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Sample records for community-associated cmrsa-10 usa-300

  1. CodY Deletion Enhances In Vivo Virulence of Community-Associated Methicillin-Resistant Staphylococcus aureus Clone USA300

    PubMed Central

    Boyle-Vavra, Susan; Roux, Agnès; Ebine, Kazumi; Sonenshein, Abraham L.; Daum, Robert S.

    2012-01-01

    The Staphylococcus aureus global regulator CodY responds to nutrient availability by controlling the expression of target genes. In vitro, CodY represses the transcription of virulence genes, but it is not known if CodY also represses virulence in vivo. The dominant community-associated methicillin-resistant S. aureus (CA-MRSA) clone, USA300, is hypervirulent and has increased transcription of global regulators and virulence genes; these features are reminiscent of a strain defective in CodY. Sequence analysis revealed, however, that the codY genes of USA300 and other sequenced S. aureus isolates are not significantly different from the codY genes in strains known to have active CodY. codY was expressed in USA300, as well as in other pulsotypes assessed. Deletion of codY from a USA300 clinical isolate resulted in modestly increased expression of the global regulators agr and saeRS, as well as the gene encoding the toxin alpha-hemolysin (hla). A substantial increase (>30-fold) in expression of the lukF-PV gene, encoding part of the Panton-Valentine leukocidin (PVL), was observed in the codY mutant. All of these expression differences were reversed by complementation with a functional codY gene. Moreover, purified CodY protein bound upstream of the lukSF-PV operon, indicating that CodY directly represses expression of lukSF-PV. Deletion of codY increased the virulence of USA300 in necrotizing pneumonia and skin infection. Interestingly, deletion of lukSF-PV from the codY mutant did not attenuate virulence, indicating that the hypervirulence of the codY mutant was not explained by overexpression of PVL. These results demonstrate that CodY is active in USA300 and that CodY-mediated repression restrains the virulence of USA300. PMID:22526672

  2. Virulence strategies of the dominant USA300 lineage of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA).

    PubMed

    Thurlow, Lance R; Joshi, Gauri S; Richardson, Anthony R

    2012-06-01

    Methicillin-resistant Staphylococcus aureus (MRSA) poses a serious threat to worldwide health. Historically, MRSA clones have strictly been associated with hospital settings, and most hospital-associated MRSA (HA-MRSA) disease resulted from a limited number of virulent clones. Recently, MRSA has spread into the community causing disease in otherwise healthy people with no discernible contact with healthcare environments. These community-associated MRSA clones (CA-MRSA) are phylogenetically distinct from traditional HA-MRSA clones, and CA-MRSA strains seem to exhibit hypervirulence and more efficient host : host transmission. Consequently, CA-MRSA clones belonging to the USA300 lineage have become dominant sources of MRSA infections in North America. The rise of this successful USA300 lineage represents an important step in the evolution of emerging pathogens and a great deal of effort has been exerted to understand how these clones evolved. Here, we review much of the recent literature aimed at illuminating the source of USA300 success and broadly categorize these findings into three main categories: newly acquired virulence genes, altered expression of common virulence determinants and alterations in protein sequence that increase fitness. We argue that none of these evolutionary events alone account for the success of USA300, but rather their combination may be responsible for the rise and spread of CA-MRSA.

  3. Role of lipase from community-associated methicillin-resistant Staphylococcus aureus strain USA300 in hydrolyzing triglycerides into growth-inhibitory free fatty acids.

    PubMed

    Cadieux, Brigitte; Vijayakumaran, Vithooshan; Bernards, Mark A; McGavin, Martin J; Heinrichs, David E

    2014-12-01

    Part of the human host innate immune response involves the secretion of bactericidal lipids on the skin and delivery of triglycerides into abscesses to control invading pathogens. Two Staphylococcus aureus lipases, named SAL1 and SAL2, were identified in the community-associated methicillin-resistant S. aureus strain USA300, which, presumably, are produced and function to degrade triglycerides to release free fatty acids. We show that the SAL2 lipase is one of the most abundant proteins secreted by USA300 and is proteolytically processed from the 72-kDa proSAL2 to the 44-kDa mature SAL2 by the metalloprotease aureolysin. We show that spent culture supernatants had lipase activity on both short- and long-chain fatty acid substrates and that deletion of gehB, encoding SAL2, resulted in the complete loss of these activities. With the use of gas chromatography-mass spectrometry, we show that SAL2 hydrolyzed trilinolein to linoleic acid, a fatty acid with known antistaphylococcal properties. When added to cultures of USA300, trilinolein and, to a lesser extent, triolein inhibited growth in a SAL2-dependent manner. This effect was shown to be due to the enzymatic activity of SAL2 on these triglycerides, since the catalytically inactive SAL2 Ser412Ala mutant was incapable of hydrolyzing the triglycerides or yielding delayed growth in their presence. Overall, these results reveal that SAL2 hydrolyzes triglycerides of both short- and long-chain fatty acids and that the released free fatty acids have the potential to cause significant delays in growth, depending on the chemical nature of the free fatty acid. PMID:25225262

  4. Role of lipase from community-associated methicillin-resistant Staphylococcus aureus strain USA300 in hydrolyzing triglycerides into growth-inhibitory free fatty acids.

    PubMed

    Cadieux, Brigitte; Vijayakumaran, Vithooshan; Bernards, Mark A; McGavin, Martin J; Heinrichs, David E

    2014-12-01

    Part of the human host innate immune response involves the secretion of bactericidal lipids on the skin and delivery of triglycerides into abscesses to control invading pathogens. Two Staphylococcus aureus lipases, named SAL1 and SAL2, were identified in the community-associated methicillin-resistant S. aureus strain USA300, which, presumably, are produced and function to degrade triglycerides to release free fatty acids. We show that the SAL2 lipase is one of the most abundant proteins secreted by USA300 and is proteolytically processed from the 72-kDa proSAL2 to the 44-kDa mature SAL2 by the metalloprotease aureolysin. We show that spent culture supernatants had lipase activity on both short- and long-chain fatty acid substrates and that deletion of gehB, encoding SAL2, resulted in the complete loss of these activities. With the use of gas chromatography-mass spectrometry, we show that SAL2 hydrolyzed trilinolein to linoleic acid, a fatty acid with known antistaphylococcal properties. When added to cultures of USA300, trilinolein and, to a lesser extent, triolein inhibited growth in a SAL2-dependent manner. This effect was shown to be due to the enzymatic activity of SAL2 on these triglycerides, since the catalytically inactive SAL2 Ser412Ala mutant was incapable of hydrolyzing the triglycerides or yielding delayed growth in their presence. Overall, these results reveal that SAL2 hydrolyzes triglycerides of both short- and long-chain fatty acids and that the released free fatty acids have the potential to cause significant delays in growth, depending on the chemical nature of the free fatty acid.

  5. USA300 Methicillin-Resistant Staphylococcus aureus, United States, 2000-2013.

    PubMed

    Carrel, Margaret; Perencevich, Eli N; David, Michael Z

    2015-11-01

    In the United States, methicillin-resistant Staphylococcus aureus (MRSA) with the USA300 pulsed-field gel electrophoresis type causes most community-associated MRSA infections and is an increasingly common cause of health care-associated MRSA infections. USA300 probably emerged during the early 1990s. To assess the spatiotemporal diffusion of USA300 MRSA and USA100 MRSA throughout the United States, we systematically reviewed 354 articles for data on 33,543 isolates, of which 8,092 were classified as USA300 and 2,595 as USA100. Using the biomedical literature as a proxy for USA300 prevalence among genotyped MRSA samples, we found that USA300 was isolated during 2000 in several states, including California, Texas, and midwestern states. The geographic mean center of USA300 MRSA then shifted eastward from 2000 to 2013. Analyzing genotyping studies enabled us to track the emergence of a new, successful MRSA type in space and time across the country.

  6. USA300 Methicillin-Resistant Staphylococcus aureus, United States, 2000–2013

    PubMed Central

    Perencevich, Eli N.; David, Michael Z.

    2015-01-01

    In the United States, methicillin-resistant Staphylococcus aureus (MRSA) with the USA300 pulsed-field gel electrophoresis type causes most community-associated MRSA infections and is an increasingly common cause of health care–associated MRSA infections. USA300 probably emerged during the early 1990s. To assess the spatiotemporal diffusion of USA300 MRSA and USA100 MRSA throughout the United States, we systematically reviewed 354 articles for data on 33,543 isolates, of which 8,092 were classified as USA300 and 2,595 as USA100. Using the biomedical literature as a proxy for USA300 prevalence among genotyped MRSA samples, we found that USA300 was isolated during 2000 in several states, including California, Texas, and midwestern states. The geographic mean center of USA300 MRSA then shifted eastward from 2000 to 2013. Analyzing genotyping studies enabled us to track the emergence of a new, successful MRSA type in space and time across the country. PMID:26484389

  7. Complete nucleotide sequence analysis of plasmids in strains of Staphylococcus aureus clone USA300 reveals a high level of identity among isolates with closely related core genome sequences.

    PubMed

    Kennedy, Adam D; Porcella, Stephen F; Martens, Craig; Whitney, Adeline R; Braughton, Kevin R; Chen, Liang; Craig, Carly T; Tenover, Fred C; Kreiswirth, Barry N; Musser, James M; DeLeo, Frank R

    2010-12-01

    A community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) strain known as pulsed-field type USA300 (USA300) is epidemic in the United States. Previous comparative whole-genome sequencing studies demonstrated that there has been recent clonal emergence of a subset of USA300 isolates, which comprise the epidemic clone. Although the core genomes of these isolates are closely related, the level of diversity among USA300 plasmids was not resolved. Inasmuch as these plasmids might contribute to significant gene diversity among otherwise closely related USA300 isolates, we performed de novo sequencing of endogenous plasmids from 10 previously characterized USA300 clinical isolates obtained from different geographic locations in the United States. All isolates tested contained small (2- to 3-kb) and/or large (27- to 30-kb) plasmids. The large plasmids encoded heavy metal and/or antimicrobial resistance elements, including those that confer resistance to cadmium, bacitracin, macrolides, penicillin, kanamycin, and streptothricin, although all isolates were sensitive to minocycline, doxycycline, trimethoprim-sulfamethoxazole, vancomycin, teicoplanin, and linezolid. One of the USA300 isolates contained an archaic plasmid that encoded staphylococcal enterotoxins R, J, and P. Notably, the large plasmids (27 to 28 kb) from 8 USA300 isolates--those that comprise the epidemic USA300 clone--were virtually identical (99% identity) and similar to a large plasmid from strain USA300_TCH1516 (a previously sequenced USA300 strain from Houston, TX). These plasmids are largely divergent from the 37-kb plasmid of FPR3757, the first sequenced USA300 strain. The high level of plasmid sequence identity among the majority of closely related USA300 isolates is consistent with the recent clonal emergence hypothesis for USA300.

  8. USA300 and USA500 Clonal Lineages of Staphylococcus aureus Do Not Produce a Capsular Polysaccharide Due to Conserved Mutations in the cap5 Locus

    PubMed Central

    Li, Xue; Alam, Md Tauqeer; Read, Timothy D.; Sieth, Julia; Cywes-Bentley, Colette; Dobbins, Ginette; David, Michael Z.; Kumar, Neha; Eells, Samantha J.; Miller, Loren G.; Boxrud, David J.; Chambers, Henry F.; Lynfield, Ruth; Lee, Jean C.; Daum, Robert S.

    2015-01-01

    ABSTRACT The surface capsular polysaccharide (CP) is a virulence factor that has been used as an antigen in several successful vaccines against bacterial pathogens. A vaccine has not yet been licensed against Staphylococcus aureus, although two multicomponent vaccines that contain CP antigens are in clinical trials. In this study, we evaluated CP production in USA300 methicillin-resistant S. aureus (MRSA) isolates that have become the predominant community-associated MRSA clones in the United States. We found that all 167 USA300 MRSA and 50 USA300 methicillin-susceptible S. aureus (MSSA) isolates were CP negative (CP−). Moreover, all 16 USA500 isolates, which have been postulated to be the progenitor lineage of USA300, were also CP−. Whole-genome sequence analysis of 146 CP− USA300 MRSA isolates revealed they all carry a cap5 locus with 4 conserved mutations compared with strain Newman. Genetic complementation experiments revealed that three of these mutations (in the cap5 promoter, cap5D nucleotide 994, and cap5E nucleotide 223) ablated CP production in USA300 and that Cap5E75 Asp, located in the coenzyme-binding domain, is essential for capsule production. All but three USA300 MSSA isolates had the same four cap5 mutations found in USA300 MRSA isolates. Most isolates with a USA500 pulsotype carried three of these four USA300-specific mutations, suggesting the fourth mutation occurred in the USA300 lineage. Phylogenetic analysis of the cap loci of our USA300 isolates as well as publicly available genomes from 41 other sequence types revealed that the USA300-specific cap5 mutations arose sequentially in S. aureus in a common ancestor of USA300 and USA500 isolates. PMID:25852165

  9. Interactions of methicillin resistant Staphylococcus aureus USA300 and Pseudomonas aeruginosa in polymicrobial wound infection.

    PubMed

    Pastar, Irena; Nusbaum, Aron G; Gil, Joel; Patel, Shailee B; Chen, Juan; Valdes, Jose; Stojadinovic, Olivera; Plano, Lisa R; Tomic-Canic, Marjana; Davis, Stephen C

    2013-01-01

    Understanding the pathology resulting from Staphylococcus aureus and Pseudomonas aeruginosa polymicrobial wound infections is of great importance due to their ubiquitous nature, increasing prevalence, growing resistance to antimicrobial agents, and ability to delay healing. Methicillin-resistant S. aureus USA300 is the leading cause of community-associated bacterial infections resulting in increased morbidity and mortality. We utilized a well-established porcine partial thickness wound healing model to study the synergistic effects of USA300 and P. aeruginosa on wound healing. Wound re-epithelialization was significantly delayed by mixed-species biofilms through suppression of keratinocyte growth factor 1. Pseudomonas showed an inhibitory effect on USA300 growth in vitro while both species co-existed in cutaneous wounds in vivo. Polymicrobial wound infection in the presence of P. aeruginosa resulted in induced expression of USA300 virulence factors Panton-Valentine leukocidin and α-hemolysin. These results provide evidence for the interaction of bacterial species within mixed-species biofilms in vivo and for the first time, the contribution of virulence factors to the severity of polymicrobial wound infections.

  10. Toward an understanding of the evolution of Staphylococcus aureus strain USA300 during colonization in community households.

    PubMed

    Uhlemann, Anne-Catrin; Kennedy, Adam D; Martens, Craig; Porcella, Stephen F; Deleo, Frank R; Lowy, Franklin D

    2012-01-01

    Staphylococcus aureus is a frequent cause of serious infections and also a human commensal. The emergence of community-associated methicillin-resistant S. aureus led to a dramatic increase in skin and soft tissue infections worldwide. This epidemic has been driven by a limited number of clones, such as USA300 in the United States. To better understand the extent of USA300 evolution and diversification within communities, we performed comparative whole-genome sequencing of three clinical and five colonizing USA300 isolates collected longitudinally from three unrelated households over a 15-month period. Phylogenetic analysis that incorporated additional geographically diverse USA300 isolates indicated that all but one likely arose from a common recent ancestor. Although limited genetic adaptation occurred over the study period, the greatest genetic heterogeneity occurred between isolates from different households and within one heavily colonized household. This diversity allowed for a more accurate tracking of interpersonal USA300 transmission. Sequencing of persisting USA300 isolates revealed mutations in genes involved in major aspects of S. aureus function: adhesion, cell wall biosynthesis, virulence, and carbohydrate metabolism. Genetic variations also included accumulation of multiple polymorphisms within select genes of two multigene operons, suggestive of small genome rearrangements rather than de novo single point mutations. Such rearrangements have been underappreciated in S. aureus and may represent novel means of strain variation. Subtle genetic changes may contribute to USA300 fitness and persistence. Elucidation of small genome rearrangements reveals a potentially new and intriguing mechanism of directed S. aureus genome diversification in environmental niches and during pathogen-host interactions.

  11. Toward an understanding of the evolution of Staphylococcus aureus strain USA300 during colonization in community households.

    PubMed

    Uhlemann, Anne-Catrin; Kennedy, Adam D; Martens, Craig; Porcella, Stephen F; Deleo, Frank R; Lowy, Franklin D

    2012-01-01

    Staphylococcus aureus is a frequent cause of serious infections and also a human commensal. The emergence of community-associated methicillin-resistant S. aureus led to a dramatic increase in skin and soft tissue infections worldwide. This epidemic has been driven by a limited number of clones, such as USA300 in the United States. To better understand the extent of USA300 evolution and diversification within communities, we performed comparative whole-genome sequencing of three clinical and five colonizing USA300 isolates collected longitudinally from three unrelated households over a 15-month period. Phylogenetic analysis that incorporated additional geographically diverse USA300 isolates indicated that all but one likely arose from a common recent ancestor. Although limited genetic adaptation occurred over the study period, the greatest genetic heterogeneity occurred between isolates from different households and within one heavily colonized household. This diversity allowed for a more accurate tracking of interpersonal USA300 transmission. Sequencing of persisting USA300 isolates revealed mutations in genes involved in major aspects of S. aureus function: adhesion, cell wall biosynthesis, virulence, and carbohydrate metabolism. Genetic variations also included accumulation of multiple polymorphisms within select genes of two multigene operons, suggestive of small genome rearrangements rather than de novo single point mutations. Such rearrangements have been underappreciated in S. aureus and may represent novel means of strain variation. Subtle genetic changes may contribute to USA300 fitness and persistence. Elucidation of small genome rearrangements reveals a potentially new and intriguing mechanism of directed S. aureus genome diversification in environmental niches and during pathogen-host interactions. PMID:23104992

  12. Dissemination of Methicillin-Resistant Staphylococcus aureus (MRSA), USA300 Sequence Type 8 Lineage in Latin-America

    PubMed Central

    Reyes, Jinnethe; Rincón, Sandra; Díaz, Lorena; Panesso, Diana; Contreras, Germán A.; Zurita, Jeannete; Carrillo, Carlos; Rizzi, Adele; Guzmán, Manuel; Adachi, Javier; Chowdhury, Shahreen; Murray, Barbara E.; Arias, Cesar A.

    2009-01-01

    Background Methicillin-resistant Staphylococus aureus (MRSA) is an important nosocomial and community-associated (CA) pathogen. Recently, a variant of the MRSA USA300 clone emerged and disseminated in South-America causing important clinical problems. Methods S. aureus isolates were prospectively collected (2006 to 2008) from 32 tertiary hospitals in Colombia, Ecuador, Peru, and Venezuela. MRSA isolates were subjected to antimicrobial susceptibility testing, pulsed field gel electrophoresis (PFGE), and categorized as healthcare-associated (HA)-like or CA-like clones based on genotypic characteristics and detection of genes encoding the Panton-Valentine leukocidin (PVL) and staphylococcal cassette mec (SCCmec) IV. Additionally, MLST of representative isolates of each major CA-MRSA pulsotype, and detection of USA300-associated toxins and the arcA gene were performed in all isolates categorized as CA-MRSA. Results A total of 1570 S. aureus were included; 651 were MRSA (41%), with the highest rates of MRSA isolation in Peru (62%), and lowest in Venezuela (26%) and 71%, 27%, and 2% were classified as HA-like, CA-like, and non-CA/HA-like clones, respectively. Only 9 MRSA isolates were confirmed to have reduced susceptibility to glycopeptides (GISA phenotype). The most common pulsotype (designated ComA) amongst the CA-like MRSA strains was found in 96% of isolates with the majority (81%) having ≤6 bands difference with the USA300-0114 strain. Representative isolates of this clone were ST8 but, unlike the USA300-0114 strain, they harbored a different SCCmec IV subtype and lacked arcA (an indicator of the arginine catabolic mobile element (ACME)). Conclusion A variant CA-MRSA USA300 clone has now become established in South America and, in some countries, is endemic in hospital settings. PMID:19911971

  13. Alpha-toxin induces programmed cell death of human T cells, B cells, and monocytes during USA300 infection.

    PubMed

    Nygaard, Tyler K; Pallister, Kyler B; DuMont, Ashley L; DeWald, Mark; Watkins, Robert L; Pallister, Erik Q; Malone, Cheryl; Griffith, Shannon; Horswill, Alexander R; Torres, Victor J; Voyich, Jovanka M

    2012-01-01

    This investigation examines the influence of alpha-toxin (Hla) during USA300 infection of human leukocytes. Survival of an USA300 isogenic deletion mutant of hla (USA300Δhla) in human blood was comparable to the parental wild-type strain and polymorphonuclear leukocyte (PMN) plasma membrane permeability caused by USA300 did not require Hla. Flow cytometry analysis of peripheral blood mononuclear cells (PBMCs) following infection by USA300, USA300Δhla, and USA300Δhla transformed with a plasmid over-expressing Hla (USA300Δhla Comp) demonstrated this toxin plays a significant role inducing plasma membrane permeability of CD14(+), CD3(+), and CD19(+) PBMCs. Rapid plasma membrane permeability independent of Hla was observed for PMNs, CD14(+) and CD19(+) PBMCs following intoxication with USA300 supernatant while the majority of CD3(+) PBMC plasma membrane permeability induced by USA300 required Hla. Addition of recombinant Hla to USA300Δhla supernatant rescued CD3(+) and CD19(+) PBMC plasma membrane permeability generated by USA300 supernatant. An observed delay in plasma membrane permeability caused by Hla in conjunction with Annexin V binding and ApoBrdU Tunel assays examining PBMCs intoxicated with recombinant Hla or infected with USA300, USA300Δhla, USA300Δhla Comp, and USA300ΔsaeR/S suggest Hla induces programmed cell death of monocytes, B cells, and T cells that results in plasma membrane permeability. Together these findings underscore the importance of Hla during S. aureus infection of human tissue and specifically demonstrate Hla activity during USA300 infection triggers programmed cell death of human monocytes, T cells and B cells that leads to plasma membrane permeability.

  14. Emergence of Panton-Valentine leucocidin-positive ST8-methicillin-resistant Staphylococcus aureus (USA300 clone) in Korea causing healthcare-associated and hospital-acquired bacteraemia.

    PubMed

    Jung, J; Song, E H; Park, S Y; Lee, S-R; Park, S-J; Sung, H; Kim, M-N; Kim, S-H; Lee, S-O; Choi, S-H; Woo, J H; Kim, Y S; Chong, Y P

    2016-08-01

    Panton-Valentine leucocidin (PVL)-positive sequence type (ST)8-MRSA-SCCmec IVa (USA300) is the epidemic strain of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) in North America. USA300 is extremely rare in South Korea, and PVL-negative ST72 SCCmec type IVc is the predominant CA-MRSA clone. In a multicentre, prospective cohort study of S. aureus bacteraemia, we identified PVL-positive ST8-MRSA isolates by performing multilocus sequence typing and PCR for PVL. We analyzed the clinical characteristics of patients with PVL-positive ST8-MRSA bacteraemia, and performed SCCmec, spa, and agr typing, PCR for arginine catabolic mobile element (ACME), virulence gene profiling, and pulsed-field gel electrophoresis (PFGE). Among a total of 818 MRSA isolates, we identified ten isolates of PVL-positive ST8-MRSA (USA300) (3 from Hospital D, 4 from Hospital G, and 3 from Hospital A), all of which involved exclusively healthcare-associated (5 isolates) and hospital-acquired bacteraemia (5 isolates). This strain accounted for 8~10 % of the hospital-acquired MRSA bacteraemia in Hospitals D and G. Bacteraemia of unknown origin was the most common type of infection followed by pneumonia. All the isolates were SCCmec type IVa, spa type t008, and agr group I. Eight of the isolates harboured ACME. In a PFGE analysis, four isolates were identical to the USA300 control strain, five differed by a single band, and the remaining one differed by two bands. All the isolates were pulsed-field type USA300. This is the first report of healthcare-associated and hospital-acquired bacteraemia caused by USA300 in South Korea. USA300 seems to be an emerging hospital clone in this country. PMID:27209287

  15. Deferoxamine mesylate enhances virulence of community-associated methicillin resistant Staphylococcus aureus.

    PubMed

    Arifin, Andrew J; Hannauer, Mélissa; Welch, Ian; Heinrichs, David E

    2014-11-01

    Staphylococcus aureus is a leading cause of bacterial infections. Strains of community-associated methicillin-resistant S. aureus (CA-MRSA), such as USA300, display enhanced virulence and fitness. Patients suffering from iron overload diseases often undergo iron chelation therapy with deferoxamine mesylate (DFO). Here, we show that USA300 uses this drug to acquire iron. We further demonstrate that mice administered DFO I.P., versus those not administered DFO, had significantly higher bacterial burden in livers and kidneys after I.V. challenge with USA300, associated with increased abscess formation and tissue destruction. The virulence of USA300 mutants defective for DFO uptake was not affected by DFO treatment.

  16. Evolution of virulence in epidemic community-associated methicillin-resistant Staphylococcus aureus.

    PubMed

    Li, Min; Diep, Binh An; Villaruz, Amer E; Braughton, Kevin R; Jiang, Xiaofei; DeLeo, Frank R; Chambers, Henry F; Lu, Yuan; Otto, Michael

    2009-04-01

    Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) has recently emerged worldwide. The United States, in particular, is experiencing a serious epidemic of CA-MRSA that is almost entirely caused by an extraordinarily infectious strain named USA300. However, the molecular determinants underlying the pathogenic success of CA-MRSA are mostly unknown. To gain insight into the evolution of the exceptional potential of USA300 to cause disease, we compared the phylogeny and virulence of USA300 with that of closely related MRSA clones. We discovered that the sublineage from which USA300 evolved is characterized by a phenotype of high virulence that is clearly distinct from other MRSA strains. Namely, USA300 and its progenitor, USA500, had high virulence in animal infection models and the capacity to evade innate host defense mechanisms. Furthermore, our results indicate that increased virulence in the USA300/USA500 sublineage is attributable to differential expression of core genome-encoded virulence determinants, such as phenol-soluble modulins and alpha-toxin. Notably, the fact that the virulence phenotype of USA300 was already established in its progenitor indicates that acquisition of mobile genetic elements has played a limited role in the evolution of USA300 virulence and points to a possibly different role of those elements. Thus, our results highlight the importance of differential gene expression in the evolution of USA300 virulence. This finding calls for a profound revision of our notion about CA-MRSA pathogenesis at the molecular level and has important implications for design of therapeutics directed against CA-MRSA.

  17. Phosphatidylinositol-Specific Phospholipase C Contributes to Survival of Staphylococcus aureus USA300 in Human Blood and Neutrophils

    PubMed Central

    White, Mark J.; Boyd, Jeffrey M.

    2014-01-01

    Staphylococcus aureus is an important human pathogen that employs a large repertoire of secreted virulence factors to promote disease pathogenesis. Many strains of S. aureus possess a plc gene that encodes a phosphatidylinositol (PI)-specific phospholipase C (PI-PLC) capable of hydrolyzing PI and cleaving glycosyl-PI (GPI)-linked proteins from cell surfaces. Despite being secreted by virulent staphylococci, the contribution of PI-PLC to the capacity of S. aureus to cause disease remains undefined. Our goal in these studies was to understand PI-PLC in the context of S. aureus biology. Among a collection of genetically diverse clinical isolates of S. aureus, community-associated methicillin-resistant S. aureus (CA-MRSA) USA300 secreted the most PI-PLC. Screening a collection of two-component system (TCS) mutants of S. aureus, we identified both the agr quorum-sensing system and the SrrAB TCS to be positive regulators of plc gene expression. Real-time PCR and PI-PLC enzyme assays of the TCS mutants, coupled with SrrA promoter binding studies, demonstrated that SrrAB was the predominant transcriptional activator of plc. Furthermore, plc regulation was linked to oxidative stress both in vitro and in vivo in a SrrAB-dependent manner. A Δplc mutant in a CA-MRSA USA300 background exhibited a survival defect in human whole blood and in isolated neutrophils. However, the same mutant strain displayed no survival defect in murine models of infection or murine whole blood. Overall, these data identify potential links between bacterial responses to the host innate immune system and to oxidative stress and suggest how PI-PLC could contribute to the pathogenesis of S. aureus infections. PMID:24452683

  18. Community-associated methicillin-resistant Staphylococcus aureus, Iowa, USA.

    PubMed

    Van De Griend, Philip; Herwaldt, Loreen A; Alvis, Bret; DeMartino, Mary; Heilmann, Kristopher; Doern, Gary; Winokur, Patricia; Vonstein, Diana DeSalvo; Diekema, Daniel

    2009-10-01

    We performed antimicrobial drug susceptibility testing and molecular typing on invasive methicillin-resistant Staphylococcus aureus (MRSA) isolates (n = 1,666) submitted to the University of Iowa Hygienic Laboratory during 1999-2006 as part of a statewide surveillance system. All USA300 and USA400 isolates were resistant to USA300 or USA400 increased significantly from 1999-2005 through 2006 (p<0.0001). During 2006, the incidence of invasive community-associated (CA)-MRSA infections was highest in the summer (p = 0.0004). Age <69 years was associated with an increased risk for invasive CA-MRSA infection (odds ratio [OR] 5.1, 95% confidence interval [CI] 2.06-12.64), and hospital exposure was associated with decreased risk (OR 0.07, 95% CI 0.01-0.51). PMID:19861049

  19. Phenol-Soluble Modulins Contribute to Early Sepsis Dissemination Not Late Local USA300-Osteomyelitis Severity in Rabbits

    PubMed Central

    Davido, Benjamin; Saleh-Mghir, Azzam; Laurent, Frédéric; Danel, Claire; Couzon, Florence; Gatin, Laure; Vandenesch, François; Rasigade, Jean-Philippe; Crémieux, Anne-Claude

    2016-01-01

    Introduction In bone and joint infections (BJIs), bacterial toxins are major virulence factors: Panton—Valentine leukocidin (PVL) expression leads to severe local damage, including bone distortion and abscesses, while α-hemolysin (Hla) production is associated with severe sepsis-related mortality. Recently, other toxins, namely phenol-soluble modulins (PSMs) expressed by community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) strain USA300 (LAC WT) were shown to have ex vivo intracellular cytotoxic activity after S. aureus invasion of osteoblasts, but their in vivo contribution in a relatively PVL-sensitive osteomyelitis model remains poorly elucidated. Materials and Methods We compared the outcomes of experimental rabbit osteomyelitises induced with pvl+hla+psms+ LAC WT and its isogenic Δpsm derivatives (LAC Δpsmα and LAC Δpsmαβhld) using an inoculum of 3 × 108 CFUs. Mortality, hematogenous spread (blood culture, spleen and kidney), lung and bone involvements were assessed in two groups (non-survivors of severe sepsis and survivors sacrificed on day (D) 14). Results Severe sepsis-related mortality tended to be lower for Δpsm derivatives (Kaplan—Meier curves, P = .06). Non-survivors’ bone LAC-Δpsmα (6.9 log10 CFUs/g of bone, P = .04) or -Δpsmαβhld (6.86 log10 CFUs/g of bone, P = .014) densities were significantly higher than LAC WT (6.43 log10 CFUs/g of bone). Conversely, lung Δpsmαβhld CFUs were significantly lower than LAC WT (P = .04). LAC Δpsmα, Δpsmαβhld and WT induced similar bone damage in D14 survivors, with comparable bacterial densities (respectively: 5.89, 5.91, and 6.15 log10 CFUs/g of bone). Meanwhile, pulmonary histological scores of inflammation were significantly higher for LAC Δpsmα- and Δpsmαβhld-infected rabbits compared to LAC WT (P = .04 and .01, respectively) but with comparable lung bacterial densities. Conclusion Our experimental results showed that deactivating PSM peptides significantly

  20. Staphylococcus aureus Strain USA300 Perturbs Acquisition of Lysosomal Enzymes and Requires Phagosomal Acidification for Survival inside Macrophages

    PubMed Central

    Tranchemontagne, Zachary R.; Camire, Ryan B.; O'Donnell, Vanessa J.; Baugh, Jessfor

    2015-01-01

    Methicillin-resistant Staphylococcus aureus (MRSA) causes invasive, drug-resistant skin and soft tissue infections. Reports that S. aureus bacteria survive inside macrophages suggest that the intramacrophage environment may be a niche for persistent infection; however, mechanisms by which the bacteria might evade macrophage phagosomal defenses are unclear. We examined the fate of the S. aureus-containing phagosome in THP-1 macrophages by evaluating bacterial intracellular survival and phagosomal acidification and maturation and by testing the impact of phagosomal conditions on bacterial viability. Multiple strains of S. aureus survived inside macrophages, and in studies using the MRSA USA300 clone, the USA300-containing phagosome acidified rapidly and acquired the late endosome and lysosome protein LAMP1. However, fewer phagosomes containing live USA300 bacteria than those containing dead bacteria associated with the lysosomal hydrolases cathepsin D and β-glucuronidase. Inhibiting lysosomal hydrolase activity had no impact on intracellular survival of USA300 or other S. aureus strains, suggesting that S. aureus perturbs acquisition of lysosomal enzymes. We examined the impact of acidification on S. aureus intramacrophage viability and found that inhibitors of phagosomal acidification significantly impaired USA300 intracellular survival. Inhibition of macrophage phagosomal acidification resulted in a 30-fold reduction in USA300 expression of the staphylococcal virulence regulator agr but had little effect on expression of sarA, saeR, or sigB. Bacterial exposure to acidic pH in vitro increased agr expression. Together, these results suggest that S. aureus survives inside macrophages by perturbing normal phagolysosome formation and that USA300 may sense phagosomal conditions and upregulate expression of a key virulence regulator that enables its intracellular survival. PMID:26502911

  1. Demography and Intercontinental Spread of the USA300 Community-Acquired Methicillin-Resistant Staphylococcus aureus Lineage

    PubMed Central

    Glaser, Philippe; Martins-Simões, Patrícia; Villain, Adrien; Barbier, Maxime; Tristan, Anne; Bouchier, Christiane; Ma, Laurence; Bes, Michele; Laurent, Frederic; Guillemot, Didier; Wirth, Thierry

    2016-01-01

    ABSTRACT Community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA) was recognized worldwide during the 1990s; in less than a decade, several genetically distinct CA-MRSA lineages carrying Panton-Valentine leukocidin genes have emerged on every continent. Most notably, in the United States, the sequence type 18-IV (ST8-IV) clone known as USA300 has become highly prevalent, outcompeting methicillin-susceptible S. aureus (MSSA) and other MRSA strains in both community and hospital settings. CA-MRSA bacteria are much less prevalent in Europe, where the European ST80-IV European CA-MRSA clone, USA300 CA-MRSA strains, and other lineages, such as ST22-IV, coexist. The question that arises is whether the USA300 CA-MRSA present in Europe (i) was imported once or on very few occasions, followed by a broad geographic spread, anticipating an increased prevalence in the future, or (ii) derived from multiple importations with limited spreading success. In the present study, we applied whole-genome sequencing to a collection of French USA300 CA-MRSA strains responsible for sporadic cases and micro-outbreaks over the past decade and United States ST8 MSSA and MRSA isolates. Genome-wide phylogenetic analysis demonstrated that the population structure of the French isolates is the product of multiple introductions dating back to the onset of the USA300 CA-MRSA clone in North America. Coalescent-based demography of the USA300 lineage shows that a strong expansion occurred during the 1990s concomitant with the acquisition of the arginine catabolic mobile element and antibiotic resistance, followed by a sharp decline initiated around 2008, reminiscent of the rise-and-fall pattern previously observed in the ST80 lineage. A future expansion of the USA300 lineage in Europe is therefore very unlikely. PMID:26884428

  2. Capsaicin Protects Mice from Community-Associated Methicillin-Resistant Staphylococcus aureus Pneumonia

    PubMed Central

    Xing, Yan; Leng, Bingfeng; Dong, Jing; Li, Hongen; Luo, Mingjing; Zhang, Yu; Dai, Xiaohan; Luo, Yonghuang; Deng, Xuming

    2012-01-01

    Background α-toxin is one of the major virulence factors secreted by most Staphylococcus aureus strains, which played a central role in the pathogenesis of S. aureus pneumonia. The aim of this study was to investigate the impact of capsaicin on the production of α-toxin by community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) strain USA 300 and to further assess its performance in the treatment of CA-MRSA pneumonia in a mouse model. Methodology/Principal Findings The in vitro effects of capsaicin on α-toxin production by S. aureus USA 300 were determined using hemolysis, western blot, and real-time RT-PCR assays. The influence of capsaicin on the α-toxin-mediated injury of human alveolar epithelial cells was determined using viability and cytotoxicity assays. Mice were infected intranasally with S. aureus USA300; the in vivo protective effects of capsaicin against S. aureus pneumonia were assessed by monitoring the mortality, histopathological changes and cytokine levels. Low concentrations of capsaicin substantially decreased the production of α-toxin by S. aureus USA 300 without affecting the bacterial viability. The addition of capsaicin prevented α-toxin-mediated human alveolar cell (A549) injury in co-culture with S. aureus. Furthermore, the in vivo experiments indicated that capsaicin protected mice from CA-MRSA pneumonia caused by strain USA 300. Conclusions/Significance Capsaicin inhibits the production of α-toxin by CA-MRSA strain USA 300 in vitro and protects mice from CA-MRSA pneumonia in vivo. However, the results need further confirmation with other CA-MRSA lineages. This study supports the views of anti-virulence as a new antibacterial approach for chemotherapy. PMID:22427935

  3. The impact of α-toxin on host cell plasma membrane permeability and cytokine expression during human blood infection by CA-MRSA USA300

    PubMed Central

    Nygaard, Tyler K.; Pallister, Kyler B.; Zurek, Oliwia W.; Voyich, Jovanka M.

    2013-01-01

    This investigation examines the influence of α-toxin (Hla) expression by CA-MRSA on host immune cell integrity and cytokine expression during infection of human blood. Flow cytometry analysis of human blood infected by Staphylococcus aureus PFGE type USA300 or a USA300Δhla demonstrated that Hla expression significantly increased plasma membrane permeability of human CD14+ monocytes. The increased susceptibility of human CD14+ monocytes to Hla toxicity paralleled the high cell-surface expression on these cell types of ADAM10. USA300 rapidly associated with PMNs and monocytes but not T cells following inoculation of human blood. Transcription analysis indicated a strong up-regulation of proinflammatory cytokine transcription following infection of human blood by USA300 and USA300Δhla. CBAs and ELISAs determined that IL-6, IL-10, TNF-α, IFN-γ, IL-1β, IL-8, and IL-4 are significantly up-regulated during the initial phases of human blood infection by USA300 relative to mock-infected blood but failed to distinguish any significant differences in secreted cytokine protein concentrations during infection by USA300Δhla relative to USA300. Collectively, these findings demonstrate that expression of Hla by USA300 has a significant impact on human CD14+ monocyte plasma membrane integrity but is not exclusively responsible for the proinflammatory cytokine profile induced by USA300 during the initial stages of human blood infection. PMID:24026286

  4. The impact of α-toxin on host cell plasma membrane permeability and cytokine expression during human blood infection by CA-MRSA USA300.

    PubMed

    Nygaard, Tyler K; Pallister, Kyler B; Zurek, Oliwia W; Voyich, Jovanka M

    2013-11-01

    This investigation examines the influence of α-toxin (Hla) expression by CA-MRSA on host immune cell integrity and cytokine expression during infection of human blood. Flow cytometry analysis of human blood infected by Staphylococcus aureus PFGE type USA300 or a USA300Δhla demonstrated that Hla expression significantly increased plasma membrane permeability of human CD14(+) monocytes. The increased susceptibility of human CD14(+) monocytes to Hla toxicity paralleled the high cell-surface expression on these cell types of ADAM10. USA300 rapidly associated with PMNs and monocytes but not T cells following inoculation of human blood. Transcription analysis indicated a strong up-regulation of proinflammatory cytokine transcription following infection of human blood by USA300 and USA300Δhla. CBAs and ELISAs determined that IL-6, IL-10, TNF-α, IFN-γ, IL-1β, IL-8, and IL-4 are significantly up-regulated during the initial phases of human blood infection by USA300 relative to mock-infected blood but failed to distinguish any significant differences in secreted cytokine protein concentrations during infection by USA300Δhla relative to USA300. Collectively, these findings demonstrate that expression of Hla by USA300 has a significant impact on human CD14(+) monocyte plasma membrane integrity but is not exclusively responsible for the proinflammatory cytokine profile induced by USA300 during the initial stages of human blood infection.

  5. Phloretin derived from apple can reduce alpha-hemolysin expression in methicillin-resistant Staphylococcus aureus USA300.

    PubMed

    Zhou, Xuan; Liu, Shui; Li, Wenhua; Zhang, Bing; Liu, Bowen; Liu, Yan; Deng, Xuming; Peng, Liping

    2015-08-01

    Methicillin-resistant Staphylococcus aureus (MRSA) has become increasingly important because it is the most common cause of hospital-acquired infections, which have become globally epidemic. Our study specifically focused on the MRSA strain USA300, which was shown in 2014 to be responsible for the most current pandemic of highly virulent MRSA in the United States. We aimed to evaluate the in vitro effect of phloretin on USA300. Susceptibility testing, western blotting assays, hemolysis assays and real-time RT-PCR were employed to examine the in vitro effects of phloretin on alpha-hemolysin (Hla) production when the bacterium was co-cultured with phloretin. The protective effect of phloretin against the USA300-mediated injury of human alveolar epithelial cells (A549) was tested using the live/dead analysis and cytotoxicity assays. We showed that sub-inhibitory concentrations of phloretin have no effect on bacterial viability; however, they can markedly inhibit the production of Hla in culture supernatants and the transcriptional levels of hla (the gene encoding Hla) and agrA (the accessory gene regulator). Phloretin, at a final concentration of 16 µg/ml, could protect A549 cells from injury caused by USA300 in the co-culture system. Our study suggests that phloretin might have a potential application in the development of treatment for MRSA infections. PMID:26026280

  6. Nuclease Modulates Biofilm Formation in Community-Associated Methicillin-Resistant Staphylococcus aureus

    PubMed Central

    Kiedrowski, Megan R.; Kavanaugh, Jeffrey S.; Malone, Cheryl L.; Mootz, Joe M.; Voyich, Jovanka M.; Smeltzer, Mark S.; Bayles, Kenneth W.; Horswill, Alexander R.

    2011-01-01

    Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) is an emerging contributor to biofilm-related infections. We recently reported that strains lacking sigma factor B (sigB) in the USA300 lineage of CA-MRSA are unable to develop a biofilm. Interestingly, when spent media from a USA300 sigB mutant was incubated with other S. aureus strains, biofilm formation was inhibited. Following fractionation and mass spectrometry analysis, the major anti-biofilm factor identified in the spent media was secreted thermonuclease (Nuc). Considering reports that extracellular DNA (eDNA) is an important component of the biofilm matrix, we investigated the regulation and role of Nuc in USA300. The expression of the nuc gene was increased in a sigB mutant, repressed by glucose supplementation, and was unaffected by the agr quorum-sensing system. A FRET assay for Nuc activity was developed and confirmed the regulatory results. A USA300 nuc mutant was constructed and displayed an enhanced biofilm-forming capacity, and the nuc mutant also accumulated more high molecular weight eDNA than the WT and regulatory mutant strains. Inactivation of nuc in the USA300 sigB mutant background partially repaired the sigB biofilm-negative phenotype, suggesting that nuc expression contributes to the inability of the mutant to form biofilm. To test the generality of the nuc mutant biofilm phenotypes, the mutation was introduced into other S. aureus genetic backgrounds and similar increases in biofilm formation were observed. Finally, using multiple S. aureus strains and regulatory mutants, an inverse correlation between Nuc activity and biofilm formation was demonstrated. Altogether, our findings confirm the important role for eDNA in the S. aureus biofilm matrix and indicates Nuc is a regulator of biofilm formation. PMID:22096493

  7. Systematic Surveillance Detects Multiple Silent Introductions and Household Transmission of Methicillin-Resistant Staphylococcus aureus USA300 in the East of England

    PubMed Central

    Toleman, Michelle S.; Reuter, Sandra; Coll, Francesc; Harrison, Ewan M.; Blane, Beth; Brown, Nicholas M.; Török, M. Estée; Parkhill, Julian; Peacock, Sharon J.

    2016-01-01

    Background. The spread of USA300 methicillin-resistant Staphylococcus aureus (MRSA) across the United States resulted in an epidemic of infections. In Europe, only sporadic cases or small clusters of USA300 infections are described, and its prevalence in England is unknown. We conducted prospective surveillance for USA300 in the east of England. Methods. We undertook a 12-month prospective observational cohort study of all individuals with MRSA isolated from community and hospital samples submitted to a microbiology laboratory. At least 1 MRSA isolate from each individual underwent whole-genome sequencing. USA300 was identified on the basis of sequence analysis, and phylogenetic comparisons were made between these and USA300 genomes from the United States. Results. Between April 2012 and April 2013, we sequenced 2283 MRSA isolates (detected during carriage screening and in clinical samples) from 1465 individuals. USA300 was isolated from 24 cases (1.6%). Ten cases (42%) had skin and soft tissue infection, and 2 cases had invasive disease. Phylogenetic analyses identified multiple introductions and household transmission of USA300. Conclusions. Use of a diagnostic laboratory as a sentinel for surveillance has identified repeated introductions of USA300 in eastern England in 2012–2013, with evidence for limited transmission. Our results show how systematic surveillance could provide an early warning of strain emergence and dissemination. PMID:27122590

  8. Noninvasive in vivo imaging to evaluate immune responses and antimicrobial therapy against Staphylococcus aureus and USA300 MRSA skin infections.

    PubMed

    Cho, John S; Zussman, Jamie; Donegan, Niles P; Ramos, Romela Irene; Garcia, Nairy C; Uslan, Daniel Z; Iwakura, Yoichiro; Simon, Scott I; Cheung, Ambrose L; Modlin, Robert L; Kim, Jenny; Miller, Lloyd S

    2011-04-01

    Staphylococcus aureus skin infections represent a significant public health threat because of the emergence of antibiotic-resistant strains such as methicillin-resistant S. aureus (MRSA). As greater understanding of protective immune responses and more effective antimicrobial therapies are needed, a S. aureus skin wound infection model was developed in which full-thickness scalpel cuts on the backs of mice were infected with a bioluminescent S. aureus (methicillin sensitive) or USA300 community-acquired MRSA strain and in vivo imaging was used to noninvasively monitor the bacterial burden. In addition, the infection-induced inflammatory response was quantified using in vivo fluorescence imaging of LysEGFP mice. Using this model, we found that both IL-1α and IL-1β contributed to host defense during a wound infection, whereas IL-1β was more critical during an intradermal S. aureus infection. Furthermore, treatment of a USA300 MRSA skin infection with retapamulin ointment resulted in up to 85-fold reduction in bacterial burden and a 53% decrease in infection-induced inflammation. In contrast, mupirocin ointment had minimal clinical activity against this USA300 strain, resulting in only a 2-fold reduction in bacterial burden. Taken together, this S. aureus wound infection model provides a valuable preclinical screening method to investigate cutaneous immune responses and the efficacy of topical antimicrobial therapies.

  9. Detection of a New Community Genotype Methicillin-Resistant Staphylococcus aureus Clone That Is Unrelated to the USA300 Clone and That Causes Pediatric Infections in Colombia

    PubMed Central

    Marquez-Ortiz, Ricaurte Alejandro; Alvarez-Olmos, Martha I.; Leal, Aura Lucia; Castro, Betsy Esperanza; Vanegas, Natasha

    2013-01-01

    The dissemination of a clone of community genotype methicillin-resistant Staphylococcus aureus (CG-MRSA) that is related to USA300 has been reported in Latin America. We recently detected isolates of a new clone of CG-MRSA (spa type t1635 and ACME-negative) that was genetically unrelated to the USA300 clone and that causes infections in children in Colombia. This finding indicates the appearance of a new clone of CG-MRSA in our region. PMID:23241375

  10. Recurrent Furunculosis Caused by a Community-Acquired Staphylococcus aureus Strain Belonging to the USA300 Clone

    PubMed Central

    Balachandra, Shirish; Pardos de la Gandara, Maria; Salvato, Scott; Urban, Tracie; Parola, Claude; Khalida, Chamanara; Kost, Rhonda G.; Evering, Teresa H.; Pastagia, Mina; D'Orazio, Brianna M.; Tomasz, Alexander; de Lencastre, Herminia

    2015-01-01

    Background: A 24-year-old female with recurrent skin and soft tissue infections (SSTI) was enrolled as part of a multicenter observational cohort study conducted by a practice-based research network (PBRN) on community-acquired methicillin-resistant Staphylococcus aureus (CA-MRSA). Methods: Strains were characterized by pulsed-field gel electrophoresis (PFGE), spa typing, and multilocus sequence typing. MRSA strains were analyzed for SCCmec type and the presence of the Panton-Valentine leukocidin (PVL) and arginine catabolic mobile element (ACME) using PCR. Results: In the first episode, S. aureus was recovered from the wound and inguinal folds; in the second, S. aureus was recovered from a lower abdomen furuncle, inguinal folds, and patellar fold. Molecular typing identified CA-MRSA clone USA300 in all samples as spa-type t008, ST8, SCCmecIVa, and a typical PFGE pattern. The strain carried virulence genes pvl and ACME type I. Five SSTI episodes were documented despite successful resolution by antibiotic treatment, with and without incision and drainage. Conclusions: The source of the USA300 strain remains unknown. The isolate may represent a persistent strain capable of surviving extensive antibiotic pressure or a persistent environmental reservoir may be the source, possibly in the patient's household, from which bacteria were repeatedly introduced into the skin flora with subsequent infections. PMID:25668150

  11. The Lantibiotic NAI-107 Efficiently Rescues Drosophila melanogaster from Infection with Methicillin-Resistant Staphylococcus aureus USA300

    PubMed Central

    Mojsoska, Biljana; Cruz, João C. S.; Donadio, Stefano; Jenssen, Håvard

    2016-01-01

    We used the fruit fly Drosophila melanogaster as a cost-effective in vivo model to evaluate the efficacy of novel antibacterial peptides and peptoids for treatment of methicillin-resistant Staphylococcus aureus (MRSA) infections. A panel of peptides with known antibacterial activity in vitro and/or in vivo was tested in Drosophila. Although most peptides and peptoids that were effective in vitro failed to rescue lethal effects of S. aureus infections in vivo, we found that two lantibiotics, nisin and NAI-107, rescued adult flies from fatal infections. Furthermore, NAI-107 rescued mortality of infection with the MRSA strain USA300 with an efficacy equivalent to that of vancomycin, a widely applied antibiotic for the treatment of serious MRSA infections. These results establish Drosophila as a useful model for in vivo drug evaluation of antibacterial peptides. PMID:27381394

  12. The Lantibiotic NAI-107 Efficiently Rescues Drosophila melanogaster from Infection with Methicillin-Resistant Staphylococcus aureus USA300.

    PubMed

    Thomsen, Thomas T; Mojsoska, Biljana; Cruz, João C S; Donadio, Stefano; Jenssen, Håvard; Løbner-Olesen, Anders; Rewitz, Kim

    2016-09-01

    We used the fruit fly Drosophila melanogaster as a cost-effective in vivo model to evaluate the efficacy of novel antibacterial peptides and peptoids for treatment of methicillin-resistant Staphylococcus aureus (MRSA) infections. A panel of peptides with known antibacterial activity in vitro and/or in vivo was tested in Drosophila Although most peptides and peptoids that were effective in vitro failed to rescue lethal effects of S. aureus infections in vivo, we found that two lantibiotics, nisin and NAI-107, rescued adult flies from fatal infections. Furthermore, NAI-107 rescued mortality of infection with the MRSA strain USA300 with an efficacy equivalent to that of vancomycin, a widely applied antibiotic for the treatment of serious MRSA infections. These results establish Drosophila as a useful model for in vivo drug evaluation of antibacterial peptides. PMID:27381394

  13. Phenotypes and Virulence among Staphylococcus aureus USA100, USA200, USA300, USA400, and USA600 Clonal Lineages

    PubMed Central

    King, Jessica M.; Kulhankova, Katarina; Stach, Christopher S.; Vu, Bao G.

    2016-01-01

    ABSTRACT Staphylococcus aureus diseases affect ~500,000 individuals per year in the United States. Worldwide, the USA100, USA200, USA400, and USA600 lineages cause many of the life-threatening S. aureus infections, such as bacteremia, infective endocarditis, pneumonia, toxic shock syndrome, and surgical site infections. However, the virulence mechanisms associated with these clonal lineages, in particular the USA100 and USA600 isolates, have been severely understudied. We investigated the virulence of these strains, in addition to strains in the USA200, USA300, and USA400 types, in well-established in vitro assays and in vivo in the rabbit model of infective endocarditis and sepsis. We show in the infective endocarditis and sepsis model that strains in the USA100 and USA600 lineages cause high lethality and are proficient in causing native valve infective endocarditis. Strains with high cytolytic activity or producing toxic shock syndrome toxin 1 (TSST-1) or staphylococcal enterotoxin C (SEC) caused lethal sepsis, even with low cytolytic activity. Strains in the USA100, USA200, USA400, and USA600 lineages consistently contained genes that encode for the enterotoxin gene cluster proteins, SEC, or TSST-1 and were proficient at causing infective endocarditis, while the USA300 strains lacked these toxins and were deficient in promoting vegetation growth. The USA100, USA200, and USA400 strains in our collection formed strong biofilms in vitro, whereas the USA200 and USA600 strains exhibited increased blood survival. Hence, infective endocarditis and lethal sepsis are multifactorial and not intrinsic to any one individual clonal group, further highlighting the importance of expanding our knowledge of S. aureus pathogenesis to clonal lineages causative of invasive disease. IMPORTANCE S. aureus is the leading cause of infective endocarditis in the developed world, affecting ~40,000 individuals each year in the United States, and the second leading cause of bacteremia (D

  14. Pediatric Staphylococcus aureus Isolate Genotypes and Infections from the Dawn of the Community-Associated Methicillin-Resistant S. aureus Epidemic Era in Chicago, 1994 to 1997

    PubMed Central

    Acree, Mary Ellen; Sieth, Julia J.; Boxrud, Dave J.; Dobbins, Ginette; Lynfield, Ruth; Boyle-Vavra, Susan; Daum, Robert S.

    2015-01-01

    Widespread infections with community-associated (CA) methicillin-resistant Staphylococcus aureus (MRSA) have occurred in the United States with the dissemination of the USA300 strain beginning in 2000. We examined 105 isolates obtained from children treated at the University of Chicago from 1994 to 1997 (75 methicillin-susceptible S. aureus [MSSA] and 30 MRSA isolates) in order to investigate for possible evidence of USA300 during this period. Infections were defined epidemiologically based on medical record review. The isolates underwent multilocus sequence typing (MLST), as well as assays for the Panton-Valentine leukocidin (PVL) genes, the protein A gene (spa), and arcA and opp3, proxy markers for the arginine catabolic mobile element (ACME), characteristic of USA300 MRSA. MRSA isolates also underwent staphylococcal cassette chromosome mec (SCCmec) typing and pulsed-field gel electrophoresis (PFGE) subtyping. MSSA isolates belonged to 17 sequence type (ST) groups. The 12 epidemiologically defined CA-MRSA infection isolates were either ST1 (n = 4) or ST8 (n = 8). They belonged to 3 different PFGE types: USA100 (n = 1), USA400 (n = 5), and USA500 (n = 6). Among the CA-MRSA infection isolates, 8 (67%) were PVL+. None of the MRSA or MSSA isolates contained arcA or opp3. Only one MRSA isolate was USA300 by PFGE. This was a health care-associated (HA) MRSA isolate, negative for PVL, that carried SCCmec type II. USA300 with its characteristic features was not identified in the collection from the years 1994 to 1997. PMID:26019202

  15. Global epidemiology of community-associated methicillin resistant Staphylococcus aureus (CA-MRSA).

    PubMed

    Mediavilla, José R; Chen, Liang; Mathema, Barun; Kreiswirth, Barry N

    2012-10-01

    During the 1990s, various reports of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) infections appeared in the literature, caused by novel strains genetically distinct from traditional healthcare-associated MRSA (HA-MRSA). Numerous lineages of CA-MRSA have since emerged on every continent, several of which have spread internationally, most notably USA300. CA-MRSA strains are increasingly implicated in nosocomial infections, and may eventually displace HA-MRSA strains in hospitals. Consequently, distinctions based on clinical epidemiology and susceptibility are becoming less relevant, arguing in favor of genotypic definitions. We review the current molecular epidemiology of CA-MRSA with respect to genetic diversity, global distribution, and factors related to its emergence and spread.

  16. Improved Protection in a Rabbit Model of Community-Associated Methicillin-Resistant Staphylococcus aureus Necrotizing Pneumonia upon Neutralization of Leukocidins in Addition to Alpha-Hemolysin.

    PubMed

    Diep, Binh An; Le, Vien T M; Visram, Zehra C; Rouha, Harald; Stulik, Lukas; Dip, Etyene Castro; Nagy, Gábor; Nagy, Eszter

    2016-10-01

    Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA), especially the USA300 pulsotype, is a frequent cause of skin and soft tissue infections and severe pneumonia. Despite appropriate antibiotic treatment, complications are common and pneumonia is associated with high mortality. S. aureus strains express multiple cytotoxins, including alpha-hemolysin (Hla) and up to five bicomponent leukocidins that specifically target phagocytic cells for lysis. CA-MRSA USA300 strains carry the genes for all six cytotoxins. Species specificity of the leukocidins greatly contributes to the ambiguity regarding their role in S. aureus pathogenesis. We performed a comparative analysis of the leukocidin susceptibility of human, rabbit, and mouse polymorphonuclear leukocytes (PMNs) to assess the translational value of mouse and rabbit S. aureus models. We found that mouse PMNs were largely resistant to LukSF-PV, HlgAB, and HlgCB and susceptible only to LukED, whereas rabbit and human PMNs were highly sensitive to all these cytotoxins. In the rabbit pneumonia model with a USA300 CA-MRSA strain, passive immunization with a previously identified human monoclonal antibody (MAb), Hla-F#5, which cross-neutralizes Hla, LukSF-PV, HlgAB, HlgCB, and LukED, provided full protection, whereas an Hla-specific MAb was only partially protective. In the mouse USA300 CA-MRSA pneumonia model, both types of antibodies demonstrated full protection, suggesting that Hla, but not leukocidin(s), is the principal virulence determinant in mice. As the rabbit recapitulates the high susceptibility to leukocidins characteristic of humans, this species represents a valuable model for assessing novel, cytotoxin-targeting anti-S. aureus therapeutic approaches.

  17. A Novel Core Genome-Encoded Superantigen Contributes to Lethality of Community-Associated MRSA Necrotizing Pneumonia

    PubMed Central

    Wilson, Gillian J.; Seo, Keun Seok; Cartwright, Robyn A.; Connelley, Timothy; Chuang-Smith, Olivia N.; Merriman, Joseph A.; Guinane, Caitriona M.; Park, Joo Youn; Bohach, Gregory A.; Schlievert, Patrick M.; Morrison, W. Ivan; Fitzgerald, J. Ross

    2011-01-01

    Bacterial superantigens (SAg) stimulate T-cell hyper-activation resulting in immune modulation and severe systemic illnesses such as Staphylococcus aureus toxic shock syndrome. However, all known S. aureus SAgs are encoded by mobile genetic elements and are made by only a proportion of strains. Here, we report the discovery of a novel SAg staphylococcal enterotoxin-like toxin X (SElX) encoded in the core genome of 95% of phylogenetically diverse S. aureus strains from human and animal infections, including the epidemic community-associated methicillin-resistant S. aureus (CA-MRSA) USA300 clone. SElX has a unique predicted structure characterized by a truncated SAg B-domain, but exhibits the characteristic biological activities of a SAg including Vβ-specific T-cell mitogenicity, pyrogenicity and endotoxin enhancement. In addition, SElX is expressed by clinical isolates in vitro, and during human, bovine, and ovine infections, consistent with a broad role in S. aureus infections of multiple host species. Phylogenetic analysis suggests that the selx gene was acquired horizontally by a progenitor of the S. aureus species, followed by allelic diversification by point mutation and assortative recombination resulting in at least 17 different alleles among the major pathogenic clones. Of note, SElX variants made by human- or ruminant-specific S. aureus clones demonstrated overlapping but distinct Vβ activation profiles for human and bovine lymphocytes, indicating functional diversification of SElX in different host species. Importantly, SElX made by CA-MRSA USA300 contributed to lethality in a rabbit model of necrotizing pneumonia revealing a novel virulence determinant of CA-MRSA disease pathogenesis. Taken together, we report the discovery and characterization of a unique core genome-encoded superantigen, providing new insights into the evolution of pathogenic S. aureus and the molecular basis for severe infections caused by the CA-MRSA USA300 epidemic clone. PMID

  18. Basis of virulence in a Panton-Valentine leukocidin-negative community-associated methicillin-resistant Staphylococcus aureus strain.

    PubMed

    Chen, Yan; Yeh, Anthony J; Cheung, Gordon Y C; Villaruz, Amer E; Tan, Vee Y; Joo, Hwang-Soo; Chatterjee, Som S; Yu, Yunsong; Otto, Michael

    2015-02-01

    Community-associated (CA) infections with methicillin-resistant Staphylococcus aureus (MRSA) are on a global rise. However, analysis of virulence characteristics has been limited almost exclusively to the US endemic strain USA300. CA-MRSA strains that do not produce Panton-Valentine leukocidin (PVL) have not been investigated on a molecular level. Therefore, we analyzed virulence determinants in a PVL-negative CA-MRSA strain, ST72, from Korea. Genome-wide analysis identified 3 loci that are unique to that strain, but did not affect virulence. In contrast, phenol-soluble modulins (PSMs) and the global virulence regulator Agr strongly affected lysis of neutrophils and erythrocytes, while α-toxin and Agr had a major impact on in vivo virulence. Our findings substantiate the general key roles these factors play in CA-MRSA virulence. However, our analyses also showed noticeable differences to strain USA300, inasmuch as α-toxin emerged as a much more important factor than PSMs in experimental skin infection caused by ST72.

  19. The νSaα Specific Lipoprotein Like Cluster (lpl) of S. aureus USA300 Contributes to Immune Stimulation and Invasion in Human Cells

    PubMed Central

    Nguyen, Minh Thu; Kraft, Beatrice; Yu, Wenqi; Demicrioglu, Dogan Doruk; Hertlein, Tobias; Burian, Marc; Schmaler, Mathias; Boller, Klaus; Bekeredjian-Ding, Isabelle; Ohlsen, Knut; Schittek, Birgit; Götz, Friedrich

    2015-01-01

    All Staphylococcus aureus genomes contain a genomic island, which is termed νSaα and characterized by two clusters of tandem repeat sequences, i.e. the exotoxin (set) and 'lipoprotein-like' genes (lpl). Based on their structural similarities the νSaα islands have been classified as type I to IV. The genomes of highly pathogenic and particularly epidemic S. aureus strains (USA300, N315, Mu50, NCTC8325, Newman, COL, JH1 or JH9) belonging to the clonal complexes CC5 and CC8 bear a type I νSaα island. Since the contribution of the lpl gene cluster encoded in the νSaα island to virulence is unclear to date, we deleted the entire lpl gene cluster in S. aureus USA300. The results showed that the mutant was deficient in the stimulation of pro-inflammatory cytokines in human monocytes, macrophages and keratinocytes. Purified lipoprotein Lpl1 was further shown to elicit a TLR2-dependent response. Furthermore, heterologous expression of the USA300 lpl cluster in other S. aureus strains enhanced their immune stimulatory activity. Most importantly, the lpl cluster contributed to invasion of S. aureus into human keratinocytes and mouse skin and the non-invasive S. carnosus expressing the lpl gene cluster became invasive. Additionally, in a murine kidney abscess model the bacterial burden in the kidneys was higher in wild type than in mutant mice. In this infection model the lpl cluster, thus, contributes to virulence. The present report is one of the first studies addressing the role of the νSaα encoded lpl gene cluster in staphylococcal virulence. The finding that the lpl gene cluster contributes to internalization into non-professional antigen presenting cells such as keratinocytes highlights the lpl as a new cell surface component that triggers host cell invasion by S. aureus. Increased invasion in murine skin and an increased bacterial burden in a murine kidney abscess model suggest that the lpl gene cluster serves as an important virulence factor. PMID:26083414

  20. Methicillin-Resistant Staphylococcus aureus USA300 Latin American Variant in Patients Undergoing Hemodialysis and HIV Infected in a Hospital in Bogotá, Colombia.

    PubMed

    Hidalgo, Marylin; Carvajal, Lina P; Rincón, Sandra; Faccini-Martínez, Álvaro A; Tres Palacios, Alba A; Mercado, Marcela; Palomá, Sandra L; Rayo, Leidy X; Acevedo, Jessica A; Reyes, Jinnethe; Panesso, Diana; García-Padilla, Paola; Alvarez, Carlos; Arias, Cesar A

    2015-01-01

    We aimed to determine the prevalence of MRSA colonization and examine the molecular characteristics of colonizing isolates in patients receiving hemodialysis and HIV-infected in a Colombian hospital. Patients on hemodialysis and HIV-infected were prospectively followed between July 2011 and June 2012 in Bogota, Colombia. Nasal and axillary swabs were obtained and cultured. Colonizing S. aureus isolates were identified by standard and molecular techniques. Molecular typing was performed by using pulse-field gel electrophoresis and evaluating the presence of lukF-PV/lukS-PV by PCR. A total of 29% (n = 82) of HIV-infected and 45.5% (n = 15) of patients on hemodialysis exhibited S. aureus colonization. MSSA/MRSA colonization was observed in 28% and 3.6% of the HIV patients, respectively and in 42.4% and 13.3% of the hemodialysis patients, respectively. Staphylococcal cassette chromosome mec typing showed that four MRSA isolates harbored the type IV cassette, and one type I. In the hemodialysis group, two MRSA isolates were classified as belonging to the USA300-LV genetic lineage. Conversely, in the HIV infected group, no colonizing isolates belonging to the USA300-Latin American Variant (UDA300-LV) lineage were identified. Colonizing isolates recovered from the HIV-infected group belonged to the prevalent hospital-associated clones circulating in Latin America (Chilean [n = 1] and Pediatric [n = 2]). The prevalence of MRSA colonization in the study groups was 3.6% (HIV) and 13.3% (hemodialysis). Surveillance programs should be implemented in this group of patients in order to understand the dynamics of colonization and infection in high-risk patients.

  1. Methicillin-Resistant Staphylococcus aureus USA300 Latin American Variant in Patients Undergoing Hemodialysis and HIV Infected in a Hospital in Bogotá, Colombia

    PubMed Central

    Hidalgo, Marylin; Carvajal, Lina P.; Rincón, Sandra; Faccini-Martínez, Álvaro A.; Tres Palacios, Alba A.; Mercado, Marcela; Palomá, Sandra L.; Rayo, Leidy X.; Acevedo, Jessica A.; Reyes, Jinnethe; Panesso, Diana; García-Padilla, Paola; Alvarez, Carlos; Arias, Cesar A.

    2015-01-01

    We aimed to determine the prevalence of MRSA colonization and examine the molecular characteristics of colonizing isolates in patients receiving hemodialysis and HIV-infected in a Colombian hospital. Patients on hemodialysis and HIV-infected were prospectively followed between July 2011 and June 2012 in Bogota, Colombia. Nasal and axillary swabs were obtained and cultured. Colonizing S. aureus isolates were identified by standard and molecular techniques. Molecular typing was performed by using pulse-field gel electrophoresis and evaluating the presence of lukF-PV/lukS-PV by PCR. A total of 29% (n = 82) of HIV-infected and 45.5% (n = 15) of patients on hemodialysis exhibited S. aureus colonization. MSSA/MRSA colonization was observed in 28% and 3.6% of the HIV patients, respectively and in 42.4% and 13.3% of the hemodialysis patients, respectively. Staphylococcal cassette chromosome mec typing showed that four MRSA isolates harbored the type IV cassette, and one type I. In the hemodialysis group, two MRSA isolates were classified as belonging to the USA300-LV genetic lineage. Conversely, in the HIV infected group, no colonizing isolates belonging to the USA300-Latin American Variant (UDA300-LV) lineage were identified. Colonizing isolates recovered from the HIV-infected group belonged to the prevalent hospital-associated clones circulating in Latin America (Chilean [n = 1] and Pediatric [n = 2]). The prevalence of MRSA colonization in the study groups was 3.6% (HIV) and 13.3% (hemodialysis). Surveillance programs should be implemented in this group of patients in order to understand the dynamics of colonization and infection in high-risk patients. PMID:26474075

  2. Emergence of the Epidemic Methicillin-Resistant Staphylococcus aureus Strain USA300 Coincides with Horizontal Transfer of the Arginine Catabolic Mobile Element and speG-mediated Adaptations for Survival on Skin

    PubMed Central

    Planet, Paul J.; LaRussa, Samuel J.; Dana, Ali; Smith, Hannah; Xu, Amy; Ryan, Chanelle; Uhlemann, Anne-Catrin; Boundy, Sam; Goldberg, Julia; Narechania, Apurva; Kulkarni, Ritwij; Ratner, Adam J.; Geoghegan, Joan A.; Kolokotronis, Sergios-Orestis; Prince, Alice

    2013-01-01

    ABSTRACT The arginine catabolic mobile element (ACME) is the largest genomic region distinguishing epidemic USA300 strains of methicillin-resistant Staphylococcus aureus (MRSA) from other S. aureus strains. However, the functional relevance of ACME to infection and disease has remained unclear. Using phylogenetic analysis, we have shown that the modular segments of ACME were assembled into a single genetic locus in Staphylococcus epidermidis and then horizontally transferred to the common ancestor of USA300 strains in an extremely recent event. Acquisition of one ACME gene, speG, allowed USA300 strains to withstand levels of polyamines (e.g., spermidine) produced in skin that are toxic to other closely related S. aureus strains. speG-mediated polyamine tolerance also enhanced biofilm formation, adherence to fibrinogen/fibronectin, and resistance to antibiotic and keratinocyte-mediated killing. We suggest that these properties gave USA300 a major selective advantage during skin infection and colonization, contributing to the extraordinary evolutionary success of this clone. PMID:24345744

  3. β-Lactam Resistance in Methicillin-Resistant Staphylococcus aureus USA300 Is Increased by Inactivation of the ClpXP Protease

    PubMed Central

    Bæk, Kristoffer T.; Gründling, Angelika; Mogensen, René G.; Thøgersen, Louise; Petersen, Andreas; Paulander, Wilhelm

    2014-01-01

    Methicillin-resistant Staphylococcus aureus (MRSA) has acquired the mecA gene encoding a peptidoglycan transpeptidase, penicillin binding protein 2a (PBP2a), which has decreased affinity for β-lactams. Quickly spreading and highly virulent community-acquired (CA) MRSA strains recently emerged as a frequent cause of infection in individuals without exposure to the health care system. In this study, we found that the inactivation of the components of the ClpXP protease substantially increased the β-lactam resistance level of a CA-MRSA USA300 strain, suggesting that the proteolytic activity of ClpXP controls one or more pathways modulating β-lactam resistance. These pathways do not involve the control of mecA expression, as the cellular levels of PBP2a were unaltered in the clp mutants. An analysis of the cell envelope properties of the clpX and clpP mutants revealed a number of distinct phenotypes that may contribute to the enhanced β-lactam tolerance. Both mutants displayed significantly thicker cell walls, increased peptidoglycan cross-linking, and altered composition of monomeric muropeptide species compared to those of the wild types. Moreover, changes in Sle1-mediated peptidoglycan hydrolysis and altered processing of the major autolysin Atl were observed in the clp mutants. In conclusion, the results presented here point to an important role for the ClpXP protease in controlling cell wall metabolism and add novel insights into the molecular factors that determine strain-dependent β-lactam resistance. PMID:24867990

  4. β-Lactam resistance in methicillin-resistant Staphylococcus aureus USA300 is increased by inactivation of the ClpXP protease.

    PubMed

    Bæk, Kristoffer T; Gründling, Angelika; Mogensen, René G; Thøgersen, Louise; Petersen, Andreas; Paulander, Wilhelm; Frees, Dorte

    2014-08-01

    Methicillin-resistant Staphylococcus aureus (MRSA) has acquired the mecA gene encoding a peptidoglycan transpeptidase, penicillin binding protein 2a (PBP2a), which has decreased affinity for β-lactams. Quickly spreading and highly virulent community-acquired (CA) MRSA strains recently emerged as a frequent cause of infection in individuals without exposure to the health care system. In this study, we found that the inactivation of the components of the ClpXP protease substantially increased the β-lactam resistance level of a CA-MRSA USA300 strain, suggesting that the proteolytic activity of ClpXP controls one or more pathways modulating β-lactam resistance. These pathways do not involve the control of mecA expression, as the cellular levels of PBP2a were unaltered in the clp mutants. An analysis of the cell envelope properties of the clpX and clpP mutants revealed a number of distinct phenotypes that may contribute to the enhanced β-lactam tolerance. Both mutants displayed significantly thicker cell walls, increased peptidoglycan cross-linking, and altered composition of monomeric muropeptide species compared to those of the wild types. Moreover, changes in Sle1-mediated peptidoglycan hydrolysis and altered processing of the major autolysin Atl were observed in the clp mutants. In conclusion, the results presented here point to an important role for the ClpXP protease in controlling cell wall metabolism and add novel insights into the molecular factors that determine strain-dependent β-lactam resistance.

  5. Molecular epidemiologic study of community-associated methicillin-resistant Staphylococcus aureus with Panton-Valentine leukocidin gene among family members in Japan.

    PubMed

    Uehara, Yuki; Ito, Teruyo; Ogawa, Yu; Hirotaki, Shintaro; Shoji, Takayo; Tame, Tomoyuki; Horikoshi, Yuho; Hiramatsu, Keiichi

    2015-09-01

    Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) is one of the worldwide concerns of antimicrobial chemotherapy. An accumulation of ten patients in five families (A-E) suffering from skin and soft tissue infection (SSTI) of CA-MRSA was experienced in 2012, in Fuchu-shi, Tokyo, Japan. Molecular epidemiological investigation was performed for the 10 MRSA strains obtained from 8 children and 2 of their parents to assess endemic patterns of CA-MRSA in the community. Results of molecular typing, presence of toxin genes and antimicrobial susceptibilities were analyzed combined with the patients' clinical information. Each family had its own unique MRSA strain: A, ST30-SCCmec IVd; B, ST8-SCCmec IVd; C, ST8-SCCmec IVa; D, ST8-SCCmec IVl; E, ST8-SCCmec IVl and ST858-SCCmec IVl. Seven strains from the families A-C carried Panton-Valentine leukocidin gene. Three strains from the families D and E carried toxic shock syndrome toxin gene. Strains belonged to the same family demonstrated genetically related banding patterns of pulsed-filed gel electrophoresis. The family C experienced intrafamilial transmission of USA300-0114. Our data showed the MRSA clones disseminating in this community were highly diverse. They contained USA300-0114 clone, the rapidly distributing clone in the world, as well as MRSA clones identified in Japan. Our results suggested intrafamilial transmission of MRSA could be initial phenomenon of wide transmission in a community, therefore CA-MRSA SSTI in children and their family members should be monitored closely in order to notice the spread of highly pathogenic and transmittable strains. PMID:26091885

  6. Molecular epidemiologic study of community-associated methicillin-resistant Staphylococcus aureus with Panton-Valentine leukocidin gene among family members in Japan.

    PubMed

    Uehara, Yuki; Ito, Teruyo; Ogawa, Yu; Hirotaki, Shintaro; Shoji, Takayo; Tame, Tomoyuki; Horikoshi, Yuho; Hiramatsu, Keiichi

    2015-09-01

    Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) is one of the worldwide concerns of antimicrobial chemotherapy. An accumulation of ten patients in five families (A-E) suffering from skin and soft tissue infection (SSTI) of CA-MRSA was experienced in 2012, in Fuchu-shi, Tokyo, Japan. Molecular epidemiological investigation was performed for the 10 MRSA strains obtained from 8 children and 2 of their parents to assess endemic patterns of CA-MRSA in the community. Results of molecular typing, presence of toxin genes and antimicrobial susceptibilities were analyzed combined with the patients' clinical information. Each family had its own unique MRSA strain: A, ST30-SCCmec IVd; B, ST8-SCCmec IVd; C, ST8-SCCmec IVa; D, ST8-SCCmec IVl; E, ST8-SCCmec IVl and ST858-SCCmec IVl. Seven strains from the families A-C carried Panton-Valentine leukocidin gene. Three strains from the families D and E carried toxic shock syndrome toxin gene. Strains belonged to the same family demonstrated genetically related banding patterns of pulsed-filed gel electrophoresis. The family C experienced intrafamilial transmission of USA300-0114. Our data showed the MRSA clones disseminating in this community were highly diverse. They contained USA300-0114 clone, the rapidly distributing clone in the world, as well as MRSA clones identified in Japan. Our results suggested intrafamilial transmission of MRSA could be initial phenomenon of wide transmission in a community, therefore CA-MRSA SSTI in children and their family members should be monitored closely in order to notice the spread of highly pathogenic and transmittable strains.

  7. Bacterial communities associated with the lichen symbiosis.

    PubMed

    Bates, Scott T; Cropsey, Garrett W G; Caporaso, J Gregory; Knight, Rob; Fierer, Noah

    2011-02-01

    Lichens are commonly described as a mutualistic symbiosis between fungi and "algae" (Chlorophyta or Cyanobacteria); however, they also have internal bacterial communities. Recent research suggests that lichen-associated microbes are an integral component of lichen thalli and that the classical view of this symbiotic relationship should be expanded to include bacteria. However, we still have a limited understanding of the phylogenetic structure of these communities and their variability across lichen species. To address these knowledge gaps, we used bar-coded pyrosequencing to survey the bacterial communities associated with lichens. Bacterial sequences obtained from four lichen species at multiple locations on rock outcrops suggested that each lichen species harbored a distinct community and that all communities were dominated by Alphaproteobacteria. Across all samples, we recovered numerous bacterial phylotypes that were closely related to sequences isolated from lichens in prior investigations, including those from a lichen-associated Rhizobiales lineage (LAR1; putative N(2) fixers). LAR1-related phylotypes were relatively abundant and were found in all four lichen species, and many sequences closely related to other known N(2) fixers (e.g., Azospirillum, Bradyrhizobium, and Frankia) were recovered. Our findings confirm the presence of highly structured bacterial communities within lichens and provide additional evidence that these bacteria may serve distinct functional roles within lichen symbioses.

  8. Community-associated methicillin resistant Staphylococcus aureus in south Florida hospital and recreational environments

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Strains of methicillin resistant Staphylococcus aureus (MRSA), a frequent human pathogen, may also be found in the flora of healthy persons and in the environments that they frequent. Strains of MRSA circulating in the community classified as USA 300 are now found not only in the community but also...

  9. Molecular Characterization of Community-Associated Methicillin-Resistant Staphylococcus aureus Isolated from Skin and Pus Samples of Outpatients in Japan.

    PubMed

    Yamaguchi, Tetsuo; Okamura, Sakiko; Miura, Yuri; Koyama, Shinobu; Yanagisawa, Hideji; Matsumoto, Tetsuya

    2015-08-01

    Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) is now endemic in the United States. In Japan, CA-MRSA infections and CA-MRSA surveillance have been scarcely reported. In this study, we conducted a nationwide survey of CA-MRSA in Japan. We collected MRSA strains isolated from outpatients with skin and soft-tissue infection (SSTI) at 107 medical facilities from 24 prefectures in 2010 and 2012. Among 10,385 clinical samples from SSTI patients, 3,581 S. aureus isolates (35%) were obtained and 673 of the S. aureus strains (19%) were identified as MRSA. Among 625 MRSA strains tested in this study, 266 strains (43%) and 114 strains (18%) were classified as SCCmec types IV and V, respectively. Detection of virulence genes was as follows: Panton-Valentine leukocidin (PVL) gene (57 strains, 9%), exfoliative toxin (ET) gene (179 strains, 29%), toxic shock syndrome toxin-1 (TSST-1) gene (195 strains, 31%), or none. PVL-positive strains were classified into eight sequence types (STs) (i.e., ST1, ST5, ST8, ST22, ST30, ST452, ST59, and ST154) and six clonal complexes (i.e., CC1, CC5, CC8, CC22, CC30, and CC59). Only 10 PVL-positive strains (2%) were pulsed-field type USA300 clone. There were a wide variety of CA-MRSA clones in Japan, which were different from the situation in the United States.

