabs from dogs with diarrhea or nasal/ocular discharge were tested by a nested-PCR assay specific for reoviruses, and no sample was found to contain MRV RNA, a finding that is apparently in contrast with the seroprevalence (25.77%) observed in dogs.

  5. Effects of tensile and compressive strains on response of a chondrocytic cell line embedded in type I collagen gel.

    PubMed

    Hirano, Yuji; Ishiguro, Naoki; Sokabe, Masahiro; Takigawa, Masaharu; Naruse, Keiji

    2008-01-20

    Tensile and compressive strains are commonly used in mechanobiological models. Here we report on the development of a novel three-dimensional cell-culture method, which allows both tensile and compressive loads to be applied. Preliminary results were obtained using HCS2/8 chondrocytic cells embedded in type I collagen gel. This construct was subjected to either 16% tension or 14% compression. Confocal laser scanning microscopy showed that both tension and compression caused significant cell deformation. The collagen gel-embedded HCS2/8 cells were subjected to static tension, dynamic tension, static compression or dynamic compression for 24h. Dynamic compression led to significantly decreased 5-bromo-2'-deoxyuridine incorporation compared with the control group. PCR analysis revealed upregulation of type II collagen caused by dynamic tension, upregulation of aggrecan caused by static compression, and downregulation of type II collagen and aggrecan caused by dynamic compression. Nitric oxide production was significantly increased by static tension and static compression compared with the control group. Our experimental system effectively applied several types of strain to HCS2/8 cells embedded in collagen gel. Our results suggest that the mode of mechanical strain affects the response of HCS2/8 cells.

  6. Whole-Genome Sequences of Xanthomonas euvesicatoria Strains Clarify Taxonomy and Reveal a Stepwise Erosion of Type 3 Effectors

    PubMed Central

    Barak, Jeri D.; Vancheva, Taca; Lefeuvre, Pierre; Jones, Jeffrey B.; Timilsina, Sujan; Minsavage, Gerald V.; Vallad, Gary E.; Koebnik, Ralf

    2016-01-01

    Multiple species of Xanthomonas cause bacterial spot of tomato (BST) and pepper. We sequenced five Xanthomonas euvesicatoria strains isolated from three continents (Africa, Asia, and South America) to provide a set of representative genomes with temporal and geographic diversity. LMG strains 667, 905, 909, and 933 were pathogenic on tomato and pepper, except LMG 918 elicited a hypersensitive reaction (HR) on tomato. Furthermore, LMG 667, 909, and 918 elicited a HR on Early Cal Wonder 30R containing Bs3. We examined pectolytic activity and starch hydrolysis, two tests which are useful in differentiating X. euvesicatoria from X. perforans, both causal agents of BST. LMG strains 905, 909, 918, and 933 were nonpectolytic while only LMG 918 was amylolytic. These results suggest that LMG 918 is atypical of X. euvesicatoria. Sequence analysis of all the publicly available X. euvesicatoria and X. perforans strains comparing seven housekeeping genes identified seven haplotypes with few polymorphisms. Whole genome comparison by average nucleotide identity (ANI) resulted in values of >99% among the LMG strains 667, 905, 909, 918, and 933 and X. euvesicatoria strains and >99.6% among the LMG strains and a subset of X. perforans strains. These results suggest that X. euvesicatoria and X. perforans should be considered a single species. ANI values between strains of X. euvesicatoria, X. perforans, X. allii, X. alfalfa subsp. citrumelonis, X. dieffenbachiae, and a recently described pathogen of rose were >97.8% suggesting these pathogens should be a single species and recognized as X. euvesicatoria. Analysis of the newly sequenced X. euvesicatoria strains revealed interesting findings among the type 3 (T3) effectors, relatively ancient stepwise erosion of some T3 effectors, additional X. euvesicatoria-specific T3 effectors among the causal agents of BST, orthologs of avrBs3 and avrBs4, and T3 effectors shared among xanthomonads pathogenic against various hosts. The results from

  7. Biogenic amine production by Lactococcus lactis subsp. cremoris strains in the model system of Dutch-type cheese.

    PubMed

    Flasarová, Radka; Pachlová, Vendula; Buňková, Leona; Menšíková, Anna; Georgová, Nikola; Dráb, Vladimír; Buňka, František

    2016-03-01

    The aim of this study was to compare the biogenic amine production of two starter strains of Lactococcus lactis subsp. cremoris (strains from the Culture Collection of Dairy Microorganisms - CCDM 824 and CCDM 946) with decarboxylase positive activity in a model system of Dutch-type cheese during a 90-day ripening period at 10°C. During ripening, biogenic amine and free amino acid content, microbiological characteristics and proximate chemical properties were observed. By the end of the ripening period, the putrescine content in both samples with the addition of the biogenic amine producing strain almost evened out and the concentration of putrescine was >800mg/kg. The amount of tyramine in the cheeses with the addition of the strain of CCDM 824 approached the limit of 400mg/kg by the end of ripening. In the cheeses with the addition of the strain of CCDM 946 it even exceeded 500mg/kg. In the control samples, the amount of biogenic amines was insignificant.

  8. Co-existence of multiple strains of porcine circovirus type 2 in the same pig from China.

    PubMed

    Zhai, Shao-Lun; Chen, Sheng-Nan; Wei, Zu-Zhang; Zhang, Jian-Wu; Huang, Lv; Lin, Tao; Yue, Cheng; Ran, Duo-Liang; Yuan, Shi-Shan; Wei, Wen-Kang; Long, Jin-Xue

    2011-11-13

    Pigs are often co-infected by different viral strains from the same virus. Up to now, there are few reports about co-existence of different porcine circovirus type 2 (PCV2) strains in China. The aim of this study was to evaluate it in Chinese swine herds. 118 PCV2 positive DNAs isolated from diseased pigs identified by classic PCR were re-detected using a modified differential PCR assay. The results indicated that co-existence rates of PCV2 were 32.2% (38/118) in diseased pigs and 0% (0/41) in asymptomatic pigs. Four PCV2 complete genomes were cloned from two co-infected samples and their nucleotide (nt) identities were 95%-97.3%. The phylogenetic analysis showed that four PCV2 strains were divided into different genotypes, PCV2a, PCV2b, PCV2d and PCV2e, respectively. In addition, co-existence were not detected in 41 serum samples from healthy pigs but PCV2 single infection (31.7%, 13/41) existed. These data revealed that the co-existence of different strains of PCV2 might contribute to the development of more severe clinical symptoms for pigs. This is the first report confirming the co-existence of different PCV2 strains in Chinese swine herds. Meanwhile, this study could help us to understand new infection and prevalence forms of PCV2 clinically.

  9. Comparative analyses of the 9 glycoprotein genes found in wild-type and vaccine strains of varicella-zoster virus.

    PubMed

    Storlie, Johnathan; Maresova, Lucie; Jackson, Wallen; Grose, Charles

    2008-03-01

    The complete DNA sequences of wild-type and vaccine strains of varicella-zoster virus have been published and listed in GenBank. In this comparative genomic analysis, the sequences of the 9 glycoprotein open reading frames (ORFs) were compared. They included gE (ORF68), gI (ORF 67), gC (ORF14), gH (ORF37), gL (ORF60), gB (ORF31), gK (ORF5), gM (ORF50), and gN (ORF8 or ORF9A). After realignment on the basis of newer data, the corrected gB sequence was lengthened to include 931 residues. The data showed that there were glycoprotein polymorphisms that differentiated North American/European strains from Japanese strains-for example, an additional ATG codon in the gL of all Oka strains. Also, there were a small number of coding single-nucleotide polymorphisms present only in glycoproteins of vaccine strains. Because these changes were highly conserved, the structure of the glycoprotein was unlikely to be altered.

  10. Soil type affects plant colonization, activity and catabolic gene expression of inoculated bacterial strains during phytoremediation of diesel.

    PubMed

    Afzal, Muhammad; Yousaf, Sohail; Reichenauer, Thomas G; Kuffner, Melanie; Sessitsch, Angela

    2011-02-28

    The combined use of plants and associated microorganisms has great potential for cleaning up soils contaminated with petroleum hydrocarbons. Apart from environmental conditions the physicochemical properties of the soil are the main factors influencing the survival and activity of an inoculated strain as well as the growth of plants. This study examined the effect of different soil types (sandy, loamy sand and loam) on the survival, gene abundance and catabolic gene expression of two inoculated strains (Pseudomonas sp. strain ITRI53 and Pantoea sp. strain BTRH79) in the rhizosphere and shoot interior of Italian ryegrass vegetated in diesel contaminated soils. High colonization, gene abundance and expression in loamy soils were observed. By contrast, low colonization, gene abundance and absence of gene expression in sandy soil were found. The highest levels of genes expression and hydrocarbon degradation were seen in loamy soil that had been inoculated with BTRH79 and were significantly higher compared to those in other soils. A positive correlation was observed between gene expression and hydrocarbon degradation indicating that catabolic gene expression is necessary for contaminant degradation. These results suggest that soil type influences the bacterial colonization and microbial activities and subsequently the efficiency of contaminant degradation.

  11. Investigation of the types and characteristics of the proteolytic enzymes formed by diverse strains of Proteus species.

    PubMed

    Senior, B W

    1999-07-01

    Many diverse clinical isolates of Proteus mirabilis (48 strains), P. penneri (25), P. vulgaris biogroup 2 (48) and P. vulgaris biogroup 3 (21) from man were examined for their ability to produce proteolytic enzymes and the nature and characteristics of the proteases were studied. All the P. penneri isolates, most (94-90%) of the P. mirabilis and P. vulgaris biogroup 2 isolates, but only 71% of the P. vulgaris biogroup 3 isolates, secreted proteolytic enzymes. These were detected most readily at pH 8 with gelatin as substrate. A strong correlation was found between the ability of a strain to form swarming growth and its ability to secrete proteases. Non-swarming isolates invariably appeared to be non-proteolytic. However, some isolates, particularly of P. vulgaris biogroup 3, were non-proteolytic even when they formed swarming growth. Analysis of the secreted enzymes of the different Proteus spp. on polyacrylamide-gelatin gels under various constraints of pH and other factors showed that they were all EDTA-sensitive metalloproteinases. Analysis of the kinetics of production of the proteases revealed the formation of an additional protease of undefined type and function that was cell-associated and formed before the others were secreted. The secreted protease was subsequently modified to two isoforms whose mass (53-46 kDa) varied with the Proteus spp. and the strain. There was no evidence that the secreted proteases of strains of Proteus spp. were of types other than metalloproteinases.

  12. Comparative neuropathology of ovine enterotoxemia produced by Clostridium perfringens type D wild-type strain CN1020 and its genetically modified derivatives.

    PubMed

    Garcia, J P; Giannitti, F; Finnie, J W; Manavis, J; Beingesser, J; Adams, V; Rood, J I; Uzal, F A

    2015-05-01

    Clostridium perfringens type D causes enterotoxemia in sheep and goats. The disease is mediated by epsilon toxin (ETX), which affects the cerebrovascular endothelium, increasing vascular permeability and leading to cerebral edema. In the present study, we compared the distribution and severity of the cerebrovascular changes induced in lambs by C. perfringens type D strain CN1020, its isogenic etx null mutant, and the ETX-producing complemented mutant. We also applied histochemical and immunohistochemical markers to further characterize the brain lesions induced by ETX. Both ETX-producing strains induced extensive cerebrovascular damage that did not differ significantly between each other in nature, neuroanatomic distribution, or severity. By contrast, lambs inoculated with the etx mutant or sterile, nontoxic culture medium did not develop detectable brain lesions, confirming that the neuropathologic effects observed in these infections are dependent on ETX production. Lambs treated with the wild-type and complemented strains showed perivascular and mural vascular edema, as well as serum albumin extravasation, particularly severe in the cerebral white matter, midbrain, medulla oblongata, and cerebellum. Brains of animals inoculated with the ETX-producing strains showed decreased expression of glial fibrillary acidic protein and increased expression of aquaporin-4 in the end-feet processes of the astrocytes around blood vessels. Early axonal injury was demonstrated with anti-amyloid precursor protein immunohistochemistry. Perivascular accumulation of macrophages/microglia with intracytoplasmic albumin globules was also observed in these animals. This study demonstrates that ETX is responsible for the major cerebrovascular changes in C. perfringens type D-induced disease.

  13. Phylogeography and molecular epidemiology of an epidemic strain of dengue virus type 1 in Sri Lanka.

    PubMed

    Ocwieja, Karen E; Fernando, Anira N; Sherrill-Mix, Scott; Sundararaman, Sesh A; Tennekoon, Rashika N; Tippalagama, Rashmi; Krishnananthasivam, Shivankari; Premawansa, Gayani; Premawansa, Sunil; De Silva, Aruna Dharshan

    2014-08-01

    In 2009, a severe epidemic of dengue disease occurred in Sri Lanka, with higher mortality and morbidity than any previously recorded epidemic in the country. It corresponded to a shift to dengue virus 1 as the major disease-causing serotype in Sri Lanka. Dengue disease reached epidemic levels in the next 3 years. We report phylogenetic evidence that the 2009 epidemic DENV-1 strain continued to circulate within the population and caused severe disease in the epidemic of 2012. Bayesian phylogeographic analyses suggest that the 2009 Sri Lankan epidemic DENV-1 strain may have traveled directly or indirectly from Thailand through China to Sri Lanka, and after spreading within the Sri Lankan population, it traveled to Pakistan and Singapore. Our findings delineate the dissemination route of a virulent DENV-1 strain in Asia. Understanding such routes will be of particular importance to global control efforts.

  14. Probe-based real-time PCR method for multilocus melt typing of Xylella fastidiosa strains.

    PubMed

    Brady, Jeff A; Faske, Jennifer B; Ator, Rebecca A; Castañeda-Gill, Jessica M; Mitchell, Forrest L

    2012-04-01

    Epidemiological studies of Pierce's disease (PD) can be confounded by a lack of taxonomic detail on the bacterial causative agent, Xylella fastidiosa (Xf). PD in grape is caused by strains of Xylella fastidiosa subsp. fastidiosa, but is not caused by other subspecies of Xf that typically colonize plants other than grape. Detection assays using ELISA and qPCR are effective at detecting and quantifying Xf presence or absence, but offer no information on Xf subspecies or strain identity. Surveying insects or host plants for Xf by current ELISA or qPCR methods provides only presence/absence and quantity information for any and all Xf subspecies, potentially leading to false assessments of disease threat. This study uses a series of adjacent-hybridizing DNA melt analysis probes that are capable of efficiently discriminating Xf subspecies and strain relationships in rapid real-time PCR reactions.

  15. [Current knowledge on the strain typing of the pathogenic fungus Histoplasma capsulatum var. capsulatum: a review of the findings].

    PubMed

    Reyes-Montes, M del R; Taylor, M L; Curiel-Quesada, E; Mesa-Arango, A C

    2000-12-01

    The classification of microbial strains is currently based on different typing methods, which must meet certain criteria in order to be widely used. Phenotypic and genotypic methods are being employed in the epidemiology of several fungal diseases. However, some problems associated to the phenotypic methods have fostered genotyping procedures, from DNA polymorphic diversity to gene sequencing studies, all aiming to differentiate and to relate fungal isolates or strains. Through these studies, it is possible to identify outbreaks, to detect nosocomial infection transmission, and to determine the source of infection, as well as to recognize virulent isolates. This paper is aimed at analyzing the methods recently used to type Histoplasma capsulatum, causative agent of the systemic mycosis known as histoplasmosis, in order to recommend those that yield reproducible and accurate results.

  16. A new bacteriophage typing scheme for Proteus mirabilis and Proteus vulgaris strains. 3. Analysis of lytic properties.

    PubMed

    Sekaninová, G; Rychlík, I; Kolárová, M; Pillich, J; Seménka, J; Zajícová, V

    1998-01-01

    The lytic properties of 21 bacteriophages constituting a new typing set for Proteus were examined in 507 Proteus mirabilis and 29 P. vulgaris strains isolated from patients and healthy subjects. Comparison of their morphological, serological, genetic and lytic properties showed that, in the Myoviridae and Podoviridae families, some phages were so closely related that the presence of all of them in the set was redundant. Analysis of the lytic properties revealed that some of the bacteriophages were not active enough to facilitate the differentiation of Proteus strains. The size of the final typing set was reduced from 21 to 12 phages but it was suggested that, in order to improve the differentiation capacity of the set, new phages should be included.

  17. The Effect of Fabric Type of Common Iranian Working Clothes on the Induced Cardiac and Physiological Strain Under Heat Stress.

    PubMed

    Parvari, Roh Allah; Aghaei, Habib Allah; Dehghan, Habibollah; Khademi, Abolfazl; Maracy, Mohammad Reza; Dehghan, Somayeh Farhang

    2015-01-01

    The present study compared the effect of fabric type of working clothes on heat strain responses in different levels of physical workload and under different kinds of weather conditions. Four kinds of working clothing fabric that are greatly popular in Iranian industry were assessed on 18 healthy male at 2 environments: hot and humid (dry temperature [DBt]: 35°C and relative humidity [RH]: 70%) and hot and dry (DBt: 40°C and RH: 40%). The physiological responses such as heart rate and core body temperature were reported. It was found that there were no significant differences between different types of clothing fabric on cardiac and physiological parameters. It can be recommended that 100% cotton clothing ensemble during low-workload activities and 30.2% cotton-69.8% polyester clothing ensemble during moderate-workload activities is used for Iranian workers to maintain the cardiac and physiological strains as low as possible.

  18. Complete genome sequence of the bile-resistant pigment- producing anaerobe Alistipes finegoldii type strain (AHN2437T)

    SciTech Connect

    Mavromatis, K; Stackebrandt, Erko; Munk, Christine; Lapidus, Alla L.; Nolan, Matt; Lucas, Susan; Hammon, Nancy; Deshpande, Shweta; Cheng, Jan-Fang; Tapia, Roxanne; Goodwin, Lynne A.; Pitluck, Sam; Liolios, Konstantinos; Pagani, Ioanna; Ivanova, N; Mikhailova, Natalia; Huntemann, Marcel; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam L; Hauser, Loren John; Rohde, Manfred; Gronow, Sabine; Goker, Markus; Detter, J. Chris; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter; Woyke, Tanja

    2013-01-01

    Alistipes finegoldii Rautio et al. 2003 is one of five species of Alistipes with a validly pub- lished name: family Rikenellaceae, order Bacteroidetes, class Bacteroidia, phylum Bacteroidetes. This rod-shaped and strictly anaerobic organism has been isolated mostly from human tissues. Here we describe the features of the type strain of this species, together with the complete genome sequence, and annotation. A. finegoldii is the first member of the genus Alistipes for which the complete genome sequence of its type strain is now available. The 3,734,239 bp long single replicon genome with its 3,302 protein-coding and 68 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

  19. Complete genome sequence of the bile-resistant pigment-producing anaerobe Alistipes finegoldii type strain (AHN2437(T)).

    PubMed

    Mavromatis, Konstantinos; Stackebrandt, Erko; Munk, Christine; Lapidus, Alla; Nolan, Matt; Lucas, Susan; Hammon, Nancy; Deshpande, Shweta; Cheng, Jan-Fang; Tapia, Roxanne; Goodwin, Lynne A; Pitluck, Sam; Liolios, Konstantinos; Pagani, Ioanna; Ivanova, Natalia; Mikhailova, Natalia; Huntemann, Marcel; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Rohde, Manfred; Gronow, Sabine; Göker, Markus; Detter, John C; Bristow, James; Eisen, Jonathan A; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter; Woyke, Tanja

    2013-04-15

    Alistipes finegoldii Rautio et al. 2003 is one of five species of Alistipes with a validly published name: family Rikenellaceae, order Bacteroidetes, class Bacteroidia, phylum Bacteroidetes. This rod-shaped and strictly anaerobic organism has been isolated mostly from human tissues. Here we describe the features of the type strain of this species, together with the complete genome sequence, and annotation. A. finegoldii is the first member of the genus Alistipes for which the complete genome sequence of its type strain is now available. The 3,734,239 bp long single replicon genome with its 3,302 protein-coding and 68 RNA genes is part of the G enomic E ncyclopedia of Bacteria and Archaea project.

  20. Complete genome sequence of Mesorhizobium ciceri bv. biserrulae type strain (WSM1271T)

    SciTech Connect

    Nandesena, Kemanthi; Yates, Ron; Tiwari, Ravi; O'Hara, Graham; Howieson, John; Ninawi, Mohamed; Chertkov, Olga; Detter, J. Chris; Tapia, Roxanne; Han, Cliff; Woyke, Tanja; Pitluck, Sam; Nolan, Matt; Land, Miriam L; Liolios, Konstantinos; Pati, Amrita; Copeland, A; Kyrpides, Nikos C; Ivanova, N; Goodwin, Lynne A.; Meenakshi, Uma; Reeve, Wayne

    2013-01-01

    Mesorhizobium ciceri bv. biserrulae strain WSM1271T was isolated from root nodules of the pasture legume Biserrula pelecinus growing in the Mediterranean basin. Previous studies have shown this aerobic, motile, Gram negative, non-spore-forming rod preferably nodulates B. pelecinus a legume with many beneficial agronomic attributes for sustainable agriculture in Australia. We describe the genome of Mesorhizobium ciceri bv. biserrulae strain WSM1271T consisting of a 6,264,489 bp chro-mosome and a 425,539 bp plasmid that together encode 6,470 protein-coding genes and 61 RNA-only encoding genes.

  1. Type 2 NADH Dehydrogenases in the Cyanobacterium Synechocystis sp. Strain PCC 6803 Are Involved in Regulation Rather Than Respiration

    PubMed Central

    Howitt, Crispin A.; Udall, Pacer K.; Vermaas, Wim F. J.

    1999-01-01

    Analysis of the genome of Synechocystis sp. strain PCC 6803 reveals three open reading frames (slr0851, slr1743, and sll1484) that may code for type 2 NAD(P)H dehydrogenases (NDH-2). The sequence similarity between the translated open reading frames and NDH-2s from other organisms is low, generally not exceeding 30% identity. However, NAD(P)H and flavin adenine dinucleotide binding motifs are conserved in all three putative NDH-2s in Synechocystis sp. strain PCC 6803. The three open reading frames were cloned, and deletion constructs were made for each. An expression construct containing one of the three open reading frames, slr1743, was able to functionally complement an Escherichia coli mutant lacking both NDH-1s and NDH-2s. Therefore, slr0851, slr1743, and sll1484 have been designated ndbA, ndbB, and ndbC, respectively. Strains that lacked one or more of the ndb genes were created in wild-type and photosystem (PS) I-less backgrounds. Deletion of ndb genes led to small changes in photoautotrophic growth rates and respiratory activities. Electron transfer rates into the plastoquinone pool in thylakoids in darkness were consistent with the presence of a small amount of NDH-2 activity in thylakoids. No difference was observed between wild-type and the Ndb-less strains in the banding patterns seen on native gels when stained for either NADH or NADPH dehydrogenase activity, indicating that the Ndb proteins do not accumulate to high levels. A striking phenotype of the PS I-less background strains lacking one or more of the NDH-2s is that they were able to grow at high light intensities that were lethal to the control strain but they retained normal PS II activity. We suggest that the Ndb proteins in Synechocystis sp. strain PCC 6803 are redox sensors and that they play a regulatory role responding to the redox state of the plastoquinone pool. PMID:10383967

  2. Complete Genome Sequence of Mycoplasma pneumoniae Type 2 Reference Strain FH Using Single-Molecule Real-Time Sequencing Technology

    PubMed Central

    Desai, Heta P.; Morrison, Shatavia S.; Diaz, Maureen H.; Benitez, Alvaro J.

    2017-01-01

    ABSTRACT Mycoplasma pneumoniae type 2 strain FH was previously sequenced with Illumina (FH-Illumina) and 454 (FH-454) technologies according to Xiao et al. (2015) and Krishnakumar et al. (2010). Comparative analyses revealed differences in genomic content between these sequences, including a 6-kb region absent from the FH-454 submission. Here, we present a complete genome sequence of FH sequenced with the Pacific Biosciences RSII platform. PMID:28232437

  3. Cloning, expression, and sequence analysis of the Haemophilus influenzae type b strain M43p+ pilin gene.

    PubMed Central

    Gilsdorf, J R; Marrs, C F; McCrea, K W; Forney, L J

    1990-01-01

    By using antiserum against Haemophilus influenzae type b (Hib) strain M43p+ denatured pilin, we screened a genomic library of Hib strain M43p+ and identified a clone that expressed pilin, but not assembled pili, on its surface. Southern blot analysis revealed the presence of one structural gene, which was also present in strain M42p-, a nonpiliated variant. Five exonuclease III deletion mutants, two of which had deletions that extended into the structural gene and failed to express pilin, were used to obtain the nucleotide sequence of the structural gene. The amino acid sequence of the open reading frame agrees with 38 of 40 amino acids from the published sequence of purified Hib M43p+ pilin. The pilin gene coded for a mature protein of 193 amino acids, with a calculated molecular mass of 21,101 daltons. Comparison of the Hib M43p+ pilin amino acid sequence with those of pilins of other bacteria revealed strong conservation of amino- and carboxy-terminal regions in M43p+ and Escherichia coli F17, type 1C, and several members of the P pili family, as well as Klebsiella pneumoniae type 3 MR/K, Bordetella pertussis serotype 2, and Serratia marcescens US46 fimbriae. Images PMID:1969389

  4. Molecular phylogeny of a novel human adenovirus type 8 strain causing a prolonged, multi-state keratoconjunctivitis epidemic in Germany

    PubMed Central

    Hage, Elias; Espelage, Werner; Eckmanns, Tim; Lamson, Daryl M.; Pantó, Laura; Ganzenmueller, Tina; Heim, Albert

    2017-01-01

    The German infectious disease surveillance system revealed an increase of epidemic keratoconjunctivitis (EKC) from an average of 320 cases/year (2001 to 2010) up to 2146 and 1986 cases in 2012 and 2013, respectively. From November 2011 until December 2013 (epidemic period) 85% of typed isolates were human adenovirus type 8 (HAdV-D8), whereas only low level circulation (19%) of HAdV-D8 was observed outside the epidemic period. In order to investigate whether a novel monophyletic HAdV-D8 strain prevailed during the epidemic period, complete genomic sequences of 23 HAdV-D8 isolates were generated by deep sequencing and analyzed phylogenetically. For comparison, eight HAdV-D8 isolates from outside the epidemic period were sequenced. HAdV-D8 isolates of the epidemic period had a very high sequence identity of at least 99.9% and formed a monophyletic cluster with two subclusters. A single outlier was closely related to HAdV-D8 strains isolated prior to the epidemic period. Circulation of the epidemic strain was detected as early as 2010 but not after the epidemic period in 2014. In conclusion, molecular phylogeny of complete genomic sequences proved a monophyletic HAdV-D8 epidemic. However, co-circulation of other HAdV types as well as better reporting may have contributed to the huge increase of reported cases. PMID:28084428

  5. Inulin-type fructan fermentation by bifidobacteria depends on the strain rather than the species and region in the human intestine.

    PubMed

    Selak, Marija; Rivière, Audrey; Moens, Frédéric; Van den Abbeele, Pieter; Geirnaert, Annelies; Rogelj, Irena; Leroy, Frédéric; De Vuyst, Luc

    2016-05-01

    Inulin-type fructans (ITF) are known to cause a health-promoting bifidogenic effect, although the ITF degradation capacity of bifidobacteria in different intestinal regions remains unclear. The present study aims at offering new insights into this link, making use of a collection of 190 bifidobacterial strains, encompassing strains from gut biopsies (terminal ileum and proximal colon; mucosa-associated strains) and the simulator of the human intestinal microbial ecosystem (SHIME®; proximal and distal colon vessels; lumen-associated strains). A multivariate data analysis of all fermentation data revealed four clusters corresponding with different types of ITF degradation fingerprints, which were not correlated with the region in the intestine, suggesting that the degradation of ITF is uniform along the human intestine. Strains from cluster 1 consumed fructose, while strains from cluster 2 consumed more oligofructose than fructose. Higher fructose and oligofructose consumption was characteristic for clusters 3 and 4 strains, which degraded inulin too. In general, the mucosa-associated strains from biopsy origin seemed to be more specialized in the consumption of fructose and oligofructose, while the lumen-associated strains from SHIME origin displayed a higher degradation degree of inulin. Further, intra-species variability in ITF degradation was found, indicating strain-specific variations. The coexistence of different bifidobacterial strains with different ITF degradation fingerprints within the same intestinal region suggests cooperation for the degradation of ITF, with opportunities for cross-feeding on strain and/or species level.

  6. Rapid Focused Sequencing: A Multiplexed Assay for Simultaneous Detection and Strain Typing of Bacillus anthracis, Francisella tularensis, and Yersinia pestis

    PubMed Central

    Zolotova, Anna; Tan, Eugene; Selden, Richard F.

    2013-01-01

    Background The intentional release of Bacillus anthracis in the United States in 2001 has heightened concern about the use of pathogenic microorganisms in bioterrorism attacks. Many of the deadliest bacteria, including the Class A Select Agents Bacillus anthracis, Francisella tularensis, and Yersinia pestis, are highly infectious via the pulmonary route when released in aerosolized form. Hence, rapid, sensitive, and reliable methods for detection of these biothreats and characterization of their potential impact on the exposed population are of critical importance to initiate and support rapid military, public health, and clinical responses. Methodology/Principal Findings We have developed microfluidic multiplexed PCR and sequencing assays based on the simultaneous interrogation of three pathogens per assay and ten loci per pathogen. Microfluidic separation of amplified fluorescently labeled fragments generated characteristic electrophoretic signatures for identification of each agent. The three sets of primers allowed significant strain typing and discrimination from non-pathogenic closely-related species and environmental background strains based on amplicon sizes alone. Furthermore, sequencing of the 10 amplicons per pathogen, termed “Rapid Focused Sequencing,” allowed an even greater degree of strain discrimination and, in some cases, can be used to determine virulence. Both amplification and sequencing assays were performed in microfluidic biochips developed for fast thermal cycling and requiring 7 µL per reaction. The 30-plex sequencing assay resulted in genotypic resolution of 84 representative strains belonging to each of the three biothreat species. Conclusions/Significance The microfluidic multiplexed assays allowed identification and strain differentiation of the biothreat agents Bacillus anthracis, Francisella tularensis, and Yersinia pestis and clear discrimination from closely-related species and several environmental background strains. The

  7. Mechanical properties of elytra from Tribolium castaneum wild-type and body color mutant strains

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Cuticle tanning in insects involves simultaneous cuticular hardening and pigmentation. The dynamic mechanical properties of the highly modified and cuticle-rich forewings (elytra) from Tribolium castaneum (red flour beetle) body color mutant strains were investigated to determine the relationship b...

  8. Genetic and phenotypic characterization of sylvatic dengue virus type 2 strains

    PubMed Central

    Vasilakis, Nikos; Fokam, Eric B.; Hanson, Christopher T.; Weinberg, Ethan; Sall, Amadou A.; Whitehead, Stephen S.; Hanley, Kathryn A.; Weaver, Scott C.

    2009-01-01

    The four serotypes of endemic dengue viruses (DENV) circulate between humans and peridomestic Aedes mosquitoes. At present endemic DENV infect 100 million people per year, and a third of the global population is at risk. In contrast, sylvatic DENV strains are maintained in a transmission cycle between nonhuman primates and sylvatic Aedes species, and are evolutionarily and ecologically distinct from endemic DENV strains. Phylogenetic analyses place sylvatic strains basal to each of the endemic serotypes, supporting the hypothesis that each of the endemic DENV serotypes emerged independently from sylvatic ancestors. We utilized complete genome analyses of both sylvatic and endemic DENV serotype 2 (DENV-2) to expand our understanding of their genetic relationships. A high degree of conservation was observed in both the 5′- and 3′-untranslated genome regions, whereas considerable differences at the nucleotide and amino acid levels were observed within the open reading frame. Additionally, replication of the two genotypes was compared in cultured cells, where endemic DENV strains produced a significantly higher output of progeny in human liver cells, but not in monkey kidney or mosquito cells. Understanding the genetic relationships and phenotypic differences between endemic and sylvatic DENV genotypes may provide valuable insight into DENV emergence and guide monitoring of future outbreaks. PMID:18570968

  9. Genetic and Phenotypic Characterization of Sylvatic Dengue Virus Type 4 Strains

    PubMed Central

    Rossi, S.L.; Nasar, F.; Cardosa, J.; Mayer, S.V.; Tesh, R.B; Hanley, K.A.; Weaver, S.C.; Vasilakis, Nikos

    2011-01-01

    Four serotypes of dengue virus (DENV 1-4) currently circulate between humans and domestic/peridomestic Aedes mosquitoes, resulting in 100 million infections per year. All four serotypes emerged, independently, from sylvatic progenitors transmitted among non-human primates by arboreal Aedes mosquitoes. This study investigated the genetic and phenotypic changes associated with emergence of human DENV-4 from its sylvatic ancestors. Analysis of complete genomes of 3 sylvatic and 4 human strains revealed high conservation of both the 5′- and 3′-untranslated regions but considerable divergence within the open reading frame. Additionally, the two ecotypes did not differ significantly in replication dynamics in cultured human liver (Huh-7), monkey kidney (Vero) or mosquito (C6/36) cells, although significant inter-strain variation within ecotypes was detected. These findings are in partial agreement with previous studies of DENV-2, where human strains produced a larger number of progeny than sylvatic strains in human liver cells but not in monkey or mosquito cells. PMID:22178263

  10. Epidemiological typing of Acanthamoeba strains isolated from keratitis cases in Belgium.

    PubMed

    De Jonckheere, J F

    2003-01-01

    From the corneas of nine keratitis patients and from their contact lenses, contact lens boxes and saline solutions, 15 strains of Acanthamoeba have been isolated. An Acanthamoeba strain was isolated from the swimming pool where one of the patients swam, while in the tapwater of the houses of three patients investigated, no Acanthamoeba could be detected. All the Acanthamoeba isolates from the cornea belong to genotype T4, but are different subtypes of T4. The Acanthamoeba detected on the contact lenses (and/or associated paraphernalia) of a patient are of the same subtype as that isolated from the cornea. The only Acanthamoeba strain isolated from a contact lens which was not related to an Acanthamoeba keratitis infection proved to be another genotype. A strain of Hartmannella from a cornea and two vahlkampfiids isolated from contact lenses had no connection with keratitis. This study confirms that, as found elsewhere, only Acanthamoeba genotype T4 of the 12 known Acanthamoeba genotypes is responsible for keratitis in Belgium. Most cases of Acanthamoeba keratitis cases are due to poor hygiene in the treatment (cleaning and storage) of contact lenses.

  11. Live Attenuated Mutants of Francisella tularensis Protect Rabbits against Aerosol Challenge with a Virulent Type A Strain

    PubMed Central

    Smith, Le'Kneitah P.; Cole, Kelly Stefano; Santiago, Araceli E.; Mann, Barbara J.; Barry, Eileen M.

    2014-01-01

    Francisella tularensis, a Gram-negative bacterium, is the causative agent of tularemia. No licensed vaccine is currently available for protection against tularemia, although an attenuated strain, dubbed the live vaccine strain (LVS), is given to at-risk laboratory personnel as an investigational new drug (IND). In an effort to develop a vaccine that offers better protection, recombinant attenuated derivatives of a virulent type A strain, SCHU S4, were evaluated in New Zealand White (NZW) rabbits. Rabbits vaccinated via scarification with the three attenuated derivatives (SCHU S4 ΔguaBA, ΔaroD, and ΔfipB strains) or with LVS developed a mild fever, but no weight loss was detected. Twenty-one days after vaccination, all vaccinated rabbits were seropositive for IgG to F. tularensis lipopolysaccharide (LPS). Thirty days after vaccination, all rabbits were challenged with aerosolized SCHU S4 at doses ranging from 50 to 500 50% lethal doses (LD50). All rabbits developed fevers and weight loss after challenge, but the severity was greater for mock-vaccinated rabbits. The ΔguaBA and ΔaroD SCHU S4 derivatives provided partial protection against death (27 to 36%) and a prolonged time to death compared to results for the mock-vaccinated group. In contrast, LVS and the ΔfipB strain both prolonged the time to death, but there were no survivors from the challenge. This is the first demonstration of vaccine efficacy against aerosol challenge with virulent type A F. tularensis in a species other than a rodent since the original work with LVS in the 1960s. The ΔguaBA and ΔaroD SCHU S4 derivatives warrant further evaluation and consideration as potential vaccines for tularemia and for identification of immunological correlates of protection. PMID:24614653

  12. Spreading of AbaR-type genomic islands in multidrug resistance Acinetobacter baumannii strains belonging to different clonal complexes.

    PubMed

    Ramírez, María Soledad; Vilacoba, Elisabet; Stietz, María Silvina; Merkier, Andrea Karina; Jeric, Paola; Limansky, Adriana S; Márquez, Carolina; Bello, Helia; Catalano, Mariana; Centrón, Daniela

    2013-07-01

    In order to determine the occurrence of AbaR-type genomic island in multidrug resistant Acinetobacter baumannii (MDRAb) strains circulating in Argentina, Uruguay, and Chile, we studied 51 MDRAb isolates recovered from several hospitals over 30 years. AbaR-type genomic resistance islands were found in 36 MDRAb isolates since 1986 till now. MLST technique allowed us to identify the presence of four different Clonal Complexes (109, 104, 119, 113) among the positive AbaR-type island positive strains. This is the first description of AbaR-type islands in the CC104 and CC113 that are the most widespread Clonal Complexes in Argentina. In addition, PCR mapping exposed different arrays to those previously described, evidencing the plasticity of this island. Our results evidence a widespread distribution of the AbaR-type genomic islands along the time in the MDRAb population, including the epidemic global clone 1 (GC1) as well as different clonal complexes to those already described in the literature.