  10. Heterogeneous vancomycin-intermediate susceptibility in a community-associated methicillin-resistant Staphylococcus aureus epidemic clone, in a case of Infective Endocarditis in Argentina

    PubMed Central

    2011-01-01

    Background Community-Associated Methicillin Resistant Staphylococcus aureus (CA-MRSA) has traditionally been related to skin and soft tissue infections in healthy young patients. However, it has now emerged as responsible for severe infections worldwide, for which vancomycin is one of the mainstays of treatment. Infective endocarditis (IE) due to CA-MRSA with heterogeneous vancomycin-intermediate susceptibility-(h-VISA) has been recently reported, associated to an epidemic USA 300 CA-MRSA clone. Case Presentation We describe the occurrence of h-VISA phenotype in a case of IE caused by a strain belonging to an epidemic CA-MRSA clone, distinct from USA300, for the first time in Argentina. The isolate h-VISA (SaB2) was recovered from a patient with persistent bacteraemia after a 7-day therapy with vancomycin, which evolved to fatal case of IE complicated with brain abscesses. The initial isolate-(SaB1) was fully vancomycin susceptible (VSSA). Although MRSA SaB2 was vancomycin susceptible (≤2 μg/ml) by MIC (agar and broth dilution, E-test and VITEK 2), a slight increase of MIC values between SaB1 and SaB2 isolates was detected by the four MIC methods, particularly for teicoplanin. Moreover, Sab2 was classified as h-VISA by three different screening methods [MHA5T-screening agar, Macromethod-E-test-(MET) and by GRD E-test] and confirmed by population analysis profile-(PAP). In addition, a significant increase in cell-wall thickness was revealed for SaB2 by electron microscopy. Molecular typing showed that both strains, SaB1 and SaB2, belonged to ST5 lineage, carried SCCmecIV, lacked Panton-Valentine leukocidin-(PVL) genes and had indistinguishable PFGE patterns (subtype I2), thereby confirming their isogenic nature. In addition, they were clonally related to the epidemic CA-MRSA clone (pulsotype I) detected in our country. Conclusions This report demonstrates the ability of this epidemic CA-MRSA clone, disseminated in some regions of Argentina, to produce severe and

  11. Evidence of Multiple Virulence Subtypes in Nosocomial and Community-Associated MRSA Genotypes in Companion Animals from the Upper Midwestern and Northeastern United States

    PubMed Central

    Lin, Yihan; Barker, Emily; Kislow, Jennifer; Kaldhone, Pravin; Stemper, Mary E.; Pantrangi, Madhulatha; Moore, Frances M.; Hall, Matthew; Fritsche, Thomas R.; Novicki, Thomas; Foley, Steven L.; Shukla, Sanjay K.

    2011-01-01

    Objective: Not much is known about the zoonotic transmission of methicillin-resistant Staphylococcus aureus (MRSA) in companion animals in the United States. We report the rate of prevalence of S. aureus and MRSA recovered from clinical samples of animals requiring treatment at veterinary clinics throughout the upper midwestern and northeastern United States. Design: We compared phenotypes, genotypes, and virulence profiles of the MRSA isolates identified in companion animals, such as cats, dogs, horses, and pigs, with typical human nosocomial and community-associated MRSA (CA-MRSA) genotypes to assess implied zoonotic transmission or zooanthroponosis. Five hundred thirty-three coagulase-positive staphylococci (CPS) isolates recovered between 2006 and 2008 from a variety of animal-source samples were screened for S. aureus by S. aureus-specific 16S rDNA primers and were screened for methicillin-resistance. All MRSA isolates were genotyped by pulsed-field gel electrophoresis (PFGE), multilocus sequence typing (MLST), and spa typing. They were also screened for common staphylococcal enterotoxin and adhesion genes by multiplex and singleplex PCR. Results: Among the 533 CPS isolates recovered, 66 (12.4%) were determined to be S. aureus and 24 (4.5%) were MRSA. The percent of animals that were positive for S. aureus were as follows: 6.6% (32 of 487) dogs, 39.6% (19 of 48) cats, 83.3% (10 of 12) horses, and 100% of pigs, rabbits, hamsters and rats. Notably, 36.4% of all S. aureus identified were MRSA. Methicillin-resistant S. aureus was present in clinical samples from 12 of 487 dogs (2.5%), 6 of 48 cats (12.5%), 5 of 12 horses (42%), and 1 of 2 pigs (50%). The 24 MRSA isolates resolved into 4 PFGE clones: USA100 (50%), USA300 (16.7%), USA500 (20.8%) and USA800 (12.5%) and 6 sequence types (ST5, ST8, ST105, ST830, and ST986) or 2 clonal complexes, CC5 and CC8. Five major virulence profiles (clusters A to E) were observed in these MRSA isolates. Genotypic and virulence

  12. Assessing the diversity of bacterial communities associated with plants

    PubMed Central

    Andreote, Fernando Dini; Azevedo, João Lúcio; Araújo, Welington Luiz

    2009-01-01

    Plant–bacteria interactions result from reciprocal recognition between both species. These interactions are responsible for essential biological processes in plant development and health status. Here, we present a review of the methodologies applied to investigate shifts in bacterial communities associated with plants. A description of techniques is made from initial isolations to culture-independent approaches focusing on quantitative Polymerase Chain Reaction in real time (qPCR), Denaturing Gradient Gel Electrophoresis (DGGE), clone library construction and analysis, the application of multivariate analyses to microbial ecology data and the upcoming high throughput methodologies such as microarrays and pyrosequencing. This review supplies information about the development of traditional methods and a general overview about the new insights into bacterial communities associated with plants. PMID:24031382

  13. Microbial communities associated with wet flue gas desulfurization systems.

    PubMed

    Brown, Bryan P; Brown, Shannon R; Senko, John M

    2012-01-01

    Flue gas desulfurization (FGD) systems are employed to remove SO(x) gasses that are produced by the combustion of coal for electric power generation, and consequently limit acid rain associated with these activities. Wet FGDs represent a physicochemically extreme environment due to the high operating temperatures and total dissolved solids (TDS) of fluids in the interior of the FGD units. Despite the potential importance of microbial activities in the performance and operation of FGD systems, the microbial communities associated with them have not been evaluated. Microbial communities associated with distinct process points of FGD systems at several coal-fired electricity generation facilities were evaluated using culture-dependent and -independent approaches. Due to the high solute concentrations and temperatures in the FGD absorber units, culturable halothermophilic/tolerant bacteria were more abundant in samples collected from within the absorber units than in samples collected from the makeup waters that are used to replenish fluids inside the absorber units. Evaluation of bacterial 16S rRNA genes recovered from scale deposits on the walls of absorber units revealed that the microbial communities associated with these deposits are primarily composed of thermophilic bacterial lineages. These findings suggest that unique microbial communities develop in FGD systems in response to physicochemical characteristics of the different process points within the systems. The activities of the thermophilic microbial communities that develop within scale deposits could play a role in the corrosion of steel structures in FGD systems.

  14. Microbial communities associated with wet flue gas desulfurization systems

    PubMed Central

    Brown, Bryan P.; Brown, Shannon R.; Senko, John M.

    2012-01-01

    Flue gas desulfurization (FGD) systems are employed to remove SOx gasses that are produced by the combustion of coal for electric power generation, and consequently limit acid rain associated with these activities. Wet FGDs represent a physicochemically extreme environment due to the high operating temperatures and total dissolved solids (TDS) of fluids in the interior of the FGD units. Despite the potential importance of microbial activities in the performance and operation of FGD systems, the microbial communities associated with them have not been evaluated. Microbial communities associated with distinct process points of FGD systems at several coal-fired electricity generation facilities were evaluated using culture-dependent and -independent approaches. Due to the high solute concentrations and temperatures in the FGD absorber units, culturable halothermophilic/tolerant bacteria were more abundant in samples collected from within the absorber units than in samples collected from the makeup waters that are used to replenish fluids inside the absorber units. Evaluation of bacterial 16S rRNA genes recovered from scale deposits on the walls of absorber units revealed that the microbial communities associated with these deposits are primarily composed of thermophilic bacterial lineages. These findings suggest that unique microbial communities develop in FGD systems in response to physicochemical characteristics of the different process points within the systems. The activities of the thermophilic microbial communities that develop within scale deposits could play a role in the corrosion of steel structures in FGD systems. PMID:23226147

  15. Microbial communities associated with wet flue gas desulfurization systems.

    PubMed

    Brown, Bryan P; Brown, Shannon R; Senko, John M

    2012-01-01

    Flue gas desulfurization (FGD) systems are employed to remove SO(x) gasses that are produced by the combustion of coal for electric power generation, and consequently limit acid rain associated with these activities. Wet FGDs represent a physicochemically extreme environment due to the high operating temperatures and total dissolved solids (TDS) of fluids in the interior of the FGD units. Despite the potential importance of microbial activities in the performance and operation of FGD systems, the microbial communities associated with them have not been evaluated. Microbial communities associated with distinct process points of FGD systems at several coal-fired electricity generation facilities were evaluated using culture-dependent and -independent approaches. Due to the high solute concentrations and temperatures in the FGD absorber units, culturable halothermophilic/tolerant bacteria were more abundant in samples collected from within the absorber units than in samples collected from the makeup waters that are used to replenish fluids inside the absorber units. Evaluation of bacterial 16S rRNA genes recovered from scale deposits on the walls of absorber units revealed that the microbial communities associated with these deposits are primarily composed of thermophilic bacterial lineages. These findings suggest that unique microbial communities develop in FGD systems in response to physicochemical characteristics of the different process points within the systems. The activities of the thermophilic microbial communities that develop within scale deposits could play a role in the corrosion of steel structures in FGD systems. PMID:23226147

  16. Community-Associated Methicillin-Resistant Staphylococcus aureus Case Studies

    PubMed Central

    Sowash, Madeleine G.; Uhlemann, Anne-Catrin

    2014-01-01

    Over the past decade, the emergence of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) has changed the landscape of S. aureus infections around the globe. Initially recognized for its ability to cause disease in young and healthy individuals without healthcare exposures as well as for its distinct genotype and phenotype, this original description no longer fully encompasses the diversity of CA-MRSA as it continues to expand its niche. Using four case studies, we highlight a wide range of the clinical presentations and challenges of CA-MRSA. Based on these cases we further explore the globally polygenetic background of CA-MRSA with a special emphasis on generally less characterized populations. PMID:24085688

  17. Diverse honeydew-consuming fungal communities associated with scale insects.

    PubMed

    Dhami, Manpreet K; Weir, Bevan S; Taylor, Michael W; Beggs, Jacqueline R

    2013-01-01

    Sooty mould fungi are ubiquitous, abundant consumers of insect-honeydew that have been little-studied. They form a complex of unrelated fungi that coexist and compete for honeydew, which is a chemically complex resource. In this study, we used scanning electron microscopy in combination with T-RFLP community profiling and ITS-based tag-pyrosequencing to extensively describe the sooty mould community associated with the honeydews of two ecologically important New Zealand coelostomidiid scale insects, Coelostomidia wairoensis and Ultracoelostoma brittini. We tested the influence of host plant on the community composition of associated sooty moulds, and undertook limited analyses to examine the influence of scale insect species and geographic location. We report here a previously unknown degree of fungal diversity present in this complex, with pyrosequencing detecting on average 243 operational taxonomic units across the different sooty mould samples. In contrast, T-RFLP detected only a total of 24 different "species" (unique peaks). Nevertheless, both techniques identified similar patterns of diversity suggesting that either method is appropriate for community profiling. The composition of the microbial community associated with individual scale insect species varied although the differences may in part reflect variation in host preference and site. Scanning electron microscopy visualised an intertwined mass of fungal hyphae and fruiting bodies in near-intact physical condition, but was unable to distinguish between the different fungal communities on a morphological level, highlighting the need for molecular research. The substantial diversity revealed for the first time by pyrosequencing and our inability to identify two-thirds of the diversity to further than the fungal division highlights the significant gap in our knowledge of these fungal groups. This study provides a first extensive look at the community diversity of the fungal community closely associated

  18. Complete Circular Genome Sequence of Successful ST8/SCCmecIV Community-Associated Methicillin-Resistant Staphylococcus aureus (OC8) in Russia: One-Megabase Genomic Inversion, IS256’s Spread, and Evolution of Russia ST8-IV

    PubMed Central

    Wan, Tsai-Wen; Higuchi, Wataru; Hung, Wei-Chun; Reva, Ivan V.; Singur, Olga A.; Gostev, Vladimir V.; Sidorenko, Sergey V.; Peryanova, Olga V.; Salmina, Alla B.; Reva, Galina V.; Teng, Lee-Jene; Yamamoto, Tatsuo

    2016-01-01

    ST8/SCCmecIV community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) has been a common threat, with large USA300 epidemics in the United States. The global geographical structure of ST8/SCCmecIV has not yet been fully elucidated. We herein determined the complete circular genome sequence of ST8/SCCmecIVc strain OC8 from Siberian Russia. We found that 36.0% of the genome was inverted relative to USA300. Two IS256, oppositely oriented, at IS256-enriched hot spots were implicated with the one-megabase genomic inversion (MbIN) and vSaβ split. The behavior of IS256 was flexible: its insertion site (att) sequences on the genome and junction sequences of extrachromosomal circular DNA were all divergent, albeit with fixed sizes. A similar multi-IS256 system was detected, even in prevalent ST239 healthcare-associated MRSA in Russia, suggesting IS256’s strong transmission potential and advantage in evolution. Regarding epidemiology, all ST8/SCCmecIVc strains from European, Siberian, and Far Eastern Russia, examined had MbIN, and geographical expansion accompanied divergent spa types and resistance to fluoroquinolones, chloramphenicol, and often rifampicin. Russia ST8/SCCmecIVc has been associated with life-threatening infections such as pneumonia and sepsis in both community and hospital settings. Regarding virulence, the OC8 genome carried a series of toxin and immune evasion genes, a truncated giant surface protein gene, and IS256 insertion adjacent to a pan-regulatory gene. These results suggest that unique single ST8/spa1(t008)/SCCmecIVc CA-MRSA (clade, Russia ST8-IVc) emerged in Russia, and this was followed by large geographical expansion, with MbIN as an epidemiological marker, and fluoroquinolone resistance, multiple virulence factors, and possibly a multi-IS256 system as selective advantages. PMID:27741255

  19. Shifts in soil testate amoeba communities associated with forest diversification.

    PubMed

    Bobrov, Anatoly A; Zaitsev, Andrei S; Wolters, Volkmar

    2015-05-01

    We studied changes of testate amoeba communities associated with the conversion of spruce monocultures into mixed beech-fir-spruce forests in the Southern Black Forest Mountains (Germany). In this region, forest conversion is characterized by a gradual development of beech undergrowth within thinned spruce tree stands leading to multiple age continuous cover forests with a diversified litter layer. Strong shifts in the abundance of testate amoeba observed in intermediate stages levelled off to monoculture conditions again after the final stage of the conversion process had been reached. The average number of species per conversion stage (i.e., local richness) did not respond strongly to forest conversion, but the total number of species (i.e., regional richness) was considerably higher in the initial stage than in the mixed forests, due to the large number of hygrophilous species inhabiting spruce monocultures. Functional diversity of the testate amoeba community, however, significantly increased during the conversion process. This shift was closely associated with improved C and N availability as well as higher niche diversity in the continuous cover stands. Lower soil acidity in these forests coincided with a higher relative abundance of eurytopic species. Our results suggest that testate amoeba communities are much more affected by physicochemical properties of the soil than directly by litter diversity.

  20. Community-associated methicillin-resistant Staphylococcus aureus

    PubMed Central

    DeLeo, Frank R.; Otto, Michael; Kreiswirth, Barry N.; Chambers, Henry F.

    2012-01-01

    Summary Methicillin-resistant Staphylococcus aureus (MRSA) is endemic in hospitals worldwide and a significant cause of morbidity and mortality. Healthcare-associated MRSA infections occur in individuals with predisposing risk factors for disease, such as surgery or presence of an indwelling medical device. By contrast, community-associated MRSA (CA-MRSA) infections often occur in otherwise healthy individuals who lack such risk factors. In addition, CA-MRSA infections are epidemic in some countries. These observations suggest that CA-MRSA strains are more virulent and transmissible than traditional hospital-associated MRSA strains. Relatively limited treatment options for CA-MRSA infections compound the problem of enhanced virulence and transmission. Although progress has been made toward understanding emergence of CA-MRSA, virulence, and treatment of infections, our knowledge in these areas remains incomplete. Here were review the most current knowledge in these areas and provide perspective on future outlook for prophylaxis and/or new therapies for CA-MRSA infections. PMID:20206987

  1. Viral communities associated with healthy and bleaching corals.

    PubMed

    Marhaver, Kristen L; Edwards, Robert A; Rohwer, Forest

    2008-09-01

    The coral holobiont is the integrated assemblage of the coral animal, its symbiotic algae, protists, fungi and a diverse consortium of Bacteria and Archaea. Corals are a model system for the study of symbiosis, the breakdown of which can result in disease and mortality. Little is known, however, about viruses that infect corals and their symbionts. Here we present metagenomic analyses of the viral communities associated with healthy and partially bleached specimens of the Caribbean reef-building coral Diploria strigosa. Surprisingly, herpes-like sequences accounted for 4-8% of the total sequences in each metagenome; this abundance of herpes-like sequences is unprecedented in other marine viral metagenomes. Viruses similar to those that infect algae and plants were also present in the coral viral assemblage. Among the phage identified, cyanophages were abundant in both healthy and bleaching corals and vibriophages were also present. Therefore, coral-associated viruses could potentially infect all components of the holobiont--coral, algal and microbial. Thus, we expect viruses to figure prominently in the preservation and breakdown of coral health.

  2. Community-associated methicillin-resistant Staphylococcus aureus, Canada.

    PubMed

    Mulvey, Michael R; MacDougall, Laura; Cholin, Brenda; Horsman, Greg; Fidyk, Melanie; Woods, Shirley

    2005-06-01

    A total of 184 methicillin-resistant Staphylococcus aureus (MRSA) strains were collected from patients who sought treatment primarily for skin and soft tissue infections from January 1, 1999, to March 31, 2002, in east-central Saskatchewan, Canada. Molecular subtyping analysis using pulsed-field gel electrophoresis showed 2 major clusters. Cluster A (n = 55) was composed of a multidrug-resistant MRSA strain associated with a long-term care facility and was similar to the previously reported nosocomial Canadian epidemic strain labeled CMRSA-2. Cluster B (n = 125) was associated with cases identified at community health centers and was indistinguishable from a community-associated (CA)-MRSA strain identified previously in the United States (USA400). Cluster B remained susceptible to a number of classes of antimicrobial agents and harbored the lukF-PV and lukS-PV toxin genes. Over 50% of both clonal groups displayed high-level resistance to mupirocin. This is the first report of the USA400 strain harboring the lukF-PV and lukS-PV toxin genes in Canada.

  3. Bacterial communities associated with four ctenophore genera from the German Bight (North Sea).

    PubMed

    Hao, Wenjin; Gerdts, Gunnar; Peplies, Jörg; Wichels, Antje

    2015-01-01

    Intense research has been conducted on jellyfish and ctenophores in recent years. They are increasingly recognized as key elements in the marine ecosystem that serve as critical indicators and drivers of ecosystem performance and change. However, the bacterial community associated with ctenophores is still poorly investigated. Based on automated ribosomal intergenic spacer analysis (ARISA) and 16S ribosomal RNA gene amplicon pyrosequencing, we investigated bacterial communities associated with the frequently occurring ctenophore species Mnemiopsis leidyi, Beroe sp., Bolinopsis infundibulum and Pleurobrachia pileus at Helgoland Roads in the German Bight (North Sea). We observed significant differences between the associated bacterial communities of the different ctenophore species based on ARISA patterns. With respect to bacterial taxa, all ctenophore species were dominated by Proteobacteria as revealed by pyrosequencing. Mnemiopsis leidyi and P. pileus mainly harboured Gammaproteobacteria, with Marinomonas as the dominant phylotype of M. leidyi. By contrast, Pseudoalteromonas and Psychrobacter were the most abundant Gammaproteobacteria in P. pileus. Beroe sp. was mainly dominated by Alphaproteobacteria, particularly by the genus Thalassospira. For B. infundibulum, the bacterial community was composed of Alphaproteobacteria and Gammaproteobacteria in equal parts, which consisted of the genera Thalassospira and Marinomonas. In addition, the bacterial communities associated with M. leidyi display a clear variation over time that needs further investigation. Our results indicate that the bacterial communities associated with ctenophores are highly species- specific. PMID:25764531

  4. Preventing Community-Associated Methicillin-Resistant "Staphylococcus aureus" among Student Athletes

    ERIC Educational Resources Information Center

    Many, Patricia S.

    2008-01-01

    Methicillin-resistant "Staphylococcus aureus" (MRSA) was once thought to be a bacterium causing infections in only hospitalized patients. However, a new strain of MRSA has emerged among healthy individuals who have not had any recent exposure to a hospital or to medical procedures. This new strain is known as "community-associated MRSA". Studies…

  5. Scarlet fever caused by community-associated methicillin-resistant Staphylococcus aureus.

    PubMed

    Lu, Ying-Chun; Chen, Shyi-Jou; Lo, Wen-Tsung

    2011-07-01

    We describe a previously healthy 2.5-year-old boy with staphylococcal scarlet fever associated with acute suppurative otitis media due to community-associated methicillin-resistant Staphylococcus aureus. The patient was successfully treated by spontaneous drainage in combination with trimethoprim-sulfamethoxazole therapy.

  6. New patterns of methicillin-resistant Staphylococcus aureus (MRSA) clones, community-associated MRSA genotypes behave like healthcare-associated MRSA genotypes within hospitals, Argentina.

    PubMed

    Egea, Ana L; Gagetti, Paula; Lamberghini, Ricardo; Faccone, Diego; Lucero, Celeste; Vindel, Ana; Tosoroni, Dario; Garnero, Analía; Saka, Hector A; Galas, Marcelo; Bocco, José L; Corso, Alejandra; Sola, Claudia

    2014-11-01

    Methicillin-resistant Staphylococcus aureus (MRSA) burden is increasing worldwide in hospitals [healthcare-associated (HA)-MRSA] and in communities [community-associated (CA)-MRSA]. However, the impact of CA-MRSA within hospitals remains limited, particularly in Latin America. A countrywide representative survey of S. aureus infections was performed in Argentina by analyzing 591 clinical isolates from 66 hospitals in a prospective cross-sectional, multicenter study (Nov-2009). This work involved healthcare-onset infections-(HAHO, >48 hospitalization hours) and community-onset (CO) infections [including both, infections (HACO) in patients with healthcare-associated risk-factors (HRFs) and infections (CACO) in those without HRFs]. MRSA strains were genetically typed as CA-MRSA and HA-MRSA genotypes (CA-MRSAG and HA-MRSAG) by SCCmec- and spa-typing, PFGE, MLST and virulence genes profile by PCR. Considering all isolates, 63% were from CO-infections and 55% were MRSA [39% CA-MRSAG and 16% HA-MRSAG]. A significantly higher MRSA proportion among CO- than HAHO-S. aureus infections was detected (58% vs 49%); mainly in children (62% vs 43%). The CA-MRSAG/HA-MRSAG have accounted for 16%/33% of HAHO-, 39%/13% of HACO- and 60.5%/0% of CACO-infections. Regarding the epidemiological associations identified in multivariate models for patients with healthcare-onset CA-MRSAG infections, CA-MRSAG behave like HA-MRSAG within hospitals but children were the highest risk group for healthcare-onset CA-MRSAG infections. Most CA-MRSAG belonged to two major clones: PFGE-type N-ST30-SCCmecIVc-t019-PVL(+) and PFGE-type I-ST5-IV-SCCmecIVa-t311-PVL(+) (45% each). The ST5-IV-PVL(+)/ST30-IV-PVL(+) clones have caused 31%/33% of all infections, 20%/4% of HAHO-, 43%/23% of HACO- and 35%/60% of CACO- infections, with significant differences by age groups (children/adults) and geographical regions. Importantly, an isolate belonging to USA300-0114-(ST8-SCCmecIVa-spat008-PVL(+)-ACME(+)) was detected

  7. Genotyping of community-associated methicillin resistant Staphylococcus aureus (CA-MRSA) in a tertiary care centre in Mysore, South India: ST2371-SCCmec IV emerges as the major clone.

    PubMed

    Rajan, Vineeth; Schoenfelder, Sonja M K; Ziebuhr, Wilma; Gopal, Shubha

    2015-08-01

    The burden of community-associated methicillin resistant Staphylococcus aureus (CA-MRSA) is on the rise in population and clinical settings on account of the adaptability and virulence traits of this pathogen. We characterized 45 non-duplicate CA-MRSA strains implicated mainly in skin and soft tissue infections (SSTIs) in a tertiary care hospital in Mysore, South India. All the isolates were genotyped by staphylococcal cassette chromosome mec (SCCmec) typing, staphylococcal protein A (spa) typing, accessory gene regulator (agr) typing, and multi-locus sequence typing (MLST). Four sequence types (STs) belonging to three major clonal complexes (CCs) were identified among the isolates: CC22 (ST2371 and ST22), CC1 (ST772) and CC8 (ST8). The majority (53.3%) of the isolates was of the genotype ST2371-t852-SCCmec IV [sequence type-spa type-SCCmec type], followed by ST22-t852-SCCmec IV (22.2%), ST772-t657-SCCmec V (13.3%) and ST8-t008-SCCmec IV (11.1%). ST237I, a single locus variant of ST22 (EMRSA-15 clone), has not been reported previously from any of the Asian countries. Our study also documents for the first time, the appearance of ST8-SCCmec IV (USA300) strains in India. Representative strains of the STs were further analyzed by pulsed field gel electrophoresis (PFGE). agr typing detected type I or II alleles in the majority of the isolates. All the isolates were positive for the leukotoxin gene, pvl (Panton-Valentine leukocidin) and the staphylococcal enterotoxin gene cluster, egc. Interestingly, multidrug resistance (resistance to ⩾3 classes of non-beta-lactam antibiotics) was observed in 77.8% (n=35) of the isolates. The highest (75.5%) resistance was recorded for ciprofloxacin, followed by erythromycin (53.3%), and quinupristin-dalfopristin (51.1%). Inducible clindamycin-resistance was identified in 37.7% of the isolates and it was attributed to the presence of erm(A), erm(C) and a combination of erm(A) and erm(C) genes. Isolates which showed a phenotypic

  8. Hypochlorite killing of community-associated methicillin-resistant Staphylococcus aureus.

    PubMed

    Fisher, Randall G; Chain, Rebecca L; Hair, Pamela S; Cunnion, Kenji M

    2008-10-01

    We tested in vitro hypochlorite (bleach) killing of community-associated methicillin-resistant Staphylococcus aureus isolates to determine optimal concentration and duration. For all isolates maximal killing, >3-log decrease in colony forming units (CFU), was found after 5 minutes in 2.5 microL/mL bleach. We estimate that 2.5 microL/mL bleach is approximately one-half cup of bleach in one-quarter tub of water.

  9. Hypochlorite killing of community-associated methicillin-resistant Staphylococcus aureus.

    PubMed

    Fisher, Randall G; Chain, Rebecca L; Hair, Pamela S; Cunnion, Kenji M

    2008-10-01

    We tested in vitro hypochlorite (bleach) killing of community-associated methicillin-resistant Staphylococcus aureus isolates to determine optimal concentration and duration. For all isolates maximal killing, >3-log decrease in colony forming units (CFU), was found after 5 minutes in 2.5 microL/mL bleach. We estimate that 2.5 microL/mL bleach is approximately one-half cup of bleach in one-quarter tub of water. PMID:18756186

  10. Intrarenal abscess caused by community-associated methicillin-resistant Staphylococcus aureus in a transplanted kidney.

    PubMed

    Cheung, C Y; Chan, S Y; Yeung, C S; Kwok, P C; Chak, W L; Wu, T C; Chau, K F

    2016-04-01

    Emergence of multidrug-resistant bacteria is important in solid organ transplant recipients, because it can jeopardize patient and graft survival. Methicillin-resistant Staphylococcus aureus (MRSA) infections are not rare in kidney transplant recipients. On the other hand, infections related to community-associated MRSA (CA-MRSA) strains are seldom reported in the literature. Herein, we report the first patient, to our knowledge, with CA-MRSA renal graft abscess who was successfully treated with drainage and parenteral antibiotics.

  11. Global implications of the emergence of community-associated methicillin-resistant Staphylococcus aureus in Indigenous populations.

    PubMed

    Tong, Steven Y C; McDonald, Malcolm I; Holt, Deborah C; Currie, Bart J

    2008-06-15

    The emergence of community-associated methicillin-resistant Staphylococcus aureus (MRSA) in Australia may have been facilitated by conditions in socially disadvantaged populations--particularly, remote Australian Aboriginal communities. The appearance of community-associated MRSA was first noticed in Australia during the early 1980s; subsequently, several genetically diverse strains have independently emerged from geographically distinct regions. Molecular and epidemiological studies support the role of genetic transfer of resistance determinants (SCCmecIV) in this process. Conditions in Aboriginal communities--namely, domestic crowding, poor hygiene, and high rates of scabies, pyoderma, and antibiotic use--have facilitated both the clonal expansion and de novo emergence of strains of community-associated MRSA. Combating the worldwide emergence and spread of community-associated MRSA may require novel community-level control strategies targeted at specific groups, such as remote Indigenous populations.

  12. Diversity and structure of bacterial communities associated with Phanerochaete chrysosporium during wood decay.

    PubMed

    Hervé, Vincent; Le Roux, Xavier; Uroz, Stéphane; Gelhaye, Eric; Frey-Klett, Pascale

    2014-07-01

    Wood recycling is key to forest biogeochemical cycles, largely driven by microorganisms such as white-rot fungi which naturally coexist with bacteria in the environment. We have tested whether and to what extent the diversity of the bacterial community associated with wood decay is determined by wood and/or by white-rot fungus Phanerochaete chrysosporium. We combined a microcosm approach with an enrichment procedure, using beech sawdust inoculated with or without P.chrysosporium. During 18 weeks, we used 16S rRNA gene-based pyrosequencing to monitor the forest bacterial community inoculated into these microcosms. We found bacterial communities associated with wood to be substantially less diverse than the initial forest soil inoculum. The presence of most bacterial operational taxonomic units (OTUs) varied over time and between replicates, regardless of their treatment, suggestive of the stochastic processes. However, we observed two OTUs belonging to Xanthomonadaceae and Rhizobium, together representing 50% of the relative bacterial abundance, as consistently associated with the wood substrate, regardless of fungal presence. Moreover, after 12 weeks, the bacterial community composition based on relative abundance was significantly modified by the presence of the white-rot fungus. Effectively, members of the Burkholderia genus were always associated with P.chrysosporium, representing potential taxonomic bioindicators of the white-rot mycosphere. PMID:24286477

  13. Bacterial communities associated with the ctenophores Mnemiopsis leidyi and Beroe ovata.

    PubMed

    Daniels, Camille; Breitbart, Mya

    2012-10-01

    Residing in a phylum of their own, ctenophores are gelatinous zooplankton that drift through the ocean's water column. Although ctenophores are known to be parasitized by a variety of eukaryotes, no studies have examined their bacterial associates. This study describes the bacterial communities associated with the lobate ctenophore Mnemiopsis leidyi and its natural predator Beroe ovata in Tampa Bay, Florida, USA. Investigations using terminal restriction fragment length polymorphism (T-RFLP) and cloning and sequencing of 16S rRNA genes demonstrated that ctenophore bacterial communities were distinct from the surrounding water. In addition, each ctenophore genus contained a unique microbiota. Ctenophore samples contained fewer bacterial operational taxonomic units (OTUs) by T-RFLP and lower diversity communities by 16S rRNA gene sequencing than the water column. Both ctenophore genera contained sequences related to bacteria previously described in marine invertebrates, and sequences similar to a sea anemone pathogen were abundant in B. ovata. Temporal sampling revealed that the ctenophore-associated bacterial communities varied over time, with no single OTU detected at all time points. This is the first report of distinct and dynamic bacterial communities associated with ctenophores, suggesting that these microbial consortia may play important roles in ctenophore ecology. Future work needs to elucidate the functional roles and mode of acquisition of these bacteria. PMID:22571334

  14. Bacterial Communities Associated with Culex Mosquito Larvae and Two Emergent Aquatic Plants of Bioremediation Importance

    PubMed Central

    Duguma, Dagne; Rugman-Jones, Paul; Kaufman, Michael G.; Hall, Michael W.; Neufeld, Josh D.; Stouthamer, Richard; Walton, William E.

    2013-01-01

    Microbes are important for mosquito nutrition, growth, reproduction and control. In this study, we examined bacterial communities associated with larval mosquitoes and their habitats. Specifically, we characterized bacterial communities associated with late larval instars of the western encephalitis mosquito (Culextarsalis), the submerged portions of two emergent macrophytes (California bulrush, Schoenoplectuscalifornicus and alkali bulrush, Schoenoplectusmaritimus), and the associated water columns to investigate potential differential use of resources by mosquitoes in different wetland habitats. Using next-generation sequence data from 16S rRNA gene hypervariable regions, the alpha diversity of mosquito gut microbial communities did not differ between pond mesocosms containing distinct monotypic plants. Proteobacteria, dominated by the genus Thorsellia (Enterobacteriaceae), was the most abundant phylum recovered from C. tarsalis larvae. Approximately 49% of bacterial OTUs found in larval mosquitoes were identical to OTUs recovered from the water column and submerged portions of the two bulrushes. Plant and water samples were similar to one another, both being dominated by Actinobacteria, Bacteroidetes, Cyanobacteria, Proteobacteria and Verrucomicrobia phyla. Overall, the bacterial communities within C. tarsalis larvae were conserved and did not change across sampling dates and between two distinct plant habitats. Although Thorsellia spp. dominated mosquito gut communities, overlap of mosquito gut, plant and water-column OTUs likely reveal the effects of larval feeding. Future research will investigate the role of the key indicator groups of bacteria across the different developmental stages of this mosquito species. PMID:23967314

  15. Diazotrophic potential among bacterial communities associated with wild and cultivated Agave species.

    PubMed

    Desgarennes, Damaris; Garrido, Etzel; Torres-Gomez, Miryam J; Peña-Cabriales, Juan J; Partida-Martinez, Laila P

    2014-12-01

    Agaves are major biotic resources in arid and semi-arid ecosystems. Despite their ecological, economical and cultural relevance, many aspects of the microbial communities associated with agaves are still unknown. Here, we investigated the bacterial communities associated with two Agave species by 16S rRNA- Denaturing gradient gel electrophoresis fingerprinting and sequencing. We also evaluated the effects of biotic and abiotic factors in the structure of the bacterial communities. In parallel, we isolated and characterized diazotrophic bacteria associated with agaves, as Agave soils are characterized by their low nitrogen content. Our results demonstrate that in Agave, the structure of prokaryotic assemblages was mostly influenced by the community group, where the soil, episphere, and endosphere were clearly distinct. Proteobacteria (γ and α), Actinobacteria, and Acidobacteria were the dominant phyla. Bacterial communities in the episphere of agaves were mainly influenced by the host species, whereas in the endosphere were affected by the season. Fifteen bacterial taxa were common and abundant in the endosphere of both Agave species during the dry season. Notably, some of the confirmed diazotrophic strains belonged to this group, suggesting a possible beneficial role in planta. PMID:25314594

  16. Temporal changes in the diazotrophic bacterial communities associated with Caribbean sponges Ircinia stroblina and Mycale laxissima

    PubMed Central

    Zhang, Fan; Vicente, Jan; Hill, Russell T.

    2014-01-01

    Sponges that harbor microalgal or, cyanobacterial symbionts may benefit from photosynthetically derived carbohydrates, which are rich in carbon but devoid of nitrogen, and may therefore encounter nitrogen limitation. Diazotrophic communities associated with two Caribbean sponges, Ircinia strobilina and Mycale laxissima were studied in a time series during which three individuals of each sponge were collected in four time points (5:00 AM, 12:00 noon, 5:00 PM, 10:00 PM). nifH genes were successfully amplified from the corresponding gDNA and cDNA pools and sequenced by high throughput 454 amplicon sequencing. In both sponges, over half the nifH transcripts were classified as from cyanobacteria and the remainder from heterotrophic bacteria. We found various groups of bacteria actively expressing the nifH gene during the entire day-night cycle, an indication that the nitrogen fixation potential was fully exploited by different nitrogen fixing bacteria groups associated with their hosts. This study showed for the first time the dynamic changes in the activity of the diazotrophic bacterial communities in marine sponges. Our study expands understanding of the diazotrophic groups that contribute to the fixed nitrogen pool in the benthic community. Sponge bacterial community-associated diazotrophy may have an important impact on the nitrogen biogeochemical cycle in the coral reef ecosystem. PMID:25389420

  17. Pyrosequencing reveals diverse microbial community associated with the zoanthid Palythoa australiae from the South China Sea.

    PubMed

    Sun, Wei; Zhang, Fengli; He, Liming; Li, Zhiyong

    2014-05-01

    Diverse sessile organisms inhabit the coral reef ecosystems, including corals, sponges, and sea anemones. In the past decades, scleractinian corals (Cnidaria, Anthozoa, Scleractinia) and their associated microorganisms have attracted much attention. Zoanthids (Cnidaria, Anthozoa, Zoanthidea) are commonly found in coral reefs. However, little is known about the community structure of zoanthid-associated microbiota. In this study, the microbial community associated with the zoanthid Palythoa australiae in the South China Sea was investigated by 454 pyrosequencing. As a result, 2,353 bacterial, 583 archaeal, and 36 eukaryotic microbial ribotypes were detected, respectively. A total of 22 bacterial phyla (16 formally described phyla and six candidate phyla) were recovered. Proteobacteria was the most abundant group, followed by Chloroflexi and Actinobacteria. High-abundance Rhizobiales and diverse Chloroflexi were observed in the bacterial community. The archaeal population was composed of Crenarchaeota and Euryarchaeota, with Marine Group I as the dominant lineage. In particular, Candidatus Nitrosopumilus dominated the archaeal community. Besides bacteria and archaea, the zoanthid harbored eukaryotic microorganisms including fungi and algae though their diversity was very low. This study provided the first insights into the microbial community associated with P. australiae by 454 pyrosequencing, consequently laid a basis for the understanding of the association of P. australiae-microbes symbioses.

  18. Diazotrophic potential among bacterial communities associated with wild and cultivated Agave species.

    PubMed

    Desgarennes, Damaris; Garrido, Etzel; Torres-Gomez, Miryam J; Peña-Cabriales, Juan J; Partida-Martinez, Laila P

    2014-12-01

    Agaves are major biotic resources in arid and semi-arid ecosystems. Despite their ecological, economical and cultural relevance, many aspects of the microbial communities associated with agaves are still unknown. Here, we investigated the bacterial communities associated with two Agave species by 16S rRNA- Denaturing gradient gel electrophoresis fingerprinting and sequencing. We also evaluated the effects of biotic and abiotic factors in the structure of the bacterial communities. In parallel, we isolated and characterized diazotrophic bacteria associated with agaves, as Agave soils are characterized by their low nitrogen content. Our results demonstrate that in Agave, the structure of prokaryotic assemblages was mostly influenced by the community group, where the soil, episphere, and endosphere were clearly distinct. Proteobacteria (γ and α), Actinobacteria, and Acidobacteria were the dominant phyla. Bacterial communities in the episphere of agaves were mainly influenced by the host species, whereas in the endosphere were affected by the season. Fifteen bacterial taxa were common and abundant in the endosphere of both Agave species during the dry season. Notably, some of the confirmed diazotrophic strains belonged to this group, suggesting a possible beneficial role in planta.

  19. Archaeal communities associated with roots of the common reed (Phragmites australis) in Beijing Cuihu Wetland.

    PubMed

    Liu, Yin; Li, Hong; Liu, Qun Fang; Li, Yan Hong

    2015-05-01

    The richness, phylogeny and composition of archaeal community associated with the roots of common reed (Phragmites australis) growing in the Beijing Cuihu Wetland, China was investigated using a 16S rDNA library. In total, 235 individual sequences were collected, and a phylogenetic analysis revealed that 69.4 and 11.5 % of clones were affiliated with the Euryarchaeota and the Crenarchaeota, respectively. In Euryarchaeota, the archaeal community was dominated by species in following genera: Methanobacterium in the order Methanobacteriales (60.7 %); Methanoregula and Methanospirillum in the order Methanomicrobiales (20.2 %), and Methanomethylovorans, Methanosarcina and Methanosaeta in the order Methanosarcinales (17.2 %). Of 27 sequences assigned to uncultured Crenarchaeota, 22 were grouped into Group 1.3, and five grouped into Group 1.1b. Hence, the archaeal communities associated with reed roots are largely involved in methane production, and, to a lesser extent, in ammonia oxidization. Quantification of the archaeal amoA gene indicated that ammonia oxidizing archaea were more numerous in the rhizosphere soil than in the root tissue or surrounding water. A total of 19.1 % of the sequences were unclassified, suggesting that many unidentified archaea are probably involved in the reed wetland ecosystem.

  20. Methicillin-Resistant Staphylococcus aureus Recovered from Healthcare- and Community-Associated Infections in Egypt.

    PubMed

    Abdel-Maksoud, Mohamed; El-Shokry, Mona; Ismail, Ghada; Hafez, Soad; El-Kholy, Amani; Attia, Ehab; Talaat, Maha

    2016-01-01

    Background. Methicillin-resistant Staphylococcus aureus (MRSA) has created significant epidemiological, infection-control, and therapeutic management challenges during the past three decades. Aim. To analyze the pattern of resistance of healthcare- and community-associated MRSA in Egypt and the trend of resistance of HA-MRSA over time (2005-2013). Methods. MRSA isolates were recovered from healthcare-associated (HA) and community-associated (CA) Staphylococcus aureus (S. aureus) infections. They were tested against 11 antimicrobial discs and the minimal inhibitory concentration (MIC) of vancomycin was determined. Inducible clindamycin resistance (iMLSB) was also screened using D-test. Findings. Of 631 S. aureus, MRSA was identified in 343 (76.6%) and 21 (11.5%) of HA and CA S. aureus isolates, respectively. The proportion of HA-MRSA increased significantly from 48.6% in 2005 to 86.8% in 2013 (p value < 0.001). Multidrug resistance (MDR) was observed in 85.8% of HA-MRSA and 48.6% of CA-MRSA. Vancomycin intermediate resistant S. aureus (VISA) was detected in 1.2% of HA-MRSA and none was detected in CA-MRSA. Among HA-MRSA strains, 5.3% showed iMLSB compared to 9.5% among CA-MRSA. Conclusion. The upsurge of the prevalence rates of HA-MRSA over time is alarming and urges for an effective infection control strategy and continuous monitoring of antimicrobial use.

  1. Methicillin-Resistant Staphylococcus aureus Recovered from Healthcare- and Community-Associated Infections in Egypt

    PubMed Central

    Abdel-Maksoud, Mohamed; Ismail, Ghada; Hafez, Soad; El-Kholy, Amani; Attia, Ehab; Talaat, Maha

    2016-01-01

    Background. Methicillin-resistant Staphylococcus aureus (MRSA) has created significant epidemiological, infection-control, and therapeutic management challenges during the past three decades. Aim. To analyze the pattern of resistance of healthcare- and community-associated MRSA in Egypt and the trend of resistance of HA-MRSA over time (2005–2013). Methods. MRSA isolates were recovered from healthcare-associated (HA) and community-associated (CA) Staphylococcus aureus (S. aureus) infections. They were tested against 11 antimicrobial discs and the minimal inhibitory concentration (MIC) of vancomycin was determined. Inducible clindamycin resistance (iMLSB) was also screened using D-test. Findings. Of 631 S. aureus, MRSA was identified in 343 (76.6%) and 21 (11.5%) of HA and CA S. aureus isolates, respectively. The proportion of HA-MRSA increased significantly from 48.6% in 2005 to 86.8% in 2013 (p value < 0.001). Multidrug resistance (MDR) was observed in 85.8% of HA-MRSA and 48.6% of CA-MRSA. Vancomycin intermediate resistant S. aureus (VISA) was detected in 1.2% of HA-MRSA and none was detected in CA-MRSA. Among HA-MRSA strains, 5.3% showed iMLSB compared to 9.5% among CA-MRSA. Conclusion. The upsurge of the prevalence rates of HA-MRSA over time is alarming and urges for an effective infection control strategy and continuous monitoring of antimicrobial use. PMID:27433480

  2. Community-associated methicillin-resistant Staphylococcus aureus in college residential halls.

    PubMed

    Tonn, Katelynn; Ryan, Timothy J

    2013-01-01

    Methicillin-resistant Staphylococcus aureus (MRSA) was once a predominantly hospital-acquired organism but community-associated MRSA (CA-MRSA) has become a concern in athletics, prisons, and other nonclinical closed populations. As such, college residential hall occupants and workers may be at elevated risk of spreading or contracting MRSA. Environmental samples were obtained to identify the occurrence of MRSA on surfaces in bathrooms of 15 university residential halls. Sterile swabs and BBL CHROMagar plates were used to sample seven categories of potentially contaminated surfaces in each location. Frequencies and descriptive statistics were prepared. All sites had at least one positive sample for MRSA, and shower floors displayed the greatest prevalence (50%). These results indicate areas for heightened sanitation, and illustrate CA-MRSA potential from such surfaces. The need for hygiene education of affected persons about skin and soft tissue infections like MRSA, and intervention opportunities for public health professionals, are discussed.

  3. Prevalence of community-associated methicillin-resistant Staphylococcus aureus in high school wrestling environments.

    PubMed

    Stanforth, Bethany; Krause, Andrew; Starkey, Chad; Ryan, Timothy J

    2010-01-01

    Methicillin-resistant Staphylococcus Aureus (MRSA) was predominantly a hospital-acquired organism; recently, however, community-associated MRSA (CA-MRSA) has been causing outbreaks in otherwise healthy individuals involved in athletics. As such, CA-MRSA is of emerging concern to sanitarians and public health officials. Secondary school athletic trainers and student athletes may be at elevated risk of spreading or contracting MRSA. The absence of proper hygiene protocols or equipment may further increase this risk. In the study discussed in this article, environmental samples were obtained to identify the prevalence of MRSA on surfaces in high school athletic training and wrestling facilities mats in nine rural Ohio high schools. Frequencies and descriptive statistics were prepared. All nine (100%) of the sites tested had at least one positive sample for the presence of MRSA. The need for heightened sanitation, hygiene education of affected persons about skin and soft tissue infections like MRSA, and intervention opportunities for public health professionals are discussed.

  4. Specific Microbial Communities Associate with the Rhizosphere of Welwitschia mirabilis, a Living Fossil

    PubMed Central

    De Maayer, Pieter; Oberholster, Tanzelle; Henschel, Joh; Louw, Michele K.; Cowan, Don

    2016-01-01

    Welwitschia mirabilis is an ancient and rare plant distributed along the western coast of Namibia and Angola. Several aspects of Welwitschia biology and ecology have been investigated, but very little is known about the microbial communities associated with this plant. This study reports on the bacterial and fungal communities inhabiting the rhizosphere of W. mirabilis and the surrounding bulk soil. Rhizosphere communities were dominated by sequences of Alphaproteobacteria and Euromycetes, while Actinobacteria, Alphaproteobacteria, and fungi of the class Dothideomycetes jointly dominated bulk soil communities. Although microbial communities within the rhizosphere and soil samples were highly variable, very few “species” (OTUs defined at a 97% identity cut-off) were shared between these two environments. There was a small ‘core’ rhizosphere bacterial community (formed by Nitratireductor, Steroidobacter, Pseudonocardia and three Phylobacteriaceae) that together with Rhizophagus, an arbuscular mycorrhizal fungus, and other putative plant growth-promoting microbes may interact synergistically to promote Welwitschia growth. PMID:27064484

  5. Huanglongbing alters the structure and functional diversity of microbial communities associated with citrus rhizosphere.

    PubMed

    Trivedi, Pankaj; He, Zhili; Van Nostrand, Joy D; Albrigo, Gene; Zhou, Jizhong; Wang, Nian

    2012-02-01

    The diversity and stability of bacterial communities present in the rhizosphere heavily influence soil and plant quality and ecosystem sustainability. The goal of this study is to understand how 'Candidatus Liberibacter asiaticus' (known to cause Huanglongbing, HLB) influences the structure and functional potential of microbial communities associated with the citrus rhizosphere. Clone library sequencing and taxon/group-specific quantitative real-time PCR results showed that 'Ca. L. asiaticus' infection restructured the native microbial community associated with citrus rhizosphere. Within the bacterial community, phylum Proteobacteria with various genera typically known as successful rhizosphere colonizers were significantly greater in clone libraries from healthy samples, whereas phylum Acidobacteria, Actinobacteria and Firmicutes, typically more dominant in the bulk soil were higher in 'Ca. L. asiaticus'-infected samples. A comprehensive functional microarray GeoChip 3.0 was used to determine the effects of 'Ca. L. asiaticus' infection on the functional diversity of rhizosphere microbial communities. GeoChip analysis showed that HLB disease has significant effects on various functional guilds of bacteria. Many genes involved in key ecological processes such as nitrogen cycling, carbon fixation, phosphorus utilization, metal homeostasis and resistance were significantly greater in healthy than in the 'Ca. L. asiaticus'-infected citrus rhizosphere. Our results showed that the microbial community of the 'Ca. L. asiaticus'-infected citrus rhizosphere has shifted away from using more easily degraded sources of carbon to the more recalcitrant forms. Overall, our study provides evidence that the change in plant physiology mediated by 'Ca. L. asiaticus' infection could elicit shifts in the composition and functional potential of rhizosphere microbial communities. In the long term, these fluctuations might have important implications for the productivity and sustainability

  6. Microbial Communities Associated with the Larval Gut and Eggs of the Western Corn Rootworm

    PubMed Central

    Dematheis, Flavia; Kurtz, Benedikt; Vidal, Stefan; Smalla, Kornelia

    2012-01-01

    Background The western corn rootworm (WCR) is one of the economically most important pests of maize. A better understanding of microbial communities associated with guts and eggs of the WCR is required in order to develop new pest control strategies, and to assess the potential role of the WCR in the dissemination of microorganisms, e.g., mycotoxin-producing fungi. Methodology/Principal Findings Total community (TC) DNA was extracted from maize rhizosphere, WCR eggs, and guts of larvae feeding on maize roots grown in three different soil types. Denaturing gradient gel electrophoresis (DGGE) and sequencing of 16S rRNA gene and ITS fragments, PCR-amplified from TC DNA, were used to investigate the fungal and bacterial communities, respectively. Microorganisms in the WCR gut were not influenced by the soil type. Dominant fungal populations in the gut were affiliated to Fusarium spp., while Wolbachia was the most abundant bacterial genus. Identical ribosomal sequences from gut and egg samples confirmed a transovarial transmission of Wolbachia sp. Betaproteobacterial DGGE indicated a stable association of Herbaspirillum sp. with the WCR gut. Dominant egg-associated microorganisms were the bacterium Wolbachia sp. and the fungus Mortierella gamsii. Conclusion/Significance The soil type-independent composition of the microbial communities in the WCR gut and the dominance of only a few microbial populations suggested either a highly selective environment in the gut lumen or a high abundance of intracellular microorganisms in the gut epithelium. The dominance of Fusarium species in the guts indicated WCR larvae as vectors of mycotoxin-producing fungi. The stable association of Herbaspirillum sp. with WCR gut systems and the absence of corresponding sequences in WCR eggs suggested that this bacterium was postnatally acquired from the environment. The present study provided new insights into the microbial communities associated with larval guts and eggs of the WCR. However

  7. Huanglongbing, a systemic disease, restructures the bacterial community associated with citrus roots.

    PubMed

    Trivedi, Pankaj; Duan, Yongping; Wang, Nian

    2010-06-01

    To examine the effect of pathogens on the diversity and structure of plant-associated bacterial communities, we carried out a molecular analysis using citrus and huanglongbing as a host-disease model. 16S rRNA gene clone library analysis of citrus roots revealed shifts in microbial diversity in response to pathogen infection. The clone library of the uninfected root samples has a majority of phylotypes showing similarity to well-known plant growth-promoting bacteria, including Caulobacter, Burkholderia, Lysobacter, Pantoea, Pseudomonas, Stenotrophomonas, Bacillus, and Paenibacillus. Infection by "Candidatus Liberibacter asiaticus" restructured the native microbial community associated with citrus roots and led to the loss of detection of most phylotypes while promoting the growth of bacteria such as Methylobacterium and Sphingobacterium. In pairwise comparisons, the clone library from uninfected roots contained significantly higher 16S rRNA gene diversity, as reflected in the higher Chao 1 richness estimation (P community associated with citrus roots.

  8. Huanglongbing alters the structure and functional diversity of microbial communities associated with citrus rhizosphere

    PubMed Central

    Trivedi, Pankaj; He, Zhili; Van Nostrand, Joy D; Albrigo, Gene; Zhou, Jizhong; Wang, Nian

    2012-01-01

    The diversity and stability of bacterial communities present in the rhizosphere heavily influence soil and plant quality and ecosystem sustainability. The goal of this study is to understand how ‘Candidatus Liberibacter asiaticus' (known to cause Huanglongbing, HLB) influences the structure and functional potential of microbial communities associated with the citrus rhizosphere. Clone library sequencing and taxon/group-specific quantitative real-time PCR results showed that ‘Ca. L. asiaticus' infection restructured the native microbial community associated with citrus rhizosphere. Within the bacterial community, phylum Proteobacteria with various genera typically known as successful rhizosphere colonizers were significantly greater in clone libraries from healthy samples, whereas phylum Acidobacteria, Actinobacteria and Firmicutes, typically more dominant in the bulk soil were higher in ‘Ca. L. asiaticus'-infected samples. A comprehensive functional microarray GeoChip 3.0 was used to determine the effects of ‘Ca. L. asiaticus' infection on the functional diversity of rhizosphere microbial communities. GeoChip analysis showed that HLB disease has significant effects on various functional guilds of bacteria. Many genes involved in key ecological processes such as nitrogen cycling, carbon fixation, phosphorus utilization, metal homeostasis and resistance were significantly greater in healthy than in the ‘Ca. L. asiaticus'-infected citrus rhizosphere. Our results showed that the microbial community of the ‘Ca. L. asiaticus'-infected citrus rhizosphere has shifted away from using more easily degraded sources of carbon to the more recalcitrant forms. Overall, our study provides evidence that the change in plant physiology mediated by ‘Ca. L. asiaticus' infection could elicit shifts in the composition and functional potential of rhizosphere microbial communities. In the long term, these fluctuations might have important implications for the productivity and

  9. Association Between Outpatient Antibiotic Prescribing Practices and Community-Associated Clostridium difficile Infection

    PubMed Central

    Dantes, Raymund; Mu, Yi; Hicks, Lauri A.; Cohen, Jessica; Bamberg, Wendy; Beldavs, Zintars G.; Dumyati, Ghinwa; Farley, Monica M.; Holzbauer, Stacy; Meek, James; Phipps, Erin; Wilson, Lucy; Winston, Lisa G.; McDonald, L. Clifford; Lessa, Fernanda C.

    2015-01-01

    Background. Antibiotic use predisposes patients to Clostridium difficile infections (CDI), and approximately 32% of these infections are community-associated (CA) CDI. The population-level impact of antibiotic use on adult CA-CDI rates is not well described. Methods. We used 2011 active population- and laboratory-based surveillance data from 9 US geographic locations to identify adult CA-CDI cases, defined as C difficile-positive stool specimens (by toxin or molecular assay) collected from outpatients or from patients ≤3 days after hospital admission. All patients were surveillance area residents and aged ≥20 years with no positive test ≤8 weeks prior and no overnight stay in a healthcare facility ≤12 weeks prior. Outpatient oral antibiotic prescriptions dispensed in 2010 were obtained from the IMS Health Xponent database. Regression models examined the association between outpatient antibiotic prescribing and adult CA-CDI rates. Methods. Healthcare providers prescribed 5.2 million courses of antibiotics among adults in the surveillance population in 2010, for an average of 0.73 per person. Across surveillance sites, antibiotic prescription rates (0.50–0.88 prescriptions per capita) and unadjusted CA-CDI rates (40.7–139.3 cases per 100 000 persons) varied. In regression modeling, reducing antibiotic prescribing rates by 10% among persons ≥20 years old was associated with a 17% (95% confidence interval, 6.0%–26.3%; P = .032) decrease in CA-CDI rates after adjusting for age, gender, race, and type of diagnostic assay. Reductions in prescribing penicillins and amoxicillin/clavulanic acid were associated with the greatest decreases in CA-CDI rates. Conclusions and Relevance. Community-associated CDI prevention should include reducing unnecessary outpatient antibiotic use. A modest reduction of 10% in outpatient antibiotic prescribing can have a disproportionate impact on reducing CA-CDI rates. PMID:26509182

  10. Seasonal Changes in the Rhizosphere Microbial Communities Associated with Field-Grown Genetically Modified Canola (Brassica napus)

    PubMed Central

    Dunfield, Kari E.; Germida, James J.

    2003-01-01

    The introduction of transgenic plants into agricultural ecosystems has raised the question of the ecological impact of these plants on nontarget organisms, such as soil bacteria. Although differences in both the genetic structure and the metabolic function of the microbial communities associated with some transgenic plant lines have been established, it remains to be seen whether these differences have an ecological impact on the soil microbial communities. We conducted a 2-year, multiple-site field study in which rhizosphere samples associated with a transgenic canola variety and a conventional canola variety were sampled at six times throughout the growing season. The objectives of this study were to identify differences between the rhizosphere microbial community associated with the transgenic plants and the rhizosphere microbial community associated with the conventional canola plants and to determine whether the differences were permanent or depended on the presence of the plant. Community-level physiological profiles, fatty acid methyl ester profiles, and terminal amplified ribosomal DNA restriction analysis profiles of rhizosphere microbial communities were compared to the profiles of the microbial community associated with an unplanted, fallow field plot. Principal-component analysis showed that there was variation in the microbial community associated with both canola variety and growth season. Importantly, while differences between the microbial communities associated with the transgenic plant variety were observed at several times throughout the growing season, all analyses indicated that when the microbial communities were assessed after winter, there were no differences between microbial communities from field plots that contained harvested transgenic canola plants and microbial communities from field plots that did not contain plants during the field season. Hence, the changes in the microbial community structure associated with genetically modified

  11. Exploring cultivable Bacteria from the prokaryotic community associated with the carnivorous sponge Asbestopluma hypogea.

    PubMed

    Dupont, Samuel; Carre-Mlouka, Alyssa; Domart-Coulon, Isabelle; Vacelet, Jean; Bourguet-Kondracki, Marie-Lise

    2014-04-01

    Combining culture-dependent and independent approaches, we investigated for the first time the cultivable fraction of the prokaryotic community associated with the carnivorous sponge Asbestopluma hypogea. The heterotrophic prokaryotes isolated from this tiny sponge were compared between specimens freshly collected from cave and maintained in aquarium. Overall, 67 isolates obtained in pure culture were phylogenetically affiliated to the bacterial phyla Proteobacteria, Bacteroidetes, Actinobacteria, and Firmicutes. This cultivable diversity was lower than the prokaryotic diversity obtained by previous pyrosequencing study and comparable to that of another Mediterranean demosponge, the filter-feeding Phorbas tenacior. Furthermore, using fluorescence in situ hybridization, we visualized bacterial and archaeal cells, confirming the presence of both prokaryotes in A. hypogea tissue. Approximately 16% of the bacterial isolates tested positive for chitinolytic activity, suggesting potential microbial involvement in the digestion processes of crustacean prey by this carnivorous sponge. Additionally, 6% and 16% of bacterial isolates revealed antimicrobial and antioxidant activities, respectively. One Streptomyces sp. S1CA strain was identified as a promising candidate for the production of antimicrobial and antioxidant secondary metabolites as well as chitinolytic enzymes. Implications in the context of the sponge biology and prey-feeding strategy are discussed.

  12. Risk Factors for Community-Associated Staphylococcus aureus Skin Infection in Children of Maui

    PubMed Central

    Seifried, Steven E

    2012-01-01

    The prevalence of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) infection, and Staphylococcus aureus (S. aureus) infection overall, has dramatically increased in the past 10 years. Children and Native Hawaiians and Pacific Islanders (NHPI) are disproportionately affected by CA-MRSA infection. The purpose of this case-control study was to identify risk factors for CA-S. aureus skin infections in children of Maui, Hawai‘i, as a foundation for reducing the transmission of these infections. Survey data were obtained from patients in pediatric clinician offices over an 8-month period. NHPI participants were well-represented as 58% of cases and 54% of controls. Chi-square analysis and logistic regression were used to identify risk factors. Significant risk factors predictive of infection among all participants were (a) skin abrasions or wounds, (b) household contact, and (c) overweight or obesity. Risk factors predictive of infection among NHPI were (a) skin abrasions or wounds, (b) antibiotic use within 6 months, (c) overweight or obesity, and (d) a history of eczema or other skin disorder. The role of overweight or obesity in S. aureus skin infections among NHPI has not been identified in previous research and indicates a focus for additional education. Further research is needed to better understand the role of eczema, antibiotic use, overweight and obesity, and socio-cultural factors in these infections. PMID:22900237

  13. Diversity of endophytic fungal community associated with Piper hispidum (Piperaceae) leaves.

    PubMed

    Orlandelli, R C; Alberto, R N; Rubin Filho, C J; Pamphile, J A

    2012-05-22

    Tropical and subtropical plants are rich in endophytic community diversity. Endophytes, mainly fungi and bacteria, inhabit the healthy plant tissues without causing any damage to the hosts. These fungi can be useful for biological control of pathogens and plant growth promotion. Some plants of the genus Piper are hosts of endophytic microorganisms; however, there is little information about endophytes on Piper hispidum, a medicinal shrub used as an insecticide, astringent, diuretic, stimulant, liver treatment, and for stopping hemorrhages. We isolated the fungal endophyte community associated with P. hispidum leaves from plants in a Brazilian forest remnant. The endophytic diversity was examined based on sequencing of the ITS1-5.8S-ITS2 region of rDNA. A high colonization frequency was obtained, as expected for tropical angiosperms. Isolated endophytes were divided into 66 morphogroups, demonstrating considerable diversity. We identified 21 isolates, belonging to 11 genera (Alternaria, Bipolaris, Colletotrichum, Glomerella, Guignardia, Lasiodiplodia, Marasmius, Phlebia, Phoma, Phomopsis, and Schizophyllum); one isolate was identified only to the order level (Diaporthales). Bipolaris was the most frequent genus among the identified endophytes. Phylogenetic analysis confirmed the molecular identification of some isolates to genus level while for others it was confirmed at the species level.

  14. Antibiotic-Induced Change of Bacterial Communities Associated with the Copepod Nitocra spinipes

    PubMed Central

    Edlund, Anna; Ek, Karin; Breitholtz, Magnus; Gorokhova, Elena

    2012-01-01

    Environmental pressures, such as physical factors, diet and contaminants may affect interactions between microbial symbionts and their multicellular hosts. Despite obvious relevance, effects of antimicrobial contaminants on host-symbiont relations in non-target aquatic organisms are largely unknown. We show that exposure to antibiotics had negative effects on survival and juvenile development of the copepod Nitocra spinipes and caused significant alterations in copepod-associated bacterial communities. The significant positive correlations between indices of copepod development and bacterial diversity indicate that disruption of the microflora was likely to be an important factor behind retarded juvenile development in the experimental animals. Moreover, as evidenced by ribotype distribution in the bacterial clone libraries, the exposure to antibiotics caused a shift in dominance from Betaproteobacteria to Cardinium bacteria; the latter have been shown to cause reproductive manipulations in various terrestrial arthropods. Thus, in addition to providing evidence that the antibiotic-induced perturbation of the microbial community associates with reductions in fitness-related traits of the host, this study is the first record of a copepod serving as a host for endosymbiotic Cardinium. Taken together, our results suggest that (1) antimicrobial substances and possibly other stressors can affect micobiome and symbiont-mediated interactions in copepods and other hosts, and (2) Cardinium endosymbionts may occur in other copepods and affect reproduction of their hosts. PMID:22427962

  15. Analysis of bacterial communities associated with the benthic amphipod Diporeia in the Laurentian Great Lakes Basin.

    PubMed

    Winters, Andrew D; Marsh, Terence L; Brenden, Travis O; Faisal, Mohamed

    2015-01-01

    Bacterial communities play important roles in the biological functioning of crustaceans, yet little is known about their diversity, structure, and dynamics. This study was conducted to investigate the bacterial communities associated with the benthic amphipod Diporeia, an important component in the Great Lakes foodweb that has been declining over the past 3 decades. In this study, the combination of 16S rRNA gene sequencing and terminal restriction fragment length polymorphism revealed a total of 175 and 138 terminal restriction fragments (T-RFs) in Diporeia samples following treatment with the endonucleases HhaI and MspI, respectively. Relatively abundant and prevalent T-RFs were affiliated with the genera Flavobacterium and Pseudomonas and the class Betaproteobacteria. T-RFs affiliated with the order Rickettsiales were also detected. A significant difference in T-RF presence and abundance (P = 0.035) was detected among profiles generated for Diporeia collected from 4 sites in Lake Michigan. Comparison of profiles generated for Diporeia samples collected in 2 years from lakes Superior and Michigan showed a significant change in diversity for Lake Superior Diporeia but not Lake Michigan Diporeia. Profiles from one Lake Michigan site contained multiple unique T-RFs compared with other Lake Michigan Diporeia profiles, most notably one that represents the genus Methylotenera. This study generated the most extensive list of bacteria associated with Diporeia and sheds useful insights on the microbiome of Great Lakes Diporeia that may help to reveal potential causes of the decline of Diporeia populations.

  16. Bacterial community associated to the pine wilt disease insect vectors Monochamus galloprovincialis and Monochamus alternatus

    PubMed Central

    Alves, Marta; Pereira, Anabela; Matos, Patrícia; Henriques, Joana; Vicente, Cláudia; Aikawa, Takuya; Hasegawa, Koichi; Nascimento, Francisco; Mota, Manuel; Correia, António; Henriques, Isabel

    2016-01-01

    Monochamus beetles are the dispersing vectors of the nematode Bursaphelenchus xylophilus, the causative agent of pine wilt disease (PWD). PWD inflicts significant damages in Eurasian pine forests. Symbiotic microorganisms have a large influence in insect survival. The aim of this study was to characterize the bacterial community associated to PWD vectors in Europe and East Asia using a culture-independent approach. Twenty-three Monochamus galloprovincialis were collected in Portugal (two different locations); twelve Monochamus alternatus were collected in Japan. DNA was extracted from the insects’ tracheas for 16S rDNA analysis through denaturing gradient gel electrophoresis and barcoded pyrosequencing. Enterobacteriales, Pseudomonadales, Vibrionales and Oceanospirilales were present in all samples. Enterobacteriaceae was represented by 52.2% of the total number of reads. Twenty-three OTUs were present in all locations. Significant differences existed between the microbiomes of the two insect species while for M. galloprovincialis there were no significant differences between samples from different Portuguese locations. This study presents a detailed description of the bacterial community colonizing the Monochamus insects’ tracheas. Several of the identified bacterial groups were described previously in association with pine trees and B. xylophilus, and their previously described functions suggest that they may play a relevant role in PWD. PMID:27045340

  17. Community-Associated Methicillin-Resistant Staphylococcus aureus: Epidemiology and Clinical Consequences of an Emerging Epidemic

    PubMed Central

    David, Michael Z.; Daum, Robert S.

    2010-01-01

    Summary: Staphylococcus aureus is an important cause of skin and soft-tissue infections (SSTIs), endovascular infections, pneumonia, septic arthritis, endocarditis, osteomyelitis, foreign-body infections, and sepsis. Methicillin-resistant S. aureus (MRSA) isolates were once confined largely to hospitals, other health care environments, and patients frequenting these facilities. Since the mid-1990s, however, there has been an explosion in the number of MRSA infections reported in populations lacking risk factors for exposure to the health care system. This increase in the incidence of MRSA infection has been associated with the recognition of new MRSA clones known as community-associated MRSA (CA-MRSA). CA-MRSA strains differ from the older, health care-associated MRSA strains; they infect a different group of patients, they cause different clinical syndromes, they differ in antimicrobial susceptibility patterns, they spread rapidly among healthy people in the community, and they frequently cause infections in health care environments as well. This review details what is known about the epidemiology of CA-MRSA strains and the clinical spectrum of infectious syndromes associated with them that ranges from a commensal state to severe, overwhelming infection. It also addresses the therapy of these infections and strategies for their prevention. PMID:20610826

  18. Molecular profiling of rhizosphere bacterial communities associated with Prosopis juliflora and Parthenium hysterophorus.

    PubMed

    Jothibasu, K; Chinnadurai, C; Sundaram, Sp; Kumar, K; Balachandar, Dananjeyan

    2012-03-01

    Prosopis juliflora and Parthenium hysterophorus are the two arid, exotic weeds of India that are characterized by distinct, profuse growth even in nutritionally poor soils and environmentally stressed conditions. Owing to the exceptional growth nature of these two plants, they are believed to harbor some novel bacterial communities with wide adaptability in their rhizosphere. Hence, in the present study, the bacterial communities associated with the rhizosphere of Prosopis and Parthenium were characterized by clonal 16S rRNA gene sequence analysis. The culturable microbial counts in the rhizosphere of these two plants were higher than bulk soils, possibly influenced by the root exudates of these two plants. The phylogenetic analysis of V1_V2 domains of the 16S rRNA gene indicated a wider range of bacterial communities present in the rhizosphere of these two plants than in bulk soils and the predominant genera included Acidobacteria, Gammaproteobacteria, and Bacteriodetes in the rhizosphere of Prosopis, and Acidobacteria, Betaproteobacteria, and Nitrospirae in the Parthenium rhizosphere. The diversity of bacterial communities was more pronounced in the Parthenium rhizosphere than in the Prosopis rhizosphere. This culture-independent bacterial analysis offered extensive possibilities of unraveling novel microbes in the rhizospheres of Prosopis and Parthenium with genes for diverse functions, which could be exploited for nutrient transformation and stress tolerance in cultivated crops.

  19. Bacterial communities associated with aerobic degradation of polybrominated diphenyl ethers from river sediments.

    PubMed

    Yang, Chu-Wen; Huang, Huang-Wen; Chao, Wei-Liang; Chang, Bea-Ven

    2015-03-01

    Polybrominated diphenyl ethers (PBDEs) are persistent organic pollutants and have therefore drawn much environmental concern. We aimed to compare aerobic degradation of different PBDE congeners under various treatments and reveal the bacterial community associated with PBDE degradation in sediment. Results of this study indicate that degradation rates of BDE-15 were enhanced 45.1 and 81.3 % with the addition of suspended and microencapsulated Pseudomonas sp., respectively. However, the degradation rates of BDE-28, BDE-47, BDE-99, and BDE-100 did not differ among experimental treatments. Degradation rates of PBDE congeners were in the order of BDE-15 > BDE-28 > BDE-47 > BDE-99 > BDE-100. Using a pyrosequencing-based metagenomic approach, we found that addition of various treatments altered the microbial community composition in the sediment. Twenty-four bacterial genera associated with degradation of PBDEs; six are the core bacterial genera common among PBDE degraders. The diverse bacterial composition among different PBDE congener degradation indicates different combinations of bacteria involved in degradation of different PBDE congeners.

  20. The economic burden of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA).

    PubMed

    Lee, B Y; Singh, A; David, M Z; Bartsch, S M; Slayton, R B; Huang, S S; Zimmer, S M; Potter, M A; Macal, C M; Lauderdale, D S; Miller, L G; Daum, R S

    2013-06-01

    The economic impact of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) remains unclear. We developed an economic simulation model to quantify the costs associated with CA-MRSA infection from the societal and third-party payer perspectives. A single CA-MRSA case costs third-party payers $2277-$3200 and society $7070-$20 489, depending on patient age. In the United States (US), CA-MRSA imposes an annual burden of $478 million to 2.2 billion on third-party payers and $1.4-13.8 billion on society, depending on the CA-MRSA definitions and incidences. The US jail system and Army may be experiencing annual total costs of $7-11 million ($6-10 million direct medical costs) and $15-36 million ($14-32 million direct costs), respectively. Hospitalization rates and mortality are important cost drivers. CA-MRSA confers a substantial economic burden on third-party payers and society, with CA-MRSA-attributable productivity losses being major contributors to the total societal economic burden. Although decreasing transmission and infection incidence would decrease costs, even if transmission were to continue at present levels, early identification and appropriate treatment of CA-MRSA infections before they progress could save considerable costs.

  1. Effects of Host Plant Factors on the Bacterial Communities Associated with Two Whitefly Sibling Species

    PubMed Central

    Su, Ming-Ming; Guo, Lei; Tao, Yun-Li; Zhang, You-Jun; Wan, Fang-Hao; Chu, Dong

    2016-01-01

    Background Although discrepancy in the specific traits and ecological characteristics of Bemisia tabaci between species are partially attributed to the B. tabaci-associated bacteria, the factors that affect the diversity of B. tabaci-associated bacteria are not well-understood. We used the metagenomic approach to characterize the B. tabaci-associated bacterial community because the approach is an effective tool to identify the bacteria. Methodology and Results To investigate the effects of the host plant and a virus, tomato yellow leaf curl virus (TYLCV), on the bacterial communities of B. tabaci sibling species B and Q, we analyzed the bacterial communities associated with whitefly B and Q collected from healthy cotton, healthy tomato, and TYLCV-infected tomato. The analysis used miseq-based sequencing of a variable region of the bacterial 16S rDNA gene. For the bacteria associated with B. tabaci, we found that the influence of the host plant species was greater than that of the whitefly cryptic species. With further analysis of host plants infected with the TYLCV, the virus had no significant effects on the B. tabaci-associated bacterial community. Conclusions The effects of different plant hosts and TYLCV-infection on the diversity of B. tabaci-associated bacterial communities were successfully analyzed in this study. To explain why B. tabaci sibling species with different host ranges differ in performance, the analysis of the bacterial community may be essential to the explanation. PMID:27008327

  2. Comparison of microbial communities associated with three Atlantic ultramafic hydrothermal systems.

    PubMed

    Roussel, Erwan G; Konn, Cécile; Charlou, Jean-Luc; Donval, Jean-Pierre; Fouquet, Yves; Querellou, Joël; Prieur, Daniel; Bonavita, Marie-Anne Cambon

    2011-09-01

    The distribution of Archaea and methanogenic, methanotrophic and sulfate-reducing communities in three Atlantic ultramafic-hosted hydrothermal systems (Rainbow, Ashadze, Lost City) was compared using 16S rRNA gene and functional gene (mcrA, pmoA and dsrA) clone libraries. The overall archaeal community was diverse and heterogeneously distributed between the hydrothermal sites and the types of samples analyzed (seawater, hydrothermal fluid, chimney and sediment). The Lost City hydrothermal field, characterized by high alkaline warm fluids (pH>11; T<95 °C), harbored a singular archaeal diversity mostly composed of unaffiliated Methanosarcinales. The archaeal communities associated with the recently discovered Ashadze 1 site, one of the deepest active hydrothermal fields known (4100 m depth), showed significant differences between the two different vents analyzed and were characterized by putative extreme halophiles. Sequences related to the rarely detected Nanoarchaeota phylum and Methanopyrales order were also retrieved from the Rainbow and Ashadze hydrothermal fluids. However, the methanogenic Methanococcales was the most widely distributed hyper/thermophilic archaeal group among the hot and acidic ultramafic-hosted hydrothermal system environments. Most of the lineages detected are linked to methane and hydrogen cycling, suggesting that in ultramafic-hosted hydrothermal systems, large methanogenic and methanotrophic communities could be fuelled by hydrothermal fluids highly enriched in methane and hydrogen.

  3. Diversity of endophytic fungal community associated with Piper hispidum (Piperaceae) leaves.

    PubMed

    Orlandelli, R C; Alberto, R N; Rubin Filho, C J; Pamphile, J A

    2012-01-01

    Tropical and subtropical plants are rich in endophytic community diversity. Endophytes, mainly fungi and bacteria, inhabit the healthy plant tissues without causing any damage to the hosts. These fungi can be useful for biological control of pathogens and plant growth promotion. Some plants of the genus Piper are hosts of endophytic microorganisms; however, there is little information about endophytes on Piper hispidum, a medicinal shrub used as an insecticide, astringent, diuretic, stimulant, liver treatment, and for stopping hemorrhages. We isolated the fungal endophyte community associated with P. hispidum leaves from plants in a Brazilian forest remnant. The endophytic diversity was examined based on sequencing of the ITS1-5.8S-ITS2 region of rDNA. A high colonization frequency was obtained, as expected for tropical angiosperms. Isolated endophytes were divided into 66 morphogroups, demonstrating considerable diversity. We identified 21 isolates, belonging to 11 genera (Alternaria, Bipolaris, Colletotrichum, Glomerella, Guignardia, Lasiodiplodia, Marasmius, Phlebia, Phoma, Phomopsis, and Schizophyllum); one isolate was identified only to the order level (Diaporthales). Bipolaris was the most frequent genus among the identified endophytes. Phylogenetic analysis confirmed the molecular identification of some isolates to genus level while for others it was confirmed at the species level. PMID:22653631

  4. Changes in cystic fibrosis airway microbial community associated with a severe decline in lung function.

    PubMed

    Paganin, Patrizia; Fiscarelli, Ersilia Vita; Tuccio, Vanessa; Chiancianesi, Manuela; Bacci, Giovanni; Morelli, Patrizia; Dolce, Daniela; Dalmastri, Claudia; De Alessandri, Alessandra; Lucidi, Vincenzina; Taccetti, Giovanni; Mengoni, Alessio; Bevivino, Annamaria

    2015-01-01

    Cystic fibrosis (CF) is a genetic disease resulting in chronic polymicrobial infections of the airways and progressive decline in lung function. To gain insight into the underlying causes of severe lung diseases, we aimed at comparing the airway microbiota detected in sputum of CF patients with stable lung function (S) versus those with a substantial decline in lung function (SD). Microbiota composition was investigated by using culture-based and culture-independent methods, and by performing multivariate and statistical analyses. Culture-based methods identified some microbial species associated with a worse lung function, i.e. Pseudomonas aeruginosa, Rothia mucilaginosa, Streptococcus pneumoniae and Candida albicans, but only the presence of S. pneumoniae and R. mucilaginosa was found to be associated with increased severe decline in forced expiratory volume in 1 second (FEV1). Terminal-Restriction Fragment Length Polymorphism (T-RFLP) analysis revealed a higher bacterial diversity than that detected by culture-based methods. Molecular signatures with a statistically significant odds ratio for SD status were detected, and classified as Pseudomonas, Burkholderia and Shewanella, while for other Terminal Restriction Fragments (T-RFs) no species assignation was achieved. The analysis of T-RFLP data using ecological biodiversity indices showed reduced Evenness in SD patients compared to S ones, suggesting an impaired ecology of the bacterial community in SD patients. Statistically significant differences of the ecological biodiversity indices among the three sub-groups of FEV1 (normal/mild vs moderate vs severe) were also found, suggesting that the patients with moderate lung disease experienced changes in the airway assembly of taxa. Overall, changes in CF airway microbial community associated with a severe lung function decline were detected, allowing us to define some discriminatory species as well as some discriminatory T-RFs that represent good candidates for the

  5. Oxacillin alters the toxin expression profile of community-associated methicillin-resistant Staphylococcus aureus.

    PubMed

    Rudkin, Justine K; Laabei, Maisem; Edwards, Andrew M; Joo, Hwang-Soo; Otto, Michael; Lennon, Katrina L; O'Gara, James P; Waterfield, Nicholas R; Massey, Ruth C

    2014-01-01

    The emergence of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) is a growing cause for concern. These strains are more virulent than health care-associated MRSA (HA-MRSA) due to higher levels of toxin expression. In a previous study, we showed that the high-level expression of PBP2a, the alternative penicillin binding protein encoded by the mecA gene on type II staphylococcal cassette chromosome mec (SCCmec) elements, reduced toxicity by interfering with the Agr quorum sensing system. This was not seen in strains carrying the CA-MRSA-associated type IV SCCmec element. These strains express significantly lower levels of PBP2a than the other MRSA type, which may explain their relatively high toxicity. We hypothesized that as oxacillin is known to increase mecA expression levels, it may be possible to attenuate the toxicity of CA-MRSA by using this antibiotic. Subinhibitory oxacillin concentrations induced PBP2a expression, repressed Agr activity, and, as a consequence, decreased phenol-soluble modulin (PSM) secretion by CA-MRSA strains. However, consistent with other studies, oxacillin also increased the expression levels of alpha-toxin and Panton-Valentine leucocidin (PVL). The net effect of these changes on the ability to lyse diverse cell types was tested, and we found that where the PSMs and alpha-toxin are important, oxacillin reduced overall lytic activity, but where PVL is important, it increased lytic activity, demonstrating the pleiotropic effect of oxacillin on toxin expression by CA-MRSA.