  13. Regulation of Type IV Pili Contributes to Surface Behaviors of Historical and Epidemic Strains of Clostridium difficile

    PubMed Central

    Purcell, Erin B.; McKee, Robert W.; Bordeleau, Eric; Burrus, Vincent

    2015-01-01

    ABSTRACT The intestinal pathogen Clostridium difficile is an urgent public health threat that causes antibiotic-associated diarrhea and is a leading cause of fatal nosocomial infections in the United States. C. difficile rates of recurrence and mortality have increased in recent years due to the emergence of so-called “hypervirulent” epidemic strains. A great deal of the basic biology of C. difficile has not been characterized. Recent findings that flagellar motility, toxin synthesis, and type IV pilus (TFP) formation are regulated by cyclic diguanylate (c-di-GMP) reveal the importance of this second messenger for C. difficile gene regulation. However, the function(s) of TFP in C. difficile remains largely unknown. Here, we examine TFP-dependent phenotypes and the role of c-di-GMP in controlling TFP production in the historical 630 and epidemic R20291 strains of C. difficile. We demonstrate that TFP contribute to C. difficile biofilm formation in both strains, but with a more prominent role in R20291. Moreover, we report that R20291 is capable of TFP-dependent surface motility, which has not previously been described in C. difficile. The expression and regulation of the pilA1 pilin gene differs between R20291 and 630, which may underlie the observed differences in TFP-mediated phenotypes. The differences in pilA1 expression are attributable to greater promoter-driven transcription in R20291. In addition, R20291, but not 630, upregulates c-di-GMP levels during surface-associated growth, suggesting that the bacterium senses its substratum. The differential regulation of surface behaviors in historical and epidemic C. difficile strains may contribute to the different infection outcomes presented by these strains. IMPORTANCE How Clostridium difficile establishes and maintains colonization of the host bowel is poorly understood. Surface behaviors of C. difficile are likely relevant during infection, representing possible interactions between the bacterium and the

  14. Genotypic Diversity and Population Structure of Vibrio vulnificus Strains Isolated in Taiwan and Korea as Determined by Multilocus Sequence Typing

    PubMed Central

    Kim, Hye-Jin; Cho, Jae-Chang

    2015-01-01

    The genetic diversity and population structure of Vibrio vulnificus isolates from Korea and Taiwan were investigated using PCR-based assays targeting putative virulence-related genes and multilocus sequence typing (MLST). BOX-PCR genomic fingerprinting identified 52 unique genotypes in 84 environmental and clinical V. vulnificus isolates. The majority (> 50%) of strains had pathogenic genotypes for all loci tested; moreover, many environmental strains had pathogenic genotypes. Although significant (p < 0.05) inter-relationships among the genotypes were observed, the association between genotype and strain source (environmental or clinical) was not significant, indicating that genotypic characteristics alone are not sufficient to predict the isolation source or the virulence of a given V. vulnificus strain and vice versa. MLST revealed 23–35 allelic types per locus analyzed, resulting in a total of 44 unique sequence types (STs). Two major monophyletic groups (lineages A and B) corresponding to the two known lineages of V. vulnificus were observed; lineage A had six STs that were exclusively environmental, whereas lineage B had STs from both environmental and clinical sources. Pathogenic and nonpathogenic genotypes predominated in MLST lineages B and A, respectively. In addition, V. vulnificus was shown to be in linkage disequilibrium (p < 0.05), although two different recombination tests (PHI and Sawyer’s tests) detected significant evidence of recombination. Tajima’s D test also indicated that V. vulnificus might be comprised of recently sub-divided lineages. These results suggested that the two lineages revealed by MLST correspond to two distinct ecotypes of V. vulnificus. PMID:26599487

  15. Transcriptome Profiling of Wild-Type and pga-Knockout Mutant Strains Reveal the Role of Exopolysaccharide in Aggregatibacter actinomycetemcomitans.

    PubMed

    Shanmugam, Mayilvahanan; El Abbar, Faiha; Ramasubbu, Narayanan

    2015-01-01

    Exopolysaccharides have a diverse set of functions in most bacteria including a mechanistic role in protecting bacteria against environmental stresses. Among the many functions attributed to the exopolysaccharides, biofilm formation, antibiotic resistance, immune evasion and colonization have been studied most extensively. The exopolysaccharide produced by many Gram positive as well as Gram negative bacteria including the oral pathogen Aggregatibacter actinomycetemcomitans is the homopolymer of β(1,6)-linked N-acetylglucosamine. Recently, we reported that the PGA-deficient mutant of A. actinomycetemcomitans failed to colonize or induce bone resorption in a rat model of periodontal disease, and the colonization genes, apiA and aae, were significantly down regulated in the mutant strain. To understand the role of exopolysaccharide and the pga locus in the global expression of A. actinomycetemcomitans, we have used comparative transcriptome profiling to identify differentially expressed genes in the wild-type strain in relation to the PGA-deficient strain. Transcriptome analysis revealed that about 50% of the genes are differently expressed (P < 0.05 and fold change >1.5). Our study demonstrated that the absence of the pga locus affects the genes involved in peptidoglycan recycling, glycogen storage, and virulence. Further, using confocal microscopy and plating assays, we show that the viability of pga mutant strain is significantly reduced during biofilm growth. Thus, this study highlights the importance of pga genes and the exopolysaccharide in the virulence of A. actinomycetemcomitans.

  16. Poles Apart: Arctic and Antarctic Octadecabacter strains Share High Genome Plasticity and a New Type of Xanthorhodopsin

    PubMed Central

    Vollmers, John; Voget, Sonja; Dietrich, Sascha; Gollnow, Kathleen; Smits, Maike; Meyer, Katja; Brinkhoff, Thorsten; Simon, Meinhard; Daniel, Rolf

    2013-01-01

    The genus Octadecabacter is a member of the ubiquitous marine Roseobacter clade. The two described species of this genus, Octadecabacter arcticus and Octadecabacter antarcticus, are psychrophilic and display a bipolar distribution. Here we provide the manually annotated and finished genome sequences of the type strains O. arcticus 238 and O. antarcticus 307, isolated from sea ice of the Arctic and Antarctic, respectively. Both genomes exhibit a high genome plasticity caused by an unusually high density and diversity of transposable elements. This could explain the discrepancy between the low genome synteny and high 16S rRNA gene sequence similarity between both strains. Numerous characteristic features were identified in the Octadecabacter genomes, which show indications of horizontal gene transfer and may represent specific adaptations to the habitats of the strains. These include a gene cluster encoding the synthesis and degradation of cyanophycin in O. arcticus 238, which is absent in O. antarcticus 307 and unique among the Roseobacter clade. Furthermore, genes representing a new subgroup of xanthorhodopsins as an adaptation to icy environments are present in both Octadecabacter strains. This new xanthorhodopsin subgroup differs from the previously characterized xanthorhodopsins of Salinibacter ruber and Gloeobacter violaceus in phylogeny, biogeography and the potential to bind 4-keto-carotenoids. Biochemical characterization of the Octadecabacter xanthorhodopsins revealed that they function as light-driven proton pumps. PMID:23671678

  17. Variability of human immunodeficiency virus type 1 group O strains isolated from Cameroonian patients living in France.

    PubMed Central

    Loussert-Ajaka, I; Chaix, M L; Korber, B; Letourneur, F; Gomas, E; Allen, E; Ly, T D; Brun-Vézinet, F; Simon, F; Saragosti, S

    1995-01-01

    Human immunodeficiency virus type 1 (HIV-1) nucleotide sequences encoding p24Gag and the Env C2V3 region were obtained from seven patients who were selected on the basis of having paradoxical seronegativity on a subset of HIV enzyme-linked immunosorbent assay detection kits and having atypical Western blot (immunoblot) reactivity. Sequence analyses showed that all of these strains were more closely related to the recently described Cameroonian HIV isolates of group O (HIV-1 outlier) than to group M (HIV-1 major). All seven patients had Cameroonian origins but were living in France at the time the blood samples were taken. Characterization of a large number of group M strains has to date revealed eight distinct genetic subtypes (A to H). Genetic distances between sequences from available group O isolates were generally comparable to those observed in M intersubtype sequence comparisons, showing that the group O viruses are genetically very diverse. Analysis of sequences from these seven new viral strains, combined with the three previously characterized group O strains, revealed few discernable phylogenetic clustering patterns among the 10 patients' viral sequences. The level of diversity among group O sequences suggests that they may have a comparable (or greater) age than the M group sequences, although for unknown reasons, the latter group dispersed first and is the dominant lineage in the pandemic. PMID:7637010

  18. Variability of human immunodeficiency virus type 1 group O strains isolated from Cameroonian patients living in France.

    PubMed

    Loussert-Ajaka, I; Chaix, M L; Korber, B; Letourneur, F; Gomas, E; Allen, E; Ly, T D; Brun-Vézinet, F; Simon, F; Saragosti, S

    1995-09-01

    Human immunodeficiency virus type 1 (HIV-1) nucleotide sequences encoding p24Gag and the Env C2V3 region were obtained from seven patients who were selected on the basis of having paradoxical seronegativity on a subset of HIV enzyme-linked immunosorbent assay detection kits and having atypical Western blot (immunoblot) reactivity. Sequence analyses showed that all of these strains were more closely related to the recently described Cameroonian HIV isolates of group O (HIV-1 outlier) than to group M (HIV-1 major). All seven patients had Cameroonian origins but were living in France at the time the blood samples were taken. Characterization of a large number of group M strains has to date revealed eight distinct genetic subtypes (A to H). Genetic distances between sequences from available group O isolates were generally comparable to those observed in M intersubtype sequence comparisons, showing that the group O viruses are genetically very diverse. Analysis of sequences from these seven new viral strains, combined with the three previously characterized group O strains, revealed few discernable phylogenetic clustering patterns among the 10 patients' viral sequences. The level of diversity among group O sequences suggests that they may have a comparable (or greater) age than the M group sequences, although for unknown reasons, the latter group dispersed first and is the dominant lineage in the pandemic.

  19. Typing of field rabies virus strains in FR Yugoslavia by limited sequence analysis and monoclonal antibodies.

    PubMed

    Stankov, S

    2001-01-01

    A total of 32 rabies virus isolates (15 of fox, 14 of cat and 3 of dog origin) from the territory of FR Yugoslavia were collected from December 1996 till February 1998 and analyzed by limited sequencing of N gene and by indirect immunofluorescence and a panel of 20 antinucleocapsid monoclonal antibodies (MAbs). All examined strains were characterized as sylvatic fox strains. Two main genetic variants were detected, 15 isolates belonging to Group I, 14 belonging to Group II, while the remaining 3 could not be classified into any group. This classification was confirmed by MAbs. The obtained results indicate at least two independent cycles of rabies transmission, probably resulting from multiple modes of transmission to the territories now belonging to FR Yugoslavia.

  20. Pattern recognition of genomic features with microarrays: site typing of Mycobacterium tuberculosis strains

    PubMed Central

    Raychaudhuri, Soumya; Stuart, Joshua M.; Liu, Xuemin; Small, Peter M.; Altman, Russ B.

    2009-01-01

    Mycobacterium tuberculosis (M. tb.) strains differ in the number and locations of a transposon-like insertion sequence known as IS6110. Accurate detection of this sequence can be used as a fingerprint for individual strains, but can be difficult because of noisy data. In this paper, we propose a non-parametric discriminant analysis method for predicting the locations of the IS6110 sequence from microarray data. Polymerase chain reaction extension products generated from primers specific for the insertion sequence are hybridized to a microarray containing targets corresponding to each open reading frame in M. tb. To test for insertion sites, we use microarray intensity values extracted from small windows of contiguous open reading frames. Rank-transformation of spot intensities and first-order differences in local windows provide enough information to reliably determine the presence of an insertion sequence. The non-parametric approach outperforms all other methods tested in this study. PMID:10977090

  1. Presence of Legionellaceae in warm water supplies and typing of strains by polymerase chain reaction.

    PubMed Central

    Zietz, B.; Wiese, J.; Brengelmann, F.; Dunkelberg, H.

    2001-01-01

    Outbreaks of Legionnaire's disease present a public health challenge especially because fatal outcomes still remain frequent. The aim of this study was to describe the abundance and epidemiology of Legionellaceae in the human-made environment. Water was sampled from hot-water taps in private and public buildings across the area of Göttingen, Germany, including distant suburbs. Following isolation, we used polymerase chain reaction in order to generate strain specific banding profiles of legionella isolates. In total, 70 buildings were examined. Of these 18 (26%) had the bacterium in at least one water sample. Legionella pneumophila serogroups 1, 4, 5 and 6 could be identified in the water samples. Most of the buildings were colonized solely by one distinct strain, as proven by PCR. In three cases equal patterns were found in separate buildings. There were two buildings in this study where isolates with different serogroups were found at the same time. PMID:11293675

  2. Failure strain and mechanical property data for the Type IIIA waste tank liners

    SciTech Connect

    Thomas, J.K.

    1992-06-01

    The SRS Waste Tanks at the Savannah River Site to be employed in the In-Tank Precipitation (ITP) process are undergoing a structural evaluation in order to define their response to a hypothetical deflagration accident. This report provides mechanical property data to support the structural analyses, and characterizes the impact of mechanical property variability and materials degradation on the failure strain of the primary liner.

  3. Antimicrobial resistance profiles of dairy and clinical isolates and type strains of enterococci.

    PubMed

    de Fátima Silva Lopes, Maria; Ribeiro, Tânia; Abrantes, Marta; Figueiredo Marques, José Joaquim; Tenreiro, Rogério; Crespo, Maria Teresa Barreto

    2005-08-25

    The susceptibility to 30 antimicrobial agents was determined by the disk diffusion method for a collection of 172 enterococcal strains, including 96 isolates from dairy sources, 50 isolates of human and veterinary origin, and 26 reference strains from 24 different enterococcal species. Results were analysed by hierarchic numerical methods to cluster strains and to group antimicrobials according to similarity profiles. Resistance to 17 of the 30 antimicrobials showed to be correlated, leading to four groups reflecting the mode of action: quinolones (ofloxacin, enrofloxacin, ciprofloxacin and norfloxacin); macrolides (erythromycin, spiramycin), phenicols (cloramphenicol) and tetracyclins (tetracycline, oxytetracyclin); aminoglycosides (gentamicin, kanamycin) and lincosamides (clindamycin); penicillins (amoxicillin, ampicillin, penicillin G, piperacillin) and carbapenems (imipenem). Overall, the genus Enterococcus behaved as resistant to lincomycin, colistin, polimixin B and, with a few exceptions in dairy isolates, to methicillin. In general, all isolates were susceptible to vancomycin, cloramphenicol and fusidic acid. Clusters containing only dairy isolates were susceptible to the majority of antimicrobials tested, as opposed to clusters constituted only by clinical enterococcal isolates. Among the clinical isolates, 62% were highly multiresistant. Low level gentamicin resistance was found to be associated with clinical enterococci. Among dairy isolates, those that clustered with clinical isolates were both resistant to gentamicin and identified as Enterococcus faecalis. Resistance to macrolides, quinolones, penicillins and imipenem was found to be associated also with clinical environments, mainly with multiresistant isolates, contrary to what is generally agreed as a characteristic of the genus. Veterinary clinical isolates were mainly grouped with the multiresistant clinical human isolates. The 26 reference enterococcal strains were distributed in clusters with

  4. Streptococcus equi subspecies equi in horses in Israel: seroprevalence and strain types

    PubMed Central

    Tirosh-Levy, S.; Blum, S. E.; Steward, K. F.; Waller, A. S.; Steinman, A.

    2016-01-01

    The purpose of this cross-sectional study was to determine the seroprevalence of Streptococcus equi in Israel, to monitor seropositive horses over time and to identify archived strains that were recovered from Israeli horses. A serological survey of 200 healthy horses on 20 farms throughout Israel was performed to detect recent exposure to S equi antigens A and C via indirect ELISA. Seroprevalence was 9.5 per cent (19/200) and positive horses were found in 30 per cent (6/20) of the farms. Sixteen horses that returned a positive serology result were retested three and six months later. Most (12/16) positive horses remained positive, which suggests the presence of animals with persistent infection. Molecular characterisation of S equi strains by sequencing of the SeM gene of 16 archived isolates of S equi that were recovered from clinical cases of strangles between 2008 and 2012 identified two strains: SeM-2 and SeM-28. PMID:27651915

  5. Effects of Pyrogallol on Growth and Cytotoxicity of Wild-Type and katG Mutant Strains of Vibrio vulnificus

    PubMed Central

    Lim, Ju Young; Kim, Choon-Mee; Rhee, Joon Haeng; Kim, Young Ran

    2016-01-01

    Vibrio vulnificus is a causative agent of fatal septicemia and necrotic wound infection and the pathogen infection became an important public health problem in many counties. Vibrio vulnificus causes RtxA1 toxin-induced acute cell death. We tried to identify natural products that inhibit the acute cytotoxicity of V. vulnificus using a lactate hydrogenase assay. A polyphenol pyrogallol protected HeLa cells from V. vulnificus-induced cytotoxicity. Pyrogallol also decreased the growth of V. vulnificus; this inhibitory effect was more significant during log phase than stationary phase. To further elucidate the inhibitory mechanism, pyrogallol-induced toxicity was compared between a V. vulnificus catalase-peroxidase mutant (katG−) and the isogenic wild-type MO6-24/O strains. No growth was observed for the katG− mutant in the presence of pyrogallol (50 μg/mL) even after 24 h, whereas the wild-type strain demonstrated growth recovery following a prolonged lag phase. Pyrogallol-mediated growth inhibition of the katG− mutant strain was partially rescued by exogenous catalase treatment. These results indicate that the mechanism by which pyrogallol inhibits the growth and cytotoxicity of V. vulnificus likely involves polyphenol-induced prooxidant damage. Taken together, these results suggest that pyrogallol has potential for development as a new paradigm drug to treat infectious diseases. PMID:27936080

  6. Molecular typing of Paenibacillus larvae strains isolated from Bulgarian apiaries based on repetitive element polymerase chain reaction (Rep-PCR).

    PubMed

    Rusenova, Nikolina; Parvanov, Parvan; Stanilova, Spaska

    2013-06-01

    The aim of the present study was to perform molecular typing of Paenibacillus larvae (P. larvae) isolates from Bulgarian apiaries with repetitive element polymerase chain reaction (rep-PCR) using BOX A1R, MBO REP1, and ERIC primers. A total of 96 isolates collected from brood combs with clinical symptoms of American foulbrood originating from apiaries located in different geographical regions of Bulgaria, a reference strain P. larvae NBIMCC 8478 and 30 commercial honey samples with Bulgarian origin were included in the study. Rep-PCR fingerprinting analysis revealed two genotypes ab and AB of P. larvae isolates from brood combs and honey samples. A combination of genotypes ab/AB was detected in one apiary and honey sample. The prevailing genotype ab was found in 78.1 % of brood combs isolates as well as in the reference strain whereas genotype AB was determined in 21.9 % of isolates. The examination of honey samples confirmed the preponderance of ab genotype which was demonstrated in 20 of 30 samples analyzed. In conclusion, the genetic epidemiology of P. larvae revealed two genotypes--ab and AB for Bulgarian strains. Developed protocols for molecular typing of P. larvae are reliable and may be used to trace the source of infection.

  7. Secretory delivery of recombinant proteins in attenuated Salmonella strains: potential and limitations of Type I protein transporters.

    PubMed

    Hahn, Heinz P; von Specht, Bernd Ulrich

    2003-07-15

    Live attenuated Salmonella strains have been extensively explored as oral delivery systems for recombinant vaccine antigens and effector proteins with immunoadjuvant and immunomodulatory potential. The feasibility of this approach was demonstrated in human vaccination trials for various antigens. However, immunization efficiencies with live vaccines are generally significantly lower compared to those monitored in parenteral immunizations with the same vaccine antigen. This is, at least partly, due to the lack of secretory expression systems, enabling large-scale extracellular delivery of vaccine and effector proteins by these strains. Because of their low complexity and the terminal location of the secretion signal in the secreted protein, Type I (ATP-binding cassette) secretion systems appear to be particularly suited for development of such recombinant extracellular expression systems. So far, the Escherichia coli hemolysin system is the only Type I secretion system, which has been adapted to recombinant protein secretion in Salmonella. However, this system has a number of disadvantages, including low secretion capacity, complex genetic regulation, and structural restriction to the secreted protein, which eventually hinder high-level in vivo delivery of recombinant vaccines and effector proteins. Thus, the development of more efficient recombinant protein secretion systems, based on Type I exporters can help to improve efficacies of live recombinant Salmonella vaccines. Type I secretion systems, mediating secretion of bacterial surface layer proteins, such as RsaA in Caulobacter crescentus, are discussed as promising candidates for improved secretory delivery systems.

  8. CodY Is a Global Regulator of Virulence-Associated Properties for Clostridium perfringens Type D Strain CN3718

    PubMed Central

    Li, Jihong; Ma, Menglin; Sarker, Mahfuzur R.; McClane, Bruce A.

    2013-01-01

    ABSTRACT CodY is known to regulate various virulence properties in several Gram-positive bacteria but has not yet been studied in the important histotoxic and intestinal pathogen Clostridium perfringens. The present study prepared an isogenic codY-null mutant in C. perfringens type D strain CN3718 by insertional mutagenesis using the Targetron system. Western blot analysis indicated that, relative to wild-type CN3718 or a complementing strain, this isogenic codY mutant produces reduced levels of epsilon toxin (ETX). Using supernatants from cultures of the wild-type, codY-null mutant, and complementing strains, CodY regulation of ETX production was shown to have cytotoxic consequences for MDCK cells. The CodY regulatory effect on ETX production was specific, since the codY-null mutant still made wild-type levels of alpha-toxin and perfringolysin O. Sialidase activity measurements and sialidase Western blot analysis of supernatants from CN3718 and its isogenic derivatives showed that CodY represses overall exosialidase activity due to a reduced presence of NanH in culture supernatants. Inactivation of the codY gene significantly decreased the adherence of CN3718 vegetative cells or spores to host Caco-2 cells. Finally, the codY mutant showed increased spore formation under vegetative growth conditions, although germination of these spores was impaired. Overall, these results identify CodY as a global regulator of many C. perfringens virulence-associated properties. Furthermore, they establish that, via CodY, CN3718 coordinately regulates many virulence-associated properties likely needed for intestinal infection. PMID:24105766

  9. New strain of human T lymphotropic virus (HTLV) type 3 in a Pygmy from Cameroon with peculiar HTLV serologic results.

    PubMed

    Calattini, Sara; Betsem, Edouard; Bassot, Sylviane; Chevalier, Sébastien Alain; Mahieux, Renaud; Froment, Alain; Gessain, Antoine

    2009-02-15

    A search for human T lymphotropic virus (HTLV) types 1 and 2 and related viruses was performed by serological and molecular means on samples obtained from 421 adult villagers from the southern Cameroon forest areas. One individual (a 56-year-old Baka Pygmy hunter) was found to be HTLV-3 infected; however, there was a low proviral load in blood cells. Complete sequence analysis of this virus (HTLV-3Lobak18) indicated a close relationship to human HTLV-3Pyl43 and simian STLV-3CTO604 strains. Plasma samples from Lobak18, the HTLV-3 infected individual, exhibited a peculiar "HTLV-2-like" pattern on Western blot analysis and were serologically untypeable by line immunoassay. These results were different from those for the 2 previously reported HTLV-3 strains, raising questions about serological confirmation of infection with such retroviruses.

  10. Evaluation of the correlation of caspofungin MICs and treatment outcome in murine infections by wild type strains of Candida parapsilosis.

    PubMed

    Salas, Valentina; Pastor, F Javier; Capilla, Javier; Sutton, Deanna A; Mayayo, Emilio; Fothergill, Annette W; Rinaldi, Michael G; Guarro, Josep

    2013-09-01

    We have evaluated the in vitro activity of caspofungin against 36 wild-type strains of Candida parapsilosis sensu stricto using 3 techniques: broth microdilution, disk diffusion, and the determination of minimal fungicidal concentration (MFC). The first 2 methods showed a good in vitro activity of caspofungin, but the MFCs were ≥2 dilutions above their corresponding MICs. In a murine model of disseminated infection, we evaluated the efficacy of caspofungin at 5 mg/kg against 8 strains of C. parapsilosis representing different degrees of in vitro susceptibility (0.12-1 μg/mL). All the isolates responded to treatment and (1→3)-β-D-glucan levels were reduced in all the cases; however, the study revealed differences among isolates, since caspofungin reduced the tissue burden of mice infected with isolates with MICs ≤0.5 μg/mL but was less effective against those with MICs of 1 μg/mL.

  11. A distinct type of alcohol dehydrogenase, adh4+, complements ethanol fermentation in an adh1-deficient strain of Schizosaccharomyces pombe.

    PubMed

    Sakurai, Masao; Tohda, Hideki; Kumagai, Hiromichi; Giga-Hama, Yuko

    2004-03-01

    In the fission yeast Schizosaccharomyces pombe, only one alcohol dehydrogenase gene, adh1(+), has been identified. To elucidate the influence of adh1(+) on ethanol fermentation, we constructed the adh1 null strain (delta adh1). The delta adh1 cells still produced ethanol and grew fermentatively as the wild-type cells. Both DNA microarray and RT-PCR analysis demonstrated that this ethanol production is caused by the enhanced expression of a Saccharomyces cerevisiae ADH4-like gene product (SPAC5H10.06C named adh4(+)). Since the strain lacking both adh1 and adh4 genes (delta adh1 delta adh4) showed non-fermentative retarded growth, only these two ADHs produce ethanol for fermentative growth. This is the first observation that a S. cerevisiae ADH4-like alcohol dehydrogenase functions in yeast ethanol fermentation.

  12. Computational classification of different wild-type zebrafish strains based on their variation in light-induced locomotor response.

    PubMed

    Gao, Yuan; Zhang, Gaonan; Jelfs, Beth; Carmer, Robert; Venkatraman, Prahatha; Ghadami, Mohammad; Brown, Skye A; Pang, Chi Pui; Leung, Yuk Fai; Chan, Rosa H M; Zhang, Mingzhi

    2016-02-01

    Zebrafish larvae display a rapid and characteristic swimming behaviour after abrupt light onset or offset. This light-induced locomotor response (LLR) has been widely used for behavioural research and drug screening. However, the locomotor responses have long been shown to be different between different wild-type (WT) strains. Thus, it is critical to define the differences in the WT LLR to facilitate accurate interpretation of behavioural data. In this investigation, we used support vector machine (SVM) models to classify LLR data collected from three WT strains: AB, TL and TLAB (a hybrid of AB and TL), during early embryogenesis, from 3 to 9 days post-fertilisation (dpf). We analysed both the complete dataset and a subset of the data during the first 30after light change. This initial period of activity is substantially driven by vision, and is also known as the visual motor response (VMR). The analyses have resulted in three major conclusions: First, the LLR is different between the three WT strains, and at different developmental stages. Second, the distinguishable information in the VMR is comparable to, if not better than, the full dataset for classification purposes. Third, the distinguishable information of WT strains in the light-onset response differs from that in the light-offset response. While the classification accuracies were higher for the light-offset than light-onset response when using the complete LLR dataset, a reverse trend was observed when using a shorter VMR dataset. Together, our results indicate that one should use caution when extrapolating interpretations of LLR/VMR obtained from one WT strain to another.

  13. A Killed, Genetically Engineered Derivative of a Wild-Type Extraintestinal Pathogenic E. coli strain is a Vaccine Candidate

    PubMed Central

    Russo, Thomas A.; Beanan, Janet M.; Olson, Ruth; Genagon, Stacy A.; MacDonald, Ulrike; Cope, John J.; Davidson, Bruce A.; Johnston, Brian; Johnson, James R.

    2007-01-01

    Infections due to extraintestinal pathogenic E. coli (ExPEC) result in significant morbidity, mortality and increased healthcare costs. An efficacious vaccine against ExPEC would be desirable. In this report we explore the use of killed-whole E. coli as a vaccine immunogen. Given the diversity of capsule and O-antigens in ExPEC we have hypothesized that alternative targets are viable vaccine candidates. We have also hypothesized that immunization with a genetically engineered strain that is deficient in the capsule and O-antigen will generate a greater immune response against antigens other than the capsular and O-antigen epitopes than a wild-type strain. Lastly, we hypothesize that mucosal immunization with killed E. coli has the potential to generate a significant immune response. In this study we demonstrated that nasal immunization with a formalin-killed ExPEC derivative deficient in capsule and O-antigen results in a significantly greater overall humoral response compared to its wild-type derivative (which demonstrates that capsule and/or the O-antigen impede the development of an optimal humoral immune response) and a significantly greater immune response against non-capsular and O-antigen epitopes. These antibodies also bound to a subset of heterologous ExPEC strains and enhanced neutrophil-mediated bactericidal activity against the homologous and a heterologous strain. Taken together these studies support the concept that formalin-killed genetically engineered ExPEC derivatives are whole cell vaccine candidates to prevent infections due to ExPEC. PMID:17306426

  14. Three types of taxis used in the response of Acidovorax sp. strain JS42 to 2-nitrotoluene.

    PubMed

    Rabinovitch-Deere, Christine A; Parales, Rebecca E

    2012-04-01

    Acidovorax sp. strain JS42 is able to utilize 2-nitrotoluene (2NT) as its sole carbon, nitrogen, and energy source. We report here that strain JS42 is chemotactic to 2NT and that the response is increased when cells are grown on compounds such as 2NT that are known to induce the first step of 2NT degradation. Assays with JS42 mutants unable to oxidize 2NT showed that the first step of 2NT metabolism was required for the induced response, but not for a portion of the constitutive response, indicating that 2NT itself is an attractant. The 2NT metabolite nitrite was shown to be a strong attractant for strain JS42, and sufficient nitrite was produced during the taxis assay to account for a large part of the induced response. A mutant with an inactivated ntdY gene, which is located adjacent to the 2NT degradation genes and codes for a putative methyl-accepting chemotaxis protein, showed a defect in taxis toward 2NT that may involve a reduced response to nitrite. Responses of a mutant defective for the energy-taxis receptor, Aer, indicated that a functional aer gene is required for a substantial part of the wild-type induced response to 2NT. In summary, strain JS42 utilizes three types of taxis to sense and respond to 2NT: constitutive 2NT-specific chemotaxis to directly sense 2NT, metabolism-dependent nitrite-specific chemotaxis that may be mediated by NtdY, and energy taxis mediated by Aer.

  15. Three Types of Taxis Used in the Response of Acidovorax sp. Strain JS42 to 2-Nitrotoluene

    PubMed Central

    Rabinovitch-Deere, Christine A.

    2012-01-01

    Acidovorax sp. strain JS42 is able to utilize 2-nitrotoluene (2NT) as its sole carbon, nitrogen, and energy source. We report here that strain JS42 is chemotactic to 2NT and that the response is increased when cells are grown on compounds such as 2NT that are known to induce the first step of 2NT degradation. Assays with JS42 mutants unable to oxidize 2NT showed that the first step of 2NT metabolism was required for the induced response, but not for a portion of the constitutive response, indicating that 2NT itself is an attractant. The 2NT metabolite nitrite was shown to be a strong attractant for strain JS42, and sufficient nitrite was produced during the taxis assay to account for a large part of the induced response. A mutant with an inactivated ntdY gene, which is located adjacent to the 2NT degradation genes and codes for a putative methyl-accepting chemotaxis protein, showed a defect in taxis toward 2NT that may involve a reduced response to nitrite. Responses of a mutant defective for the energy-taxis receptor, Aer, indicated that a functional aer gene is required for a substantial part of the wild-type induced response to 2NT. In summary, strain JS42 utilizes three types of taxis to sense and respond to 2NT: constitutive 2NT-specific chemotaxis to directly sense 2NT, metabolism-dependent nitrite-specific chemotaxis that may be mediated by NtdY, and energy taxis mediated by Aer. PMID:22286989

  16. Differences in susceptibility to develop parameters of diabetic nephropathy in four mouse strains with type 1 diabetes.

    PubMed

    Franzén, Stephanie; Friederich-Persson, Malou; Fasching, Angelica; Hansell, Peter; Nangaku, Masaomi; Palm, Fredrik

    2014-05-15

    One-third of diabetes mellitus patients develop diabetic nephropathy, and with underlying mechanisms unknown it is imperative that diabetic animal models resemble human disease. The present study investigated the susceptibility to develop diabetic nephropathy in four commonly used and commercially available mouse strains with type 1 diabetes to determine the suitability of each strain. Type 1 diabetes was induced in C57Bl/6, NMRI, BALB/c, and 129Sv mice by alloxan, and conscious glomerular filtration rate, proteinuria, and oxidative stress levels were measured in control and diabetic animals at baseline and after 5 and 10 wk. Histological alterations were analyzed using periodic acid-Schiff staining. Diabetic C57Bl/6 displayed increased glomerular filtration rate, i.e., hyperfiltration, whereas all other parameters remained unchanged. Diabetic NMRI developed the most pronounced hyperfiltration as well as increased oxidative stress and proteinuria but without glomerular damage. Diabetic BALB/c did not develop hyperfiltration but presented with pronounced proteinuria, increased oxidative stress, and glomerular damage. Diabetic 129Sv displayed proteinuria and increased oxidative stress without glomerular hyperfiltration or damage. However, all strains displayed intrastrain correlation between oxidative stress and proteinuria. In conclusion, diabetic C57Bl/6 and NMRI both developed glomerular hyperfiltration but neither presented with histological damage, although NMRI developed low-degree proteinuria. Thus these strains may be suitable when investigating the mechanism causing hyperfiltration. Neither BALB/c nor 129Sv developed hyperfiltration although both developed pronounced proteinuria. However, only BALB/c developed detectable histological damage. Thus BALB/c may be suitable when studying the roles of proteinuria and histological alterations for the progression of diabetic nephropathy.

  17. Core Genome Multilocus Sequence Typing for Identification of Globally Distributed Clonal Groups and Differentiation of Outbreak Strains of Listeria monocytogenes

    PubMed Central

    Gonzalez-Escalona, Narjol; Hammack, Thomas S.; Allard, Marc W.; Strain, Errol A.; Brown, Eric W.

    2016-01-01

    ABSTRACT Many listeriosis outbreaks are caused by a few globally distributed clonal groups, designated clonal complexes or epidemic clones, of Listeria monocytogenes, several of which have been defined by classic multilocus sequence typing (MLST) schemes targeting 6 to 8 housekeeping or virulence genes. We have developed and evaluated core genome MLST (cgMLST) schemes and applied them to isolates from multiple clonal groups, including those associated with 39 listeriosis outbreaks. The cgMLST clusters were congruent with MLST-defined clonal groups, which had various degrees of diversity at the whole-genome level. Notably, cgMLST could distinguish among outbreak strains and epidemiologically unrelated strains of the same clonal group, which could not be achieved using classic MLST schemes. The precise selection of cgMLST gene targets may not be critical for the general identification of clonal groups and outbreak strains. cgMLST analyses further identified outbreak strains, including those associated with recent outbreaks linked to contaminated French-style cheese, Hispanic-style cheese, stone fruit, caramel apple, ice cream, and packaged leafy green salad, as belonging to major clonal groups. We further developed lineage-specific cgMLST schemes, which can include accessory genes when core genomes do not possess sufficient diversity, and this provided additional resolution over species-specific cgMLST. Analyses of isolates from different common-source listeriosis outbreaks revealed various degrees of diversity, indicating that the numbers of allelic differences should always be combined with cgMLST clustering and epidemiological evidence to define a listeriosis outbreak. IMPORTANCE Classic multilocus sequence typing (MLST) schemes targeting internal fragments of 6 to 8 genes that define clonal complexes or epidemic clones have been widely employed to study L. monocytogenes biodiversity and its relation to pathogenicity potential and epidemiology. We demonstrated

  18. Molecular Typing and Presence of Genetic Markers Among Strains of Banana Finger-Tip Rot Pathogen, Burkholderia cenocepacia, in Taiwan.

    PubMed

    Lee, Yung-An; Chan, Chih-Wen

    2007-02-01

    ABSTRACT Burkholderia cenocepacia (genomovar III of B. cepacia complex), the causal agent of banana finger-tip rot, is a common plant-associated bacterium but also an important opportunistic pathogen of humans. To better understand the nature of B. cenocepacia from banana, the genetic variation among B. cenocepacia isolates from various banana-growing regions in southern Taiwan was examined. Forty-four serial isolates recovered from diseased banana stigmata from three banana-growing regions during the periods ranging from 2002 to 2004 were investigated. All B. cenocepacia isolates picked from quinate-yeast extract tetracycline-polymyxin semiselective medium could cause onion maceration and were polymerase chain reaction (PCR) positive for bcscV, which is a type III secretion gene present in all members of the B. cepacia complex except B. cepacia (formerly genomovar I). Genetic diversity was assessed using recA PCR restriction fragment length polymorphism, recA nucleotide sequence analysis, and pulsed-field gel electrophoresis assays. The assays revealed the genetic variability among the isolates and also allowed us to trace the relationship among isolates. The isolates all were assigned to genomovar III and consisted of two groups, A and B, which corresponded to recA lineage IIIA and IIIB. The group B strains were separated into B1 and B2 subgroups and the B1 strains were further divided into distinct lineages. The B1 strains were the most frequently detected and occurred in all regions tested. There was no significant difference between strains from each subgroup in the virulence on banana fingers of cv. Cavendish. PCR assays were further used to determine whether B. cenocepacia from banana contained the cable pilus subunit gene (cblA), IS1356, and B. cepacia epidemic strain marker (BCESM), which are DNA markers associated with epidemic B. cepacia clinic strains. The results indicated that cblA and IS1356 were absent but the BCESM was found in all isolates. The

  19. Glaciimonas alpina sp. nov. isolated from alpine glaciers and reclassification of Glaciimonas immobilis Cr9-12 as the type strain of Glaciimonas alpina sp. nov.