  6. Metagenomic Analysis of the Bacterial Community Associated with the Taproot of Sugar Beet

    PubMed Central

    Tsurumaru, Hirohito; Okubo, Takashi; Okazaki, Kazuyuki; Hashimoto, Megumi; Kakizaki, Kaori; Hanzawa, Eiko; Takahashi, Hiroyuki; Asanome, Noriyuki; Tanaka, Fukuyo; Sekiyama, Yasuyo; Ikeda, Seishi; Minamisawa, Kiwamu

    2015-01-01

    We analyzed a metagenome of the bacterial community associated with the taproot of sugar beet (Beta vulgaris L.) in order to investigate the genes involved in plant growth-promoting traits (PGPTs), namely 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase, indole acetic acid (IAA), N2 fixation, phosphate solubilization, pyrroloquinoline quinone, siderophores, and plant disease suppression as well as methanol, sucrose, and betaine utilization. The most frequently detected gene among the PGPT categories encoded β-1,3-glucanase (18 per 105 reads), which plays a role in the suppression of plant diseases. Genes involved in phosphate solubilization (e.g., for quinoprotein glucose dehydrogenase), methanol utilization (e.g., for methanol dehydrogenase), siderophore production (e.g. isochorismate pyruvate lyase), and ACC deaminase were also abundant. These results suggested that such PGPTs are crucially involved in supporting the growth of sugar beet. In contrast, genes for IAA production (iaaM and ipdC) were less abundant (~1 per 105 reads). N2 fixation genes (nifHDK) were not detected; bacterial N2 -fixing activity was not observed in the 15N2 -feeding experiment. An analysis of nitrogen metabolism suggested that the sugar beet microbiome mainly utilized ammonium and nitroalkane as nitrogen sources. Thus, N2 fixation and IAA production did not appear to contribute to sugar beet growth. Taxonomic assignment of this metagenome revealed the high abundance of Mesorhizobium, Bradyrhizobium, and Streptomyces, suggesting that these genera have ecologically important roles in the taproot of sugar beet. Bradyrhizobium-assigned reads in particular were found in almost all categories of dominant PGPTs with high abundance. The present study revealed the characteristic functional genes in the taproot-associated microbiome of sugar beet, and suggest the opportunity to select sugar beet growth-promoting bacteria. PMID:25740621

  7. Dynamics of bacterial and fungal communities associated with eggshells during incubation

    PubMed Central

    Grizard, Stéphanie; Dini-Andreote, Francisco; Tieleman, B Irene; Salles, Joana F

    2014-01-01

    Microorganisms are closely associated with eggs and may play a determinant role in embryo survival. Yet, the majority of studies focusing on this association relied on culture-based methodology, eventually leading to a skewed assessment of microbial communities. By targeting the 16S rRNA gene and internal transcribed spacer (ITS) region, we, respectively, described bacterial and fungal communities on eggshells of the homing pigeon Columba livia. We explored their structure, abundance, and composition. Firstly, we showed that sampling technique affected the outcome of the results. While broadly used, the egg swabbing procedure led to a lower DNA extraction efficiency and provided different profiles of bacterial communities than those based on crushed eggshell pieces. Secondly, we observed shifts in bacterial and fungal communities during incubation. At late incubation, bacterial communities showed a reduction in diversity, while their abundance increased, possibly due to the competitive advantage of some species. When compared to their bacterial counterparts, fungal communities also decreased in diversity at late incubation. In that case, however, the decline was associated with a diminution of their overall abundance. Conclusively, our results showed that although incubation might inhibit microbial growth when compared to unincubated eggs, we observed the selective growth of specific bacterial species during incubation. Moreover, we showed that fungi are a substantial component of the microbial communities associated with eggshells and require further investigations in avian ecology. Identifying the functional roles of these microorganisms is likely to provide news insights into the evolutionary strategies that control embryo survival. We aimed to describe the dynamics of bacterial and fungal communities on homing pigeon eggshell surfaces. We investigated these communities at early and late incubation stages. PMID:24772289

  8. An assessment of microbial communities associated with surface mining-disturbed overburden.

    PubMed

    Poncelet, Dominique M; Cavender, Nicole; Cutright, Teresa J; Senko, John M

    2014-03-01

    To assess the microbiological changes that occur during the maturation of overburden that has been disturbed by surface mining of coal, a surface mining-disturbed overburden unit in southeastern Ohio, USA was characterized. Overburden from the same unit that had been disturbed for 37 and 16 years were compared to undisturbed soil from the same region. Overburden and soil samples were collected as shallow subsurface cores from each subregion of the mined area (i.e., land 16 years and 37 years post-mining, and unmined land). Chemical and mineralogical characteristics of overburden samples were determined, as were microbial respiration rates. The composition of microbial communities associated with overburden and soil were determined using culture-independent, nucleic acid-based approaches. Chemical and mineralogical evaluation of overburden suggested that weathering of disturbed overburden gave rise to a setting with lower pH and more oxidized chemical constituents. Overburden-associated microbial biomass and respiration rates increased with time after overburden disturbance. Evaluation of 16S rRNA gene libraries that were produced by "next-generation" sequencing technology revealed that recently disturbed overburden contained an abundance of phylotypes attributable to sulfur-oxidizing Limnobacter spp., but with increasing time post-disturbance, overburden-associated microbial communities developed a structure similar to that of undisturbed soil, but retained characteristics of more recently disturbed overburden. Our results indicate that over time, the biogeochemical weathering of disturbed overburden leads to the development of geochemical conditions and microbial communities that approximate those of undisturbed soil, but that this transition is incomplete after 37 years of overburden maturation.

  9. Differentiation of clonal complex 59 community-associated methicillin-resistant Staphylococcus aureus in Western Australia.

    PubMed

    Coombs, Geoffrey W; Monecke, Stefan; Ehricht, Ralf; Slickers, Peter; Pearson, Julie C; Tan, Hui-Leen; Christiansen, Keryn J; O'Brien, Frances G

    2010-05-01

    Clonal complex 59 (CC59) community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) strains were characterized using pulsed-field gel electrophoresis, spa typing, multilocus sequence typing, diagnostic DNA microarrays, and PCRs targeting staphylococcal cassette chromosome mec (SCCmec) elements and Panton-Valentine leukocidin (PVL). Six distinct groups within CC59 were characterized. At least seven different variants of SCCmec elements were identified (IVa [2B], IVb [2B], IVd [2B], IV variant [2B], IVa [2B&5], V variant [5C2], and V [5C2&5]). (The structural type is indicated by a Roman numeral, with a lowercase letter indicating the subtype, and the ccr complex and the mec complex are indicated by an Arabic numeral and an uppercase letter, respectively. Where there is an extra ccr element, this is indicated by "&" and an Arabic numeral designating the ccr type.) The first group is similar to the American sequence type 59 (ST59) MRSA-IV CA-MRSA strain USA1000. The second group includes a PVL-negative ST87 strain with an SCCmec element of subtype IVb (2B). The third group comprises PVL-variable ST59 MRSA-IV strains harboring multiple SCCmec IV subtypes. PVL-negative ST59 MRSA strains with multiple or composite SCCmec elements (IVa [2B&5]) form the fourth group. Group 5 corresponds to the internationally known "Taiwan clone," a PVL-positive strain with a variant SCCmec element (V [5C2&5]). This strain proved to be the most common CC59 MRSA strain isolated in Western Australia. Finally, group 6 encompasses the ST59 MRSA-V variant (5C2). The differentiation of CC59 into groups and strains indicates a rapid evolution and spread of SCCmec elements. Observed differences between groups of strains as well as intrastrain variability within a group facilitate the tracing of their spread. PMID:20211891

  10. Metagenomic analysis of the bacterial community associated with the taproot of sugar beet.

    PubMed

    Tsurumaru, Hirohito; Okubo, Takashi; Okazaki, Kazuyuki; Hashimoto, Megumi; Kakizaki, Kaori; Hanzawa, Eiko; Takahashi, Hiroyuki; Asanome, Noriyuki; Tanaka, Fukuyo; Sekiyama, Yasuyo; Ikeda, Seishi; Minamisawa, Kiwamu

    2015-01-01

    We analyzed a metagenome of the bacterial community associated with the taproot of sugar beet (Beta vulgaris L.) in order to investigate the genes involved in plant growth-promoting traits (PGPTs), namely 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase, indole acetic acid (IAA), N2 fixation, phosphate solubilization, pyrroloquinoline quinone, siderophores, and plant disease suppression as well as methanol, sucrose, and betaine utilization. The most frequently detected gene among the PGPT categories encoded β-1,3-glucanase (18 per 10(5) reads), which plays a role in the suppression of plant diseases. Genes involved in phosphate solubilization (e.g., for quinoprotein glucose dehydrogenase), methanol utilization (e.g., for methanol dehydrogenase), siderophore production (e.g. isochorismate pyruvate lyase), and ACC deaminase were also abundant. These results suggested that such PGPTs are crucially involved in supporting the growth of sugar beet. In contrast, genes for IAA production (iaaM and ipdC) were less abundant (~1 per 10(5) reads). N2 fixation genes (nifHDK) were not detected; bacterial N2 -fixing activity was not observed in the (15)N2 -feeding experiment. An analysis of nitrogen metabolism suggested that the sugar beet microbiome mainly utilized ammonium and nitroalkane as nitrogen sources. Thus, N2 fixation and IAA production did not appear to contribute to sugar beet growth. Taxonomic assignment of this metagenome revealed the high abundance of Mesorhizobium, Bradyrhizobium, and Streptomyces, suggesting that these genera have ecologically important roles in the taproot of sugar beet. Bradyrhizobium-assigned reads in particular were found in almost all categories of dominant PGPTs with high abundance. The present study revealed the characteristic functional genes in the taproot-associated microbiome of sugar beet, and suggest the opportunity to select sugar beet growth-promoting bacteria.

  11. Soil pathogen communities associated with native and non-native Phragmites australis populations in freshwater wetlands.

    PubMed

    Nelson, Eric B; Karp, Mary Ann

    2013-12-01

    Soil pathogens are believed to be major contributors to negative plant-soil feedbacks that regulate plant community dynamics and plant invasions. While the theoretical basis for pathogen regulation of plant communities is well established within the plant-soil feedback framework, direct experimental evidence for pathogen community responses to plants has been limited, often relying largely on indirect evidence based on above-ground plant responses. As a result, specific soil pathogen responses accompanying above-ground plant community dynamics are largely unknown. Here, we examine the oomycete pathogens in soils conditioned by established populations of native noninvasive and non-native invasive haplotypes of Phragmites australis (European common reed). Our aim was to assess whether populations of invasive plants harbor unique communities of pathogens that differ from those associated with noninvasive populations and whether the distribution of taxa within these communities may help to explain invasive success. We compared the composition and abundance of pathogenic and saprobic oomycete species over a 2-year period. Despite a diversity of oomycete taxa detected in soils from both native and non-native populations, pathogen communities from both invaded and noninvaded soils were dominated by species of Pythium. Pathogen species that contributed the most to the differences observed between invaded and noninvaded soils were distributed between invaded and noninvaded soils. However, the specific taxa in invaded soils responsible for community differences were distinct from those in noninvaded soils that contributed to community differences. Our results indicate that, despite the phylogenetic relatedness of native and non-native P. australis haplotypes, pathogen communities associated with the dominant non-native haplotype are distinct from those of the rare native haplotype. Pathogen taxa that dominate either noninvaded or invaded soils suggest different potential

  12. Molecular survey of bacterial communities associated with bacterial chondronecrosis with osteomyelitis (BCO) in broilers.

    PubMed

    Jiang, Tieshan; Mandal, Rabindra K; Wideman, Robert F; Khatiwara, Anita; Pevzner, Igal; Min Kwon, Young

    2015-01-01

    Bacterial chondronecrosis with osteomyelitis (BCO) is recognized as an important cause of lameness in commercial broiler chickens (meat-type chickens). Relatively little is known about the microbial communities associated with BCO. This study was conducted to increase our understanding of the microbial factors associated with BCO using a culture-independent approach. Using Illumina sequencing of the hyper-variable region V6 in the 16S rRNA gene, we characterized the bacterial communities in 97 femoral or tibial heads from normal and lame broilers carefully selected to represent diverse variations in age, line, lesion type, floor type, clinical status and bone type. Our in-depth survey based on 14 million assembled sequence reads revealed that complex bacterial communities exist in all samples, including macroscopically normal bones from clinically healthy birds. Overall, Proteobacteria (mean 90.9%) comprised the most common phylum, followed by Firmicutes (6.1%) and Actinobacteria (2.6%), accounting for more than 99% of all reads. Statistical analyses demonstrated that there are differences in bacterial communities in different types of bones (femur vs. tibia), lesion types (macroscopically normal femora or tibiae vs. those with pathognomonic BCO lesions), and among individual birds. This analysis also showed that BCO samples overrepresented genera Staphylococcus, whose species have been frequently isolated in BCO samples in previous studies. Rarefaction analysis demonstrated the general tendency that increased severities of BCO lesions were associated with reduced species diversity in both femoral and tibial samples when compared to macroscopically normal samples. These observations suggest that certain bacterial subgroups are preferentially selected in association with the development of BCO lesions. Understanding the microbial species associated with BCO will identify opportunities for understanding and modulating the pathogenesis of this form of lameness in

  13. Changes in cystic fibrosis airway microbial community associated with a severe decline in lung function.

    PubMed

    Paganin, Patrizia; Fiscarelli, Ersilia Vita; Tuccio, Vanessa; Chiancianesi, Manuela; Bacci, Giovanni; Morelli, Patrizia; Dolce, Daniela; Dalmastri, Claudia; De Alessandri, Alessandra; Lucidi, Vincenzina; Taccetti, Giovanni; Mengoni, Alessio; Bevivino, Annamaria

    2015-01-01

    Cystic fibrosis (CF) is a genetic disease resulting in chronic polymicrobial infections of the airways and progressive decline in lung function. To gain insight into the underlying causes of severe lung diseases, we aimed at comparing the airway microbiota detected in sputum of CF patients with stable lung function (S) versus those with a substantial decline in lung function (SD). Microbiota composition was investigated by using culture-based and culture-independent methods, and by performing multivariate and statistical analyses. Culture-based methods identified some microbial species associated with a worse lung function, i.e. Pseudomonas aeruginosa, Rothia mucilaginosa, Streptococcus pneumoniae and Candida albicans, but only the presence of S. pneumoniae and R. mucilaginosa was found to be associated with increased severe decline in forced expiratory volume in 1 second (FEV1). Terminal-Restriction Fragment Length Polymorphism (T-RFLP) analysis revealed a higher bacterial diversity than that detected by culture-based methods. Molecular signatures with a statistically significant odds ratio for SD status were detected, and classified as Pseudomonas, Burkholderia and Shewanella, while for other Terminal Restriction Fragments (T-RFs) no species assignation was achieved. The analysis of T-RFLP data using ecological biodiversity indices showed reduced Evenness in SD patients compared to S ones, suggesting an impaired ecology of the bacterial community in SD patients. Statistically significant differences of the ecological biodiversity indices among the three sub-groups of FEV1 (normal/mild vs moderate vs severe) were also found, suggesting that the patients with moderate lung disease experienced changes in the airway assembly of taxa. Overall, changes in CF airway microbial community associated with a severe lung function decline were detected, allowing us to define some discriminatory species as well as some discriminatory T-RFs that represent good candidates for the

  14. Macroinvertebrates communities associated with the decomposition of Phragmites australis and Fucus vesiculosus in transitional systems

    NASA Astrophysics Data System (ADS)

    Lopes, Marta Lobão; Martins, Patrícia; Rodrigues, Ana Maria; Quintino, Victor

    2013-10-01

    The decomposition rates of a macrophyte (Phragmites australis) and an alga (Fucus vesiculosus) and the associated macrofauna communities were studied along a full salinity gradient, using the leaf-bag technique and four sampling times (days 3, 7, 15 and 30). A control was set up using an artificial substrate. A subsequent study conducted in the mesohaline part of the salinity gradient also included empty bags as procedure control. The decay rates of the alga and the macrophyte were significantly different, the alga decaying faster, and presented an opposite trend along the salinity gradient, with the faster decay rate for reed in the less saline areas and for the alga in the euhaline part of the gradient. The fauna associated with the decaying and the artificial substrate showed equally well the benthic succession from the marine to the freshwater areas, in all sampling times. Arthropods were dominant in all substrates along the estuarine gradient and replaced by annelids in freshwater. No significant differences were found between the benthic communities associated with P. australis and F. vesiculosus, despite the strong differences in the decay rates, suggesting that these do not seem to be primarily related to the benthic colonizers. Although the organic substrates sustained a more abundant fauna, the benthic communities did not show significant differences between the organic and the artificial substrates, especially at the level of the species composition, suggesting that the macroinvertebrates may colonize both substrates to feed on the biofilm and/or to seek shelter. The strongly impoverished benthic community sampled by the empty bags reinforced this idea.

  15. Ecology and biogeography of bacterial communities associated with chloroethene-contaminated aquifers.

    PubMed

    Rossi, Pierre; Shani, Noam; Kohler, Florian; Imfeld, Gwenaël; Holliger, Christof

    2012-01-01

    Massive usage, along with careless handling, storage, spills, and leakages made chloroethenes (CEs) one of the most abundant classes of groundwater contaminants. Anaerobic organohalide respiring bacteria (OHRB) can couple reductive dechlorination of CEs with energy conservation, a central microbial process in (enhanced) natural attenuation of CE-contaminated aquifers. Spatial variability of OHRB guild members present in contaminated sites has not yet been investigated in detail and it is not known whether the spatial localization of contaminated sites could impact differentially remediation capacities. The goal of this study was to investigate how spatially distant microbial communities responded to the presence of CEs. Bacterial communities associated with five geographically distant European CE-contaminated aquifers were analyzed with terminal restriction fragment length polymorphism. Numerical ecology tools were used to assess the separate and combined effects on the communities of their spatial localization, their local environmental conditions and their contaminant concentrations. Three spatial scales were used for the assessment of the structuration of the communities as a function of geographical distances, namely at the aquifer scale, at medium (50 km) and long (ca. 1000 km) distances between aquifers. As a result, bacterial communities were structured with an almost identical contribution by both the geographical position of the aquifer and local environmental variables, especially electron donors and acceptors. The impact of environmental factors decreased with distance between aquifers, with the concomitant increase in importance of a geographical factor. Contrastingly, CEs contributed at a low extent at the medium scale and became important only when all aquifers were considered together, at a large geographical scale, suggesting that distant communities were structured partially by a common niche specialization in organohalide respiration.

  16. A study of community-associated methicillin-resistant Staphylococcus aureus in patients with pyoderma

    PubMed Central

    Venniyil, Prasanth V.; Ganguly, Satyaki; Kuruvila, Sheela; Devi, Sheela

    2016-01-01

    Background: Health care–associated methicillin-resistant Staphylococcus aureus(HA-MRSA) are resistant to multiple antibiotics, therefore infections caused by them are difficult to treat resulting in high morbidity and mortality. While most of the research activities and public health initiatives are focused on HA-MRSA, the newly emerging pathogen, community-associated methicillin-resistant Staphylococcus aureus(CA-MRSA) is gaining in significance in respect to patient morbidity. There is a significant paucity of data regarding CA-MRSA in the developing parts of the world. Aim: To study the proportions of HA-MRSA and CA-MRSA infections among patients with culture-proven S. aureus infection and to find out how many of these patients showed presence of MRSA in nasal cultures of healthy contacts. Materials and Methods: Clinical details of 227 patients were recorded in the study, such as the duration and recurrence of the infection, history of antibiotic intake, and the presence of other medical illnesses. A pus swab was taken from each lesion and sent for culture and sensitivity. If the culture grew S. aureus, they were screened for methicillin resistance. A swab from the anterior nares of the healthy contact of each patient, whenever available, was collected and it was screened for MRSA. Results: Furunculosis was most common among the primary pyodermas (53/134; 39. 5%). Out of 239 pus culture samples obtained from 227 patients, 192 (84.58%) grew S. aureus; of these 150 (78.12%) were methicillin-sensitive S. aureus (MSSA), whereas 42 (21.98%) were MRSA. Out of the 42 MRSA isolated, 33 turned out to be CA-MRSA (78%) and 9 (22%) were HA-MRSA. Nasal swabs of healthy contacts of 34 MRSA patients were cultured. Out of them, two grew MRSA in the culture. Conclusion: The isolation rate of S. aureus was high in our study. Furthermore, our study, although hospital based, clearly indicated the substantial magnitude of the CA-MRSA problem in the local population. PMID:27294048

  17. Community-associated Staphylococcus aureus pneumonia among Greek children: epidemiology, molecular characteristics, treatment, and outcome.

    PubMed

    Doudoulakakis, A G; Bouras, D; Drougka, E; Kazantzi, M; Michos, A; Charisiadou, A; Spiliopoulou, I; Lebessi, E; Tsolia, M

    2016-07-01

    Staphylococcus aureus is an infrequent cause of community-associated (CA-SA) pneumonia in children. The aim of this study was to evaluate the clinical, epidemiological, microbiological, and molecular characteristics of CA-SA pneumonia among children hospitalized in two large tertiary care referral centers during an 8-year period. Cases of CA-SA pneumonia admitted between 2007 and 2014 were retrospectively examined through medical record review. Molecular investigation was performed for available strains; mecA, Panton-Valentine leukocidin (PVL) (lukS-lukF-PV), and fibronectin binding protein A (fnbA) genes were detected by polymerase chain reaction (PCR). Clones were assigned by agr groups, pulsed-field gel electrophoresis (PFGE), SCCmec, and multilocus sequencing typing (MLST). In total, 41 cases were recorded (boys, 61 %), with a median age of 4.3 months (range, 1-175). Methicillin-resistant S. aureus (MRSA) accounted for 31 cases (75.6 %). Complications included empyema (25/41, 61 %), pneumatoceles (7/41, 17 %), and lung abscess (1/41, 2.5 %). Intensive care unit (ICU) admission was required in 58.5 %. Two deaths occurred (4.9 %). Definitive therapy was based on vancomycin with or without other antibiotics (55.9 %), followed by clindamycin and linezolid (26.5 % each). All isolates were susceptible to vancomycin (MIC90 2 mg/L, range 1-2), teicoplanin, and linezolid, whereas 26.8 % were resistant to clindamycin. Among the 25 studied strains, 20 were mecA-positive (MRSA), carrying also the fnbA gene. Of these, 90 % belonged to the ST80-IV/agr3/PVL-positive clone. Methicillin-susceptible S. aureus (MSSA) strains showed polyclonality, 3/5 were PVL-positive, and 3/5 were fnbA-positive. MRSA and particularly the ST80-IV clone predominated among staphylococcal pneumonia cases in children. Treatment provided was effective in all but two patients, despite the relatively high minimum inhibitory concentration (MIC) of vancomycin and a high resistance to

  18. Genetic and functional diversity of soil microbial communities associated to grapevine plants and wine quality

    NASA Astrophysics Data System (ADS)

    Mocali, Stefano; Fabiano, Arturo; Kuramae, Eiko; de Hollander, Matias; Kowalchuck, George; Vignozzi, Nadia; Valboa, Giuseppe; Pastorelli, Roberta; Fornasier, Flavio; Priori, Simone; Costantini, Edoardo

    2014-05-01

    Introduction Despite the economic importance of vineyards in Italy, the wine sector is facing severe challenges from increased global competition and climate changes. The quality of the grape at harvest has a strong direct impact on final wine quality and the strong relationship between wine composition, aroma, taste and soil properties has been outlined in the "Terroir concept". However, information on the impact of soil microbial communities on soil functions, grapevine plants and wine quality is still lacking. Objectives The aim of this study was to explore the composition and the potential functions of soil microbial communities associated to grapevine plants grown in two soils which showed similar physical, chemical and hydrological properties but which provided a different wine quality. Materials and Methods Soils from two sites of the Chianti region in Tuscany (BRO11 and BRO12) cultivated with the grapevine cultivar Sangiovese with contrasting wine quality were examined by means of a structural and functional approach: specifically, GeoChip microarrays, pyrosequencing of 16S rRNA and 18S rRNA genes, enzyme assays and measurements of some soil biological properties, such as microbial biomass C and soil respiration, were carried out. Results Enzyme assays and soil biological analyses revealed a higher biological activity in BRO11 as compared to BRO12. The structure of soil microbial communities, assessed using 16S and 18S rRNA gene-targeted pyrosequencing, revealed a higher presence of Actinobacteria in the BRO12 than in the BRO11 soil where, in contrast, the alfa-Proteobacteria are more abundant. GeoChip microarray analyses revealed a consistent difference in genes involved in S cycling, with a significant overrepresentation of sulfur-oxidation genes in BRO11 and increased levels of sulfate reduction genes BRO12. These results are consistent with the high content of sulfates and the abundance of Firmicutes such as Sulfobacillus thermosulfidooxidans in the BRO

  19. Endophytic Fungal Communities Associated with Vascular Plants in the High Arctic Zone Are Highly Diverse and Host-Plant Specific.

    PubMed

    Zhang, Tao; Yao, Yi-Feng

    2015-01-01

    This study assessed the diversity and distribution of endophytic fungal communities associated with the leaves and stems of four vascular plant species in the High Arctic using 454 pyrosequencing with fungal-specific primers targeting the ITS region. Endophytic fungal communities showed high diversity. The 76,691 sequences obtained belonged to 250 operational taxonomic units (OTUs). Of these OTUs, 190 belonged to Ascomycota, 50 to Basidiomycota, 1 to Chytridiomycota, and 9 to unknown fungi. The dominant orders were Helotiales, Pleosporales, Capnodiales, and Tremellales, whereas the common known fungal genera were Cryptococcus, Rhizosphaera, Mycopappus, Melampsora, Tetracladium, Phaeosphaeria, Mrakia, Venturia, and Leptosphaeria. Both the climate and host-related factors might shape the fungal communities associated with the four Arctic plant species in this region. These results suggested the presence of an interesting endophytic fungal community and could improve our understanding of fungal evolution and ecology in the Arctic terrestrial ecosystems. PMID:26067836

  20. Endophytic Fungal Communities Associated with Vascular Plants in the High Arctic Zone Are Highly Diverse and Host-Plant Specific.

    PubMed

    Zhang, Tao; Yao, Yi-Feng

    2015-01-01

    This study assessed the diversity and distribution of endophytic fungal communities associated with the leaves and stems of four vascular plant species in the High Arctic using 454 pyrosequencing with fungal-specific primers targeting the ITS region. Endophytic fungal communities showed high diversity. The 76,691 sequences obtained belonged to 250 operational taxonomic units (OTUs). Of these OTUs, 190 belonged to Ascomycota, 50 to Basidiomycota, 1 to Chytridiomycota, and 9 to unknown fungi. The dominant orders were Helotiales, Pleosporales, Capnodiales, and Tremellales, whereas the common known fungal genera were Cryptococcus, Rhizosphaera, Mycopappus, Melampsora, Tetracladium, Phaeosphaeria, Mrakia, Venturia, and Leptosphaeria. Both the climate and host-related factors might shape the fungal communities associated with the four Arctic plant species in this region. These results suggested the presence of an interesting endophytic fungal community and could improve our understanding of fungal evolution and ecology in the Arctic terrestrial ecosystems.

  1. Endophytic Fungal Communities Associated with Vascular Plants in the High Arctic Zone Are Highly Diverse and Host-Plant Specific

    PubMed Central

    Zhang, Tao; Yao, Yi-Feng

    2015-01-01

    This study assessed the diversity and distribution of endophytic fungal communities associated with the leaves and stems of four vascular plant species in the High Arctic using 454 pyrosequencing with fungal-specific primers targeting the ITS region. Endophytic fungal communities showed high diversity. The 76,691 sequences obtained belonged to 250 operational taxonomic units (OTUs). Of these OTUs, 190 belonged to Ascomycota, 50 to Basidiomycota, 1 to Chytridiomycota, and 9 to unknown fungi. The dominant orders were Helotiales, Pleosporales, Capnodiales, and Tremellales, whereas the common known fungal genera were Cryptococcus, Rhizosphaera, Mycopappus, Melampsora, Tetracladium, Phaeosphaeria, Mrakia, Venturia, and Leptosphaeria. Both the climate and host-related factors might shape the fungal communities associated with the four Arctic plant species in this region. These results suggested the presence of an interesting endophytic fungal community and could improve our understanding of fungal evolution and ecology in the Arctic terrestrial ecosystems. PMID:26067836

  2. Water quality and communities associated with macrophytes in a shallow water-supply reservoir on an aquaculture farm.

    PubMed

    Sipaúba-Tavares, L H; Dias, S G

    2014-05-01

    Plankton communities and macrofauna associated to aquatic macrophyte stands in a shallow water-supply reservoir (21°14'09″S; 48°18'38″W) on an aquaculture farm were compared to evaluate the relationship between organism densities and some abiotic features of the reservoir. Water and communities associated were sampled at two sites, one in an area with the predominance of Eichhornia azurea (Sw.) Kunth and the other with the predominance of Salvinia auriculata Aublet. Communities associated with macrophytes were sampled with floating quadrants (0.5 m2); the macrophytes were washed and plankton and macrofauna were fixated with 4% formalin and 1% lugol iodine; the specimens were then identified and counted. Plankton and macrofauna communities associated with S. auriculata and E. azurea had a similar diversity of species but different (p<0.05) in the abundance of associated organisms. Eichhornia azurea had the highest contents in dry and wet weight, total phosphorus, total nitrogen and organic matter. Planktonic algae were directly correlated with biomass of E. azurea. The taxa with highest densities were Rotifera and Zygnematophyceae. Results showed that the environmental variables associated with macrophytes presence in the shallow reservoir is a strong predictor of favourable conditions to maintain great diversity plankton community and macrofauna associated with plants. The role of macrophytes is important for not only stabilising the clear-water state and maintaining high diversity of organisms associated, but also it seems to be a good alternative to maintaining desirable water-supply quality for aquaculture farms.

  3. Ex situ diet influences the bacterial community associated with the skin of red-eyed tree frogs (Agalychnis callidryas).

    PubMed

    Antwis, Rachael E; Haworth, Rachel L; Engelmoer, Daniel J P; Ogilvy, Victoria; Fidgett, Andrea L; Preziosi, Richard F

    2014-01-01

    Amphibians support symbiotic bacterial communities on their skin that protect against a range of infectious pathogens, including the amphibian chytrid fungus. The conditions under which amphibians are maintained in captivity (e.g. diet, substrate, enrichment) in ex situ conservation programmes may affect the composition of the bacterial community. In addition, ex situ amphibian populations may support different bacterial communities in comparison to in situ populations of the same species. This could have implications for the suitability of populations intended for reintroduction, as well as the success of probiotic bacterial inoculations intended to provide amphibians with a bacterial community that resists invasion by the chytrid fungus. We aimed to investigate the effect of a carotenoid-enriched diet on the culturable bacterial community associated with captive red-eyed tree frogs (Agalychnis callidryas) and make comparisons to bacteria isolated from a wild population from the Chiquibul Rainforest in Belize. We successfully showed carotenoid availability influences the overall community composition, species richness and abundance of the bacterial community associated with the skin of captive frogs, with A. callidryas fed a carotenoid-enriched diet supporting a greater species richness and abundance of bacteria than those fed a carotenoid-free diet. Our results suggest that availability of carotenoids in the diet of captive frogs is likely to be beneficial for the bacterial community associated with the skin. We also found wild A. callidryas hosted more than double the number of different bacterial species than captive frogs with very little commonality between species. This suggests frogs in captivity may support a reduced and diverged bacterial community in comparison to wild populations of the same species, which could have particular relevance for ex situ conservation projects.

  4. Water quality and communities associated with macrophytes in a shallow water-supply reservoir on an aquaculture farm.

    PubMed

    Sipaúba-Tavares, L H; Dias, S G

    2014-05-01

    Plankton communities and macrofauna associated to aquatic macrophyte stands in a shallow water-supply reservoir (21°14'09″S; 48°18'38″W) on an aquaculture farm were compared to evaluate the relationship between organism densities and some abiotic features of the reservoir. Water and communities associated were sampled at two sites, one in an area with the predominance of Eichhornia azurea (Sw.) Kunth and the other with the predominance of Salvinia auriculata Aublet. Communities associated with macrophytes were sampled with floating quadrants (0.5 m2); the macrophytes were washed and plankton and macrofauna were fixated with 4% formalin and 1% lugol iodine; the specimens were then identified and counted. Plankton and macrofauna communities associated with S. auriculata and E. azurea had a similar diversity of species but different (p<0.05) in the abundance of associated organisms. Eichhornia azurea had the highest contents in dry and wet weight, total phosphorus, total nitrogen and organic matter. Planktonic algae were directly correlated with biomass of E. azurea. The taxa with highest densities were Rotifera and Zygnematophyceae. Results showed that the environmental variables associated with macrophytes presence in the shallow reservoir is a strong predictor of favourable conditions to maintain great diversity plankton community and macrofauna associated with plants. The role of macrophytes is important for not only stabilising the clear-water state and maintaining high diversity of organisms associated, but also it seems to be a good alternative to maintaining desirable water-supply quality for aquaculture farms. PMID:25166326

  5. Ex situ diet influences the bacterial community associated with the skin of red-eyed tree frogs (Agalychnis callidryas).

    PubMed

    Antwis, Rachael E; Haworth, Rachel L; Engelmoer, Daniel J P; Ogilvy, Victoria; Fidgett, Andrea L; Preziosi, Richard F

    2014-01-01

    Amphibians support symbiotic bacterial communities on their skin that protect against a range of infectious pathogens, including the amphibian chytrid fungus. The conditions under which amphibians are maintained in captivity (e.g. diet, substrate, enrichment) in ex situ conservation programmes may affect the composition of the bacterial community. In addition, ex situ amphibian populations may support different bacterial communities in comparison to in situ populations of the same species. This could have implications for the suitability of populations intended for reintroduction, as well as the success of probiotic bacterial inoculations intended to provide amphibians with a bacterial community that resists invasion by the chytrid fungus. We aimed to investigate the effect of a carotenoid-enriched diet on the culturable bacterial community associated with captive red-eyed tree frogs (Agalychnis callidryas) and make comparisons to bacteria isolated from a wild population from the Chiquibul Rainforest in Belize. We successfully showed carotenoid availability influences the overall community composition, species richness and abundance of the bacterial community associated with the skin of captive frogs, with A. callidryas fed a carotenoid-enriched diet supporting a greater species richness and abundance of bacteria than those fed a carotenoid-free diet. Our results suggest that availability of carotenoids in the diet of captive frogs is likely to be beneficial for the bacterial community associated with the skin. We also found wild A. callidryas hosted more than double the number of different bacterial species than captive frogs with very little commonality between species. This suggests frogs in captivity may support a reduced and diverged bacterial community in comparison to wild populations of the same species, which could have particular relevance for ex situ conservation projects. PMID:24416427

  6. Ex situ Diet Influences the Bacterial Community Associated with the Skin of Red-Eyed Tree Frogs (Agalychnis callidryas)

    PubMed Central

    Antwis, Rachael E.; Haworth, Rachel L.; Engelmoer, Daniel J. P.; Ogilvy, Victoria; Fidgett, Andrea L.; Preziosi, Richard F.

    2014-01-01

    Amphibians support symbiotic bacterial communities on their skin that protect against a range of infectious pathogens, including the amphibian chytrid fungus. The conditions under which amphibians are maintained in captivity (e.g. diet, substrate, enrichment) in ex situ conservation programmes may affect the composition of the bacterial community. In addition, ex situ amphibian populations may support different bacterial communities in comparison to in situ populations of the same species. This could have implications for the suitability of populations intended for reintroduction, as well as the success of probiotic bacterial inoculations intended to provide amphibians with a bacterial community that resists invasion by the chytrid fungus. We aimed to investigate the effect of a carotenoid-enriched diet on the culturable bacterial community associated with captive red-eyed tree frogs (Agalychnis callidryas) and make comparisons to bacteria isolated from a wild population from the Chiquibul Rainforest in Belize. We successfully showed carotenoid availability influences the overall community composition, species richness and abundance of the bacterial community associated with the skin of captive frogs, with A. callidryas fed a carotenoid-enriched diet supporting a greater species richness and abundance of bacteria than those fed a carotenoid-free diet. Our results suggest that availability of carotenoids in the diet of captive frogs is likely to be beneficial for the bacterial community associated with the skin. We also found wild A. callidryas hosted more than double the number of different bacterial species than captive frogs with very little commonality between species. This suggests frogs in captivity may support a reduced and diverged bacterial community in comparison to wild populations of the same species, which could have particular relevance for ex situ conservation projects. PMID:24416427

  7. Characterization of the bacterial community associated with body wall lesions of Tripneustes gratilla (Echinoidea) using culture-independent methods.

    PubMed

    Becker, Pierre T; Gillan, David C; Eeckhaut, Igor

    2009-02-01

    The bacterial community associated with skin lesions of the sea urchin Tripneustes gratilla was investigated using 16S ribosomal RNA gene cloning and fluorescent in situ hybridization (FISH). All clones were classified in the Alphaproteobacteria, Gammaproteobacteria and Cytophaga-Flexibacter-Bacteroides (CFB) bacteria. Most of the Alphaproteobacteria were related to the Roseobacter lineage and to bacteria implicated in marine diseases. The majority of the Gammaproteobacteria were identified as Vibrio while CFB represented only 9% of the total clones. FISH analyses showed that Alphaproteobacteria, CFB bacteria and Gammaproteobacteria accounted respectively for 43%, 38% and 19% of the DAPI counts. The importance of the methods used is emphasized. PMID:19041326

  8. Stability of the rhizosphere and endophytic bacterial communities associated with Arabidopsis thaliana (L.) Heynh under impact of cosmic factors

    NASA Astrophysics Data System (ADS)

    Kordium, V. A.; Adamchuk-Chala, N. I.; Moshinec, H. V.

    The orbital experiment will involve a growing of Arabidopsis plant seed to seed in the presence of a plant probiotic bacteria consortium introduced into the system The purpose of experiment is to characterize microbial community associated with Arabidopsis thaliana and determine how consortium of introduced bacteria along with the endemic plant-associated bacteria influences the plant development reproductive system and seed formation in spaceflight conditions The first study will be an examination of the survival of model bacteria in on the inoculated plant The second complex study is to examine the plant traits in particular the ultrastructure of root statocytes in order to determine whether the plant development proceeds normally under microgravity conditions on background of introduced bacteria and to assess the structural changes occurring in the cotyledons generative organs and seeds The third set of observations will concern studies of the structure of microbial community associated with Arabidopsis plants with traditional and molecular tools The fourth part of the work will be an examination of mobile genetic elements that can play a role in adaptation of bacteria to the spaceflight conditions however they may affect the stability of bacterial endo- and rhizosphere communities The final part of the proposal initiates the study of possible risk of the bacterial consortium use for a plant inoculation in spaceflight conditions An evaluation of this risk will be performed via examination of expression of the Klebsiella

  9. Bacterial communities associated with Porites white patch syndrome (PWPS) on three western Indian Ocean (WIO) coral reefs.

    PubMed

    Séré, Mathieu G; Tortosa, Pablo; Chabanet, Pascale; Turquet, Jean; Quod, Jean-Pascal; Schleyer, Michael H

    2013-01-01

    The scleractinian coral Porites lutea, an important reef-building coral on western Indian Ocean reefs (WIO), is affected by a newly-reported white syndrome (WS) the Porites white patch syndrome (PWPS). Histopathology and culture-independent molecular techniques were used to characterise the microbial communities associated with this emerging disease. Microscopy showed extensive tissue fragmentation generally associated with ovoid basophilic bodies resembling bacterial aggregates. Results of 16S rRNA sequence analysis revealed a high variability between bacterial communities associated with PWPS-infected and healthy tissues in P. lutea, a pattern previously reported in other coral diseases such as black band disease (BBD), white band disease (WBD) and white plague diseases (WPD). Furthermore, substantial variations in bacterial communities were observed at the different sampling locations, suggesting that there is no strong bacterial association in Porites lutea on WIO reefs. Several sequences affiliated with potential pathogens belonging to the Vibrionaceae and Rhodobacteraceae were identified, mainly in PWPS-infected coral tissues. Among them, only two ribotypes affiliated to Shimia marina (NR043300.1) and Vibrio hepatarius (NR025575.1) were consistently found in diseased tissues from the three geographically distant sampling localities. The role of these bacterial species in PWPS needs to be tested experimentally.

  10. Highly heterogeneous bacterial communities associated with the South China Sea reef corals Porites lutea, Galaxea fascicularis and Acropora millepora.

    PubMed

    Li, Jie; Chen, Qi; Zhang, Si; Huang, Hui; Yang, Jian; Tian, Xin-Peng; Long, Li-Juan

    2013-01-01

    Coral harbor diverse and specific bacteria play significant roles in coral holobiont function. Bacteria associated with three of the common and phylogenetically divergent reef-building corals in the South China Sea, Porites lutea, Galaxea fascicularis and Acropora millepora, were investigated using 454 barcoded-pyrosequencing. Three colonies of each species were sampled, and 16S rRNA gene libraries were constructed individually. Analysis of pyrosequencing libraries showed that bacterial communities associated with the three coral species were more diverse than previous estimates based on corals from the Caribbean Sea, Indo-Pacific reefs and the Red Sea. Three candidate phyla, including BRC1, OD1 and SR1, were found for the first time in corals. Bacterial communities were separated into three groups: P. lutea and G. fascicular, A. millepora and seawater. P. lutea and G. fascicular displayed more similar bacterial communities, and bacterial communities associated with A. millepora differed from the other two coral species. The three coral species shared only 22 OTUs, which were distributed in Alphaproteobacteria, Deltaproteobacteria, Gammaproteobacteria, Chloroflexi, Actinobacteria, Acidobacteria and an unclassified bacterial group. The composition of bacterial communities within each colony of each coral species also showed variation. The relatively small common and large specific bacterial communities in these corals implies that bacterial associations may be structured by multiple factors at different scales and that corals may associate with microbes in terms of similar function, rather than identical species.

  11. Highly Heterogeneous Bacterial Communities Associated with the South China Sea Reef Corals Porites lutea, Galaxea fascicularis and Acropora millepora

    PubMed Central

    Li, Jie; Chen, Qi; Zhang, Si; Huang, Hui; Yang, Jian; Tian, Xin-Peng; Long, Li-Juan

    2013-01-01

    Coral harbor diverse and specific bacteria play significant roles in coral holobiont function. Bacteria associated with three of the common and phylogenetically divergent reef-building corals in the South China Sea, Porites lutea, Galaxea fascicularis and Acropora millepora, were investigated using 454 barcoded-pyrosequencing. Three colonies of each species were sampled, and 16S rRNA gene libraries were constructed individually. Analysis of pyrosequencing libraries showed that bacterial communities associated with the three coral species were more diverse than previous estimates based on corals from the Caribbean Sea, Indo-Pacific reefs and the Red Sea. Three candidate phyla, including BRC1, OD1 and SR1, were found for the first time in corals. Bacterial communities were separated into three groups: P. lutea and G. fascicular, A. millepora and seawater. P. lutea and G. fascicular displayed more similar bacterial communities, and bacterial communities associated with A. millepora differed from the other two coral species. The three coral species shared only 22 OTUs, which were distributed in Alphaproteobacteria, Deltaproteobacteria, Gammaproteobacteria, Chloroflexi, Actinobacteria, Acidobacteria and an unclassified bacterial group. The composition of bacterial communities within each colony of each coral species also showed variation. The relatively small common and large specific bacterial communities in these corals implies that bacterial associations may be structured by multiple factors at different scales and that corals may associate with microbes in terms of similar function, rather than identical species. PMID:23940737

  12. New and emerging concepts in managing and preventing community-associated methicillin-resistant Staphylococcus aureus infections.

    PubMed

    Gupta, Aditya K; Lyons, Danika C A; Rosen, Ted

    2015-11-01

    Methicillin-resistant Staphylococcus aureus (MRSA) infections occurring within communities are increasing and can affect healthy individuals who have had little to no experience with hospital or healthcare settings (community-associated MRSA, CA-MRSA). CA-MRSA infections have multiple presentations which can make diagnosis and timely treatment difficult yet often manifest as a skin and soft tissue infection (SSTI) requiring dermatological intervention. There is emerging evidence of multiple environmental sources of bacteria that may contribute to recurrence. As with other infections, preventing transmission and recurrence depends on adherence to hand-washing and personal hygiene practices. Pharmaceutical intervention should be culture- rather than empirically-guided. The goal of this review is to provide dermatologists with a brief summary of the diagnostic features of CA-MRSA infections and updated strategies for management and prevention of transmission and recurrence of CA-MRSA infections, infections likely to present to dermatology offices.

  13. Bacterial communities associated with host-adapted populations of pea aphids revealed by deep sequencing of 16S ribosomal DNA.

    PubMed

    Gauthier, Jean-Pierre; Outreman, Yannick; Mieuzet, Lucie; Simon, Jean-Christophe

    2015-01-01

    Associations between microbes and animals are ubiquitous and hosts may benefit from harbouring microbial communities through improved resource exploitation or resistance to environmental stress. The pea aphid, Acyrthosiphon pisum, is the host of heritable bacterial symbionts, including the obligate endosymbiont Buchnera aphidicola and several facultative symbionts. While obligate symbionts supply aphids with key nutrients, facultative symbionts influence their hosts in many ways such as protection against natural enemies, heat tolerance, color change and reproduction alteration. The pea aphid also encompasses multiple plant-specialized biotypes, each adapted to one or a few legume species. Facultative symbiont communities differ strongly between biotypes, although bacterial involvement in plant specialization is uncertain. Here, we analyse the diversity of bacterial communities associated with nine biotypes of the pea aphid complex using amplicon pyrosequencing of 16S rRNA genes. Combined clustering and phylogenetic analyses of 16S sequences allowed identifying 21 bacterial OTUs (Operational Taxonomic Unit). More than 98% of the sequencing reads were assigned to known pea aphid symbionts. The presence of Wolbachia was confirmed in A. pisum while Erwinia and Pantoea, two gut associates, were detected in multiple samples. The diversity of bacterial communities harboured by pea aphid biotypes was very low, ranging from 3 to 11 OTUs across samples. Bacterial communities differed more between than within biotypes but this difference did not correlate with the genetic divergence between biotypes. Altogether, these results confirm that the aphid microbiota is dominated by a few heritable symbionts and that plant specialization is an important structuring factor of bacterial communities associated with the pea aphid complex. However, since we examined the microbiota of aphid samples kept a few generations in controlled conditions, it may be that bacterial diversity was

  14. Bacterial communities associated with host-adapted populations of pea aphids revealed by deep sequencing of 16S ribosomal DNA.

    PubMed

    Gauthier, Jean-Pierre; Outreman, Yannick; Mieuzet, Lucie; Simon, Jean-Christophe

    2015-01-01

    Associations between microbes and animals are ubiquitous and hosts may benefit from harbouring microbial communities through improved resource exploitation or resistance to environmental stress. The pea aphid, Acyrthosiphon pisum, is the host of heritable bacterial symbionts, including the obligate endosymbiont Buchnera aphidicola and several facultative symbionts. While obligate symbionts supply aphids with key nutrients, facultative symbionts influence their hosts in many ways such as protection against natural enemies, heat tolerance, color change and reproduction alteration. The pea aphid also encompasses multiple plant-specialized biotypes, each adapted to one or a few legume species. Facultative symbiont communities differ strongly between biotypes, although bacterial involvement in plant specialization is uncertain. Here, we analyse the diversity of bacterial communities associated with nine biotypes of the pea aphid complex using amplicon pyrosequencing of 16S rRNA genes. Combined clustering and phylogenetic analyses of 16S sequences allowed identifying 21 bacterial OTUs (Operational Taxonomic Unit). More than 98% of the sequencing reads were assigned to known pea aphid symbionts. The presence of Wolbachia was confirmed in A. pisum while Erwinia and Pantoea, two gut associates, were detected in multiple samples. The diversity of bacterial communities harboured by pea aphid biotypes was very low, ranging from 3 to 11 OTUs across samples. Bacterial communities differed more between than within biotypes but this difference did not correlate with the genetic divergence between biotypes. Altogether, these results confirm that the aphid microbiota is dominated by a few heritable symbionts and that plant specialization is an important structuring factor of bacterial communities associated with the pea aphid complex. However, since we examined the microbiota of aphid samples kept a few generations in controlled conditions, it may be that bacterial diversity was

  15. Transient Shifts in Bacterial Communities Associated with the Temperate Gorgonian Paramuricea clavata in the Northwestern Mediterranean Sea

    PubMed Central

    La Rivière, Marie; Roumagnac, Marie; Garrabou, Joaquim; Bally, Marc

    2013-01-01

    Background Bacterial communities that are associated with tropical reef-forming corals are being increasingly recognized for their role in host physiology and health. However, little is known about the microbial diversity of the communities associated with temperate gorgonian corals, even though these communities are key structural components of the ecosystem. In the Northwestern Mediterranean Sea, gorgonians undergo recurrent mass mortalities, but the potential relationship between these events and the structure of the associated bacterial communities remains unexplored. Because microbial assemblages may contribute to the overall health and disease resistance of their host, a detailed baseline of the associated bacterial diversity is required to better understand the functioning of the gorgonian holobiont. Methodology/Principal Findings The bacterial diversity associated with the gorgonian Paramuricea clavata was determined using denaturing gradient gel electrophoresis, terminal-restriction fragment length polymorphism and the construction of clone libraries of the bacterial 16S ribosomal DNA. Three study sites were monitored for 4 years to assess the variability of communities associated with healthy colonies. Bacterial assemblages were highly dominated by one Hahellaceae-related ribotype and exhibited low diversity. While this pattern was mostly conserved through space and time, in summer 2007, a deep shift in microbiota structure toward increased bacterial diversity and the transient disappearance of Hahellaceae was observed. Conclusion/Significance This is the first spatiotemporal study to investigate the bacterial diversity associated with a temperate shallow gorgonian. Our data revealed an established relationship between P. clavata and a specific bacterial group within the Oceanospirillales. These results suggest a potential symbiotic role of Hahellaceae in the host-microbe association, as recently suggested for tropical corals. However, a transient

  16. Emergence and Characterization of Community-Associated Methicillin-Resistant Staphyloccocus aureus Infections in Denmark, 1999 to 2006▿

    PubMed Central

    Larsen, A. R.; Stegger, M.; Böcher, S.; Sørum, M.; Monnet, D. L.; Skov, R. L.

    2009-01-01

    The epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) infections has changed worldwide. From being strictly nosocomial, MRSA is now frequently found as a community-associated (CA) pathogen. Denmark has been a low-prevalence country for MRSA since the mid-1970s but has in recent years experienced an increasing number of CA-MRSA cases. The aim of this study was to describe the emergence of CA-MRSA infections in Denmark. All Danish MRSA specimens and corresponding clinical data from 1999 to 2006 were investigated. Isolates were analyzed by antibiotic resistance and molecular typing and were assigned to clonal complexes (CC). Clinical data were extracted from discharge summaries and general practitioners' notes, from which assessments of community association were made for all infected cases. CA-MRSA cases constituted 29.4% of all MRSA infections (n = 1,790) and an increasing proportion of the annual numbers of MRSA infections during the study period. CA-MRSA was associated with a young age, skin and soft tissue infections, and non-Danish origin. Transmission between household members was frequently reported. Molecular typing showed >60 circulating clones, where 89.4% of the isolates belonged to five CC (CC80, CC8, CC30, CC5, and CC22), 81.2% carried staphylococcal cassette chromosome mec IV, and 163/244 (69.4%) were positive for Panton-Valentine leukocidin. Clinical and microbiological characteristics indicated that import of MRSA occurs frequently. Resistance to ≥3 antibiotic classes was observed for 48.8% of the isolates. The emergence of CA-MRSA in Denmark was caused by diverse strains, both well-known and new CA-MRSA strains. The results suggest multiple introductions of MRSA as an important source for CA-MRSA infections in Denmark. PMID:18971362

  17. Molecular epidemiology and antimicrobial susceptibility profiles of methicillin-resistant Staphylococcus aureus blood culture isolates: results of the Quebec Provincial Surveillance Programme.

    PubMed

    Lévesque, S; Bourgault, A M; Galarneau, L A; Moisan, D; Doualla-Bell, F; Tremblay, C

    2015-05-01

    The objectives of this study were to characterize methicillin-resistant Staphylococcus aureus (MRSA) blood culture isolates and to determine their relative importance in both nosocomial and community-acquired infections. A total of 535 MRSA blood culture isolates were analysed. In vitro susceptibility to 14 agents was determined. The genes nuc, mecA and coding for PVL toxin were identified by PCR. All isolates were characterized by PFGE or spa typing to assess their genomic relationships. Most MRSA isolates were retrieved from nosocomial bloodstream infections (474, 89%) and were of the CMRSA2 genotype. Healthcare-associated (HA)-MRSA bloodstream infections were associated with older age (70-89 years, P = 0·002) and most often secondary to central line infections (P = 0·005). Among MRSA strains associated with community-acquired (CA)-MRSA, 28·8% were isolated in intravenous drug users. CA-MRSA genotypes were more frequently found in young adults (20-39 years, P < 0·0001) with skin/soft tissue as the primary sources of infection (P = 0·006). CMRSA10 genotype was the predominant CA-MRSA strain. All MRSA isolates were susceptible to doxycycline, tigecycline, trimethoprim/sulfamethoxazole and vancomycin. Both the presence of the genes coding for PVL toxin (89·8%) and susceptibility to clindamycin (86·5%) were predictive of CA-MRSA genotypes. Whereas in the USA, HA-MRSA have been replaced by USA300 (CMRSA10) clone as the predominant MRSA strain type in positive blood cultures from hospitalized patients, this phenomenon has not been observed in the province of Quebec. PMID:25140694

  18. Molecular epidemiology and antimicrobial susceptibility profiles of methicillin-resistant Staphylococcus aureus blood culture isolates: results of the Quebec Provincial Surveillance Programme.

    PubMed

    Lévesque, S; Bourgault, A M; Galarneau, L A; Moisan, D; Doualla-Bell, F; Tremblay, C

    2015-05-01

    The objectives of this study were to characterize methicillin-resistant Staphylococcus aureus (MRSA) blood culture isolates and to determine their relative importance in both nosocomial and community-acquired infections. A total of 535 MRSA blood culture isolates were analysed. In vitro susceptibility to 14 agents was determined. The genes nuc, mecA and coding for PVL toxin were identified by PCR. All isolates were characterized by PFGE or spa typing to assess their genomic relationships. Most MRSA isolates were retrieved from nosocomial bloodstream infections (474, 89%) and were of the CMRSA2 genotype. Healthcare-associated (HA)-MRSA bloodstream infections were associated with older age (70-89 years, P = 0·002) and most often secondary to central line infections (P = 0·005). Among MRSA strains associated with community-acquired (CA)-MRSA, 28·8% were isolated in intravenous drug users. CA-MRSA genotypes were more frequently found in young adults (20-39 years, P < 0·0001) with skin/soft tissue as the primary sources of infection (P = 0·006). CMRSA10 genotype was the predominant CA-MRSA strain. All MRSA isolates were susceptible to doxycycline, tigecycline, trimethoprim/sulfamethoxazole and vancomycin. Both the presence of the genes coding for PVL toxin (89·8%) and susceptibility to clindamycin (86·5%) were predictive of CA-MRSA genotypes. Whereas in the USA, HA-MRSA have been replaced by USA300 (CMRSA10) clone as the predominant MRSA strain type in positive blood cultures from hospitalized patients, this phenomenon has not been observed in the province of Quebec.

  19. Comparative Metagenomic Profiling of Symbiotic Bacterial Communities Associated with Ixodes persulcatus, Ixodes pavlovskyi and Dermacentor reticulatus Ticks

    PubMed Central

    Kurilshikov, Alexander; Livanova, Natalya N.; Fomenko, Nataliya V.; Tupikin, Alexey E.; Rar, Vera A.; Kabilov, Marsel R.; Livanov, Stanislav G.; Tikunova, Nina V.

    2015-01-01

    Ixodes persulcatus, Ixodes pavlovskyi, and Dermacentor reticulatus ticks inhabiting Western Siberia are responsible for the transmission of a number of etiological agents that cause human and animal tick-borne diseases. Because these ticks are abundant in the suburbs of large cities, agricultural areas, and popular tourist sites and frequently attack people and livestock, data regarding the microbiomes of these organisms are required. Using metagenomic 16S profiling, we evaluate bacterial communities associated with I. persulcatus, I. pavlovskyi, and D. reticulatus ticks collected from the Novosibirsk region of Russia. A total of 1214 ticks were used for this study. DNA extracted from the ticks was pooled according to tick species and sex. Sequencing of the V3-V5 domains of 16S rRNA genes was performed using the Illumina Miseq platform. The following bacterial genera were prevalent in the examined communities: Acinetobacter (all three tick species), Rickettsia (I. persulcatus and D. reticulatus) and Francisella (D. reticulatus). B. burgdorferi sensu lato and B. miyamotoi sequences were detected in I. persulcatus and I. pavlovskyi but not in D. reticulatus ticks. The pooled samples of all tick species studied contained bacteria from the Anaplasmataceae family, although their occurrence was low. DNA from A. phagocytophilum and Candidatus Neoehrlichia mikurensis was first observed in I. pavlovskyi ticks. Significant inter-species differences in the number of bacterial taxa as well as intra-species diversity related to tick sex were observed. The bacterial communities associated with the I. pavlovskyi ticks displayed a higher biodiversity compared with those of the I. persulcatus and D. reticulatus ticks. Bacterial community structure was also diverse across the studied tick species, as shown by permutational analysis of variance using the Bray-Curtis dissimilarity metric (p = 0.002). Between-sex variation was confirmed by PERMANOVA testing in I. persulcatus (p = 0

  20. Spirochaetes dominate the microbial community associated with the red coral Corallium rubrum on a broad geographic scale

    PubMed Central

    van de Water, Jeroen A. J. M.; Melkonian, Rémy; Junca, Howard; Voolstra, Christian R.; Reynaud, Stéphanie; Allemand, Denis; Ferrier-Pagès, Christine

    2016-01-01

    Mass mortality events in populations of the iconic red coral Corallium rubrum have been related to seawater temperature anomalies that may have triggered microbial disease development. However, very little is known about the bacterial community associated with the red coral. We therefore aimed to provide insight into this species’ bacterial assemblages using Illumina MiSeq sequencing of 16S rRNA gene amplicons generated from samples collected at five locations distributed across the western Mediterranean Sea. Twelve bacterial species were found to be consistently associated with the red coral, forming a core microbiome that accounted for 94.6% of the overall bacterial community. This core microbiome was particularly dominated by bacteria of the orders Spirochaetales and Oceanospirillales, in particular the ME2 family. Bacteria belonging to these orders have been implicated in nutrient cycling, including nitrogen, carbon and sulfur. While Oceanospirillales are common symbionts of marine invertebrates, our results identify members of the Spirochaetales as other important dominant symbiotic bacterial associates within Anthozoans. PMID:27263657

  1. Community-Associated Methicillin-Resistant Staphylococcus aureus Lacking PVL, as a Cause of Severe Invasive Infection Treated with Linezolid

    PubMed Central

    Gavino, Alexandra; Miragaia, Maria; Varandas, Luis; de Lencastre, Herminia; Brito, Maria Joao

    2013-01-01

    Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) is an emerging public health problem worldwide. Severe invasive infections have been described, mostly associated with the presence of Panton-Valentine leukocidin (PVL). In Portugal limited information exists regarding CA-MRSA infections. In this study we describe the case of a previously healthy 12-year-old female, sport athlete, who presented to the hospital with acetabulofemoral septic arthritis, myositis, fasciitis, acetabulum osteomyelitis, and pneumonia. The MRSA isolated from blood and synovial fluid was PVL negative and staphylococcal enterotoxin type P (SEP) and type L (SEL) positive, with a vancomycin MIC of 1.0 mg/L and resistant to clindamycin and ciprofloxacin. The patient was submitted to multiple surgical drainages and started on vancomycin, rifampicin, and gentamycin. Due to persistence of fever and no microbiological clearance, linezolid was started with improvement. This is one of the few reported cases of severe invasive infection caused by CA-MRSA in Portugal, which was successfully treated with linezolid. In spite of the severity of infection, the MRSA isolate did not produce PVL. PMID:23509655

  2. Metabolic and molecular characterization of bacterial community associated to Patagonian Chilean oligotrophic-lakes of quaternary glacial origin.

    PubMed

    Leon, Carla; Campos, Víctor; Urrutia, Roberto; Mondaca, María-Angélica

    2012-04-01

    The Patagonian Lakes have particular environmental conditions with or without intermittent disturbances. The study of the microorganisms present in aquatic ecosystems has increased notably because they can be used as micro-scale bioindicators of, among others, anthropogenic pollution and climatic change. The aim of the work was to compare the composition of the bacterial communities associated with sediments of three Patagonian Lakes with different geomorphologic patterns and disturbances. The lake sediments were characterized by molecular techniques, physiology profiles and physico-chemical analyses. The metabolic and physiological profiles of the microbial community demonstrated that non-impacted Tranquilo Lake is statistically different to impacted Bertrand and Plomo Lakes. Similar results were detected by DGGE profiles. FISH results demonstrated that betaproteobacteria showed the highest count in the Tranquilo Lake while gammaproteobacteria showed the highest counts in the Bertrand and Plomo Lakes, indicating that their sediments are highly dystrophic. The results demonstrate differences in the metabolic activity and structural and functional composition of bacterial communities of the studied lakes, which have different geomorphological patterns due to disturbances such as volcanic activity and the climatic change.

  3. Novel Phenol-soluble Modulin Derivatives in Community-associated Methicillin-resistant Staphylococcus aureus Identified through Imaging Mass Spectrometry*

    PubMed Central

    Gonzalez, David J.; Okumura, Cheryl Y.; Hollands, Andrew; Kersten, Roland; Akong-Moore, Kathryn; Pence, Morgan A.; Malone, Cheryl L.; Derieux, Jaclyn; Moore, Bradley S.; Horswill, Alexander R.; Dixon, Jack E.; Dorrestein, Pieter C.; Nizet, Victor

    2012-01-01

    Staphylococcus aureus causes a wide range of human disease ranging from localized skin and soft tissue infections to potentially lethal systemic infections. S. aureus has the biosynthetic ability to generate numerous virulence factors that assist in circumventing the innate immune system during disease pathogenesis. Recent studies have uncovered a set of extracellular peptides produced by community-associated methicillin-resistant S. aureus (CA-MRSA) with homology to the phenol-soluble modulins (PSMs) from Staphylococcus epidermidis. CA-MRSA PSMs contribute to skin infection and recruit and lyse neutrophils, and truncated versions of these peptides possess antimicrobial activity. In this study, novel CA-MRSA PSM derivatives were discovered by the use of microbial imaging mass spectrometry. The novel PSM derivatives are compared with their parent full-length peptides for changes in hemolytic, cytolytic, and neutrophil-stimulating activity. A potential contribution of the major S. aureus secreted protease aureolysin in processing PSMs is demonstrated. Finally, we show that PSM processing occurs in multiple CA-MRSA strains by structural confirmation of additional novel derivatives. This work demonstrates that IMS can serve as a useful tool to go beyond genome predictions and expand our understanding of the important family of small peptide virulence factors. PMID:22371493

  4. In vitro activity of beta-lactam antibiotics to community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA).

    PubMed

    Germel, C; Haag, A; Söderquist, B

    2012-04-01

    Community-associated (CA) MRSA often display low MIC values against oxacillin. The in vitro activity of various beta-lactam antibiotics against heterogeneous CA-MRSA (n = 98) isolated in a low endemic area was determined by Etest, and Mueller-Hinton agar (MUHAP) was compared with Mueller-Hinton agar supplemented with 2% NaCl (MUHSP). In general, the CA-MRSA isolates showed higher MIC values for the various beta-lactam antibiotics on MUHSP compared with MUHAP. MIC values for oxacillin ranged from 1 to >256 mg/L on MUHSP. Cephalothin, representing the first generation of cephalosporins, showed MICs from 0.75 to 96 mg/L and the MIC(50) and MIC(90) for cefuroxime, cefotaxime and cefepime, representing the second, third and fourth generations, respectively, were rather high. However, the MIC(50) and MIC(90) for ceftobiprole (fifth generation) were 1.5 and 2 mg/L, respectively, on MUHSP. The MIC(50) and MIC(90) for imipenem were 0.75 and 2 mg/L, respectively, on MUHSP. Only 3/98 (3%) CA-MRSA isolates showed a MIC >4 mg/L. Consequently, low MIC values for imipenem, lower than those of the newly developed fifth generation cephalosporins, were found among CA-MRSA. These findings may be considered for further studies including clinical trials in order to evaluate carbapenems as a potential treatment option for infections caused by CA-MRSA.

  5. Virulence determinants associated with the Asian community-associated methicillin-resistant Staphylococcus aureus lineage ST59.

    PubMed

    Li, Min; Dai, Yingxin; Zhu, Yuanjun; Fu, Chih-Lung; Tan, Vee Y; Wang, Yanan; Wang, Xing; Hong, Xufen; Liu, Qian; Li, Tianming; Qin, Juanxiu; Ma, Xiaowei; Fang, Jingyuan; Otto, Michael

    2016-06-14

    Understanding virulence is vital for the development of novel therapeutics to target infections with community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA), which cause an ongoing epidemic in the United States and are on a global rise. However, what defines virulence particularly of global CA-MRSA lineages is poorly understood. Threatening a vast population, the predominant Asian CA-MRSA lineage ST59 is of major epidemiological importance. However, there have been no molecular analyses using defined virulence gene deletion mutants in that lineage as of yet. Here, we compared virulence in skin, lung, and blood infection models of ST59 CA-MRSA isolates with geographically matched hospital-associated MRSA isolates. We selected a representative ST59 CA-MRSA isolate based on toxin expression and virulence characteristics, and produced isogenic gene deletion mutants of important CA-MRSA virulence determinants (α-toxin, PSM α, Agr) in that isolate for in-vitro and in-vivo analyses. Our results demonstrate strongly enhanced virulence of ST59 CA-MRSA over hospital-associated lineages, supporting the notion that enhanced virulence is characteristic for CA-MRSA. Furthermore, they show strong and significant contribution of Agr, α-toxin, and PSMα to pathogenesis of ST59 CA-MRSA skin, lung, and blood infection, emphasizing the value of drug development efforts targeted toward those virulence determinants.

  6. Virulence determinants associated with the Asian community-associated methicillin-resistant Staphylococcus aureus lineage ST59

    PubMed Central

    Li, Min; Dai, Yingxin; Zhu, Yuanjun; Fu, Chih-Lung; Tan, Vee Y.; Wang, Yanan; Wang, Xing; Hong, Xufen; Liu, Qian; Li, Tianming; Qin, Juanxiu; Ma, Xiaowei; Fang, Jingyuan; Otto, Michael

    2016-01-01

    Understanding virulence is vital for the development of novel therapeutics to target infections with community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA), which cause an ongoing epidemic in the United States and are on a global rise. However, what defines virulence particularly of global CA-MRSA lineages is poorly understood. Threatening a vast population, the predominant Asian CA-MRSA lineage ST59 is of major epidemiological importance. However, there have been no molecular analyses using defined virulence gene deletion mutants in that lineage as of yet. Here, we compared virulence in skin, lung, and blood infection models of ST59 CA-MRSA isolates with geographically matched hospital-associated MRSA isolates. We selected a representative ST59 CA-MRSA isolate based on toxin expression and virulence characteristics, and produced isogenic gene deletion mutants of important CA-MRSA virulence determinants (α-toxin, PSM α, Agr) in that isolate for in-vitro and in-vivo analyses. Our results demonstrate strongly enhanced virulence of ST59 CA-MRSA over hospital-associated lineages, supporting the notion that enhanced virulence is characteristic for CA-MRSA. Furthermore, they show strong and significant contribution of Agr, α-toxin, and PSMα to pathogenesis of ST59 CA-MRSA skin, lung, and blood infection, emphasizing the value of drug development efforts targeted toward those virulence determinants. PMID:27296890

  7. Role of the ESAT-6 secretion system in virulence of the emerging community-associated Staphylococcus aureus lineage ST398

    PubMed Central

    Wang, Yanan; Hu, Mo; Liu, Qian; Qin, Juanxiu; Dai, Yingxin; He, Lei; Li, Tianming; Zheng, Bing; Zhou, Fan; Yu, Kaiwen; Fang, Jingyuan; Liu, Xiaoyun; Otto, Michael; Li, Min

    2016-01-01

    Novel Staphylococcus aureus clones continue to emerge that cause infections in otherwise healthy people. One example is the sequence type (ST) 398 lineage, which we show here is increasing in importance as a significant cause of community-associated (CA) human infections in China. We have a profound lack of understanding about what determines the considerable virulence potential of such newly emerging clones. Information about the contribution to virulence of the more recently discovered ESAT-6 secretion system (ESS) has remained particularly scarce. The Chinese ST398 isolates exhibited significantly increased expression of ESS genes as compared to predominant hospital-associated clones, which we found is likely due to increased expression of the accessory gene regulator (Agr) system and control of ESS by Agr. Importantly, deletion of essB in ST398 resulted in significantly reduced resistance to neutrophil killing and decreased virulence in murine skin and blood infection models. Our results demonstrate a key function of ESS in promoting virulence and mechanisms of resistance to innate host defense in an important emerging CA-S. aureus lineage. They suggest that ESS has a so far underestimated role in promoting aggressive virulence and epidemiological success of S. aureus. PMID:27112266

  8. Molecular diversity of the methanotrophic bacteria communities associated with disused tin-mining ponds in Kampar, Perak, Malaysia.

    PubMed

    Sow, S L S; Khoo, G; Chong, L K; Smith, T J; Harrison, P L; Ong, H K A

    2014-10-01

    In a previous study, notable differences of several physicochemical properties, as well as the community structure of ammonia oxidizing bacteria as judged by 16S rRNA gene analysis, were observed among several disused tin-mining ponds located in the town of Kampar, Malaysia. These variations were associated with the presence of aquatic vegetation as well as past secondary activities that occurred at the ponds. Here, methane oxidizing bacteria (MOB), which are direct participants in the nutrient cycles of aquatic environments and biological indicators of environmental variations, have been characterised via analysis of pmoA functional genes in the same environments. The MOB communities associated with disused tin-mining ponds that were exposed to varying secondary activities were examined in comparison to those in ponds that were left to nature. Comparing the sequence and phylogenetic analysis of the pmoA clone libraries at the different ponds (idle, lotus-cultivated and post-aquaculture), we found pmoA genes indicating the presence of type I and type II MOB at all study sites, but type Ib sequences affiliated with the Methylococcus/Methylocaldum lineage were most ubiquitous (46.7 % of clones). Based on rarefaction analysis and diversity indices, the disused mining pond with lotus culture was observed to harbor the highest richness of MOB. However, varying secondary activity or sample type did not show a strong variation in community patterns as compared to the ammonia oxidizers in our previous study.

  9. Effect of copper tolerant Elsholtzia splendens on bacterial community associated with Commelina communis on a copper mine spoil.

    PubMed

    Yang, Ruyi; Guo, Fuyu; Li, Jing; Su, Nannan; Shao, Zongyuan; Zan, Shuting

    2016-08-01

    Facilitation, or positive plant-plant interaction, has received increasing concern from ecologists over the last two decades. Facilitation may occur through direct mitigation of severe environments or indirect mediation by a third participant from the same or different trophic levels. The copper (Cu) tolerant species Elsholtzia splendens facilitates the establishment and growth of co-occurring Commelina communis through indirect enrichment of microbial activity. However, whether and how E. splendens impacts the microbial community that is associated with C. communis is less known. We characterized the soil bacterial community in the rhizosphere of C. communis in the absence and presence of E. splendens using PCR-DGGE (polymerase chain reaction-denaturing gradient gel electrophoresis) and sequencing. The result showed that the richness of the bacterial community increased, but diversity and evenness remained similar, in the presence of E. splendens. Chloroflexi, Acidobacteria and Proteobacteria were the most dominant bacteria. The relative abundance of dominant and minor bacterial groups showed distinctly different responses to E. splendens. Principal component analysis and redundancy analysis indicated that variation of the bacterial community was determined by multiple factors and might be driven by the tested soil parameters collectively, or alternatively changed through plant root exudates or other microorganisms. Our results enhance the understanding of how the bacterial community associated with a beneficiary plant responds to a benefactor plant and suggests that the changes of bacterial community composition may have far-reaching influence on plant-soil feedback and the aboveground plant community in the long run. PMID:27521948

  10. Plant-by-plant variations of bacterial communities associated with leaves of the nickel hyperaccumulator Alyssum bertolonii Desv.

    PubMed

    Mengoni, Alessio; Pini, Francesco; Huang, Li-Nan; Shu, Wen-Sheng; Bazzicalupo, Marco

    2009-10-01

    Bacteria associated with tissues of metal-hyperaccumulating plants are of great interest due to the multiple roles they may play with respect to plant growth and resistance to heavy metals. The variability of bacterial communities associated with plant tissues of three populations of Alyssum bertolonii, a Ni hyperaccumulator endemic of serpentine outcrops of Central Italy, was investigated. Terminal-restriction fragment length polymorphism (T-RFLP) analysis of bacterial 16S rRNA genes was applied to DNA extracted from leaf tissues of 30 individual plants from three geographically separated serpentine outcrops. Moreover, T-RFLP fingerprinting was also performed on DNA extracted from the same soils from which the plants were collected. Fifty-nine unique terminal-restriction fragments (TRFs) were identified, with more than half of the taxonomically interpreted TRFs assigned to Alpha- and Gamma-Proteobacteria and Clostridia. Data were then used to define the extent of variation of bacterial communities due to single plants or to plant populations. Results indicated a very high plant-by-plant variation of leaf-associated community (more than 93% of total variance observed). However, a core (numerically small) of plant-specific TRFs was found. This work demonstrates that plant-associated bacterial communities represent a large reservoir of biodiversity and that the high variability existing between plants, even from the same population, should be taken into account in future studies on association between bacteria and metal-hyperaccumulating plants. PMID:19479304

  11. Host Species and Environmental Effects on Bacterial Communities Associated with Drosophila in the Laboratory and in the Natural Environment

    PubMed Central

    Staubach, Fabian; Baines, John F.; Künzel, Sven; Bik, Elisabeth M.; Petrov, Dmitri A.

    2013-01-01

    The fruit fly Drosophila is a classic model organism to study adaptation as well as the relationship between genetic variation and phenotypes. Although associated bacterial communities might be important for many aspects of Drosophila biology, knowledge about their diversity, composition, and factors shaping them is limited. We used 454-based sequencing of a variable region of the bacterial 16S ribosomal RNA gene to characterize the bacterial communities associated with wild and laboratory Drosophila isolates. In order to specifically investigate effects of food source and host species on bacterial communities, we analyzed samples from wild Drosophila melanogaster and D. simulans collected from a variety of natural substrates, as well as from adults and larvae of nine laboratory-reared Drosophila species. We find no evidence for host species effects in lab-reared flies; instead, lab of origin and stochastic effects, which could influence studies of Drosophila phenotypes, are pronounced. In contrast, the natural Drosophila–associated microbiota appears to be predominantly shaped by food substrate with an additional but smaller effect of host species identity. We identify a core member of this natural microbiota that belongs to the genus Gluconobacter and is common to all wild-caught flies in this study, but absent from the laboratory. This makes it a strong candidate for being part of what could be a natural D. melanogaster and D. simulans core microbiome. Furthermore, we were able to identify candidate pathogens in natural fly isolates. PMID:23967097

  12. Nasal carriage screening of community-associated methicillin resistant Staphylococcus aureus in healthy children of a developing country

    PubMed Central

    Mobasherizadeh, Sina; Shojaei, Hasan; Havaei, Seyed Asghar; Mostafavizadeh, Kamyar; Davoodabadi, Fazlollah; Khorvash, Farzin; Kushki, Ali Mehrabi; Daei-Naser, Abbas; Ghanbari, Fahimeh

    2016-01-01

    Background: The rapid emergence and spread of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) has raised considerable public health concern in both developed and developing countries. The current study aimed to address the extent of this phenomenon in healthy preschool children of a developing country. Materials and Methods: We conducted a prospective study from April 2013 to March 2014 on 410 healthy 2-6 years old preschool children in Isfahan, Iran. Demographic medical data and nasal samples were collected from the participating children. Isolates were identified as S. aureus and MRSA based on microbiological and molecular tests, including the presence of eap and mecA genes. Results: The overall prevalence of S. aureus and CA-MRSA nasal carriage was 28% (115/410) and 6.1% (25/410), respectively. The identity of isolates was confirmed by molecular assay. The factors that were independently associated with nasal carriage of S. aureus were: Children crowding in day-care nurseries and income level of families. A total of 20/90 (22.2%) of methicillin-susceptible S. aureus and all 25 CA-MRSA displayed multiple drug resistance to 3–8 antibiotics. Conclusions: The current report reflects issues and concerns that the high rate of colonization by CA-MRSA in Iranian healthy children provides obliging evidence that MRSA have established a foothold in the community and are emerging as important health threatening pathogens. It is suggested that we need more effective infection control measures to prevent transmission of nasal CA-MRSA in healthy preschool children.

  13. Molecular Profiling of Rhizosphere Microbial Communities Associated with Healthy and Diseased Black Spruce (Picea mariana) Seedlings Grown in a Nursery

    PubMed Central

    Filion, M.; Hamelin, R. C.; Bernier, L.; St-Arnaud, M.

    2004-01-01

    Bacterial and fungal populations associated with the rhizosphere of healthy black spruce (Picea mariana) seedlings and seedlings with symptoms of root rot were characterized by cloned rRNA gene sequence analysis. Triplicate bacterial and fungal rRNA gene libraries were constructed, and 600 clones were analyzed by amplified ribosomal DNA restriction analysis and grouped into operational taxonomical units (OTUs). A total of 84 different bacterial and 31 different fungal OTUs were obtained and sequenced. Phylogenetic analyses indicated that the different OTUs belonged to a wide range of bacterial and fungal taxa. For both groups, pairwise comparisons revealed that there was greater similarity between replicate libraries from each treatment than between libraries from different treatments. Significant differences between pooled triplicate samples from libraries of genes from healthy seedlings and pooled triplicate samples from libraries of genes from diseased seedlings were also obtained for both bacteria and fungi, clearly indicating that the rhizosphere-associated bacterial and fungal communities of healthy and diseased P. mariana seedlings were different. The communities associated with healthy and diseased seedlings also showed distinct ecological parameters as indicated by the calculated diversity, dominance, and evenness indices. Among the main differences observed at the community level, there was a higher proportion of Acidobacteria, Gammaproteobacteria, and Homobasidiomycetes clones associated with healthy seedlings, while the diseased-seedling rhizosphere harbored a higher proportion of Actinobacteria, Sordariomycetes, and environmental clones. The methodological approach described in this study appears promising for targeting potential rhizosphere-competent biological control agents against root rot diseases occurring in conifer nurseries. PMID:15184155

  14. Staphylococcus aureus spa type t437: identification of the most dominant community-associated clone from Asia across Europe.

    PubMed

    Glasner, C; Pluister, G; Westh, H; Arends, J P; Empel, J; Giles, E; Laurent, F; Layer, F; Marstein, L; Matussek, A; Mellmann, A; Pérez-Vásquez, M; Ungvári, E; Yan, X; Žemličková, H; Grundmann, H; van Dijl, J M

    2015-02-01

    Methicillin-resistant Staphylococcus aureus (MRSA) belonging to the multilocus sequence type clonal complex 59 (MLST CC59) is the predominant community-associated MRSA clone in Asia. This clone, which is primarily linked with the spa type t437, has so far only been reported in low numbers among large epidemiological studies in Europe. Nevertheless, the overall numbers identified in some Northern European reference laboratories have increased during the past decade. To determine whether the S. aureus t437 clone is present in other European countries, and to assess its genetic diversity across Europe, we analysed 147 S. aureus t437 isolates from 11 European countries collected over a period of 11 years using multiple locus variable number tandem repeat fingerprinting/analysis (MLVF/MLVA) and MLST. Additionally 16 S. aureus t437 isolates from healthy carriers and patients from China were included. Most isolates were shown to be monophyletic with 98% of the isolates belonging to the single MLVA complex 621, to which nearly all included isolates from China also belonged. More importantly, all MLST-typed isolates belonged to CC59. Our study implies that the European S. aureus t437 population represents a genetically tight cluster, irrespective of the year, country and site of isolation. This underpins the view that S. aureus CC59 has been introduced into several European countries, not being restricted to particular geographical regions or specific host environments. The European S. aureus t437 isolates thus bear the general hallmarks of a high-risk clone. PMID:25658555

  15. Origin and ecological selection of core and food-specific bacterial communities associated with meat and seafood spoilage.

    PubMed

    Chaillou, Stéphane; Chaulot-Talmon, Aurélie; Caekebeke, Hélène; Cardinal, Mireille; Christieans, Souad; Denis, Catherine; Desmonts, Marie Hélène; Dousset, Xavier; Feurer, Carole; Hamon, Erwann; Joffraud, Jean-Jacques; La Carbona, Stéphanie; Leroi, Françoise; Leroy, Sabine; Lorre, Sylvie; Macé, Sabrina; Pilet, Marie-France; Prévost, Hervé; Rivollier, Marina; Roux, Dephine; Talon, Régine; Zagorec, Monique; Champomier-Vergès, Marie-Christine

    2015-05-01

    The microbial spoilage of meat and seafood products with short shelf lives is responsible for a significant amount of food waste. Food spoilage is a very heterogeneous process, involving the growth of various, poorly characterized bacterial communities. In this study, we conducted 16S ribosomal RNA gene pyrosequencing on 160 samples of fresh and spoiled foods to comparatively explore the bacterial communities associated with four meat products and four seafood products that are among the most consumed food items in Europe. We show that fresh products are contaminated in part by a microbiota similar to that found on the skin and in the gut of animals. However, this animal-derived microbiota was less prevalent and less abundant than a core microbiota, psychrotrophic in nature, mainly originated from the environment (water reservoirs). We clearly show that this core community found on meat and seafood products is the main reservoir of spoilage bacteria. We also show that storage conditions exert strong selective pressure on the initial microbiota: alpha diversity in fresh samples was 189±58 operational taxonomic units (OTUs) but dropped to 27±12 OTUs in spoiled samples. The OTU assemblage associated with spoilage was shaped by low storage temperatures, packaging and the nutritional value of the food matrix itself. These factors presumably act in tandem without any hierarchical pattern. Most notably, we were also able to identify putative new clades of dominant, previously undescribed bacteria occurring on spoiled seafood, a finding that emphasizes the importance of using culture-independent methods when studying food microbiota. PMID:25333463

  16. Incidence and risk factors for community-associated methicillin-resistant Staphylococcus aureus in New York City, 2006-2012.

    PubMed

    Baker, P; Cohen, B; Liu, J; Larson, E

    2016-04-01

    This study aims to describe changes in incidence and risk factors for community-associated methicillin resistant Staphylococcus aureus (CA-MRSA) infections upon admission to two New York City hospitals from 2006 to 2012. We examined the first hospitalization for adult patients using electronic health record and administrative data and determined the annual incidence/1000 admissions of total S. aureus, total MRSA, and CA-MRSA (within 48 h of admission) in clinical specimens over the study period. Logistic regression was used to identify factors associated with CA-MRSA in 2006 and 2012. In 137 350 admissions, the incidence of S. aureus, MRSA, and CA-MRSA/1000 admissions were 15·6, 7·0, and 3·5, respectively. The total S. aureus and MRSA isolations decreased significantly over the study period (27% and 25%, respectively) while CA-MRSA incidence was unchanged. CA-MRSA increased as a proportion of all MRSA between 2006 (46%) and 2012 (62%), and was most frequently isolated from respiratory (1·5/1000) and blood (0·7/1000) cultures. Logistic regression analysis of factors associated with isolation of CA-MRSA showed that age ⩾65 years [odds ratio (OR) 2·3, 95% confidence interval (CI) 1·2-4·5], male gender (OR 1·8, 95% CI 1·2-2·8) and history of renal failure (OR 2·6, 95% CI 1·6-4·2) were significant predictors of infection in 2006. No predictors were identified in 2012.