    PubMed

    Frasson, David; Udovičić, Matije; Frey, Beat; Lapanje, Aleš; Zhang, De-Chao; Margesin, Rosa; Sievers, Martin

    2015-06-01

    Psychrophilic bacterial strains were isolated from alpine glaciers in Switzerland and characterized taxonomically. On the basis of phylogenetic analysis of partial 16S rRNA and rpoB genes, three of those strains, strain 79 ( = CCOS 247), strain 4/58 ( = CCOS 250) and strain 4/56 ( = CCOS 258) clustered together with strain Cr9-12T and separately from the type strains Glaciimonas immobilis Cr9-30T and Glaciimonas singularis LMG 27070T. Strain Cr9-12T has been previously described as a strain of G. immobilis. The three newly isolated strains were compared phenotypically with strain Cr9-12T and with the type strains of the species G. immobilis and G. singularis. Cr9-12T and the three novel strains from an alpine glacier in Switzerland were Gram-stain-negative, non-motile, rod-shaped and psychrophilic and showed good growth throughout a temperature range of 1-20 °C and characteristically oxidized d-mannitol, l-fucose and bromosuccinic acid. The predominant cellular fatty acids of strain Cr9-12T and the three novel strains were summed feature 3 (C16 : 1ω7c and/or iso-C15 : 0 2-OH), C16 : 0 and C18 : 1ω7c. The respiratory quinone of these strains was ubiquinone 8 (UQ-8). The genomic DNA G+C content of Cr9-12T was 49.2 mol%. The combined data from phenotypic, phylogenetic and DNA-DNA relatedness studies strongly support the reclassification of strain Cr9-12T as representing a novel species. This strain and the isolates 79 ( = CCOS 247), 4/58 ( = CCOS 250) and 4/56 ( = CCOS 258) are representatives of a novel species of the genus Glaciimonas, for which the name Glaciimonas alpina sp. nov. is proposed. The type strain of Glaciimonas alpina is Cr9-12T ( = CCOS 761T = DSM 22814T).

  20. Complete genome sequence of Methanospirillum hungatei type strain JF1

    SciTech Connect

    Gunsalus, Robert; Cook, Lauren E.; Crable, Bryan R.; Rohlin, Lars; McDonald, Erin; Mouttaki, Housna; Sieber, Jessica R.; Poweleit, Nicole; Zhou, Hong; Lapidus, Alla; Daligault, Hajnalka E.; Land, Miriam L.; Gilna, Paul; Ivanova, Natalia; Kyripides, Nikos; Culley, David E.; McInerney, Michael J.

    2016-01-06

    Methanospirillum hungatei strain JF1 is a hydrogenotrophic methanogen that belongs to the order Methanomicrobiales. Members of the genus Methanospirillum are commonly encountered in syntrophic association with fermenting microorganisms. M. hungatei serves as the model partner organism in laboratory cocultures that syntrophically oxidize fatty and aromatic acids. Furthermore, when grown syntrophically, M. hungatei rapidly uses the hydrogen or formate produced by its syntrophic partner and maintains the concentration of these metabolites at very low levels so that the degradation of the syntrophic substrate is thermodynamically favorable.

  1. Strain glass transition in a multifunctional β-type Ti alloy

    NASA Astrophysics Data System (ADS)

    Wang, Yu; Gao, Jinghui; Wu, Haijun; Yang, Sen; Ding, Xiangdong; Wang, Dong; Ren, Xiaobing; Wang, Yunzhi; Song, Xiaoping; Gao, Jianrong

    2014-02-01

    Recently, a class of multifunctional Ti alloys called GUM metals attracts tremendous attentions for their superior mechanical behaviors (high strength, high ductility and superelasticity) and novel physical properties (Invar effect, Elinvar effect and low modulus). The Invar and Elinvar effects are known to originate from structural or magnetic transitions, but none of these transitions were found in the GUM metals. This challenges our fundamental understanding of their physical properties. In this study, we show that the typical GUM metal Ti-23Nb-0.7Ta-2Zr-1.2O (at%) alloy undergoes a strain glass transition, where martensitic nano-domains are frozen gradually over a broad temperature range by random point defects. These nano-domains develop strong texture after cold rolling, which causes the lattice elongation in the rolling direction associated with the transition upon cooling and leads to its Invar effect. Moreover, its Elinvar effect and low modulus can also be explained by the nano-domain structure of strain glass.

  2. Strain and Magnetization Properties of High Subelement Count Tube-Type Nb3Sn Strands

    SciTech Connect

    Peng, X.; Ghosh, A.; Gregory, E.; Tomsic, M.; Sumption, M.D.; Lu, X.F.; Cheggour, N.; Stauffer, T.C.; Goodrich, L.F.; Splett, J.D.

    2011-08-03

    A tubular technique for economical production of Nb{sub 3}Sn material with large numbers of subelements is being explored by Supergenics I LLC and Hyper Tech Research Inc. The number of subelements was increased to 919 (744 subelements plus 175 Cu filaments) by increasing the size at which restacking is carried out. The product exhibited no fabrication problems and was drawn down and tested at a wire diameter of 0.42 mm, where the subelements are 10 {micro}m in diameter. Recently we increased the subelement number to 1387 (1248 subelements plus 139 Cu filaments), which gives a subelement size of 12 {micro}m in 0.7 mm diameter wires. Heat treatment (HT) of different subelement restacks has been investigated, and the best results of critical current and stability are presented. The strain tolerance of the strands with 192 and 744 subelements was also tested, and the strand with fine subelement size showed a high intrinsic irreversible strain limit.

  3. Human salivary aggregation in Streptococcus intermedius type g strains: relationship with IgA.

    PubMed

    Yamaguchi, Taihei

    2004-06-01

    Bacterial aggregation is an important step in elimination from the human body to protect against infection. Streptococcus intermedius K1K aggregates in human saliva. In this study, the salivary agglutinin was identified. The aggregation level was very strong in sonic-treated saliva and 1-microm filtrate. Preincubation of human saliva with anti-human alpha chain serum or anti-human whole saliva serum completely inhibited aggregation, but preincubation with anti-human micro chain serum or anti-Fc fragment of human IgG serum had no effect. Agglutinin of human saliva that could aggregate the strain K1K was purified using DEAE-Sepharose CL-6B, Phenyl-Sepharose CL-4B and Sephacryl S200HR gel filtration. Purified salivary agglutinin was characterized with electrophoresis and immunological techniques, indicating that purified material was IgA. Bacterial aggregation was dependent on the presence of calcium. Saliva filtrate specimens from eight healthy men and eight women showed different aggregation activities. Three men and one woman had little activity. These data show that the present bacterial aggregation was an immunoreaction between IgA in saliva and the bacteria dependent on the levels of calcium. In addition, the IgA in human saliva related with possible calcium-dependent antigen(s) on the surface of strain K1K.

  4. A Geobacter sulfurreducens strain expressing pseudomonas aeruginosa type IV pili localizes OmcS on pili but is deficient in Fe(III) oxide reduction and current production.

    PubMed

    Liu, Xing; Tremblay, Pier-Luc; Malvankar, Nikhil S; Nevin, Kelly P; Lovley, Derek R; Vargas, Madeline

    2014-02-01

    The conductive pili of Geobacter species play an important role in electron transfer to Fe(III) oxides, in long-range electron transport through current-producing biofilms, and in direct interspecies electron transfer. Although multiple lines of evidence have indicated that the pili of Geobacter sulfurreducens have a metal-like conductivity, independent of the presence of c-type cytochromes, this claim is still controversial. In order to further investigate this phenomenon, a strain of G. sulfurreducens, designated strain PA, was constructed in which the gene for the native PilA, the structural pilin protein, was replaced with the PilA gene of Pseudomonas aeruginosa PAO1. Strain PA expressed and properly assembled P. aeruginosa PilA subunits into pili and exhibited a profile of outer surface c-type cytochromes similar to that of a control strain expressing the G. sulfurreducens PilA. Surprisingly, the strain PA pili were decorated with the c-type cytochrome OmcS in a manner similar to the control strain. However, the strain PA pili were 14-fold less conductive than the pili of the control strain, and strain PA was severely impaired in Fe(III) oxide reduction and current production. These results demonstrate that the presence of OmcS on pili is not sufficient to confer conductivity to pili and suggest that there are unique structural features of the G. sulfurreducens PilA that are necessary for conductivity.

  5. A Geobacter sulfurreducens Strain Expressing Pseudomonas aeruginosa Type IV Pili Localizes OmcS on Pili but Is Deficient in Fe(III) Oxide Reduction and Current Production

    PubMed Central

    Liu, Xing; Tremblay, Pier-Luc; Malvankar, Nikhil S.; Nevin, Kelly P.; Vargas, Madeline

    2014-01-01

    The conductive pili of Geobacter species play an important role in electron transfer to Fe(III) oxides, in long-range electron transport through current-producing biofilms, and in direct interspecies electron transfer. Although multiple lines of evidence have indicated that the pili of Geobacter sulfurreducens have a metal-like conductivity, independent of the presence of c-type cytochromes, this claim is still controversial. In order to further investigate this phenomenon, a strain of G. sulfurreducens, designated strain PA, was constructed in which the gene for the native PilA, the structural pilin protein, was replaced with the PilA gene of Pseudomonas aeruginosa PAO1. Strain PA expressed and properly assembled P. aeruginosa PilA subunits into pili and exhibited a profile of outer surface c-type cytochromes similar to that of a control strain expressing the G. sulfurreducens PilA. Surprisingly, the strain PA pili were decorated with the c-type cytochrome OmcS in a manner similar to the control strain. However, the strain PA pili were 14-fold less conductive than the pili of the control strain, and strain PA was severely impaired in Fe(III) oxide reduction and current production. These results demonstrate that the presence of OmcS on pili is not sufficient to confer conductivity to pili and suggest that there are unique structural features of the G. sulfurreducens PilA that are necessary for conductivity. PMID:24296506

  6. [Investigation of OXA type beta-lactamases and PFGE patterns in Acinetobacter baumannii strains resistant to carbapenems].

    PubMed

    Keyik, Serafettin; Arslan, Uğur; Türk Dağı, Hatice; Seyhan, Tuba; Fındık, Duygu

    2014-10-01

    Acinetobacter baumannii is an important opportunistic and multidrug-resistant pathogen leading to nosocomial infections. Over the last 10 years, a significant and threatening increase in resistance to carbapenems, mainly due to the dissemination of class D beta-lactamases, has been reported in A.baumannii worldwide. The most common types of beta-lactamases causing carbapenem resistance in A.baumannii are the OXA-23, OXA-24, OXA-40, OXA-58 and OXA-143 type serine beta-lactamases. The aim of this study was to investigate the presence of OXA type beta-lactamases in carbapenem-resistant A.baumannii strains and the clonal relationship between the strains. A total of 105 non-duplicate carbapenem-resistant A.baumannii strains isolated from various clinical samples (68 blood, 18 bronchoalveolar lavage, 13 drainage, 3 urine, 2 cerebrospinal fluid and 1 catheter samples) in the Microbiology Laboratories of Selcuk University, Meram (2009-2012) and Selcuklu (2007-2008) Medical School Hospitals, were included in the study. The isolates were identified by conventional methods and Phoenix 100 BD (BD Diagnostic, USA) and Vitek II (bioMerieux, France) automated systems. Carbapenem susceptibility test was performed by Kirby-Bauer disk diffusion method according to the CLSI standards. bla(OXA 23-like), bla(OXA 24-like), bla(OXA 58-like) and bla(OXA 51-like) genes were amplified by multiplex PCR assay and clonal relatedness was investigated by pulsed-field gel electrophoresis (PFGE) using ApaI enzyme. The bla(OXA 51-like) gene was determined in all carbapenem-resistant A.baumannii isolates, while the bla(OXA 23-like) and bla(OXA 58-like) genes were detected in 46.6% and 53.3% of isolates, respectively. However bla(OXA 24-like) gene was not demonstrated in any isolates. bla(OXA 23-like) gene was determined in both Meram and Selcuklu Medical School hospitals, but bla(OXA 58-like) gene was detected only in Meram Medical School hospital. PFGE analysis of the isolates revealed 32 different

  7. Complete genome sequence of the moderately thermophilic mineral-sulfide-oxidizing firmicute Sulfobacillus acidophilus type strain (NALT)

    SciTech Connect

    Anderson, Iain; Chertkov, Olga; Chen, Amy; Saunders, Elizabeth H; Lapidus, Alla L.; Nolan, Matt; Lucas, Susan; Hammon, Nancy; Deshpande, Shweta; Cheng, Jan-Fang; Han, Cliff; Tapia, Roxanne; Goodwin, Lynne A.; Pitluck, Sam; Liolios, Konstantinos; Pagani, Ioanna; Ivanova, N; Mikhailova, Natalia; Pati, Amrita; Palaniappan, Krishna; Land, Miriam L; Pan, Chongle; Rohde, Manfred; Pukall, Rudiger; Goker, Markus; Detter, J. Chris; Woyke, Tanja; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter; Mavromatis, K

    2012-01-01

    Sulfobacillus acidophilus Norris et al. 1996 is a member of the genus Sulfobacillus which comprises five species of the order Clostridiales. Sulfobacillus species are of interest for comparison to other sulfur and iron oxidizers and also have biomining applications. This is the first completed genome sequence of a type strain of the genus Sulfobacillus, and the second published genome of a member of the species S. acidophilus. The genome, which consists of one chromosome and one plasmid with a total size of 3,557,831 bp, harbors 3,626 protein-coding and 69 RNA genes, and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  8. Alcoholic fermentation by wild-type Hansenula polymorpha and Saccharomyces cerevisiae versus recombinant strains with an elevated level of intracellular glutathione.

    PubMed

    Grabek-Lejko, Dorota; Kurylenko, Olena O; Sibirny, Vladimir A; Ubiyvovk, Vira M; Penninckx, Michel; Sibirny, Andriy A

    2011-11-01

    The ability of baker's yeast Saccharomyces cerevisiae and of the thermotolerant methylotrophic yeast Hansenula polymorpha to produce ethanol during alcoholic fermentation of glucose was compared between wild-type strains and recombinant strains possessing an elevated level of intracellular glutathione (GSH) due to overexpression of the first gene of GSH biosynthesis, gamma-glutamylcysteine synthetase, or of the central regulatory gene of sulfur metabolism, MET4. The analyzed strains of H. polymorpha with an elevated pool of intracellular GSH were found to accumulate almost twice as much ethanol as the wild-type strain during glucose fermentation, in contrast to GSH1-overexpressing S. cerevisiae strains, which also possessed an elevated pool of GSH. The ethanol tolerance of the GSH-overproducing strains was also determined. For this, the wild-type strain and transformants with an elevated GSH pool were compared for their viability upon exposure to exogenous ethanol. Unexpectedly, both S. cerevisiae and H. polymorpha transformants with a high GSH pool proved more sensitive to exogenous ethanol than the corresponding wild-type strains.

  9. Complete genome sequencing of a multidrug-resistant and human-invasive Salmonella enterica serovar Typhimurium strain of the emerging sequence type 213 genotype

    DOE PAGES

    Calva, Edmundo; Silva, Claudia; Zaidi, Mussaret B.; ...

    2015-06-18

    Salmonella enterica subsp. enterica serovar Typhimurium strain YU39 was isolated in 2005 in the state of Yucatán, Mexico, from a human systemic infection. The YU39 strain is representative of the multidrug-resistant emergent sequence type 213 (ST213) genotype. The YU39 complete genome is composed of a chromosome and seven plasmids.

  10. Complete Genome Sequence of Salmonella enterica Serovar Typhimurium Strain YU15 (Sequence Type 19) Harboring the Salmonella Genomic Island 1 and Virulence Plasmid pSTV

    PubMed Central

    Calva, Edmundo; Puente, José L.; Zaidi, Mussaret B.

    2016-01-01

    The complete genome of Salmonella enterica subsp. enterica serovar Typhimurium sequence type 19 (ST19) strain YU15, isolated in Yucatán, Mexico, from a human baby stool culture, was determined using PacBio technology. The chromosome contains five intact prophages and the Salmonella genomic island 1 (SGI1). This strain carries the Salmonella virulence plasmid pSTV. PMID:27081132

  11. Complete Genome Sequencing of a Multidrug-Resistant and Human-Invasive Salmonella enterica Serovar Typhimurium Strain of the Emerging Sequence Type 213 Genotype

    PubMed Central

    Calva, Edmundo; Zaidi, Mussaret B.; Sanchez-Flores, Alejandro; Estrada, Karel; Silva, Genivaldo G. Z.; Soto-Jiménez, Luz M.; Wiesner, Magdalena; Fernández-Mora, Marcos; Edwards, Robert A.

    2015-01-01

    Salmonella enterica subsp. enterica serovar Typhimurium strain YU39 was isolated in 2005 in the state of Yucatán, Mexico, from a human systemic infection. The YU39 strain is representative of the multidrug-resistant emergent sequence type 213 (ST213) genotype. The YU39 complete genome is composed of a chromosome and seven plasmids. PMID:26089426

  12. Draft Genome Sequences of Four Bacterial Strains Isolated from a Polymicrobial Culture of Naked (N-Type) Emiliania huxleyi CCMP1516

    PubMed Central

    Orata, Fabini D.; Rosana, Albert Remus R.; Xu, Yue; Simkus, Danielle N.; Bramucci, Anna R.; Boucher, Yan

    2016-01-01

    Strains of Sulfitobacter spp., Erythrobacter sp., and Marinobacter sp. were isolated from a polymicrobial culture of the naked (N-type) haptophyte Emiliania huxleyi strain CCMP1516. The genomes encode genes for the production of phytohormones, vitamins, and the consumption of their hosts’ metabolic by-products, suggesting symbiotic interactions within this polymicrobial culture. PMID:27417846

  13. Draft Genome Sequences of Seven Bacterial Strains Isolated from a Polymicrobial Culture of Coccolith-Bearing (C-Type) Emiliania huxleyi M217

    PubMed Central

    Rosana, Albert Remus R.; Orata, Fabini D.; Xu, Yue; Simkus, Danielle N.; Bramucci, Anna R.; Boucher, Yan

    2016-01-01

    Strains of Rhodobacteraceae, Sphingomonadales, Alteromonadales, and Bacteroidetes were isolated from a polymicrobial culture of the coccolith-forming (C-type) haptophyte Emiliania huxleyi strain M217. The genomes encode genes for the production of algal growth factors and the consumption of their hosts’ metabolic by-products, suggesting that the polymicrobial culture harbors many symbiotic interactions. PMID:27417845

  14. Anomalous radial and angular strain relaxation around dilute p-, isoelectronic-, and n-type dopants in Si crystal

    NASA Astrophysics Data System (ADS)

    Zhao, Mingshu; Dong, Juncai; Chen, Dongliang

    2017-02-01

    Doping is widely applied in yielding desirable properties and functions in silicon technology; thus, fully understanding the relaxation mechanism for lattice-mismatch strain is of fundamental importance. Here we systematically study the local lattice distortion near dilute IIIA-, IVA-, and VA-group substitutional dopants in Si crystal using density functional theory, and anomalous radial and angular strain relaxation modes are first revealed. Both the nearest-neighbor (NN) bond-distances and the tetrahedral bond-angles are found to exhibit completely opposite dependence on the electronic configurations for the low Z (Z<26) and high Z (Z>26) dopants. More surprisingly, negative and positive angular shifts for the second NN twelve Si2 atoms are unveiled surrounding the p- and n-type dopants, respectively. While electron localization function shows that the doped hole and electron are highly localized near the dopants, hence being responsible for the abnormal angular shifts, a universal radial strain relaxation mechanism dominated by a competition of the Coulomb interactions among the ion-core, bond-charge, and the localized hole or electron is also proposed. These findings may prove to be instrumental in precise design of silicon-based solotronics.

  15. Type I interferon induction is correlated with attenuation of a South American eastern equine encephalitis virus strain in mice

    PubMed Central

    Gardner, Christina L.; Yin, Jun; Burke, Crystal W.; Klimstra, William B.; Ryman, Kate D.

    2009-01-01

    North American eastern equine encephalitis virus (NA-EEEV) strains cause high mortality in humans, whereas South American strains (SA-EEEV) are typically avirulent. To clarify mechanisms of SA-EEEV attenuation, we compared mouse-attenuated BeAr436087 SA-EEEV, considered an EEEV vaccine candidate, with mouse-virulent NA-EEEV strain, FL93-939. Although attenuated, BeAr436087 initially replicated more efficiently than FL93-939 in lymphoid and other tissues, inducing systemic IFN-α/β release, whereas FL93-939 induced little. BeAr436087 was more virulent than FL93-939 in IFN-α/β-deficient mice, confirming that type I IFN responses determined attenuation, but the viruses were similarly sensitive to IFN-α/β priming in vitro. Infection with BeAr436087 protected against FL93-939 disease/death, even when given 8 h afterward, suggesting that the environment produced by BeAr436087 infection attenuated FL93-939. We conclude that avoidance of IFN-α/β induction is factor for FL93-939. Furthermore, BeAr436087 could be used for vaccination and therapeutic treatment in the event of exposure to NA-EEEV during a bioterrorism attack. PMID:19539968

  16. Complete genome sequence of the orange-red pigmented, radioresistant Deinococcus proteolyticus type strain (MRP(T)).

    PubMed

    Copeland, Alex; Zeytun, Ahmet; Yassawong, Montri; Nolan, Matt; Lucas, Susan; Hammon, Nancy; Deshpande, Shweta; Cheng, Jan-Fang; Han, Cliff; Tapia, Roxanne; Goodwin, Lynne A; Pitluck, Sam; Mavromatis, Konstantinos; Liolios, Konstantinos; Pagani, Ioanna; Ivanova, Natalia; Mikhailova, Natalia; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Jeffries, Cynthia D; Brambilla, Evelyne-Marie; Rohde, Manfred; Sikorski, Johannes; Pukall, Rüdiger; Göker, Markus; Detter, John C; Woyke, Tanja; Bristow, James; Eisen, Jonathan A; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter; Lapidus, Alla

    2012-05-25

    Deinococcus proteolyticus (ex Kobatake et al. 1973) Brook and Murray 1981 is one of currently 47 species in the genus Deinococcus within the family Deinococcaceae. Strain MRP(T) was isolated from feces of Lama glama and possesses extreme radiation resistance, a trait is shares with various other species of the genus Deinococcus, with D. proteolyticus being resistant up to 1.5 Mrad of gamma radiation. Strain MRP(T) is of further interest for its carotenoid pigment. The genome presented here is only the fifth completed genome sequence of a member of the genus Deinococcus (and the forth type strain) to be published, and will hopefully contribute to a better understanding of how members of this genus adapted to high gamma- or UV ionizing-radiation. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 2,886,836 bp long genome with its four large plasmids of lengths 97 kbp, 132 kbp, 196 kbp and 315 kbp harbors 2,741 protein-coding and 58 RNA genes and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  17. High-quality draft genome sequence of the Thermus amyloliquefaciens type strain YIM 77409T with an incomplete denitrification pathway

    DOE PAGES

    Zhou, En -Min; Murugapiran, Senthil K.; Mefferd, Chrisabelle C.; ...

    2016-02-27

    Thermus amyloliquefaciens type strain YIM 77409T is a thermophilic, Gram-negative, non-motile and rod-shaped bacterium isolated from Niujie Hot Spring in Eryuan County, Yunnan Province, southwest China. In the present study we describe the features of strain YIM 77409T together with its genome sequence and annotation. The genome is 2,160,855 bp long and consists of 6 scaffolds with 67.4 % average GC content. A total of 2,313 genes were predicted, comprising 2,257 protein-coding and 56 RNA genes. The genome is predicted to encode a complete glycolysis, pentose phosphate pathway, and tricarboxylic acid cycle. Additionally, a large number of transporters and enzymesmore » for heterotrophy highlight the broad heterotrophic lifestyle of this organism. Furthermore, a denitrification gene cluster included genes predicted to encode enzymes for the sequential reduction of nitrate to nitrous oxide, consistent with the incomplete denitrification phenotype of this strain.« less

  18. Molecular typing of nosocomial Staphylococcus aureus strains associated to biofilm based on the coagulase and protein A gene polymorphisms

    PubMed Central

    Salehzadeh, Ali; Zamani, Hojjatolah; Langeroudi, Maedeh Keshtkar; Mirzaie, Amir

    2016-01-01

    Objective(s): Staphylococcus aureus is an important bacterial pathogen responsible for a variety numbers of nosocomial and community acquired infections. Biofilm formation is regarded as an important factor in the establishment of S. aureus infection. The contribution of the genetic background of S. aureus to biofilm formation is poorly understood. The aim of the present work was to genotype S. aureus strains associated to biofilm based on the coagulase and protein A genes and to evaluate the association between the genetic background and the biofilm forming ability of clinical S. aureus isolates. Materials and Methods: A total number of 100 S. aureus were isolated from nosocomial infections and biofilm formation capability was investigated using phenotypic assay and molecular detection of biofilm associated genes. The strains were genotyped based on coagulase (coa) and protein A (spa) gene polymorphisms using restriction fragments length polymorphism-polymerase chain reaction (RFLP-PCR). Results: RFLP-PCR of coa gene generated two types and three subtypes. Amplification of spa gene resulted in two banding patterns and their restriction digestion generated three subtypes. The combined coa and spa RFLP patterns generated nine genotypes (G1-G9). The genotypes G4 and G1 were the most prevalent (32.1% and 24.3%, respectively). Conclusion: High clonal diversity of S. aureus strains able to produce biofilm was observed. Biofilm formation correlates with the spa and coa clonal lineage in our population and testing for multiple gene polymorphisms could be employed for local epidemiologic purposes. PMID:28096965

  19. Cell type specificity and mechanism of control of a gene may be reverted in different strains of Dictyostelium discoideum.

    PubMed

    Mangiarotti, G; Giorda, R

    2000-06-21

    Twelve genes which are expressed exclusively in pre-spore cells of Dictyostelium strain AX3 are expressed exclusively in pre-stalk cells of strain AX2. One gene has the opposite behavior: it is expressed in pre-stalk cells in AX3 and in pre-spore cells in AX2. The change in cell type specificity involves a change in the mechanism of control of gene expression. When they are expressed in pre-stalk cells, genes are controlled at the level of transcription, whilst in pre-spore cells, they are controlled at the level of mRNA stability. Genes expressed in pre-stalk cells in strain AX2, fused with an AX2 pre-spore specific promoter, become regulated at the level of mRNA stability. These findings indicate that at least a group of pre-stalk mRNAs possess the cis-destabilizing element typical of pre-spore mRNAs, though they are not destabilized in disaggregated cells. This is due to the fact that ribosomal protein S6, phosphorylation of which is responsible for controlling the stability of pre-spore mRNAs, is not dephosphorylated in disaggregated pre-stalk cells. These cells lack an S6 phosphatase activity which has been purified from disaggregated pre-spore cells.

  20. Sialidases Affect the Host Cell Adherence and Epsilon Toxin-Induced Cytotoxicity of Clostridium perfringens Type D Strain CN3718

    PubMed Central

    Li, Jihong; Sayeed, Sameera; Robertson, Susan; Chen, Jianming; McClane, Bruce A.

    2011-01-01

    Clostridium perfringens type B or D isolates, which cause enterotoxemias or enteritis in livestock, produce epsilon toxin (ETX). ETX is exceptionally potent, earning it a listing as a CDC class B select toxin. Most C. perfringens strains also express up to three different sialidases, although the possible contributions of those enzymes to type B or D pathogenesis remain unclear. Type D isolate CN3718 was found to carry two genes (nanI and nanJ) encoding secreted sialidases and one gene (nanH) encoding a cytoplasmic sialidase. Construction in CN3718 of single nanI, nanJ and nanH null mutants, as well as a nanI/nanJ double null mutant and a triple sialidase null mutant, identified NanI as the major secreted sialidase of this strain. Pretreating MDCK cells with NanI sialidase, or with culture supernatants of BMC206 (an isogenic CN3718 etx null mutant that still produces sialidases) enhanced the subsequent binding and cytotoxic effects of purified ETX. Complementation of BMC207 (an etx/nanH/nanI/nanJ null mutant) showed this effect is mainly attributable to NanI production. Contact between BMC206 and certain mammalian cells (e.g., enterocyte-like Caco-2 cells) resulted in more rapid sialidase production and this effect involved increased transcription of BMC206 nanI gene. BMC206 was shown to adhere to some (e.g. Caco-2 cells), but not all mammalian cells, and this effect was dependent upon sialidase, particularly NanI, expression. Finally, the sialidase activity of NanI (but not NanJ or NanH) could be enhanced by trypsin. Collectively these in vitro findings suggest that, during type D disease originating in the intestines, trypsin may activate NanI, which (in turn) could contribute to intestinal colonization by C. perfringens type D isolates and also increase ETX action. PMID:22174687

  1. V3 variability can influence the ability of an antibody to neutralize or enhance infection by diverse strains of human immunodeficiency virus type 1.

    PubMed Central

    Kliks, S C; Shioda, T; Haigwood, N L; Levy, J A

    1993-01-01

    Human monoclonal antibodies (mAbs) to two contiguous epitopes in the V3 loop of the human immunodeficiency virus type 1 (HIV-1) envelope have shown different effects on three distinct strains of the virus: neutralization, enhancement, or resistance to both processes. Only one amino acid in the mAb epitopes proximal to the crown of the V3 loop was different among these three strains. Substitution of this amino acid in the neutralizable strain with the amino acid of the neutralization-resistant strain or the enhanceable strain resulted in loss of both activities. The conversion of this single amino acid in the neutralization-resistant strain to that of the amino acid found in the neutralization-sensitive strain did not confer the ability for the virus to be neutralized. However, additional changes in neighboring amino acids in the V3 loop succeeded in conferring the neutralization capability. These observations indicate that one antibody species can exert three different effects on various HIV-1 strains. They could explain the emergence of neutralization "escape" variants in the presence of the neutralizing antibodies. Moreover, the results suggest caution in immunization of individuals with the envelope region from one strain since the antibodies induced may show a neutralizing effect against the homologous strain but enhancing effects against other unrelated strains. Images Fig. 4 PMID:7505441

  2. Identification of concomitant infection with Chlamydia trachomatis IncA-negative mutant and wild-type strains by genomic, transcriptional, and biological characterizations.

    PubMed

    Suchland, Robert J; Jeffrey, Brendan M; Xia, Minsheng; Bhatia, Ajay; Chu, Hencelyn G; Rockey, Daniel D; Stamm, Walter E

    2008-12-01

    Clinical isolates of Chlamydia trachomatis that lack IncA on their inclusion membrane form nonfusogenic inclusions and have been associated with milder, subclinical infections in patients. The molecular events associated with the generation of IncA-negative strains and their roles in chlamydial sexually transmitted infections are not clear. We explored the biology of the IncA-negative strains by analyzing their genomic structure, transcription, and growth characteristics in vitro and in vivo in comparison with IncA-positive C. trachomatis strains. Three clinical samples were identified that contained a mixture of IncA-positive and -negative same-serovar C. trachomatis populations, and two more such pairs were found in serial isolates from persistently infected individuals. Genomic sequence analysis of individual strains from each of two serovar-matched pairs showed that these pairs were very similar genetically. In contrast, the genome sequence of an unmatched IncA-negative strain contained over 5,000 nucleotide polymorphisms relative to the genome sequence of a serovar-matched but otherwise unlinked strain. Transcriptional analysis, in vitro culture kinetics, and animal modeling demonstrated that IncA-negative strains isolated in the presence of a serovar-matched wild-type strain are phenotypically more similar to the wild-type strain than are IncA-negative strains isolated in the absence of a serovar-matched wild-type strain. These studies support a model suggesting that a change from an IncA-positive strain to the previously described IncA-negative phenotype may involve multiple steps, the first of which involves a translational inactivation of incA, associated with subsequent unidentified steps that lead to the observed decrease in transcript level, differences in growth rate, and differences in mouse infectivity.

  3. Genome sequence of the homoacetogenic bacterium Holophaga foetida type strain (TMBS4T)

    SciTech Connect

    Anderson, Iain; Held, Brittany; Lapidus, Alla L.; Nolan, Matt; Lucas, Susan; Tice, Hope; Glavina Del Rio, Tijana; Cheng, Jan-Fang; Han, Cliff; Tapia, Roxanne; Goodwin, Lynne A.; Pitluck, Sam; Liolios, Konstantinos; Mavromatis, K; Pagani, Ioanna; Ivanova, N; Mikhailova, Natalia; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam L; Brambilla, Evelyne-Marie; Rohde, Manfred; Spring, Stefan; Goker, Markus; Detter, J. Chris; Woyke, Tanja; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Klenk, Hans-Peter; Kyrpides, Nikos C

    2012-01-01

    Holophaga foetida Liesack et al. 1994 is a member to the genomically so far poorly characterized family Holophagaceae in the class Holophagae within the phylum Acidibacteria. H. foetida is of interest for its ability to anaerobically degrade aromatic compounds and for its production of volatile sulfur compounds through a unique pathway. The genome of H. foetida strain TMBS4T is the first sequenced genome of a member of the class Holophagae. Here we describe the features of this organism, together with the complete genome sequence (improved high quality draft), and annotation. The 4,127,237 bp long chromosome with its 3,615 protein-coding and 57 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  4. A combinational approach of multilocus sequence typing and other molecular typing methods in unravelling the epidemiology of Erysipelothrix rhusiopathiae strains from poultry and mammals.

    PubMed

    Janßen, Traute; Voss, Matthias; Kühl, Michael; Semmler, Torsten; Philipp, Hans-Christian; Ewers, Christa

    2015-07-21

    Erysipelothrix rhusiopathiae infections re-emerged as a matter of great concern particularly in the poultry industry. In contrast to porcine isolates, molecular epidemiological traits of avian E. rhusiopathiae isolates are less well known. Thus, we aimed to (i) develop a multilocus sequence typing (MLST) scheme for E. rhusiopathiae, (ii) study the congruence of strain grouping based on pulsed-field gel electrophoresis (PFGE) and MLST, (iii) determine the diversity of the dominant immunogenic protein SpaA, and (iv) examine the distribution of genes putatively linked with virulence among field isolates from poultry (120), swine (24) and other hosts (21), including humans (3). Using seven housekeeping genes for MLST analysis we determined 72 sequence types (STs) among 165 isolates. This indicated an overall high diversity, though 34.5% of all isolates belonged to a single predominant ST-complex, STC9, which grouped strains from birds and mammals, including humans, together. PFGE revealed 58 different clusters and congruence with the sequence-based MLST-method was not common. Based on polymorphisms in the N-terminal hyper-variable region of SpaA the isolates were classified into five groups, which followed the phylogenetic background of the strains. More than 90% of the isolates harboured all 16 putative virulence genes tested and only intI, encoding an internalin-like protein, showed infrequent distribution. MLST data determined E. rhusiopathiae as weakly clonal species with limited host specificity. A common evolutionary origin of isolates as well as shared SpaA variants and virulence genotypes obtained from avian and mammalian hosts indicates common reservoirs, pathogenic pathways and immunogenic properties of the pathogen.

  5. Human T Cell Lymphotropic Virus Type 2a Strains Among HIV Type 1-Coinfected Patients from Brazil Have Originated Mostly from Brazilian Amerindians

    PubMed Central

    Magri, Mariana Cavalheiro; Brigido, Luis Fernando de Macedo; Morimoto, Helena Kaminami

    2013-01-01

    Abstract The human T cell lymphotropic virus type 2 (HTLV-2) is found mainly in Amerindians and in intravenous drug users (IDUs) from urban areas of the United States, Europe, and Latin America. Worldwide, HTLV-2a and HTLV-2b subtypes are the most prevalent. Phylogenetic analysis of HTLV-2 isolates from Brazil showed the HTLV-2a subtype, variant -2c, which spread from Indians to the general population and IDUs. The present study searched for the types of HTLV-2 that predominate among HIV-1-coinfected patients from southern and southeastern Brazil. Molecular characterization of the LTR, env, and tax regions of 38 isolates confirmed the HTLV-2c variant in 37 patients, and one HTLV-2b in a patient from Paraguay. Phylogenetic analysis of sequences showed different clades of HTLV-2 associated with risk factors and geographic region. These clades could represent different routes of virus transmission and/or little diverse evolutionary rates of virus. Taking into account the results obtained in the present study and the lack of the prototypic North American HTLV-2a strain and HTLV-2b subtypes commonly detected among HIV-coinfected individuals worldwide, we could speculate on the introduction of Brazilian HTLV-2 strains in such populations before the introduction of HIV. PMID:23484539

  6. High resolution melting curve analysis as a new tool for rapid identification of canine parvovirus type 2 strains.

    PubMed

    Bingga, Gali; Liu, Zhicheng; Zhang, Jianfeng; Zhu, Yujun; Lin, Lifeng; Ding, Shuangyang; Guo, Pengju

    2014-01-01

    A high resolution melting (HRM) curve method was developed to identify canine parvovirus type 2 (CPV-2) strains by nested PCR. Two sets of primers, CPV-426F/426R and CPV-87R/87F, were designed that amplified a 52 bp and 53 bp product from the viral VP2 capsid gene. The region amplified by CPV-426F/426R included the A4062G and T4064A mutations in CPV-2a, CPV-2b and CPV-2c. The region amplified by CPV-87F/87R included the A3045T mutation in the vaccine strains of CPV-2 and CPV-2a, CPV-2b and CPV-2c. Faecal samples were obtained from 30 dogs that were CPV antigen-positive. The DNA was isolated from the faecal samples and PCR-amplified using the two sets of primers, and genotyped by HRM curve analysis. The PCR-HRM assay was able to distinguish single nucleotide polymorphisms between CPV-2a, CPV-2b and CPV-2c using CPV-426F/426R. CPV-2a was distinguished from CPV-2b and CPV-2c by differences in the melting temperature. CPV-2b and CPV-2c could be distinguished based on the shape of the melting curve after generating heteroduplexes using a CPV-2b reference sample. The vaccine strains of CPV-2 were identified using CPV-87F/87R. Conventional methods for genotyping CPV strains are labor intensive, expensive or time consuming; the present PCR-based HRM assay might be an attractive alternative.