  17. Incidence and risk factors for community-associated methicillin-resistant Staphylococcus aureus in New York City, 2006-2012.

    PubMed

    Baker, P; Cohen, B; Liu, J; Larson, E

    2016-04-01

    This study aims to describe changes in incidence and risk factors for community-associated methicillin resistant Staphylococcus aureus (CA-MRSA) infections upon admission to two New York City hospitals from 2006 to 2012. We examined the first hospitalization for adult patients using electronic health record and administrative data and determined the annual incidence/1000 admissions of total S. aureus, total MRSA, and CA-MRSA (within 48 h of admission) in clinical specimens over the study period. Logistic regression was used to identify factors associated with CA-MRSA in 2006 and 2012. In 137 350 admissions, the incidence of S. aureus, MRSA, and CA-MRSA/1000 admissions were 15·6, 7·0, and 3·5, respectively. The total S. aureus and MRSA isolations decreased significantly over the study period (27% and 25%, respectively) while CA-MRSA incidence was unchanged. CA-MRSA increased as a proportion of all MRSA between 2006 (46%) and 2012 (62%), and was most frequently isolated from respiratory (1·5/1000) and blood (0·7/1000) cultures. Logistic regression analysis of factors associated with isolation of CA-MRSA showed that age ⩾65 years [odds ratio (OR) 2·3, 95% confidence interval (CI) 1·2-4·5], male gender (OR 1·8, 95% CI 1·2-2·8) and history of renal failure (OR 2·6, 95% CI 1·6-4·2) were significant predictors of infection in 2006. No predictors were identified in 2012. PMID:26364503

  18. Origin and ecological selection of core and food-specific bacterial communities associated with meat and seafood spoilage

    PubMed Central

    Chaillou, Stéphane; Chaulot-Talmon, Aurélie; Caekebeke, Hélène; Cardinal, Mireille; Christieans, Souad; Denis, Catherine; Hélène Desmonts, Marie; Dousset, Xavier; Feurer, Carole; Hamon, Erwann; Joffraud, Jean-Jacques; La Carbona, Stéphanie; Leroi, Françoise; Leroy, Sabine; Lorre, Sylvie; Macé, Sabrina; Pilet, Marie-France; Prévost, Hervé; Rivollier, Marina; Roux, Dephine; Talon, Régine; Zagorec, Monique; Champomier-Vergès, Marie-Christine

    2015-01-01

    The microbial spoilage of meat and seafood products with short shelf lives is responsible for a significant amount of food waste. Food spoilage is a very heterogeneous process, involving the growth of various, poorly characterized bacterial communities. In this study, we conducted 16S ribosomal RNA gene pyrosequencing on 160 samples of fresh and spoiled foods to comparatively explore the bacterial communities associated with four meat products and four seafood products that are among the most consumed food items in Europe. We show that fresh products are contaminated in part by a microbiota similar to that found on the skin and in the gut of animals. However, this animal-derived microbiota was less prevalent and less abundant than a core microbiota, psychrotrophic in nature, mainly originated from the environment (water reservoirs). We clearly show that this core community found on meat and seafood products is the main reservoir of spoilage bacteria. We also show that storage conditions exert strong selective pressure on the initial microbiota: alpha diversity in fresh samples was 189±58 operational taxonomic units (OTUs) but dropped to 27±12 OTUs in spoiled samples. The OTU assemblage associated with spoilage was shaped by low storage temperatures, packaging and the nutritional value of the food matrix itself. These factors presumably act in tandem without any hierarchical pattern. Most notably, we were also able to identify putative new clades of dominant, previously undescribed bacteria occurring on spoiled seafood, a finding that emphasizes the importance of using culture-independent methods when studying food microbiota. PMID:25333463

  19. Nasal carriage screening of community-associated methicillin resistant Staphylococcus aureus in healthy children of a developing country

    PubMed Central

    Mobasherizadeh, Sina; Shojaei, Hasan; Havaei, Seyed Asghar; Mostafavizadeh, Kamyar; Davoodabadi, Fazlollah; Khorvash, Farzin; Kushki, Ali Mehrabi; Daei-Naser, Abbas; Ghanbari, Fahimeh

    2016-01-01

    Background: The rapid emergence and spread of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) has raised considerable public health concern in both developed and developing countries. The current study aimed to address the extent of this phenomenon in healthy preschool children of a developing country. Materials and Methods: We conducted a prospective study from April 2013 to March 2014 on 410 healthy 2-6 years old preschool children in Isfahan, Iran. Demographic medical data and nasal samples were collected from the participating children. Isolates were identified as S. aureus and MRSA based on microbiological and molecular tests, including the presence of eap and mecA genes. Results: The overall prevalence of S. aureus and CA-MRSA nasal carriage was 28% (115/410) and 6.1% (25/410), respectively. The identity of isolates was confirmed by molecular assay. The factors that were independently associated with nasal carriage of S. aureus were: Children crowding in day-care nurseries and income level of families. A total of 20/90 (22.2%) of methicillin-susceptible S. aureus and all 25 CA-MRSA displayed multiple drug resistance to 3–8 antibiotics. Conclusions: The current report reflects issues and concerns that the high rate of colonization by CA-MRSA in Iranian healthy children provides obliging evidence that MRSA have established a foothold in the community and are emerging as important health threatening pathogens. It is suggested that we need more effective infection control measures to prevent transmission of nasal CA-MRSA in healthy preschool children. PMID:27656613

  20. Metagenomic profiling reveals lignocellulose degrading system in a microbial community associated with a wood-feeding beetle.

    PubMed

    Scully, Erin D; Geib, Scott M; Hoover, Kelli; Tien, Ming; Tringe, Susannah G; Barry, Kerrie W; Glavina del Rio, Tijana; Chovatia, Mansi; Herr, Joshua R; Carlson, John E

    2013-01-01

    The Asian longhorned beetle (Anoplophoraglabripennis) is an invasive, wood-boring pest that thrives in the heartwood of deciduous tree species. A large impediment faced by A. glabripennis as it feeds on woody tissue is lignin, a highly recalcitrant biopolymer that reduces access to sugars and other nutrients locked in cellulose and hemicellulose. We previously demonstrated that lignin, cellulose, and hemicellulose are actively deconstructed in the beetle gut and that the gut harbors an assemblage of microbes hypothesized to make significant contributions to these processes. While lignin degrading mechanisms have been well characterized in pure cultures of white rot basidiomycetes, little is known about such processes in microbial communities associated with wood-feeding insects. The goals of this study were to develop a taxonomic and functional profile of a gut community derived from an invasive population of larval A. glabripennis collected from infested host trees and to identify genes that could be relevant for the digestion of woody tissue and nutrient acquisition. To accomplish this goal, we taxonomically and functionally characterized the A. glabripennis midgut microbiota through amplicon and shotgun metagenome sequencing and conducted a large-scale comparison with the metagenomes from a variety of other herbivore-associated communities. This analysis distinguished the A. glabripennis larval gut metagenome from the gut communities of other herbivores, including previously sequenced termite hindgut metagenomes. Genes encoding enzymes were identified in the A. glabripennis gut metagenome that could have key roles in woody tissue digestion including candidate lignin degrading genes (laccases, dye-decolorizing peroxidases, novel peroxidases and β-etherases), 36 families of glycoside hydrolases (such as cellulases and xylanases), and genes that could facilitate nutrient recovery, essential nutrient synthesis, and detoxification. This community could serve as a

  1. Metagenomic Profiling Reveals Lignocellulose Degrading System in a Microbial Community Associated with a Wood-Feeding Beetle

    PubMed Central

    Scully, Erin D.; Geib, Scott M.; Hoover, Kelli; Tien, Ming; Tringe, Susannah G.; Barry, Kerrie W.; Glavina del Rio, Tijana; Chovatia, Mansi; Herr, Joshua R.; Carlson, John E.

    2013-01-01

    The Asian longhorned beetle (Anoplophoraglabripennis) is an invasive, wood-boring pest that thrives in the heartwood of deciduous tree species. A large impediment faced by A. glabripennis as it feeds on woody tissue is lignin, a highly recalcitrant biopolymer that reduces access to sugars and other nutrients locked in cellulose and hemicellulose. We previously demonstrated that lignin, cellulose, and hemicellulose are actively deconstructed in the beetle gut and that the gut harbors an assemblage of microbes hypothesized to make significant contributions to these processes. While lignin degrading mechanisms have been well characterized in pure cultures of white rot basidiomycetes, little is known about such processes in microbial communities associated with wood-feeding insects. The goals of this study were to develop a taxonomic and functional profile of a gut community derived from an invasive population of larval A. glabripennis collected from infested host trees and to identify genes that could be relevant for the digestion of woody tissue and nutrient acquisition. To accomplish this goal, we taxonomically and functionally characterized the A. glabripennis midgut microbiota through amplicon and shotgun metagenome sequencing and conducted a large-scale comparison with the metagenomes from a variety of other herbivore-associated communities. This analysis distinguished the A. glabripennis larval gut metagenome from the gut communities of other herbivores, including previously sequenced termite hindgut metagenomes. Genes encoding enzymes were identified in the A. glabripennis gut metagenome that could have key roles in woody tissue digestion including candidate lignin degrading genes (laccases, dye-decolorizing peroxidases, novel peroxidases and β-etherases), 36 families of glycoside hydrolases (such as cellulases and xylanases), and genes that could facilitate nutrient recovery, essential nutrient synthesis, and detoxification. This community could serve as a

  2. Spatial and Species Variations in Bacterial Communities Associated with Corals from the Red Sea as Revealed by Pyrosequencing

    PubMed Central

    Lee, On On; Yang, Jiangke; Bougouffa, Salim; Wang, Yong; Batang, Zenon; Tian, Renmao; Al-Suwailem, Abdulaziz

    2012-01-01

    Microbial associations with corals are common and are most likely symbiotic, although their diversity and relationships with environmental factors and host species remain unclear. In this study, we adopted a 16S rRNA gene tag-pyrosequencing technique to investigate the bacterial communities associated with three stony Scleractinea and two soft Octocorallia corals from three locations in the Red Sea. Our results revealed highly diverse bacterial communities in the Red Sea corals, with more than 600 ribotypes detected and up to 1,000 species estimated from a single coral species. Altogether, 21 bacterial phyla were recovered from the corals, of which Gammaproteobacteria was the most dominant group, and Chloroflexi, Chlamydiae, and the candidate phylum WS3 were reported in corals for the first time. The associated bacterial communities varied greatly with location, where environmental conditions differed significantly. Corals from disturbed areas appeared to share more similar bacterial communities, but larger variations in community structures were observed between different coral species from pristine waters. Ordination methods identified salinity and depth as the most influential parameters affecting the abundance of Vibrio, Pseudoalteromonas, Serratia, Stenotrophomonas, Pseudomonas, and Achromobacter in the corals. On the other hand, bacteria such as Chloracidobacterium and Endozoicomonas were more sensitive to the coral species, suggesting that the host species type may be influential in the associated bacterial community, as well. The combined influences of the coral host and environmental factors on the associated microbial communities are discussed. This study represents the first comparative study using tag-pyrosequencing technology to investigate the bacterial communities in Red Sea corals. PMID:22865078

  3. Origin and ecological selection of core and food-specific bacterial communities associated with meat and seafood spoilage.

    PubMed

    Chaillou, Stéphane; Chaulot-Talmon, Aurélie; Caekebeke, Hélène; Cardinal, Mireille; Christieans, Souad; Denis, Catherine; Desmonts, Marie Hélène; Dousset, Xavier; Feurer, Carole; Hamon, Erwann; Joffraud, Jean-Jacques; La Carbona, Stéphanie; Leroi, Françoise; Leroy, Sabine; Lorre, Sylvie; Macé, Sabrina; Pilet, Marie-France; Prévost, Hervé; Rivollier, Marina; Roux, Dephine; Talon, Régine; Zagorec, Monique; Champomier-Vergès, Marie-Christine

    2015-05-01

    The microbial spoilage of meat and seafood products with short shelf lives is responsible for a significant amount of food waste. Food spoilage is a very heterogeneous process, involving the growth of various, poorly characterized bacterial communities. In this study, we conducted 16S ribosomal RNA gene pyrosequencing on 160 samples of fresh and spoiled foods to comparatively explore the bacterial communities associated with four meat products and four seafood products that are among the most consumed food items in Europe. We show that fresh products are contaminated in part by a microbiota similar to that found on the skin and in the gut of animals. However, this animal-derived microbiota was less prevalent and less abundant than a core microbiota, psychrotrophic in nature, mainly originated from the environment (water reservoirs). We clearly show that this core community found on meat and seafood products is the main reservoir of spoilage bacteria. We also show that storage conditions exert strong selective pressure on the initial microbiota: alpha diversity in fresh samples was 189±58 operational taxonomic units (OTUs) but dropped to 27±12 OTUs in spoiled samples. The OTU assemblage associated with spoilage was shaped by low storage temperatures, packaging and the nutritional value of the food matrix itself. These factors presumably act in tandem without any hierarchical pattern. Most notably, we were also able to identify putative new clades of dominant, previously undescribed bacteria occurring on spoiled seafood, a finding that emphasizes the importance of using culture-independent methods when studying food microbiota.

  4. Characterization and Comparison of 2 Distinct Epidemic Community-Associated Methicillin-Resistant Staphylococcus aureus Clones of ST59 Lineage

    PubMed Central

    Chen, Chih-Jung; Unger, Clemens; Hoffmann, Wolfgang; Lindsay, Jodi A.; Huang, Yhu-Chering; Götz, Friedrich

    2013-01-01

    Sequence type (ST) 59 is an epidemic lineage of community-associated (CA) methicillin-resistant Staphylococcus aureus (MRSA) isolates. Taiwanese CA-MRSA isolates belong to ST59 and can be grouped into 2 distinct clones, a virulent Taiwan clone and a commensal Asian-Pacific clone. The Taiwan clone carries the Panton–Valentine leukocidin (PVL) genes and the staphylococcal chromosomal cassette mec (SCCmec) VT, and is frequently isolated from patients with severe disease. The Asian-Pacific clone is PVL-negative, carries SCCmec IV, and a frequent colonizer of healthy children. Isolates of both clones were characterized by their ability to adhere to respiratory A549 cells, cytotoxicity to human neutrophils, and nasal colonization of a murine and murine sepsis models. Genome variation was determined by polymerase chain reaction of selected virulence factors and by multi-strain whole genome microarray. Additionally, the expression of selected factors was compared between the 2 clones. The Taiwan clone showed a much higher cytotoxicity to the human neutrophils and caused more severe septic infections with a high mortality rate in the murine model. The clones were indistinguishable in their adhesion to A549 cells and persistence of murine nasal colonization. The microarray data revealed that the Taiwan clone had lost the ø3-prophage that integrates into the β-hemolysin gene and includes staphylokinase- and enterotoxin P-encoding genes, but had retained the genes for human immune evasion, scn and chps. Production of the virulence factors did not differ significantly in the 2 clonal groups, although more α-toxin was expressed in Taiwan clone isolates from pneumonia patients. In conclusion, the Taiwan CA-MRSA clone was distinguished by enhanced virulence in both humans and an animal infection model. The evolutionary acquisition of PVL, the higher expression of α-toxin, and possibly the loss of a large portion of the β-hemolysin-converting prophage likely contribute to

  5. High-density livestock operations, crop field application of manure, and risk of community-associated methicillin-resistant Staphylococcus aureus infection, Pennsylvania, USA

    PubMed Central

    Casey, Joan A.; Curriero, Frank C.; Cosgrove, Sara E.; Nachman, Keeve E.; Schwartz, Brian S.

    2015-01-01

    Context Nearly 80% of antibiotics in the United States are sold for use in livestock feeds. The manure produced by these livestock contains antibiotic-resistant bacteria, resistance genes, and antibiotics, and is subsequently applied to crop fields where it may put community members at risk for antibiotic-resistant infections. Objective To assess the association between individual exposure to swine and dairy/veal industrial agriculture and risk of methicillin-resistant Staphylococcus aureus (MRSA) infection. Design, Setting, and Participants A population-based, nested case-control study of Geisinger primary care patients in Pennsylvania from 2005–2010. Incident MRSA cases were identified using electronic health records, classified as community-associated or healthcare-associated, and frequency-matched to randomly selected controls and patients with skin and soft tissue infection. Nutrient management plans were used to create two exposure variables: seasonal crop field manure application and number of livestock at the operation. In a sub-study we collected 200 isolates from patients stratified by location of diagnosis and proximity to livestock operations. Main outcome measures Community-associated MRSA, healthcare associated-MRSA, and skin and soft tissue infection status (with no history of MRSA) compared to controls. Results From 446,480 patients, 1539 community-associated MRSA, 1335 healthcare-associated MRSA, 2895 skin and soft tissue infection cases, and 2914 controls were included. After adjustment for MRSA risk factors, the highest quartile of swine crop field exposure was significantly associated with community-associated MRSA, healthcare-associated MRSA, and skin and soft tissue infection case status (adjusted odds ratio, 1.38 [95% CI, 1.13–1.69], 1.30 [95% CI, 1.05–1.61], and 1.37 [95% CI, 1.18–1.60], respectively); and there was a trend of increasing odds across quartiles for each outcome (all P for trend ≤0.01). There were similar but weaker

  6. Seed-colonizing bacterial communities associated with the suppression of Pythium seedling disease in a municipal biosolids compost.

    PubMed

    Chen, Mei-Hsing; Jack, Allison L H; McGuire, I Cristina; Nelson, Eric B

    2012-05-01

    This study was designed to characterize seed-colonizing microbial communities that were previously shown to be involved in the suppression of seedling disease caused by Pythium ultimum in a municipal biosolids compost. Selective microbial inhibitors were employed to inactivate portions of the microbial community associated with seed germinated in a compost medium to evaluate their impact on disease suppression. After initial screenings for toxicity to both cucumber and P. ultimum, six selective inhibitors were eventually used to assess the impact of seed treatment on the reduction of bacterial and fungal populations and on disease suppression. Rifampicin was the most effective inhibitor for inactivating disease suppression. Bacterial communities that colonized cucumber seed sown in compost medium for 8 h and seed sown in compost medium for 8 h followed by a 3-h treatment of either rifampicin at 500 ppm or water were dislodged from seed surfaces and subjected to RNA extraction and reverse transcription to cDNA. Differences in the composition of seed-colonizing bacterial communities were assessed using terminal restriction fragment length polymorphisms (T-RFLP) of polymerase chain reaction-amplified 16S rDNA genes. T-RFLP profiles revealed a diversity of distinct bacterial taxa, a number of which dominate seed surfaces within 8 h of sowing. Analysis of similarity (ANOSIM) using terminal restriction fragment (T-RF) presence or absence showed that community profiles of nontreated and water-treated seed were quite similar whereas community profiles from rifampicin-treated seed were distinct. Differences in community profiles based on T-RF abundance (peak height and peak area) indicated that all treatments were unique (ANOSIM, all pairwise comparisons P < 0.05) Peaks heights and areas of relatively few T-RFs were reduced to zero following rifampicin treatment and 34 T-RFs explained 85% of the observed difference between treatments. Tentative taxon assignments for each of

  7. Invasion Is a Community Affair: Clandestine Followers in the Bacterial Community Associated to Green Algae, Caulerpa racemosa, Track the Invasion Source

    PubMed Central

    Aires, Tania; Serrão, Ester A.; Kendrick, Gary; Duarte, Carlos M.; Arnaud-Haond, Sophie

    2013-01-01

    Biological invasions rank amongst the most deleterious components of global change inducing alterations from genes to ecosystems. The genetic characteristics of introduced pools of individuals greatly influence the capacity of introduced species to establish and expand. The recently demonstrated heritability of microbial communities associated to individual genotypes of primary producers makes them a potentially essential element of the evolution and adaptability of their hosts. Here, we characterized the bacterial communities associated to native and non-native populations of the marine green macroalga Caulerparacemosa through pyrosequencing, and explored their potential role on the strikingly invasive trajectory of their host in the Mediterranean. The similarity of endophytic bacterial communities from the native Australian range and several Mediterranean locations confirmed the origin of invasion and revealed distinct communities associated to a second Mediterranean variety of C. racemosa long reported in the Mediterranean. Comparative analysis of these two groups demonstrated the stability of the composition of bacterial communities through the successive steps of introduction and invasion and suggested the vertical transmission of some major bacterial OTUs. Indirect inferences on the taxonomic identity and associated metabolism of bacterial lineages showed a striking consistency with sediment upheaval conditions associated to the expansion of their invasive host and to the decline of native species. These results demonstrate that bacterial communities can be an effective tracer of the origin of invasion and support their potential role in their eukaryotic host’s adaptation to new environments. They put forward the critical need to consider the 'meta-organism' encompassing both the host and associated micro-organisms, to unravel the origins, causes and mechanisms underlying biological invasions. PMID:23874625

  8. Characteristics of Community-Associated Methicillin-Resistant Staphylococcus aureus (CA-MRSA) Strains Isolated from Skin and Soft-Tissue Infections in Uruguay

    PubMed Central

    Pardo, Lorena; Machado, Virginia; Mollerach, Marta; Mota, María Inés; Tuchscherr, Lorena P. N.; Gadea, Pilar; Gardella, Noella; Sordelli, Daniel O.; Vola, Magdalena; Schelotto, Felipe; Varela, Gustavo

    2009-01-01

    We analyzed 90 nonduplicates community-associated methicillin-resistant S. aureus (CA-MRSA) strains isolated from skin and soft-tissue infections. All strains were mecA positive. Twenty-four of the 90 strains showed inducible macrolide-lincosamide-streptogramin B resistance. All strains produced α-toxin; 96% and 100% of them displayed positive results for lukS-F and cna genes, respectively. Eigthy-five strains expressed capsular polysaccharide serotype 8. Six different pulsotypes were discriminated by pulsed-field gel electrophoresis (PFGE) and three predominant groups of CA-MRSA strains (1, 2, and 4) were identified, in agreement with phenotypic and genotypic characteristics. Strains of group 1 (pulsotype A, CP8+, and Panton-Valentine leukocidin (PVL)+) were the most frequently recovered and exhibited a PFGE band pattern identical to other CA-MRSA strains previously isolated in Uruguay and Brazil. Three years after the first local CA-MRSA report, these strains are still producing skin and soft-tissue infections demonstrating the stability over time of this community-associated emerging pathogen. PMID:20016669

  9. Archaeal and Bacterial Communities Associated with the Surface Mucus of Caribbean Corals Differ in Their Degree of Host Specificity and Community Turnover Over Reefs.

    PubMed

    Frade, Pedro R; Roll, Katharina; Bergauer, Kristin; Herndl, Gerhard J

    2016-01-01

    Comparative studies on the distribution of archaeal versus bacterial communities associated with the surface mucus layer of corals have rarely taken place. It has therefore remained enigmatic whether mucus-associated archaeal and bacterial communities exhibit a similar specificity towards coral hosts and whether they vary in the same fashion over spatial gradients and between reef locations. We used microbial community profiling (terminal-restriction fragment length polymorphism, T-RFLP) and clone library sequencing of the 16S rRNA gene to compare the diversity and community structure of dominant archaeal and bacterial communities associating with the mucus of three common reef-building coral species (Porites astreoides, Siderastrea siderea and Orbicella annularis) over different spatial scales on a Caribbean fringing reef. Sampling locations included three reef sites, three reef patches within each site and two depths. Reference sediment samples and ambient water were also taken for each of the 18 sampling locations resulting in a total of 239 samples. While only 41% of the bacterial operational taxonomic units (OTUs) characterized by T-RFLP were shared between mucus and the ambient water or sediment, for archaeal OTUs this percentage was 2-fold higher (78%). About half of the mucus-associated OTUs (44% and 58% of bacterial and archaeal OTUs, respectively) were shared between the three coral species. Our multivariate statistical analysis (ANOSIM, PERMANOVA and CCA) showed that while the bacterial community composition was determined by habitat (mucus, sediment or seawater), host coral species, location and spatial distance, the archaeal community composition was solely determined by the habitat. This study highlights that mucus-associated archaeal and bacterial communities differ in their degree of community turnover over reefs and in their host-specificity. PMID:26788724

  10. Complete nucleotide sequences of bla(CTX-M)-harboring IncF plasmids from community-associated Escherichia coli strains in the United States.

    PubMed

    Li, Jun-Jie; Spychala, Caressa N; Hu, Fupin; Sheng, Ji-Fang; Doi, Yohei

    2015-01-01

    Community-associated infections due to Escherichia coli producing CTX-M-type extended-spectrum β-lactamases are increasingly recognized in the United States. The bla(CTX-M) genes are frequently carried on IncF group plasmids. In this study, bla(CTX-M-15)-harboring plasmids pCA14 (sequence type 131 [ST131]) and pCA28 (ST44) and bla(CTX-M-14)-harboring plasmid pCA08 (ST131) were sequenced and characterized. The three plasmids were closely related to other IncFII plasmids from continents outside the United States in the conserved backbone region and multiresistance regions (MRRs). Each of the bla(CTX-M-15)-carrying plasmids pCA14 and pCA28 belonged to F31:A4:B1 (FAB [FII, FIA, FIB] formula) and showed a high level of similarity (92% coverage of pCA14 and 99% to 100% nucleotide identity), suggesting a possible common origin. The blaC(TX-M-14)-carrying plasmid pCA08 belonged to F2:A2:B20 and was highly similar to pKF3-140 from China (88% coverage of pCA08 and 99% to 100% nucleotide identity). All three plasmids carried multiple antimicrobial resistance genes and modules associated with virulence and biochemical pathways, which likely confer selective advantages for their host strains. The bla(CTX-M)-carrying IncFII-IA-IB plasmids implicated in community-associated infections in the United States shared key structural features with those identified from other continents, underscoring the global nature of this plasmid epidemic.

  11. Archaeal and Bacterial Communities Associated with the Surface Mucus of Caribbean Corals Differ in Their Degree of Host Specificity and Community Turnover Over Reefs

    PubMed Central

    Frade, Pedro R.; Roll, Katharina; Bergauer, Kristin; Herndl, Gerhard J.

    2016-01-01

    Comparative studies on the distribution of archaeal versus bacterial communities associated with the surface mucus layer of corals have rarely taken place. It has therefore remained enigmatic whether mucus-associated archaeal and bacterial communities exhibit a similar specificity towards coral hosts and whether they vary in the same fashion over spatial gradients and between reef locations. We used microbial community profiling (terminal-restriction fragment length polymorphism, T-RFLP) and clone library sequencing of the 16S rRNA gene to compare the diversity and community structure of dominant archaeal and bacterial communities associating with the mucus of three common reef-building coral species (Porites astreoides, Siderastrea siderea and Orbicella annularis) over different spatial scales on a Caribbean fringing reef. Sampling locations included three reef sites, three reef patches within each site and two depths. Reference sediment samples and ambient water were also taken for each of the 18 sampling locations resulting in a total of 239 samples. While only 41% of the bacterial operational taxonomic units (OTUs) characterized by T-RFLP were shared between mucus and the ambient water or sediment, for archaeal OTUs this percentage was 2-fold higher (78%). About half of the mucus-associated OTUs (44% and 58% of bacterial and archaeal OTUs, respectively) were shared between the three coral species. Our multivariate statistical analysis (ANOSIM, PERMANOVA and CCA) showed that while the bacterial community composition was determined by habitat (mucus, sediment or seawater), host coral species, location and spatial distance, the archaeal community composition was solely determined by the habitat. This study highlights that mucus-associated archaeal and bacterial communities differ in their degree of community turnover over reefs and in their host-specificity. PMID:26788724

  12. Archaeal and Bacterial Communities Associated with the Surface Mucus of Caribbean Corals Differ in Their Degree of Host Specificity and Community Turnover Over Reefs.

    PubMed

    Frade, Pedro R; Roll, Katharina; Bergauer, Kristin; Herndl, Gerhard J

    2016-01-01

    Comparative studies on the distribution of archaeal versus bacterial communities associated with the surface mucus layer of corals have rarely taken place. It has therefore remained enigmatic whether mucus-associated archaeal and bacterial communities exhibit a similar specificity towards coral hosts and whether they vary in the same fashion over spatial gradients and between reef locations. We used microbial community profiling (terminal-restriction fragment length polymorphism, T-RFLP) and clone library sequencing of the 16S rRNA gene to compare the diversity and community structure of dominant archaeal and bacterial communities associating with the mucus of three common reef-building coral species (Porites astreoides, Siderastrea siderea and Orbicella annularis) over different spatial scales on a Caribbean fringing reef. Sampling locations included three reef sites, three reef patches within each site and two depths. Reference sediment samples and ambient water were also taken for each of the 18 sampling locations resulting in a total of 239 samples. While only 41% of the bacterial operational taxonomic units (OTUs) characterized by T-RFLP were shared between mucus and the ambient water or sediment, for archaeal OTUs this percentage was 2-fold higher (78%). About half of the mucus-associated OTUs (44% and 58% of bacterial and archaeal OTUs, respectively) were shared between the three coral species. Our multivariate statistical analysis (ANOSIM, PERMANOVA and CCA) showed that while the bacterial community composition was determined by habitat (mucus, sediment or seawater), host coral species, location and spatial distance, the archaeal community composition was solely determined by the habitat. This study highlights that mucus-associated archaeal and bacterial communities differ in their degree of community turnover over reefs and in their host-specificity.

  13. Composition and structure of the Chironomidae (Insecta: Diptera) community associated with bryophytes in a first-order stream in the Atlantic forest, Brazil.

    PubMed

    Rosa, B F J V; Dias-Silva, M V D; Alves, R G

    2013-02-01

    This study describes the structure of the Chironomidae community associated with bryophytes in a first-order stream located in a biological reserve of the Atlantic Forest, during two seasons. Samples of bryophytes adhered to rocks along a 100-m stretch of the stream were removed with a metal blade, and 200-mL pots were filled with the samples. The numerical density (individuals per gram of dry weight), Shannon's diversity index, Pielou's evenness index, the dominance index (DI), and estimated richness were calculated for each collection period (dry and rainy). Linear regression analysis was employed to test the existence of a correlation between rainfall and the individual's density and richness. The high numerical density and richness of Chironomidae taxa observed are probably related to the peculiar conditions of the bryophyte habitat. The retention of larvae during periods of higher rainfall contributed to the high density and richness of Chironomidae larvae. The rarefaction analysis showed higher richness in the rainy season related to the greater retention of food particles. The data from this study show that bryophytes provide stable habitats for the colonization by and refuge of Chironomidae larvae, mainly under conductions of faster water flow and higher precipitation. PMID:23949708

  14. [Community associated-methicillin-resistant Staphylococcus aureus (SAMR-AC): comunication of the first four pediatric cases in the Roberto del Rio Children's Hospital].

    PubMed

    Acuña, Mirta; Benadof, Dona; Jadue, Carla; Hormazábal, Juan C; Alarcón, Pedro; Contreras, Julio; Torres, Ramón; Mülchi, Cristóbal; Aguayo, Carolina; Fernández, Jorge; Araya, Pamela

    2015-06-01

    Staphylococcus aureus is a known pathogen in pediatric patients that produces skin infections, cutaneous abscess, cellulitis and osteoarticular infections. Most of these infections are produced by a meticilin susceptible strain. The community associated methicillin resistant Staphylococcus aureus was published for the first time in 1993, ever since then is has been recognized as a cosmopolite pathogen. The first report in Latin America was published in 2003, and in Chile in 2008 from adult patients that have reported traveling to other countries. The following series describes four pediatric cases, all school-aged children, diagnosed since 2012 with clinical followups and molecular studies. Two cases presented as osteomyelitis of the lower extremity; and one presented as arm cellulitis. These three cases had Panton Valentine leukocidine (PV-L) negative strains from the clone complex 8. The last case presented a renal abscess, the strain was PV-L positive from the clone complex 30. This case series constitutes the first pediatric case report in Chile. PMID:26230445

  15. The role of primary care prescribers in the diagnosis and management of community-associated methicillin-resistant Staphylococcus aureus skin and soft tissue infections.

    PubMed

    Lawrence, Kenneth R; Golik, Monica V; Davidson, Lisa

    2009-01-01

    Nosocomial infections caused by methicillin-resistant Staphylococcus aureus were first reported in the United States in the early 1960s. Beginning in the 1990s, healthy individuals from the community with no risk factors for resistant bacteria began presenting with methicillin-resistant Staphylococcus aureus infections, acquiring the name "community-associated methicillin-resistant Staphylococcus aureus" (CA-MRSA). CA-MRSA has a tendency to affect the skin and skin structures, generally in the form of abscesses and furuncles, carbuncles, and cellulitis. Cases of invasive infections including bacteremia, endocarditis, and necrotizing pneumonia have also been reported. A patient complaint of a "spider bite" is frequently associated with CA-MRSA. CA-MRSA and the traditional health care-associated methicillin-resistant Staphylococcus aureus are distinguished by their genetic composition, virulence factors, and susceptibility patterns to non-beta-lactam antibiotics. Appropriate management of CA-MRSA skin and skin structure infections includes incision and drainage of infected tissue and appropriate antimicrobial therapy. It has been suggested that when prevalence of CA-MRSA within a community eclipses 10%-15%, empiric use of non-beta-lactam antibiotics with in vitro activity against CA-MRSA be initiated when treating skin and skin structure infections. CA-MRSA retains susceptibility to a range of older antibiotics available in oral formulations such as minocycline, doxycycline, sulfamethoxazole-trimethoprim, moxifloxacin, levofloxacin, and clindamycin. Local susceptibility patterns and individual patient factors should guide the selection of antibiotics. PMID:19617720

  16. The role of primary care prescribers in the diagnosis and management of community-associated methicillin-resistant Staphylococcus aureus skin and soft tissue infections.

    PubMed

    Lawrence, Kenneth R; Golik, Monica V; Davidson, Lisa

    2009-01-01

    Nosocomial infections caused by methicillin-resistant Staphylococcus aureus were first reported in the United States in the early 1960s. Beginning in the 1990s, healthy individuals from the community with no risk factors for resistant bacteria began presenting with methicillin-resistant Staphylococcus aureus infections, acquiring the name "community-associated methicillin-resistant Staphylococcus aureus" (CA-MRSA). CA-MRSA has a tendency to affect the skin and skin structures, generally in the form of abscesses and furuncles, carbuncles, and cellulitis. Cases of invasive infections including bacteremia, endocarditis, and necrotizing pneumonia have also been reported. A patient complaint of a "spider bite" is frequently associated with CA-MRSA. CA-MRSA and the traditional health care-associated methicillin-resistant Staphylococcus aureus are distinguished by their genetic composition, virulence factors, and susceptibility patterns to non-beta-lactam antibiotics. Appropriate management of CA-MRSA skin and skin structure infections includes incision and drainage of infected tissue and appropriate antimicrobial therapy. It has been suggested that when prevalence of CA-MRSA within a community eclipses 10%-15%, empiric use of non-beta-lactam antibiotics with in vitro activity against CA-MRSA be initiated when treating skin and skin structure infections. CA-MRSA retains susceptibility to a range of older antibiotics available in oral formulations such as minocycline, doxycycline, sulfamethoxazole-trimethoprim, moxifloxacin, levofloxacin, and clindamycin. Local susceptibility patterns and individual patient factors should guide the selection of antibiotics.

  17. Characterization of bacterial communities associated with Brassica napus L. growing on a Zn-contaminated soil and their effects on root growth.

    PubMed

    Montalbán, Blanca; Croes, Sarah; Weyens, Nele; Lobo, M Carmen; Pérez-Sanz, Araceli; Vangronsveld, Jaco

    2016-10-01

    The interaction between plant growth-promoting bacteria (PGPB) and plants can enhance biomass production and metal tolerance of the host plants. This work aimed at isolating and characterizing the cultivable bacterial community associated with Brassica napus growing on a Zn-contaminated site, for selecting cultivable PGPB that might enhance biomass production and metal tolerance of energy crops. The effects of some of these bacterial strains on root growth of B. napus exposed to increasing Zn and Cd concentrations were assessed. A total of 426 morphologically different bacterial strains were isolated from the soil, the rhizosphere, and the roots and stems of B. napus. The diversity of the isolated bacterial populations was similar in rhizosphere and roots, but lower in soil and stem compartments. Burkoholderia, Alcaligenes, Agrococcus, Polaromonas, Stenotrophomonas, Serratia, Microbacterium, and Caulobacter were found as root endophytes exclusively. The inoculation of seeds with Pseudomonas sp. strains 228 and 256, and Serratia sp. strain 246 facilitated the root development of B. napus at 1,000 µM Zn. Arthrobacter sp. strain 222, Serratia sp. strain 246, and Pseudomonas sp. 228 and 262 increased the root length at 300 µM Cd. PMID:27159736

  18. Response of the bacterial community associated with a cosmopolitan marine diatom to crude oil shows a preference for the biodegradation of aromatic hydrocarbons.

    PubMed

    Mishamandani, Sara; Gutierrez, Tony; Berry, David; Aitken, Michael D

    2016-06-01

    Emerging evidence shows that hydrocarbonoclastic bacteria (HCB) may be commonly found associated with phytoplankton in the ocean, but the ecology of these bacteria and how they respond to crude oil remains poorly understood. Here, we used a natural diatom-bacterial assemblage to investigate the diversity and response of HCB associated with a cosmopolitan marine diatom, Skeletonema costatum, to crude oil. Pyrosequencing analysis and qPCR revealed a dramatic transition in the diatom-associated bacterial community, defined initially by a short-lived bloom of Methylophaga (putative oil degraders) that was subsequently succeeded by distinct groups of HCB (Marinobacter, Polycyclovorans, Arenibacter, Parvibaculum, Roseobacter clade), including putative novel phyla, as well as other groups with previously unqualified oil-degrading potential. Interestingly, these oil-enriched organisms contributed to the apparent and exclusive biodegradation of substituted and non-substituted polycyclic aromatic hydrocarbons (PAHs), thereby suggesting that the HCB community associated with the diatom is tuned to specializing in the degradation of PAHs. Furthermore, the formation of marine oil snow (MOS) in oil-amended incubations was consistent with its formation during the Deepwater Horizon oil spill. This work highlights the phycosphere of phytoplankton as an underexplored biotope in the ocean where HCB may contribute importantly to the biodegradation of hydrocarbon contaminants in marine surface waters. PMID:26184578

  19. Composition and structure of the Chironomidae (Insecta: Diptera) community associated with bryophytes in a first-order stream in the Atlantic forest, Brazil.

    PubMed

    Rosa, B F J V; Dias-Silva, M V D; Alves, R G

    2013-02-01

    This study describes the structure of the Chironomidae community associated with bryophytes in a first-order stream located in a biological reserve of the Atlantic Forest, during two seasons. Samples of bryophytes adhered to rocks along a 100-m stretch of the stream were removed with a metal blade, and 200-mL pots were filled with the samples. The numerical density (individuals per gram of dry weight), Shannon's diversity index, Pielou's evenness index, the dominance index (DI), and estimated richness were calculated for each collection period (dry and rainy). Linear regression analysis was employed to test the existence of a correlation between rainfall and the individual's density and richness. The high numerical density and richness of Chironomidae taxa observed are probably related to the peculiar conditions of the bryophyte habitat. The retention of larvae during periods of higher rainfall contributed to the high density and richness of Chironomidae larvae. The rarefaction analysis showed higher richness in the rainy season related to the greater retention of food particles. The data from this study show that bryophytes provide stable habitats for the colonization by and refuge of Chironomidae larvae, mainly under conductions of faster water flow and higher precipitation.

  20. Characterization of the Bacterial Community Associated with Larvae and Adults of Anoplophora chinensis Collected in Italy by Culture and Culture-Independent Methods

    PubMed Central

    Rizzi, Aurora; Crotti, Elena; Lupi, Daniela; Daffonchio, Daniele

    2013-01-01

    The wood-boring beetle Anoplophora chinensis Forster, native to China, has recently spread to North America and Europe causing serious damage to ornamental and forest trees. The gut microbial community associated with these xylophagous beetles is of interest for potential biotechnological applications in lignocellulose degradation and development of pest-control measures. In this study the gut bacterial community of larvae and adults of A. chinensis, collected from different host trees in North Italy, was investigated by both culture and culture-independent methods. Larvae and adults harboured a moderately diverse bacterial community, dominated by Proteobacteria, Actinobacteria, and Firmicutes. The gammaproteobacterial family Enterobacteriaceae (genera Gibbsiella, Enterobacter, Raoultella, and Klebsiella) was the best represented. The abundance of such bacteria in the insect gut is likely due to the various metabolic abilities of Enterobacteriaceae, including fermentation of carbohydrates derived from lignocellulose degradation and contribution to nitrogen intake by nitrogen-fixing activity. In addition, bacteria previously shown to have some lignocellulose-degrading activity were detected at a relatively low level in the gut. These bacteria possibly act synergistically with endogenous and fungal enzymes in lignocellulose breakdown. The detection of actinobacterial symbionts could be explained by a possible role in the detoxification of secondary plant metabolites and/or protection against pathogens. PMID:24069601

  1. Characterization of bacterial communities associated with Brassica napus L. growing on a Zn-contaminated soil and their effects on root growth.

    PubMed

    Montalbán, Blanca; Croes, Sarah; Weyens, Nele; Lobo, M Carmen; Pérez-Sanz, Araceli; Vangronsveld, Jaco

    2016-10-01

    The interaction between plant growth-promoting bacteria (PGPB) and plants can enhance biomass production and metal tolerance of the host plants. This work aimed at isolating and characterizing the cultivable bacterial community associated with Brassica napus growing on a Zn-contaminated site, for selecting cultivable PGPB that might enhance biomass production and metal tolerance of energy crops. The effects of some of these bacterial strains on root growth of B. napus exposed to increasing Zn and Cd concentrations were assessed. A total of 426 morphologically different bacterial strains were isolated from the soil, the rhizosphere, and the roots and stems of B. napus. The diversity of the isolated bacterial populations was similar in rhizosphere and roots, but lower in soil and stem compartments. Burkoholderia, Alcaligenes, Agrococcus, Polaromonas, Stenotrophomonas, Serratia, Microbacterium, and Caulobacter were found as root endophytes exclusively. The inoculation of seeds with Pseudomonas sp. strains 228 and 256, and Serratia sp. strain 246 facilitated the root development of B. napus at 1,000 µM Zn. Arthrobacter sp. strain 222, Serratia sp. strain 246, and Pseudomonas sp. 228 and 262 increased the root length at 300 µM Cd.

  2. Comparison of microbial communities associated with phase-separation-induced hydrothermal fluids at the Yonaguni Knoll IV hydrothermal field, the Southern Okinawa Trough.

    PubMed

    Nunoura, Takuro; Takai, Ken

    2009-03-01

    Microbial communities associated with a variety of hydrothermal emissions at the Yonaguni Knoll IV hydrothermal field, the southernmost Okinawa Trough, were analyzed by culture-dependent and -independent techniques. In this hydrothermal field, dozens of vent sites hosting physically and chemically distinct hydrothermal fluids were observed. Variability in the gas content and formation in the hydrothermal fluids was observed and could be controlled by the potential subseafloor phase-separation and -partition processes. The hydrogen concentration in the hydrothermal fluids was also variable (0.8-3.6 mmol kg(-1)) among the chimney sites, but was unusually high as compared with those in other Okinawa Trough hydrothermal fields. Despite the physical and chemical variabilities of the hydrothermal fluids, the microbial communities were relatively similar among the habitats. Based on both culture-dependent and -independent analyses of the microbial community structures, members of Thermococcales, Methanococcales and Desulfurococcales likely represent the predominant archaeal components, while members of Nautiliaceae and Thioreductoraceae are considered to dominate the bacterial population. Most of the abundant microbial components appear to be chemolithotrophs sustained by hydrogen oxidation. The relatively consistent microbial communities found in this study could have been because of the sufficient input of hydrogen from the hydrothermal fluids rather than other chemical properties.

  3. Characterization of Microbial Communities Associated With Deep-Sea Hydrothermal Vent Animals of the East Pacific Rise and the Galápagos Rift

    NASA Astrophysics Data System (ADS)

    Ward, N.; Page, S.; Heidelberg, J.; Eisen, J. A.; Fraser, C. M.

    2002-12-01

    The composition of microbial communities associated with deep-sea hydrothermal vent animals is of interest because of the key role of bacterial symbionts in driving the chemosynthetic food chain of the vent system, and also because bacterial biofilms attached to animal exterior surfaces may play a part in settlement of larval forms. Sequence analysis of 16S ribosomal RNA (rRNA) genes from such communities provides a snapshot of community structure, as this gene is present in all Bacteria and Archaea, and a useful phylogenetic marker for both cultivated microbial species, and uncultivated species such as many of those found in the deep-sea environment. Specimens of giant tube worms (Riftia pachyptila), mussels (Bathymodiolus thermophilus), and clams (Calyptogena magnifica) were collected during the 2002 R/V Atlantis research cruises to the East Pacific Rise (9N) and Galápagos Rift. Microbial biofilms attached to the exterior surfaces of individual animals were sampled, as were tissues known to harbor chemosynthetic bacterial endosymbionts. Genomic DNA was extracted from the samples using a commercially available kit, and 16S rRNA genes amplified from the mixed bacterial communities using the polymerase chain reaction (PCR) and oligonucleotide primers targeting conserved terminal regions of the 16S rRNA gene. The PCR products obtained were cloned into a plasmid vector and the recombinant plasmids transformed into cells of Escherichia coli. Individual cloned 16S rRNA genes were sequenced at the 5' end of the gene (the most phylogenetically informative region in most taxa) and the sequence data compared to publicly available gene sequence databases, to allow a preliminary assignment of clones to taxonomic groups within the Bacteria and Archaea, and to determine the overall composition and phylogenetic diversity of the animal-associated microbial communities. Analysis of Riftia pachyptila exterior biofilm samples revealed the presence of members of the delta and

  4. Adaptive change inferred from genomic population analysis of the ST93 epidemic clone of community-associated methicillin-resistant Staphylococcus aureus.

    PubMed

    Stinear, Timothy P; Holt, Kathryn E; Chua, Kyra; Stepnell, Justin; Tuck, Kellie L; Coombs, Geoffrey; Harrison, Paul Francis; Seemann, Torsten; Howden, Benjamin P

    2014-02-01

    Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) has emerged as a major public health problem around the world. In Australia, ST93-IV[2B] is the dominant CA-MRSA clone and displays significantly greater virulence than other S. aureus. Here, we have examined the evolution of ST93 via genomic analysis of 12 MSSA and 44 MRSA ST93 isolates, collected from around Australia over a 17-year period. Comparative analysis revealed a core genome of 2.6 Mb, sharing greater than 99.7% nucleotide identity. The accessory genome was 0.45 Mb and comprised additional mobile DNA elements, harboring resistance to erythromycin, trimethoprim, and tetracycline. Phylogenetic inference revealed a molecular clock and suggested that a single clone of methicillin susceptible, Panton-Valentine leukocidin (PVL) positive, ST93 S. aureus likely spread from North Western Australia in the early 1970s, acquiring methicillin resistance at least twice in the mid 1990s. We also explored associations between genotype and important MRSA phenotypes including oxacillin MIC and production of exotoxins (α-hemolysin [Hla], δ-hemolysin [Hld], PSMα3, and PVL). High-level expression of Hla is a signature feature of ST93 and reduced expression in eight isolates was readily explained by mutations in the agr locus. However, subtle but significant decreases in Hld were also noted over time that coincided with decreasing oxacillin resistance and were independent of agr mutations. The evolution of ST93 S. aureus is thus associated with a reduction in both exotoxin expression and oxacillin MIC, suggesting MRSA ST93 isolates are under pressure for adaptive change. PMID:24482534

  5. Adaptive Change Inferred from Genomic Population Analysis of the ST93 Epidemic Clone of Community-Associated Methicillin-Resistant Staphylococcus aureus

    PubMed Central

    Stinear, Timothy P.; Holt, Kathryn E.; Chua, Kyra; Stepnell, Justin; Tuck, Kellie L.; Coombs, Geoffrey; Harrison, Paul Francis; Seemann, Torsten; Howden, Benjamin P.

    2014-01-01

    Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) has emerged as a major public health problem around the world. In Australia, ST93-IV[2B] is the dominant CA-MRSA clone and displays significantly greater virulence than other S. aureus. Here, we have examined the evolution of ST93 via genomic analysis of 12 MSSA and 44 MRSA ST93 isolates, collected from around Australia over a 17-year period. Comparative analysis revealed a core genome of 2.6 Mb, sharing greater than 99.7% nucleotide identity. The accessory genome was 0.45 Mb and comprised additional mobile DNA elements, harboring resistance to erythromycin, trimethoprim, and tetracycline. Phylogenetic inference revealed a molecular clock and suggested that a single clone of methicillin susceptible, Panton-Valentine leukocidin (PVL) positive, ST93 S. aureus likely spread from North Western Australia in the early 1970s, acquiring methicillin resistance at least twice in the mid 1990s. We also explored associations between genotype and important MRSA phenotypes including oxacillin MIC and production of exotoxins (α-hemolysin [Hla], δ-hemolysin [Hld], PSMα3, and PVL). High-level expression of Hla is a signature feature of ST93 and reduced expression in eight isolates was readily explained by mutations in the agr locus. However, subtle but significant decreases in Hld were also noted over time that coincided with decreasing oxacillin resistance and were independent of agr mutations. The evolution of ST93 S. aureus is thus associated with a reduction in both exotoxin expression and oxacillin MIC, suggesting MRSA ST93 isolates are under pressure for adaptive change. PMID:24482534

  6. Microbiological and molecular epidemiological analyses of community-associated methicillin-resistant Staphylococcus aureus at a tertiary care hospital in Japan.

    PubMed

    Inomata, Shinya; Yano, Hisakazu; Tokuda, Koichi; Kanamori, Hajime; Endo, Shiro; Ishizawa, Chiyuki; Ogawa, Miho; Ichimura, Sadahiro; Shimojima, Masahiro; Kakuta, Risako; Ozawa, Daiki; Aoyagi, Tetsuji; Gu, Yoshiaki; Hatta, Masumitsu; Oshima, Kengo; Nakashima, Kazutoshi; Kaku, Mitsuo

    2015-10-01

    Molecular characterization of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) is generally conducted referred to staphylococcal cassette chromosome mec (SCCmec) type IV or V. CA-MRSA is now a cause of concern since such strains have been isolated not only from individuals in a community but also from patients in healthcare settings. The aim of this study was to analyze microbiological and molecular epidemiological features of CA-MRSA strains at a Japanese tertiary care hospital using PCR based-open reading frame typing (POT). This technique allows for molecular classification into CA-MRSA (POT-CA) and hospital-associated (HA-) MRSA (POT-HA) with clonal discrimination. Clinical MRSA isolates obtained from consecutive patients between October 1, 2012 and September 30, 2013 at the hospital were analyzed in combination with the clinical definition for CA-MRSA by the Centers for Disease Control and Prevention and POT. Of 219 isolates (76 clonal groups), 64 (29.3%) were clinical-HA/POT-CA isolates (22 clonal groups). Some clones of them accumulated in this hospital and might be involved in nosocomial transmission. Virulent factors of the isolates were analyzed, and only one (1.6%) Panton-Valentine leukocidin gene positive isolate but no arginine catabolic mobile element genes positive isolate were found in clinical-HA/POT-CA. Additionally, clinical-HA/POT-CA isolates showed higher antimicrobial susceptibility than clinical-HA/POT-HA, especially to minocycline, doxycycline, and amikacin. The most frequent genotype of molecular CA-MRSA was multi-locus sequence type 5-SCCmecIV, previously not detected in Japan. Although CA-MRSA at this hospital showed low virulence and higher antimicrobial susceptibility, the risk of nosocomial infection from them should be recognized, requiring stricter infection control measures.

  7. Prospective Multicenter Study of Community-Associated Skin and Skin Structure Infections due to Methicillin-Resistant Staphylococcus aureus in Buenos Aires, Argentina

    PubMed Central

    López Furst, María José; de Vedia, Lautaro; Fernández, Silvina; Gardella, Noella; Ganaha, María Cristina; Prieto, Sergio; Carbone, Edith; Lista, Nicolás; Rotryng, Flavio; Morera, Graciana I.; Mollerach, Marta; Stryjewski, Martín E.

    2013-01-01

    Background Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) is now the most common cause of skin and skin structure infections (SSSI) in several world regions. In Argentina prospective, multicenter clinical studies have only been conducted in pediatric populations. Objective Primary: describe the prevalence, clinical and demographic characteristics of adult patients with community acquired SSSI due to MRSA; secondary: molecular evaluation of CA-MRSA strains. Patients with MRSA were compared to those without MRSA. Materials and Methods Prospective, observational, multicenter, epidemiologic study, with molecular analysis, conducted at 19 sites in Argentina (18 in Buenos Aires) between March 2010 and October 2011. Patients were included if they were ≥14 years, were diagnosed with SSSI, a culture was obtained, and there had no significant healthcare contact identified. A logistic regression model was used to identify factors associated with CA-MRSA. Pulse field types, SCCmec, and PVL status were also determined. Results A total of 311 patients were included. CA-MRSA was isolated in 70% (218/311) of patients. Clinical variables independently associated with CA-MRSA were: presence of purulent lesion (OR 3.29; 95%CI 1.67, 6.49) and age <50 years (OR 2.39; 95%CI 1.22, 4.70). The vast majority of CA-MRSA strains causing SSSI carried PVL genes (95%) and were SCCmec type IV. The sequence type CA-MRSA ST30 spa t019 was the predominant clone. Conclusions CA-MRSA is now the most common cause of SSSI in our adult patients without healthcare contact. ST30, SCCmec IV, PVL+, spa t019 is the predominant clone in Buenos Aires, Argentina. PMID:24324543

  8. Staphylococcus aureus and Community-Associated Methicillin-Resistant Staphylococcus aureus (CA-MRSA) in and Around Therapeutic Whirlpools in College Athletic Training Rooms

    PubMed Central

    Kahanov, Leamor; Kim, Young Kyun; Eberman, Lindsey; Dannelly, Kathleen; Kaur, Haninder; Ramalinga, A.

    2015-01-01

    Context: Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) has become a leading cause of skin and soft tissue infection in the nonhospitalized community. Care of the athletes in athletic training rooms is specifically designed with equipment tailored to the health care needs of the athletes, yet recent studies indicate that CA-MRSA is still prevalent in athletic facilities and that cleaning methods may not be optimal. Objective: To investigate the prevalence of Staphylococcus aureus and CA-MRSA in and around whirlpools in the athletic training room. Design: Cross-sectional study. Setting: National Collegiate Athletic Association Division I university. Patients or Other Participants: Student-athletes (n = 109) consisting of 46 men (42%) and 63 women (58%) representing 6 sports. Main Outcome Measure(s): Presence of MRSA and Staphylococcus aureus in and around the whirlpool structures relative to sport and number of athletes using the whirlpools. Results: We identified Staphylococcus aureus in 22% (n = 52/240) of the samples and MRSA in 0.8% (n = 2/240). A statistically significant difference existed between the number of athletes using the whirlpool and the presence of Staphylococcus aureus in and around the whirlpools (F2,238 = 2.445, P = .007). However, Staphylococcus aureus was identified regardless of whether multiple athletes used a whirlpool or no athletes used a whirlpool. We did not identify a relationship between the number of athletes who used a whirlpool and Staphylococcus aureus or MRSA density (P = .134). Conclusions: Staphylococcus aureus and MRSA were identified in and around the whirlpools. Transmission of the bacteria can be reduced by following the cleaning and disinfecting protocols recommended by the Centers for Disease Control and Prevention. Athletic trainers should use disinfectants registered by the Environmental Protection Agency to sanitize all whirlpools between uses. PMID:25710853

  9. Infections Caused By Community-Associated Methicillin-Resistant Staphylococcus Aureus European Clone (ST80) In Slovenia Between 2006 And 2013

    PubMed Central

    Jurca, Tomaž; Harlander, Tatjana; Košir, Marta; Zajc, Urška; Golob, Majda; Zdovc, Irena; Košnik1, Irena Grmek

    2016-01-01

    Abstract Introduction According to the existing literature, a heterogeneous sequence type (ST) or clones of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) circulate in Europe. In Europe, the European clone that belongs to sequence type ST80 is predominant. Methods The aim of the study was to investigate the phenotypic and genotypic characteristics and epidemiological data of CA-MRSA ST80 and its occurrence in Slovenia. We retrospectively analyzed those CA-MRSA isolates that were isolated during microbiological procedures in microbiological laboratories between 2006 and 2013. Only CA-MRSA isolates from the national collection of CA-MRSA strains that belonged to ST80 (European clone) were analyzed. We determined the Pantone-Valentine leukocidin (PVL), mec A genes, exfoliative toxin genes and type of staphylococcal cassette chromosome (SCCmec) by polymerase chain reaction (PCR). We determined also spa type and sequence type. Results ST80 was confirmed in only 2 (0.5%) out of 385 CA-MRSA isolates, collected in a national collection of CAMRSA. Both isolates were positive for the PVL genes, mec A gene, exfoliative toxin type D gene and SCCmec IV. One CA-MRSA isolate was confirmed in a wound swab taken from a 47-year-old male, and the second was isolated from blood cultures of a 69-year-old female. No epidemiological connections between them were found. Conclusions In Slovenia CA-MRSA infections caused by ST80 are rare. In the future, it is necessary that a surveillance study of CA-MRSA at the national level continues and CA-MRSA be considered as a public health threat. PMID:27284382

  10. Adaptive change inferred from genomic population analysis of the ST93 epidemic clone of community-associated methicillin-resistant Staphylococcus aureus.

    PubMed

    Stinear, Timothy P; Holt, Kathryn E; Chua, Kyra; Stepnell, Justin; Tuck, Kellie L; Coombs, Geoffrey; Harrison, Paul Francis; Seemann, Torsten; Howden, Benjamin P

    2014-02-01

    Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) has emerged as a major public health problem around the world. In Australia, ST93-IV[2B] is the dominant CA-MRSA clone and displays significantly greater virulence than other S. aureus. Here, we have examined the evolution of ST93 via genomic analysis of 12 MSSA and 44 MRSA ST93 isolates, collected from around Australia over a 17-year period. Comparative analysis revealed a core genome of 2.6 Mb, sharing greater than 99.7% nucleotide identity. The accessory genome was 0.45 Mb and comprised additional mobile DNA elements, harboring resistance to erythromycin, trimethoprim, and tetracycline. Phylogenetic inference revealed a molecular clock and suggested that a single clone of methicillin susceptible, Panton-Valentine leukocidin (PVL) positive, ST93 S. aureus likely spread from North Western Australia in the early 1970s, acquiring methicillin resistance at least twice in the mid 1990s. We also explored associations between genotype and important MRSA phenotypes including oxacillin MIC and production of exotoxins (α-hemolysin [Hla], δ-hemolysin [Hld], PSMα3, and PVL). High-level expression of Hla is a signature feature of ST93 and reduced expression in eight isolates was readily explained by mutations in the agr locus. However, subtle but significant decreases in Hld were also noted over time that coincided with decreasing oxacillin resistance and were independent of agr mutations. The evolution of ST93 S. aureus is thus associated with a reduction in both exotoxin expression and oxacillin MIC, suggesting MRSA ST93 isolates are under pressure for adaptive change.

  11. Targeted Intranasal Mupirocin To Prevent Colonization and Infection by Community-Associated Methicillin-Resistant Staphylococcus aureus Strains in Soldiers: a Cluster Randomized Controlled Trial▿

    PubMed Central

    Ellis, Michael W.; Griffith, Matthew E.; Dooley, David P.; McLean, Joseph C.; Jorgensen, James H.; Patterson, Jan E.; Davis, Kepler A.; Hawley, Joshua S.; Regules, Jason A.; Rivard, Robert G.; Gray, Paula J.; Ceremuga, Julia M.; DeJoseph, Mary A.; Hospenthal, Duane R.

    2007-01-01

    Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) is an emerging pathogen that primarily manifests as uncomplicated skin and soft tissue infections. We conducted a cluster randomized, double-blind, placebo-controlled trial to determine whether targeted intranasal mupirocin therapy in CA-MRSA-colonized soldiers could prevent infection in the treated individual and prevent new colonization and infection within their study groups. We screened 3,447 soldiers comprising 14 training classes for CA-MRSA colonization from January to December 2005. Each training class was randomized to either the mupirocin or placebo study group, and the participants identified as CA-MRSA colonized were treated with either mupirocin or placebo. All participants underwent repeat screening after 8 to 10 weeks and were monitored for 16 weeks for development of infection. Of 3,447 participants screened, 134 (3.9%) were initially colonized with CA-MRSA. Five of 65 (7.7%; 95% confidence interval [95% CI], 4.0% to 11.4%) placebo-treated participants and 7 of 66 (10.6%; 95% CI, 7.9% to 13.3%) mupirocin-treated participants developed infections; the difference in the infection rate of the placebo- and mupirocin-treated groups was −2.9% (95% CI, −7.5% to 1.7%). Of those not initially colonized with CA-MRSA, 63 of 1,459 (4.3%; 95% CI, 2.7% to 5.9%) of the placebo group and 56 of 1,607 (3.5%; 95% CI, 2.6% to 5.2%) of the mupirocin group developed infections; the difference in the infection rate of the placebo and mupirocin groups was 0.8% (95% CI, −1.0% to 2.7%). Of 3,447 participants, 3,066 (89%) were available for the second sampling and completed follow-up. New CA-MRSA colonization occurred in 24 of 1,459 (1.6%; 95% CI, 0.05% to 2.8%) of the placebo group participants and 23 of 1,607 (1.4%; 95% CI, 0.05% to 2.3%) of the mupirocin group participants; the difference in the infection rate of the placebo and mupirocin groups was 0.2% (95% CI, −1.3% to 1.7%). Despite CA

  12. Comparative Molecular Characteristics of Community-Associated and Healthcare-Associated Methicillin-Resistant Staphylococcus aureus Isolates From Adult Patients in Northern Taiwan.

    PubMed

    Chen, Yi-Jen; Liu, Kuan-Liang; Chen, Chih-Jung; Huang, Yhu-Chering

    2015-12-01

    Methicillin-resistant Staphylococcus aureus (MRSA) is an important nosocomial pathogen in hospitals, and increases rapidly in the community, named as community-associated MRSA (CA-MRSA). We conducted a prospective/retrospective study to understand the epidemiology, antimicrobial susceptibility, and molecular characteristics of MRSA infections in adult patients in Taiwan.From March to June, 2012, all clinical MRSA isolates were prospectively collected from adult patients in a tertiary hospital in northern Taiwan. Selective isolates were further characterized. We reviewed the detailed medical record of each case retrospectively.A total of 857 clinical isolates were collected from 555 patients. A total of 749 isolates from 453 patients were classified as healthcare-associated (HA)-MRSA and 108 isolates from 102 patients as CA-MRSA by the epidemiologic criteria. Compared to HA-MRSA, CA-MRSA isolates were significantly more frequently identified from pus (78% vs 28%, P < 0.001) and less frequently from sputum (4.6% vs 43.8%, P < 0.001) and blood (3.7% vs 15%, P = 0.002). CA-MRSA isolates were more susceptible to all antibiotics tested. A total of 102 CA-MRSA and 101 HA-MRSA isolates were characterized, showing significantly different molecular characteristics between CA and HA isolates (P < 0.001). The clone of sequence type (ST) 59/t437 complex, with 2 pulsotypes, accounted for 70% of CA isolates. Three major clones were identified from HA-MRSA isolates, namely clonal complex (CC) 59 (32.7%), CC239 (29.7%), and CC5 (24.8%). Among HA isolates, a significant difference was also seen between community-onset and hospital-onset MRSA isolates in terms of the source of specimens, antibiotic susceptibility patterns, and molecular characteristics.CA-MRSA isolates from adults in northern Taiwan were genetically significantly different from HA isolates. The community clones, CC59, spread into hospitals.

  13. Phylogenetic survey of metabolically active microbial communities associated with the deep-sea coral Lophelia pertusa from the Apulian plateau, Central Mediterranean Sea

    NASA Astrophysics Data System (ADS)

    Yakimov, Michail M.; Cappello, Simone; Crisafi, Ermanno; Tursi, Angelo; Savini, Alessandra; Corselli, Cesare; Scarfi, Simona; Giuliano, Laura

    2006-01-01

    Living deep-water coral assemblages were discovered recently inhabiting the Mediterranean Sea between the depths of 300 and 1000 m off the Cape of Santa Maria di Leuca (Apulian platform, Ionian Sea). This living assemblage was dominated by two colonial scleractinian corals, Lophelia pertusa and Madrepora oculata. Two other corals, Desmophyllum crystagalli and Stenocyathus vermiformis were also recovered from this site, but were much less common. The composition of the metabolically active fraction of the microbial community associated with living specimens of L. pertusa was determined. Dead corals, proximal sediments and overlying seawater were also sampled and analyzed. Complementary 16S ribosomal DNA (crDNA) was obtained from total RNA extracted from all samples that had been subjected to reverse transcription-PCR amplification. Domain-specific 16S PCR primers were used to construct four different 16S crDNA libraries containing 45 Archaea and 201 Bacteria clones. Using Archaea-specific primers, no amplification products were obtained from any coral samples (live and dead). Living specimens of L. pertusa seem to possess a specific microbial community different from that of dead coral and sediment samples. The majority of all coral-associated riboclones was related to the Holophaga-Acidobacterium and Nitrospira divisions (80%). Moreover, more than 12% of all coral-associated riboclones formed a separate deep-branching cluster within the α- Proteobacteria with no known close relatives. The metabolically active fraction of the bacterial community colonizing the dead corals was dominated by Proteobacteria related to the gamma and epsilon subdivisions (74% and 26% of all clones, respectively). Phylogenetic analysis of the Archaea clone library retrieved from proximal sediments indicated an exclusive dominance by the members of Crenarchaea Marine Group I (MGI), a lineage of unculturable microorganisms, widely distributed in marine habitats. In contrast, bacterial

  14. Multidrug-resistant clones of community-associated meticillin-resistant Staphylococcus aureus isolated from Chinese children and the resistance genes to clindamycin and mupirocin.

    PubMed

    Wang, Lijuan; Liu, Yingchao; Yang, Yonghong; Huang, Guoying; Wang, Chuanqing; Deng, Li; Zheng, Yuejie; Fu, Zhou; Li, Changcong; Shang, Yunxiao; Zhao, Changan; Sun, Mingjiao; Li, Xiangmei; Yu, Sangjie; Yao, Kaihu; Shen, Xuzhuang

    2012-09-01

    This study aimed to correlate the multidrug resistance (MDR) and sequence type (ST) clones of community-associated (CA) meticillin-resistant Staphylococcus aureus (MRSA) to identify the genes responsible for clindamycin and mupirocin resistance in S. aureus isolates from paediatric hospitals in mainland China. A total of 435 S. aureus isolates were collected. Compared with CA meticillin-susceptible S. aureus (MSSA), the resistance rates of CA-MRSA to ciprofloxacin, chloramphenicol, gentamicin and tetracycline were higher (19.0 vs 2.6 %, P<0.001; 14.7 vs 3.1 %, P<0.001; 14.7 vs 3.1 %, P<0.01; and 46.0 vs 13.3 %, P<0.001, respectively). Compared with hospital-associated (HA)-MRSA, the resistance rates of CA-MRSA to ciprofloxacin, gentamicin, rifampicin, tetracycline and trimethoprim-sulfamethoxazole were lower (19 vs 94.8 %, P<0.001; 14.7 vs 84.4 %, P<0.001; 5.5 vs 88.3 %, P<0.001; 46 vs 94.8 %, P<0.001; and 1.8 vs 9.1 %, P<0.01, respectively). The resistance rates of CA-MRSA, HA-MRSA and CA-MSSA to clindamycin (92.0, 77.9 and 64.1 %, respectively) and erythromycin (85.9, 77.9 and 63.1 %, respectively) were high. The MDR rates (resistance to three or more non-β-lactams) were 49.6, 100 and 14 % in the CA-MRSA, HA-MRSA and CA-MSSA isolates, respectively. Five of seven ST clones in the CA-MRSA isolates, namely ST59, ST338, ST45, ST910 and ST965, had MDR rates of >50 % (67.9, 87.5, 100, 50 and 83.3 %, respectively). The constitutive phenotype of macrolide-lincosamide-streptogramin B (MLS(B)) resistance (69 %) and the ermB gene (38.1 %) predominated among the MLS(B)-resistant CA S. aureus strains. The resistance rate to mupirocin was 2.3 % and plasmids carrying the mupA gene varied in size between 23 and 54.2 kb in six strains with high-level resistance as determined by Southern blot analysis. The present study showed that resistance to non-β-lactams, especially to clindamycin, is high in CA-MRSA isolates from Chinese children and that

  15. Presence of Methicillin-Resistant Staphylococcus aureus in Pigs in Peru

    PubMed Central

    Arriola, Carmen S.; Güere, Mariella E.; Larsen, Jesper; Skov, Robert L.; Gilman, Robert H.; Gonzalez, Armando E.; Silbergeld, Ellen K.

    2011-01-01

    We report the first detection of methicillin-resistant Staphylococcus aureus isolates in pigs in Peru. The isolates belong to a livestock-associated lineage previously reported in North America and Europe, CC398, and a highly virulent USA300-like ST8-IV variant, which is the predominant community-associated lineage in Latin America. PMID:22174831

  16. In vitro activity of oritavancin against community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA), vancomycin-intermediate S. aureus (VISA), vancomycin-resistant S. aureus (VRSA) and daptomycin-non-susceptible S. aureus (DNSSA).

    PubMed

    Saravolatz, Louis D; Pawlak, Joan; Johnson, Leonard B

    2010-07-01

    Isolates of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA), vancomycin-intermediate S. aureus (VISA), vancomycin-resistant S. aureus (VRSA) and daptomycin non-susceptible S. aureus (DNSSA) are increasing in frequency and new antistaphylococcal therapies are needed. Microdilution testing using Mueller-Hinton broth was used to determine the minimal inhibitory concentrations (MICs) of oritavancin and nine additional antimicrobial agents against 92 CA-MRSA, 23 VISA, 7 DNSSA and 10 VRSA isolates. Minimal bactericidal concentrations were also determined. Pulsed-field gel electrophoresis (PFGE) was performed. Staphylococcal cassette chromosome mec (SCCmec) typing as well as assays for Panton-Valentine leukocidin (PVL) and arginine catabolic mobile element (ACME) genes were performed. Oritavancin was more bactericidal than any of the other comparators against CA-MRSA and demonstrated excellent activity against VRSA and VISA.

  17. Emerging ST121/agr4 community-associated methicillin-resistant Staphylococcus aureus (MRSA) with strong adhesin and cytolytic activities: trigger for MRSA pneumonia and fatal aspiration pneumonia in an influenza-infected elderly.

    PubMed

    Wan, T-W; Tomita, Y; Saita, N; Konno, K; Iwao, Y; Hung, W-C; Teng, L-J; Yamamoto, T

    2016-09-01

    The pathogenesis of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) pneumonia in influenza-infected elderly individuals has not yet been elucidated in detail. In the present study, a 92-year-old man infected with influenza developed CA-MRSA pneumonia. His CA-MRSA was an emerging type, originated in ST121/agr4 S. aureus, with diversities of Panton-Valentine leucocidin (PVL)(-)/spat5110/SCCmecV(+) versus PVL(+)/spat159((etc.))/SCCmec (-), but with common virulence potentials of strong adhesin and cytolytic activities. Resistance to erythromycin/clindamycin (inducible-type) and gentamicin was detected. Pneumonia improved with the administration of levofloxacin, but with the subsequent development of fatal aspiration pneumonia. Hence, characteristic CA-MRSA with strong adhesin and cytolytic activities triggered influenza-related sequential complications.

  18. Plant community associations of two invasive thistles

    PubMed Central

    Rauschert, Emily S.J.; Shea, Katriona; Goslee, Sarah

    2015-01-01

    In order to combat the growing problems associated with biological invasions, many researchers have focused on identifying which communities are most vulnerable to invasion by exotic species. However, once established, invasive species can significantly change the composition of the communities that they invade. The first step to disentangling the direction of causality is to discern whether a relationship with other vegetation exists at all. Carduus nutans and C. acanthoides are similar invasive thistles, which have caused substantial economic damage worldwide. We assessed the associations between the thistles and the standing flora in four sites in central Pennsylvania in which they co-occur. After sampling nearly 2000 plots of 1 m2, we used partial Mantel tests to assess the differences in vegetation between thistle and non-thistle plots after accounting for location, and non-metric multidimensional scaling to visualize differences among plots and sites. We found significant differences in community composition in plots with and without Carduus thistles. The non-native species Sisymbrium officinale and Coronilla varia were consistently associated with the presence of Carduus thistles. Several species were associated with areas that were free of Carduus thistles, including an important non-native pasture species (Trifolium repens). We found no evidence for differences in composition between plots with C. nutans versus C. acanthoides, suggesting that they have similar associations with the vegetation community. We conclude that even at the within-field scale, areas invaded by Carduus thistles have different vegetation associations than uninvaded areas, allowing us to target future research about the role of vegetation structure in resisting and responding to invasion. PMID:26038126

  19. Plant community associations of two invasive thistles.

    PubMed

    Rauschert, Emily S J; Shea, Katriona; Goslee, Sarah

    2015-01-01

    In order to combat the growing problems associated with biological invasions, many researchers have focused on identifying which communities are most vulnerable to invasion by exotic species. However, once established, invasive species can significantly change the composition of the communities that they invade. The first step to disentangling the direction of causality is to discern whether a relationship with other vegetation exists at all. Carduus nutans and C. acanthoides are similar invasive thistles, which have caused substantial economic damage worldwide. We assessed the associations between the thistles and the standing flora in four sites in central Pennsylvania in which they co-occur. After sampling nearly 2000 plots of 1 m(2), we used partial Mantel tests to assess the differences in vegetation between thistle and non-thistle plots after accounting for location, and non-metric multidimensional scaling to visualize differences among plots and sites. We found significant differences in community composition in plots with and without Carduus thistles. The non-native species Sisymbrium officinale and Coronilla varia were consistently associated with the presence of Carduus thistles. Several species were associated with areas that were free of Carduus thistles, including an important non-native pasture species (Trifolium repens). We found no evidence for differences in composition between plots with C. nutans versus C. acanthoides, suggesting that they have similar associations with the vegetation community. We conclude that even at the within-field scale, areas invaded by Carduus thistles have different vegetation associations than uninvaded areas, allowing us to target future research about the role of vegetation structure in resisting and responding to invasion.

  20. Isolation and characterization of a thermophilic, obligately anaerobic and heterotrophic marine Chloroflexi bacterium from a Chloroflexi-dominated microbial community associated with a Japanese shallow hydrothermal system, and proposal for Thermomarinilinea lacunofontalis gen. nov., sp. nov.

    PubMed

    Nunoura, Takuro; Hirai, Miho; Miyazaki, Masayuki; Kazama, Hiromi; Makita, Hiroko; Hirayama, Hisako; Furushima, Yasuo; Yamamoto, Hiroyuki; Imachi, Hiroyuki; Takai, Ken

    2013-01-01

    A novel marine thermophilic and heterotrophic Anaerolineae bacterium in the phylum Chloroflexi, strain SW7(T), was isolated from an in situ colonization system deployed in the main hydrothermal vent of the Taketomi submarine hot spring field located on the southern part of Yaeyama Archipelago, Japan. The microbial community associated with the hydrothermal vent was predominated by thermophilic heterotrophs such as Thermococcaceae and Anaerolineae, and the next dominant population was thermophilic sulfur oxidizers. Both aerobic and anaerobic hydrogenotrophs including methanogens were detected as minor populations. During the culture-dependent viable count analysis in this study, an Anaerolineae strain SW7(T) was isolated from an enrichment culture at a high dilution rate. Strain SW7(T) was an obligately anaerobic heterotroph that grew with fermentation and had non-motile thin rods 3.5-16.5 μm in length and 0.2 μm in width constituting multicellular filaments. Growth was observed between 37-65°C (optimum 60°C), pH 5.5-7.3 (optimum pH 6.0), and 0.5-3.5% (w/v) NaCl concentration (optimum 1.0%). Based on the physiological and phylogenetic features of a new isolate, we propose a new species representing a novel genus Thermomarinilinea: the type strain of Thermomarinilinea lacunofontalis sp. nov., is SW7(T) (=JCM15506(T)=KCTC5908(T)). PMID:23666537

  1. A comparison of clinical outcomes between healthcare-associated infections due to community-associated methicillin-resistant Staphylococcus aureus strains and healthcare-associated methicillin-resistant S. aureus strains

    PubMed Central

    EELLS, S. J.; MCKINNELL, J.A.; WANG, A. A.; GREEN, N. L.; WHANG, D.; O'HARA, P.; BROWN, M. L.; MILLER, L. G.

    2013-01-01

    SUMMARY There are limited data examining whether outcomes of MRSA healthcare-associated infections (HAIs) are worse when caused by community-associated strains compared to healthcare-associated strains. We reviewed all patient charts at our institution from 1999 to 2009 that had MRSA first isolated only after 72 hours of hospitalization (n=724). Of these, 384 patients had an MRSA-HAI by CDC criteria. Treatment failure was similar in those infected with a phenotypically CA-MRSA strain compared to a phenotypically HA-MRSA strain (23% vs. 15%, P=0.10) as was 30-day mortality (16% vs. 19%, P=0.57). Independent risk factors associated with (p<0.05) treatment failure were higher Charlson Comorbidity Index, higher APACHE II score, and no anti-MRSA treatment. These factors were also associated with 30-day mortality, as were female gender, older age, MRSA bloodstream infection, MRSA pneumonia, and HIV. Our findings suggest that clinical and host factors, not MRSA strain type, predict treatment failure and death in hospitalized patients with MRSA-HAIs. PMID:23217979

  2. Prevalence of community-associated meticillin-resistant Staphylococcus aureus and Panton-Valentine leucocidin-positive S. aureus in general practice patients with skin and soft tissue infections in the northern and southern regions of The Netherlands.

    PubMed

    Mithoe, D; Rijnders, M I A; Roede, B M; Stobberingh, E; Möller, A V M

    2012-03-01

    The purpose of this investigation was to determine the prevalence of community-associated meticillin-resistant Staphylococcus aureus (CA-MRSA) and Panton-Valentine leucocidin (PVL)-positive S. aureus in general practice (GP) patients with skin and soft tissue infections (SSTI) in the northern (Groningen and Drenthe) and southern (Limburg) regions of The Netherlands. Secondary objectives were to assess the possible risk factors for patients with SSTI caused by S. aureus and PVL-positive S. aureus using a questionnaire-based survey. From 2007 to 2008, wound and nose cultures were obtained from patients with SSTI in general practice. These swabs were analysed for the presence of S. aureus and the antibiotic susceptibility was determined. The presence of the PVL toxin gene was determined by polymerase chain reaction (PCR) and the genetic background with the use of spa typing. A survey was performed to detect risk factors for S. aureus infection and for the presence of PVL toxin.S. aureus was isolated from 219 out of 314 (70%) patients with SSTI, of which two (0.9%) patients were MRSA-positive. In 25 (11%) patients, the PVL toxin gene was found. A higher prevalence of PVL-positive S. aureus of patients with SSTI was found in the northern region compared to the south (p < 0.05). Regional differences were found in the spa types of PVL-positive S. aureus isolates, and for PVL-negative S. aureus isolates, the genetic background was similar in both regions. The prevalence of CA-MRSA in GP patients with SSTI in The Netherlands is low. Regional differences were found in the prevalence of PVL-positive S. aureus isolates from GP patients with SSTI. Household contacts having similar symptoms were found to be a risk factor for SSTI with S. aureus.

  3. Emergence of community-associated methicillin-resistant Staphylococcus aureus strains in the neonatal intensive care unit: an infection prevention and patient safety challenge.

    PubMed

    Reich, P J; Boyle, M G; Hogan, P G; Johnson, A J; Wallace, M A; Elward, A M; Warner, B B; Burnham, C-A D; Fritz, S A

    2016-07-01

    Methicillin-resistant Staphylococcus aureus (MRSA) infections cause significant morbidity and mortality in neonatal intensive care units (NICUs). We characterized the clinical and molecular epidemiology of MRSA strains colonizing NICU patients. Nasal MRSA isolates (n = 250, from 96 NICU patients) recovered through active surveillance from 2009 to 2014 were characterized with staphylococcal cassette chromosome mec (SCCmec) typing and detection of mupA (marker of high-level mupirocin resistance) and qacA/B (marker associated with chlorhexidine resistance). Factors associated with community-associated (CA-) or healthcare-associated (HA-) MRSA were evaluated. The overall prevalence of MRSA nasal colonization was 3.9%. Of 96 neonates in our retrospective cohort, 60 (63%) were colonized with CA-MRSA strains and 35 (36%) were colonized with HA-MRSA strains. Patients colonized with HA-MRSA were more likely to develop MRSA infections than patients colonized with CA-MRSA (13/35, 37% versus 8/60, 13%; p 0.007), although the interval from colonization to infection was shorter in CA-MRSA-colonized infants (median 0 days, range -1 to 4 versus HA-MRSA-colonized infants, 7 days, -1 to 43; p 0.005). Maternal peripartum antibiotics were associated with CA-MRSA colonization (adjusted odds ratio (aOR) 8.7; 95% CI 1.7-45.0); intubation and surgical procedures were associated with HA-MRSA colonization (aOR 7.8; 95% CI 1.3-47.6 and aOR 6.0; 95% CI 1.4-24.4, respectively). Mupirocin- and chlorhexidine-resistant MRSA was isolated from four and eight patients, respectively; carriage of a mupirocin-resistant strain precluded decolonization. CA-MRSA strains are prominent in the NICU and associated with distinct risk factors. Given community reservoirs for MRSA acquisition and transmission, novel infection prevention strategies are needed.