  7. Characterization of bacteriophages Cp1 and Cp2, the strain-typing agents for Xanthomonas axonopodis pv. citri.

    PubMed

    Ahmad, Abdelmonim Ali; Ogawa, Megumi; Kawasaki, Takeru; Fujie, Makoto; Yamada, Takashi

    2014-01-01

    The strains of Xanthomonas axonopodis pv. citri, the causative agent of citrus canker, are historically classified based on bacteriophage (phage) sensitivity. Nearly all X. axonopodis pv. citri strains isolated from different regions in Japan are lysed by either phage Cp1 or Cp2; Cp1-sensitive (Cp1(s)) strains have been observed to be resistant to Cp2 (Cp2(r)) and vice versa. In this study, genomic and molecular characterization was performed for the typing agents Cp1 and Cp2. Morphologically, Cp1 belongs to the Siphoviridae. Genomic analysis revealed that its genome comprises 43,870-bp double-stranded DNA (dsDNA), with 10-bp 3'-extruding cohesive ends, and contains 48 open reading frames. The genomic organization was similar to that of Xanthomonas phage phiL7, but it lacked a group I intron in the DNA polymerase gene. Cp2 resembles morphologically Escherichia coli T7-like phages of Podoviridae. The 42,963-bp linear dsDNA genome of Cp2 contained terminal repeats. The Cp2 genomic sequence has 40 open reading frames, many of which did not show detectable homologs in the current databases. By proteomic analysis, a gene cluster encoding structural proteins corresponding to the class III module of T7-like phages was identified on the Cp2 genome. Therefore, Cp1 and Cp2 were found to belong to completely different virus groups. In addition, we found that Cp1 and Cp2 use different molecules on the host cell surface as phage receptors and that host selection of X. axonopodis pv. citri strains by Cp1 and Cp2 is not determined at the initial stage by binding to receptors.

  8. Draft Genome Sequence of an Extended-Spectrum-β-Lactamase-Positive Hypervirulent Klebsiella pneumoniae Strain with Novel Sequence Type 2318 Isolated from a Neonate

    PubMed Central

    Shankar, Chaitra; Santhanam, Sridhar; Kumar, Manish; Gupta, Vijay; Devanga Ragupathi, Naveen Kumar

    2016-01-01

    Antimicrobial resistance among hypervirulent Klebsiella pneumoniae is increasingly reported. Here, we report the draft genome sequence of a hypervirulent K. pneumoniae strain isolated from a neonate with sepsis belonging to novel sequence type 2318 (ST2318). PMID:27834717

  9. Distribution of Clostridium botulinum Type E Strains in Nunavik, Northern Quebec, Canada

    PubMed Central

    Leclair, Daniel; Farber, Jeffrey M.; Doidge, Bill; Blanchfield, Burke; Suppa, Sandy; Pagotto, Franco

    2013-01-01

    The distribution and levels of Clostridium botulinum type E were determined from field sites used by Inuit hunters for butchering seals along the coast of Nunavik. The incidence rates of C. botulinum type E in shoreline soil along the coast were 0, 50, and 87.5% among samples tested for the Hudson Strait, Hudson Bay, and Ungava Bay regions, respectively. Spores were detected in seawater or coastal rock surfaces from 17.6% of butchering sites, almost all of which were located in southern Ungava Bay. Concentrations of C. botulinum type E along the Ungava Bay coast were significantly higher than on the coasts of Hudson Strait and Hudson Bay, with the highest concentrations (270 to 1,800/kg of sample) found near butchering sites located along the mouths of large rivers. The Koksoak River contained high levels of C. botulinum type E, with the highest median concentration (270/kg) found in sediments of the marine portion of the river. C. botulinum type E was found in the intestinal contents (4.4%) and skins (1.4%) of seals. A high genetic biodiversity of C. botulinum type E isolates was observed among the 21 butchering sites and their surroundings along the Nunavik coastline, with 83% of isolates (44/53) yielding distinct pulsed-field gel electrophoresis genotypes. Multiple sources of C. botulinum type E may be involved in the contamination of seal meat during butchering in this region, but the risk of contamination appears to be much higher from environmental sources along the shoreline of southern Ungava Bay and the sediments of the Koksoak River. PMID:23160120

  10. Distribution of Clostridium botulinum type E strains in Nunavik, Northern Quebec, Canada.

    PubMed

    Leclair, Daniel; Farber, Jeffrey M; Doidge, Bill; Blanchfield, Burke; Suppa, Sandy; Pagotto, Franco; Austin, John W

    2013-01-01

    The distribution and levels of Clostridium botulinum type E were determined from field sites used by Inuit hunters for butchering seals along the coast of Nunavik. The incidence rates of C. botulinum type E in shoreline soil along the coast were 0, 50, and 87.5% among samples tested for the Hudson Strait, Hudson Bay, and Ungava Bay regions, respectively. Spores were detected in seawater or coastal rock surfaces from 17.6% of butchering sites, almost all of which were located in southern Ungava Bay. Concentrations of C. botulinum type E along the Ungava Bay coast were significantly higher than on the coasts of Hudson Strait and Hudson Bay, with the highest concentrations (270 to 1,800/kg of sample) found near butchering sites located along the mouths of large rivers. The Koksoak River contained high levels of C. botulinum type E, with the highest median concentration (270/kg) found in sediments of the marine portion of the river. C. botulinum type E was found in the intestinal contents (4.4%) and skins (1.4%) of seals. A high genetic biodiversity of C. botulinum type E isolates was observed among the 21 butchering sites and their surroundings along the Nunavik coastline, with 83% of isolates (44/53) yielding distinct pulsed-field gel electrophoresis genotypes. Multiple sources of C. botulinum type E may be involved in the contamination of seal meat during butchering in this region, but the risk of contamination appears to be much higher from environmental sources along the shoreline of southern Ungava Bay and the sediments of the Koksoak River.

  11. Sexual reproduction and mating-type-mediated strain development in the penicillin-producing fungus Penicillium chrysogenum.

    PubMed

    Böhm, Julia; Hoff, Birgit; O'Gorman, Céline M; Wolfers, Simon; Klix, Volker; Binger, Danielle; Zadra, Ivo; Kürnsteiner, Hubert; Pöggeler, Stefanie; Dyer, Paul S; Kück, Ulrich

    2013-01-22

    Penicillium chrysogenum is a filamentous fungus of major medical and historical importance, being the original and present-day industrial source of the antibiotic penicillin. The species has been considered asexual for more than 100 y, and despite concerted efforts, it has not been possible to induce sexual reproduction, which has prevented sexual crosses being used for strain improvement. However, using knowledge of mating-type (MAT) gene organization, we now describe conditions under which a sexual cycle can be induced leading to production of meiotic ascospores. Evidence of recombination was obtained using both molecular and phenotypic markers. The identified heterothallic sexual cycle was used for strain development purposes, generating offspring with novel combinations of traits relevant to penicillin production. Furthermore, the MAT1-1-1 mating-type gene, known primarily for a role in governing sexual identity, was also found to control transcription of a wide range of genes with biotechnological relevance including those regulating penicillin production, hyphal morphology, and conidial formation. These discoveries of a sexual cycle and MAT gene function are likely to be of broad relevance for manipulation of other asexual fungi of economic importance.

  12. Characterization of Three nef-Defective Human Immunodeficiency Virus Type 1 Strains Associated with Long-Term Nonprogression

    PubMed Central

    Rhodes, David I.; Ashton, Lesley; Solomon, Ajantha; Carr, Andrew; Cooper, David; Kaldor, John; Deacon, Nicholas

    2000-01-01

    Long-term survivors (LTS) of human immunodeficiency virus type 1 (HIV-1) infection provide an opportunity to investigate both viral and host factors that influence the rate of disease progression. We have identified three HIV-1-infected individuals in Australia who have been infected for over 11 years with viruses that contain deletions in the nef and nef-long terminal repeat (nef/LTR) overlap regions. These viruses differ from each other and from other nef-defective strains of HIV-1 previously identified in Australia. One individual, LTS 3, is infected with a virus containing a nef gene with a deletion of 29 bp from the nef/LTR overlap region, resulting in a truncated Nef open reading frame. In addition to the Nef defect, only viruses containing truncated Vif open reading frames of 37 or 69 amino acids could be detected in peripheral blood mononuclear cells isolated from this patient. LTS 3 had a viral load of less than 20 copies of RNA/ml of plasma. The other two long-term survivors, LTS 9 and LTS 11, had loads of less than 200 copies of RNA/ml of plasma and are infected with viruses with larger deletions in both the nef alone and nef/LTR overlap regions. These viruses contain wild-type vif, vpu, and vpr accessory genes. All three strains of virus had envelope sequences characteristic of macrophagetropic viruses. These findings further indicate the reduced pathogenic potential of nef-defective viruses. PMID:11044102

  13. Infection of monocyte-derived macrophages with human immunodeficiency virus type 1 (HIV-1). Monocyte-tropic and lymphocyte-tropic strains of HIV-1 show distinctive patterns of replication in a panel of cell types.

    PubMed

    Collman, R; Hassan, N F; Walker, R; Godfrey, B; Cutilli, J; Hastings, J C; Friedman, H; Douglas, S D; Nathanson, N

    1989-10-01

    To characterize the host range of different strains of HIV-1, we have used four types of cells, primary monocyte-derived macrophages (MDM), primary PBL, a promonocyte cell line (U937), and a CD4+ T cell line (SUP-T1). These cells were infected with three prototype strains of HIV-1, a putative lymphocyte-tropic strain (IIIB), and two putative monocyte-tropic strains (SF162 and DV). Infections were monitored by assays for infectious virus, for cell-free and cell-associated viral antigen (p24), and for the proportion of cells infected by immunohistochemical staining. It was concluded that: (a) the use of four different cell types provides a useful biological matrix for distinguishing the tropism of different strains of HIV-1; this matrix yields more information than the infection of any single cell type. (b) A monocyte-tropic strain of HIV-1, such as strain SF162, shows a reciprocal host range when compared with a lymphocyte-tropic strain such as IIIB; strain SF162 replicates well in primary MDM but not in U937 or SUP-T1 cells, while strain IIIB replicates well in both U937 and SUP-T1 cells but not in MDM. (c) Both lymphocyte-tropic and monocyte-tropic strains of HIV-1 replicate well in PBL. (d) The promonocyte cell line, U937, and the T cell line, SUP-T1, differ markedly from primary cells, such as MDM and PBL, in their ability to support the replication of different strains of HIV-1; these cell lines cannot be used as surrogates for primary cells in host range studies of HIV-1 strains.

  14. Characterization of a novel gene for strain typing reveals substructuring of Aspergillus fumigatus across North America

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Fifty five epidemiologically linked Aspergillus fumigatus isolates obtained from six nosocomial outbreaks of invasive aspergillosis were sub-typed by sequencing the polymorphic region of the gene encoding a putative cell surface protein, Afu3g08990 (denoted as CSP). Comparative sequence analysis sh...

  15. Genomic sequence and virulence comparison of four type 2 porcine reproductive and respiratory syndrome virus strains

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Porcine reproductive and respiratory syndrome virus (PRRSV) is a ubiquitous and costly virus that exhibits substantial sequence and virulence disparity among diverse isolates. In this study, we compared the whole genomic sequence and virulence of 4 North American Type 2 PRRSV isolates. Among the 4 i...

  16. Molecular Strain Typing of Mycobacterium tuberculosis: a Review of Frequently Used Methods

    PubMed Central

    2016-01-01

    Tuberculosis, caused by the bacterium Mycobacterium tuberculosis, remains one of the most serious global health problems. Molecular typing of M. tuberculosis has been used for various epidemiologic purposes as well as for clinical management. Currently, many techniques are available to type M. tuberculosis. Choosing the most appropriate technique in accordance with the existing laboratory conditions and the specific features of the geographic region is important. Insertion sequence IS6110-based restriction fragment length polymorphism (RFLP) analysis is considered the gold standard for the molecular epidemiologic investigations of tuberculosis. However, other polymerase chain reaction-based methods such as spacer oligonucleotide typing (spoligotyping), which detects 43 spacer sequence-interspersing direct repeats (DRs) in the genomic DR region; mycobacterial interspersed repetitive units–variable number tandem repeats, (MIRU-VNTR), which determines the number and size of tandem repetitive DNA sequences; repetitive-sequence-based PCR (rep-PCR), which provides high-throughput genotypic fingerprinting of multiple Mycobacterium species; and the recently developed genome-based whole genome sequencing methods demonstrate similar discriminatory power and greater convenience. This review focuses on techniques frequently used for the molecular typing of M. tuberculosis and discusses their general aspects and applications. PMID:27709842

  17. Complete genome sequence of Deinococcus maricopensis type strain (LB-34T)

    SciTech Connect

    Pukall, Rudiger; Zeytun, Ahmet; Lucas, Susan; Lapidus, Alla L.; Hammon, Nancy; Deshpande, Shweta; Nolan, Matt; Cheng, Jan-Fang; Pitluck, Sam; Liolios, Konstantinos; Pagani, Ioanna; Mikhailova, Natalia; Ivanova, N; Mavromatis, K; Pati, Amrita; Tapia, Roxanne; Han, Cliff; Goodwin, Lynne A.; Chen, Amy; Palaniappan, Krishna; Land, Miriam L; Hauser, Loren John; Chang, Yun-Juan; Jeffries, Cynthia; Brambilla, Evelyne-Marie; Rohde, Manfred; Goker, Markus; Detter, J. Chris; Woyke, Tanja; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter

    2011-01-01

    Deinococcus maricopensis (Rainey and da Costa 2005) is a member of the genus Deinococcus, which is comprised of 44 validly named species and is located within the deeply branching bacterial phylum Deinococcus Thermus. Strain LB-34T was isolated from a soil sample from the Sonoran Desert in Arizona. Various species of the genus Deinococcus are characterized by extreme radiation resistance, with D. maricopensis being resistant in excess of 10 kGy. Even though the genomes of three Deinococcus species, D. radiodurans, D. geothermalis and D. deserti, have already been published, no special physiological characteristic is currently known that is unique to this group. It is therefore of special interest to analyze the genomes of additional species of the genus Deinococcus to better understand how these species adapted to gamma- or UV ionizing-radiation. The 3,498,530 bp long genome of D. maricopensis with its 3,301 protein-coding and 66 RNA genes consists of one circular chromosome and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  18. Molecular strain typing of Brucella abortus isolates from Italy by two VNTR allele sizing technologies.

    PubMed

    De Santis, Riccardo; Ancora, Massimo; De Massis, Fabrizio; Ciammaruconi, Andrea; Zilli, Katiuscia; Di Giannatale, Elisabetta; Pittiglio, Valentina; Fillo, Silvia; Lista, Florigio

    2013-10-01

    Brucellosis, one of the most important re-emerging zoonoses in many countries, is caused by bacteria belonging to the genus Brucella. Furthermore these bacteria represent potential biological warfare agents and the identification of species and biovars of field strains may be crucial for tracing back source of infection, allowing to discriminate naturally occurring outbreaks instead of bioterrorist events. In the last years, multiple-locus variable-number tandem repeat analysis (MLVA) has been proposed as complement of the classical biotyping methods and it has been applied for genotyping large collections of Brucella spp. At present, the MLVA band profiles may be resolved by automated or manual procedures. The Lab on a chip technology represents a valid alternative to standard genotyping techniques (as agarose gel electrophoresis) and it has been previously used for Brucella genotyping. Recently, a new high-throughput genotyping analysis system based on capillary gel electrophoresis, the QIAxcel, has been described. The aim of the study was to evaluate the ability of two DNA sizing equipments, the QIAxcel System and the Lab chip GX, to correctly call alleles at the sixteen loci including one frequently used MLVA assay for Brucella genotyping. The results confirmed that these technologies represent a meaningful advancement in high-throughput Brucella genotyping. Considering the accuracy required to confidently resolve loci discrimination, QIAxcel shows a better ability to measure VNTR allele sizes compared to LabChip GX.

  19. Bovine mastitis Staphylococcus aureus: antibiotic susceptibility profile, resistance genes and molecular typing of methicillin-resistant and methicillin-sensitive strains in China.

    PubMed

    Wang, Dengfeng; Wang, Zhicai; Yan, Zuoting; Wu, Jianyong; Ali, Tariq; Li, Jianjun; Lv, Yanli; Han, Bo

    2015-04-01

    The emergence of methicillin-resistant Staphylococcus aureus (MRSA) infection in dairy animals is of great concern for livestock and public health. The aim of present study was to detect new trends of methicillin-resistant Staphylococcus aureus (MRSA) and methicillin-sensitive Staphylococcus aureus (MSSA) towards antibiotic susceptibility, resistance genes and molecular typing by methods of disc diffusion, multiplex PCR assay and multilocus sequence typing (MLST). A total of 219 S. aureus strains were isolated from bovine mastitis cases from six provinces of China, including 34 MRSA strains. The results revealed that more than 70% isolated strains showed resistance to various antibiotics, and multiple-drugs resistance to more than five categories of antibiotics was found more common. The ermC was the most prevalent resistance gene, followed by other genes; however, ermA was the least frequently detected gene. Twenty-eight mecA-negative MRSA and six mecA-positive MRSA strains were detected, and in which three strains were ST97-MRSA-IV, others were ST965-MRSA-IV, ST6-MRSA-IV and ST9-MRSA-SCCmec-NT. The mecA-negative MRSA strains were found resistant to most of the antibiotics, and harbored aac(6')/aph(2''), aph(3')-III and tetM genes higher than MSSA strains. The resistance to most of the antibiotics was significantly higher in MRSA than in MSSA strains. The MLST profiles showed that these strains mainly belonged to CC5, CC398, CC121 and CC50 lineage, especially within ST97 and ST398, while some novel sequence types (ST2154, ST2165 and ST2166) were identified and deposited in the MLST database. This indicates that the resistance of S. aureus is becoming more complicated by changes in multi-drug resistance mechanism and appearance of mecA-negative MRSA isolates, and importantly, MRSA-IV strains in different MLST types are emerging.

  20. A multiplex reverse transcription-nested polymerase chain reaction for detection and differentiation of wild-type and vaccine strains of canine distemper virus.

    PubMed

    Si, Wei; Zhou, Shun; Wang, Zhao; Cui, Shang-jin

    2010-05-01

    A multiplex reverse transcription-nested polymerase chain reaction (RT-nPCR) method was developed for the detection and differentiation of wild-type and vaccine strains of canine distemper virus (CDV). A pair of primers (P1 and P4) specific for CDV corresponding to the highly conserved region of the CDV genome were used as a common primer pair in the first-round PCR of the nested PCR. Primers P2 specific for CDV wild-type strains, were used as the forward primer together with the common reverse primer P4 in the second round of nested PCR. Primers P3, P5 specific for CDV wild-type strain or vaccine strain, were used as the forward primer together with the common reverse primer P4+P6 in the second round of nested PCR. A fragment of 177 bp was amplified from vaccine strain genomic RNA, and a fragment of 247 bp from wild-type strain genomic RNA in the RT-nPCR, and two fragments of 247 bp and 177 bp were amplified from the mixed samples of vaccine and wild-type strains. No amplification was achieved for uninfected cells, or cells infected with Newcastle disease virus (NDV), canine parvovirus (CPV), canine coronavirus (CCV), rabies virus (RV), or canine adenovirus (CAV). The RT-nPCR method was used to detect 30 field samples suspected of canine distemper from Heilongjiang and Jilin Provinces, and 51 samples in Shandong province. As a result of 30 samples, were found to be wild-type-like, and 5 to be vaccine-strain-like. The RT-nPCR method can be used to effectively detect and differentiate wild-type CDV-infected dogs from dogs vaccinated with CDV vaccine, and thus can be used in clinical detection and epidemiological surveillance.