  4. Healthcare- and Community-Associated Methicillin-Resistant Staphylococcus aureus (MRSA) and Fatal Pneumonia with Pediatric Deaths in Krasnoyarsk, Siberian Russia: Unique MRSA's Multiple Virulence Factors, Genome, and Stepwise Evolution.

    PubMed

    Khokhlova, Olga E; Hung, Wei-Chun; Wan, Tsai-Wen; Iwao, Yasuhisa; Takano, Tomomi; Higuchi, Wataru; Yachenko, Svetlana V; Teplyakova, Olga V; Kamshilova, Vera V; Kotlovsky, Yuri V; Nishiyama, Akihito; Reva, Ivan V; Sidorenko, Sergey V; Peryanova, Olga V; Reva, Galina V; Teng, Lee-Jene; Salmina, Alla B; Yamamoto, Tatsuo

    2015-01-01

    Methicillin-resistant Staphylococcus aureus (MRSA) is a common multidrug-resistant (MDR) pathogen. We herein discussed MRSA and its infections in Krasnoyarsk, Siberian Russia between 2007 and 2011. The incidence of MRSA in 3,662 subjects was 22.0% and 2.9% for healthcare- and community-associated MRSA (HA- and CA-MRSA), respectively. The 15-day mortality rates for MRSA hospital- and community-acquired pneumonia (HAP and CAP) were 6.5% and 50%, respectively. MRSA CAP cases included pediatric deaths; of the MRSA pneumonia episodes available, ≥27.3% were associated with bacteremia. Most cases of HA-MRSA examined exhibited ST239/spa3(t037)/SCCmecIII.1.1.2 (designated as ST239Kras), while all CA-MRSA cases examined were ST8/spa1(t008)/SCCmecIV.3.1.1(IVc) (designated as ST8Kras). ST239Kras and ST8Kras strongly expressed cytolytic peptide (phenol-soluble modulin α, PSMα; and δ-hemolysin, Hld) genes, similar to CA-MRSA. ST239Kras pneumonia may have been attributed to a unique set of multiple virulence factors (MVFs): toxic shock syndrome toxin-1 (TSST-1), elevated PSMα/Hld expression, α-hemolysin, the staphylococcal enterotoxin SEK/SEQ, the immune evasion factor SCIN/SAK, and collagen adhesin. Regarding ST8Kras, SEA was included in MVFs, some of which were common to ST239Kras. The ST239Kras (strain OC3) genome contained: a completely unique phage, φSa7-like (W), with no att repetition; S. aureus pathogenicity island SaPI2R, the first TSST-1 gene-positive (tst+) SaPI in the ST239 lineage; and a super copy of IS256 (≥22 copies/genome). ST239Kras carried the Brazilian SCCmecIII.1.1.2 and United Kingdom-type tst. ST239Kras and ST8Kras were MDR, with the same levofloxacin resistance mutations; small, but transmissible chloramphenicol resistance plasmids spread widely enough to not be ignored. These results suggest that novel MDR and MVF+ HA- and CA-MRSA (ST239Kras and ST8Kras) emerged in Siberian Russia (Krasnoyarsk) associated with fatal pneumonia, and also with ST

  5. Molecular Evolutionary Pathways toward Two Successful Community-Associated but Multidrug-Resistant ST59 Methicillin-Resistant Staphylococcus aureus Lineages in Taiwan: Dynamic Modes of Mobile Genetic Element Salvages.

    PubMed

    Hung, Wei-Chun; Wan, Tsai-Wen; Kuo, Yu-Chia; Yamamoto, Tatsuo; Tsai, Jui-Chang; Lin, Yu-Tzu; Hsueh, Po-Ren; Teng, Lee-Jene

    2016-01-01

    Clonal complex 59 (CC59) Staphylococcus aureus in Taiwan includes both methicillin-susceptible S. aureus (MSSA) and methicillin-resistant S. aureus (MRSA). As the most prominent community-associated MRSA (CA-MRSA) in Taiwan, CC59 has two major clones characterized as PVL-negative SCCmec IV (carrying the staphylococcal cassette chromosome mec IV but Panton-Valentine leukocidin-negative) and PVL-positive SCCmec V (5C2&5). We investigated the drug resistance, phylogeny and the distribution and sequence variation of SCCmec, staphylococcal bacteriophage φSA3, genomic island νSaβ and MES (an enterococcal mobile genetic element conferring multidrug resistance) in 195 CC59 S. aureus. Sequencing and PCR mapping revealed that all of the CC59/SCCmec V (5C2&5) MRSA strains had acquired MESPM1 or its segregants, and obtained a φSA3-related fragment in νSaβ. In contrast, MES6272-2 and MES4578, which showed gentamicin resistance that was not encoded by MESPM1, were dominant in SCCmec IVg MRSA. Translocation of a whole φSA3 into νSaβ instead of only a φSA3-related fragment was common in SCCmec IVg MRSA. However, the non-subtype-g SCCmec IV MRSA (SCCmec IVa is the major) still carried MES and νSaβ structures similar to those in SCCmec V (5C2&5) MRSA. A minimum spanning tree constructed by multiple-locus variable-number tandem repeat analysis revealed that SCCmec IVg MRSA and SCCmec V (5C2&5) MRSA grouped respectively in two major clades. The CC59 MSSA was equally distributed among the two clades, while the non-subtype-g SCCmec IV MRSA mostly clustered with SCCmec V (5C2&5) MRSA. Our findings strongly suggest that CC59 MSSA acquired divergent mobile genetic elements and evolved to SCCmec IVg MRSA and SCCmec V (5C2&5) MRSA/non-subtype-g SCCmec IV MRSA independently. The evolutionary history of CC59 S. aureus explains how mobile genetic elements increase the antimicrobial resistance and virulence and contribute to the success of CA-MRSA in Taiwan. PMID:27606427

  6. Molecular Evolutionary Pathways toward Two Successful Community-Associated but Multidrug-Resistant ST59 Methicillin-Resistant Staphylococcus aureus Lineages in Taiwan: Dynamic Modes of Mobile Genetic Element Salvages

    PubMed Central

    Hung, Wei-Chun; Wan, Tsai-Wen; Kuo, Yu-Chia; Yamamoto, Tatsuo; Tsai, Jui-Chang; Lin, Yu-Tzu; Hsueh, Po-Ren; Teng, Lee-Jene

    2016-01-01

    Clonal complex 59 (CC59) Staphylococcus aureus in Taiwan includes both methicillin-susceptible S. aureus (MSSA) and methicillin-resistant S. aureus (MRSA). As the most prominent community-associated MRSA (CA-MRSA) in Taiwan, CC59 has two major clones characterized as PVL-negative SCCmec IV (carrying the staphylococcal cassette chromosome mec IV but Panton-Valentine leukocidin-negative) and PVL-positive SCCmec V (5C2&5). We investigated the drug resistance, phylogeny and the distribution and sequence variation of SCCmec, staphylococcal bacteriophage φSA3, genomic island νSaβ and MES (an enterococcal mobile genetic element conferring multidrug resistance) in 195 CC59 S. aureus. Sequencing and PCR mapping revealed that all of the CC59/SCCmec V (5C2&5) MRSA strains had acquired MESPM1 or its segregants, and obtained a φSA3-related fragment in νSaβ. In contrast, MES6272-2 and MES4578, which showed gentamicin resistance that was not encoded by MESPM1, were dominant in SCCmec IVg MRSA. Translocation of a whole φSA3 into νSaβ instead of only a φSA3-related fragment was common in SCCmec IVg MRSA. However, the non-subtype-g SCCmec IV MRSA (SCCmec IVa is the major) still carried MES and νSaβ structures similar to those in SCCmec V (5C2&5) MRSA. A minimum spanning tree constructed by multiple-locus variable-number tandem repeat analysis revealed that SCCmec IVg MRSA and SCCmec V (5C2&5) MRSA grouped respectively in two major clades. The CC59 MSSA was equally distributed among the two clades, while the non-subtype-g SCCmec IV MRSA mostly clustered with SCCmec V (5C2&5) MRSA. Our findings strongly suggest that CC59 MSSA acquired divergent mobile genetic elements and evolved to SCCmec IVg MRSA and SCCmec V (5C2&5) MRSA/non-subtype-g SCCmec IV MRSA independently. The evolutionary history of CC59 S. aureus explains how mobile genetic elements increase the antimicrobial resistance and virulence and contribute to the success of CA-MRSA in Taiwan. PMID:27606427

  7. Healthcare- and Community-Associated Methicillin-Resistant Staphylococcus aureus (MRSA) and Fatal Pneumonia with Pediatric Deaths in Krasnoyarsk, Siberian Russia: Unique MRSA's Multiple Virulence Factors, Genome, and Stepwise Evolution.

    PubMed

    Khokhlova, Olga E; Hung, Wei-Chun; Wan, Tsai-Wen; Iwao, Yasuhisa; Takano, Tomomi; Higuchi, Wataru; Yachenko, Svetlana V; Teplyakova, Olga V; Kamshilova, Vera V; Kotlovsky, Yuri V; Nishiyama, Akihito; Reva, Ivan V; Sidorenko, Sergey V; Peryanova, Olga V; Reva, Galina V; Teng, Lee-Jene; Salmina, Alla B; Yamamoto, Tatsuo

    2015-01-01

    Methicillin-resistant Staphylococcus aureus (MRSA) is a common multidrug-resistant (MDR) pathogen. We herein discussed MRSA and its infections in Krasnoyarsk, Siberian Russia between 2007 and 2011. The incidence of MRSA in 3,662 subjects was 22.0% and 2.9% for healthcare- and community-associated MRSA (HA- and CA-MRSA), respectively. The 15-day mortality rates for MRSA hospital- and community-acquired pneumonia (HAP and CAP) were 6.5% and 50%, respectively. MRSA CAP cases included pediatric deaths; of the MRSA pneumonia episodes available, ≥27.3% were associated with bacteremia. Most cases of HA-MRSA examined exhibited ST239/spa3(t037)/SCCmecIII.1.1.2 (designated as ST239Kras), while all CA-MRSA cases examined were ST8/spa1(t008)/SCCmecIV.3.1.1(IVc) (designated as ST8Kras). ST239Kras and ST8Kras strongly expressed cytolytic peptide (phenol-soluble modulin α, PSMα; and δ-hemolysin, Hld) genes, similar to CA-MRSA. ST239Kras pneumonia may have been attributed to a unique set of multiple virulence factors (MVFs): toxic shock syndrome toxin-1 (TSST-1), elevated PSMα/Hld expression, α-hemolysin, the staphylococcal enterotoxin SEK/SEQ, the immune evasion factor SCIN/SAK, and collagen adhesin. Regarding ST8Kras, SEA was included in MVFs, some of which were common to ST239Kras. The ST239Kras (strain OC3) genome contained: a completely unique phage, φSa7-like (W), with no att repetition; S. aureus pathogenicity island SaPI2R, the first TSST-1 gene-positive (tst+) SaPI in the ST239 lineage; and a super copy of IS256 (≥22 copies/genome). ST239Kras carried the Brazilian SCCmecIII.1.1.2 and United Kingdom-type tst. ST239Kras and ST8Kras were MDR, with the same levofloxacin resistance mutations; small, but transmissible chloramphenicol resistance plasmids spread widely enough to not be ignored. These results suggest that novel MDR and MVF+ HA- and CA-MRSA (ST239Kras and ST8Kras) emerged in Siberian Russia (Krasnoyarsk) associated with fatal pneumonia, and also with ST

  8. Healthcare- and Community-Associated Methicillin-Resistant Staphylococcus aureus (MRSA) and Fatal Pneumonia with Pediatric Deaths in Krasnoyarsk, Siberian Russia: Unique MRSA's Multiple Virulence Factors, Genome, and Stepwise Evolution

    PubMed Central

    Khokhlova, Olga E.; Hung, Wei-Chun; Wan, Tsai-Wen; Iwao, Yasuhisa; Takano, Tomomi; Higuchi, Wataru; Yachenko, Svetlana V.; Teplyakova, Olga V.; Kamshilova, Vera V.; Kotlovsky, Yuri V.; Nishiyama, Akihito; Reva, Ivan V.; Sidorenko, Sergey V.; Peryanova, Olga V.; Reva, Galina V.; Teng, Lee-Jene; Salmina, Alla B.; Yamamoto, Tatsuo

    2015-01-01

    Methicillin-resistant Staphylococcus aureus (MRSA) is a common multidrug-resistant (MDR) pathogen. We herein discussed MRSA and its infections in Krasnoyarsk, Siberian Russia between 2007 and 2011. The incidence of MRSA in 3,662 subjects was 22.0% and 2.9% for healthcare- and community-associated MRSA (HA- and CA-MRSA), respectively. The 15-day mortality rates for MRSA hospital- and community-acquired pneumonia (HAP and CAP) were 6.5% and 50%, respectively. MRSA CAP cases included pediatric deaths; of the MRSA pneumonia episodes available, ≥27.3% were associated with bacteremia. Most cases of HA-MRSA examined exhibited ST239/spa3(t037)/SCCmecIII.1.1.2 (designated as ST239Kras), while all CA-MRSA cases examined were ST8/spa1(t008)/SCCmecIV.3.1.1(IVc) (designated as ST8Kras). ST239Kras and ST8Kras strongly expressed cytolytic peptide (phenol-soluble modulin α, PSMα; and δ-hemolysin, Hld) genes, similar to CA-MRSA. ST239Kras pneumonia may have been attributed to a unique set of multiple virulence factors (MVFs): toxic shock syndrome toxin-1 (TSST-1), elevated PSMα/Hld expression, α-hemolysin, the staphylococcal enterotoxin SEK/SEQ, the immune evasion factor SCIN/SAK, and collagen adhesin. Regarding ST8Kras, SEA was included in MVFs, some of which were common to ST239Kras. The ST239Kras (strain OC3) genome contained: a completely unique phage, φSa7-like (W), with no att repetition; S. aureus pathogenicity island SaPI2R, the first TSST-1 gene-positive (tst+) SaPI in the ST239 lineage; and a super copy of IS256 (≥22 copies/genome). ST239Kras carried the Brazilian SCCmecIII.1.1.2 and United Kingdom-type tst. ST239Kras and ST8Kras were MDR, with the same levofloxacin resistance mutations; small, but transmissible chloramphenicol resistance plasmids spread widely enough to not be ignored. These results suggest that novel MDR and MVF+ HA- and CA-MRSA (ST239Kras and ST8Kras) emerged in Siberian Russia (Krasnoyarsk) associated with fatal pneumonia, and also with ST

  9. Molecular tracing of the emergence, diversification, and transmission of S. aureus sequence type 8 in a New York community.

    PubMed

    Uhlemann, Anne-Catrin; Dordel, Janina; Knox, Justin R; Raven, Kathy E; Parkhill, Julian; Holden, Matthew T G; Peacock, Sharon J; Lowy, Franklin D

    2014-05-01

    During the last 2 decades, community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) strains have dramatically increased the global burden of S. aureus infections. The pandemic sequence type (ST)8/pulsed-field gel type USA300 is the dominant CA-MRSA clone in the United States, but its evolutionary history and basis for biological success are incompletely understood. Here, we use whole-genome sequencing of 387 ST8 isolates drawn from an epidemiological network of CA-MRSA infections and colonizations in northern Manhattan to explore short-term evolution and transmission patterns. Phylogenetic analysis predicted that USA300 diverged from a most common recent ancestor around 1993. We found evidence for multiple introductions of USA300 and reconstructed the phylogeographic spread of isolates across neighborhoods. Using pair-wise single-nucleotide polymorphism distances as a measure of genetic relatedness between isolates, we observed that most USA300 isolates had become endemic in households, indicating their critical role as reservoirs for transmission and diversification. Using the maximum single-nucleotide polymorphism variability of isolates from within households as a threshold, we identified several possible transmission networks beyond households. Our study also revealed the evolution of a fluoroquinolone-resistant subpopulation in the mid-1990s and its subsequent expansion at a time of high-frequency outpatient antibiotic use. This high-resolution phylogenetic analysis of ST8 has documented the genomic changes associated with USA300 evolution and how some of its recent evolution has been shaped by antibiotic use. By integrating whole-genome sequencing with detailed epidemiological analyses, our study provides an important framework for delineating the full diversity and spread of USA300 and other emerging pathogens in large urban community populations. PMID:24753569

  10. Molecular tracing of the emergence, diversification, and transmission of S. aureus sequence type 8 in a New York community.

    PubMed

    Uhlemann, Anne-Catrin; Dordel, Janina; Knox, Justin R; Raven, Kathy E; Parkhill, Julian; Holden, Matthew T G; Peacock, Sharon J; Lowy, Franklin D

    2014-05-01

    During the last 2 decades, community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) strains have dramatically increased the global burden of S. aureus infections. The pandemic sequence type (ST)8/pulsed-field gel type USA300 is the dominant CA-MRSA clone in the United States, but its evolutionary history and basis for biological success are incompletely understood. Here, we use whole-genome sequencing of 387 ST8 isolates drawn from an epidemiological network of CA-MRSA infections and colonizations in northern Manhattan to explore short-term evolution and transmission patterns. Phylogenetic analysis predicted that USA300 diverged from a most common recent ancestor around 1993. We found evidence for multiple introductions of USA300 and reconstructed the phylogeographic spread of isolates across neighborhoods. Using pair-wise single-nucleotide polymorphism distances as a measure of genetic relatedness between isolates, we observed that most USA300 isolates had become endemic in households, indicating their critical role as reservoirs for transmission and diversification. Using the maximum single-nucleotide polymorphism variability of isolates from within households as a threshold, we identified several possible transmission networks beyond households. Our study also revealed the evolution of a fluoroquinolone-resistant subpopulation in the mid-1990s and its subsequent expansion at a time of high-frequency outpatient antibiotic use. This high-resolution phylogenetic analysis of ST8 has documented the genomic changes associated with USA300 evolution and how some of its recent evolution has been shaped by antibiotic use. By integrating whole-genome sequencing with detailed epidemiological analyses, our study provides an important framework for delineating the full diversity and spread of USA300 and other emerging pathogens in large urban community populations.

  11. Evidence for Community Transmission of Community-Associated but Not Health-Care-Associated Methicillin-Resistant Staphylococcus Aureus Strains Linked to Social and Material Deprivation: Spatial Analysis of Cross-sectional Data

    PubMed Central

    Tosas Auguet, Olga; Betley, Jason R.; Stabler, Richard A.; Patel, Amita; Ioannou, Avgousta; Marbach, Helene; Hearn, Pasco; Aryee, Anna; Goldenberg, Simon D.; Otter, Jonathan A.; Desai, Nergish; Karadag, Tacim; Grundy, Chris; Gaunt, Michael W.; Cooper, Ben S.; Edgeworth, Jonathan D.; Kypraios, Theodore

    2016-01-01

    Background Identifying and tackling the social determinants of infectious diseases has become a public health priority following the recognition that individuals with lower socioeconomic status are disproportionately affected by infectious diseases. In many parts of the world, epidemiologically and genotypically defined community-associated (CA) methicillin-resistant Staphylococcus aureus (MRSA) strains have emerged to become frequent causes of hospital infection. The aim of this study was to use spatial models with adjustment for area-level hospital attendance to determine the transmission niche of genotypically defined CA- and health-care-associated (HA)-MRSA strains across a diverse region of South East London and to explore a potential link between MRSA carriage and markers of social and material deprivation. Methods and Findings This study involved spatial analysis of cross-sectional data linked with all MRSA isolates identified by three National Health Service (NHS) microbiology laboratories between 1 November 2011 and 29 February 2012. The cohort of hospital-based NHS microbiology diagnostic services serves 867,254 usual residents in the Lambeth, Southwark, and Lewisham boroughs in South East London, United Kingdom (UK). Isolates were classified as HA- or CA-MRSA based on whole genome sequencing. All MRSA cases identified over 4 mo within the three-borough catchment area (n = 471) were mapped to small geographies and linked to area-level aggregated socioeconomic and demographic data. Disease mapping and ecological regression models were used to infer the most likely transmission niches for each MRSA genetic classification and to describe the spatial epidemiology of MRSA in relation to social determinants. Specifically, we aimed to identify demographic and socioeconomic population traits that explain cross-area extra variation in HA- and CA-MRSA relative risks following adjustment for hospital attendance data. We explored the potential for associations with

  12. Evidence for Community Transmission of Community-Associated but Not Health-Care-Associated Methicillin-Resistant Staphylococcus Aureus Strains Linked to Social and Material Deprivation: Spatial Analysis of Cross-sectional Data

    PubMed Central

    Tosas Auguet, Olga; Betley, Jason R.; Stabler, Richard A.; Patel, Amita; Ioannou, Avgousta; Marbach, Helene; Hearn, Pasco; Aryee, Anna; Goldenberg, Simon D.; Otter, Jonathan A.; Desai, Nergish; Karadag, Tacim; Grundy, Chris; Gaunt, Michael W.; Cooper, Ben S.; Edgeworth, Jonathan D.; Kypraios, Theodore

    2016-01-01

    Background Identifying and tackling the social determinants of infectious diseases has become a public health priority following the recognition that individuals with lower socioeconomic status are disproportionately affected by infectious diseases. In many parts of the world, epidemiologically and genotypically defined community-associated (CA) methicillin-resistant Staphylococcus aureus (MRSA) strains have emerged to become frequent causes of hospital infection. The aim of this study was to use spatial models with adjustment for area-level hospital attendance to determine the transmission niche of genotypically defined CA- and health-care-associated (HA)-MRSA strains across a diverse region of South East London and to explore a potential link between MRSA carriage and markers of social and material deprivation. Methods and Findings This study involved spatial analysis of cross-sectional data linked with all MRSA isolates identified by three National Health Service (NHS) microbiology laboratories between 1 November 2011 and 29 February 2012. The cohort of hospital-based NHS microbiology diagnostic services serves 867,254 usual residents in the Lambeth, Southwark, and Lewisham boroughs in South East London, United Kingdom (UK). Isolates were classified as HA- or CA-MRSA based on whole genome sequencing. All MRSA cases identified over 4 mo within the three-borough catchment area (n = 471) were mapped to small geographies and linked to area-level aggregated socioeconomic and demographic data. Disease mapping and ecological regression models were used to infer the most likely transmission niches for each MRSA genetic classification and to describe the spatial epidemiology of MRSA in relation to social determinants. Specifically, we aimed to identify demographic and socioeconomic population traits that explain cross-area extra variation in HA- and CA-MRSA relative risks following adjustment for hospital attendance data. We explored the potential for associations with

  13. Bacterial Communities Associated with Different Anthurium andraeanum L. Plant Tissues

    PubMed Central

    Sarria-Guzmán, Yohanna; Chávez-Romero, Yosef; Gómez-Acata, Selene; Montes-Molina, Joaquín Adolfo; Morales-Salazar, Eleacin; Dendooven, Luc; Navarro-Noya, Yendi E.

    2016-01-01

    Plant-associated microbes have specific beneficial functions and are considered key drivers for plant health. The bacterial community structure of healthy Anthurium andraeanum L. plants was studied by 16S rRNA gene pyrosequencing associated with different plant parts and the rhizosphere. A limited number of bacterial taxa, i.e., Sinorhizobium, Fimbriimonadales, and Gammaproteobacteria HTCC2089 were enriched in the A. andraeanum rhizosphere. Endophytes were more diverse in the roots than in the shoots, whereas all shoot endophytes were found in the roots. Streptomyces, Flavobacterium succinicans, and Asteroleplasma were only found in the roots, Variovorax paradoxus only in the stem, and Fimbriimonas 97%-OTUs only in the spathe, i.e., considered specialists, while Brevibacillus, Lachnospiraceae, Pseudomonas, and Pseudomonas pseudoalcaligenes were generalist and colonized all plant parts. The anaerobic diazotrophic bacteria Lachnospiraceae, Clostridium sp., and Clostridium bifermentans colonized the shoot system. Phylotypes belonging to Pseudomonas were detected in the rhizosphere and in the substrate (an equiproportional mixture of soil, cow manure, and peat), and dominated the endosphere. Pseudomonas included nine 97%-OTUs with different patterns of distribution and phylogenetic affiliations with different species. P. pseudoalcaligenes and P. putida dominated the shoots, but were also found in the roots and rhizosphere. P. fluorescens was present in all plant parts, while P. resinovorans, P. denitrificans, P. aeruginosa, and P. stutzeri were only detected in the substrate and rhizosphere. The composition of plant-associated bacterial communities is generally considered to be suitable as an indicator of plant health. PMID:27524305

  14. Highly Variable Bacterial Communities Associated with the Octocoral Antillogorgia elisabethae

    PubMed Central

    Robertson, Veronica; Haltli, Brad; McCauley, Erin P.; Overy, David P.; Kerr, Russell G.

    2016-01-01

    Antillogorgia elisabethae (synonymous with Pseudopterogorgia elisabethae) is a common branching octocoral in Caribbean reef ecosystems. A. elisabethae is a rich source of anti-inflammatory diterpenes, thus this octocoral has been the subject of numerous natural product investigations, yet relatively little is known regarding the composition, diversity and the geographic and temporal stability of its microbiome. To characterize the composition, diversity and stability of bacterial communities of Bahamian A. elisabethae populations, 17 A. elisabethae samples originating from five sites within The Bahamas were characterized by 16S rDNA pyrosequencing. A. elisabethae bacterial communities were less diverse and distinct from those of surrounding seawater samples. Analyses of α- and β-diversity revealed that A. elisabethae bacterial communities were highly variable between A. elisabethae samples from The Bahamas. This contrasts results obtained from a previous study of three specimens collected from Providencia Island, Colombia, which found A. elisabethae bacterial communities to be highly structured. Taxa belonging to the Rhodobacteriales, Rhizobiales, Flavobacteriales and Oceanospiralles were identified as potential members of the A. elisabethae core microbiome. PMID:27681917

  15. Study of methanogen communities associated with different rumen protozoal populations.

    PubMed

    Belanche, Alejandro; de la Fuente, Gabriel; Newbold, Charles J

    2014-12-01

    Protozoa-associated methanogens (PAM) are considered one of the most active communities in the rumen methanogenesis. This experiment investigated whether methanogens are sequestrated within rumen protozoa, and structural differences between rumen free-living methanogens and PAM. Rumen protozoa were harvested from totally faunated sheep, and six protozoal fractions (plus free-living microorganisms) were generated by sequential filtration. Holotrich-monofaunated sheep were also used to investigate the holotrich-associated methanogens. Protozoal size determined the number of PAM as big protozoa had 1.7-3.3 times more methanogen DNA than smaller protozoa, but also more endosymbiotic bacteria (2.2- to 3.5-fold times). Thus, similar abundance of methanogens with respect to total bacteria were observed across all protozoal fractions and free-living microorganisms, suggesting that methanogens are not accumulated within rumen protozoa in a greater proportion to that observed in the rumen as a whole. All rumen methanogen communities had similar diversity (22.2 ± 3.4 TRFs). Free-living methanogens composed a conserved community (67% similarity within treatment) in the rumen with similar diversity but different structures than PAM (P < 0.05). On the contrary, PAM constituted a more variable community (48% similarity), which differed between holotrich and total protozoa (P < 0.001). Thus, PAM constitutes a community, which requires further investigation as part of methane mitigation strategies.

  16. The bacterial communities associated with honey bee (Apis mellifera) foragers.

    PubMed

    Corby-Harris, Vanessa; Maes, Patrick; Anderson, Kirk E

    2014-01-01

    The honey bee is a key pollinator species in decline worldwide. As part of a commercial operation, bee colonies are exposed to a variety of agricultural ecosystems throughout the year and a multitude of environmental variables that may affect the microbial balance of individuals and the hive. While many recent studies support the idea of a core microbiota in guts of younger in-hive bees, it is unknown whether this core is present in forager bees or the pollen they carry back to the hive. Additionally, several studies hypothesize that the foregut (crop), a key interface between the pollination environment and hive food stores, contains a set of 13 lactic acid bacteria (LAB) that inoculate collected pollen and act in synergy to preserve pollen stores. Here, we used a combination of 454 based 16S rRNA gene sequencing of the microbial communities of forager guts, crops, and corbicular pollen and crop plate counts to show that (1) despite a very different diet, forager guts contain a core microbiota similar to that found in younger bees, (2) corbicular pollen contains a diverse community dominated by hive-specific, environmental or phyllosphere bacteria that are not prevalent in the gut or crop, and (3) the 13 LAB found in culture-based studies are not specific to the crop but are a small subset of midgut or hindgut specific bacteria identified in many recent 454 amplicon-based studies. The crop is dominated by Lactobacillus kunkeei, and Alpha 2.2 (Acetobacteraceae), highly osmotolerant and acid resistant bacteria found in stored pollen and honey. Crop taxa at low abundance include core hindgut bacteria in transit to their primary niche, and potential pathogens or food spoilage organisms seemingly vectored from the pollination environment. We conclude that the crop microbial environment is influenced by worker task, and may function in both decontamination and inoculation.

  17. The bacterial communities associated with honey bee (Apis mellifera) foragers.

    PubMed

    Corby-Harris, Vanessa; Maes, Patrick; Anderson, Kirk E

    2014-01-01

    The honey bee is a key pollinator species in decline worldwide. As part of a commercial operation, bee colonies are exposed to a variety of agricultural ecosystems throughout the year and a multitude of environmental variables that may affect the microbial balance of individuals and the hive. While many recent studies support the idea of a core microbiota in guts of younger in-hive bees, it is unknown whether this core is present in forager bees or the pollen they carry back to the hive. Additionally, several studies hypothesize that the foregut (crop), a key interface between the pollination environment and hive food stores, contains a set of 13 lactic acid bacteria (LAB) that inoculate collected pollen and act in synergy to preserve pollen stores. Here, we used a combination of 454 based 16S rRNA gene sequencing of the microbial communities of forager guts, crops, and corbicular pollen and crop plate counts to show that (1) despite a very different diet, forager guts contain a core microbiota similar to that found in younger bees, (2) corbicular pollen contains a diverse community dominated by hive-specific, environmental or phyllosphere bacteria that are not prevalent in the gut or crop, and (3) the 13 LAB found in culture-based studies are not specific to the crop but are a small subset of midgut or hindgut specific bacteria identified in many recent 454 amplicon-based studies. The crop is dominated by Lactobacillus kunkeei, and Alpha 2.2 (Acetobacteraceae), highly osmotolerant and acid resistant bacteria found in stored pollen and honey. Crop taxa at low abundance include core hindgut bacteria in transit to their primary niche, and potential pathogens or food spoilage organisms seemingly vectored from the pollination environment. We conclude that the crop microbial environment is influenced by worker task, and may function in both decontamination and inoculation. PMID:24740297

  18. Woody stem galls interact with foliage to affect community associations.

    PubMed

    Cooper, W R; Rieske, L K

    2009-04-01

    Gall wasps (Hymenoptera: Cynipidae) hijack the physiology of their host plant to produce galls that house wasps throughout their immature stages. The gall-maker-host plant interaction is highly evolved, and galls represent an extended phenotype of the gall wasp. We evaluated two-way interactions between stem galls produced by Dryocosmus kuriphilus Yasumatsu on Castanea spp. (Fagales: Fagaceae) and foliage directly attached to galls (gall leaves) using gall leaf excision experiments and herbivore bioassays. Early season gall leaf excision decreased the dry weight per chamber (nutritive index) and thickness of the protective schlerenchyma layer and increased the number of empty chambers and the occurrence and size of exterior fungal lesions. Leaf excision also caused a modestly significant (alpha = 0.1) increase in the incidence of feeding chamber fungi and herbivory by Curculio sayi Gyllenhal (Coleoptera: Curculionidae), and a modest decrease in parasitoids. This study shows that gall leaves are important for stem gall development, quality, and defenses, adding support for the nutrient and enemy hypotheses. We also evaluated the effects of stem galls on the suitability of gall leaves to Lymantria dispar L. (Lepidoptera: Lymantriidae) herbivory to assess the extent of gall defenses in important source leaves. Relative growth rate of L. dispar larvae was greater on gall leaves compared with normal leaves, indicating that, despite their importance, gall leaves may be more suitable to generalist insect herbivores, suggesting limitations to the extended phenotype of the gall wasp. Our results improve our knowledge of host-cynipid interactions, gall source-sink relations, and D. kuriphilus community interactions.

  19. Fish communities associated with a complex Mississippi stream system.

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Complex habitats such as sloughs, oxbows, and wetlands provide important ecosystem services for fish communities. While human manipulation of rivers and streams for flood control often reduce this complexity, some construction practices may provide an unexpected benefit. Structures such as borrow pi...

  20. Sediment bacterial communities associated with anaerobic biodegradation of bisphenol A.

    PubMed

    Yang, Yuyin; Wang, Zhao; He, Tao; Dai, Yu; Xie, Shuguang

    2015-07-01

    Bisphenol A (BPA) is one of the endocrine-disrupting chemicals that are ubiquitous in aquatic environments. Biodegradation is a major way to clean up the BPA pollution in sediments. However, information on the effective BPA biodegradation in anaerobic sediments is still lacking. The present study investigated the biodegradation potential of BPA in river sediment under nitrate- or sulfate-reducing conditions. After 120-day incubation, a high removal of BPA (93 or 89%) was found in sediment microcosms (amended with 50 mg kg(-1) BPA) under these two anaerobic conditions. Illumina MiSeq sequencing analysis indicated that Proteobacteria, Bacteroidetes, Chloroflexi, Firmicutes, Gemmatimonadetes, and Actinobacteria were the major bacterial groups in BPA-degrading sediments. The shift in bacterial community structure could occur with BPA biodegradation.

  1. Highly Variable Bacterial Communities Associated with the Octocoral Antillogorgia elisabethae.

    PubMed

    Robertson, Veronica; Haltli, Brad; McCauley, Erin P; Overy, David P; Kerr, Russell G

    2016-01-01

    Antillogorgia elisabethae (synonymous with Pseudopterogorgia elisabethae) is a common branching octocoral in Caribbean reef ecosystems. A. elisabethae is a rich source of anti-inflammatory diterpenes, thus this octocoral has been the subject of numerous natural product investigations, yet relatively little is known regarding the composition, diversity and the geographic and temporal stability of its microbiome. To characterize the composition, diversity and stability of bacterial communities of Bahamian A. elisabethae populations, 17 A. elisabethae samples originating from five sites within The Bahamas were characterized by 16S rDNA pyrosequencing. A. elisabethae bacterial communities were less diverse and distinct from those of surrounding seawater samples. Analyses of α- and β-diversity revealed that A. elisabethae bacterial communities were highly variable between A. elisabethae samples from The Bahamas. This contrasts results obtained from a previous study of three specimens collected from Providencia Island, Colombia, which found A. elisabethae bacterial communities to be highly structured. Taxa belonging to the Rhodobacteriales, Rhizobiales, Flavobacteriales and Oceanospiralles were identified as potential members of the A. elisabethae core microbiome. PMID:27681917

  2. Study of methanogen communities associated with different rumen protozoal populations

    PubMed Central

    Belanche, Alejandro; de la Fuente, Gabriel; Newbold, Charles J

    2014-01-01

    Protozoa-associated methanogens (PAM) are considered one of the most active communities in the rumen methanogenesis. This experiment investigated whether methanogens are sequestrated within rumen protozoa, and structural differences between rumen free-living methanogens and PAM. Rumen protozoa were harvested from totally faunated sheep, and six protozoal fractions (plus free-living microorganisms) were generated by sequential filtration. Holotrich-monofaunated sheep were also used to investigate the holotrich-associated methanogens. Protozoal size determined the number of PAM as big protozoa had 1.7–3.3 times more methanogen DNA than smaller protozoa, but also more endosymbiotic bacteria (2.2- to 3.5-fold times). Thus, similar abundance of methanogens with respect to total bacteria were observed across all protozoal fractions and free-living microorganisms, suggesting that methanogens are not accumulated within rumen protozoa in a greater proportion to that observed in the rumen as a whole. All rumen methanogen communities had similar diversity (22.2 ± 3.4 TRFs). Free-living methanogens composed a conserved community (67% similarity within treatment) in the rumen with similar diversity but different structures than PAM (P < 0.05). On the contrary, PAM constituted a more variable community (48% similarity), which differed between holotrich and total protozoa (P < 0.001). Thus, PAM constitutes a community, which requires further investigation as part of methane mitigation strategies. PMID:25195951

  3. The pathogenic persona of community-associated oral streptococci.

    PubMed

    Whitmore, Sarah E; Lamont, Richard J

    2011-07-01

    The mitis group streptococci (MGS) are widespread in the oral cavity and are traditionally associated with oral health. However, these organisms have many attributes that contribute to the development of pathogenic oral communities. MGS adhere rapidly to saliva-coated tooth surfaces, thereby providing an attachment substratum for more overtly pathogenic organisms such as Porphyromonas gingivalis, and the two species assemble into heterotypic communities. Close physical association facilitates physiologic support, and pathogens such as Aggregatibacter actinomycetemcomitans display resource partitioning to favour carbon sources generated by streptococcal metabolism. MGS exchange information with community members through a number of interspecies signalling systems including AI-2 and contact dependent mechanisms. Signal transduction systems induced in P. gingivalis are based on protein dephosphorylation mediated by the tyrosine phosphatase Ltp1, and converge on a LuxR-family transcriptional regulator, CdhR. Phenotypic responses in P. gingivalis include regulation of hemin uptake systems and gingipain activity, processes that are intimately linked to the virulence of the organism. Furthermore, communities of S. gordonii with P. gingivalis or with A. actinomycetemcomitans are more pathogenic in animal models than the constituent species alone. We propose that MGS should be considered accessory pathogens, organisms whose pathogenic potential only becomes evident in the context of a heterotypic microbial community.

  4. Microbial community associated with the colonial ascidian Cystodytes dellechiajei.

    PubMed

    Martínez-García, Manuel; Díaz-Valdés, Marta; Wanner, Gerhard; Ramos-Esplá, Alfonso; Antón, Josefa

    2007-02-01

    The ascidian Cystodytes dellechiajei (Della Valle, 1877) (phylum Chordata, class Ascidiacea, family Polycitoridae) is a colonial tunicate that inhabits benthic rock environments in the Atlantic, Pacific and Indian Oceans, as well as the Mediterranean Sea. Its life cycle has two phases, the adult sessile colony and the free-living larva. Both adult zooids and larvae are surrounded by a protective tunic that contains several eukaryotic cell lines, is composed mainly of acidic mucopolysacharides associated with collagen and elastin-like proteins, and is covered by a thin cuticle. The microbiota associated with the tunic tissues of adult colonies and larva of C. dellechiajei has been examined by optical, confocal and electron microscopy and by fluorescence in situ hybridization (FISH), denaturing gradient gel electrophoresis (DGGE), and 16S rRNA gene clone library analysis. Microscopy analyses indicated the presence inside the tunic, both for the adult and the larva, of a dense community of Bacteria while only the external surface of colony cuticle was colonized by diatoms, rodophyte algae and prokaryotic-like epiphytes. Transmission electron microscopy showed tunic eukaryotic cells that were engulfing and lysing bacteria. 16S rRNA gene analyses (DGGE and clone libraries) and FISH indicated that the community inside the tunic tissues of the adults and larvae was dominated by Alphaproteobacteria. Bacteria belonging to the phyla Gammaproteobacteria and Bacteroidetes were also detected in the adults. Many of the 16S rRNA gene sequences in the tunic tissues were related to known aerobic anoxygenic phototrophs (AAP), like Roseobacter sp. and Erythrobacter sp. In order to check whether the gene pufM, coding for the M subunit of the reaction centre complex of aerobic anoxygenic photosynthesis, was being expressed inside the ascidian tissues, two libraries, one for an adult colony and one for larva, of cDNA from the expressed pufM gene were also constructed. The sequences most frequently (64% for colony and 67% for larva) retrieved from these libraries presented > 90% aa identity with the pufM gene product of the Roseobacter-like group, a cluster of AAP widely detected in marine planktonic environments.

  5. Highly Variable Bacterial Communities Associated with the Octocoral Antillogorgia elisabethae

    PubMed Central

    Robertson, Veronica; Haltli, Brad; McCauley, Erin P.; Overy, David P.; Kerr, Russell G.

    2016-01-01

    Antillogorgia elisabethae (synonymous with Pseudopterogorgia elisabethae) is a common branching octocoral in Caribbean reef ecosystems. A. elisabethae is a rich source of anti-inflammatory diterpenes, thus this octocoral has been the subject of numerous natural product investigations, yet relatively little is known regarding the composition, diversity and the geographic and temporal stability of its microbiome. To characterize the composition, diversity and stability of bacterial communities of Bahamian A. elisabethae populations, 17 A. elisabethae samples originating from five sites within The Bahamas were characterized by 16S rDNA pyrosequencing. A. elisabethae bacterial communities were less diverse and distinct from those of surrounding seawater samples. Analyses of α- and β-diversity revealed that A. elisabethae bacterial communities were highly variable between A. elisabethae samples from The Bahamas. This contrasts results obtained from a previous study of three specimens collected from Providencia Island, Colombia, which found A. elisabethae bacterial communities to be highly structured. Taxa belonging to the Rhodobacteriales, Rhizobiales, Flavobacteriales and Oceanospiralles were identified as potential members of the A. elisabethae core microbiome.

  6. Yeast communities associated with artisanal mezcal fermentations from Agave salmiana.

    PubMed

    Verdugo Valdez, A; Segura Garcia, L; Kirchmayr, M; Ramírez Rodríguez, P; González Esquinca, A; Coria, R; Gschaedler Mathis, A

    2011-11-01

    The aims of this work were to characterize the fermentation process of mezcal from San Luis Potosi, México and identify the yeasts present in the fermentation using molecular culture-dependent methods (RFLP of the 5.8S-ITS and sequencing of the D1/D2 domain) and also by using a culture-independent method (DGGE). The alcoholic fermentations of two separate musts obtained from Agave salmiana were analyzed. Sugar, ethanol and major volatile compounds concentrations were higher in the first fermentation, which shows the importance of having a quality standard for raw materials, particularly in the concentration of fructans, in order to produce fermented Agave salmiana must with similar characteristics. One hundred ninety-two (192) different yeast colonies were identified, from those present on WL agar plates, by RFLP analysis of the ITS1-5.8S- ITS2 from the rRNA gene, with restriction endonucleases, HhaI, HaeIII and HinfI. The identified yeasts were: Saccharomyces cerevisiae, Kluyveromyces marxianus, Pichia kluyveri, Zygosaccharomyces bailii, Clavispora lusitaniae, Torulaspora delbrueckii, Candida ethanolica and Saccharomyces exiguus. These identifications were confirmed by sequencing the D1-D2 region of the 26S rRNA gene. With the PCR-DGGE method, bands corresponding to S. cerevisiae, K. marxianus and T. delbrueckii were clearly detected, confirming the results obtained with classic techniques.

  7. Fungal community associated with genetically modified poplar during metal phytoremediation.

    PubMed

    Hur, Moonsuk; Lim, Young Woon; Yu, Jae Jeong; Cheon, Se Uk; Choi, Young Im; Yoon, Seok-Hwan; Park, Sang-Cheol; Kim, Dong-Il; Yi, Hana

    2012-12-01

    Due to the increasing demand for phytoremediation, many transgenic poplars have been developed to enhance the bioremediation of heavy metals. However, structural changes to indigenous fungal communities by genetically modified organisms (GMO) presents a major ecological issue, due to the important role of fungi for plant growth in natural environments. To evaluate the effect of GM plant use on environmental fungal soil communities, extensive sequencing-based community analysis was conducted, while controlling the influence of plant clonality, plant age, soil condition, and harvesting season. The rhizosphere soils of GM and wild type (WT) poplars at a range of growth stages were sampled together with unplanted, contaminated soil, and the fungal community structures were investigated by pyrosequencing the D1/D2 region of the 28S rRNA gene. The results show that the overall structure of the rhizosphere fungal community was not significantly influenced by GM poplars. However, the presence of GM specific taxa, and faster rate of community change during poplar growth, appeared to be characteristic of the GM plant-induced effects on soil-born fungal communities. The results of this study provide additional information about the potential effects of GM poplar trees aged 1.5-3 years, on the soil fungal community.

  8. Diversity of Methicillin-Resistant Staphylococcus aureus (MRSA) Strains Isolated from Inpatients of 30 Hospitals in Orange County, California

    PubMed Central

    Hudson, Lyndsey O.; Murphy, Courtney R.; Spratt, Brian G.; Enright, Mark C.; Elkins, Kristen; Nguyen, Christopher; Terpstra, Leah; Gombosev, Adrijana; Kim, Diane; Hannah, Paul; Mikhail, Lydia; Alexander, Richard; Moore, Douglas F.; Huang, Susan S.

    2013-01-01

    There is a need for a regional assessment of the frequency and diversity of MRSA to determine major circulating clones and the extent to which community and healthcare MRSA reservoirs have mixed. We conducted a prospective cohort study of inpatients in Orange County, California, systematically collecting clinical MRSA isolates from 30 hospitals, to assess MRSA diversity and distribution. All isolates were characterized by spa typing, with selective PFGE and MLST to relate spa types with major MRSA clones. We collected 2,246 MRSA isolates from hospital inpatients. This translated to 91/10,000 inpatients with MRSA and an Orange County population estimate of MRSA inpatient clinical cultures of 86/100,000 people. spa type genetic diversity was heterogeneous between hospitals, and relatively high overall (72%). USA300 (t008/ST8), USA100 (t002/ST5) and a previously reported USA100 variant (t242/ST5) were the dominant clones across all Orange County hospitals, representing 83% of isolates. Fifteen hospitals isolated more t008 (USA300) isolates than t002/242 (USA100) isolates, and 12 hospitals isolated more t242 isolates than t002 isolates. The majority of isolates were imported into hospitals. Community-based infection control strategies may still be helpful in stemming the influx of traditionally community-associated strains, particularly USA300, into the healthcare setting. PMID:23637976

  9. Staphylococcus aureus Colonization Among Household Contacts of Patients With Skin Infections: Risk Factors, Strain Discordance, and Complex Ecology

    PubMed Central

    Miller, Loren G.; Eells, Samantha J.; Taylor, Alexis R.; David, Michael Z.; Ortiz, Nancy; Zychowski, Diana; Kumar, Neha; Cruz, Denise; Boyle-Vavra, Susan; Daum, Robert S.

    2012-01-01

    Background. The USA300 methicillin resistant Staphylococcus aureus (MRSA) genetic background has rapidly emerged as the predominant cause of community-associated S. aureus infections in the U.S. However, epidemiologic characteristics of S. aureus household transmission are poorly understood. Methods. We performed a cross-sectional study of adults and children with S. aureus skin infections and their household contacts in Los Angeles and Chicago. Subjects were surveyed for S. aureus colonization of the nares, oropharynx, and inguinal region and risk factors for S. aureus disease. All isolates underwent genetic typing. Results. We enrolled 1162 persons (350 index patients and 812 household members). The most common infection isolate characteristic was ST8/SCCmec IV, PVL+ MRSA (USA300) (53%). S. aureus colonized 40% (137/350) of index patients and 50% (405/812) of household contacts. A nares-only survey would have missed 48% of S. aureus and 51% of MRSA colonized persons. Sixty-five percent of households had >1 S. aureus genetic background identified and 26% of MRSA isolates in household contacts were discordant with the index patients' infecting MRSA strain type. Factors independently associated (P < .05) with the index strain type colonizing household contacts were recent skin infection, recent cephalexin use, and USA300 genetic background. Conclusions. In our study population, USA300 MRSA appeared more transmissible among household members compared with other S. aureus genetic backgrounds. Strain distribution was complex; >1 S. aureus genetic background was present in many households. S. aureus decolonization strategies may need to address extra-nasal colonization and the consequences of eradicating S. aureus genetic backgrounds infrequently associated with infection. PMID:22474221

  10. 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

  11. 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

  12. Survey of community-associated-methicillin-Resistant Staphylococcus aureus in Slovenia: identification of community-associated and livestock-associated clones.

    PubMed

    Dermota, U; Mueller-Premru, M; Švent-Kučina, N; Petrovič, Ž; Ribič, H; Rupnik, M; Janežič, S; Zdovc, I; Grmek-Košnik, I

    2015-09-01

    The epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) in Slovenia is poorly documented. The aim of this study was to investigate susceptibility patterns, virulence gene profile and clonality among MRSA isolates with positive screened resistance phenotype for CA-MRSA collected from patients in Slovenia, from January 2010 to December 2010. We included only MRSA isolates that were resistant to cefoxitin and oxacillin, and susceptible to at least two of the following four antibiotics: ciprofloxacin, erythromycin, clindamycin or gentamicin (presumptive CA-MRSA). Altogether 151 isolates fulfilled our screening phenotypic definition, 126 MRSA isolates were classified as CA-MRSA and 25 as HA-MRSA. Thirty-six per cent of them were resistant to ciprofloxacin, 24% to clindamycin, 33% to erythromycin and 13% to gentamicin. The mecA gene was detected in 150 isolates, while the mecC gene only in 1 isolate. The MRSA isolates were classified to 19 different clones. The most prevalent sequence types were ST5 (26.4%), ST45 (25.2%), ST22 (10.6%), ST398 (9.9%), ST8 (5.9%), ST7 (4.6%), ST1 (3.9%), ST152/377 (3.3%), ST228 (2.6%) and ST2883 (1.3%). The ST6, ST9, ST30, ST72, ST88, ST111, ST130, ST225 and ST772 were identified sporadically. The Panton-Valentine leukocidin (PVL) gene was detected in 13 (8.6%) isolates that belonged to ST5, ST7, ST8, ST22, ST72, ST88, ST 152/377 and ST772. Our results show high variability of CA-MRSA circulating in Slovenia and also the presence of LA-MRSA clones.

  13. Molecular epidemiology of community-onset methicillin-resistant Staphylococcus aureus infections in Israel.

    PubMed

    Biber, A; Parizade, M; Taran, D; Jaber, H; Berla, E; Rubin, C; Rahav, G; Glikman, D; Regev-Yochay, G

    2015-08-01

    Data on community-associated (CA) methicillin-resistant Staphylococcus aureus (MRSA) in Israel are scarce. The objective of this study was to characterize the major CA-MRSA clones in Israel. All clinical MRSA isolates detected in the community during a period of 2.5 years (2011-2013) from individuals insured by a major health maintenance organization in Israel were collected, with additional data from medical records. Antibiotic susceptibility patterns and staphylococcal chromosomal cassette mec (SCCmec) typing were determined. SCCmec IV and V isolates were further typed by pulsed-field gel electrophoresis (PFGE), spa typing, and detection of a panel of toxin genes. MRSA were detected in 280 patients, mostly from skin infections. Patients with SCCmec IV (n = 120, 43 %) were younger (p < 0.0001) and reported less contact with healthcare facilities. Almost all isolates were trimethoprim-sulfamethoxazole susceptible (98 %). spa-CC032, a typical nosocomial MRSA clone, accounted for 28 % of SCCmec IV. The two major CA-MRSA clones were t008 USA300 (13 %) and t991 (10 %); t991 was isolated mainly from children (75 %), was Panton-Valentine leukocidin (PVL) negative but eta-positive, and was typically susceptible to most antibiotic groups. PVL-positive strains (n = 31) included mainly USA300 (52 %) and t019 (13 %). While multiple genetic lineages were evident among community-onset MRSA in Israel, approximately 20 % are typical CA-MRSA clones, mainly USA300 and a local clone, t991.

  14. Autophagy mediates tolerance to Staphylococcus aureus alpha-toxin.

    PubMed

    Maurer, Katie; Reyes-Robles, Tamara; Alonzo, Francis; Durbin, Joan; Torres, Victor J; Cadwell, Ken

    2015-04-01

    Resistance and tolerance are two defense strategies employed by the host against microbial threats. Autophagy-mediated degradation of bacteria has been extensively described as a major resistance mechanism. Here we find that the dominant function of autophagy proteins during infections with the epidemic community-associated methicillin-resistant Staphylococcus aureus USA300 is to mediate tolerance rather than resistance. Atg16L1 hypomorphic mice (Atg16L1(HM)), which have reduced autophagy, were highly susceptible to lethality in both sepsis and pneumonia models of USA300 infection. Autophagy confers protection by limiting the damage caused by α-toxin, particularly to endothelial cells. Remarkably, Atg16L1(HM) mice display enhanced survival rather than susceptibility upon infection with α-toxin-deficient S. aureus. These results identify an essential role for autophagy in tolerance to Staphylococcal disease and highlight how a single virulence factor encoded by a pathogen can determine whether a given host factor promotes tolerance or resistance.

  15. Host and Environmental Specificity in Bacterial Communities Associated to Two Highly Invasive Marine Species (Genus Asparagopsis).

    PubMed

    Aires, Tânia; Serrão, Ester A; Engelen, Aschwin H

    2016-01-01

    As habitats change due to global and local pressures, population resilience, and adaptive processes depend not only on their gene pools but also on their associated bacteria communities. The hologenome can play a determinant role in adaptive evolution of higher organisms that rely on their bacterial associates for vital processes. In this study, we focus on the associated bacteria of the two most invasive seaweeds in southwest Iberia (coastal mainland) and nearby offshore Atlantic islands, Asparagopsis taxiformis and Asparagopsis armata. Bacterial communities were characterized using 16S rRNA barcoding through 454 next generation sequencing and exploratory shotgun metagenomics to provide functional insights and a backbone for future functional studies. The bacterial community composition was clearly different between the two species A. taxiformis and A. armata and between continental and island habitats. The latter was mainly due to higher abundances of Acidimicrobiales, Sphingomonadales, Xanthomonadales, Myxococcales, and Alteromonadales on the continent. Metabolic assignments for these groups contained a higher number of reads in functions related to oxidative stress and resistance to toxic compounds, more precisely heavy metals. These results are in agreement with their usual association with hydrocarbon degradation and heavy-metals detoxification. In contrast, A. taxiformis from islands contained more bacteria related to oligotrophic environments which might putatively play a role in mineralization of dissolved organic matter. The higher number of functional assignments found in the metagenomes of A. taxiformis collected from Cape Verde Islands suggest a higher contribution of bacteria to compensate nutrient limitation in oligotrophic environments. Our results show that Asparagopsis-associated bacterial communities have host-specificity and are modulated by environmental conditions. Whether this environmental effect reflects the host's selective requirements or the locally available bacteria remains to be addressed. However, the known functional capacities of these bacterial communities indicate their potential for eco-physiological functions that could be valuable for the host fitness.

  16. Changes in microbial communities associated with gas hydrates in subseafloor sediments from the Nankai Trough.

    PubMed

    Katayama, Taiki; Yoshioka, Hideyoshi; Takahashi, Hiroshi A; Amo, Miki; Fujii, Tetsuya; Sakata, Susumu

    2016-08-01

    Little is known about the microbial distribution patterns in subseafloor sediments. This study examines microbial diversity and activities in sediments of the Nankai Trough, where biogenic gas hydrates are deposited. Illumina sequencing of 16S rRNA genes revealed that the prokaryotic community structure is correlated with hydrate occurrence and depth but not with the sedimentary facies. The bacterial phyla 'Atribacteria' lineage JS1 and Chloroflexi dominated in all samples, whereas lower taxonomic units of Chloroflexi accounted for community variation related to hydrate saturation. In archaeal communities, 'Bathyarchaeota' was significantly abundant in the hydrate-containing samples, whereas Marine Benthic Group-B dominated in the upper sediments without hydrates. mcrA gene sequences assigned to deeply branching groups and ANME-1 were detected only in hydrate-containing samples. A predominance of hydrogenotrophic methanogens, Methanomicrobiales and Methanobacteriales, over acetoclastic methanogens was found throughout the depth. Incubation tests on hydrate-containing samples with a stable isotope tracer showed anaerobic methane oxidation activities under both low- and seawater-like salinity conditions. These results indicate that the distribution patterns of microorganisms involved in carbon cycling changed with gas hydrate occurrence, possibly because of the previous hydrate dissociation followed by pore water salinity decrease in situ, as previously proposed by a geochemical study at the study site. PMID:27170363

  17. Comparative Analysis of Prokaryotic Communities Associated with Organic and Conventional Farming Systems.

    PubMed

    Pershina, Elizaveta; Valkonen, Jari; Kurki, Päivi; Ivanova, Ekaterina; Chirak, Evgeny; Korvigo, Ilia; Provorov, Nykolay; Andronov, Evgeny

    2015-01-01

    One of the most important challenges in agriculture is to determine the effectiveness and environmental impact of certain farming practices. The aim of present study was to determine and compare the taxonomic composition of the microbiomes established in soil following long-term exposure (14 years) to a conventional and organic farming systems (CFS and OFS accordingly). Soil from unclared forest next to the fields was used as a control. The analysis was based on RT-PCR and pyrosequencing of 16S rRNA genes of bacteria and archaea. The number of bacteria was significantly lower in CFS than in OFS and woodland. The highest amount of archaea was detected in woodland, whereas the amounts in CFS and OFS were lower and similar. The most common phyla in the soil microbial communities analyzed were Proteobacteria (57.9%), Acidobacteria (16.1%), Actinobacteria (7.9%), Verrucomicrobia (2.0%), Bacteroidetes (2.7%) and Firmicutes (4.8%). Woodland soil differed from croplands in the taxonomic composition of microbial phyla. Croplands were enriched with Proteobacteria (mainly the genus Pseudomonas), while Acidobacteria were detected almost exclusively in woodland soil. The most pronounced differences between the CFS and OFS microbiomes were found within the genus Pseudomonas, which significantly (p<0,05) increased its number in CFS soil compared to OFS. Other differences in microbiomes of cropping systems concerned minor taxa. A higher relative abundance of bacteria belonging to the families Oxalobacteriaceae, Koribacteriaceae, Nakamurellaceae and genera Ralstonia, Paenibacillus and Pedobacter was found in CFS as compared with OFS. On the other hand, microbiomes of OFS were enriched with proteobacteria of the family Comamonadaceae (genera Hylemonella) and Hyphomicrobiaceae, actinobacteria from the family Micrococcaceae, and bacteria of the genera Geobacter, Methylotenera, Rhizobium (mainly Rhizobium leguminosarum) and Clostridium. Thus, the fields under OFS and CFS did not differ greatly for the composition of the microbiome. These results, which were also confirmed by cluster analysis, indicated that microbial communities in the field soil do not necessarily differ largely between conventional and organic farming systems.

  18. Impact of Phanerochaete chrysosporium on the Functional Diversity of Bacterial Communities Associated with Decaying Wood.

    PubMed

    Hervé, Vincent; Ketter, Elodie; Pierrat, Jean-Claude; Gelhaye, Eric; Frey-Klett, Pascale

    2016-01-01

    Bacteria and fungi naturally coexist in various environments including forest ecosystems. While the role of saprotrophic basidiomycetes in wood decomposition is well established, the influence of these fungi on the functional diversity of the wood-associated bacterial communities has received much less attention. Based on a microcosm experiment, we tested the hypothesis that both the presence of the white-rot fungus Phanerochaete chrysosporium and the wood, as a growth substrate, impacted the functional diversity of these bacterial communities. Microcosms containing sterile sawdust were inoculated with a microbial inoculum extracted from a forest soil, in presence or in absence of P. chrysosporium and subsequently, three enrichment steps were performed. First, bacterial strains were isolated from different microcosms previously analyzed by 16S rRNA gene-based pyrosequencing. Strains isolated from P. chrysosporium mycosphere showed less antagonism against this fungus compared to the strains isolated from the initial forest soil inoculum, suggesting a selection by the fungus of less inhibitory bacterial communities. Moreover, the presence of the fungus in wood resulted in a selection of cellulolytic and xylanolytic bacterial strains, highlighting the role of mycospheric bacteria in wood decomposition. Additionally, the proportion of siderophore-producing bacteria increased along the enrichment steps, suggesting an important role of bacteria in iron mobilization in decaying-wood. Finally, taxonomic identification of 311 bacterial isolates revealed, at the family level, strong similarities with the high-throughput sequencing data as well as with other studies in terms of taxonomic composition of the wood-associated bacterial community, highlighting that the isolated strains are representative of the wood-associated bacterial communities.

  19. Continous application of bioorganic fertilizer induced resilient culturable bacteria community associated with banana Fusarium wilt suppression.

    PubMed

    Fu, Lin; Ruan, Yunze; Tao, Chengyuan; Li, Rong; Shen, Qirong

    2016-01-01

    Fusarium wilt of banana always drives farmers to find new land for banana cultivation due to the comeback of the disease after a few cropping years. A novel idea for solving this problem is the continuous application of bioorganic fertilizer (BIO), which should be practiced from the beginning of banana planting. In this study, BIO was applied in newly reclaimed fields to pre-control banana Fusarium wilt and the culturable rhizobacteria community were evaluated using Biolog Ecoplates and culture-dependent denaturing gradient gel electrophoresis (CD-DGGE). The results showed that BIO application significantly reduced disease incidences and increased crop yields, respectivly. And the stabilized general bacterial metabolic potential, especially for the utilization of carbohydrates, carboxylic acids and phenolic compounds, was induced by BIO application. DGGE profiles demonstrated that resilient community structure of culturable rhizobacteria with higher richness and diversity were observed in BIO treated soils. Morever, enriched culturable bacteria affiliated with Firmicutes, Gammaproteobacteria and Actinobacteria were also detected. In total, continuous application of BIO effectively suppressed Fusarium wilt disease by stabilizing culturable bacterial metabolic potential and community structure. This study revealed a new method to control Fusarium wilt of banana for long term banana cultivation. PMID:27306096

  20. Fungal Communities Associated with the Biodegradation of Polyester Polyurethane Buried under Compost at Different Temperatures

    PubMed Central

    Zafar, Urooj; Houlden, Ashley

    2013-01-01

    Plastics play an essential role in the modern world due to their low cost and durability. However, accumulation of plastic waste in the environment causes wide-scale pollution with long-lasting effects, making plastic waste management expensive and problematic. Polyurethanes (PUs) are heteropolymers that made up ca. 7% of the total plastic production in Europe in 2011. Polyester PUs in particular have been extensively reported as susceptible to microbial biodegradation in the environment, particularly by fungi. In this study, we investigated the impact of composting on PUs, as composting is a microbially rich process that is increasingly being used for the processing of green waste and food waste as an economically viable alternative to landfill disposal. PU coupons were incubated for 12 weeks in fresh compost at 25°C, 45°C, and 50°C to emulate the thermophilic and maturation stages of the composting process. Incubation at all temperatures caused significant physical deterioration of the polyester PU coupons and was associated with extensive fungal colonization. Terminal restriction fragment length polymorphism (TRFLP) analysis and pyrosequencing of the fungal communities on the PU surface and in the surrounding compost revealed that the population on the surface of PU was different from the surrounding compost community, suggesting enrichment and selection. The most dominant fungi identified from the surfaces of PU coupons by pyrosequencing was Fusarium solani at 25°C, while at both 45°C and 50°C, Candida ethanolica was the dominant species. The results of this preliminary study suggest that the composting process has the potential to biodegrade PU waste if optimized further in the future. PMID:24056469

  1. Recent changes in phytoplankton communities associated with rapid regional climate change along the western Antarctic Peninsula.

    PubMed

    Montes-Hugo, Martin; Doney, Scott C; Ducklow, Hugh W; Fraser, William; Martinson, Douglas; Stammerjohn, Sharon E; Schofield, Oscar

    2009-03-13

    The climate of the western shelf of the Antarctic Peninsula (WAP) is undergoing a transition from a cold-dry polar-type climate to a warm-humid sub-Antarctic-type climate. Using three decades of satellite and field data, we document that ocean biological productivity, inferred from chlorophyll a concentration (Chl a), has significantly changed along the WAP shelf. Summertime surface Chl a (summer integrated Chl a approximately 63% of annually integrated Chl a) declined by 12% along the WAP over the past 30 years, with the largest decreases equatorward of 63 degrees S and with substantial increases in Chl a occurring farther south. The latitudinal variation in Chl a trends reflects shifting patterns of ice cover, cloud formation, and windiness affecting water-column mixing. Regional changes in phytoplankton coincide with observed changes in krill (Euphausia superba) and penguin populations.

  2. Analysis of the bacterial communities associated with different drinking water treatment processes.

    PubMed

    Zeng, Dan-Ning; Fan, Zhen-Yu; Chi, Liang; Wang, Xia; Qu, Wei-Dong; Quan, Zhe-Xue

    2013-09-01

    A drinking water plant was surveyed to determine the bacterial composition of different drinking water treatment processes (DWTP). Water samples were collected from different processing steps in the plant (i.e., coagulation, sedimentation, sand filtration, and chloramine disinfection) and from distantly piped water. The samples were pyrosequensed using sample-specific oligonucleotide barcodes. The taxonomic composition of the microbial communities of different DWTP and piped water was dominated by the phylum Proteobacteria. Additionally, a large proportion of the sequences were assigned to the phyla Actinobacteria and Bacteroidetes. The piped water exhibited increasing taxonomic diversity, including human pathogens such as the Mycobacterium, which revealed a threat to the safety of drinking water. Surprisingly, we also found that a sister group of SAR11 (LD12) persisted throughout the DWTP, which was always detected in freshwater aquatic systems. Moreover, Polynucleobacter, Rhodoferax, and a group of Actinobacteria, hgcI clade, were relatively consistent throughout the processes. It is concluded that smaller-size microorganisms tended to survive against the present treatment procedure. More improvement should be made to ensure the long-distance transmission drinking water.

  3. Biodiversity of Prokaryotic Communities Associated with the Ectoderm of Ectopleura crocea (Cnidaria, Hydrozoa)

    PubMed Central

    Di Camillo, Cristina Gioia; Luna, Gian Marco; Bo, Marzia; Giordano, Giuseppe; Corinaldesi, Cinzia; Bavestrello, Giorgio

    2012-01-01

    The surface of many marine organisms is colonized by complex communities of microbes, yet our understanding of the diversity and role of host-associated microbes is still limited. We investigated the association between Ectopleura crocea (a colonial hydroid distributed worldwide in temperate waters) and prokaryotic assemblages colonizing the hydranth surface. We used, for the first time on a marine hydroid, a combination of electron and epifluorescence microscopy and 16S rDNA tag pyrosequencing to investigate the associated prokaryotic diversity. Dense assemblages of prokaryotes were associated with the hydrant surface. Two microbial morphotypes were observed: one horseshoe-shaped and one fusiform, worm-like. These prokaryotes were observed on the hydrozoan epidermis, but not in the portions covered by the perisarcal exoskeleton, and their abundance was higher in March while decreased in late spring. Molecular analyses showed that assemblages were dominated by Bacteria rather than Archaea. Bacterial assemblages were highly diversified, with up to 113 genera and 570 Operational Taxonomic Units (OTUs), many of which were rare and contributed to <0.4%. The two most abundant OTUs, likely corresponding to the two morphotypes present on the epidermis, were distantly related to Comamonadaceae (genus Delftia) and to Flavobacteriaceae (genus Polaribacter). Epibiontic bacteria were found on E. crocea from different geographic areas but not in other hydroid species in the same areas, suggesting that the host-microbe association is species-specific. This is the first detailed report of bacteria living on the hydrozoan epidermis, and indeed the first study reporting bacteria associated with the epithelium of E. crocea. Our results provide a starting point for future studies aiming at clarifying the role of this peculiar hydrozoan-bacterial association. PMID:22768172

  4. Crohn associated microbial communities associated to colonic mucosal biopsies in patients of the western Mediterranean.

    PubMed

    Vidal, Roberto; Ginard, Daniel; Khorrami, Sam; Mora-Ruiz, Merit; Munoz, Raul; Hermoso, Marcela; Díaz, Sara; Cifuentes, Ana; Orfila, Alejandro; Rosselló-Móra, Ramon

    2015-09-01

    Next generation sequencing approaches allow the retrieval of several orders of magnitude larger numbers of amplified single sequences in 16S rRNA diversity surveys than classical methods. However, the sequences are only partial and thus lack sufficient resolution for a reliable identification. The OPU approach used here, based on a tandem combination of high quality 454 sequences (mean >500 nuc) applying strict OTU thresholds, and phylogenetic inference based on parsimony additions to preexisting trees, seemed to improve the identification yields at the species and genus levels. A total of thirteen biopsies of Crohn-diagnosed patients (CD) and seven healthy controls (HC) were studied. In most of the cases (73%), sequences were affiliated to known species or genera and distinct microbial patterns could be distinguished among the CD subjects, with a common depletion of Clostridia and either an increased presence of Bacteroidetes (CD1) or an anomalous overrepresentation of Proteobacteria (CD2). Faecalibacterium prausnitzii presence was undetectable in CD, whereas Bacteroides vulgatus-B. dorei characterized HC and some CD groups. Altogether, the results showed that a microbial composition with predominance of Clostridia followed by Bacteroidetes, with F. prausnitzii and B. vulgatus-B. dorei as major key bacteria, characterized what could be considered a balanced structure in HC. The depletion of Clostridia seemed to be a common trait in CD. PMID:26275394

  5. Identification and ecology of bacterial communities associated with necroses of three cactus species.

    PubMed

    Foster, J L; Fogleman, J C

    1993-01-01

    To compare the bacterial communities residing in necrotic tissues of columnar cacti of the Sonoran Desert, isolates from 39 organ pipe, 19 saguaro, and 16 senita cacti were obtained. The isolates were clustered into 28 conspecific groups on the basis of their fatty acid profiles. The distributions of the individual bacterial isolates varied among cactus species. Seven of the 28 species groups were unique to a particular cactus species, whereas 8 species groups were found in all three cacti. The effective number of bacterial species for each cactus species was positively correlated with both the chemical complexity and glucose concentration of the plant tissues. The effective number of bacterial species and bacterial distribution patterns were compared with those known for communities of cactophilic yeasts. The observed bacterial distribution patterns are most likely due to differences in the chemical compositions of the three cactus species. PMID:8439142

  6. A baseline study of benthic community associated with Amphioxus Sand in subtropical Hong Kong.

    PubMed

    Chen, Y; Cheung, S G; Shin, P K S

    2013-07-15

    An annual investigation on the seasonal changes of benthic community structure associated with Amphioxus Sand was conducted at two sites in the eastern waters of subtropical Hong Kong, where three species of amphioxus, Branchiostoma belcheri, B. japonicum and B. malayanum coexist. A total of 84 species and 4169 individuals were recorded at Tai Long Wan, whereas a total of 87 species and 3915 individuals were recorded at Pak Lap Wan. Benthic polychaetes were dominant, including high abundance of Onuphis eremita and Prionospio malmgreni. Results of cluster analysis showed significant community structures between the two areas because of difference in sediment granulometry. However, temporal changes within these Amphioxus Sand communities were minimal. In general, the Amphioxus Sand communities in Hong Kong showed higher species richness of Polychaeta as compared with similar studies elsewhere, possibly implying an increased level of organic pollution in Hong Kong waters. PMID:23622836

  7. Prevalence of inducible clindamycin resistance among community-associated staphylococcal isolates in central Serbia.

    PubMed

    Aleksandra, A D; Misic, M S; Mira, Z V; Violeta, N M; Dragana, I T; Zoran, B M; Dejan, V S; Milanko, S D; Dejan, B D

    2014-01-01

    The emergence of resistance to most antimicrobial agents in staphylococci indicates the need for new effective agents in the treatment of staphylococcal infections. Clindamycin is considered to be one safe, effective and less costly agent. We analysed 482 staphylococcal isolates. Detection of inducible clindamycin resistance was performed by the D-test, while the presence of methylases genes: erm (A), erm (B) and erm (C), as well as, macrolide efflux gene mef was determined by polymerase chain reaction. Inducible clindamycin resistance phenotype was significantly higher in Staphylococcus aureus (S. aureus) strains then in coagulase-negative staphylococci (CNS). Among analysed S. aureus isolates, the predominance of the erm (C) gene, followed by the erm (A) gene were detected. These results indicate that the D-test should be routinely performed on each staphylococcal isolates. PMID:24399388

  8. Comparative Analysis of Prokaryotic Communities Associated with Organic and Conventional Farming Systems

    PubMed Central

    Pershina, Elizaveta; Valkonen, Jari; Kurki, Päivi; Ivanova, Ekaterina; Chirak, Evgeny; Korvigo, Ilia; Provorov, Nykolay; Andronov, Evgeny

    2015-01-01

    One of the most important challenges in agriculture is to determine the effectiveness and environmental impact of certain farming practices. The aim of present study was to determine and compare the taxonomic composition of the microbiomes established in soil following long-term exposure (14 years) to a conventional and organic farming systems (CFS and OFS accordingly). Soil from unclared forest next to the fields was used as a control. The analysis was based on RT-PCR and pyrosequencing of 16S rRNA genes of bacteria and archaea. The number of bacteria was significantly lower in CFS than in OFS and woodland. The highest amount of archaea was detected in woodland, whereas the amounts in CFS and OFS were lower and similar. The most common phyla in the soil microbial communities analyzed were Proteobacteria (57.9%), Acidobacteria (16.1%), Actinobacteria (7.9%), Verrucomicrobia (2.0%), Bacteroidetes (2.7%) and Firmicutes (4.8%). Woodland soil differed from croplands in the taxonomic composition of microbial phyla. Croplands were enriched with Proteobacteria (mainly the genus Pseudomonas), while Acidobacteria were detected almost exclusively in woodland soil. The most pronounced differences between the CFS and OFS microbiomes were found within the genus Pseudomonas, which significantly (p<0,05) increased its number in CFS soil compared to OFS. Other differences in microbiomes of cropping systems concerned minor taxa. A higher relative abundance of bacteria belonging to the families Oxalobacteriaceae, Koribacteriaceae, Nakamurellaceae and genera Ralstonia, Paenibacillus and Pedobacter was found in CFS as compared with OFS. On the other hand, microbiomes of OFS were enriched with proteobacteria of the family Comamonadaceae (genera Hylemonella) and Hyphomicrobiaceae, actinobacteria from the family Micrococcaceae, and bacteria of the genera Geobacter, Methylotenera, Rhizobium (mainly Rhizobium leguminosarum) and Clostridium. Thus, the fields under OFS and CFS did not differ greatly for the composition of the microbiome. These results, which were also confirmed by cluster analysis, indicated that microbial communities in the field soil do not necessarily differ largely between conventional and organic farming systems. PMID:26684619

  9. Microbial communities associated with tree bark foliose lichens: a perspective on their microecology.

    PubMed

    Anderson, O Roger

    2014-01-01

    Tree-bark, foliose lichens occur widely on a global scale. In some locales, such as forests, they contribute a substantial amount of biomass. However, there are few research reports on microbial communities including eukaryotic microbes associated with foliose lichens. Lichens collected from tree bark at 11 locations (Florida, New York State, Germany, Australia, and the Arctic) were examined to determine the density and C-biomass of bacteria and some eukaryotic microbes, i.e. heterotrophic nanoflagellates (HNF) and amoeboid protists. A rich microbial diversity was found, including large plasmodial slime molds, in some cases exceeding 100 μm in size. The densities of HNF and amoeboid protists were each positively correlated with densities of bacteria, r = 0.84 and 0.80, respectively (p < 0.01, N = 11 for each analysis) indicating a likely bacterial-based food web. Microbial densities (number/g lichen dry weight) varied markedly across the geographic sampling sites: bacteria (0.7-13.1 × 10(8) ), HNF (0.2-6.8 × 10(6) ) and amoeboid protists (0.4-4.6 × 10(3) ). The ranges in C-biomass (μg/g lichen dry weight) across the 11 sites were: bacteria (8.8-158.5), HNF (0.03-0.85), and amoeboid protists (0.08-540), the latter broad range was due particularly to absence or presence of large slime mold plasmodia. PMID:24734903

  10. Soil microbial communities associated to plant rhizospheres in an organic farming system in Alabama

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The microbial communities under different organic crop rhizospheres (0-10 and 10-20 cm) were characterized using fatty acid methyl ester (FAME) and pyrosequencing techniques. The soil was a silt loam (12.8% clay, 71.8% silt and15.4% sand). Soils at this site are characterized as having pH of ~6.53, ...

  11. Soil Microbial Communities associated to Plant Rhizospheres in an Organic Farming System in Alabama

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The microbial communities under different organic crop rhizospheres (0-10 and 10-20 cm) were characterized using fatty acid methyl ester (FAME) and pyrosequencing techniques. The soil was a silt loam (12.8% clay, 71.8% silt and15.4% sand). Soils at this site are characterized as having pH of ~6.53,...

  12. Functional congruence of rhizosphere microbial communities associated to leguminous tree from Brazilian semiarid region.

    PubMed

    Taketani, Rodrigo Gouvêa; Kavamura, Vanessa Nessner; Mendes, Rodrigo; Melo, Itamar Soares

    2015-02-01

    Semiarid environments are characterized by the uneven spread of rain throughout the year. This leads to the establishment of a biota that can go through long periods without rain. In order to understand the dynamics of rhizosphere microbial communities across these contrasting seasons in Caatinga, we used the Ion Torrent platform to sequence the metagenome of the rhizosphere of a native leguminous plant (Mimosa tenuiflora). The annotation indicated that most abundant groups detected were the Actinobacteria and Proteobacteria, and the dominant functional groups were carbohydrate and protein metabolisms, and that in the wet season, the communities carried carbohydrate and amino acid metabolisms.The major differences observed between seasons were higher abundance of genes related to carbohydrate and amino acid metabolisms in the rainy season, indicating that the populations present might be better adapted to a higher abundance of organic matter. Besides, no clear separation of samples was detected based on their taxonomic composition whereas the functional composition indicates that samples from the rain season are more related. Altogether, our results indicate that there is al arge functional stability in these communities mostly due to the selection of features that aid the biota to endure the dry season and blossom during rain. PMID:25870877

  13. Microbially influenced corrosion communities associated with fuel-grade ethanol environments.

    PubMed

    Williamson, Charles H D; Jain, Luke A; Mishra, Brajendra; Olson, David L; Spear, John R

    2015-08-01

    Microbially influenced corrosion (MIC) is a costly problem that impacts hydrocarbon production and processing equipment, water distribution systems, ships, railcars, and other types of metallic infrastructure. In particular, MIC is known to cause considerable damage to hydrocarbon fuel infrastructure including production, transportation, and storage systems, often times with catastrophic environmental contamination results. As the production and use of alternative fuels such as fuel-grade ethanol (FGE) increase, it is important to consider MIC of engineered materials exposed to these "newer fuels" as they enter existing infrastructure. Reports of suspected MIC in systems handling FGE and water prompted an investigation of the microbial diversity associated with these environments. Small subunit ribosomal RNA gene pyrosequencing surveys indicate that acetic-acid-producing bacteria (Acetobacter spp. and Gluconacetobacter spp.) are prevalent in environments exposed to FGE and water. Other microbes previously implicated in corrosion, such as sulfate-reducing bacteria and methanogens, were also identified. In addition, acetic-acid-producing microbes and sulfate-reducing microbes were cultivated from sampled environments containing FGE and water. Results indicate that complex microbial communities form in these FGE environments and could cause significant MIC-related damage that may be difficult to control. How to better manage these microbial communities will be a defining aspect of improving mitigation of global infrastructure corrosion.

  14. Impact of Phanerochaete chrysosporium on the Functional Diversity of Bacterial Communities Associated with Decaying Wood

    PubMed Central

    Hervé, Vincent; Ketter, Elodie; Pierrat, Jean-Claude; Gelhaye, Eric; Frey-Klett, Pascale

    2016-01-01

    Bacteria and fungi naturally coexist in various environments including forest ecosystems. While the role of saprotrophic basidiomycetes in wood decomposition is well established, the influence of these fungi on the functional diversity of the wood-associated bacterial communities has received much less attention. Based on a microcosm experiment, we tested the hypothesis that both the presence of the white-rot fungus Phanerochaete chrysosporium and the wood, as a growth substrate, impacted the functional diversity of these bacterial communities. Microcosms containing sterile sawdust were inoculated with a microbial inoculum extracted from a forest soil, in presence or in absence of P. chrysosporium and subsequently, three enrichment steps were performed. First, bacterial strains were isolated from different microcosms previously analyzed by 16S rRNA gene-based pyrosequencing. Strains isolated from P. chrysosporium mycosphere showed less antagonism against this fungus compared to the strains isolated from the initial forest soil inoculum, suggesting a selection by the fungus of less inhibitory bacterial communities. Moreover, the presence of the fungus in wood resulted in a selection of cellulolytic and xylanolytic bacterial strains, highlighting the role of mycospheric bacteria in wood decomposition. Additionally, the proportion of siderophore-producing bacteria increased along the enrichment steps, suggesting an important role of bacteria in iron mobilization in decaying-wood. Finally, taxonomic identification of 311 bacterial isolates revealed, at the family level, strong similarities with the high-throughput sequencing data as well as with other studies in terms of taxonomic composition of the wood-associated bacterial community, highlighting that the isolated strains are representative of the wood-associated bacterial communities. PMID:26824755

  15. Archaeal communities associated with shallow to deep subseafloor sediments of the New Caledonia Basin.

    PubMed

    Roussel, Erwan G; Sauvadet, Anne-Laure; Chaduteau, Carine; Fouquet, Yves; Charlou, Jean-Luc; Prieur, Daniel; Cambon Bonavita, Marie-Anne

    2009-09-01

    The distribution of the archaeal communities in deep subseafloor sediments [0-36 m below the seafloor (mbsf)] from the New Caledonia and Fairway Basins was investigated using DNA- and RNA-derived 16S rRNA clone libraries, functional genes and denaturing gradient gel electrophoresis (DGGE). A new method, Co-Migration DGGE (CM-DGGE), was developed to access selectively the active archaeal diversity. Prokaryotic cell abundances at the open-ocean sites were on average approximately 3.5 times lower than at a site under terrestrial influence. The sediment surface archaeal community (0-1.5 mbsf) was characterized by active Marine Group 1 (MG-1) Archaea that co-occurred with ammonia monooxygenase gene (amoA) sequences affiliated to a group of uncultured sedimentary Crenarchaeota. However, the anoxic subsurface methane-poor sediments (below 1.5 mbsf) were dominated by less active archaeal communities, such as the Thermoplasmatales, Marine Benthic Group D and other lineages probably involved in the methane cycle (Methanosarcinales, ANME-2 and DSAG/MBG-B). Moreover, the archaeal diversity of some sediment layers was restricted to only one lineage (Uncultured Euryarchaeota, DHVE6, MBG-B, MG-1 and SAGMEG). Sequences forming two clusters within the Thermococcales order were also present in these cold subseafloor sediments, suggesting that these uncultured putative thermophilic archaeal communities might have originated from a different environment. This study shows a transition between surface and subsurface sediment archaeal communities.

  16. Changes in microbial communities associated with gas hydrates in subseafloor sediments from the Nankai Trough.

    PubMed

    Katayama, Taiki; Yoshioka, Hideyoshi; Takahashi, Hiroshi A; Amo, Miki; Fujii, Tetsuya; Sakata, Susumu

    2016-08-01

    Little is known about the microbial distribution patterns in subseafloor sediments. This study examines microbial diversity and activities in sediments of the Nankai Trough, where biogenic gas hydrates are deposited. Illumina sequencing of 16S rRNA genes revealed that the prokaryotic community structure is correlated with hydrate occurrence and depth but not with the sedimentary facies. The bacterial phyla 'Atribacteria' lineage JS1 and Chloroflexi dominated in all samples, whereas lower taxonomic units of Chloroflexi accounted for community variation related to hydrate saturation. In archaeal communities, 'Bathyarchaeota' was significantly abundant in the hydrate-containing samples, whereas Marine Benthic Group-B dominated in the upper sediments without hydrates. mcrA gene sequences assigned to deeply branching groups and ANME-1 were detected only in hydrate-containing samples. A predominance of hydrogenotrophic methanogens, Methanomicrobiales and Methanobacteriales, over acetoclastic methanogens was found throughout the depth. Incubation tests on hydrate-containing samples with a stable isotope tracer showed anaerobic methane oxidation activities under both low- and seawater-like salinity conditions. These results indicate that the distribution patterns of microorganisms involved in carbon cycling changed with gas hydrate occurrence, possibly because of the previous hydrate dissociation followed by pore water salinity decrease in situ, as previously proposed by a geochemical study at the study site.

  17. Identification and characterization of microbial biofilm communities associated with corroded oil pipeline surfaces.

    PubMed

    Lenhart, Tiffany R; Duncan, Kathleen E; Beech, Iwona B; Sunner, Jan A; Smith, Whitney; Bonifay, Vincent; Biri, Bernadette; Suflita, Joseph M

    2014-01-01

    Microbially influenced corrosion (MIC) has long been implicated in the deterioration of carbon steel in oil and gas pipeline systems. The authors sought to identify and characterize sessile biofilm communities within a high-temperature oil production pipeline, and to compare the profiles of the biofilm community with those of the previously analyzed planktonic communities. Eubacterial and archaeal 16S rRNA sequences of DNA recovered from extracted pipeline pieces, termed 'cookies,' revealed the presence of thermophilic sulfidogenic anaerobes, as well as mesophilic aerobes. Electron microscopy and elemental analysis of cookies confirmed the presence of sessile cells and chemical constituents consistent with corrosive biofilms. Mass spectrometry of cookie acid washes identified putative hydrocarbon metabolites, while surface profiling revealed pitting and general corrosion damage. The results suggest that in an established closed system, the biofilm taxa are representative of the planktonic eubacterial and archaeal community, and that sampling and monitoring of the planktonic bacterial population can offer insight into biocorrosion activity. Additionally, hydrocarbon biodegradation is likely to sustain these communities. The importance of appropriate sample handling and storage procedures to oilfield MIC diagnostics is highlighted.

  18. Diversity and bioprospecting of fungal communities associated with endemic and cold-adapted macroalgae in Antarctica

    PubMed Central

    Godinho, Valéria M; Furbino, Laura E; Santiago, Iara F; Pellizzari, Franciane M; Yokoya, Nair S; Pupo, Diclá; Alves, Tânia MA; S Junior, Policarpo A; Romanha, Alvaro J; Zani, Carlos L; Cantrell, Charles L; Rosa, Carlos A; Rosa, Luiz H

    2013-01-01

    We surveyed the distribution and diversity of fungi associated with eight macroalgae from Antarctica and their capability to produce bioactive compounds. The collections yielded 148 fungal isolates, which were identified using molecular methods as belonging to 21 genera and 50 taxa. The most frequent taxa were Geomyces species (sp.), Penicillium sp. and Metschnikowia australis. Seven fungal isolates associated with the endemic Antarctic macroalgae Monostroma hariotii (Chlorophyte) displayed high internal transcribed spacer sequences similarities with the psychrophilic pathogenic fungus Geomyces destructans. Thirty-three fungal singletons (66%) were identified, representing rare components of the fungal communities. The fungal communities displayed high diversity, richness and dominance indices; however, rarefaction curves indicated that not all of the fungal diversity present was recovered. Penicillium sp. UFMGCB 6034 and Penicillium sp. UFMGCB 6120, recovered from the endemic species Palmaria decipiens (Rhodophyte) and M. hariotii, respectively, yielded extracts with high and selective antifungal and/or trypanocidal activities, in which a preliminary spectral analysis using proton nuclear magnetic resonance spectroscopy indicated the presence of highly functionalised aromatic compounds. These results suggest that the endemic and cold-adapted macroalgae of Antarctica shelter a rich, diversity and complex fungal communities consisting of a few dominant indigenous or mesophilic cold-adapted species, and a large number of rare and/or endemic taxa, which may provide an interesting model of algal–fungal interactions under extreme conditions as well as a potential source of bioactive compounds. PMID:23702515

  19. The bacterial communities associated with fecal types and body weight of rex rabbits.

    PubMed

    Zeng, Bo; Han, Shushu; Wang, Ping; Wen, Bin; Jian, Wensu; Guo, Wei; Yu, Zhiju; Du, Dan; Fu, Xiangchao; Kong, Fanli; Yang, Mingyao; Si, Xiaohui; Zhao, Jiangchao; Li, Ying

    2015-01-01

    Rex rabbit is an important small herbivore for fur and meat production. However, little is known about the gut microbiota in rex rabbit, especially regarding their relationship with different fecal types and growth of the hosts. We characterized the microbiota of both hard and soft feces from rex rabbits with high and low body weight by using the Illumina MiSeq platform targeting the V4 region of the 16S rDNA. High weight rex rabbits possess distinctive microbiota in hard feces, but not in soft feces, from the low weight group. We detected the overrepresentation of several genera such as YS2/Cyanobacteria, and Bacteroidales and underrepresentation of genera such as Anaeroplasma spp. and Clostridiaceae in high weight hard feces. Between fecal types, several bacterial taxa such as Ruminococcaceae, and Akkermansia spp. were enriched in soft feces. PICRUSt analysis revealed that metabolic pathways such as "stilbenoid, diarylheptanoid, gingerol biosynthesis" were enriched in high weight rabbits, and pathways related to "xenobiotics biodegradation" and "various types of N-glycan biosynthesis" were overrepresented in rabbit soft feces. Our study provides foundation to generate hypothesis aiming to test the roles that different bacterial taxa play in the growth and caecotrophy of rex rabbits.

  20. Fungal Community Associated with Dactylopius (Hemiptera: Coccoidea: Dactylopiidae) and Its Role in Uric Acid Metabolism.

    PubMed

    Vera-Ponce de León, Arturo; Sanchez-Flores, Alejandro; Rosenblueth, Mónica; Martínez-Romero, Esperanza

    2016-01-01

    We studied fungal species associated with the carmine cochineal Dactylopius coccus and other non-domesticated Dactylopius species using culture-dependent and -independent methods. Thirty seven fungi were isolated in various culture media from insect males and females from different developmental stages and Dactylopius species. 26S rRNA genes and ITS sequences, from cultured fungal isolates revealed different species of Cryptococcus, Rhodotorula, Debaryomyces, Trametes, and Penicillium, which are genera newly associated with Dactylopius. Uric acid (UA) and uricase activity were detected in tissues extracts from different insect developmental stages. However, accumulation of high UA levels and low uricase activities were found only after antifungal treatments, suggesting an important role of fungal species in its metabolism. Additionally, uricolytic fungal isolates were identified and characterized that presumably are involved in nitrogen recycling metabolism. After metagenomic analyses from D. coccus gut and hemolymph DNA and from two published data sets, we confirmed the presence of fungal genes involved in UA catabolism, suggesting that fungi help in the nitrogen recycling process in Dactylopius by uricolysis. All these results show the importance of fungal communities in scale insects such as Dactylopius. PMID:27446001

  1. Bacterial communities associated with larval development of stable flies (Diptera: Muscidae).

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Background: Adult stable flies are hematophagous parasites that preferentially feed on cattle. Persistent attacks and painful bites of the adults contribute to an economic impact of ~$2 billion/yr on the US cattle industry. Although stable flies are important livestock pests, relatively little is ...

  2. Moisture parameters and fungal communities associated with gypsum drywall in buildings.

    PubMed

    Dedesko, Sandra; Siegel, Jeffrey A

    2015-01-01

    Uncontrolled excess moisture in buildings is a common problem that can lead to changes in fungal communities. In buildings, moisture parameters can be classified by location and include assessments of moisture in the air, at a surface, or within a material. These parameters are not equivalent in dynamic indoor environments, which makes moisture-induced fungal growth in buildings a complex occurrence. In order to determine the circumstances that lead to such growth, it is essential to have a thorough understanding of in situ moisture measurement, the influence of building factors on moisture parameters, and the levels of these moisture parameters that lead to indoor fungal growth. Currently, there are disagreements in the literature on this topic. A literature review was conducted specifically on moisture-induced fungal growth on gypsum drywall. This review revealed that there is no consistent measurement approach used to characterize moisture in laboratory and field studies, with relative humidity measurements being most common. Additionally, many studies identify a critical moisture value, below which fungal growth will not occur. The values defined by relative humidity encompassed the largest range, while those defined by moisture content exhibited the highest variation. Critical values defined by equilibrium relative humidity were most consistent, and this is likely due to equilibrium relative humidity being the most relevant moisture parameter to microbial growth, since it is a reasonable measure of moisture available at surfaces, where fungi often proliferate. Several sources concur that surface moisture, particularly liquid water, is the prominent factor influencing microbial changes and that moisture in the air and within a material are of lesser importance. However, even if surface moisture is assessed, a single critical moisture level to prevent fungal growth cannot be defined, due to a number of factors, including variations in fungal genera and/or species, temperature, and nutrient availability. Despite these complexities, meaningful measurements can still be made to inform fungal growth by making localised, long-term, and continuous measurements of surface moisture. Such an approach will capture variations in a material's surface moisture, which could provide insight on a number of conditions that could lead to fungal proliferation. PMID:26642923

  3. Fungal Community Associated with Dactylopius (Hemiptera: Coccoidea: Dactylopiidae) and Its Role in Uric Acid Metabolism

    PubMed Central

    Vera-Ponce de León, Arturo; Sanchez-Flores, Alejandro; Rosenblueth, Mónica; Martínez-Romero, Esperanza

    2016-01-01

    We studied fungal species associated with the carmine cochineal Dactylopius coccus and other non-domesticated Dactylopius species using culture-dependent and -independent methods. Thirty seven fungi were isolated in various culture media from insect males and females from different developmental stages and Dactylopius species. 26S rRNA genes and ITS sequences, from cultured fungal isolates revealed different species of Cryptococcus, Rhodotorula, Debaryomyces, Trametes, and Penicillium, which are genera newly associated with Dactylopius. Uric acid (UA) and uricase activity were detected in tissues extracts from different insect developmental stages. However, accumulation of high UA levels and low uricase activities were found only after antifungal treatments, suggesting an important role of fungal species in its metabolism. Additionally, uricolytic fungal isolates were identified and characterized that presumably are involved in nitrogen recycling metabolism. After metagenomic analyses from D. coccus gut and hemolymph DNA and from two published data sets, we confirmed the presence of fungal genes involved in UA catabolism, suggesting that fungi help in the nitrogen recycling process in Dactylopius by uricolysis. All these results show the importance of fungal communities in scale insects such as Dactylopius. PMID:27446001

  4. Population structure of microbial communities associated with two deep, anaerobic, alkaline aquifers.

    PubMed Central

    Fry, N K; Fredrickson, J K; Fishbain, S; Wagner, M; Stahl, D A

    1997-01-01

    Microbial communities of two deep (1,270 and 316 m) alkaline (pH 9.94 and 8.05), anaerobic (Eh, -137 and -27 mV) aquifers were characterized by rRNA-based analyses. Both aquifers, the Grande Ronde (GR) and Priest rapids (PR) formations, are located within the Columbia River Basalt Group in south-central Washington, and sulfidogenesis and methanogenesis characterize the GR and PR formations, respectively. RNA was extracted from microorganisms collected from groundwater by ultrafiltration through hollow-fiber membranes and hybridized to taxon-specific oligonucleotide probes. Of the three domains, Bacteria dominated both communities, making up to 92.0 and 64.4% of the total rRNA from the GR and PR formations, respectively. Eucarya comprised 5.7 and 14.4%, and Archaea comprised 1.8% and 2.5%, respectively. The gram-positive target group was found in both aquifers, 11.7% in GR and 7.6% in PR. Two probes were used to target sulfate- and/or metal-reducing bacteria within the delta subclass of Proteobacteria. The Desulfobacter groups was present (0.3%) only in the high-sulfate groundwater (GR). However, comparable hybridization to a probe selective for the desulfovibrios and some metal-reducing bacteria was found in both aquifers, 2.5 and 2.9% from the GR and PR formations, respectively. Selective PCR amplification and sequencing of the desulfovibrio/metal-reducing group revealed a predominance of desulfovibrios in both systems (17 of 20 clones), suggesting that their environmental distribution is not restricted by sulfate availability. PMID:9097447

  5. Weak habitat specificity in ectomycorrhizal communities associated with Salix herbacea and Salix polaris in alpine tundra.

    PubMed

    Ryberg, Martin; Andreasen, Mathias; Björk, Robert G

    2011-05-01

    This study explores mid-alpine ectomycorrhizal communities on Salix herbacea and Salix polaris in plant communities differing in nutrient status and snow conditions. Plant species were identified by tracking roots back to above ground structures while fungal species were identified using molecular methods. The fungi were identified to 34 molecular operational taxonomic units (MOTUs)/species but species accumulation curves indicated that the communities were only partially sampled. The estimated total species richness was 49 (±9 SD) MOTUs/species. No significant ectomycorrhizal community specificity was found between the two plant species and only weak specificity between different plant communities. Furthermore, no difference in proportion of colonized root tips could be demonstrated between plant communities. However, some fungal taxa showed tendencies to associate with specific environmental conditions. Sebacinaceae, Inocybe egenula, Russula cf. emetica, and a Tomentella sp. were found in meadow communities but not in the heath communities. Sistotrema cf. alboluteum and Tomentella cf. terrestris were only found in the dry and mesic heath communities. Classifications into exploration types showed that the contact type is more abundant in the dry heath community than the other communities. Cenococcum geophilum was the most common species but Cortinarius spp., Russula spp., Tomentella spp., and Lactarius spp. were also common. This study confirms that alpine communities are rich in ectomycorrhizal fungi including species from a wide variety of fungal lineages and also show that many dominant species have wide ecological amplitude.

  6. Impact of Phanerochaete chrysosporium on the Functional Diversity of Bacterial Communities Associated with Decaying Wood.

    PubMed

    Hervé, Vincent; Ketter, Elodie; Pierrat, Jean-Claude; Gelhaye, Eric; Frey-Klett, Pascale

    2016-01-01

    Bacteria and fungi naturally coexist in various environments including forest ecosystems. While the role of saprotrophic basidiomycetes in wood decomposition is well established, the influence of these fungi on the functional diversity of the wood-associated bacterial communities has received much less attention. Based on a microcosm experiment, we tested the hypothesis that both the presence of the white-rot fungus Phanerochaete chrysosporium and the wood, as a growth substrate, impacted the functional diversity of these bacterial communities. Microcosms containing sterile sawdust were inoculated with a microbial inoculum extracted from a forest soil, in presence or in absence of P. chrysosporium and subsequently, three enrichment steps were performed. First, bacterial strains were isolated from different microcosms previously analyzed by 16S rRNA gene-based pyrosequencing. Strains isolated from P. chrysosporium mycosphere showed less antagonism against this fungus compared to the strains isolated from the initial forest soil inoculum, suggesting a selection by the fungus of less inhibitory bacterial communities. Moreover, the presence of the fungus in wood resulted in a selection of cellulolytic and xylanolytic bacterial strains, highlighting the role of mycospheric bacteria in wood decomposition. Additionally, the proportion of siderophore-producing bacteria increased along the enrichment steps, suggesting an important role of bacteria in iron mobilization in decaying-wood. Finally, taxonomic identification of 311 bacterial isolates revealed, at the family level, strong similarities with the high-throughput sequencing data as well as with other studies in terms of taxonomic composition of the wood-associated bacterial community, highlighting that the isolated strains are representative of the wood-associated bacterial communities. PMID:26824755

  7. Vegetation communities associated with the 100-Area and 200-Area facilities on the Hanford Site

    SciTech Connect

    Stegen, J.A.

    1994-01-17

    The Hanford Site, Benton County, Washington, lies within the broad semi-arid shrub-steppe vegetation zone of the Columbia Basin. Thirteen different habitat types on the Hanford Site have been mapped in Habitat Types on the Hanford Site: Wildlife and Plant Species of Concern (Downs et al. 1993). In a broad sense, this classification is correct. On a smaller scale, however, finer delineations are possible. This study was conducted to determine the plant communities and estimate vegetation cover in and directly adjacent to the 100 and 200 Areas, primarily in relation to waste sites, as part of a comprehensive ecological study for the Compensation Environmental Response, Compensation, and Liability Act (CERCLA) characterization of the 100 and 200 Areas. During the summer of 1993, field surveys were conducted and a map of vegetation communities in each area, including dominant species associations, was produced. The field surveys consisted of qualitative community delineations. The community delineations described were made by field reconnaissance and are qualitative in nature. The delineations were made by visually determining the dominant plant species or vegetation types and were based on the species most apparent at the time of inspection. Additionally, 38 transects were run in these plant communities to try to obtain a more accurate representation of the community. Because habitat disturbances from construction/operations activities continue to occur in these areas, users of this information should be cautious in applying these maps without a current ground survey. This work will complement large-scale habitat maps of the Hanford Site.

  8. Fish communities associated with cold-water corals vary with depth and substratum type

    NASA Astrophysics Data System (ADS)

    Milligan, Rosanna J.; Spence, Gemma; Roberts, J. Murray; Bailey, David M.

    2016-08-01

    Understanding the processes that drive the distribution patterns of organisms and the scales over which these processes operate are vital when considering the effective management of species with high commercial or conservation value. In the deep sea, the importance of scleractinian cold-water corals (CWCs) to fish has been the focus of several studies but their role remains unclear. We propose this may be due to the confounding effects of multiple drivers operating over multiple spatial scales. The aims of this study were to investigate the role of CWCs in shaping fish community structure and individual species-habitat associations across four spatial scales in the NE Atlantic ranging from "regions" (separated by >500 km) to "substratum types" (contiguous). Demersal fish and substratum types were quantified from three regions: Logachev Mounds, Rockall Bank and Hebrides Terrace Seamount (HTS). PERMANOVA analyses showed significant differences in community composition between all regions which were most likely caused by differences in depths. Within regions, significant variation in community composition was recorded at scales of c. 20-3500 m. CWCs supported significantly different fish communities to non-CWC substrata at Rockall Bank, Logachev and the HTS. Single-species analyses using generalised linear mixed models showed that Sebastes sp. was strongly associated with CWCs at Rockall Bank and that Neocyttus helgae was more likely to occur in CWCs at the HTS. Depth had a significant effect on several other fish species. The results of this study suggest that the importance of CWCs to fish is species-specific and depends on the broader spatial context in which the substratum is found. The precautionary approach would be to assume that CWCs are important for associated fish, but must acknowledge that CWCs in different depths will not provide redundancy or replication within spatially-managed conservation networks.

  9. Invertebrate communities associated with hard bottom habitats in the South Atlantic Bight

    NASA Astrophysics Data System (ADS)

    Wenner, E. L.; Knott, D. M.; Van Dolah, R. F.; Burrell, V. G.

    1983-08-01

    Epibenthic invertebrates associated with nine hard bottom areas in the South Atlantic Bight between South Carolina and northern Florida were collected with dredge, trawl, suction and grab samplers to evaluate species composition, biomass, abundance, diversity, spatial distributions, and seasonality (winter and summer). Species composition changed noticeably with depth and season. Inner and outer shelf stations were least similar in species composition. Middle shelf areas were transitional and contained taxa characteristic of both inner and outer sites. Bryozoa (88 taxa), Cnidaria (85 taxa), Porifera (67 taxa), Annelida (261 taxa) and Mollusca (203 taxa) represented the richest taxonomic groups of the 1175 taxa collected. Both diversity (1175 total taxa) and biomass (1995 kg total) of invertebrates from hard bottom areas exceeded those reported in the literature for sand bottom communities. Sponges accounted for >60% of the total invertebrate biomass collected by dredge and trawl during both seasons. High diversity values were attributed primarily to habitat complexity and did not exhibit any discernible pattern with depth or latitude.

  10. SMALL MAMMAL COMMUNITIES ASSOCIATED WITH BLACK-TAILED PRAIRIE DOG COLONIES. (R829091)

    EPA Science Inventory

    The perspectives, information and conclusions conveyed in research project abstracts, progress reports, final reports, journal abstracts and journal publications convey the viewpoints of the principal investigator and may not represent the views and policies of ORD and EPA. Concl...

  11. Virulence and biodegradation potential of dynamic microbial communities associated with decaying Cladophora in Great Lakes

    USGS Publications Warehouse

    Chun, Chan Lan; Peller, Julie R.; Shively, Dawn; Byappanahalli, Muruleedhara N.; Whitman, Richard L.; Staley, Christopher; Zhang, Qian; Ishii, Satoshi; Sadowsky, Michael J.

    2017-01-01

    Cladophora mats that accumulate and decompose along shorelines of the Great Lakes create potential threats to the health of humans and wildlife. The decaying algae create a low oxygen and redox potential environment favoring growth and persistence of anaerobic microbial populations, including Clostridium botulinum, the causal agent of botulism in humans, birds, and other wildlife. In addition to the diverse population of microbes, a dynamic chemical environment is generated, which involves production of numerous organic and inorganic substances, many of which are believed to be toxic to the sand and aquatic biotic communities. In this study, we used 16S-rDNA-based-amplicon sequencing and microfluidic-based quantitative PCR approaches to characterize the bacterial community structure and the abundances of human pathogens associated with Cladophora at different stages (up to 90 days) of algal decay in laboratory microcosms. Oxygen levels were largely depleted after a few hours of incubation. As Cladophora decayed, the algal microbial biodiversity decreased within 24 h, and the mat transitioned from an aerobic to anaerobic environment. There were increasing abundances of enteric and pathogenic bacteria during decomposition of Cladophora, including Acinetobacter, Enterobacter, Kluyvera, Cedecea, and others. In contrast, there were no or very few sequences (< 0.07%) assigned to such groups in fresh Cladophora samples. Principal coordinate analysis indicated that the bacterial community structure was dynamic and changed significantly with decay time. Knowledge of microbial communities and chemical composition of decaying algal mats is critical to our further understanding of the role that Cladophora plays in a beach ecosystem's structure and function, including the algal role in trophic interactions. Based on these findings, public and environmental health concerns should be considered when decaying Cladophora mats accumulate Great Lakes shorelines.

  12. Characterization of Bacterial Communities Associated with the Tyrian Purple Producing Gland in a Marine Gastropod

    PubMed Central

    Ngangbam, Ajit Kumar; Baten, Abdul; Waters, Daniel L. E.; Whalan, Steve; Benkendorff, Kirsten

    2015-01-01

    Dicathais orbita is a marine mollusc recognised for the production of anticancer compounds that are precursors to Tyrian purple. This study aimed to assess the diversity and identity of bacteria associated with the Tyrian purple producing hypobranchial gland, in comparison with foot tissue, using a high-throughput sequencing approach. Taxonomic and phylogenetic analysis of variable region V1-V3 of 16S rRNA bacterial gene amplicons in QIIME and MEGAN were carried out. This analysis revealed a highly diverse bacterial assemblage associated with the hypobranchial gland and foot tissues of D. orbita. The dominant bacterial phylum in the 16S rRNA bacterial profiling data set was Proteobacteria followed by Bacteroidetes, Tenericutes and Spirochaetes. In comparison to the foot, the hypobranchial gland had significantly lower bacterial diversity and a different community composition, based on taxonomic assignment at the genus level. A higher abundance of indole producing Vibrio spp. and the presence of bacteria with brominating capabilities in the hypobranchial gland suggest bacteria have a potential role in biosynthesis of Tyrian purple in D. orbita. PMID:26488885

  13. Microbial Communities Associated with Biogenic Iron Oxide Mineralization in Circumneutral pH Environments

    NASA Astrophysics Data System (ADS)

    Chan, C. S.; Banfield, J. F.

    2002-12-01

    Lithotrophic growth on iron is a metabolism that has been found in a variety of neutral pH environments and is likely important in sustaining life in microaerophilic solutions, especially those low in organics. The composition of the microbial communities, especially the organisms that are responsible for iron oxidation, and carbon and nitrogen fixation, are not known, yet the ability to recognize these contributions is vital to our understanding of iron cycling in natural environments. Our approach has been to study the microbial community structure, mineralogy, and geochemistry of ~20 cm thick, 100's meters long, fluffy iron oxide-encrusted biological mats growing in the Piquette Mine tunnel, and to compare the results to those from geochemically similar environments. In situ measurements (Hydrolab) and geochemical characterization of bulk water samples and peepers (dialysis sampling vials) indicate that the environment is microaerobic, with micromolar levels of iron, high carbonate and sulfate, and typical groundwater nitrate and nitrite concentrations. 16S rDNA clone libraries show that the microbial mat and water contain communities with considerable diversity within the Bacterial domain, a large proportion of Nitrospira and Betaproteobacteria, and no Archaea. Because clone library data are not necessarily indicative of actual abundance, fluorescence in-situ hybridization (FISH) was performed on water, mat, and sediment samples from the Piquette mine and two circumneutral iron- and carbonate-rich springs in the Oregon Cascade Range. Domain- and phylum-level probes were chosen based on the clone library results (Nitrospira, Beta- and Gammaproteobacteria, Acidobacteria, Actinobacteria, Chloroflexi, and Planctomyces). FISH data reveal spatial associations between specific microbial groups and mineralized structures. The organisms responsible for making the mineralized sheaths that compose the bulk of the iron oxide mat are Betaproteobacteria (probably Leptothrix spp.). However, only a small proportion of the cells in the mat reside within the sheaths. Most are located on or around the sheaths, which provide a physical framework for the community. Preliminary results from FISH experiments on the iron-rich spring samples show some similarities, including an abundance of Betaproteobacteria. Enrichment and isolation experiments are being performed to identify the iron-oxidizing organisms. Iron-oxidizers have been enriched from all sites. In some cultures it has been difficult to isolate the iron-oxidizing organisms from a non-iron-oxidizing heterotroph, possibly indicating co-dependence. Knowledge of the microbial community structure and the metabolic activities of key members will enable us to better understand the processes and chemical conditions which generate iron oxide deposits found in the geologic record on Earth and possibly extraterrestrial habitats.

  14. Biogas production using anaerobic groundwater containing a subterranean microbial community associated with the accretionary prism

    PubMed Central

    Baito, Kyohei; Imai, Satomi; Matsushita, Makoto; Otani, Miku; Sato, Yu; Kimura, Hiroyuki

    2015-01-01

    In a deep aquifer associated with an accretionary prism, significant methane (CH4) is produced by a subterranean microbial community. Here, we developed bioreactors for producing CH4 and hydrogen (H2) using anaerobic groundwater collected from the deep aquifer. To generate CH4, the anaerobic groundwater amended with organic substrates was incubated in the bioreactor. At first, H2 was detected and accumulated in the gas phase of the bioreactor. After the H2 decreased, rapid CH4 production was observed. Phylogenetic analysis targeting 16S rRNA genes revealed that the H2-producing fermentative bacterium and hydrogenotrophic methanogen were predominant in the reactor. The results suggested that syntrophic biodegradation of organic substrates by the H2-producing fermentative bacterium and the hydrogenotrophic methanogen contributed to the CH4 production. For H2 production, the anaerobic groundwater, amended with organic substrates and an inhibitor of methanogens (2-bromoethanesulfonate), was incubated in a bioreactor. After incubation for 24 h, H2 was detected from the gas phase of the bioreactor and accumulated. Bacterial 16S rRNA gene analysis suggested the dominance of the H2-producing fermentative bacterium in the reactor. Our study demonstrated a simple and rapid CH4 and H2 production utilizing anaerobic groundwater containing an active subterranean microbial community. PMID:25267392

  15. Invertebrate communities associated with Bangia atropurpurea and Cladophora glomerata in western Lake Erie

    USGS Publications Warehouse

    Chilton, E.W.; Lowe, R.L.; Schurr, K.M.

    1986-01-01

    The appearance of the marine alga Bangia atropurpurea (Rhodophyta) in Lake Erie has been followed by its rapid dispersal throughout the eulittoral zone of the lake. Bangia was extensively sampled to determine its suitability as a habitat for littoral organisms. Present data indicate that the only organisms capable of maintaining populations on Bangia filaments are larval Chironomidae. Cladophora supports a larger and more diverse community. It is concluded that the mucilaginous cell wall of Bangia provides a less stable substrate for attached or clinging organisms than does the cellulose cell wall of Cladophora. The presence of Bangia in the littoral zone of Lake Erie results in a reduction of the quantity and diversity of algal epiphytes and may negatively impact the littoral food web.

  16. Host and Environmental Specificity in Bacterial Communities Associated to Two Highly Invasive Marine Species (Genus Asparagopsis)

    PubMed Central

    Aires, Tânia; Serrão, Ester A.; Engelen, Aschwin H.

    2016-01-01

    As habitats change due to global and local pressures, population resilience, and adaptive processes depend not only on their gene pools but also on their associated bacteria communities. The hologenome can play a determinant role in adaptive evolution of higher organisms that rely on their bacterial associates for vital processes. In this study, we focus on the associated bacteria of the two most invasive seaweeds in southwest Iberia (coastal mainland) and nearby offshore Atlantic islands, Asparagopsis taxiformis and Asparagopsis armata. Bacterial communities were characterized using 16S rRNA barcoding through 454 next generation sequencing and exploratory shotgun metagenomics to provide functional insights and a backbone for future functional studies. The bacterial community composition was clearly different between the two species A. taxiformis and A. armata and between continental and island habitats. The latter was mainly due to higher abundances of Acidimicrobiales, Sphingomonadales, Xanthomonadales, Myxococcales, and Alteromonadales on the continent. Metabolic assignments for these groups contained a higher number of reads in functions related to oxidative stress and resistance to toxic compounds, more precisely heavy metals. These results are in agreement with their usual association with hydrocarbon degradation and heavy-metals detoxification. In contrast, A. taxiformis from islands contained more bacteria related to oligotrophic environments which might putatively play a role in mineralization of dissolved organic matter. The higher number of functional assignments found in the metagenomes of A. taxiformis collected from Cape Verde Islands suggest a higher contribution of bacteria to compensate nutrient limitation in oligotrophic environments. Our results show that Asparagopsis-associated bacterial communities have host-specificity and are modulated by environmental conditions. Whether this environmental effect reflects the host's selective requirements or the locally available bacteria remains to be addressed. However, the known functional capacities of these bacterial communities indicate their potential for eco-physiological functions that could be valuable for the host fitness. PMID:27148239

  17. Ascomycete fungal communities associated with early decaying leaves of Spartina spp. from central California estuaries.

    PubMed

    Lyons, Justine I; Alber, Merryl; Hollibaugh, James T

    2010-02-01

    Ascomycetous fungi play an important role in the early stages of decomposition of Spartina alterniflora, but their role in the decomposition of other Spartina species has not been investigated. Here we use fingerprint (terminal restriction fragment length polymorphism) and phylogenetic analyses of the 18S to 28S internal transcribed spacer region to compare the composition of the ascomycete fungal communities on early decay blades of Spartina species (Spartina alterniflora, Spartina densiflora, Spartina foliosa, and a hybrid (S. alterniflora x S. foliosa)) collected from three salt marshes in San Francisco Bay and one in Tomales Bay, California, USA. Phaeosphaeria spartinicola was found on all samples collected and was often dominant. Two other ascomycetes, Phaeosphaeria halima and Mycosphaerella sp. strain 2, were also common. These three species are the same ascomycetes previously identified as the dominant fungal decomposers on S. alterniflora on the east coast. Ascomycetes appeared to exhibit varying degrees of host specificity, demonstrated by grouping patterns on phylogenetic trees. Neither the exotic S. alterniflora nor the hybrid supported fungal flora different from that of the native S. foliosa. However, S. densiflora had a significantly different fungal community than the other species, and hosted at least two unique ascomycetes. Significant differences in the fungal decomposer communities were also detected within species (two clones of S. foliosa), but these were minor and may be due to morphological differences among the plants.

  18. Microbial communities associated with Antarctic snow pack and their biogeochemical implications.

    PubMed

    Antony, Runa; Sanyal, Aritri; Kapse, Neelam; Dhakephalkar, Prashant K; Thamban, Meloth; Nair, Shanta

    2016-11-01

    Snow ecosystems represent a large part of the Earth's biosphere and harbour diverse microbial communities. Despite our increased knowledge of snow microbial communities, the question remains as to their functional potential, particularly with respect to their role in adapting to and modifying the specific snow environment. In this work, we investigated the diversity and functional capabilities of microorganisms from 3 regions of East Antarctica, with respect to compounds present in snow and tested whether their functional signature reflected the snow environment. A diverse assemblage of bacteria (Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes, Deinococcus-Thermus, Planctomycetes, Verrucomicrobia), archaea (Euryarchaeota), and eukarya (Basidiomycota, Ascomycota, Cryptomycota and Rhizaria) were detected through culture-dependent and -independent methods. Although microbial communities observed in the three snow samples were distinctly different, all isolates tested produced one or more of the following enzymes: lipase, protease, amylase, β-galactosidase, cellulase, and/or lignin modifying enzyme. This indicates that the snow pack microbes have the capacity to degrade organic compounds found in Antarctic snow (proteins, lipids, carbohydrates, lignin), thus highlighting their potential to be involved in snow chemistry.

  19. Microbially influenced corrosion communities associated with fuel-grade ethanol environments.

    PubMed

    Williamson, Charles H D; Jain, Luke A; Mishra, Brajendra; Olson, David L; Spear, John R

    2015-08-01

    Microbially influenced corrosion (MIC) is a costly problem that impacts hydrocarbon production and processing equipment, water distribution systems, ships, railcars, and other types of metallic infrastructure. In particular, MIC is known to cause considerable damage to hydrocarbon fuel infrastructure including production, transportation, and storage systems, often times with catastrophic environmental contamination results. As the production and use of alternative fuels such as fuel-grade ethanol (FGE) increase, it is important to consider MIC of engineered materials exposed to these "newer fuels" as they enter existing infrastructure. Reports of suspected MIC in systems handling FGE and water prompted an investigation of the microbial diversity associated with these environments. Small subunit ribosomal RNA gene pyrosequencing surveys indicate that acetic-acid-producing bacteria (Acetobacter spp. and Gluconacetobacter spp.) are prevalent in environments exposed to FGE and water. Other microbes previously implicated in corrosion, such as sulfate-reducing bacteria and methanogens, were also identified. In addition, acetic-acid-producing microbes and sulfate-reducing microbes were cultivated from sampled environments containing FGE and water. Results indicate that complex microbial communities form in these FGE environments and could cause significant MIC-related damage that may be difficult to control. How to better manage these microbial communities will be a defining aspect of improving mitigation of global infrastructure corrosion. PMID:26092755

  20. Endophytic fungi community associated with the dicotyledonous plant Colobanthus quitensis (Kunth) Bartl. (Caryophyllaceae) in Antarctica.

    PubMed

    Rosa, Luiz Henrique; Almeida Vieira, Mariana de Lourdes; Santiago, Iara Furtado; Rosa, Carlos Augusto

    2010-07-01

    This work describes the distribution and diversity of fungal endophytes associated with leaves of Colobanthus quitensis, a dicotyledonous plant that lives in Antarctica. A total of 188 fungal isolates were obtained from six different sites located across a 25.5-km transect through Admiralty Bay, at King George Island. The ITS1-5.8S-ITS2 nuclear ribosomal gene was sequenced and the endophytic fungi were identified as species belonging to the genera Aspergillus, Cadophora, Davidiella, Entrophospora, Fusarium, Geomyces, Gyoerffyella, Microdochium, Mycocentrospora, and Phaeosphaeria. Davidiella tassiana was the prevalent species with 20.2% abundance. The endophytic fungal community showed low richness and high dominance indexes. Eleven endophytic taxa (58%) were fungi able to produce melanin in their hyphae, which may confer resistance against freezing temperatures and high rates of UV radiation and may increase their fitness in the extreme conditions of the Antarctic environment. In addition, phytopathogenic and decomposer species associated with healthy leaves of C. quitensis were found. The results obtained in this work show that C. quitensis is an interesting reservoir of saprobic and pathogenic fungal species, and could be a community model for further ecological and evolutionary studies, as well as studies of the adaptation mechanisms these microorganisms have to the extreme conditions in Antarctica. PMID:20455944

  1. Changes in soil oribatid communities associated with conversion from conventional to organic agriculture.

    PubMed

    Khalil, Mohamed A; Al-Assiuty, Abdel-Naieem I M; van Straalen, Nico M; Al-Assiuty, Basma A

    2016-02-01

    We investigated the effects of switching from conventional management to organic management on the abundance and community composition of soil-living oribatid mites in clover fields in an experimental agricultural station at Al-Fayoum, Egypt. The site had two adjacent fields with identical vegetation cover but different management. Fifteen random soil samples were collected monthly from each of three plots per field, from October to March. We characterized the soils with respect to various physicochemical variables as well as fungal community composition, and estimated mite densities through core sampling. Organic fields had a significantly more abundant oribatid community than did conventional fields. Also the abundance of soil fungi was greater in the organically managed field. Organic management promoted common oribatid mite species with a wide ecological amplitude that already had a high abundance where such common species are more responsive to changes in agricultural management. However, some species of mite responded indifferent or negative to the switch from conventional to organic management. Overall, the differences between the two ecological systems were mainly quantitative. Species diversities of both mite and fungal communities did not differ much between the two management systems. Diversity (H0) and equitability (E) of soil oribatid communities were higher in conventional plots than in the organic plots during the first 2 months but indistinguishable thereafter. Our study confirmed that organic management stimulates soilorganic matter build-up, with positive effects on both fungal and oribatid mite abundance and possible long-term effects on soil function.

  2. Fungal Community Associated with Dactylopius (Hemiptera: Coccoidea: Dactylopiidae) and Its Role in Uric Acid Metabolism.

    PubMed

    Vera-Ponce de León, Arturo; Sanchez-Flores, Alejandro; Rosenblueth, Mónica; Martínez-Romero, Esperanza

    2016-01-01

    We studied fungal species associated with the carmine cochineal Dactylopius coccus and other non-domesticated Dactylopius species using culture-dependent and -independent methods. Thirty seven fungi were isolated in various culture media from insect males and females from different developmental stages and Dactylopius species. 26S rRNA genes and ITS sequences, from cultured fungal isolates revealed different species of Cryptococcus, Rhodotorula, Debaryomyces, Trametes, and Penicillium, which are genera newly associated with Dactylopius. Uric acid (UA) and uricase activity were detected in tissues extracts from different insect developmental stages. However, accumulation of high UA levels and low uricase activities were found only after antifungal treatments, suggesting an important role of fungal species in its metabolism. Additionally, uricolytic fungal isolates were identified and characterized that presumably are involved in nitrogen recycling metabolism. After metagenomic analyses from D. coccus gut and hemolymph DNA and from two published data sets, we confirmed the presence of fungal genes involved in UA catabolism, suggesting that fungi help in the nitrogen recycling process in Dactylopius by uricolysis. All these results show the importance of fungal communities in scale insects such as Dactylopius.

  3. [The yeast community associated with the digestive tract of the German cockroach Blattella germanica L].

    PubMed

    Zheltikova, T M; Glushakova, A M; Alesho, N A

    2011-01-01

    Data on the yeasts colonizing the digestive tract ofa German cockroach have been first obtained. Cockroach cultures are used in the commercial production of allergy vaccines to treat patients sensitized to cockroach allergens. The enteric microflora of the insects can bring nonshared antigens into the composition of the agents manufactured. An investigation established that out of 10 yeast species isolated from the digestive tract of the cockroaches fed sterile food, 6 species (Candida glabrata, Cryptococcus magnus, Debaryomyces hansenii, Metschikowia pulcherrima, Phodo-torula glutinis, Rhodotorula mucilaginosa) were isolated from both the digestive tract and excrements and 4 (Candida oleophila, Candida shehatae, Cryptococcus albidus, Pichia membmnaefciens) were only from the digestive tract. It seems that the yeast is either digested or inactivated in the digestive tract of the insects and loses their capacity to grow When the cockroaches were fed sterile food for a long time (at least a month), all yeasts virtually disappeared from the digestive tract of the insects except for Candida glabrata, C.shehatae, and Rh.mucilaginosa. However, only C.glabrata achieved a great deal (10(7)-10(8) CFU/g) of cockroaches (both imagoes and larvae of 5-7 ages), which statistically significantly decreased by no less than three orders of magnitude in the excrements after passing through the digestive tract.

  4. Functional congruence of rhizosphere microbial communities associated to leguminous tree from Brazilian semiarid region.

    PubMed

    Taketani, Rodrigo Gouvêa; Kavamura, Vanessa Nessner; Mendes, Rodrigo; Melo, Itamar Soares

    2015-02-01

    Semiarid environments are characterized by the uneven spread of rain throughout the year. This leads to the establishment of a biota that can go through long periods without rain. In order to understand the dynamics of rhizosphere microbial communities across these contrasting seasons in Caatinga, we used the Ion Torrent platform to sequence the metagenome of the rhizosphere of a native leguminous plant (Mimosa tenuiflora). The annotation indicated that most abundant groups detected were the Actinobacteria and Proteobacteria, and the dominant functional groups were carbohydrate and protein metabolisms, and that in the wet season, the communities carried carbohydrate and amino acid metabolisms.The major differences observed between seasons were higher abundance of genes related to carbohydrate and amino acid metabolisms in the rainy season, indicating that the populations present might be better adapted to a higher abundance of organic matter. Besides, no clear separation of samples was detected based on their taxonomic composition whereas the functional composition indicates that samples from the rain season are more related. Altogether, our results indicate that there is al arge functional stability in these communities mostly due to the selection of features that aid the biota to endure the dry season and blossom during rain.

  5. Composition of Bacterial Communities Associated with Aurelia aurita Changes with Compartment, Life Stage, and Population

    PubMed Central

    Weiland-Bräuer, Nancy; Neulinger, Sven C.; Pinnow, Nicole; Künzel, Sven; Baines, John F.

    2015-01-01

    The scyphozoan Aurelia aurita is recognized as a key player in marine ecosystems and a driver of ecosystem change. It is thus intensely studied to address ecological questions, although its associations with microorganisms remain so far undescribed. In the present study, the microbiota associated with A. aurita was visualized with fluorescence in situ hybridization (FISH) analysis, and community structure was analyzed with respect to different life stages, compartments, and populations of A. aurita by 16S rRNA gene amplicon sequencing. We demonstrate that the composition of the A. aurita microbiota is generally highly distinct from the composition of communities present in ambient water. Comparison of microbial communities from different developmental stages reveals evidence for life stage-specific community patterns. Significant restructuring of the microbiota during strobilation from benthic polyp to planktonic life stages is present, arguing for a restructuring during the course of metamorphosis. Furthermore, the microbiota present in different compartments of the adult medusa (exumbrella mucus and gastric cavity) display significant differences, indicating body part-specific colonization. A novel Mycoplasma strain was identified in both compartment-specific microbiota and is most likely present inside the epithelium as indicated by FISH analysis of polyps, indicating potential endosymbiosis. Finally, comparison of polyps of different populations kept under the same controlled laboratory conditions in the same ambient water showed population-specific community patterns, most likely due the genetic background of the host. In conclusion, the presented data indicate that the associated microbiota of A. aurita may play important functional roles, e.g., during the life cycle. PMID:26116680

  6. Vertical structure of the phytoplankton community associated with a coastal plume in the Gulf of Mexico

    USGS Publications Warehouse

    Wawrik, B.; Paul, J.H.; Campbell, L.; Griffin, D.; Houchin, L.; Fuentes-Ortega, A.; Muller-Karger, F.

    2003-01-01

    Low salinity plumes of coastal origin are occasionally found far offshore, where they display a distinct color signature detectable by satellites. The impact of such plumes on carbon fixation and phytoplankton community structure in vertical profiles and on basin wide scales is poorly understood. On a research cruise in June 1999, ocean-color satellite-images (Sea-viewing Wide Field-of-view Sensor, SeaWiFS) were used in locating a Mississippi River plume in the eastern Gulf of Mexico. Profiles sampled within and outside of the plume were analyzed using flow cytometry, HPLC pigment analysis and primary production using 14C incorporation. Additionally, RubisCO large subunit (rbcL) gene expression was measured by hybridization of extracted RNA using 3 full-length RNA gene probes specific for individual phytoplankton clades. We also used a combination of RT-PCR/PCR and TA cloning in order to generate cDNA and DNA rbcL clone libraries from samples taken in the plume. Primary productivity was greatest in the low salinity surface layer of the plume. The plume was also associated with high Synechococcus counts and a strong peak in Form IA rbcL expression. Form IB rbcL (green algal) mRNA was abundant at the subsurface chlorophyll maximum (SCM), whereas Form ID rbcL (chromophytic) expression showed little vertical structure. Phylogenetic analysis of cDNA libraries demonstrated the presence of Form IA rbcL Synechococcus phylotypes in the plume. Below the plume, 2 spatially separated and genetically distinct rbcL clades of Prochlorococcus were observed. This indicated the presence of the high- and low-light adapted clades of Prochlorococcus. A large and very diverse clade of Prymnesiophytes was distributed throughout the water column, whereas a clade of closely related prasinophytes may have dominated at the SCM. These data indicate that the Mississippi river plume may dramatically alter the surface picoplankton composition of the Gulf of Mexico, with Synechococcus displacing Prochlorococcus in the surface waters.

  7. Microbial communities associated with tree bark foliose lichens: a perspective on their microecology.

    PubMed

    Anderson, O Roger

    2014-01-01

    Tree-bark, foliose lichens occur widely on a global scale. In some locales, such as forests, they contribute a substantial amount of biomass. However, there are few research reports on microbial communities including eukaryotic microbes associated with foliose lichens. Lichens collected from tree bark at 11 locations (Florida, New York State, Germany, Australia, and the Arctic) were examined to determine the density and C-biomass of bacteria and some eukaryotic microbes, i.e. heterotrophic nanoflagellates (HNF) and amoeboid protists. A rich microbial diversity was found, including large plasmodial slime molds, in some cases exceeding 100 μm in size. The densities of HNF and amoeboid protists were each positively correlated with densities of bacteria, r = 0.84 and 0.80, respectively (p < 0.01, N = 11 for each analysis) indicating a likely bacterial-based food web. Microbial densities (number/g lichen dry weight) varied markedly across the geographic sampling sites: bacteria (0.7-13.1 × 10(8) ), HNF (0.2-6.8 × 10(6) ) and amoeboid protists (0.4-4.6 × 10(3) ). The ranges in C-biomass (μg/g lichen dry weight) across the 11 sites were: bacteria (8.8-158.5), HNF (0.03-0.85), and amoeboid protists (0.08-540), the latter broad range was due particularly to absence or presence of large slime mold plasmodia.

  8. Continous application of bioorganic fertilizer induced resilient culturable bacteria community associated with banana Fusarium wilt suppression

    PubMed Central

    Fu, Lin; Ruan, Yunze; Tao, Chengyuan; Li, Rong; Shen, Qirong

    2016-01-01

    Fusarium wilt of banana always drives farmers to find new land for banana cultivation due to the comeback of the disease after a few cropping years. A novel idea for solving this problem is the continuous application of bioorganic fertilizer (BIO), which should be practiced from the beginning of banana planting. In this study, BIO was applied in newly reclaimed fields to pre-control banana Fusarium wilt and the culturable rhizobacteria community were evaluated using Biolog Ecoplates and culture-dependent denaturing gradient gel electrophoresis (CD-DGGE). The results showed that BIO application significantly reduced disease incidences and increased crop yields, respectivly. And the stabilized general bacterial metabolic potential, especially for the utilization of carbohydrates, carboxylic acids and phenolic compounds, was induced by BIO application. DGGE profiles demonstrated that resilient community structure of culturable rhizobacteria with higher richness and diversity were observed in BIO treated soils. Morever, enriched culturable bacteria affiliated with Firmicutes, Gammaproteobacteria and Actinobacteria were also detected. In total, continuous application of BIO effectively suppressed Fusarium wilt disease by stabilizing culturable bacterial metabolic potential and community structure. This study revealed a new method to control Fusarium wilt of banana for long term banana cultivation. PMID:27306096

  9. Impact of amendments on microbial communities associated with nitrogen mineralization in poultry litter

    Technology Transfer Automated Retrieval System (TEKTRAN)

    As energy costs increase poultry litter is an ever more valuable commodity. Reducing ammonia volatilization from poultry litter becomes important not only to reduce ventilation costs and improve bird performance but also to retain the nutrient value of the litter as a fertilizer. The goal of this r...

  10. The bacterial communities associated with fecal types and body weight of rex rabbits

    PubMed Central

    Zeng, Bo; Han, Shushu; Wang, Ping; Wen, Bin; Jian, Wensu; Guo, Wei; Yu, Zhiju; Du, Dan; Fu, Xiangchao; Kong, Fanli; Yang, Mingyao; Si, Xiaohui; Zhao, Jiangchao; Li, Ying

    2015-01-01

    Rex rabbit is an important small herbivore for fur and meat production. However, little is known about the gut microbiota in rex rabbit, especially regarding their relationship with different fecal types and growth of the hosts. We characterized the microbiota of both hard and soft feces from rex rabbits with high and low body weight by using the Illumina MiSeq platform targeting the V4 region of the 16S rDNA. High weight rex rabbits possess distinctive microbiota in hard feces, but not in soft feces, from the low weight group. We detected the overrepresentation of several genera such as YS2/Cyanobacteria, and Bacteroidales and underrepresentation of genera such as Anaeroplasma spp. and Clostridiaceae in high weight hard feces. Between fecal types, several bacterial taxa such as Ruminococcaceae, and Akkermansia spp. were enriched in soft feces. PICRUSt analysis revealed that metabolic pathways such as “stilbenoid, diarylheptanoid, gingerol biosynthesis” were enriched in high weight rabbits, and pathways related to “xenobiotics biodegradation” and “various types of N-glycan biosynthesis” were overrepresented in rabbit soft feces. Our study provides foundation to generate hypothesis aiming to test the roles that different bacterial taxa play in the growth and caecotrophy of rex rabbits. PMID:25791609

  11. Temperature-Dependent Variations in Sulfate-Reducing Communities Associated with a Terrestrial Hydrocarbon Seep

    PubMed Central

    Cheng, Ting-Wen; Lin, Li-Hung; Lin, Yue-Ting; Song, Sheng-Rong; Wang, Pei-Ling

    2014-01-01

    Terrestrial hydrocarbon seeps are an important source of naturally emitted methane over geological time. The exact community compositions responsible for carbon cycling beneath these surface features remain obscure. As sulfate reduction represents an essential process for anoxic organic mineralization, this study collected muddy fluids from a high-temperature hydrocarbon seep in Taiwan and analyzed community structures of sulfate-supplemented sediment slurries incubated anoxically at elevated temperatures. The results obtained demonstrated that sulfate consumption occurred between 40°C and 80°C. Dominant potential sulfate reducers included Desulfovibrio spp., Desulfonatronum spp., Desulforhabdus spp., and Desulfotomaculum spp. at 40°C, Thermodesulfovibrio spp. at 50°C, Thermodesulfovibrio spp. and Thermacetogenium spp. at 60°C, Thermacetogenium spp. and Archaeoglobus spp. at 70°C, and Archaeoglobus spp. at 80°C. None of these potential sulfate reducers exceeded 7% of the community in the untreated sample. Since no exogenous electron donor was provided during incubation, these sulfate reducers appeared to rely on the degradation of organic matter inherited from porewater and sediments. Aqueous chemistry indicated that fluids discharged in the region represented a mixture of saline formation water and low-salinity surface water; therefore, these lines of evidence suggest that deeply-sourced, thermophilic and surface-input, mesophilic sulfate-reducing populations entrapped along the subsurface fluid transport could respond rapidly once the ambient temperature is adjusted to a range close to their individual optima. PMID:25273230

  12. Characterization of bacterial communities associated with deep-sea corals on Gulf of Alaska seamounts.

    PubMed

    Penn, Kevin; Wu, Dongying; Eisen, Jonathan A; Ward, Naomi

    2006-02-01

    Although microbes associated with shallow-water corals have been reported, deepwater coral microbes are poorly characterized. A cultivation-independent analysis of Alaskan seamount octocoral microflora showed that Proteobacteria (classes Alphaproteobacteria and Gammaproteobacteria), Firmicutes, Bacteroidetes, and Acidobacteria dominate and vary in abundance. More sampling is needed to understand the basis and significance of this variation.

  13. Bacterial communities associated with healthy and Acropora white syndrome-affected corals from American Samoa

    USGS Publications Warehouse

    Wilson, Bryan; Aeby, Greta S.; Work, Thierry M.; Bourne, David G.

    2012-01-01

    Acropora white syndrome (AWS) is characterized by rapid tissue loss revealing the white underlying skeleton and affects corals worldwide; however, reports of causal agents are conflicting. Samples were collected from healthy and diseased corals and seawater around American Samoa and bacteria associated with AWS characterized using both culture-dependent and culture-independent methods, from coral mucus and tissue slurries, respectively. Bacterial 16S rRNA gene clone libraries derived from coral tissue were dominated by the Gammaproteobacteria, and Jaccard's distances calculated between the clone libraries showed that those from diseased corals were more similar to each other than to those from healthy corals. 16S rRNA genes from 78 culturable coral mucus isolates also revealed a distinct partitioning of bacterial genera into healthy and diseased corals. Isolates identified as Vibrionaceae were further characterized by multilocus sequence typing, revealing that whilst several Vibrio spp. were found to be associated with AWS lesions, a recently described species, Vibrio owensii, was prevalent amongst cultured Vibrio isolates. Unaffected tissues from corals with AWS had a different microbiota than normal Acropora as found by others. Determining whether a microbial shift occurs prior to disease outbreaks will be a useful avenue of pursuit and could be helpful in detecting prodromal signs of coral disease prior to manifestation of lesions.

  14. Bacterial Community Associated with Organs of Shallow Hydrothermal Vent Crab Xenograpsus testudinatus near Kuishan Island, Taiwan.

    PubMed

    Yang, Shan-Hua; Chiang, Pei-Wen; Hsu, Tin-Chang; Kao, Shuh-Ji; Tang, Sen-Lin

    2016-01-01

    Shallow-water hydrothermal vents off Kueishan Island (northeastern Taiwan) provide a unique, sulfur-rich, highly acidic (pH 1.75-4.6) and variable-temperature environment. In this species-poor habitat, the crab Xenograpsus testudinatus is dominant, as it mainly feeds on zooplankton killed by sulfurous plumes. In this study, 16S ribosomal RNA gene amplicon pyrosequencing was used to investigate diversity and composition of bacteria residing in digestive gland, gill, stomach, heart, and mid-gut of X. testudinatus, as well as in surrounding seawater. Dominant bacteria were Gamma- and Epsilonproteobacteria that might be capable of autotrophic growth by oxidizing reduced sulfur compounds and are usually resident in deep-sea hydrothermal systems. Dominant bacterial OTUs in X. testudinatus had both host and potential organ specificities, consistent with a potential trophic symbiotic relationship (nutrient transfer between host and bacteria). We inferred that versatile ways to obtain nutrients may provide an adaptive advantage for X. testudinatus in this demanding environment. To our knowledge, this is the first study of bacterial communities in various organs/tissues of a crustacean in a shallow-water hydrothermal system, and as such, may be a convenient animal model for studying these systems.

  15. Bacterial Community Associated with Organs of Shallow Hydrothermal Vent Crab Xenograpsus testudinatus near Kuishan Island, Taiwan.

    PubMed

    Yang, Shan-Hua; Chiang, Pei-Wen; Hsu, Tin-Chang; Kao, Shuh-Ji; Tang, Sen-Lin

    2016-01-01

    Shallow-water hydrothermal vents off Kueishan Island (northeastern Taiwan) provide a unique, sulfur-rich, highly acidic (pH 1.75-4.6) and variable-temperature environment. In this species-poor habitat, the crab Xenograpsus testudinatus is dominant, as it mainly feeds on zooplankton killed by sulfurous plumes. In this study, 16S ribosomal RNA gene amplicon pyrosequencing was used to investigate diversity and composition of bacteria residing in digestive gland, gill, stomach, heart, and mid-gut of X. testudinatus, as well as in surrounding seawater. Dominant bacteria were Gamma- and Epsilonproteobacteria that might be capable of autotrophic growth by oxidizing reduced sulfur compounds and are usually resident in deep-sea hydrothermal systems. Dominant bacterial OTUs in X. testudinatus had both host and potential organ specificities, consistent with a potential trophic symbiotic relationship (nutrient transfer between host and bacteria). We inferred that versatile ways to obtain nutrients may provide an adaptive advantage for X. testudinatus in this demanding environment. To our knowledge, this is the first study of bacterial communities in various organs/tissues of a crustacean in a shallow-water hydrothermal system, and as such, may be a convenient animal model for studying these systems. PMID:26934591

  16. Comparative Analysis of Prokaryotic Communities Associated with Organic and Conventional Farming Systems.

    PubMed

    Pershina, Elizaveta; Valkonen, Jari; Kurki, Päivi; Ivanova, Ekaterina; Chirak, Evgeny; Korvigo, Ilia; Provorov, Nykolay; Andronov, Evgeny

    2015-01-01

    One of the most important challenges in agriculture is to determine the effectiveness and environmental impact of certain farming practices. The aim of present study was to determine and compare the taxonomic composition of the microbiomes established in soil following long-term exposure (14 years) to a conventional and organic farming systems (CFS and OFS accordingly). Soil from unclared forest next to the fields was used as a control. The analysis was based on RT-PCR and pyrosequencing of 16S rRNA genes of bacteria and archaea. The number of bacteria was significantly lower in CFS than in OFS and woodland. The highest amount of archaea was detected in woodland, whereas the amounts in CFS and OFS were lower and similar. The most common phyla in the soil microbial communities analyzed were Proteobacteria (57.9%), Acidobacteria (16.1%), Actinobacteria (7.9%), Verrucomicrobia (2.0%), Bacteroidetes (2.7%) and Firmicutes (4.8%). Woodland soil differed from croplands in the taxonomic composition of microbial phyla. Croplands were enriched with Proteobacteria (mainly the genus Pseudomonas), while Acidobacteria were detected almost exclusively in woodland soil. The most pronounced differences between the CFS and OFS microbiomes were found within the genus Pseudomonas, which significantly (p<0,05) increased its number in CFS soil compared to OFS. Other differences in microbiomes of cropping systems concerned minor taxa. A higher relative abundance of bacteria belonging to the families Oxalobacteriaceae, Koribacteriaceae, Nakamurellaceae and genera Ralstonia, Paenibacillus and Pedobacter was found in CFS as compared with OFS. On the other hand, microbiomes of OFS were enriched with proteobacteria of the family Comamonadaceae (genera Hylemonella) and Hyphomicrobiaceae, actinobacteria from the family Micrococcaceae, and bacteria of the genera Geobacter, Methylotenera, Rhizobium (mainly Rhizobium leguminosarum) and Clostridium. Thus, the fields under OFS and CFS did not differ greatly for the composition of the microbiome. These results, which were also confirmed by cluster analysis, indicated that microbial communities in the field soil do not necessarily differ largely between conventional and organic farming systems. PMID:26684619

  17. Community-associated methicillin-resistant Staphylococcus aureus in non-outbreak skin infections

    PubMed Central

    Bonesso, Mariana Fávero; Marques, Silvio Alencar; Camargo, Carlos Henrique; Fortaleza, Carlos Magno Castelo Branco; da Cunha, Maria de Lourdes Ribeiro de Souza

    2014-01-01

    The aim of this study was to determine the prevalence of Staphylococcus aureus and risk factors for the acquisition of MRSA (Methicillin Resistant Staphylococcus aureus) as the main cause of skin and soft tissue infections. S. aureus were characterized for the presence of PVL, TSST-1 and mecA genes. SCCmec typing was carried out in mecA positive strains and PFGE was performed only in these strains. During the study period, 127 outpatients attending a dermatology clinical the Botucatu Medical School, a regional tertiary hospital in Botucatu, Sao Paulo, Brazil, were diagnosed with active skin infections. A total 66 (56.9%) S. aureus strains were isolated. The methicillin resistance gene mecA was detected in seven (10.6%) S. aureus strains. The SCCmec types detected in the seven mecA-positive S. aureus strains were type Ia in one, type II in three, and type IV in three. The PVL gene was detected in 10 (15.1%) in sensitive strains. Pulsed field gel electrophoresis revealed non-clonal diversity among the isolates. The risk factors associated with MRSA acquisition in this study were previous ciprofloxacin use and working in a healthcare environment. The risk factors indicate plausible routes of CA-MRSA transmission among the subjects studied. PMID:25763047

  18. Bacterial communities associated with biofouling materials used in bench-scale hydrocarbon bioremediation.

    PubMed

    Al-Mailem, Dina; Kansour, Mayada; Radwan, Samir

    2015-03-01

    Biofouling material samples from the Arabian (Persian) Gulf, used as inocula in batch cultures, brought about crude oil and pure-hydrocarbon removal in a mineral medium. Without any added nitrogen fertilizers, the hydrocarbon-removal values were between about 10 and 50 %. Fertilization with NaNO3 alone or together with a mixture of the vitamins thiamine, pyridoxine, vitamin B12, biotin, riboflavin, and folic acid increased the hydrocarbon-removal values, to reach 90 %. Biofouling material samples harbored total bacteria in the magnitude of 10(7) cells g(-1), about 25 % of which were hydrocarbonoclastic. These numbers were enhanced by NaNO3 and vitamin amendment. The culture-independent analysis of the total bacterioflora revealed the predominance of the gammaproteobacterial genera Marinobacter, Acinetobacter, and Alcanivorax, the Flavobacteriia, Flavobacterium, Gaetbulibacter, and Owenweeksia, and the Alphaproteobacteria Tistrella, Zavarzinia, and others. Most of those bacteria are hydrocarbonoclastic. Culture-dependent analysis of hydrocarbonoclastic bacteria revealed that Marinobacter hydrocarbonoclasticus, Dietzia maris, and Gordonia bronchialis predominated in the fouling materials. In addition, each material had several more-specific hydrocarbonoclastic species, whose frequencies were enhanced by NaNO3 and vitamin fertilization. The same samples of fouling materials were used in four successive crude-oil-removal cycles without any dramatic loss of their hydrocarbon-removal potential nor of their associated hydrocarbonoclastic bacteria. In the fifth cycle, the oil-removal value was reduced by about 50 % in only one of the studied samples. This highlights how firmly biofouling materials were immobilizing the hydrocarbonoclastic bacteria.

  19. Effects of experimental lead pollution on the microbial communities associated with Sphagnum fallax (Bryophyta).

    PubMed

    Nguyen-Viet, H; Gilbert, D; Mitchell, E A D; Badot, P-M; Bernard, N

    2007-08-01

    Ecotoxicological studies usually focus on single microbial species under controlled conditions. As a result, little is known about the responses of different microbial functional groups or individual species to stresses. In an aim to assess the response of complex microbial communities to pollution in their natural habitat, we studied the effect of a simulated lead pollution on the microbial community (bacteria, cyanobacteria, protists, fungi, and micrometazoa) living on Sphagnum fallax. Mosses were grown in the laboratory with 0 (control), 625, and 2,500 microg L(-1) of Pb(2+) diluted in a standard nutrient solution and were sampled after 0, 6, 12, and 20 weeks. The biomasses of bacteria, microalgae, testate amoebae, and ciliates were dramatically and significantly decreased in both Pb addition treatments after 6, 12, and 20 weeks in comparison with the control. The biomass of cyanobacteria declined after 6 and 12 weeks in the highest Pb treatment. The biomasses of fungi, rotifers, and nematodes decreased along the duration of the experiment but were not significantly affected by lead addition. Consequently, the total microbial biomass was lower for both Pb addition treatments after 12 and 20 weeks than in the controls. The community structure was strongly modified due to changes in the densities of testate amoebae and ciliates, whereas the relative contribution of bacteria to the microbial biomass was stable. Differences in responses among the microbial groups suggest changes in the trophic links among them. The correlation between the biomass of bacteria and that of ciliates or testate amoebae increased with increasing Pb loading. We interpret this result as an effect on the grazing pathways of these predators and by the Pb effect on other potential prey (i.e., smaller protists). The community approach used here complements classical ecotoxicological studies by providing clues to the complex effect of pollutant-affecting organisms both directly and indirectly through trophic effects and could potentially find applications for pollution monitoring.

  20. Bird communities associated with succession and management of lowland conifer forests

    USGS Publications Warehouse

    Dawson, D.K.

    1979-01-01

    Data from published bird censuses were used to determine changes in avian communities in relation to plant succession, fire, type conversion, and timber management practices in lowland conifer forests in the northeastern United States. With modifications in current logging practices, habitat for the bird species that nest in undisturbed stands can be provided. Management guidelines are recommended.

  1. Genetic and functional diversity of soil microbial communities associated to grapevine plants and wine quality

    NASA Astrophysics Data System (ADS)

    Mocali, Stefano; Fabiani, Arturo; Kuramae, Eiko; de Hollander, Mattias; Kowalchuk, George A.; Vignozzi, Nadia; Valboa, Giuseppe; Costantini, Edoardo

    2013-04-01

    Despite the economic importance of vineyards in Italy, the wine sector is facing severe challenges from increased global competition and climate changes. The quality of the grape at harvest has a strong direct impact on wine final quality and the strong relationship between wine composition, aroma, taste, and soil properties has been outlined in the "Terroir concept". However, information on the impact of soil microbial communities on soil functions, grapevine plants, and wine quality is generally lacking. In the current study, soils from two close sites in Central Tuscany (BRO11 and BRO12) cultivated with the same grapevine cultivar Sangiovese, but with contrasting wine quality, were examined. Although the BRO12 site provided a better wine quality than the BRO11, the two soils showed similar physical, chemical, and hydrological properties. Also soil humidity, as determined by FDR (Frequency Domain Reflectometry) sensors, indicated a similar water availability in the first 75 cm during a three years trial (2000-2010). Interestingly, the mean three years value of the ratio between the two stable carbon isotopes 13C/12C, measured in the alcohol of the wines, was significantly higher in BRO12 than in BRO11 (-28,3‰ and -24,4‰, respectively), indicating the presence of a relatively higher water stress in the BRO11 soil. Functional GeoChip microarray analyses revealed higher presence of Actinobacteria in the BRO12 than in the BRO11 soil, where the alfa-Proteobacteria were more abundant. Furthermore, a consistent difference in genes involved in S cycling, with a significant overrepresentation of sulphur-oxidation genes in BRO11 and increased levels of sulphate reduction genes BRO12 was detected. These results are consistent with the high content of sulphates and the abundance of Firmicutes such as Sulfobacillus thermosulfidooxidans in the BRO11 soil. Therefore, the different microbiology of the two soils could be related to the different redox conditions of the two soils. The structure of soil microbial communities was assessed using 16S and 18S rRNA genes pyrosequencing and the determination of some soil microbial properties such as microbial respiration, microbial C-biomass were also determined. The role of both genetic and functional diversity of soil bacterial community on grape physiology and wine quality will be discussed.

  2. Evidence of a microbial community associated with rock varnish at Yungay, Atacama Desert, Chile

    NASA Astrophysics Data System (ADS)

    Kuhlman, Kimberly R.; Venkat, Parth; La Duc, Myron T.; Kuhlman, Gregory M.; McKay, Christopher P.

    2008-12-01

    Rock varnish is a very slow-growing nanostratigraphic coating consisting of approximately 70% fine-grained clay and 30% iron and manganese oxides that forms on the surfaces of rocks in arid and semiarid climates. The microbial diversity associated with rock varnish collected from the hyperarid Yungay region of the Atacama Desert was investigated using culture-independent biomolecular methods and an adenosine triphosphate (ATP) assay. The extraction of DNA from rock varnish collected at Yungay, a region in which little to no DNA has been extracted from the surface soil (<1 cm) to date, indicates that rock varnish may provide a niche habitat for microbial life where water is essentially absent. The clone library constructed suggests the presence of numerous phylogenetically distinct microorganisms, ranging in diversity from Cyanobacterial to á-proteobacteria lineages. The findings also show that only a few micrometers of varnish material are enough to shelter microbes like Chroococcidiopsis spp. from the intense ultraviolet radiation present in the Atacama Desert. Whether or not microorganisms are involved in its nucleation and/or growth, rock varnish appears to provide a microhabitat resembling cryptoendolithic communities seen on a larger scale.

  3. Bacterial communities associated with an occurrence of colored water in an urban drinking water distribution system.

    PubMed

    Wu, Hui Ting; Mi, Zi Long; Zhang, Jing Xu; Chen, Chao; Xie, Shu Guang

    2014-08-01

    This study aimed to investigate bacterial community in an urban drinking water distribution system (DWDS) during an occurrence of colored water. Variation in the bacterial community diversity and structure was observed among the different waters, with the predominance of Proteobacteria. While Verrucomicrobia was also a major phylum group in colored water. Limnobacter was the major genus group in colored water, but Undibacterium predominated in normal tap water. The coexistence of Limnobacter as well as Sediminibacterium and Aquabacterium might contribute to the formation of colored water.

  4. Distinct microbial communities associated with buried soils in the Siberian tundra.

    PubMed

    Gittel, Antje; Bárta, Jiří; Kohoutová, Iva; Mikutta, Robert; Owens, Sarah; Gilbert, Jack; Schnecker, Jörg; Wild, Birgit; Hannisdal, Bjarte; Maerz, Joeran; Lashchinskiy, Nikolay; Capek, Petr; Santrůčková, Hana; Gentsch, Norman; Shibistova, Olga; Guggenberger, Georg; Richter, Andreas; Torsvik, Vigdis L; Schleper, Christa; Urich, Tim

    2014-04-01

    Cryoturbation, the burial of topsoil material into deeper soil horizons by repeated freeze-thaw events, is an important storage mechanism for soil organic matter (SOM) in permafrost-affected soils. Besides abiotic conditions, microbial community structure and the accessibility of SOM to the decomposer community are hypothesized to control SOM decomposition and thus have a crucial role in SOM accumulation in buried soils. We surveyed the microbial community structure in cryoturbated soils from nine soil profiles in the northeastern Siberian tundra using high-throughput sequencing and quantification of bacterial, archaeal and fungal marker genes. We found that bacterial abundances in buried topsoils were as high as in unburied topsoils. In contrast, fungal abundances decreased with depth and were significantly lower in buried than in unburied topsoils resulting in remarkably low fungal to bacterial ratios in buried topsoils. Fungal community profiling revealed an associated decrease in presumably ectomycorrhizal (ECM) fungi. The abiotic conditions (low to subzero temperatures, anoxia) and the reduced abundance of fungi likely provide a niche for bacterial, facultative anaerobic decomposers of SOM such as members of the Actinobacteria, which were found in significantly higher relative abundances in buried than in unburied topsoils. Our study expands the knowledge on the microbial community structure in soils of Northern latitude permafrost regions, and attributes the delayed decomposition of SOM in buried soils to specific microbial taxa, and particularly to a decrease in abundance and activity of ECM fungi, and to the extent to which bacterial decomposers are able to act as their functional substitutes.

  5. Distinct microbial communities associated with buried soils in the Siberian tundra

    PubMed Central

    Gittel, Antje; Bárta, Jiří; Kohoutová, Iva; Mikutta, Robert; Owens, Sarah; Gilbert, Jack; Schnecker, Jörg; Wild, Birgit; Hannisdal, Bjarte; Maerz, Joeran; Lashchinskiy, Nikolay; Čapek, Petr; Šantrůčková, Hana; Gentsch, Norman; Shibistova, Olga; Guggenberger, Georg; Richter, Andreas; Torsvik, Vigdis L; Schleper, Christa; Urich, Tim

    2014-01-01

    Cryoturbation, the burial of topsoil material into deeper soil horizons by repeated freeze–thaw events, is an important storage mechanism for soil organic matter (SOM) in permafrost-affected soils. Besides abiotic conditions, microbial community structure and the accessibility of SOM to the decomposer community are hypothesized to control SOM decomposition and thus have a crucial role in SOM accumulation in buried soils. We surveyed the microbial community structure in cryoturbated soils from nine soil profiles in the northeastern Siberian tundra using high-throughput sequencing and quantification of bacterial, archaeal and fungal marker genes. We found that bacterial abundances in buried topsoils were as high as in unburied topsoils. In contrast, fungal abundances decreased with depth and were significantly lower in buried than in unburied topsoils resulting in remarkably low fungal to bacterial ratios in buried topsoils. Fungal community profiling revealed an associated decrease in presumably ectomycorrhizal (ECM) fungi. The abiotic conditions (low to subzero temperatures, anoxia) and the reduced abundance of fungi likely provide a niche for bacterial, facultative anaerobic decomposers of SOM such as members of the Actinobacteria, which were found in significantly higher relative abundances in buried than in unburied topsoils. Our study expands the knowledge on the microbial community structure in soils of Northern latitude permafrost regions, and attributes the delayed decomposition of SOM in buried soils to specific microbial taxa, and particularly to a decrease in abundance and activity of ECM fungi, and to the extent to which bacterial decomposers are able to act as their functional substitutes. PMID:24335828

  6. Biogas production using anaerobic groundwater containing a subterranean microbial community associated with the accretionary prism.

    PubMed

    Baito, Kyohei; Imai, Satomi; Matsushita, Makoto; Otani, Miku; Sato, Yu; Kimura, Hiroyuki

    2015-09-01

    In a deep aquifer associated with an accretionary prism, significant methane (CH₄) is produced by a subterranean microbial community. Here, we developed bioreactors for producing CH₄ and hydrogen (H₂) using anaerobic groundwater collected from the deep aquifer. To generate CH₄, the anaerobic groundwater amended with organic substrates was incubated in the bioreactor. At first, H₂ was detected and accumulated in the gas phase of the bioreactor. After the H₂ decreased, rapid CH₄ production was observed. Phylogenetic analysis targeting 16S rRNA genes revealed that the H₂ -producing fermentative bacterium and hydrogenotrophic methanogen were predominant in the reactor. The results suggested that syntrophic biodegradation of organic substrates by the H₂ -producing fermentative bacterium and the hydrogenotrophic methanogen contributed to the CH₄ production. For H₂ production, the anaerobic groundwater, amended with organic substrates and an inhibitor of methanogens (2-bromoethanesulfonate), was incubated in a bioreactor. After incubation for 24 h, H₂ was detected from the gas phase of the bioreactor and accumulated. Bacterial 16S rRNA gene analysis suggested the dominance of the H₂ -producing fermentative bacterium in the reactor. Our study demonstrated a simple and rapid CH4 and H2 production utilizing anaerobic groundwater containing an active subterranean microbial community. PMID:25267392

  7. Nearshore habitat and fish community associations of coaster brook trout in Isle Royale, Lake Superior

    USGS Publications Warehouse

    Gorman, O.T.; Moore, S.A.; Carlson, A.J.; Quinlan, H.R.

    2008-01-01

    We characterized the nearshore habitat and fish community composition of approximately 300 km of shoreline within and adjacent to the major embayments of Isle Royale, Lake Superior. Sampling yielded 17 species, of which 12 were widespread and represented a common element of the Lake Superior fish community, including cisco Coregonus artedi, lake whitefish C. clupeaformis, round whitefish Prosopium cylindraceum, lake trout Salvelinus namaycush, rainbow smelt Osmerus mordax, lake chub Couesius plumbeus, longnose sucker Catostomus catostomus, white sucker C. commersonii, trout-perch Percopsis omiscomaycus, ninespine stickleback Pungitius pungitius, burbot Lota lota, and slimy sculpin Cottus cognatus. The presence of brook trout S. fontinalis in an embayment was associated with the common species of the Isle Royale nearshore fish community, particularly cisco, longnose sucker, and round whitefish. However, brook trout were present in only five embayments and were common only in Tobin Harbor. Most Isle Royale embayments had broadly overlapping ranges of nearshore habitats. Within embayments, fish were distributed along a habitat gradient from less-protected rocky habitat near the mouth to highly protected habitat with mixed and finer substrates at the head. Embayments with brook trout had greater mean protection from the open lake, greater variation in depth, greater mean cover, and higher mean frequencies of large substrates (cobble, boulder, and bedrock). Within those embayments, brook trout were associated with habitat patches with higher mean frequencies of small substrates (particularly sand and coarse gravel). Within Tobin Harbor, brook trout were associated with midembayment habitat and species assemblages, especially those locations with a mixture of sand, gravel, and cobble substrates, an absence of bedrock, and the presence of round whitefish, white sucker, and trout-perch. Comparison of embayments with the model, Tobin Harbor, showed that six embayments without brook trout had very similar arrays of habitat. However, four embayments with brook trout had relatively different arrays of habitat from Tobin Harbor. These results suggest that there is potential for further recovery of brook trout populations across Isle Royale nearshore habitats. ?? Copyright by the American Fisheries Society 2008.

  8. Bacterial Community Associated with Organs of Shallow Hydrothermal Vent Crab Xenograpsus testudinatus near Kuishan Island, Taiwan

    PubMed Central

    Yang, Shan-Hua; Chiang, Pei-Wen; Hsu, Tin-Chang; Kao, Shuh-Ji; Tang, Sen-Lin

    2016-01-01

    Shallow-water hydrothermal vents off Kueishan Island (northeastern Taiwan) provide a unique, sulfur-rich, highly acidic (pH 1.75–4.6) and variable-temperature environment. In this species-poor habitat, the crab Xenograpsus testudinatus is dominant, as it mainly feeds on zooplankton killed by sulfurous plumes. In this study, 16S ribosomal RNA gene amplicon pyrosequencing was used to investigate diversity and composition of bacteria residing in digestive gland, gill, stomach, heart, and mid-gut of X. testudinatus, as well as in surrounding seawater. Dominant bacteria were Gamma- and Epsilonproteobacteria that might be capable of autotrophic growth by oxidizing reduced sulfur compounds and are usually resident in deep-sea hydrothermal systems. Dominant bacterial OTUs in X. testudinatus had both host and potential organ specificities, consistent with a potential trophic symbiotic relationship (nutrient transfer between host and bacteria). We inferred that versatile ways to obtain nutrients may provide an adaptive advantage for X. testudinatus in this demanding environment. To our knowledge, this is the first study of bacterial communities in various organs/tissues of a crustacean in a shallow-water hydrothermal system, and as such, may be a convenient animal model for studying these systems. PMID:26934591

  9. Crohn associated microbial communities associated to colonic mucosal biopsies in patients of the western Mediterranean.

    PubMed

    Vidal, Roberto; Ginard, Daniel; Khorrami, Sam; Mora-Ruiz, Merit; Munoz, Raul; Hermoso, Marcela; Díaz, Sara; Cifuentes, Ana; Orfila, Alejandro; Rosselló-Móra, Ramon

    2015-09-01

    Next generation sequencing approaches allow the retrieval of several orders of magnitude larger numbers of amplified single sequences in 16S rRNA diversity surveys than classical methods. However, the sequences are only partial and thus lack sufficient resolution for a reliable identification. The OPU approach used here, based on a tandem combination of high quality 454 sequences (mean >500 nuc) applying strict OTU thresholds, and phylogenetic inference based on parsimony additions to preexisting trees, seemed to improve the identification yields at the species and genus levels. A total of thirteen biopsies of Crohn-diagnosed patients (CD) and seven healthy controls (HC) were studied. In most of the cases (73%), sequences were affiliated to known species or genera and distinct microbial patterns could be distinguished among the CD subjects, with a common depletion of Clostridia and either an increased presence of Bacteroidetes (CD1) or an anomalous overrepresentation of Proteobacteria (CD2). Faecalibacterium prausnitzii presence was undetectable in CD, whereas Bacteroides vulgatus-B. dorei characterized HC and some CD groups. Altogether, the results showed that a microbial composition with predominance of Clostridia followed by Bacteroidetes, with F. prausnitzii and B. vulgatus-B. dorei as major key bacteria, characterized what could be considered a balanced structure in HC. The depletion of Clostridia seemed to be a common trait in CD.