  1. Complete genome sequence of Nocardiopsis dassonvillei type strain (IMRU 509T)

    SciTech Connect

    Sun, Hui; Lapidus, Alla L.; Nolan, Matt; Lucas, Susan; Glavina Del Rio, Tijana; Tice, Hope; Cheng, Jan-Fang; Tapia, Roxanne; Han, Cliff; Goodwin, Lynne A.; Pitluck, Sam; Pagani, Ioanna; Ivanova, N; Mavromatis, K; Mikhailova, Natalia; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam L; Hauser, Loren John; Chang, Yun-Juan; Jeffries, Cynthia; Djao, Olivier Duplex; Rohde, Manfred; Sikorski, Johannes; Goker, Markus; Woyke, Tanja; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter

    2010-01-01

    Nocardiopsis dassonvillei (Brocq-Rousseau 1904) Meyer 1976 is the type species of the genus Nocardiopsis, which in turn is the type genus of the family Nocardiopsaceae. This species is of interest because of its ecological versatility. Members of N. dassonvillei have been isolated from a large variety of natural habitats such as soil and marine sediments, from different plant and animal materials as well as from human patients. Moreover, representatives of the genus Nocardiopsis participate actively in biopolymer degradation. This is the first complete genome sequence in the family Nocardiopsaceae. Here we describe the features of this organism, together with the complete genome sequence and annotation. The 6,543,312 bp long genome consist of a 5.77 Mbp chromosome and a 0.78 Mbp plasmid and with its 5,570 protein-coding and 77 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  2. Genome Sequence of a Novel Porcine Circovirus Type 2 Strain That Reemerged in Southern China

    PubMed Central

    Zhou, Xia; Lin, Tao; Zhang, He; Lv, Dian-Hong; Wen, Xiao-Hui; Zhou, Xiu-Rong; Jia, Chun-Ling; Tu, Du; Zhu, Xue-Liang; Chen, Qin-Ling

    2017-01-01

    ABSTRACT Here, we describe a novel porcine circovirus type 2 (PCV2) variant (GD2014) found in the Guangdong province, southern China. Its complete genome is 1,766 nucleotides and contained a 708-nucleotide open reading frame 2 (ORF2). Sequence analysis suggested that GD2014 is closest to JS2015 originating from the Jiangsu province of China and belongs to the PCV2d genotype. PMID:28209816

  3. Detection, identification and typing of Acidithiobacillus species and strains: a review.

    PubMed

    Nuñez, Harold; Covarrubias, Paulo C; Moya-Beltrán, Ana; Issotta, Francisco; Atavales, Joaquín; Acuña, Lillian G; Johnson, D Barrie; Quatrini, Raquel

    2016-09-01

    The genus Acidithiobacillus comprises several species of Gram-negative acidophilic bacteria that thrive in natural and man-made low pH environments in a variety of geo-climatic contexts. Beyond their fundamental interest as model extreme acidophiles, these bacteria are involved in the processing of minerals and the desulfurization of coal and natural gas, and are also sources of environmental pollution due to their generation of acid mine drainage and corrosion of cement and concrete structures. Acidithiobacillus spp. are therefore considered a biotechnologically relevant group of bacteria, and their identification and screening in natural and industrial environments is of great concern. Several molecular typing methodologies have been instrumental in improving knowledge of the inherent diversity of acidithiobacilli by providing information on the genetic subtypes sampled in public and private culture collections; more recently, they have provided specific insight into the diversity of acidithiobacilli present in industrial and natural environments. The aim of this review is to provide an overview of techniques used in molecular detection, identification and typing of Acidithiobacillus spp. These methods will be discussed in the context of their contribution to the general and specific understanding of the role of the acidithiobacilli in microbial ecology and industrial biotechnology. Emerging opportunities for industrial and environmental surveillance of acidithiobacilli using next-generation molecular typing methodologies are also reviewed.

  4. Multilocus sequence typing is a reliable alternative method to DNA fingerprinting for discriminating among strains of Candida albicans.

    PubMed

    Robles, Juan C; Koreen, Larry; Park, Steven; Perlin, David S

    2004-06-01

    Multilocus sequence typing (MLST) has emerged as a powerful new DNA-typing tool for the evaluation of intraspecies genetic relatedness. This method relies on DNA sequence analysis of nucleotide polymorphisms in housekeeping genes and has shown a high degree of intraspecies discriminatory power for bacterial and fungal pathogens. However, the results of the MLST scheme for Candida albicans have heretofore never been formally compared to those of other established typing techniques. To assess the value of MLST relative to those of other DNA fingerprinting tools for discriminating among strains of C. albicans, we applied it to a previously well-characterized set of 29 C. albicans isolates evaluated by the random amplified polymorphic DNA (RAPD), multilocus enzyme electrophoresis (MLEE), and Ca3 Southern hybridization probe techniques. MLST identified three clusters of genetically related isolates, with 82.3% direct concordance with MLEE, 82.7% with RAPD analysis, and 86.2% with the Ca3 Southern hybridization technique. When MLST was applied to a subset of 22 isolates of unrelated origins, it identified 21 independent diploid sequence types (DSTs), resulting in a discriminatory power of 99.6%. These DSTs were 96.9, 99.6, and 99.6% concordant with the genotypes identified by RAPD analysis, MLEE, and Ca3 Southern hybridization, respectively. These results demonstrate that MLST is a highly effective technique that performs at least comparably to other established DNA fingerprinting techniques.

  5. Prolonged Growth of a Clinical Staphylococcus aureus Strain Selects for a Stable Small-Colony-Variant Cell Type

    PubMed Central

    Bui, Long M. G.; Hoffmann, Peter; Turnidge, John D.; Zilm, Peter S.

    2014-01-01

    An undetermined feature of Staphylococcus aureus pathogenesis is its persistence and then relapse of disease. This has been explained by its switch to alternative lifestyles, mainly as biofilm or small-colony variants (SCVs). Studying the native characteristics of SCVs has been problematic due to their reversion to the parental lifestyle. We have observed that for a number of S. aureus strains as they switch to an SCV lifestyle, there is the formation of an extracellular matrix. We focused our analysis on one strain, WCH-SK2. For bacterial survival in the host, the combination of low nutrients and the prolonged time frame forms a stress that selects for a specific cell type from the population. In this context, we used steady-state growth conditions with low nutrients and a controlled low growth rate for a prolonged time and with methylglyoxal. These conditions induced S. aureus WCH-SK2 into a stable SCV cell type; the cells did not revert after subculturing. Analysis revealed these cells possessed a metabolic and surface profile that was different from those of previously described SCVs or biofilm cells. The extracellular matrix was protein and extracellular DNA but not polysaccharide. The SCV cells induced expression of certain surface proteins (such as Ebh) and synthesis of lantibiotics while downregulating factors that stimulate the immune response (leucocidin, capsule, and carotenoid). Our data reveal cell heterogeneity within an S. aureus population and under conditions that resemble long-term survival in the host have identified a previously unnoticed S. aureus cell type with a distinctive metabolic and molecular profile. PMID:25385795

  6. Molecular Typing of Mycobacterium Tuberculosis Complex by 24-Locus Based MIRU-VNTR Typing in Conjunction with Spoligotyping to Assess Genetic Diversity of Strains Circulating in Morocco

    PubMed Central

    Bouklata, Nada; Supply, Philip; Jaouhari, Sanae; Charof, Reda; Seghrouchni, Fouad; Sadki, Khalid; El Achhab, Youness; Nejjari, Chakib; Filali-Maltouf, Abdelkarim

    2015-01-01

    Background Standard 24-locus Mycobacterial Interspersed Repetitive Unit Variable Number Tandem Repeat (MIRU-VNTR) typing allows to get an improved resolution power for tracing TB transmission and predicting different strain (sub) lineages in a community. Methodology During 2010–2012, a total of 168 Mycobacterium tuberculosis Complex (MTBC) isolates were collected by cluster sampling from 10 different Moroccan cities, and centralized by the National Reference Laboratory of Tuberculosis over the study period. All isolates were genotyped using spoligotyping, and a subset of 75 was genotyped using 24-locus based MIRU-VNTR typing, followed by first line drug susceptibility testing. Corresponding strain lineages were predicted using MIRU-VNTRplus database. Principal Findings Spoligotyping resulted in 137 isolates in 18 clusters (2–50 isolates per cluster: clustering rate of 81.54%) corresponding to a SIT number in the SITVIT database, while 31(18.45%) patterns were unique of which 10 were labelled as “unknown” according to the same database. The most prevalent spoligotype family was LAM; (n = 81 or 48.24% of isolates, dominated by SIT42, n = 49), followed by Haarlem (23.80%), T superfamily (15.47%), >Beijing (2.97%), > U clade (2.38%) and S clade (1.19%). Subsequent 24-Locus MIRU-VNTR typing identified 64 unique types and 11 isolates in 5 clusters (2 to 3isolates per cluster), substantially reducing clusters defined by spoligotyping only. The single cluster of three isolates corresponded to two previously treated MDR-TB cases and one new MDR-TB case known to be contact a same index case and belonging to a same family, albeit residing in 3 different administrative regions. MIRU-VNTR loci 4052, 802, 2996, 2163b, 3690, 1955, 424, 2531, 2401 and 960 were highly discriminative in our setting (HGDI >0.6). Conclusions 24-locus MIRU-VNTR typing can substantially improve the resolution of large clusters initially defined by spoligotyping alone and predominating in Morocco

  7. Complete genome sequence of Xylanimonas cellulosilytica type strain (XIL07T)

    SciTech Connect

    Foster, Brian; Pukall, Rudiger; Abt, Birte; Nolan, Matt; Glavina Del Rio, Tijana; Chen, Feng; Lucas, Susan; Tice, Hope; Pitluck, Sam; Cheng, Jan-Fang; Chertkov, Olga; Brettin, Thomas S; Han, Cliff; Detter, J C; Bruce, David; Goodwin, Lynne A.; Ivanova, N; Mavromatis, K; Pati, Amrita; Mikhailova, Natalia; Chen, Amy; Palaniappan, Krishna; Land, Miriam L; Hauser, Loren John; Chang, Yun-Juan; Jeffries, Cynthia; Chain, Patrick S. G.; Rohde, Manfred; Goker, Markus; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter; Lapidus, Alla L.

    2010-01-01

    Xylanimonas cellulosilytica Rivas et al. 2003 is the type species of the genus Xylanimonas of the actinobacterial family Promicromonosporaceae. The species X. cellulosilytica is of interest because of its ability to hydrolyze cellulose and xylan. Here we describe the features of this organism, together with the complete genome sequence, and annotation. This is the first complete genome sequence of a member of the large family Promicromonosporaceae, and the 3,831,380 bp long genome (one chromosome plus an 88,604 bp long plasmid) with its 3485 protein-coding and 61 RNA genes is part of the Genomic Encyclopedia of Bacteria and Archaea project.

  8. Complete genome sequence of Riemerella anatipestifer type strain (BrunerT)

    SciTech Connect

    Mavromatis, K; Lu, Megan; Misra, Monica; Lapidus, Alla L.; Nolan, Matt; Lucas, Susan; Hammon, Nancy; Deshpande, Shweta; Cheng, Jan-Fang; Tapia, Roxanne; Han, Cliff; Goodwin, Lynne A.; Pitluck, Sam; Liolios, Konstantinos; Pagani, Ioanna; Ivanova, N; Mikhailova, Natalia; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam L; Hauser, Loren John; Chang, Yun-Juan; Jeffries, Cynthia; Detter, J. Chris; Brambilla, Evelyne-Marie; Rohde, Manfred; Goker, Markus; Gronow, Sabine; Woyke, Tanja; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Klenk, Hans-Peter; Kyrpides, Nikos C

    2011-01-01

    Riemerella anatipestifer (Hendrickson and Hilbert 1932) Segers et al. 1993 is the type species of the genus Riemerella, which belongs to the family Flavobacteriaceae. The species is of interest because of the position of the genus in the phylogenetic tree and because of its role as a pathogen of commercially important avian species worldwide. This is the first completed genome sequence of a member of the genus Riemerella. The 2,155,121 bp long genome with its 2,001 protein-coding and 51 RNA genes consists of one circular chromosome and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  9. Complete genome sequence of the facultatively anaerobic, appendaged bacterium Muricauda ruestringensis type strain (B1(T)).

    PubMed

    Huntemann, Marcel; Teshima, Hazuki; Lapidus, Alla; Nolan, Matt; Lucas, Susan; Hammon, Nancy; Deshpande, Shweta; Cheng, Jan-Fang; Tapia, Roxanne; Goodwin, Lynne A; Pitluck, Sam; Liolios, Konstantinos; Pagani, Ioanna; Ivanova, Natalia; Mavromatis, Konstantinos; Mikhailova, Natalia; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Pan, Chongle; Brambilla, Evelyne-Marie; Rohde, Manfred; Spring, Stefan; Göker, Markus; Detter, John C; Bristow, James; Eisen, Jonathan A; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter; Woyke, Tanja

    2012-05-25

    Muricauda ruestringensis Bruns et al. 2001 is the type species of the genus Muricauda, which belongs to the family Flavobacteriaceae in the phylum Bacteroidetes. The species is of interest because of its isolated position in the genomically unexplored genus Muricauda, which is located in a part of the tree of life containing not many organisms with sequenced genomes. The genome, which consists of a circular chromosome of 3,842,422 bp length with a total of 3,478 protein-coding and 47 RNA genes, is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  10. Complete genome sequence of the facultatively anaerobic, appendaged bacterium Muricauda ruestringensis type strain (B1T)

    SciTech Connect

    Huntemann, Marcel; Teshima, Hazuki; Lapidus, Alla L.; Nolan, Matt; Lucas, Susan; Hammon, Nancy; Deshpande, Shweta; Cheng, Jan-Fang; Tapia, Roxanne; Goodwin, Lynne A.; Pitluck, Sam; Liolios, Konstantinos; Pagani, Ioanna; Ivanova, N; Mavromatis, K; Mikhailova, Natalia; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam L; Hauser, Loren John; Pan, Chongle; Brambilla, Evelyne-Marie; Rohde, Manfred; Spring, Stefan; Goker, Markus; Detter, J. Chris; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter; Woyke, Tanja

    2012-01-01

    Muricauda ruestringensis Bruns et al. 2001 is the type species of the genus Muricauda, which belongs to the family Flavobacteriaceae in the phylum Bacteroidetes. The species is of interest because of its isolated position in the genomically unexplored genus Muricauda, which is located in a part of the tree of life containing not many organisms with sequenced genomes. The genome, which consists of a circular chromosome of 3,842,422 bp length with a total of 3,478 protein-coding and 47 RNA genes, is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  11. Complete genome sequence of the facultatively anaerobic, appendaged bacterium Muricauda ruestringensis type strain (B1T)

    PubMed Central

    Huntemann, Marcel; Teshima, Hazuki; Lapidus, Alla; Nolan, Matt; Lucas, Susan; Hammon, Nancy; Deshpande, Shweta; Cheng, Jan-Fang; Tapia, Roxanne; Goodwin, Lynne A.; Pitluck, Sam; Liolios, Konstantinos; Pagani, Ioanna; Ivanova, Natalia; Mavromatis, Konstantinos; Mikhailova, Natalia; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam; Hauser, Loren; Pan, Chongle; Brambilla, Evelyne-Marie; Rohde, Manfred; Spring, Stefan; Göker, Markus; Detter, John C.; Bristow, James; Eisen, Jonathan A.; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C.; Klenk, Hans-Peter; Woyke, Tanja

    2012-01-01

    Muricauda ruestringensis Bruns et al. 2001 is the type species of the genus Muricauda, which belongs to the family Flavobacteriaceae in the phylum Bacteroidetes. The species is of interest because of its isolated position in the genomically unexplored genus Muricauda, which is located in a part of the tree of life containing not many organisms with sequenced genomes. The genome, which consists of a circular chromosome of 3,842,422 bp length with a total of 3,478 protein-coding and 47 RNA genes, is a part of the Genomic Encyclopedia of Bacteria and Archaea project. PMID:22768362

  12. Complete genome sequence of Paludibacter propionicigenes type strain (WB4T)

    SciTech Connect

    Gronow, Sabine; Munk, Christine; Lapidus, Alla L.; Nolan, Matt; Lucas, Susan; Hammon, Nancy; Deshpande, Shweta; Cheng, Jan-Fang; Tapia, Roxanne; Han, Cliff; Goodwin, Lynne A.; Pitluck, Sam; Liolios, Konstantinos; Ivanova, N; Mavromatis, K; Mikhailova, Natalia; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Land, Miriam L; Hauser, Loren John; Chang, Yun-Juan; Jeffries, Cynthia; Brambilla, Evelyne-Marie; Rohde, Manfred; Goker, Markus; Detter, J. Chris; Woyke, Tanja; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter

    2011-01-01

    Paludibacter propionicigenes Ueki et al. 2006 is the type species of the genus Paludibacter, which belongs to the family Porphyromonadaceae. The species is of interest because of the position it occupies in the tree of life where it can be found in close proximity to members of the genus Dysgonomonas. This is the first completed genome sequence of a member of the genus Paludibacter and the third sequence from the family Porphyromonadaceae. The 3,685,504 bp long genome with its 3,054 protein-coding and 64 RNA genes consists of one circular chromosome and is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  13. Complete genome sequence of Calditerrivibrio nitroreducens type strain (Yu37-1T)

    SciTech Connect

    Pitluck, Sam; Sikorski, Johannes; Zeytun, Ahmet; Lapidus, Alla L.; Nolan, Matt; Lucas, Susan; Hammon, Nancy; Deshpande, Shweta; Cheng, Jan-Fang; Tapia, Roxanne; Han, Cliff; Goodwin, Lynne A.; Liolios, Konstantinos; Pagani, Ioanna; Ivanova, N; Mavromatis, K; Pati, Amrita; Chen, Amy; Palaniappan, Krishna; Hauser, Loren John; Chang, Yun-Juan; Jeffries, Cynthia; Detter, J. Chris; Brambilla, Evelyne-Marie; Ngatchou, Olivier Duplex; Rohde, Manfred; Spring, Stefan; Goker, Markus; Woyke, Tanja; Bristow, James; Eisen, Jonathan; Markowitz, Victor; Hugenholtz, Philip; Kyrpides, Nikos C; Klenk, Hans-Peter; Land, Miriam L

    2011-01-01

    Calditerrivibrio nitroreducens Iino et al. 2008 is the type species of the genus Calditerrivibrio. The species is of interest because of its important role in the nitrate cycle as nitrate reducer and for its isolated phylogenetic position in the Tree of Life. Here we describe the features of this organism, together with the complete genome sequence and annotation. This is the third complete genome sequence of a member of the family Deferribacteraceae. The 2,216,552 bp long genome with its 2,128 protein-coding and 50 RNA genes is a part of the Genomic Encyclopedia of Bacteria and Archaea project.

  14. Complete genome sequence of Odoribacter splanchnicus type strain (1651/6T)

    SciTech Connect

    Goker, Markus; Gronow, Sabine; Zeytun, Ahmet; Nolan, Matt; Lucas, Susan; Lapidus, Alla L.;