  10. Bacterial Communities Associated with Atherosclerotic Plaques from Russian Individuals with Atherosclerosis

    PubMed Central

    Ziganshina, Elvira E.; Sharifullina, Dilyara M.; Lozhkin, Andrey P.; Khayrullin, Rustem N.; Ignatyev, Igor M.; Ziganshin, Ayrat M.

    2016-01-01

    Atherosclerosis is considered a chronic disease of the arterial wall and is the major cause of severe disease and death among individuals all over the world. Some recent studies have established the presence of bacteria in atherosclerotic plaque samples and suggested their possible contribution to the development of cardiovascular disease. The main objective of this preliminary pilot study was to better understand the bacterial diversity and abundance in human atherosclerotic plaques derived from common carotid arteries of individuals with atherosclerosis (Russian nationwide group) and contribute towards the further identification of a main group of atherosclerotic plaque bacteria by 454 pyrosequencing their 16S ribosomal RNA (16S rRNA) genes. The applied approach enabled the detection of bacterial DNA in all atherosclerotic plaques. We found that distinct members of the order Burkholderiales were present at high levels in all atherosclerotic plaques obtained from patients with atherosclerosis with the genus Curvibacter being predominant in all plaque samples. Moreover, unclassified Burkholderiales as well as members of the genera Propionibacterium and Ralstonia were typically the most significant taxa for all atherosclerotic plaques. Other genera such as Burkholderia, Corynebacterium and Sediminibacterium as well as unclassified Comamonadaceae, Oxalobacteraceae, Rhodospirillaceae, Bradyrhizobiaceae and Burkholderiaceae were always found but at low relative abundances of the total 16S rRNA gene population derived from all samples. Also, we found that some bacteria found in plaque samples correlated with some clinical parameters, including total cholesterol, alanine aminotransferase and fibrinogen levels. Finally, our study indicates that some bacterial agents at least partially may be involved in affecting the development of cardiovascular disease through different mechanisms. PMID:27736997

  11. Microbial communities associated with Antarctic snow pack and their biogeochemical implications.

    PubMed

    Antony, Runa; Sanyal, Aritri; Kapse, Neelam; Dhakephalkar, Prashant K; Thamban, Meloth; Nair, Shanta

    2016-11-01

    Snow ecosystems represent a large part of the Earth's biosphere and harbour diverse microbial communities. Despite our increased knowledge of snow microbial communities, the question remains as to their functional potential, particularly with respect to their role in adapting to and modifying the specific snow environment. In this work, we investigated the diversity and functional capabilities of microorganisms from 3 regions of East Antarctica, with respect to compounds present in snow and tested whether their functional signature reflected the snow environment. A diverse assemblage of bacteria (Proteobacteria, Actinobacteria, Firmicutes, Bacteroidetes, Deinococcus-Thermus, Planctomycetes, Verrucomicrobia), archaea (Euryarchaeota), and eukarya (Basidiomycota, Ascomycota, Cryptomycota and Rhizaria) were detected through culture-dependent and -independent methods. Although microbial communities observed in the three snow samples were distinctly different, all isolates tested produced one or more of the following enzymes: lipase, protease, amylase, β-galactosidase, cellulase, and/or lignin modifying enzyme. This indicates that the snow pack microbes have the capacity to degrade organic compounds found in Antarctic snow (proteins, lipids, carbohydrates, lignin), thus highlighting their potential to be involved in snow chemistry. PMID:27664737

  12. Host and Environmental Specificity in Bacterial Communities Associated to Two Highly Invasive Marine Species (Genus Asparagopsis).

    PubMed

    Aires, Tânia; Serrão, Ester A; Engelen, Aschwin H

    2016-01-01

    As habitats change due to global and local pressures, population resilience, and adaptive processes depend not only on their gene pools but also on their associated bacteria communities. The hologenome can play a determinant role in adaptive evolution of higher organisms that rely on their bacterial associates for vital processes. In this study, we focus on the associated bacteria of the two most invasive seaweeds in southwest Iberia (coastal mainland) and nearby offshore Atlantic islands, Asparagopsis taxiformis and Asparagopsis armata. Bacterial communities were characterized using 16S rRNA barcoding through 454 next generation sequencing and exploratory shotgun metagenomics to provide functional insights and a backbone for future functional studies. The bacterial community composition was clearly different between the two species A. taxiformis and A. armata and between continental and island habitats. The latter was mainly due to higher abundances of Acidimicrobiales, Sphingomonadales, Xanthomonadales, Myxococcales, and Alteromonadales on the continent. Metabolic assignments for these groups contained a higher number of reads in functions related to oxidative stress and resistance to toxic compounds, more precisely heavy metals. These results are in agreement with their usual association with hydrocarbon degradation and heavy-metals detoxification. In contrast, A. taxiformis from islands contained more bacteria related to oligotrophic environments which might putatively play a role in mineralization of dissolved organic matter. The higher number of functional assignments found in the metagenomes of A. taxiformis collected from Cape Verde Islands suggest a higher contribution of bacteria to compensate nutrient limitation in oligotrophic environments. Our results show that Asparagopsis-associated bacterial communities have host-specificity and are modulated by environmental conditions. Whether this environmental effect reflects the host's selective requirements or the locally available bacteria remains to be addressed. However, the known functional capacities of these bacterial communities indicate their potential for eco-physiological functions that could be valuable for the host fitness. PMID:27148239

  13. Bacterial Communities Associated with Subsurface Geochemical Processes in Continental Serpentinite Springs

    PubMed Central

    Morrill, Penny L.; Szponar, Natalie; Schrenk, Matthew O.

    2013-01-01

    Reactions associated with the geochemical process of serpentinization can generate copious quantities of hydrogen and low-molecular-weight organic carbon compounds, which may provide energy and nutrients to sustain subsurface microbial communities independently of the photosynthetically supported surface biosphere. Previous microbial ecology studies have tested this hypothesis in deep sea hydrothermal vents, such as the Lost City hydrothermal field. This study applied similar methods, including molecular fingerprinting and tag sequencing of the 16S rRNA gene, to ultrabasic continental springs emanating from serpentinizing ultramafic rocks. These molecular surveys were linked with geochemical measurements of the fluids in an interdisciplinary approach designed to distinguish potential subsurface organisms from those derived from surface habitats. The betaproteobacterial genus Hydrogenophaga was identified as a likely inhabitant of transition zones where hydrogen-enriched subsurface fluids mix with oxygenated surface water. The Firmicutes genus Erysipelothrix was most strongly correlated with geochemical factors indicative of subsurface fluids and was identified as the most likely inhabitant of a serpentinization-powered subsurface biosphere. Both of these taxa have been identified in multiple hydrogen-enriched subsurface habitats worldwide, and the results of this study contribute to an emerging biogeographic pattern in which Betaproteobacteria occur in near-surface mixing zones and Firmicutes are present in deeper, anoxic subsurface habitats. PMID:23584766

  14. Microbial Communities Associated with Anaerobic Benzene Degradation in a Petroleum-Contaminated Aquifer

    PubMed Central

    Rooney-Varga, Juliette N.; Anderson, Robert T.; Fraga, Jocelyn L.; Ringelberg, David; Lovley, Derek R.

    1999-01-01

    Microbial community composition associated with benzene oxidation under in situ Fe(III)-reducing conditions in a petroleum-contaminated aquifer located in Bemidji, Minn., was investigated. Community structure associated with benzene degradation was compared to sediment communities that did not anaerobically oxidize benzene which were obtained from two adjacent Fe(III)-reducing sites and from methanogenic and uncontaminated zones. Denaturing gradient gel electrophoresis of 16S rDNA sequences amplified with bacterial or Geobacteraceae-specific primers indicated significant differences in the composition of the microbial communities at the different sites. Most notable was a selective enrichment of microorganisms in the Geobacter cluster seen in the benzene-degrading sediments. This finding was in accordance with phospholipid fatty acid analysis and most-probable-number–PCR enumeration, which indicated that members of the family Geobacteraceae were more numerous in these sediments. A benzene-oxidizing Fe(III)-reducing enrichment culture was established from benzene-degrading sediments and contained an organism closely related to the uncultivated Geobacter spp. This genus contains the only known organisms that can oxidize aromatic compounds with the reduction of Fe(III). Sequences closely related to the Fe(III) reducer Geothrix fermentans and the aerobe Variovorax paradoxus were also amplified from the benzene-degrading enrichment and were present in the benzene-degrading sediments. However, neither G. fermentans nor V. paradoxus is known to oxidize aromatic compounds with the reduction of Fe(III), and there was no apparent enrichment of these organisms in the benzene-degrading sediments. These results suggest that Geobacter spp. play an important role in the anaerobic oxidation of benzene in the Bemidji aquifer and that molecular community analysis may be a powerful tool for predicting a site’s capacity for anaerobic benzene degradation. PMID:10388703

  15. Metagenomic analysis of the microbial community associated with the coral Porites astreoides.

    PubMed

    Wegley, Linda; Edwards, Robert; Rodriguez-Brito, Beltran; Liu, Hong; Rohwer, Forest

    2007-11-01

    The coral holobiont is a dynamic assemblage of the coral animal, zooxanthellae, endolithic algae and fungi, Bacteria,Archaea and viruses. Zooxanthellae and some Bacteria form relatively stable and species-specific associations with corals. Other associations are less specific; coral-associated Archaea differ from those in the water column, but the same archaeal species may be found on different coral species. It has been hypothesized that the coral animal can adapt to differing ecological niches by 'switching' its microbial associates. In the case of corals and zooxanthellae, this has been termed adaptive bleaching and it has important implications for carbon cycling within the coral holobiont and ultimately the survival of coral reefs. However, the roles of other components of the coral holobiont are essentially unknown. To better understand these other coral associates, a fractionation procedure was used to separate the microbes, mitochondria and viruses from the coral animal cells and zooxanthellae. The resulting metagenomic DNA was sequenced using pyrosequencing. Fungi, Bacteria and phage were the most commonly identified organisms in the metagenome. Three of the four fungal phyla were represented, including a wide diversity of fungal genes involved in carbon and nitrogen metabolism, suggesting that the endolithic community is more important than previously appreciated. In particular, the data suggested that endolithic fungi could be converting nitrate and nitrite to ammonia, which would enable fixed nitrogen to cycle within the coral holobiont. The most prominent bacterial groups were Proteobacteria (68%), Firmicutes (10%), Cyanobacteria (7%) and Actinobacteria (6%). Functionally, the bacterial community was primarily heterotrophic and included a number of pathways for the degradation of aromatic compounds, the most abundant being the homogentisate pathway. The most abundant phage family was the ssDNA Microphage and most of the eukaryotic viruses were most closely related to those known to infect aquatic organisms. This study provides a metabolic and taxonomic snapshot of microbes associated with the reef-building coral Porites astreoides and presents a basis for understanding how coral-microbial interactions structure the holobiont and coral reefs. PMID:17922755

  16. Introduction of Electronic Referral from Community Associated with More Timely Review by Secondary Services

    PubMed Central

    Warren, J.; White, S.; Day, K.J.; Gu, Y.; Pollock, M.

    2011-01-01

    Background Electronic referral (eReferral) from community into public secondary healthcare services was introduced to 30 referring general medical practices and 28 hospital based services in late 2007. Objectives To measure the extent of uptake of eReferral and its association with changes in referral processing. Methods Analysis of transactional data from the eReferral message service and the patient information management system of the affected hospital; interview of clinical, operational and management stakeholders. Results eReferral use rose steadily to 1000 transactions per month in 2008, thereafter showing moderate growth to 1200 per month in 2010. Rate of eReferral from the community in 2010 is estimated at 56% of total referrals to the hospital from general practice, and as 71% of referrals from those having done at least one referral electronically. Referral latency from letter date to hospital triage improves significantly from 2007 to 2009 (p<0.001), from a paper referral median of 8 days (inter-quartile range, IQR: 4–14) in 2007 to an eReferral median of 5 days (IQR: 2–9) and paper referral median of 6 days (IQR: 2–12) in 2009. Specialists upgrade the referrer-assigned eReferral priority in 19.2% of cases and downgrade it 18.6% of the time. Clinical users appreciate improvement of referral visibility (status and content access); however, both general practitioners and specialists point out system usability issues. Discussion With eReferrals, a referral’s status can be checked, and its content read, by any authorized user at any time. The period of eReferral uptake was associated with significant speed-up in referral processing without changes in staffing levels. The eReferral system provides a foundation for further innovation in the community-secondary interface, such as electronic decision support and shared care planning systems. Conclusions We observed substantial rapid voluntary uptake of eReferrals associated with faster, more reliable and more transparent referral processing. PMID:23616895

  17. The dominant Australian community-acquired methicillin-resistant Staphylococcus aureus clone ST93-IV [2B] is highly virulent and genetically distinct.

    PubMed

    Chua, Kyra Y L; Seemann, Torsten; Harrison, Paul F; Monagle, Shaun; Korman, Tony M; Johnson, Paul D R; Coombs, Geoffrey W; Howden, Brian O; Davies, John K; Howden, Benjamin P; Stinear, Timothy P

    2011-01-01

    Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) USA300 has spread rapidly across North America, and CA-MRSA is also increasing in Australia. However, the dominant Australian CA-MRSA strain, ST93-IV [2B] appears distantly related to USA300 despite strikingly similar clinical and epidemiological profiles. Here, we compared the virulence of a recent Australian ST93 isolate (JKD6159) to other MRSA, including USA300, and found that JKD6159 was the most virulent in a mouse skin infection model. We fully sequenced the genome of JKD6159 and confirmed that JKD6159 is a distinct clone with 7616 single nucleotide polymorphisms (SNPs) distinguishing this strain from all other S. aureus genomes. Despite its high virulence there were surprisingly few virulence determinants. However, genes encoding α-hemolysin, Panton-Valentine leukocidin (PVL) and α-type phenol soluble modulins were present. Genome comparisons revealed 32 additional CDS in JKD6159 but none appeared to encode new virulence factors, suggesting that this clone's enhanced pathogenicity could lie within subtler genome changes, such as SNPs within regulatory genes. To investigate the role of accessory genome elements in CA-MRSA epidemiology, we next sequenced three additional Australian non-ST93 CA-MRSA strains and compared them with JKD6159, 19 completed S. aureus genomes and 59 additional S. aureus genomes for which unassembled genome sequence data was publicly available (82 genomes in total). These comparisons showed that despite its distinctive genotype, JKD6159 and other CA-MRSA clones (including USA300) share a conserved repertoire of three notable accessory elements (SSCmecIV, PVL prophage, and pMW2). This study demonstrates that the genetically distinct ST93 CA-MRSA from Australia is highly virulent. Our comparisons of geographically and genetically diverse CA-MRSA genomes suggest that apparent convergent evolution in CA-MRSA may be better explained by the rapid dissemination of a

  18. The Spl Serine Proteases Modulate Staphylococcus aureus Protein Production and Virulence in a Rabbit Model of Pneumonia

    PubMed Central

    Salgado-Pabon, Wilmara; Meyerholz, David K.; White, Mark J.; Schlievert, Patrick M.

    2016-01-01

    ABSTRACT The Spl proteases are a group of six serine proteases that are encoded on the νSaβ pathogenicity island and are unique to Staphylococcus aureus. Despite their interesting biochemistry, their biological substrates and functions in virulence have been difficult to elucidate. We found that an spl operon mutant of the community-associated methicillin-resistant S. aureus USA300 strain LAC induced localized lung damage in a rabbit model of pneumonia, characterized by bronchopneumonia observed histologically. Disease in the mutant-infected rabbits was restricted in distribution compared to that in wild-type USA300-infected rabbits. We also found that SplA is able to cleave the mucin 16 glycoprotein from the surface of the CalU-3 lung cell line, suggesting a possible mechanism for wild-type USA300 spreading pneumonia to both lungs. Investigation of the secreted and surface proteomes of wild-type USA300 and the spl mutant revealed multiple alterations in metabolic proteins and virulence factors. This study demonstrates that the Spls modulate S. aureus physiology and virulence, identifies a human target of SplA, and suggests potential S. aureus targets of the Spl proteases. IMPORTANCE Staphylococcus aureus is a versatile human pathogen that produces an array of virulence factors, including several proteases. Of these, six proteases called the Spls are the least characterized. Previous evidence suggests that the Spls are expressed during human infection; however, their function is unknown. Our study shows that the Spls are required for S. aureus to cause disseminated lung damage during pneumonia. Further, we present the first example of a human protein cut by an Spl protease. Although the Spls were predicted not to cut staphylococcal proteins, we also show that an spl mutant has altered abundance of both secreted and surface-associated proteins. This work provides novel insight into the function of Spls during infection and their potential ability to degrade

  19. Community-based intervention to manage an outbreak of MRSA skin infections in a county jail.

    PubMed

    Elias, Abdallah F; Chaussee, Michael S; McDowell, Emily J; Huntington, Mark K

    2010-07-01

    This article describes a community-based intervention to manage an outbreak of community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) skin infections in a midwestern county jail. A systematic investigation conducted by a family medicine residency program identified 64 total cases and 19 MRSA cases between January 1 and December 31, 2007. Factors contributing to MRSA transmission included inadequate surveillance, lack of antibacterial soap, and a defective laundry process. All 19 isolates were CA-MRSA and all seven tested by pulsed-field gel electrophoresis (PFGE) were USA300. Four of the seven isolates showed variation of their PFGE patterns. A primary care approach using community-based resources effectively reduced the number of cases in this heterogeneous outbreak of CA-MRSA, with the last MRSA being isolated in October 2007. PMID:20466702

  20. Comparison of automated repetitive-sequence-based polymerase chain reaction and spa typing versus pulsed-field gel electrophoresis for molecular typing of methicillin-resistant Staphylococcus aureus.

    PubMed

    Church, Deirdre L; Chow, Barbara L; Lloyd, Tracie; Gregson, Daniel B

    2011-01-01

    Automated repetitive polymerase chain reaction (PCR) (DiversiLab, bioMérieux, St. Laurent, Quebec, Canada) and single locus sequence typing of the Staphylococcus protein A (spa) gene with spa-type assignment by StaphType RIDOM software were compared to pulsed-field gel electrophoresis (PFGE) as the "gold standard" method for methicillin-resistant Staphylococcus aureus (MRSA) typing. Fifty-four MRSA isolates were typed by all methods: 10 of known PFGE CMRSA type and 44 clinical isolates. Correct assignment of CMRSA type or cluster occurred for 47 of 54 (87%) of the isolates when using a rep-PCR similarity index (SI) of ≥95%. Rep-PCR gave 7 discordant results [CMRSA1 (3), CMRSA2 (1), CMRSA4 (1), and CMRSA10 (2)], and some CMRSA clusters were not distinguished (CMRSA10/5/9, CMRSA 7/8, and CMRSA3/6). Several spa types occurred within a single PFGE or repetitive PCR types among the 19 different spa types found. spa type t037 was shared by CMRSA3 and CMRSA6 strains, and CMRSA9 and most CMRSA10 strains shared spa type t008. Time to results for PFGE, repetitive PCR, and spa typing was 3-4 days, 24 h, and 48 h, respectively. The annual costs of using spa or repetitive PCR were 2.4× and 1.9× higher, respectively, than PFGE but routine use of spa typing would lower annual labor costs by 0.10 full-time equivalents compared to PFGE. Repetitive PCR is a good method for rapid outbreak screening, but MRSA isolates that share the same repetitive PCR or PFGE patterns can be distinguished by spa typing.

  1. Trends in Methicillin-Resistant Staphylococcus aureus Anovaginal Colonization in Pregnant Women in 2005 versus 2009▿

    PubMed Central

    Top, Karina A.; Huard, Richard C.; Fox, Zachary; Wu, Fann; Whittier, Susan; Della-Latta, Phyllis; Saiman, Lisa; Ratner, Adam J.

    2010-01-01

    In 2005, the prevalence of methicillin-resistant Staphylococcus aureus (MRSA) anovaginal colonization in pregnant women at our center (Columbia University Medical Center) was 0.5%, and MRSA-colonized women were less likely to carry group B streptococcus (GBS). In this study, our objectives were to identify changing trends in the prevalence of MRSA and methicillin-susceptible S. aureus (MSSA) anovaginal colonization in pregnant women, to assess the association between MRSA and GBS colonization, and to characterize the MRSA strains. From February to July 2009, Lim broths from GBS surveillance samples were cultured for S. aureus. MRSA strains were identified by resistance to cefoxitin and characterized by MicroScan, staphylococcal cassette chromosome mec (SCCmec) typing, pulsed-field gel electrophoresis (PFGE), spa typing, and Panton-Valentine leukocidin PCR. A total of 2,921 specimens from different patients were analyzed. The prevalences of MSSA, MRSA, and GBS colonization were 11.8%, 0.6% and 23.3%, respectively. GBS colonization was associated with S. aureus colonization (odds ratio [OR], 1.9; 95% confidence interval [95% CI], 1.5 to 2.4). The frequencies of GBS colonization were similar in MRSA-positive (34.2%) versus MRSA-negative patients (21.8%) (P = 0.4). All MRSA isolates from 2009 and 13/14 isolates from 2005 were SCCmec type IV or V, consistent with community-associated MRSA; 12/18 (2009) and 0/14 (2005) isolates were the USA300 clone. Levofloxacin resistance increased from 14.3% (2005) to 55.6% (2009) (P = 0.028). In conclusion, the prevalence of MRSA anovaginal colonization in pregnant women in New York City, NY, remained stable from 2005 to 2009, and USA300 emerged as the predominant clone with a significant increase in levofloxacin-resistant isolates. PMID:20686089

  2. Genome-wide Annotation, Identification, and Global Transcriptomic Analysis of Regulatory or Small RNA Gene Expression in Staphylococcus aureus

    PubMed Central

    Weiss, Andy; Broach, William H.; Wiemels, Richard E.; Mogen, Austin B.; Rice, Kelly C.

    2016-01-01

    ABSTRACT In Staphylococcus aureus, hundreds of small regulatory or small RNAs (sRNAs) have been identified, yet this class of molecule remains poorly understood and severely understudied. sRNA genes are typically absent from genome annotation files, and as a consequence, their existence is often overlooked, particularly in global transcriptomic studies. To facilitate improved detection and analysis of sRNAs in S. aureus, we generated updated GenBank files for three commonly used S. aureus strains (MRSA252, NCTC 8325, and USA300), in which we added annotations for >260 previously identified sRNAs. These files, the first to include genome-wide annotation of sRNAs in S. aureus, were then used as a foundation to identify novel sRNAs in the community-associated methicillin-resistant strain USA300. This analysis led to the discovery of 39 previously unidentified sRNAs. Investigating the genomic loci of the newly identified sRNAs revealed a surprising degree of inconsistency in genome annotation in S. aureus, which may be hindering the analysis and functional exploration of these elements. Finally, using our newly created annotation files as a reference, we perform a global analysis of sRNA gene expression in S. aureus and demonstrate that the newly identified tsr25 is the most highly upregulated sRNA in human serum. This study provides an invaluable resource to the S. aureus research community in the form of our newly generated annotation files, while at the same time presenting the first examination of differential sRNA expression in pathophysiologically relevant conditions. PMID:26861020

  3. Spatial Homogeneity of Bacterial Communities Associated with the Surface Mucus Layer of the Reef-Building Coral Acropora palmata.

    PubMed

    Kemp, Dustin W; Rivers, Adam R; Kemp, Keri M; Lipp, Erin K; Porter, James W; Wares, John P

    2015-01-01

    Coral surface mucus layer (SML) microbiota are critical components of the coral holobiont and play important roles in nutrient cycling and defense against pathogens. We sequenced 16S rRNA amplicons to examine the structure of the SML microbiome within and between colonies of the threatened Caribbean reef-building coral Acropora palmata in the Florida Keys. Samples were taken from three spatially distinct colony regions--uppermost (high irradiance), underside (low irradiance), and the colony base--representing microhabitats that vary in irradiance and water flow. Phylogenetic diversity (PD) values of coral SML bacteria communities were greater than surrounding seawater and lower than adjacent sediment. Bacterial diversity and community composition was consistent among the three microhabitats. Cyanobacteria, Bacteroidetes, Alphaproteobacteria, and Proteobacteria, respectively were the most abundant phyla represented in the samples. This is the first time spatial variability of the surface mucus layer of A. palmata has been studied. Homogeneity in the microbiome of A. palmata contrasts with SML heterogeneity found in other Caribbean corals. These findings suggest that, during non-stressful conditions, host regulation of SML microbiota may override diverse physiochemical influences induced by the topographical complexity of A. palmata. Documenting the spatial distribution of SML microbes is essential to understanding the functional roles these microorganisms play in coral health and adaptability to environmental perturbations. PMID:26659364

  4. Deciphering Cyanide-Degrading Potential of Bacterial Community Associated with the Coking Wastewater Treatment Plant with a Novel Draft Genome.

    PubMed

    Wang, Zhiping; Liu, Lili; Guo, Feng; Zhang, Tong

    2015-10-01

    Biotreatment processes fed with coking wastewater often encounter insufficient removal of pollutants, such as ammonia, phenols, and polycyclic aromatic hydrocarbons (PAHs), especially for cyanides. However, only a limited number of bacterial species in pure cultures have been confirmed to metabolize cyanides, which hinders the improvement of these processes. In this study, a microbial community of activated sludge enriched in a coking wastewater treatment plant was analyzed using 454 pyrosequencing and Illumina sequencing to characterize the potential cyanide-degrading bacteria. According to the classification of these pyro-tags, targeting V3/V4 regions of 16S rRNA gene, half of them were assigned to the family Xanthomonadaceae, implying that Xanthomonadaceae bacteria are well-adapted to coking wastewater. A nearly complete draft genome of the dominant bacterium was reconstructed from metagenome of this community to explore cyanide metabolism based on analysis of the genome. The assembled 16S rRNA gene from this draft genome showed that this bacterium was a novel species of Thermomonas within Xanthomonadaceae, which was further verified by comparative genomics. The annotation using KEGG and Pfam identified genes related to cyanide metabolism, including genes responsible for the iron-harvesting system, cyanide-insensitive terminal oxidase, cyanide hydrolase/nitrilase, and thiosulfate:cyanide transferase. Phylogenetic analysis showed that these genes had homologs in previously identified genomes of bacteria within Xanthomonadaceae and even presented similar gene cassettes, thus implying an inherent cyanide-decomposing potential. The findings of this study expand our knowledge about the bacterial degradation of cyanide compounds and will be helpful in the remediation of cyanides contamination. PMID:25910603

  5. Dissemination of multiple MRSA clones among community-associated methicillin-resistant Staphylococcus aureus infections from Japanese children with impetigo.

    PubMed

    Hisata, Ken; Ito, Teruyo; Matsunaga, Nobuaki; Komatsu, Mitsutaka; Jin, Jingxun; Li, Shanshuang; Watanabe, Shinya; Shimizu, Toshiaki; Hiramatsu, Keiichi

    2011-10-01

    The proportion of MRSA strains that cause skin and soft infections has recently increased. In 3 months we have characterized 17 MRSA strains isolated from children with impetigo at a Japanese hospital. Seventeen MRSA strains belonged to 7 clones defined by clonal complex (CC) in MLST genotype and type of SCCmec, which were rarely identified among healthcare-associated MRSA: CC 91-SCCmecIIb (4 strains); CC91-SCCmecIIn (2 strains); CC91-SCCmecIVa (2 strains); CC91-SCCmecV (4 strains); CC88-SCCmecIVg (3 strains); CC1-SCCmecIVc (1 strain); and CC5-SCCmecIVn (1 strain). Although one strain belonged to CC5, which has been commonly identified in healthcare-associated MRSA, it did not carry type II SCCmec, but carried type IV SCCmec. Fourteen of the 17 strains carried exfoliative toxin a or b gene, and none carried Panton-Valentine leukocidine gene. Furthermore, we determined the entire nucleotide sequences of two type V SCCmec elements carried by strains JCSC5952, a CC91 strain, and TSGH17, a Taiwanese CC59 strain. The structure of SCCmecJCSC5952 was more than 99% homologous in nucleotide identity with those of Taiwanese PVL-positive ST59 MRSA strains TSGH17 and PM1, which were designated as type V (5C2&5). Identification of multiple MRSA clones distinct from those disseminating at the hospital suggests that MRSA strains might be emerging in the community from MSSA strains by acquiring SCCmec elements on various occasions. Carriage of the similar type V(5C2&5) SCCmec element by strains of distinct genetic backgrounds, CC91 and CC59, suggested horizontal transfer of the SCCmec element.

  6. High Prevalence and Resistance Patterns of Community-Associated Methicillin-Resistant Staphylococcus Aureus in the Pomoravlje Region, Serbia.

    PubMed

    Lepsanovic, Zorica; Jeremic, Ljiljana Petrovic; Lazic, Srdjan; Cirkovic, Ivana

    2016-03-01

    With a view to estimating the prevalence and resistance patterns of CA-MRSA in one region of Serbia, we performed an analysis of MRSA isolates from healthy people and hospitalised patients. The detection of CA-MRSA was carried out by SCCmec typing. In MRSA isolates from hospitalised patients SCCmec types IV and V were found in 76% of the strains. Similar percentage (80%) of CA-MRSA genotypes was present in healthy people. SCCmec type V harbouring MRSA was the most successful clone. Higher prevalence of type V in hospitalised patients to that in healthy people (70% vs 54%) may indicate nosocomial transmissions in at least some hospital units. All MRSA strains from hospitalised patients were resistant to one or more non-β-lactam antibiotics while 52% were multi-resistant. In isolates from healthy people, 16% were sensitive to all non-β-lactam antibiotics and 40% were multi-resistant. Similar percentage of multi-resistant CA- and HA-genotypes occurred in a particular environment (53% vs 50% in hospitalised patients, and 37.5% vs 37.5% in healthy people) indicating selective pressure of antibiotics as a leading force conferring antibiotic resistance. High prevalence of CA-MRSA and high resistance rate both in hospitals and the community suggest that this pathogen has been present in the Pomoravlje Region, central Serbia for years.

  7. The Widespread Presence of a Multidrug-Resistant Escherichia coli ST131 Clade among Community-Associated and Hospitalized Patients

    PubMed Central

    den Reijer, P. Martijn; van Burgh, Sebastian; Burggraaf, Arjan; Ossewaarde, Jacobus M.; van der Zee, Anneke

    2016-01-01

    Background & Aims The extent of entry of multidrug-resistant Escherichia coli from the community into the hospital and subsequent clonal spread amongst patients is unclear. To investigate the extent and direction of clonal spread of these bacteria within a large teaching hospital, we prospectively genotyped multidrug-resistant E. coli obtained from community- and hospital associated patient groups and compared the distribution of diverse genetic markers. Methods A total of 222 E. coli, classified as multi-drug resistant according to national guidelines, were retrieved from both screening (n = 184) and non-screening clinical cultures (n = 38) from outpatients and patients hospitalized for various periods. All isolates were routinely genotyped using an amplified fragment length polymorphism (AFLP) assay and real-time PCR for CTX-M genes. Multi-locus sequence typing was additionally performed to confirm clusters. Based on demographics, patients were categorized into two groups: patients that were not hospitalized or less than 72 hours at time of strain isolation (group I) and patients that were hospitalized for at least 72 hours (group II). Results Genotyping showed that most multi-drug resistant E. coli either had unique AFLP profiles or grouped in small clusters of maximally 8 isolates. We identified one large ST131 clade comprising 31% of all isolates, containing several AFLP clusters with similar profiles. Although different AFLP clusters were found in the two patient groups, overall genetic heterogeneity was similar (35% vs 28% of isolates containing unique AFLP profiles, respectively). In addition, similar distributions of CTX-M groups, including CTX-M 15 (40% and 44% of isolates in group I and II, respectively) and ST131 (32% and 30% of isolates, respectively) were found. Conclusion We conclude that multi-drug resistant E. coli from the CTX-M 15 associated lineage ST131 are widespread amongst both community- and hospital associated patient groups, with similar genetic diversity and similar distributions of genetic markers. PMID:26930662

  8. Deep-sea faunal communities associated with a lost intermodal shipping container in the Monterey Bay National Marine Sanctuary, CA.

    PubMed

    Taylor, Josi R; DeVogelaere, Andrew P; Burton, Erica J; Frey, Oren; Lundsten, Lonny; Kuhnz, Linda A; Whaling, P J; Lovera, Christopher; Buck, Kurt R; Barry, James P

    2014-06-15

    Carrying assorted cargo and covered with paints of varying toxicity, lost intermodal containers may take centuries to degrade on the deep seafloor. In June 2004, scientists from Monterey Bay Aquarium Research Institute (MBARI) discovered a recently lost container during a Remotely Operated Vehicle (ROV) dive on a sediment-covered seabed at 1281 m depth in Monterey Bay National Marine Sanctuary (MBNMS). The site was revisited by ROV in March 2011. Analyses of sediment samples and high-definition video indicate that faunal assemblages on the container's exterior and the seabed within 10 m of the container differed significantly from those up to 500 m. The container surface provides hard substratum for colonization by taxa typically found in rocky habitats. However, some key taxa that dominate rocky areas were absent or rare on the container, perhaps related to its potential toxicity or limited time for colonization and growth. Ecological effects appear to be restricted to the container surface and the benthos within ∼10 m.

  9. Characterization of geographically distinct bacterial communities associated with coral mucus produced by Acropora spp. and Porites spp.

    PubMed

    McKew, B A; Dumbrell, A J; Daud, S D; Hepburn, L; Thorpe, E; Mogensen, L; Whitby, C

    2012-08-01

    Acropora and Porites corals are important reef builders in the Indo-Pacific and Caribbean. Bacteria associated with mucus produced by Porites spp. and Acropora spp. from Caribbean (Punta Maroma, Mexico) and Indo-Pacific (Hoga and Sampela, Indonesia) reefs were determined. Analysis of pyrosequencing libraries showed that bacterial communities from Caribbean corals were significantly more diverse (H', 3.18 to 4.25) than their Indonesian counterparts (H', 2.54 to 3.25). Dominant taxa were Gammaproteobacteria, Alphaproteobacteria, Firmicutes, and Cyanobacteria, which varied in relative abundance between coral genera and region. Distinct coral host-specific communities were also found; for example, Clostridiales were dominant on Acropora spp. (at Hoga and the Mexican Caribbean) compared to Porites spp. and seawater. Within the Gammproteobacteria, Halomonas spp. dominated sequence libraries from Porites spp. (49%) and Acropora spp. (5.6%) from the Mexican Caribbean, compared to the corresponding Indonesian coral libraries (<2%). Interestingly, with the exception of Porites spp. from the Mexican Caribbean, there was also a ubiquity of Psychrobacter spp., which dominated Acropora and Porites libraries from Indonesia and Acropora libraries from the Caribbean. In conclusion, there was a dominance of Halomonas spp. (associated with Acropora and Porites [Mexican Caribbean]), Firmicutes (associated with Acropora [Mexican Caribbean] and with Acropora and Porites [Hoga]), and Cyanobacteria (associated with Acropora and Porites [Hoga] and Porites [Sampela]). This is also the first report describing geographically distinct Psychrobacter spp. associated with coral mucus. In addition, the predominance of Clostridiales associated with Acropora spp. provided additional evidence for coral host-specific microorganisms.

  10. Characterization of Geographically Distinct Bacterial Communities Associated with Coral Mucus Produced by Acropora spp. and Porites spp.

    PubMed Central

    McKew, B. A.; Dumbrell, A. J.; Daud, S. D.; Hepburn, L.; Thorpe, E.; Mogensen, L.

    2012-01-01

    Acropora and Porites corals are important reef builders in the Indo-Pacific and Caribbean. Bacteria associated with mucus produced by Porites spp. and Acropora spp. from Caribbean (Punta Maroma, Mexico) and Indo-Pacific (Hoga and Sampela, Indonesia) reefs were determined. Analysis of pyrosequencing libraries showed that bacterial communities from Caribbean corals were significantly more diverse (H′, 3.18 to 4.25) than their Indonesian counterparts (H′, 2.54 to 3.25). Dominant taxa were Gammaproteobacteria, Alphaproteobacteria, Firmicutes, and Cyanobacteria, which varied in relative abundance between coral genera and region. Distinct coral host-specific communities were also found; for example, Clostridiales were dominant on Acropora spp. (at Hoga and the Mexican Caribbean) compared to Porites spp. and seawater. Within the Gammproteobacteria, Halomonas spp. dominated sequence libraries from Porites spp. (49%) and Acropora spp. (5.6%) from the Mexican Caribbean, compared to the corresponding Indonesian coral libraries (<2%). Interestingly, with the exception of Porites spp. from the Mexican Caribbean, there was also a ubiquity of Psychrobacter spp., which dominated Acropora and Porites libraries from Indonesia and Acropora libraries from the Caribbean. In conclusion, there was a dominance of Halomonas spp. (associated with Acropora and Porites [Mexican Caribbean]), Firmicutes (associated with Acropora [Mexican Caribbean] and with Acropora and Porites [Hoga]), and Cyanobacteria (associated with Acropora and Porites [Hoga] and Porites [Sampela]). This is also the first report describing geographically distinct Psychrobacter spp. associated with coral mucus. In addition, the predominance of Clostridiales associated with Acropora spp. provided additional evidence for coral host-specific microorganisms. PMID:22636010

  11. Phylogenetic and Functional Diversity of Microbial Communities Associated with Subsurface Sediments of the Sonora Margin, Guaymas Basin

    PubMed Central

    Vigneron, Adrien; Cruaud, Perrine; Roussel, Erwan G.; Pignet, Patricia; Caprais, Jean-Claude; Callac, Nolwenn; Ciobanu, Maria-Cristina; Godfroy, Anne; Cragg, Barry A.; Parkes, John R.; Van Nostrand, Joy D.; He, Zhili; Zhou, Jizhong; Toffin, Laurent

    2014-01-01

    Subsurface sediments of the Sonora Margin (Guaymas Basin), located in proximity of active cold seep sites were explored. The taxonomic and functional diversity of bacterial and archaeal communities were investigated from 1 to 10 meters below the seafloor. Microbial community structure and abundance and distribution of dominant populations were assessed using complementary molecular approaches (Ribosomal Intergenic Spacer Analysis, 16S rRNA libraries and quantitative PCR with an extensive primers set) and correlated to comprehensive geochemical data. Moreover the metabolic potentials and functional traits of the microbial community were also identified using the GeoChip functional gene microarray and metabolic rates. The active microbial community structure in the Sonora Margin sediments was related to deep subsurface ecosystems (Marine Benthic Groups B and D, Miscellaneous Crenarchaeotal Group, Chloroflexi and Candidate divisions) and remained relatively similar throughout the sediment section, despite defined biogeochemical gradients. However, relative abundances of bacterial and archaeal dominant lineages were significantly correlated with organic carbon quantity and origin. Consistently, metabolic pathways for the degradation and assimilation of this organic carbon as well as genetic potentials for the transformation of detrital organic matters, hydrocarbons and recalcitrant substrates were detected, suggesting that chemoorganotrophic microorganisms may dominate the microbial community of the Sonora Margin subsurface sediments. PMID:25099369

  12. Phylogenetic and functional diversity of microbial communities associated with subsurface sediments of the Sonora Margin, Guaymas Basin.

    PubMed

    Vigneron, Adrien; Cruaud, Perrine; Roussel, Erwan G; Pignet, Patricia; Caprais, Jean-Claude; Callac, Nolwenn; Ciobanu, Maria-Cristina; Godfroy, Anne; Cragg, Barry A; Parkes, John R; Van Nostrand, Joy D; He, Zhili; Zhou, Jizhong; Toffin, Laurent

    2014-01-01

    Subsurface sediments of the Sonora Margin (Guaymas Basin), located in proximity of active cold seep sites were explored. The taxonomic and functional diversity of bacterial and archaeal communities were investigated from 1 to 10 meters below the seafloor. Microbial community structure and abundance and distribution of dominant populations were assessed using complementary molecular approaches (Ribosomal Intergenic Spacer Analysis, 16S rRNA libraries and quantitative PCR with an extensive primers set) and correlated to comprehensive geochemical data. Moreover the metabolic potentials and functional traits of the microbial community were also identified using the GeoChip functional gene microarray and metabolic rates. The active microbial community structure in the Sonora Margin sediments was related to deep subsurface ecosystems (Marine Benthic Groups B and D, Miscellaneous Crenarchaeotal Group, Chloroflexi and Candidate divisions) and remained relatively similar throughout the sediment section, despite defined biogeochemical gradients. However, relative abundances of bacterial and archaeal dominant lineages were significantly correlated with organic carbon quantity and origin. Consistently, metabolic pathways for the degradation and assimilation of this organic carbon as well as genetic potentials for the transformation of detrital organic matters, hydrocarbons and recalcitrant substrates were detected, suggesting that chemoorganotrophic microorganisms may dominate the microbial community of the Sonora Margin subsurface sediments.

  13. Dynamics of indigenous bacterial communities associated with crude oil degradation in soil microcosms during nutrient-enhanced bioremediation.

    PubMed

    Chikere, Chioma B; Surridge, Karen; Okpokwasili, Gideon C; Cloete, Thomas E

    2012-03-01

    Bacterial population dynamics were examined during bioremediation of an African soil contaminated with Arabian light crude oil and nutrient enrichment (biostimulation). Polymerase chain reaction followed by denaturing gradient gel electrophoresis (DGGE) were used to generate bacterial community fingerprints of the different treatments employing the 16S ribosomal ribonucleic acid (rRNA) gene as molecular marker. The DGGE patterns of the nutrient-amended soils indicated the presence of distinguishable bands corresponding to the oil-contaminated-nutrient-enriched soils, which were not present in the oil-contaminated and pristine control soils. Further characterization of the dominant DGGE bands after excision, reamplification and sequencing revealed that Corynebacterium spp., Dietzia spp., Rhodococcus erythropolis sp., Nocardioides sp., Low G+C (guanine plus cytosine) Gram positive bacterial clones and several uncultured bacterial clones were the dominant bacterial groups after biostimulation. Prominent Corynebacterium sp. IC10 sequence was detected across all nutrient-amended soils but not in oil-contaminated control soil. Total heterotrophic and hydrocarbon utilizing bacterial counts increased significantly in the nutrient-amended soils 2 weeks post contamination whereas oil-contaminated and pristine control soils remained fairly stable throughout the experimental period. Gas chromatographic analysis of residual hydrocarbons in biostimulated soils showed marked attenuation of contaminants starting from the second to the sixth week after contamination whereas no significant reduction in hydrocarbon peaks were seen in the oil-contaminated control soil throughout the 6-week experimental period. Results obtained indicated that nutrient amendment of oil-contaminated soil selected and enriched the bacterial communities mainly of the Actinobacteria phylogenetic group capable of surviving in toxic contamination with concomitant biodegradation of the hydrocarbons. The present study therefore demonstrated that the soil investigated harbours hydrocarbon-degrading bacterial populations which can be biostimulated to achieve effective bioremediation of oil-contaminated soil.

  14. Diversity of endophytic and rhizoplane bacterial communities associated with exotic Spartina alterniflora and native mangrove using Illumina amplicon sequencing.

    PubMed

    Hong, Youwei; Liao, Dan; Hu, Anyi; Wang, Han; Chen, Jinsheng; Khan, Sardar; Su, Jianqiang; Li, Hu

    2015-10-01

    Root-associated microbial communities are very important for biogeochemical cycles in wetland ecosystems and help to elaborate the mechanisms of plant invasions. In the estuary of Jiulong River (China), Spartina alterniflora has widely invaded Kandelia obovata-dominated habitats, offering an opportunity to study the influence of root-associated bacteria. The community structures of endophytic and rhizosphere bacteria associated with selected plant species were investigated using the barcoded Illumina paired-end sequencing technique. The diversity indices of bacteria associated with the roots of S. alterniflora were higher than those of the transition stands and K. obovata monoculture. Using principal coordinate analysis with UniFrac metrics, the comparison of β-diversity showed that all samples could be significantly clustered into 3 major groups, according to the bacteria communities of origin. Four phyla, namely Proteobacteria, Bacteroidetes, Chloroflexi, and Firmicutes, were enriched in the rhizoplane of both salt marsh plants, while they shared higher abundances of Cyanobacteria and Proteobacteria among endophytic bacteria. Members of the phyla Spirochaetes and Chloroflexi were found among the endophytic bacteria of S. alterniflora and K. obovata, respectively. One of the interesting findings was that endophytes were more sensitive in response to plant invasion than were rhizosphere bacteria. With linear discriminate analysis, we found some predominant rhizoplane and endophytic bacteria, including Methylococcales, Pseudoalteromonadacea, Clostridium, Vibrio, and Desulfovibrio, which have the potential to affect the carbon, nitrogen, and sulfur cycles. Thus, the results provide clues to the isolation of functional bacteria and the effects of root-associated microbial groups on S. alterniflora invasions. PMID:26223001

  15. Comparative Evaluation of Anaerobic Bacterial Communities Associated with Roots of Submerged Macrophytes Growing in Marine or Brackish Water Sediments

    EPA Science Inventory

    Sediment microbial communities are important for seagrass growth and carbon cycling, however relatively few studies have addressed the composition of prokaryotic communities in seagrass bed sediments. Selective media were used enumerate culturable anaerobic bacteria associated ...

  16. Seasonal variation in nifH abundance and expression of cyanobacterial communities associated with boreal feather mosses.

    PubMed

    Warshan, Denis; Bay, Guillaume; Nahar, Nurun; Wardle, David A; Nilsson, Marie-Charlotte; Rasmussen, Ulla

    2016-09-01

    Dinitrogen (N2)-fixation by cyanobacteria living in symbiosis with pleurocarpous feather mosses (for example, Pleurozium schreberi and Hylocomium splendens) represents the main pathway of biological N input into N-depleted boreal forests. Little is known about the role of the cyanobacterial community in contributing to the observed temporal variability of N2-fixation. Using specific nifH primers targeting four major cyanobacterial clusters and quantitative PCR, we investigated how community composition, abundance and nifH expression varied by moss species and over the growing seasons. We evaluated N2-fixation rates across nine forest sites in June and September and explored the abundance and nifH expression of individual cyanobacterial clusters when N2-fixation is highest. Our results showed temporal and host-dependent variations of cyanobacterial community composition, nifH gene abundance and expression. N2-fixation was higher in September than June for both moss species, explained by higher nifH gene expression of individual clusters rather than higher nifH gene abundance or differences in cyanobacterial community composition. In most cases, 'Stigonema cluster' made up less than 29% of the total cyanobacterial community, but accounted for the majority of nifH gene expression (82-94% of total nifH expression), irrespective of sampling date or moss species. Stepwise multiple regressions showed temporal variations in N2-fixation being greatly explained by variations in nifH expression of the 'Stigonema cluster'. These results suggest that Stigonema is potentially the most influential N2-fixer in symbiosis with boreal forest feather mosses. PMID:26918665

  17. Bacterial Community Associated with the Intestinal Tract of Chinese Mitten Crab (Eriocheir sinensis) Farmed in Lake Tai, China

    PubMed Central

    Chen, Xiaobing; Di, Panpan; Wang, Hongming; Li, Bailin; Pan, Yingjie; Yan, Shuling; Wang, Yongjie

    2015-01-01

    Chinese mitten crab (CMC, Eriocheir sinensis) is an economically valuable species in South-East Asia that has been widely farmed in China. Characterization of the intestinal bacterial diversity of CMC will provide insights into the aquaculturing of CMCs. Based on the analysis of cloned 16S rRNA genes from culture-independent CMC gut bacteria, 124 out of 128 different clones reveal >95% nucleotide similarity to the species belonging to the four phyla of Tenericutes, Bacteroidetes, Firmicutes and Proteobacteria; one clone shows 91% sequence similarity to the member of TM7 (a candidate phylum without cultured representatives). Fluorescent in situ hybridization also reveals the abundance of Bacteroidetes in crab intestine. Electron micrographs show that spherical and filamentous bacteria are closely associated with the microvillus brush border of the midgut epithelium and are often inserted into the space between the microvilli using a stalk-like cell appendage. In contrast, the predominant rod-shaped bacteria in the hindgut are tightly attached to the epithelium surface by an unusual pili-like structure. Both 16S rRNA gene denaturing gel gradient electrophoresis and metagenome library indicate that the CMC Mollicutes group 2 appears to be present in both the midgut and hindgut with no significant difference in abundance. The CMC Mollicutes group 1, however, was found mostly in the midgut of CMCs. The CMC gut Mollicutes phylotypes appear to be most closely related to Mollicutes symbionts detected in the gut of isopods (Crustacea: Isopoda). Overall, the results suggest that CMCs harbor diverse, novel and specific gut bacteria, which are likely to live in close relationships with the CMC host. PMID:25875449

  18. Macrofaunal communities associated with chemosynthetic habitats from the U.S. Atlantic margin: A comparison among depth and habitat types

    USGS Publications Warehouse

    Bourque, Jill R.; Robertson, Craig M.; Brooke, Sandra; Demopoulos, Amanda

    2016-01-01

    Hydrocarbon seeps support distinct benthic communities capable of tolerating extreme environmental conditions and utilizing reduced chemical compounds for nutrition. In recent years, several locations of methane seepage have been mapped along the U.S. Atlantic continental slope. In 2012 and 2013, two newly discovered seeps were investigated in this region: a shallow site near Baltimore Canyon (BCS, 366–412 m) and a deep site near Norfolk Canyon (NCS, 1467–1602 m), with both sites containing extensive chemosynthetic mussel bed and microbial mat habitats. Sediment push cores, suction samples, and Ekman box cores were collected to quantify the abundance, diversity, and community structure of benthic macrofauna (>300 μm) in mussel beds, mats, and slope habitats at both sites. Community data from the deep site were also assessed in relation to the associated sediment environment (organic carbon and nitrogen, stable carbon and nitrogen isotopes, grain size, and depth). Infaunal assemblages and densities differed both between depths and among habitat types. Macrofaunal densities in microbial mats were four times greater than those present in mussel beds and slope sediments and were dominated by the annelid families Dorvilleidae, Capitellidae, and Tubificidae, while mussel habitats had higher proportions of crustaceans. Diversity was lower in BCS microbial mat habitats, but higher in mussel and slope sediments compared to NCS habitats. Multivariate statistical analysis revealed specific sediment properties as important for distinguishing the macrofaunal communities, including larger grain sizes present within NCS microbial mat habitats and depleted stable carbon isotopes (δ13C) in sediments present at mussel beds. These results suggest that habitat differences in the quality and source of organic matter are driving the observed patterns in the infaunal assemblages, including high β diversity and high variability in the macrofaunal community composition. This study is the first investigation of seep infauna along the U.S. Atlantic slope north of the Blake Ridge Diapir and provides a baseline for future regional comparisons to other seep habitats along the Atlantic margin.

  19. Changes in deep-sea carbonate-hosted microbial communities associated with high and low methane flux

    NASA Astrophysics Data System (ADS)

    Case, D. H.; Steele, J. A.; Chadwick, G.; Mendoza, G. F.; Levin, L. A.; Orphan, V. J.

    2012-12-01

    Methane seeps on continental shelves are rich in authigenic carbonates built of methane-derived carbon. These authigenic carbonates are home to micro- and macroscopic communities whose compositions are thus far poorly constrained but are known to broadly depend on local methane flux. The formation of authigenic carbonates is itself a result of microbial metabolic activity, as associations of anaerobic methane oxidizing archaea (ANME) and sulfate reducing bacteria (SRB) in the sediment subsurface increase both dissolved inorganic carbon (DIC) and alkalinity in pore waters. This 1:1 increase in DIC and alkalinity promotes the precipitation of authigenic carbonates. In this study, we performed in situ manipulations to test the response of micro- and macrofaunal communities to a change in methane flux. Methane-derived authigenic carbonates from two locations at Hydrate Ridge, OR, USA (depth range 595-604 mbsl), were transplanted from "active" cold seep sites (high methane flux) to "inactive" background sites (low methane flux), and vise versa, for one year. Community diversity surveys using T-RFLP and 16S rRNA clone libraries revealed how both bacterial and archaeal assemblages respond to this change in local environment, specifically demonstrating reproducible shifts in different ANME groups (ANME-1 vs. ANME-2). Animal assemblage composition also shifted during transplantation; gastropod representation increased (relative to control rocks) when substrates were moved from inactive to active sites and polychaete, crustacean and echinoderm representation increased when substrates were moved from active to inactive sites. Combined with organic and inorganic carbon δ13C measurements and mineralogy, this unique in situ experiment demonstrates that authigenic carbonates are viable habitats, hosting microbial and macrofaunal communities capable of responding to changes in external environment over relatively short time periods.

  20. Influence of Solar Radiation and Biotic Interactions on Bacterial and Eukaryotic Communities Associated with Sewage Decomposition in Ambient Water - Poster

    EPA Science Inventory

    Sewage and ambient water both consist of a highly complex array of bacteria and eukaryotic microbes. When these communities are mixed, the persistence of sewage-derived pathogens in environmental waters can represent a significant public health concern. Solar radiation and biotic...

  1. Influence of solar radiation and biotic interactions on bacterial and eukaryotic communities associated with sewage decomposition in ambient water

    EPA Science Inventory

    Sewage and ambient water both consist of a highly complex array of bacteria and eukaryotic microbes. When these communities are mixed, the persistence of sewage-derived pathogens in environmental waters can represent a significant public health concern. Solar radiation and biot...

  2. Deep-sea faunal communities associated with a lost intermodal shipping container in the Monterey Bay National Marine Sanctuary, CA.

    PubMed

    Taylor, Josi R; DeVogelaere, Andrew P; Burton, Erica J; Frey, Oren; Lundsten, Lonny; Kuhnz, Linda A; Whaling, P J; Lovera, Christopher; Buck, Kurt R; Barry, James P

    2014-06-15

    Carrying assorted cargo and covered with paints of varying toxicity, lost intermodal containers may take centuries to degrade on the deep seafloor. In June 2004, scientists from Monterey Bay Aquarium Research Institute (MBARI) discovered a recently lost container during a Remotely Operated Vehicle (ROV) dive on a sediment-covered seabed at 1281 m depth in Monterey Bay National Marine Sanctuary (MBNMS). The site was revisited by ROV in March 2011. Analyses of sediment samples and high-definition video indicate that faunal assemblages on the container's exterior and the seabed within 10 m of the container differed significantly from those up to 500 m. The container surface provides hard substratum for colonization by taxa typically found in rocky habitats. However, some key taxa that dominate rocky areas were absent or rare on the container, perhaps related to its potential toxicity or limited time for colonization and growth. Ecological effects appear to be restricted to the container surface and the benthos within ∼10 m. PMID:24793778

  3. The bacterial community associated with the leech Myzobdella lugubris Leidy 1851 (Hirudinea: Piscicolidae) from Lake Erie, Michigan, USA.

    PubMed

    Schulz, C; Faisal, M

    2010-06-01

    Leeches are widespread in the Great Lakes Basin, yet their potential to harbor disease-causing agents has not been investigated. The purpose of this study was to identify the bacterial community of the commonly occurring leech, Myzobdella lugubris, within the Lake Erie Watershed. Leech samples were collected from the pectoral fins of channel catfish, Ictalurus punctatus, and freshwater drum, Aplodinotus grunniens, from Lake Erie in commercial trap nets and pooled into two samples based on host attachment. Bacteria from within the viscera of M. lugubris were identified by sequencing their 16S rRNA (rDNA) gene of amplified community bacterial DNA extracted from pooled leech homogenate samples and were checked for similarity in two public databases: the Ribosomal Database Project and BLAST. Bacteria belonging to the phylum Bacteroidetes, beta-proteobacteria, Verrucomicrobia, and unclassified Bacteria were present in the leech samples. A large number of bacteria found within leeches attached to channel catfish consisted of sequences that could not be classified beyond the Domain Bacteria. However, many of these sequences were homologous (< 45%) to the phylum Bacteroidetes. One of the five genera detected in the leech homogenates was Flavobacterium psychrophilum, a serious fish pathogen that causes Bacterial Cold Water Disease. While the occurrence of genera varies, bacteria associated with the two fish species were similar.

  4. Changes in the Structure of the Microbial Community Associated with Nannochloropsis salina following Treatments with Antibiotics and Bioactive Compounds.

    PubMed

    Geng, Haifeng; Tran-Gyamfi, Mary B; Lane, Todd W; Sale, Kenneth L; Yu, Eizadora T

    2016-01-01

    Open microalgae cultures host a myriad of bacteria, creating a complex system of interacting species that influence algal growth and health. Many algal microbiota studies have been conducted to determine the relative importance of bacterial taxa to algal culture health and physiological states, but these studies have not characterized the interspecies relationships in the microbial communities. We subjected Nanochroloropsis salina cultures to multiple chemical treatments (antibiotics and quorum sensing compounds) and obtained dense time-series data on changes to the microbial community using 16S gene amplicon metagenomic sequencing (21,029,577 reads for 23 samples) to measure microbial taxa-taxa abundance correlations. Short-term treatment with antibiotics resulted in substantially larger shifts in the microbiota structure compared to changes observed following treatment with signaling compounds and glucose. We also calculated operational taxonomic unit (OTU) associations and generated OTU correlation networks to provide an overview of possible bacterial OTU interactions. This analysis identified five major cohesive modules of microbiota with similar co-abundance profiles across different chemical treatments. The Eigengenes of OTU modules were examined for correlation with different external treatment factors. This correlation-based analysis revealed that culture age (time) and treatment types have primary effects on forming network modules and shaping the community structure. Additional network analysis detected Alteromonadeles and Alphaproteobacteria as having the highest centrality, suggesting these species are "keystone" OTUs in the microbial community. Furthermore, we illustrated that the chemical tropodithietic acid, which is secreted by several species in the Alphaproteobacteria taxon, is able to drastically change the structure of the microbiota within 3 h. Taken together, these results provide valuable insights into the structure of the microbiota associated with N. salina cultures and how these structures change in response to chemical perturbations. PMID:27507966

  5. Diversity and Composition of Airborne Fungal Community Associated with Particulate Matters in Beijing during Haze and Non-haze Days.

    PubMed

    Yan, Dong; Zhang, Tao; Su, Jing; Zhao, Li-Li; Wang, Hao; Fang, Xiao-Mei; Zhang, Yu-Qin; Liu, Hong-Yu; Yu, Li-Yan

    2016-01-01

    To assess the diversity and composition of airborne fungi associated with particulate matters (PMs) in Beijing, China, a total of 81 PM samples were collected, which were derived from PM2.5, PM10 fractions, and total suspended particles during haze and non-haze days. The airborne fungal community in these samples was analyzed using the Illumina Miseq platform with fungi-specific primers targeting the internal transcribed spacer 1 region of the large subunit rRNA gene. A total of 797,040 reads belonging to 1633 operational taxonomic units were observed. Of these, 1102 belonged to Ascomycota, 502 to Basidiomycota, 24 to Zygomycota, and 5 to Chytridiomycota. The dominant orders were Pleosporales (29.39%), Capnodiales (27.96%), Eurotiales (10.64%), and Hypocreales (9.01%). The dominant genera were Cladosporium, Alternaria, Fusarium, Penicillium, Sporisorium, and Aspergilus. Analysis of similarities revealed that both particulate matter sizes (R = 0.175, p = 0.001) and air quality levels (R = 0.076, p = 0.006) significantly affected the airborne fungal community composition. The relative abundance of many fungal genera was found to significantly differ among various PM types and air quality levels. Alternaria and Epicoccum were more abundant in total suspended particles samples, Aspergillus in heavy-haze days and PM2.5 samples, and Malassezia in PM2.5 samples and heavy-haze days. Canonical correspondence analysis and permutation tests showed that temperature (p < 0.01), NO2 (p < 0.01), PM10 (p < 0.01), SO2(p < 0.01), CO (p < 0.01), and relative humidity (p < 0.05) were significant factors that determine airborne fungal community composition. The results suggest that diverse airborne fungal communities are associated with particulate matters and may provide reliable data for studying the responses of human body to the increasing level of air pollution in Beijing.

  6. Headwater riparian invertebrate communities associated with red alder and conifer wood and leaf litter in southeastern Alaska

    USGS Publications Warehouse

    LeSage, C.M.; Merritt, R.W.; Wipfli, M.S.

    2005-01-01

    We examined how management of young upland forests in southeastern Alaska affect riparian invertebrate taxa richness, density, and biomass, in turn, potentially influencing food abundance for fish and wildlife. Southeastern Alaska forests are dominated by coniferous trees including Sitka spruce (Picea sitchensis (Bong.) Carr.), western hemlock (Tsuga heterophylla (Raf.) Sarg.), with mixed stands of red cedar (Thuja plicata Donn.). Red alder (Alnus rubra Bong.) is hypothesized to influence the productivity of young-growth conifer forests and through forest management may provide increased riparian invertebrate abundance. To compare and contrast invertebrate densities between coniferous and alder riparian habitats, leaf litter and wood debris (early and late decay classes) samples were collected along eleven headwater streams on Prince of Wales Island, Alaska, during the summers of 2000 and 2001. Members of Acarina and Collembola were the most abundant taxa collected in leaf litter with alder litter having significantly higher mean taxa richness than conifer litter. Members of Acarina were the most abundant group collected on wood debris and alder wood had significantly higher mean taxa richness and biomass than conifer wood. Alder wood debris in more advanced decay stages had the highest mean taxa richness and biomass, compared to other wood types, while conifer late decay wood debris had the highest densities of invertebrates. The inclusion of alder in young-growth conifer forests can benefit forest ecosystems by enhancing taxa richness and biomass of riparian forest invertebrates. ?? 2005 by the Northwest Scientific Association. All rights reserved.

  7. Simultaneous selection of soil electroactive bacterial communities associated to anode and cathode in a two-chamber Microbial Fuel Cell

    NASA Astrophysics Data System (ADS)

    Chiellini, Carolina; Bacci, Giovanni; Fani, Renato; Mocali, Stefano

    2016-04-01

    Different bacteria have evolved strategies to transfer electrons over their cell surface to (or from) their extracellular environment. This electron transfer enables the use of these bacteria in bioelectrochemical systems (BES) such as Microbial Fuel Cells (MFCs). In MFC research the biological reactions at the cathode have long been a secondary point of interest. However, bacterial biocathodes in MFCs represent a potential advantage compared to traditional cathodes, for both their low costs and their low impact on the environment. The main challenge in biocathode set-up is represented by the selection of a bacterial community able to efficiently accept electrons from the electrode, starting from an environmental matrix. In this work, a constant voltage was supplied on a two-chamber MFC filled up with soil over three weeks in order to simultaneously select an electron donor bacterial biomass on the anode and an electron acceptor biomass on the cathode, starting from the same soil. Next Generation Sequencing (NGS) analysis was performed to characterize the bacterial community of the initial soil, in the anode, in the cathode and in the control chamber not supplied with any voltage. Results highlighted that both the MFC conditions and the voltage supply affected the soil bacterial communities, providing a selection of different bacterial groups preferentially associated to the anode (Betaproteobacteria, Bacilli and Clostridia) and to the cathode (Actinobacteria and Alphaproteobacteria). These results confirmed that several electroactive bacteria are naturally present within a top soil and, moreover, different soil bacterial genera could provide different electrical properties.

  8. High Prevalence and Resistance Patterns of Community-Associated Methicillin-Resistant Staphylococcus Aureus in the Pomoravlje Region, Serbia.

    PubMed

    Lepsanovic, Zorica; Jeremic, Ljiljana Petrovic; Lazic, Srdjan; Cirkovic, Ivana

    2016-03-01

    With a view to estimating the prevalence and resistance patterns of CA-MRSA in one region of Serbia, we performed an analysis of MRSA isolates from healthy people and hospitalised patients. The detection of CA-MRSA was carried out by SCCmec typing. In MRSA isolates from hospitalised patients SCCmec types IV and V were found in 76% of the strains. Similar percentage (80%) of CA-MRSA genotypes was present in healthy people. SCCmec type V harbouring MRSA was the most successful clone. Higher prevalence of type V in hospitalised patients to that in healthy people (70% vs 54%) may indicate nosocomial transmissions in at least some hospital units. All MRSA strains from hospitalised patients were resistant to one or more non-β-lactam antibiotics while 52% were multi-resistant. In isolates from healthy people, 16% were sensitive to all non-β-lactam antibiotics and 40% were multi-resistant. Similar percentage of multi-resistant CA- and HA-genotypes occurred in a particular environment (53% vs 50% in hospitalised patients, and 37.5% vs 37.5% in healthy people) indicating selective pressure of antibiotics as a leading force conferring antibiotic resistance. High prevalence of CA-MRSA and high resistance rate both in hospitals and the community suggest that this pathogen has been present in the Pomoravlje Region, central Serbia for years. PMID:27020871

  9. Bacterial communities associated with production facilities of two newly drilled thermogenic natural gas wells in the Barnett Shale (Texas, USA).

    PubMed

    Davis, James P; Struchtemeyer, Christopher G; Elshahed, Mostafa S

    2012-11-01

    We monitored the bacterial communities in the gas-water separator and water storage tank of two newly drilled natural gas wells in the Barnett Shale in north central Texas, using a 16S rRNA gene pyrosequencing approach over a period of 6 months. Overall, the communities were composed mainly of moderately halophilic and halotolerant members of the phyla Firmicutes and Proteobacteria (classes Βeta-, Gamma-, and Epsilonproteobacteria) in both wells at all sampling times and locations. Many of the observed lineages were encountered in prior investigations of microbial communities from various fossil fluid formations and production facilities. In all of the samples, multiple H(2)S-producing lineages were encountered; belonging to the sulfate- and sulfur-reducing class Deltaproteobacteria, order Clostridiales, and phylum Synergistetes, as well as the thiosulfate-reducing order Halanaerobiales. The bacterial communities from the separator and tank samples bore little resemblance to the bacterial communities in the drilling mud and hydraulic-fracture waters that were used to drill these wells, suggesting the in situ development of the unique bacterial communities in such well components was in response to the prevalent geochemical conditions present. Conversely, comparison of the bacterial communities on temporal and spatial scales suggested the establishment of a core microbial community in each sampled location. The results provide the first overview of bacterial dynamics and colonization patterns in newly drilled, thermogenic natural gas wells and highlights patterns of spatial and temporal variability observed in bacterial communities in natural gas production facilities.

  10. Pyrosequencing analysis of a bacterial community associated with lava-formed soil from the Gotjawal forest in Jeju, Korea

    PubMed Central

    Kim, Jong-Shik; Lee, Keun Chul; Kim, Dae-Shin; Ko, Suk-Hyung; Jung, Man-Young; Rhee, Sung-Keun; Lee, Jung-Sook

    2015-01-01

    In this study, we analyzed the bacterial diversity in soils collected from Gyorae Gotjawal forest, where globally unique topography, geology, and ecological features support a forest grown on basalt flows from 110,000 to 120,000 years ago and 40,000 to 50,000 years ago. The soils at the site are fertile, with rocky areas, and are home to endangered species of plants and animals. Rainwater penetrates to the groundwater aquifer, which is composed of 34% organic matter containing rare types of soil and no soil profile. We determined the bacterial community composition using 116,475 reads from a 454-pyrosequencing analysis. This dataset included 12,621 operational taxonomic units at 3% dissimilarity, distributed among the following groups: Proteobacteria (56.2%) with 45.7% of α-Proteobacteria, Actinobacteria (25%), Acidobacteria (10.9%), Chloroflexi (2.4%), and Bacteroidetes (0.9%). In addition, 16S rRNA gene sequences were amplified using polymerase chain reaction and domain-specific primers to construct a clone library based on 142 bacterial clones. These clones were affiliated with the following groups: Proteobacteria (56%) with 51% of α-Proteobacteria, Acidobacteria (7.8%), Actinobacteria (17.6%), Chloroflexi (2.1%), Bacilli (1.4%), Cyanobacteria (2.8%), and Planctomycetes (1.4%). Within the phylum Proteobacteria, 56 of 80 clones were tentatively identified as 12 unclassified genera. Several new genera and a new family were discovered within the Actinobacteria clones. Results from 454-pyrosequencing revealed that 57% and 34% of the sequences belonged to undescribed genera and families, respectively. The characteristics of Gotjawal soil, which are determined by lava morphology, vegetation, and groundwater penetration, might be reflected in the bacterial community composition. PMID:25604185

  11. Utilising bacterial communities associated with digested piggery effluent as a primary food source for the batch culture of Moina australiensis.

    PubMed

    Patil, Sayali S; Ward, Andrew J; Kumar, Martin S; Ball, Andrew S

    2010-05-01

    In this study, a cladoceran planktonic invertebrate, Moina australiensis was uniquely cultured in two stage digested piggery wastewater and fed associated piggery wastewater bacteria. The viability of M. australiensis cultured in digested piggery wastewater under closed dark conditions to limit phytoplankton activity was tested by determining suitable effluent total ammonia nitrogen (TAN) concentrations. The highest total M. australiensis biomass production 0.94+/-0.47g and the rate of population increase (r) 0.15+/-0.08 was recorded in the 30mgl(-1) TAN concentration treatment. The lowest 'r' values and decreased biomass production was observed with increasing TAN concentration levels. This study, also focused on profiling and quantification of the associated bacterial populations in the wastewater culture media and within the digestive tract of M. australiensis by denaturing gradient gel electrophoresis (DGGE) and real-time polymerase chain reaction (RT-PCR) which revealed the feeding specificity of M. australiensis towards "gamma-Proteobacteria." PMID:20089398

  12. High genetic diversity and variability of bacterial communities associated with the sandhopper Talitrus saltator (Montagu) (Crustacea, Amphipoda)

    NASA Astrophysics Data System (ADS)

    Mengoni, A.; Focardi, A.; Bacci, G.; Ugolini, A.

    2013-10-01

    The microbiome present in individuals of Talitrus saltator belonging to seven populations distributed along the Tuscan coast (Italy) was assessed by using Terminal-Restriction Fragment Length Polymorphism (T-RFLP) analysis of amplified 16S rRNA genes. Talitrus saltator is one of the key species of the damp band of European sandy beaches and despite of the large interest on animal-associated bacteria, only a few and preliminary data were present. Results showed a high diversity of the microbiome, composed mainly by members of Alphaproteobacteria, Gammaproteobacteria, Bacillales and Clostridiales classes. The microbiome fingerprints were highly variable among individuals, even from the same populations, the inter-individual differences accounting for 88.7% of total fingerprint variance. However, statistically significant population-specific microbiome signatures were detected, and accounted for the remaining 11.3% of total fingerprint variance. These population-specific differences were mainly attributed to sequences from members of known host-associated bacteria such as Gammaproteobacteria and Betaproteobacteria, Cytophagia and Spirochaetia. This study showed the high complexity of the microbiome associated with an amphipod species and on the inter-individual microbiome variation with potential importance for understanding amphipod trophic and ecologic processes.

  13. The gut bacterial communities associated with lab-raised and field-collected ants of Camponotus fragilis (Formicidae: Formicinae).

    PubMed

    He, Hong; Wei, Cong; Wheeler, Diana E

    2014-09-01

    Camponotus is the second largest ant genus and known to harbor the primary endosymbiotic bacteria of the genus Blochmannia. However, little is known about the effect of diet and environment changes on the gut bacterial communities of these ants. We investigated the intestinal bacterial communities in the lab-raised and field-collected ants of Camponotus fragilis which is found in the southwestern United States and northern reaches of Mexico. We determined the difference of gut bacterial composition and distribution among the crop, midgut, and hindgut of the two types of colonies. Number of bacterial species varied with the methods of detection and the source of the ants. Lab-raised ants yielded 12 and 11 species using classical microbial culture methods and small-subunit rRNA genes (16S rRNAs) polymerase chain reaction-restriction fragment-length polymorphism analysis, respectively. Field-collected ants yielded just 4 and 1-3 species using the same methods. Most gut bacterial species from the lab-raised ants were unevenly distributed among the crop, midgut, and hindgut, and each section had its own dominant bacterial species. Acetobacter was the prominent bacteria group in crop, accounting for about 55 % of the crop clone library. Blochmannia was the dominant species in midgut, nearly reaching 90 % of the midgut clone library. Pseudomonas aeruginosa dominated the hindgut, accounting for over 98 % of the hindgut clone library. P. aeruginosa was the only species common to all three sections. A comparison between lab-raised and field-collected ants, and comparison with other species, shows that gut bacterial communities vary with local environment and diet. The bacterial species identified here were most likely commensals with little effect on their hosts or mild pathogens deleterious to colony health.

  14. Diversity and Composition of Airborne Fungal Community Associated with Particulate Matters in Beijing during Haze and Non-haze Days

    PubMed Central

    Yan, Dong; Zhang, Tao; Su, Jing; Zhao, Li-Li; Wang, Hao; Fang, Xiao-Mei; Zhang, Yu-Qin; Liu, Hong-Yu; Yu, Li-Yan

    2016-01-01

    To assess the diversity and composition of airborne fungi associated with particulate matters (PMs) in Beijing, China, a total of 81 PM samples were collected, which were derived from PM2.5, PM10 fractions, and total suspended particles during haze and non-haze days. The airborne fungal community in these samples was analyzed using the Illumina Miseq platform with fungi-specific primers targeting the internal transcribed spacer 1 region of the large subunit rRNA gene. A total of 797,040 reads belonging to 1633 operational taxonomic units were observed. Of these, 1102 belonged to Ascomycota, 502 to Basidiomycota, 24 to Zygomycota, and 5 to Chytridiomycota. The dominant orders were Pleosporales (29.39%), Capnodiales (27.96%), Eurotiales (10.64%), and Hypocreales (9.01%). The dominant genera were Cladosporium, Alternaria, Fusarium, Penicillium, Sporisorium, and Aspergilus. Analysis of similarities revealed that both particulate matter sizes (R = 0.175, p = 0.001) and air quality levels (R = 0.076, p = 0.006) significantly affected the airborne fungal community composition. The relative abundance of many fungal genera was found to significantly differ among various PM types and air quality levels. Alternaria and Epicoccum were more abundant in total suspended particles samples, Aspergillus in heavy-haze days and PM2.5 samples, and Malassezia in PM2.5 samples and heavy-haze days. Canonical correspondence analysis and permutation tests showed that temperature (p < 0.01), NO2 (p < 0.01), PM10 (p < 0.01), SO2(p < 0.01), CO (p < 0.01), and relative humidity (p < 0.05) were significant factors that determine airborne fungal community composition. The results suggest that diverse airborne fungal communities are associated with particulate matters and may provide reliable data for studying the responses of human body to the increasing level of air pollution in Beijing. PMID:27148180

  15. Beyond the Primary Influences of Parents and Peers on Very Young Adolescent Alcohol Use: Evidence of Independent Community Associations

    ERIC Educational Resources Information Center

    Smith, Dayna T.; Kelly, Adrian B.; Chan, Gary C. K.; Toumbourou, John W.; Patton, George C.; Williams, Joanne W.

    2014-01-01

    This study examined the extent to which young adolescent alcohol use was related to alcohol-related norms and law enforcement of underage alcohol use, after accounting for known strong parent and peer correlates. Our sample consisted of 7,674 students (X-bar age = 12 years) from 30 Australian communities. Two-level (individuals nested within…

  16. Seasonal variation in nifH abundance and expression of cyanobacterial communities associated with boreal feather mosses

    PubMed Central

    Warshan, Denis; Bay, Guillaume; Nahar, Nurun; Wardle, David A; Nilsson, Marie-Charlotte; Rasmussen, Ulla

    2016-01-01

    Dinitrogen (N2)-fixation by cyanobacteria living in symbiosis with pleurocarpous feather mosses (for example, Pleurozium schreberi and Hylocomium splendens) represents the main pathway of biological N input into N-depleted boreal forests. Little is known about the role of the cyanobacterial community in contributing to the observed temporal variability of N2-fixation. Using specific nifH primers targeting four major cyanobacterial clusters and quantitative PCR, we investigated how community composition, abundance and nifH expression varied by moss species and over the growing seasons. We evaluated N2-fixation rates across nine forest sites in June and September and explored the abundance and nifH expression of individual cyanobacterial clusters when N2-fixation is highest. Our results showed temporal and host-dependent variations of cyanobacterial community composition, nifH gene abundance and expression. N2-fixation was higher in September than June for both moss species, explained by higher nifH gene expression of individual clusters rather than higher nifH gene abundance or differences in cyanobacterial community composition. In most cases, ‘Stigonema cluster' made up less than 29% of the total cyanobacterial community, but accounted for the majority of nifH gene expression (82–94% of total nifH expression), irrespective of sampling date or moss species. Stepwise multiple regressions showed temporal variations in N2-fixation being greatly explained by variations in nifH expression of the ‘Stigonema cluster'. These results suggest that Stigonema is potentially the most influential N2-fixer in symbiosis with boreal forest feather mosses. PMID:26918665

  17. Macroinvertebrate communities associated with three aquatic macrophytes (Ceratophyllum demersum, Myriophyllum spicatum, and Vallisneria americana) in Lake Onalaska, Wisconsin

    USGS Publications Warehouse

    Chilton, E.W.

    1990-01-01

    The standing crop and species diversity of macroinvertebrates associated with wild celery (Vallisneria americana), Eurasian watermilfoil (Myriophyllum spicatum), and coontail (Ceratophyllum demersum) were examined in Lake Onalaska, Pool 7 of the upper Mississippi River, during summer 1983. Although Ceratophyllum generally supported the largest invertebrate standing crop (number per g plant dry weight), differences in invertebrate abundance among plant species were not consistent across time. However, the distribution of several taxa were significantly affected by plant species. Hyalella azteca (overall the most abundant species) and Enallagma spp. (the most abundant predator) were consistently most numerous in Ceratophyllum samples and least abundant in Vallisneria samples. Generally, invertebrate community composition differed significantly among plant species throughout the summer.

  18. The effect of corrosion inhibitors on microbial communities associated with corrosion in a model flow cell system.

    PubMed

    Duncan, Kathleen E; Perez-Ibarra, Beatriz Monica; Jenneman, Gary; Harris, Jennifer Busch; Webb, Robert; Sublette, Kerry

    2014-01-01

    A model flow cell system was designed to investigate pitting corrosion in pipelines associated with microbial communities. A microbial inoculum producing copious amounts of H₂S was enriched from an oil pipeline biofilm sample. Reservoirs containing a nutrient solution and the microbial inoculum were pumped continuously through six flow cells containing mild steel corrosion coupons. Two cells received corrosion inhibitor "A", two received corrosion inhibitor "B", and two ("untreated") received no additional chemicals. Coupons were removed after 1 month and analyzed for corrosion profiles and biofilm microbial communities. Coupons from replicate cells showed a high degree of similarity in pitting parameters and in microbial community profiles, as determined by 16S rRNA gene sequence libraries but differed with treatment regimen, suggesting that the corrosion inhibitors differentially affected microbial species. Viable microbial biomass values were more than 10-fold higher for coupons from flow cells treated with corrosion inhibitors than for coupons from untreated flow cells. The total number of pits >10 mils diameter and maximum pitting rate were significantly correlated with each other and the total number of pits with the estimated abundance of sequences classified as Desulfomicrobium. The maximum pitting rate was significantly correlated with the sum of the estimated abundance of Desulfomicrobium plus Clostridiales, and with the sum of the estimated abundance of Desulfomicrobium plus Betaproteobacteria. The lack of significant correlation with the estimated abundance of Deltaproteobacteria suggests not all Deltaproteobacteria species contribute equally to microbiologically influenced corrosion (MIC) and that it is not sufficient to target one bacterial group when monitoring for MIC.

  19. Culicoides Species Communities Associated with Wild Ruminant Ecosystems in Spain: Tracking the Way to Determine Potential Bridge Vectors for Arboviruses

    PubMed Central

    Talavera, Sandra; Muñoz-Muñoz, Francesc; Durán, Mauricio; Verdún, Marta; Soler-Membrives, Anna; Oleaga, Álvaro; Arenas, Antonio; Ruiz-Fons, Francisco; Estrada, Rosa; Pagès, Nitu

    2015-01-01

    The genus Culicoides Latreille 1809 is a well-known vector for protozoa, filarial worms and, above all, numerous viruses. The Bluetongue virus (BTV) and the recently emerged Schmallenberg virus (SBV) are responsible for important infectious, non-contagious, insect-borne viral diseases found in domestic ruminants and transmitted by Culicoides spp. Both of these diseases have been detected in wild ruminants, but their role as reservoirs during the vector-free season still remains relatively unknown. In fact, we tend to ignore the possibility of wild ruminants acting as a source of disease (BTV, SBV) and permitting its reintroduction to domestic ruminants during the following vector season. In this context, a knowledge of the composition of the Culicoides species communities that inhabit areas where there are wild ruminants is of major importance as the presence of a vector species is a prerequisite for disease transmission. In this study, samplings were conducted in areas inhabited by different wild ruminant species; samples were taken in both 2009 and 2010, on a monthly basis, during the peak season for midge activity (in summer and autumn). A total of 102,693 specimens of 40 different species of the genus Culicoides were trapped; these included major BTV and SBV vector species. The most abundant vector species were C. imicola and species of the Obsoletus group, which represented 15% and 11% of total numbers of specimens, respectively. At the local scale, the presence of major BTV and SBV vector species in areas with wild ruminants coincided with that of the nearest sentinel farms included in the Spanish Bluetongue Entomological Surveillance Programme, although their relative abundance varied. The data suggest that such species do not exhibit strong host specificity towards either domestic or wild ruminants and that they could consequently play a prominent role as bridge vectors for different pathogens between both types of ruminants. This finding would support the hypothesis that wild ruminants could act as reservoirs for such pathogens, and subsequently be involved in the reintroduction of disease to livestock on neighbouring farms. PMID:26510136

  20. Culicoides Species Communities Associated with Wild Ruminant Ecosystems in Spain: Tracking the Way to Determine Potential Bridge Vectors for Arboviruses.

    PubMed

    Talavera, Sandra; Muñoz-Muñoz, Francesc; Durán, Mauricio; Verdún, Marta; Soler-Membrives, Anna; Oleaga, Álvaro; Arenas, Antonio; Ruiz-Fons, Francisco; Estrada, Rosa; Pagès, Nitu

    2015-01-01

    The genus Culicoides Latreille 1809 is a well-known vector for protozoa, filarial worms and, above all, numerous viruses. The Bluetongue virus (BTV) and the recently emerged Schmallenberg virus (SBV) are responsible for important infectious, non-contagious, insect-borne viral diseases found in domestic ruminants and transmitted by Culicoides spp. Both of these diseases have been detected in wild ruminants, but their role as reservoirs during the vector-free season still remains relatively unknown. In fact, we tend to ignore the possibility of wild ruminants acting as a source of disease (BTV, SBV) and permitting its reintroduction to domestic ruminants during the following vector season. In this context, a knowledge of the composition of the Culicoides species communities that inhabit areas where there are wild ruminants is of major importance as the presence of a vector species is a prerequisite for disease transmission. In this study, samplings were conducted in areas inhabited by different wild ruminant species; samples were taken in both 2009 and 2010, on a monthly basis, during the peak season for midge activity (in summer and autumn). A total of 102,693 specimens of 40 different species of the genus Culicoides were trapped; these included major BTV and SBV vector species. The most abundant vector species were C. imicola and species of the Obsoletus group, which represented 15% and 11% of total numbers of specimens, respectively. At the local scale, the presence of major BTV and SBV vector species in areas with wild ruminants coincided with that of the nearest sentinel farms included in the Spanish Bluetongue Entomological Surveillance Programme, although their relative abundance varied. The data suggest that such species do not exhibit strong host specificity towards either domestic or wild ruminants and that they could consequently play a prominent role as bridge vectors for different pathogens between both types of ruminants. This finding would support the hypothesis that wild ruminants could act as reservoirs for such pathogens, and subsequently be involved in the reintroduction of disease to livestock on neighbouring farms.

  1. Soil moisture and chemistry influence diversity of ectomycorrhizal fungal communities associating with willow along an hydrologic gradient.

    PubMed

    Erlandson, Sonya R; Savage, Jessica A; Cavender-Bares, Jeannine M; Peay, Kabir G

    2016-01-01

    Influences of soil environment and willow host species on ectomycorrhizal fungi communities was studied across an hydrologic gradient in temperate North America. Soil moisture, organic matter and pH strongly predicted changes in fungal community composition. In contrast, increased fungal richness strongly correlated with higher plant-available phosphorus. The 93 willow trees sampled for ectomycorrhizal fungi included seven willow species. Host identity did not influence fungal richness or community composition, nor was there strong evidence of willow host preference for fungal species. Network analysis suggests that these mutualist interaction networks are not significantly nested or modular. Across a strong environmental gradient, fungal abiotic niche determined the fungal species available to associate with host plants within a habitat.

  2. Molecular phylogenetic diversity of the microbial community associated with a high-temperature petroleum reservoir at an offshore oilfield.

    PubMed

    Li, Hui; Yang, Shi-Zhong; Mu, Bo-Zhong; Rong, Zhao-Feng; Zhang, Jie

    2007-04-01

    The microbial community and its diversity in production water from a high-temperature, water-flooded petroleum reservoir of an offshore oilfield in China were characterized by 16S rRNA gene sequence analysis. The bacterial and archaeal 16S rRNA gene clone libraries were constructed from the community DNA and, using sequence analysis, 388 bacterial and 220 archaeal randomly selected clones were clustered with 60 and 28 phylotypes, respectively. The results showed that the 16S rRNA genes of bacterial clones belonged to the divisions Firmicutes, Thermotogae, Nitrospirae and Proteobacteria, whereas the archaeal library was dominated by methanogen-like rRNA genes (Methanothermobacter, Methanobacter, Methanobrevibacter and Methanococcus), with a lower percentage of clones belonging to Thermoprotei. Thermophilic microorganisms were found in the production water, as well as mesophilic microorganisms such as Pseudomonas and Acinetobacter-like clones. The thermophilic microorganisms may be common inhabitants of geothermally heated specialized subsurface environments, which have been isolated previously from a number of high-temperature petroleum reservoirs worldwide. The mesophilic microorganisms were probably introduced into the reservoir as it was being exploited. The results of this work provide further insight into the composition of microbial communities of high-temperature petroleum reservoirs at offshore oilfields.

  3. Deciphering Cyanide-Degrading Potential of Bacterial Community Associated with the Coking Wastewater Treatment Plant with a Novel Draft Genome.

    PubMed

    Wang, Zhiping; Liu, Lili; Guo, Feng; Zhang, Tong

    2015-10-01

    Biotreatment processes fed with coking wastewater often encounter insufficient removal of pollutants, such as ammonia, phenols, and polycyclic aromatic hydrocarbons (PAHs), especially for cyanides. However, only a limited number of bacterial species in pure cultures have been confirmed to metabolize cyanides, which hinders the improvement of these processes. In this study, a microbial community of activated sludge enriched in a coking wastewater treatment plant was analyzed using 454 pyrosequencing and Illumina sequencing to characterize the potential cyanide-degrading bacteria. According to the classification of these pyro-tags, targeting V3/V4 regions of 16S rRNA gene, half of them were assigned to the family Xanthomonadaceae, implying that Xanthomonadaceae bacteria are well-adapted to coking wastewater. A nearly complete draft genome of the dominant bacterium was reconstructed from metagenome of this community to explore cyanide metabolism based on analysis of the genome. The assembled 16S rRNA gene from this draft genome showed that this bacterium was a novel species of Thermomonas within Xanthomonadaceae, which was further verified by comparative genomics. The annotation using KEGG and Pfam identified genes related to cyanide metabolism, including genes responsible for the iron-harvesting system, cyanide-insensitive terminal oxidase, cyanide hydrolase/nitrilase, and thiosulfate:cyanide transferase. Phylogenetic analysis showed that these genes had homologs in previously identified genomes of bacteria within Xanthomonadaceae and even presented similar gene cassettes, thus implying an inherent cyanide-decomposing potential. The findings of this study expand our knowledge about the bacterial degradation of cyanide compounds and will be helpful in the remediation of cyanides contamination.

  4. Changes in the Structure of the Microbial Community Associated with Nannochloropsis salina following Treatments with Antibiotics and Bioactive Compounds

    DOE PAGES

    Geng, Haifeng; Tran-Gyamfi, Mary B.; Lane, Todd W.; Sale, Kenneth L.; Yu, Eizadora T.

    2016-07-26

    Open microalgae cultures host a myriad of bacteria, creating a complex system of interacting species that influence algal growth and health. Many algal microbiota studies have been conducted to determine the relative importance of bacterial taxa to algal culture health and physiological states, but these studies have not characterized the interspecies relationships in the microbial communities. Here we subjected Nanochroloropsis salina cultures to multiple chemical treatments (antibiotics and quorum sensing compounds) and obtained dense time-series data on changes to the microbial community using 16S gene amplicon metagenomic sequencing (21,029,577 reads for 23 samples) to measure microbial taxa-taxa abundance correlations. Short-termmore » treatment with antibiotics resulted in substantially larger shifts in the microbiota structure compared to changes observed following treatment with signaling compounds and glucose. We also calculated operational taxonomic unit (OTU) associations and generated OTU correlation networks to provide an overview of possible bacterial OTU interactions. This analysis identified five major cohesive modules of microbiota with similar co-abundance profiles across different chemical treatments. The Eigengenes of OTU modules were examined for correlation with different external treatment factors. This correlation-based analysis revealed that culture age (time) and treatment types have primary effects on forming network modules and shaping the community structure. Additional network analysis detected Alteromonadeles and Alphaproteobacteria as having the highest centrality, suggesting these species are “keystone” OTUs in the microbial community. Furthermore, we illustrated that the chemical tropodithietic acid, which is secreted by several species in the Alphaproteobacteria taxon, is able to drastically change the structure of the microbiota within 3 h. Lastly, taken together, these results provide valuable insights into the structure of the microbiota associated with N. salina cultures and how these structures change in response to chemical perturbations.« less

  5. Vertical dynamics of the aquifer microbial community associated with groundwater chemistry in the artificial recharge site in Korea

    NASA Astrophysics Data System (ADS)

    Moon, Hee Sun; Hyun, Sung Pil; Kim, Boa; Shin, Doyun; Ha, Kyoochul

    2014-05-01

    Artificial groundwater recharge offers an opportunity to better manage groundwater resources by storing water in aquifers and increasing the amount of groundwater available for abstraction during high demand periods. It is important to understand the linkage of microbial ecology to groundwater chemistry to assess changes in groundwater quality caused by artificial groundwater recharge. In this study, we investigated how the structure and diversity of this subsurface microbial community correlates with and impacts upon groundwater chemistry. Groundwater samples at two different depths (10 and 33 m) were collected from three monitoring wells (MLW 1, MLW 2 and MLW 3) in the artificial groundwater recharge demonstration site in Changwon, Korea. The groundwater samples were filtered with 0.45 um membrane filters and then used for the anion and cation analysis. A 4L of each groundwater sample was immediately filtered with 0.2 um membrane filters and the filters were used for DNA extraction using Fast DNA Spin Kit for soil (MP Bio, USA). Further molecular work processes including pyrosequencing were carried out at Chunlab, Inc. (Seoul, Korea). Pyrosequencing results showed all major phyla were OD 1, OD3, and OD 11 in shallow groundwater samples while Proteobacteria (β-proteobacteria and δ-proteobacteria) and Bacterioidetes were dominant phyla in deep groundwater. The Shannon diversity index indicated that the microbial community was much more diverse in shallow groundwater than in deep groundwater. Heat map and hierarchical cluster analysis based on the relative abundance of OTUs at genus level showed a clear distinction between shallow and deep groundwater. Differences in the vertical community structure were driven by the major species such as Sufuicurvum sp., Pseudomonas sp., Acidiferrobacter sp., Gallionella sp., and Ferribacterium sp. The results show that several distinct factors such as iron and sulfate concentration control the vertical composition of microbial communities in this aquifer. In conclusion, iron and sulfur chemistry combined with microbial community structure is useful in predicting groundwater ecology and groundwater quality changes caused by the surface water injection in the artificial recharge of aquifers.

  6. Changes in the Structure of the Microbial Community Associated with Nannochloropsis salina following Treatments with Antibiotics and Bioactive Compounds

    PubMed Central

    Geng, Haifeng; Tran-Gyamfi, Mary B.; Lane, Todd W.; Sale, Kenneth L.; Yu, Eizadora T.

    2016-01-01

    Open microalgae cultures host a myriad of bacteria, creating a complex system of interacting species that influence algal growth and health. Many algal microbiota studies have been conducted to determine the relative importance of bacterial taxa to algal culture health and physiological states, but these studies have not characterized the interspecies relationships in the microbial communities. We subjected Nanochroloropsis salina cultures to multiple chemical treatments (antibiotics and quorum sensing compounds) and obtained dense time-series data on changes to the microbial community using 16S gene amplicon metagenomic sequencing (21,029,577 reads for 23 samples) to measure microbial taxa-taxa abundance correlations. Short-term treatment with antibiotics resulted in substantially larger shifts in the microbiota structure compared to changes observed following treatment with signaling compounds and glucose. We also calculated operational taxonomic unit (OTU) associations and generated OTU correlation networks to provide an overview of possible bacterial OTU interactions. This analysis identified five major cohesive modules of microbiota with similar co-abundance profiles across different chemical treatments. The Eigengenes of OTU modules were examined for correlation with different external treatment factors. This correlation-based analysis revealed that culture age (time) and treatment types have primary effects on forming network modules and shaping the community structure. Additional network analysis detected Alteromonadeles and Alphaproteobacteria as having the highest centrality, suggesting these species are “keystone” OTUs in the microbial community. Furthermore, we illustrated that the chemical tropodithietic acid, which is secreted by several species in the Alphaproteobacteria taxon, is able to drastically change the structure of the microbiota within 3 h. Taken together, these results provide valuable insights into the structure of the microbiota associated with N. salina cultures and how these structures change in response to chemical perturbations. PMID:27507966

  7. Structural Diversity of Bacterial Communities Associated with Bloom-Forming Freshwater Cyanobacteria Differs According to the Cyanobacterial Genus

    PubMed Central

    Louati, Imen; Pascault, Noémie; Debroas, Didier; Bernard, Cécile; Humbert, Jean-François; Leloup, Julie

    2015-01-01

    The factors and processes driving cyanobacterial blooms in eutrophic freshwater ecosystems have been extensively studied in the past decade. A growing number of these studies concern the direct or indirect interactions between cyanobacteria and heterotrophic bacteria. The presence of bacteria that are directly attached or immediately adjacent to cyanobacterial cells suggests that intense nutrient exchanges occur between these microorganisms. In order to determine if there is a specific association between cyanobacteria and bacteria, we compared the bacterial community composition during two cyanobacteria blooms of Anabaena (filamentous and N2-fixing) and Microcystis (colonial and non-N2 fixing) that occurred successively within the same lake. Using high-throughput sequencing, we revealed a clear distinction between associated and free-living communities and between cyanobacterial genera. The interactions between cyanobacteria and bacteria appeared to be based on dissolved organic matter degradation and on N recycling, both for N2-fixing and non N2-fixing cyanobacteria. Thus, the genus and potentially the species of cyanobacteria and its metabolic capacities appeared to select for the bacterial community in the phycosphere. PMID:26579722

  8. Aquatic hyphomycete communities associated with decomposing alder leaf litter in reference headwater streams of the Basque Country (northern Spain).

    PubMed

    Pérez, Javier; Descals, Enrique; Pozo, Jesús

    2012-08-01

    The community of aquatic hyphomycetes associated with decomposing alder leaf litter was studied during autumn-winter in nine headwater reference streams of the Basque Country (northern Spain). In order to study the spatial variability in composition and community structure, three streams from each of three different river basins were compared. The colonization dynamics and community changes throughout the decomposition process were also followed in three of the rivers (one per basin). The taxonomic richness and community structure of these fungi varied among rivers, including similar streams of a given watershed. However, neither species diversity nor total abundance was statistically related to environmental variables. Only the conidial production of two of the species, Flagellospora curvula and Lunulospora curvula appeared to be enhanced by nitrate availability in the water. The taxonomic richness and the reproductive activity (sporulation rate) were positively related to the leaf litter decomposition rate. The changes in conidial production along the process were similar for all the streams and helped explain leaf litter quality dynamics.

  9. Culicoides Species Communities Associated with Wild Ruminant Ecosystems in Spain: Tracking the Way to Determine Potential Bridge Vectors for Arboviruses.

    PubMed

    Talavera, Sandra; Muñoz-Muñoz, Francesc; Durán, Mauricio; Verdún, Marta; Soler-Membrives, Anna; Oleaga, Álvaro; Arenas, Antonio; Ruiz-Fons, Francisco; Estrada, Rosa; Pagès, Nitu

    2015-01-01

    The genus Culicoides Latreille 1809 is a well-known vector for protozoa, filarial worms and, above all, numerous viruses. The Bluetongue virus (BTV) and the recently emerged Schmallenberg virus (SBV) are responsible for important infectious, non-contagious, insect-borne viral diseases found in domestic ruminants and transmitted by Culicoides spp. Both of these diseases have been detected in wild ruminants, but their role as reservoirs during the vector-free season still remains relatively unknown. In fact, we tend to ignore the possibility of wild ruminants acting as a source of disease (BTV, SBV) and permitting its reintroduction to domestic ruminants during the following vector season. In this context, a knowledge of the composition of the Culicoides species communities that inhabit areas where there are wild ruminants is of major importance as the presence of a vector species is a prerequisite for disease transmission. In this study, samplings were conducted in areas inhabited by different wild ruminant species; samples were taken in both 2009 and 2010, on a monthly basis, during the peak season for midge activity (in summer and autumn). A total of 102,693 specimens of 40 different species of the genus Culicoides were trapped; these included major BTV and SBV vector species. The most abundant vector species were C. imicola and species of the Obsoletus group, which represented 15% and 11% of total numbers of specimens, respectively. At the local scale, the presence of major BTV and SBV vector species in areas with wild ruminants coincided with that of the nearest sentinel farms included in the Spanish Bluetongue Entomological Surveillance Programme, although their relative abundance varied. The data suggest that such species do not exhibit strong host specificity towards either domestic or wild ruminants and that they could consequently play a prominent role as bridge vectors for different pathogens between both types of ruminants. This finding would support the hypothesis that wild ruminants could act as reservoirs for such pathogens, and subsequently be involved in the reintroduction of disease to livestock on neighbouring farms. PMID:26510136

  10. Characterization of bacterial communities associated with organic aggregates in a large, shallow, eutrophic freshwater lake (Lake Taihu, China).

    PubMed

    Tang, Xiangming; Gao, Guang; Qin, Boqiang; Zhu, Liping; Chao, Jianying; Wang, Jianjun; Yang, Guijun

    2009-08-01

    Although organic-aggregate-associated bacteria play a pivotal role in microbial food webs and in the cycling of major elements, their community composition and diversity have not been extensively studied, especially in shallow freshwater systems. This study is among the first to explore intra-lake horizontal heterogeneity of organic-aggregate-associated bacterial community composition (OABC) in the large, shallow, and eutrophic Lake Taihu. During November 2006, samples were collected at four locations representing different trophic states and food web structures. Regional variability of OABC and diversity were studied by amplified ribosomal DNA restriction analysis and comparative analysis of four large 16S ribosomal RNA clone libraries. Our results demonstrate that OABC were numerically dominated by members of the beta-proteobacteria (19.2-38.6%), Bacteroidetes (3.6-20.0%), and alpha-proteobacteria (11.5-19.2%) groups. The dominance of the Bacteroidetes group was related to algae-based aggregates. Horizontal heterogeneity of OABC exists within habitats, suggesting that the trophic state of the water and the physicochemical properties of organic aggregates (OA) play a key role. Diverse bacterial communities found on OA were substantially different from free-living ones. Comparative statistical analyses of the habitats of OA-associated bacteria highlight the potential ecological importance of the exchange between OABC and the surrounding planktonic community. Lastly, we found at least 45% of sequences closely related to ones previously found in soils, sludge, sediments, and other habitats. This demonstrates that microorganisms from terrestrial and sediment habitats are an important component of OA.

  11. Molecular Characterisation and Co-cultivation of Bacterial Biofilm Communities Associated with the Mat-Forming Diatom Didymosphenia geminata.

    PubMed

    Brandes, Josephin; Kuhajek, Jeanne M; Goodwin, Eric; Wood, Susanna A

    2016-10-01

    Didymosphenia geminata (Lyngbye) M. Schmidt is a stalked freshwater diatom that is expanding its range globally. In some rivers, D. geminata forms thick and expansive polysaccharide-dominated mats. Like other stalked diatoms, D. geminata cells attach to the substratum with a pad of adhesive extracellular polymeric substance. Research on D. geminata and other diatoms suggests that bacterial biofilm composition may contribute to successful attachment. The aim of this study was to investigate the composition and role of bacterial biofilm communities in D. geminata attachment and survival. Bacterial biofilms were collected at four sites in the main stem of a river (containing D. geminata) and in four tributaries (free of D. geminata). Samples were characterised using automated rRNA intergenic spacer analysis and high-throughput sequencing (HTS). Mat-associated bacteria were isolated and their effect on the early establishment of D. geminata cells assessed using co-culturing experiments. ARISA and HTS data showed differences in bacterial communities between samples with and without D. geminata at two of the four sites. Samples with D. geminata had a higher relative abundance of Sphingobacteria (p < 0.01) and variability in community composition was reduced. Analysis of the 76 bacteria isolated from the mat revealed 12 different strains representing 8 genera. Co-culturing of a Carnobacterium sp. with D. geminata reduced survival (p < 0.001) and attachment (p < 0.001) of D. geminata. Attachment was enhanced by Micrococcus sp. and Pseudomonas sp. (p < 0.001 and p < 0.01, respectively). These data provide evidence that bacteria play a role in the initial attachment and on-going survival of D. geminata, and may partly explain observed distribution patterns. PMID:27412380

  12. Staphylococcus aureus nuclease is an SaeRS-dependent virulence factor.

    PubMed

    Olson, Michael E; Nygaard, Tyler K; Ackermann, Laynez; Watkins, Robert L; Zurek, Oliwia W; Pallister, Kyler B; Griffith, Shannon; Kiedrowski, Megan R; Flack, Caralyn E; Kavanaugh, Jeffrey S; Kreiswirth, Barry N; Horswill, Alexander R; Voyich, Jovanka M

    2013-04-01

    Several prominent bacterial pathogens secrete nuclease (Nuc) enzymes that have an important role in combating the host immune response. Early studies of Staphylococcus aureus Nuc attributed its regulation to the agr quorum-sensing system. However, recent microarray data have indicated that nuc is under the control of the SaeRS two-component system, which is a major regulator of S. aureus virulence determinants. Here we report that the nuc gene is directly controlled by the SaeRS two-component system through reporter fusion, immunoblotting, Nuc activity measurements, promoter mapping, and binding studies, and additionally, we were unable identify a notable regulatory link to the agr system. The observed SaeRS-dependent regulation was conserved across a wide spectrum of representative S. aureus isolates. Moreover, with community-associated methicillin-resistant S. aureus (CA MRSA) in a mouse model of peritonitis, we observed in vivo expression of Nuc activity in an SaeRS-dependent manner and determined that Nuc is a virulence factor that is important for in vivo survival, confirming the enzyme's role as a contributor to invasive disease. Finally, natural polymorphisms were identified in the SaeRS proteins, one of which was linked to Nuc regulation in a CA MRSA USA300 endocarditis isolate. Altogether, our findings demonstrate that Nuc is an important S. aureus virulence factor and part of the SaeRS regulon.

  13. The agr Inhibitors Solonamide B and Analogues Alter Immune Responses to Staphylococccus aureus but Do Not Exhibit Adverse Effects on Immune Cell Functions.

    PubMed

    Baldry, Mara; Kitir, Betül; Frøkiær, Hanne; Christensen, Simon B; Taverne, Nico; Meijerink, Marjolein; Franzyk, Henrik; Olsen, Christian A; Wells, Jerry M; Ingmer, Hanne

    2016-01-01

    Staphylococcus aureus infections are becoming increasingly difficult to treat due to antibiotic resistance with the community-associated methicillin-resistant S. aureus (CA-MRSA) strains such as USA300 being of particular concern. The inhibition of bacterial virulence has been proposed as an alternative approach to treat multi-drug resistant pathogens. One interesting anti-virulence target is the agr quorum-sensing system, which regulates virulence of CA-MRSA in response to agr-encoded autoinducing peptides. Agr regulation confines exotoxin production to the stationary growth phase with concomitant repression of surface-expressed adhesins. Solonamide B, a non-ribosomal depsipeptide of marine bacterial origin, was recently identified as a putative anti-virulence compound that markedly reduced expression of α-hemolysin and phenol-soluble modulins. To further strengthen solonamide anti-virulence candidacy, we report the chemical synthesis of solonamide analogues, investigation of structure-function relationships, and assessment of their potential to modulate immune cell functions. We found that structural differences between solonamide analogues confer significant differences in interference with agr, while immune cell activity and integrity is generally not affected. Furthermore, treatment of S. aureus with selected solonamides was found to only marginally influence the interaction with fibronectin and biofilm formation, thus addressing the concern that application of compounds inducing an agr-negative state may have adverse interactions with host factors in favor of host colonization. PMID:26731096

  14. Discovery of Antivirulence Agents against Methicillin-Resistant Staphylococcus aureus

    PubMed Central

    Khodaverdian, Varandt; Pesho, Michelle; Truitt, Barbara; Bollinger, Lucy; Patel, Parita; Nithianantham, Stanley; Yu, Guanping; Delaney, Elizabeth; Jankowsky, Eckhard

    2013-01-01

    Antivirulence agents inhibit the production of disease-causing virulence factors but are neither bacteriostatic nor bactericidal. Antivirulence agents against methicillin-resistant Staphylococcus aureus (MRSA) strain USA300, the most widespread community-associated MRSA strain in the United States, were discovered by virtual screening against the response regulator AgrA, which acts as a transcription factor for the expression of several of the most prominent S. aureus toxins and virulence factors involved in pathogenesis. Virtual screening was followed by similarity searches in the databases of commercial vendors. The small-molecule compounds discovered inhibit the production of the toxins alpha-hemolysin and phenol-soluble modulin α in a dose-dependent manner without inhibiting bacterial growth. These antivirulence agents are small-molecule biaryl compounds in which the aromatic rings either are fused or are separated by a short linker. One of these compounds is the FDA-approved nonsteroidal anti-inflammatory drug diflunisal. This represents a new use for an old drug. Antivirulence agents might be useful in prophylaxis and as adjuvants in antibiotic therapy for MRSA infections. PMID:23689713

  15. Rot is a key regulator of Staphylococcus aureus biofilm formation

    PubMed Central

    Mootz, Joe M.; Benson, Meredith A.; Heim, Cortney E.; Crosby, Heidi A.; Kavanaugh, Jeffrey S.; Dunman, Paul M.; Kielian, Tammy; Torres, Victor J.; Horswill, Alexander R.

    2015-01-01

    AUTHOR SUMMARY Staphylococcus aureus is a significant cause of chronic biofilm infections on medical implants. We investigated the biofilm regulatory cascade and discovered that the repressor of toxins (Rot) is part of this pathway. A USA300 community-associated methicillin-resistant S. aureus (CA-MRSA) strain deficient in Rot was unable to form a biofilm using multiple different assays, and we found rot mutants in other strain lineages were also biofilm deficient. By performing a global analysis of transcripts and protein production controlled by Rot, we observed that all the secreted protease genes were upregulated in a rot mutant, and we hypothesized that this regulation could be responsible for the biofilm phenotype. To investigate this question, we determined that Rot bound to the protease promoters, and we observed that activity levels of these enzymes, in particular the cysteine proteases, were increased in a rot mutant. By inactivating these proteases, biofilm capacity was restored to the mutant, demonstrating they are responsible for the biofilm negative phenotype. Finally, we tested the rot mutant in a mouse catheter model of biofilm infection and observed a significant reduction in biofilm burden. Thus S. aureus uses the transcription factor Rot to repress secreted protease levels in order to build a biofilm. PMID:25612137

  16. The agr Inhibitors Solonamide B and Analogues Alter Immune Responses to Staphylococccus aureus but Do Not Exhibit Adverse Effects on Immune Cell Functions

    PubMed Central

    Baldry, Mara; Kitir, Betül; Frøkiær, Hanne; Christensen, Simon B.; Taverne, Nico; Meijerink, Marjolein; Franzyk, Henrik; Olsen, Christian A.; Wells, Jerry M.; Ingmer, Hanne

    2016-01-01

    Staphylococcus aureus infections are becoming increasingly difficult to treat due to antibiotic resistance with the community-associated methicillin-resistant S. aureus (CA-MRSA) strains such as USA300 being of particular concern. The inhibition of bacterial virulence has been proposed as an alternative approach to treat multi-drug resistant pathogens. One interesting anti-virulence target is the agr quorum-sensing system, which regulates virulence of CA-MRSA in response to agr-encoded autoinducing peptides. Agr regulation confines exotoxin production to the stationary growth phase with concomitant repression of surface-expressed adhesins. Solonamide B, a non-ribosomal depsipeptide of marine bacterial origin, was recently identified as a putative anti-virulence compound that markedly reduced expression of α-hemolysin and phenol-soluble modulins. To further strengthen solonamide anti-virulence candidacy, we report the chemical synthesis of solonamide analogues, investigation of structure–function relationships, and assessment of their potential to modulate immune cell functions. We found that structural differences between solonamide analogues confer significant differences in interference with agr, while immune cell activity and integrity is generally not affected. Furthermore, treatment of S. aureus with selected solonamides was found to only marginally influence the interaction with fibronectin and biofilm formation, thus addressing the concern that application of compounds inducing an agr-negative state may have adverse interactions with host factors in favor of host colonization. PMID:26731096

  17. Guadalupian (Middle Permian) giant bivalve Alatoconchidae from a mid-Panthalassan paleo-atoll complex in Kyushu, Japan: A unique community associated with Tethyan fusulines and corals.

    PubMed

    Isozaki, Yukio

    2006-03-01

    Unique new fossil assemblages containing the large bivalve family Alatoconchidae are recorded from the Guadalupian (Middle Permian) shallow marine limestone in Kamura, Kyushu. The large bivalves occur in the Neoschwagerina Zone and Lepidolina Zone. This discovery establishes that the biostratigraphic range of the family Alatoconchidae extends up to the top of the Lepidolina Zone (upper Capitanian of upper Guadalupian) i.e., to the end-Guadalupian extinction level. The largest Alatoconchidae in Kamura occurs in the Neoschwagerina Zone, the size of which is up to 50 cm long and 5 cm thick. Although details are still unknown, their morphology with a wing-like side projection of their valves appears very similar to that of Alatoconchidae that includes the well-known genus Shikamaia Ozaki. The bivalve-bearing Iwato Formation was derived from a mid-oceanic shallow marine carbonate build-up formed on a mid-oceanic paleo-seamount. The close association among the Alatoconchidae, typical Tethyan fusulines (Verbeekinidae) and rugose corals (Waagenophyllidae), plus their common extinction pattern suggests that the Alatoconchidae flourished in warm, shallow (photic) marine environments in low latitude areas in Panthalassa as well as Tethys. The extra-large size and double-layered shell with a translucent outer layer composed of prismatic calcite suggests that these bivalves may have hosted abundant photosynthetic algal symbionts to support their large-body metabolism.

  18. Free-living bacterial communities associated with tubeworm (Ridgeia piscesae) aggregations in contrasting diffuse flow hydrothermal vent habitats at the Main Endeavour Field, Juan de Fuca Ridge.

    PubMed

    Forget, Nathalie L; Kim Juniper, S

    2013-04-01

    We systematically studied free-living bacterial diversity within aggregations of the vestimentiferan tubeworm Ridgeia piscesae sampled from two contrasting flow regimes (High Flow and Low Flow) in the Endeavour Hydrothermal Vents Marine Protected Area (MPA) on the Juan de Fuca Ridge (Northeast Pacific). Eight samples of particulate detritus were recovered from paired tubeworm grabs from four vent sites. Most sequences (454 tag and Sanger methods) were affiliated to the Epsilonproteobacteria, and the sulfur-oxidizing genus Sulfurovum was dominant in all samples. Gammaproteobacteria were also detected, mainly in Low Flow sequence libraries, and were affiliated with known methanotrophs and decomposers. The cooccurrence of sulfur reducers from the Deltaproteobacteria and the Epsilonproteobacteria suggests internal sulfur cycling within these habitats. Other phyla detected included Bacteroidetes, Actinobacteria, Chloroflexi, Firmicutes, Planctomycetes, Verrucomicrobia, and Deinococcus-Thermus. Statistically significant relationships between sequence library composition and habitat type suggest a predictable pattern for High Flow and Low Flow environments. Most sequences significantly more represented in High Flow libraries were related to sulfur and hydrogen oxidizers, while mainly heterotrophic groups were more represented in Low Flow libraries. Differences in temperature, available energy for metabolism, and stability between High Flow and Low Flow habitats potentially explain their distinct bacterial communities.

  19. The impact of ecosystem degradation on the diversity of AM fungal communities associated to shrub species from the semiarid Spanish southeast

    NASA Astrophysics Data System (ADS)

    Barea, J. M.; Palenzuela, J.; Sánchez-Castro, I.; López-García, A.; Ferrol, M.; Azcón-Aguilar, C.

    2012-04-01

    Both the incidence of some soil environmental factors and the disturbance of natural plant communities, are often accompanied or preceded by loss of key physical-chemical and biological soil properties. In particular, plant community degradation causes disturbance of AM inoculum potential which is a critical ecological factor to help further plant developments in degraded habitats. The effect of disturbance of the vegetation cover on AM fungal population (number and diversity), is particularly relevant in the case of shrub communities, characteristics of semiarid Mediterranean ecosystems. In this context, a series of experiments have been carried out based on five representative communities of shrub species from southeast Spain. Both morphological and molecular approaches were followed for characterization of AM fungi associated to the target plant species, either as spores, extra-radical mycelia or actually colonizing their roots. The experiments can be grouped into three categories: (i) Analyzing the effect of plant cover degradation status. We demonstrated that degradation affects negatively the density and diversity of AM fungi as spores. (ii) Analyzing the community composition, and the temporal colonization dynamics, of AM fungi colonizing the roots of representative shrub species. It was found that the different co-occurring plant species are colonized by AM fungal communities of different composition, and that many AM fungal sequences detected in plant roots cannot be related to known AM fungal taxa present as spores in the rhizosphere soil. (iii) Assessing the effect of soil disturbance on AM fungal populations. It was found that, in spite of the induced perturbation, the phylotype diversity of AM fungi in receptor plants exclusively colonized by the AM propagules from the altered soil was not reduced in comparison to that of plants exclusively colonized from donor plants taken from the target ecosystem, used as inoculum source. The results will be discussed in terms of how the extent of AM fungal population changes, as induced by ecosystem disturbances, can affect AM managements.

  20. Deep 16S rRNA pyrosequencing reveals a bacterial community associated with Banana Fusarium Wilt disease suppression induced by bio-organic fertilizer application.

    PubMed

    Shen, Zongzhuan; Wang, Dongsheng; Ruan, Yunze; Xue, Chao; Zhang, Jian; Li, Rong; Shen, Qirong

    2014-01-01

    Our previous work demonstrated that application of a bio-organic fertilizer (BIO) to a banana mono-culture orchard with serious Fusarium wilt disease effectively decreased the number of soil Fusarium sp. and controlled the soil-borne disease. Because bacteria are an abundant and diverse group of soil organisms that responds to soil health, deep 16 S rRNA pyrosequencing was employed to characterize the composition of the bacterial community to investigate how it responded to BIO or the application of other common composts and to explore the potential correlation between bacterial community, BIO application and Fusarium wilt disease suppression. After basal quality control, 137,646 sequences and 9,388 operational taxonomic units (OTUs) were obtained from the 15 soil samples. Proteobacteria, Acidobacteria, Bacteroidetes, Gemmatimonadetes and Actinobacteria were the most frequent phyla and comprised up to 75.3% of the total sequences. Compared to the other soil samples, BIO-treated soil revealed higher abundances of Gemmatimonadetes and Acidobacteria, while Bacteroidetes were found in lower abundance. Meanwhile, on genus level, higher abundances compared to other treatments were observed for Gemmatimonas and Gp4. Correlation and redundancy analysis showed that the abundance of Gemmatimonas and Sphingomonas and the soil total nitrogen and ammonium nitrogen content were higher after BIO application, and they were all positively correlated with disease suppression. Cumulatively, the reduced Fusarium wilt disease incidence that was seen after BIO was applied for 1-year might be attributed to the general suppression based on a shift within the bacteria soil community, including specific enrichment of Gemmatimonas and Sphingomonas. PMID:24871319

  1. [State of infection caused by methicillin-resistant Staphylococcus aureus (MRSA) in Extremadura: susceptibility, clonality and role of community-associated MRSA].

    PubMed

    Aguadero, V; González-Velasco, C; Vindel, A; González-Velasco, M; Moreno, J J

    2014-09-01

    The correct surveillance and control of infection caused by methicillin-resistant Staphylococcus aureus (MRSA) needs of update knowledge of its specific properties in each place. Our study aims to describe the current characteristics of infection due to MRSA in Extremadura. During 2010, 309 MRSA were collected from clinical samples in our region. A susceptibility test that included 17 antibiotics tested by AST -588 card Vitek 2 ® and E -test method was performed on all isolates. A sample of 100 strains, selected by stratified random sampling, were genotyped by pulsed field electrophoresis (PFGE). The prevalence of MRSA in Extremadura was 20.2%. Don Benito-Villanueva area showed the most prevalence and a higher incidence. Merida reported the most favourable situation, with a relatively low ratios of prevalence and incidence. The community acquired reached 44 % in the region, showing predominantly in less populated areas (Navalmoral and Coria). The most common multiresistant pattern was tobramycin-levofloxacin-erythromycin (44%), followed tobramycin-erythromycin-clindamycin (20%). No linezolid, daptomycin and tigecycline resistant strains were observed, but 42 % of the MRSA strains showed decreased susceptibility vancomycin (DSV). PFGE analysis reported 27 genotypes, with 3 major genotypes: E8a (25%), E7b (17%) and E7a (12%). The post-hoc statistical analysis did not reveal significant differences in the distribution of genotypes between different areas. However it revealed some trends that should be considered.

  2. Involvement of Methicillin-Susceptible Staphylococcus aureus Related to Sequence Type 25 and Harboring pvl Genes in a Case of Carotid Cavernous Fistula after Community-Associated Sepsis

    PubMed Central

    Damasco, Paulo V.; Chamon, Raiane C.; Barbosa, Angélica T. L.; da Cunha, Sérgio; Aquino, José H. W.; Cavalcante, Fernanda S.

    2012-01-01

    Staphylococcus aureus encoding Panton-Valentine leukocidin (PVL) genes has become the cause of life-threatening infections. We describe a case of carotid cavernous fistula after bacteremia in a 12-year-old male, caused by a methicillin-susceptible S. aureus isolate carrying the pvl, fnbA, and ebpS genes and related to sequence type 25 (ST25). The patient's condition was complicated by pleural empyema and osteomyelitis in the right femur. The patient was discharged in good clinical condition after 160 days of hospitalization. PMID:22090398

  3. Bacterial communities associated with the digestive tract of the predatory ground beetle, Poecilus chalcites, and their response to laboratory rearing and antibiotic treatment

    SciTech Connect

    Michael Lehman

    2008-06-01

    Ground beetles such as Poecilus chalcites (Coleoptera: Carabidae) are beneficial insects in agricultural systems where they contribute to the control of insect and weed pests. We assessed the complexity of bacterial communities occurring in the digestive tracts of field-collected P. chalcites using terminal restriction fragment length polymorphism analyses of polymerase chain reaction-amplified 16S rRNA genes. Bacterial identification was performed by the construction of 16S rRNA gene clone libraries and sequence analysis. Intestinal bacteria in field-collected beetles were then compared to those from groups of beetles that were reared in the lab on an artificial diet with and without antibiotics. Direct cell counts estimated 1.5 × 10S bacteria per milliliter of gut. The digestive tract of field-collected P. chalcites produced an average of 4.8 terminal restriction fragments (tRF) for each beetle. The most abundant clones were affiliated with the genus Lactobacillus, followed by the taxa Enterobacteriaceae, Clostridia, and Bacteriodetes. The majority of the sequences recovered were closely related to those reported from other insect gastrointestinal tracts. Lab-reared beetles produced fewer tRF, an average of 3.1 per beetle, and a reduced number of taxa with a higher number of clones from the family Enterobacteriaceae compared to the field-collected beetles. Antibiotic treatment significantly (p < 0.05) reduced the number of tRF per beetle and selected for a less diverse set of bacterial taxa. We conclude that the digestive tract of P. chalcites is colonized by a simple community of bacteria that possess autochthonous characteristics. Laboratory-reared beetles harbored the most common bacteria found in field-collected beetles, and these bacterial communities may be manipulated in the laboratory with the addition of antibiotics to the diet to allow study of functional roles.

  4. Application of the Random Amplified Polymorphic DNA (RAPD) Fingerprinting to Analyze Genetic Variation in Community Associated-Methicillin Resistant Staphylococcus Aureus (CA-MRSA) Isolates in Iran.

    PubMed

    Mobasherizadeh, Sina; Shojaei, Hasan; Havaei, Seyed Asghar; Mostafavizadeh, Kamyar; Davoodabadi, Fazollah; Khorvash, Farzin; Ataei, Behrooz; Daei-Naser, Abbas

    2015-12-18

    The aim of this study was to apply RAPD technique to analyze the genetic variability among the Iranian CA-MRSA isolates.The RAPD amplification was implemented on 25 strains isolated from the anterior nares of 410 healthy children using four randomly selected oligonucleotide primers from the stocks available in our laboratory, including the primers 1254, GE6, OLP6 and OLP13 from our stock. The amplified PCR products were detected on a 1.5% agarose gel and subjected to further analysis to establish the band profiles and genetic relationships using the Gel Compar® program.The Iranian CA-MRSA isolates produced distinct RAPD patterns which varied based on the primer used, however, the primer 1254 revealed highly polymorphic patterns consisting 5 discernable RAPD types (RT), "RT1" (12, 48%), "RT2" (8, 32%), "RT3" (3, 12%), and "RT4 and RT5", (a single RAPD type each, 4%). Phylogenetic analysis based on RAPD profiles divided most of the CA-MRSA isolates into 2 distinct but related RAPD clusters, a small group and two single unrelated RAPD types.This study shows that the simple and cost-effective but rather difficult to optimize RAPD fingerprinting could be used to evaluate genetic and epidemiological relationships of CA-MRSA isolates on condition that the patterns are obtained from carefully optimized laboratory tests.

  5. Culture-dependent and -independent characterization of microbial communities associated with a shallow submarine hydrothermal system occurring within a coral reef off Taketomi Island, Japan.

    PubMed

    Hirayama, Hisako; Sunamura, Michinari; Takai, Ken; Nunoura, Takuro; Noguchi, Takuro; Oida, Hanako; Furushima, Yasuo; Yamamoto, Hiroyuki; Oomori, Tamotsu; Horikoshi, Koki

    2007-12-01

    Microbial communities in a shallow submarine hydrothermal system near Taketomi Island, Japan, were investigated using cultivation-based and molecular techniques. The main hydrothermal activity occurred in a craterlike basin (depth, approximately 23 m) on the coral reef seafloor. The vent fluid (maximum temperature, >52 degrees C) contained 175 microM H2S and gas bubbles mainly composed of CH4 (69%) and N2 (29%). A liquid serial dilution cultivation technique targeting a variety of metabolism types quantified each population in the vent fluid and in a white microbial mat located near the vent. The most abundant microorganisms cultivated from both the fluid and the mat were autotrophic sulfur oxidizers, including mesophilic Thiomicrospira spp. and thermophilic Sulfurivirga caldicuralii. Methane oxidizers were the second most abundant organisms in the fluid; one novel type I methanotroph exhibited optimum growth at 37 degrees C, and another novel type I methanotroph exhibited optimum growth at 45 degrees C. The number of hydrogen oxidizers cultivated only from the mat was less than the number of sulfur and methane oxidizers, although a novel mesophilic hydrogen-oxidizing member of the Epsilonproteobacteria was isolated. Various mesophilic to hyperthermophilic heterotrophs, including sulfate-reducing Desulfovibrio spp., iron-reducing Deferribacter sp., and sulfur-reducing Thermococcus spp., were also cultivated. Culture-independent 16S rRNA gene clone analysis of the vent fluid and mat revealed highly diverse archaeal communities. In the bacterial community, S. caldicuralii was identified as the predominant phylotype in the fluid (clonal frequency, 25%). Both bacterial clone libraries indicated that there were bacterial communities involved in sulfur, hydrogen, and methane oxidation and sulfate reduction. Our results indicate that there are unique microbial communities that are sustained by active chemosynthetic primary production rather than by photosynthetic production in a shallow hydrothermal system where sunlight is abundant. PMID:17921273

  6. Diversity and distribution of methane-oxidizing microbial communities associated with different faunal assemblages in a giant pockmark of the Gabon continental margin

    NASA Astrophysics Data System (ADS)

    Cambon-Bonavita, M. A.; Nadalig, T.; Roussel, E.; Delage, E.; Duperron, S.; Caprais, J. C.; Boetius, A.; Sibuet, M.

    2009-12-01

    A giant 800-m-diameter pockmark named REGAB was discovered on the Gabon continental margin actively emitting methane at a water depth of 3200 m. The microbial diversity in sediments from four different assemblages of chemosynthetic organisms, Mytilidae, Vesicomyidae, Siboglinidae and a bacterial mat, was investigated using comparative 16S rRNA gene sequence analysis. Aggregates of anaerobic methanotrophic archaea (ANME-2) and bacteria of the Desulfosarcina/Desulfococcus cluster were found in all four chemosynthetic habitats. Fluorescence in situ hybridization targeting the ANME-2/ Desulfosarcina/Desulfococcus aggregates showed their presence few centimeters (3-5 cm) below the surface of sediment. 16S rRNA gene sequences from all known marine ANME groups were detected in the pockmark sediments, as well as from both known bacterial partners. The archaeal diversity was limited to the ANME cluster for all investigated samples. The bacterial diversity included members of the Proteobacteria, Bacilliales, Cytophaga/Flavobacteria, Verrucomicrobia, JS1 and Actinobacteria clusters. Bacterial 16S rRNA gene sequences related to those of known sulphide-oxidizing symbionts were recovered from tissues of several invertebrates including vesicomyid clams and siboglinid tubeworms of REGAB.

  7. Free-living bacterial communities associated with tubeworm (Ridgeia piscesae) aggregations in contrasting diffuse flow hydrothermal vent habitats at the Main Endeavour Field, Juan de Fuca Ridge.

    PubMed

    Forget, Nathalie L; Kim Juniper, S

    2013-04-01

    We systematically studied free-living bacterial diversity within aggregations of the vestimentiferan tubeworm Ridgeia piscesae sampled from two contrasting flow regimes (High Flow and Low Flow) in the Endeavour Hydrothermal Vents Marine Protected Area (MPA) on the Juan de Fuca Ridge (Northeast Pacific). Eight samples of particulate detritus were recovered from paired tubeworm grabs from four vent sites. Most sequences (454 tag and Sanger methods) were affiliated to the Epsilonproteobacteria, and the sulfur-oxidizing genus Sulfurovum was dominant in all samples. Gammaproteobacteria were also detected, mainly in Low Flow sequence libraries, and were affiliated with known methanotrophs and decomposers. The cooccurrence of sulfur reducers from the Deltaproteobacteria and the Epsilonproteobacteria suggests internal sulfur cycling within these habitats. Other phyla detected included Bacteroidetes, Actinobacteria, Chloroflexi, Firmicutes, Planctomycetes, Verrucomicrobia, and Deinococcus-Thermus. Statistically significant relationships between sequence library composition and habitat type suggest a predictable pattern for High Flow and Low Flow environments. Most sequences significantly more represented in High Flow libraries were related to sulfur and hydrogen oxidizers, while mainly heterotrophic groups were more represented in Low Flow libraries. Differences in temperature, available energy for metabolism, and stability between High Flow and Low Flow habitats potentially explain their distinct bacterial communities. PMID:23401293

  8. Temporal evolution of bacterial communities associated with the in situ wetland-based remediation of a marine shore porphyry copper tailings deposit.

    PubMed

    Diaby, N; Dold, B; Rohrbach, E; Holliger, C; Rossi, P

    2015-11-15

    Mine tailings are a serious threat to the environment and public health. Remediation of these residues can be carried out effectively by the activation of specific microbial processes. This article presents detailed information about temporal changes in bacterial community composition during the remediation of a section of porphyry copper tailings deposited on the Bahía de Ite shoreline (Peru). An experimental remediation cell was flooded and transformed into a wetland in order to prevent oxidation processes, immobilizing metals. Initially, the top oxidation zone of the tailings deposit displayed a low pH (3.1) and high concentrations of metals, sulfate, and chloride, in a sandy grain size geological matrix. This habitat was dominated by sulfur- and iron-oxidizing bacteria, such as Leptospirillum spp., Acidithiobacillus spp., and Sulfobacillus spp., in a microbial community which structure resembled acid mine drainage environments. After wetland implementation, the cell was water-saturated, the acidity was consumed and metals dropped to a fraction of their initial respective concentrations. Bacterial communities analyzed by massive sequencing showed time-dependent changes both in composition and cell numbers. The final remediation stage was characterized by the highest bacterial diversity and evenness. Aside from classical sulfate reducers from the phyla δ-Proteobacteria and Firmicutes, community structure comprised taxa derived from very diverse habitats. The community was also characterized by an elevated proportion of rare phyla and unaffiliated sequences. Numerical ecology analysis confirmed that the temporal population evolution was driven by pH, redox, and K. Results of this study demonstrated the usefulness of a detailed follow-up of the remediation process, not only for the elucidation of the communities gradually switching from autotrophic, oxidizing to heterotrophic and reducing living conditions, but also for the long term management of the remediation wetlands. PMID:26151655

  9. Changes of Fermentation Pathways of Fecal Microbial Communities Associated with a Drug Treatment That Increases Dietary Starch in the Human Colon

    PubMed Central

    Wolin, Meyer J.; Miller, Terry L.; Yerry, Susan; Zhang, Yongchao; Bank, Shelton; Weaver, Gary A.

    1999-01-01

    Acarbose inhibits starch digestion in the human small intestine. This increases the amount of starch available for microbial fermentation to acetate, propionate, and butyrate in the colon. Relatively large amounts of butyrate are produced from starch by colonic microbes. Colonic epithelial cells use butyrate as an energy source, and butyrate causes the differentiation of colon cancer cells. In this study we investigated whether colonic fermentation pathways changed during treatment with acarbose. We examined fermentations by fecal suspensions obtained from subjects who participated in an acarbose-placebo crossover trial. After incubation with [1-13C]glucose and 12CO2 or with unlabeled glucose and 13CO2, the distribution of 13C in product C atoms was determined by nuclear magnetic resonance spectrometry and gas chromatography-mass spectrometry. Regardless of the treatment, acetate, propionate, and butyrate were produced from pyruvate formed by the Embden-Meyerhof-Parnas pathway. Considerable amounts of acetate were also formed by the reduction of CO2. Butyrate formation from glucose increased and propionate formation decreased with acarbose treatment. Concomitantly, the amounts of CO2 reduced to acetate were 30% of the total acetate in untreated subjects and 17% of the total acetate in the treated subjects. The acetate, propionate, and butyrate concentrations were 57, 20, and 23% of the total final concentrations, respectively, for the untreated subjects and 57, 13, and 30% of the total final concentrations, respectively, for the treated subjects. PMID:10388668

  10. Levels of alpha-toxin correlate with distinct phenotypic response profiles of blood mononuclear cells and with agr background of community-associated Staphylococcus aureus isolates.

    PubMed

    Mairpady Shambat, Srikanth; Haggar, Axana; Vandenesch, Francois; Lina, Gerard; van Wamel, Willem J B; Arakere, Gayathri; Svensson, Mattias; Norrby-Teglund, Anna

    2014-01-01

    Epidemiological studies of Staphylococcus aureus have shown a relation between certain clones and the presence of specific virulence genes, but how this translates into virulence-associated functional responses is not fully elucidated. Here we addressed this issue by analyses of community-acquired S. aureus strains characterized with respect to antibiotic resistance, ST types, agr types, and virulence gene profiles. Supernatants containing exotoxins were prepared from overnight bacterial cultures, and tested in proliferation assays using human peripheral blood mononuclear cells (PBMC). The strains displayed stable phenotypic response profiles, defined by either a proliferative or cytotoxic response. Although, virtually all strains elicited superantigen-mediated proliferative responses, the strains with a cytotoxic profile induced proliferation only in cultures with the most diluted supernatants. This indicated that the superantigen-response was masked by a cytotoxic effect which was also confirmed by flow cytometry analysis. The cytotoxic supernatants contained significantly higher levels of α-toxin than did the proliferative supernatants. Addition of α-toxin to supernatants characterized as proliferative switched the response into cytotoxic profiles. In contrast, no effect of Panton Valentine Leukocidin, δ-toxin or phenol soluble modulin α-3 was noted in the proliferative assay. Furthermore, a significant association between agr type and phenotypic profile was found, where agrII and agrIII strains had predominantly a proliferative profile whereas agrI and IV strains had a predominantly cytotoxic profile. The differential response profiles associated with specific S. aureus strains with varying toxin production could possibly have an impact on disease manifestations, and as such may reflect specific pathotypes.

  11. Effects of root inoculation with bacteria on the growth, Cd uptake and bacterial communities associated with rape grown in Cd-contaminated soil.

    PubMed

    Chen, Zhao-jin; Sheng, Xia-fang; He, Lin-yan; Huang, Zhi; Zhang, Wen-hui

    2013-01-15

    Two metal-resistant and plant growth-promoting bacteria (Burkholderia sp. J62 and Pseudomonas thivervalensis Y-1-3-9) were evaluated for their impacts on plant growth promotion, Cd availability in soil, and Cd uptake in rape (Brassica napus) grown in different level (0, 50, and 100 mg kg(-1)) of Cd-contaminated soils. The impacts of the bacteria on the rape-associated bacterial community structures were also evaluated using denaturing gradient gel electrophoresis (DGGE) analysis of bacterial DNA extracted from the root interior and rhizosphere and bulk soil samples collected at day 60 after inoculation. Canonical correspondence analysis (CCA) was used to have a comparative analysis of DGGE profiles. Inoculation with live bacteria not only significantly increased root (ranging from 38% to 86%), stem (ranging from 27% to 65%) and leaf (ranging from 23% to 55%) dry weights and water-extractive Cd contents (ranging from 59% to 237%) in the rhizosphere soils of the rape but also significantly increased root (ranging from 10% to 61%), stem (ranging from 41% to 57%) and leaf (ranging from 46% to 68%) total Cd uptake of rape compared to the dead bacterial-inoculated controls. DGGE and sequence analyses showed that the bacteria could colonize the rhizosphere soils and root interiors of rape plants. DGGE-CCA also showed that root interior and rhizosphere and bulk soil community profiles from the live bacteria-inoculated rape were significantly different from those from the dead bacteria-inoculated rape respectively. These results suggested that the bacteria had the potential to promote the growth and Cd uptake of rape and to influence the development of the rape-associated bacterial community structures.

  12. Temporal evolution of bacterial communities associated with the in situ wetland-based remediation of a marine shore porphyry copper tailings deposit.

    PubMed

    Diaby, N; Dold, B; Rohrbach, E; Holliger, C; Rossi, P

    2015-11-15

    Mine tailings are a serious threat to the environment and public health. Remediation of these residues can be carried out effectively by the activation of specific microbial processes. This article presents detailed information about temporal changes in bacterial community composition during the remediation of a section of porphyry copper tailings deposited on the Bahía de Ite shoreline (Peru). An experimental remediation cell was flooded and transformed into a wetland in order to prevent oxidation processes, immobilizing metals. Initially, the top oxidation zone of the tailings deposit displayed a low pH (3.1) and high concentrations of metals, sulfate, and chloride, in a sandy grain size geological matrix. This habitat was dominated by sulfur- and iron-oxidizing bacteria, such as Leptospirillum spp., Acidithiobacillus spp., and Sulfobacillus spp., in a microbial community which structure resembled acid mine drainage environments. After wetland implementation, the cell was water-saturated, the acidity was consumed and metals dropped to a fraction of their initial respective concentrations. Bacterial communities analyzed by massive sequencing showed time-dependent changes both in composition and cell numbers. The final remediation stage was characterized by the highest bacterial diversity and evenness. Aside from classical sulfate reducers from the phyla δ-Proteobacteria and Firmicutes, community structure comprised taxa derived from very diverse habitats. The community was also characterized by an elevated proportion of rare phyla and unaffiliated sequences. Numerical ecology analysis confirmed that the temporal population evolution was driven by pH, redox, and K. Results of this study demonstrated the usefulness of a detailed follow-up of the remediation process, not only for the elucidation of the communities gradually switching from autotrophic, oxidizing to heterotrophic and reducing living conditions, but also for the long term management of the remediation wetlands.

  13. Pathways of Carbon and Energy Metabolism of the Epibiotic Community Associated with the Deep-Sea Hydrothermal Vent Shrimp Rimicaris exoculata

    PubMed Central

    Hügler, Michael; Petersen, Jillian M.; Dubilier, Nicole; Imhoff, Johannes F.; Sievert, Stefan M.

    2011-01-01

    Background The shrimp Rimicaris exoculata dominates the faunal biomass at many deep-sea hydrothermal vent sites at the Mid-Atlantic Ridge. In its enlarged gill chamber it harbors a specialized epibiotic bacterial community for which a nutritional role has been proposed. Methodology/Principal Findings We analyzed specimens from the Snake Pit hydrothermal vent field on the Mid-Atlantic Ridge by complementing a 16S rRNA gene survey with the analysis of genes involved in carbon, sulfur and hydrogen metabolism. In addition to Epsilon- and Gammaproteobacteria, the epibiotic community unexpectedly also consists of Deltaproteobacteria of a single phylotype, closely related to the genus Desulfocapsa. The association of these phylogenetic groups with the shrimp was confirmed by fluorescence in situ hybridization. Based on functional gene analyses, we hypothesize that the Gamma- and Epsilonproteobacteria are capable of autotrophic growth by oxidizing reduced sulfur compounds, and that the Deltaproteobacteria are also involved in sulfur metabolism. In addition, the detection of proteobacterial hydrogenases indicates the potential for hydrogen oxidation in these communities. Interestingly, the frequency of these phylotypes in 16S rRNA gene clone libraries from the mouthparts differ from that of the inner lining of the gill chamber, indicating potential functional compartmentalization. Conclusions Our data show the specific association of autotrophic bacteria with Rimicaris exoculata from the Snake Pit hydrothermal vent field, and suggest that autotrophic carbon fixation is contributing to the productivity of the epibiotic community with the reductive tricarboxylic acid cycle as one important carbon fixation pathway. This has not been considered in previous studies of carbon fixation and stable carbon isotope composition of the shrimp and its epibionts. Furthermore, the co-occurrence of sulfur-oxidizing and sulfur-reducing epibionts raises the possibility that both may be involved in the syntrophic exchange of sulfur compounds, which could increase the overall efficiency of this epibiotic community. PMID:21249205

  14. Arctic fungal communities associated with roots of Bistorta vivipara do not respond to the same fine-scale edaphic gradients as the aboveground vegetation.

    PubMed

    Mundra, Sunil; Halvorsen, Rune; Kauserud, Håvard; Müller, Eike; Vik, Unni; Eidesen, Pernille B

    2015-03-01

    Soil conditions and microclimate are important determinants of the fine-scale distribution of plant species in the Arctic, creating locally heterogeneous vegetation. We hypothesize that root-associated fungal (RAF) communities respond to the same fine-scale environmental gradients as the aboveground vegetation, creating a coherent pattern between aboveground vegetation and RAF. We explored how RAF communities of the ectomycorrhizal (ECM) plant Bistorta vivipara and aboveground vegetation structure of arctic plants were affected by biotic and abiotic variables at 0.3-3.0-m scales. RAF communities were determined using pyrosequencing. Composition and spatial structure of RAF and aboveground vegetation in relation to collected biotic and abiotic variables were analysed by ordination and semi-variance analyses. The vegetation was spatially structured along soil C and N gradients, whereas RAF lacked significant spatial structure. A weak relationship between RAF community composition and the cover of two ECM plants, B. vivipara and S. polaris, was found, and RAF richness increased with host root length and root weight. Results suggest that the fine-scale spatial structure of RAF communities of B. vivipara and the aboveground vegetation are driven by different factors. At fine spatial scales, neighbouring ECM plants may affect RAF community composition, whereas soil nutrients gradients structure the vegetation. PMID:25483568

  15. Effects of dairy manure management in annual and perennial cropping systems on soil microbial communities associated with in situ N2O fluxes

    NASA Astrophysics Data System (ADS)

    Dunfield, Kari; Thompson, Karen; Bent, Elizabeth; Abalos, Diego; Wagner-Riddle, Claudia

    2016-04-01

    Liquid dairy manure (LDM) application and ploughing events may affect soil microbial community functioning differently between perennial and annual cropping systems due to plant-specific characteristics stimulating changes in microbial community structure. Understanding how these microbial communities change in response to varied management, and how these changes relate to in situ N2O fluxes may allow the creation of predictive models for use in the development of best management practices (BMPs) to decrease nitrogen (N) losses through choice of crop, plough, and LDM practices. Our objectives were to contrast changes in the population sizes and community structures of genes associated with nitrifier (amoA, crenamoA) and denitrifier (nirK, nirS, nosZ) communities in differently managed annual and perennial fields demonstrating variation in N2O flux, and to determine if differences in these microbial communities were linked to the observed variation in N2O fluxes. Soil was sampled in 2012 and in 2014 in a 4-ha spring-applied LDM grass-legume (perennial) plot and two 4-ha corn (annual) treatments under fall or spring LDM application. Soil DNA was extracted and used to target N-cycling genes via qPCR (n=6) and for next-generation sequencing (Illumina Miseq) (n=3). Significantly higher field-scale N2O fluxes were observed in the annual plots compared to the perennial system; however N2O fluxes increased after plough down of the perennial plot. Nonmetric multidimensional scaling (NMS) indicated differences in N-cycling communities between annual and perennial cropping systems, and some communities became similar between annual and perennial plots after ploughing. Shifts in these communities demonstrated relationships with agricultural management, which were associated with differences in N2O flux. Indicator species analysis was used to identify operational taxonomic units (OTUs) most responsible for community shifts related to management. Nitrifying and denitrifying soil bacterial communities are sensitive to agricultural management (annual or perennial crop type, LDM management, and ploughing) and communities will respond to variations in management, affecting field N2O fluxes.

  16. Characteristics of the microbial community associated with ammonia oxidation in a full-scale rockwool biofilter treating malodors from livestock manure composting.

    PubMed

    Yasuda, Tomoko; Kuroda, Kazutaka; Hanajima, Dai; Fukumoto, Yasuyuki; Waki, Miyoko; Suzuki, Kazuyoshi

    2010-01-01

    The relationship between the activity and community structure of microbes associated with the oxidation of ammonia in a full-scale rockwool biofilter was examined by kinetic, denaturing gradient gel electrophoresis (DGGE), and sequence analyses. The packing materials were sampled from two different depths at 3 sites. Estimated K(m) values were similar among depths at same sampling sites, while V(max) differed in the mid-point sample. The lower depth of this site had the highest V(max). A correspondence analysis showed the DGGE profile of ammonia-oxidizing bacterial amoA of the lower depth of the mid-point sample to be distinguishable from the others. Banding patterns at other sites were similar among depths. Banding patterns of ammonia-oxidizing archaeal amoA of the mid-point sample were also similar among depths. The results suggested an association between the ammonia-oxidizing bacterial community's composition and ammonium oxidation kinetics in samples. Sequence analysis indicated that the ammonia-oxidizing bacterial community mainly belonged to the Nitrosomonas europaea lineage and Nitrosospira cluster 3. The ammonia-oxidizing archaeal amoA-like sequences were related to those belonging to soil and sediment groups, including one with 84% nucleotide similarity with Nitrosopumilus maritimus.

  17. Molecular characterization of the endophytic fungal community associated with Eichhornia azurea (Kunth) and Eichhornia crassipes (Mart.) (Pontederiaceae) native to the Upper Paraná River floodplain, Brazil.

    PubMed

    Almeida, T T; Orlandelli, R C; Azevedo, J L; Pamphile, J A

    2015-05-11

    Endophytic fungi live in the interior of healthy plants without causing them any damage. These fungi are of biotechnological interest; they may be used in the biological control of pests and plant diseases, and in the pharmaceutical industry. The aquatic macrophytes Eichhornia azurea (Kunth) and Eichhornia crassipes (Mart.) belong to the Pontederiaceae family. The first is a fixed-floating species and the second is a free-floating species that is known for its phytoremediation potential. The fungal endophytes associated with the leaves of E. azurea and E. crassipes, native to the Upper Paraná River floodplain, Brazil, were isolated. The sequencing of the ITS1-5.8S-ITS2 region of ribosomal DNA was performed and the nucleotide sequences obtained were compared with those available in the GenBank database for the molecular identification of the isolates. The construction of phylogenetic trees was performed using the MEGA5 software. The results showed that high colonization frequencies were obtained from the 610 foliar fragments sampled from each plant: 87.86% for E. azurea and 88.85% for E. crassipes. At the genus level, it was possible to identify 19 fungal endophytes belonging to the genera Alternaria, Bipolaris, Cercospora, Diaporthe, Gibberella, Pestalotiopsis, Plectosphaerella, Phoma, and Saccharicola. Two other endophytes were identified at the species level (Microsphaeropsis arundinis). Genera Bipolaris, Cercospora, Microsphaeropsis, and Phoma were found as endophytes in the two macrophytes and the other genera were host-specific, being isolated from only one macrophyte, proving that there is a small difference in the endophytic diversity of the two Eichhornia species analyzed.

  18. Ectomycorrhizal fungal communities associated with Populus simonii and Pinus tabuliformis in the hilly-gully region of the Loess Plateau, China.

    PubMed

    Long, Dongfeng; Liu, Jianjun; Han, Qisheng; Wang, Xiaobing; Huang, Jian

    2016-01-01

    The Loess Plateau region of northwestern China has unique geological and dry/semi-dry climate characteristics. However, knowledge about ectomycorrhizal fungal (EMF) communities in the Loess Plateau is limited. In this study, we investigated EMF communities in Populus simonii and Pinus tabuliformis patches within the forest-steppe zone, in pine forests within the forest zone, and the transitional zone between them. We revealed high species richness (115 operational taxonomic units [OTUs]) of indigenous EMF resources at the Loess Plateau, of which Tomentella (35 OTUs), Inocybe (16), Sebacina (16), and Geopora (7) were the most OTU-rich lineages. EMF richness within the forest-steppe zone and the transitional zone was limited, while the natural pine forest maintained diverse EMF communities in the forest zone. The changes of EMF community richness and composition along arid eco-zones were highlighted for the complex factors including precipitation, soil factors, host, DBH, and altitude. Indicator analysis revealed that some EMF showed clear host preference and some taxa, i.e., genera Geopora and Inocybe, were dominant in drought and alkaline-saline conditions attributed to their environmental preference. This study revealed that EMF communities were quite limited in the forest-steppe zone, while the forest region contained diverse EMF communities in the Loess Plateau. PMID:27063338

  19. Deep 16S rRNA Pyrosequencing Reveals a Bacterial Community Associated with Banana Fusarium Wilt Disease Suppression Induced by Bio-Organic Fertilizer Application

    PubMed Central

    Ruan, Yunze; Xue, Chao; Zhang, Jian; Li, Rong; Shen, Qirong

    2014-01-01

    Our previous work demonstrated that application of a bio-organic fertilizer (BIO) to a banana mono-culture orchard with serious Fusarium wilt disease effectively decreased the number of soil Fusarium sp. and controlled the soil-borne disease. Because bacteria are an abundant and diverse group of soil organisms that responds to soil health, deep 16 S rRNA pyrosequencing was employed to characterize the composition of the bacterial community to investigate how it responded to BIO or the application of other common composts and to explore the potential correlation between bacterial community, BIO application and Fusarium wilt disease suppression. After basal quality control, 137,646 sequences and 9,388 operational taxonomic units (OTUs) were obtained from the 15 soil samples. Proteobacteria, Acidobacteria, Bacteroidetes, Gemmatimonadetes and Actinobacteria were the most frequent phyla and comprised up to 75.3% of the total sequences. Compared to the other soil samples, BIO-treated soil revealed higher abundances of Gemmatimonadetes and Acidobacteria, while Bacteroidetes were found in lower abundance. Meanwhile, on genus level, higher abundances compared to other treatments were observed for Gemmatimonas and Gp4. Correlation and redundancy analysis showed that the abundance of Gemmatimonas and Sphingomonas and the soil total nitrogen and ammonium nitrogen content were higher after BIO application, and they were all positively correlated with disease suppression. Cumulatively, the reduced Fusarium wilt disease incidence that was seen after BIO was applied for 1-year might be attributed to the general suppression based on a shift within the bacteria soil community, including specific enrichment of Gemmatimonas and Sphingomonas. PMID:24871319

  20. Draft Genome Sequence of Two Sphingopyxis sp. Strains, Dominant Members of the Bacterial Community Associated with a Drinking Water Distribution System Simulator

    EPA Science Inventory

    We report the draft genome of two Sphingopyxis spp. strains isolated from a chloraminated drinking water distribution system simulator. Both strains are ubiquitous residents and early colonizers of water distribution systems. Genomic annotation identified a class 1 integron (in...

  1. Diversity and Temporal Dynamics of the Epiphytic Bacterial Communities Associated with the Canopy-Forming Seaweed Cystoseira compressa (Esper) Gerloff and Nizamuddin

    PubMed Central

    Mancuso, Francesco P.; D'Hondt, Sofie; Willems, Anne; Airoldi, Laura; De Clerck, Olivier

    2016-01-01

    Canopy-forming seaweed species of the genus Cystoseira form diverse and productive habitats along temperate rocky coasts of the Mediterranean Sea. Despite numerous studies on the rich macrofauna and flora associated with Cystoseira spp., there is little knowledge about the epiphytic bacteria. We analyzed bacterial populations associated with canopies of Cystoseira compressa, over an annual vegetative cycle (May-October), and their relationships with the bacterial populations in the surrounding seawater, at intertidal rocky shores in Vasto (Chieti—Italy). The bacterial diversity was assessed using Illumina Miseq sequences of V1-V3 hypervariable regions of 16S rRNA gene. C. compressa bacterial community was dominated by sequences of Proteobacteria and Bacteroidetes, Verrucomicrobia, Actinobacteria, and Cyanobacteria especially of the Rhodobacteriaceae, Flavobacteriaceae, Sapropiraceae, Verrucomicrobiaceae, and Phyllobacteriaceae families. Seawater libraries were also dominated by Proteobacteria and Bacteroidetes sequences, especially of the Candidatus Pelagibacter (SAR11) and Rhodobacteriaceae families, but were shown to be clearly distinct from C. compressa libraries with only few species in common between the two habitats. We observed a clear successional pattern in the epiphytic bacteria of C. compressa over time. These variations were characterized by gradual addition of OTUs (Verrucomicrobia, Actinobacteria and SR1) to the community over a growing season, indicative of a temporal gradient, rather than a radical reorganization of the bacterial community. Moreover, we also found an increase in abundance over time of Rhodobacteraceae, comprising six potential pathogenic genera, Ruegeria, Nautella, Aquimarina, Loktanella, Saprospira, and Phaeobacter which seemed to be associated to aged thalli of C. compressa. These bacteria could have the potential to affect the health and ecology of the algae, suggesting the hypothesis of a possible, but still unexplored, role of the microbial communities in contributing to the extensive ongoing declines of populations of Cystoseira spp. in the Mediterranean Sea. PMID:27092130

  2. Environmental forcing and the larval fish community associated to the Atlantic bluefin tuna spawning habitat of the Balearic region (Western Mediterranean), in early summer 2005

    NASA Astrophysics Data System (ADS)

    Rodriguez, J. M.; Alvarez, I.; Lopez-Jurado, J. L.; Garcia, A.; Balbin, R.; Alvarez-Berastegui, D.; Torres, A. P.; Alemany, F.

    2013-07-01

    The Balearic region is a highly dynamic area located in the Western Mediterranean, straddling the transition between the Algerian and Provencal basins and constitutes one of the main spawning grounds for the large, migratory Atlantic bluefin (Thunnus thynnus) and other medium and small tuna species (Thunnus alalunga, Auxis rochei, Euthynnus alleteratus and Katsuwonus pelamis). In summer, despite been considered an oligotrophic region as the whole Mediterranean Sea, it harbors a relatively abundant and diverse larval fish community (LFC). In this study, we analyze the composition, abundance and the influence of abiotic and biotic factors on the horizontal structure of the LFC in the Balearic region, in early summer 2005, during the spawning season of Atlantic bluefin tuna. Hydrographically, 2005 was an unusual year with a summer situation of relatively lack of mesoscale features, weak surface currents and a general situation of high stability. A total of 128 taxa of fish larvae, belonging to 52 families, were identified. The average abundance was 1770 larvae 1000 m-3. Multivariate statistical analysis revealed LFC to have a strong horizontal structure. Cluster analysis and non-metric multidimensional scaling ordination identified two larval fish assemblages. These assemblages were mainly delineated by depth and, therefore, by the spawning location of adult fish. Our results also suggest that anticyclonic eddy boundaries constitute favourable habitats for fish larvae. Also, the scenario of higher than unusual hydrographic stability found during the cruise would be responsible for the relatively lack of mesoscale features and, consequently, for the lack of influence of these features on the horizontal distribution of fish larvae and on the horizontal structure of the LFC.

  3. Distribution, diversity and bioprospecting of bioactive compounds from cryptic fungal communities associated with endemic and cold-adapted macroalgae in Antarctica

    Technology Transfer Automated Retrieval System (TEKTRAN)

    We surveyed the distribution and diversity of fungi associated with eight macroalgae from Antarctica and their capability to produce bioactive compounds. The collections yielded 148 fungal isolates identified using molecular methods into 21 genera and 43 species. The most frequent taxa were Geomyces...

  4. Trophic ecology of the rocky shore community associated with the Ascophyllum nodosum zone (Roscoff, France): A δ 13C vs δ 15N investigation

    NASA Astrophysics Data System (ADS)

    Riera, Pascal; Escaravage, Carole; Leroux, Cédric

    2009-01-01

    This study aimed to characterize the structure and functioning of the benthic food web associated with the Ascophyllum nodosum zone of the rocky shore of Roscoff by using δ 13C and δ 15N. Several characteristics of the trophic ecology of the invertebrates associated with this mid-littoral habitat and which belong to different functional groups (e.g., grazers, filter-feeders, predators and omnivores) were highlighted. In particular, the filter feeder species (including mostly sponges) used macroalgae-derived organic matter as a substantial food requirement. The results also pointed out an important stable isotopes variability for strict coexisting primary consumers which: (1) is directly related to the high δ 15N range of the food sources; (2) makes it impossible to establish a unique trophic level scale based on δ 15N values, as previously done in coastal environments; and (3) points out the existence of major co-occurring trophic pathways which characterise the Ascophyllum nodosum habitat.

  5. Draft Genome Sequence of Two Sphingopyxis sp. Strains, Dominant Members of the Bacterial Community Associated with a Drinking Water Distribution System Simulator

    PubMed Central

    Pfaller, Stacy; Revetta, Randy P.

    2016-01-01

    We report the draft genomes of two Sphingopyxis sp. strains isolated from a chloraminated drinking water distribution system simulator. Both strains are ubiquitous residents and early colonizers of water distribution systems. Genomic annotation identified a class 1 integron (intI1) gene associated with sulfonamide (sul1) and puromycin (pac) antibiotic resistance genes. PMID:27034493

  6. Characterisation of the Bacterial and Fungal Communities Associated with Different Lesion Sizes of Dark Spot Syndrome Occurring in the Coral Stephanocoenia intersepta

    PubMed Central

    Sweet, Michael; Burn, Deborah; Croquer, Aldo; Leary, Peter

    2013-01-01

    The number and prevalence of coral diseases/syndromes are increasing worldwide. Dark Spot Syndrome (DSS) afflicts numerous coral species and is widespread throughout the Caribbean, yet there are no known causal agents. In this study we aimed to characterise the microbial communities (bacteria and fungi) associated with DSS lesions affecting the coral Stephanocoenia intersepta using nonculture molecular techniques. Bacterial diversity of healthy tissues (H), those in advance of the lesion interface (apparently healthy AH), and three sizes of disease lesions (small, medium, and large) varied significantly (ANOSIM R  = 0.052 p<0.001), apart from the medium and large lesions, which were similar in their community profile. Four bacteria fitted into the pattern expected from potential pathogens; namely absent from H, increasing in abundance within AH, and dominant in the lesions themselves. These included ribotypes related to Corynebacterium (KC190237), Acinetobacter (KC190251), Parvularculaceae (KC19027), and Oscillatoria (KC190271). Furthermore, two Vibrio species, a genus including many proposed coral pathogens, dominated the disease lesion and were absent from H and AH tissues, making them candidates as potential pathogens for DSS. In contrast, other members of bacteria from the same genus, such as V. harveyii were present throughout all sample types, supporting previous studies where potential coral pathogens exist in healthy tissues. Fungal diversity varied significantly as well, however the main difference between diseased and healthy tissues was the dominance of one ribotype, closely related to the plant pathogen, Rhytisma acerinum, a known causal agent of tar spot on tree leaves. As the corals’ symbiotic algae have been shown to turn to a darker pigmented state in DSS (giving rise to the syndromes name), the two most likely pathogens are R. acerinum and the bacterium Oscillatoria, which has been identified as the causal agent of the colouration in Black Band Disease, another widespread coral disease. PMID:23630635

  7. Target-specific PCR primers can detect and differentiate ophiostomatoid fungi from microbial communities associated with the mountain pine beetle Dendroctonus ponderosae.

    PubMed

    Khadempour, Lily; Massoumi Alamouti, Sepideh; Hamelin, Richard; Bohlmann, Jörg; Breuil, Colette

    2010-10-01

    The aim of this study was to develop DNA probes that could identify the major fungal species associated with mountain pine beetles (MPB). The beetles are closely associated with fungal species that include ophiostomatoid fungi that can be difficult to differentiate morphologically. The most frequently isolated associates are the pine pathogens Grosmannia clavigera and Leptographium longiclavatum, the less pathogenic Ophiostoma montium, and an undescribed Ceratocystiopsis species (Cop. sp.). Because growing, isolating and extracting DNA from fungi vectored by MPB can be time and labour intensive, we designed three rDNA primer sets that specifically amplify short rDNA amplicons from O. montium, Cop. sp. and the pine Leptographium clade. We also designed two primer sets on a gene of unknown function that can differentiate G. clavigera and L. longiclavatum. We tested the primers on 76 fungal isolates that included MPB associates. The primers reliably identified their targets from DNA obtained from pure fungal cultures, pulverized beetles, beetle galleries, and tree phloem inoculated with G. clavigera. The primers will facilitate large-scale work on the ecology of the MPB-fungal-lodgepole pine ecosystem, as well as phytosanitary/quarantine sample screening.

  8. Levels of Alpha-Toxin Correlate with Distinct Phenotypic Response Profiles of Blood Mononuclear Cells and with agr Background of Community-Associated Staphylococcus aureus Isolates

    PubMed Central

    Mairpady Shambat, Srikanth; Haggar, Axana; Vandenesch, Francois; Lina, Gerard; van Wamel, Willem J. B.; Arakere, Gayathri; Svensson, Mattias; Norrby-Teglund, Anna

    2014-01-01

    Epidemiological studies of Staphylococcus aureus have shown a relation between certain clones and the presence of specific virulence genes, but how this translates into virulence-associated functional responses is not fully elucidated. Here we addressed this issue by analyses of community-acquired S. aureus strains characterized with respect to antibiotic resistance, ST types, agr types, and virulence gene profiles. Supernatants containing exotoxins were prepared from overnight bacterial cultures, and tested in proliferation assays using human peripheral blood mononuclear cells (PBMC). The strains displayed stable phenotypic response profiles, defined by either a proliferative or cytotoxic response. Although, virtually all strains elicited superantigen-mediated proliferative responses, the strains with a cytotoxic profile induced proliferation only in cultures with the most diluted supernatants. This indicated that the superantigen-response was masked by a cytotoxic effect which was also confirmed by flow cytometry analysis. The cytotoxic supernatants contained significantly higher levels of α-toxin than did the proliferative supernatants. Addition of α-toxin to supernatants characterized as proliferative switched the response into cytotoxic profiles. In contrast, no effect of Panton Valentine Leukocidin, δ-toxin or phenol soluble modulin α-3 was noted in the proliferative assay. Furthermore, a significant association between agr type and phenotypic profile was found, where agrII and agrIII strains had predominantly a proliferative profile whereas agrI and IV strains had a predominantly cytotoxic profile. The differential response profiles associated with specific S. aureus strains with varying toxin production could possibly have an impact on disease manifestations, and as such may reflect specific pathotypes. PMID:25166615

  9. Intra-field variability in microbial community associated with phase-separation-controlled hydrothermal fluid chemistry in the Mariner field, the southern Lau Basin

    NASA Astrophysics Data System (ADS)

    Takai, K.; Ishibashi, J.; Lupton, J.; Ueno, Y.; Nunoura, T.; Hirayama, H.; Horikoshi, K.; Suzuki, R.; Hamasaki, H.; Suzuki, Y.

    2006-12-01

    A newly discovered hydrothermal field called the Mariner field at the northernmost central Valu Fa Ridge (VFR) in the Lau Basin was explored and characterized by geochemical and microbiological surveys. The hydrothermal fluid (max. 365 u^C) emitting from the most vigorous vent site (Snow chimney) was boiling just beneath the seafloor at a water depth of 1908 m and two end-members of hydrothermal fluid were identified. Mineral and fluid chemistry of typical brine-rich (Snow chimney and Monk chimney) and vapor-rich (Crab Restaurant chimney) hydrothermal fluids and the host chimney structures were analyzed. Microbial community structures in three chimney structures were also investigated by culture-dependent and - independent analyses. The 16S rRNA gene clone analysis revealed that both bacterial and archaeal rRNA gene communities at the chimney surface zones were different among three chimneys. The bacterial and archaeal rRNA gene communities of the Snow chimney surface were very similar with those in the dead chimneys, suggesting concurrence of metal sulfide deposition at the inside and weathering at the surface potentially due to its large structure and size. Cultivation analysis demonstrated the significant variation in culturability of various microbial components, particularly of thermophilic H2- and/or S-oxidizing chemolithoautotrophs such as the genera Aquifex and Persephonella, among the chimney sites. The culturability of these chemolithoautotrophs might be associated with the input of gaseous energy and carbon sources like H2S, H2 and CH4 from the hydrothermal fluids, and might be affected by phase-separation- controlled fluid chemistry. In addition, inter-fields comparison of microbial community structures determined by cultivation analysis revealed novel characteristics of the microbial communities in the Mariner field of the Lau Basin among the global deep-sea hydrothermal systems.

  10. Diversity and Temporal Dynamics of the Epiphytic Bacterial Communities Associated with the Canopy-Forming Seaweed Cystoseira compressa (Esper) Gerloff and Nizamuddin.

    PubMed

    Mancuso, Francesco P; D'Hondt, Sofie; Willems, Anne; Airoldi, Laura; De Clerck, Olivier

    2016-01-01

    Canopy-forming seaweed species of the genus Cystoseira form diverse and productive habitats along temperate rocky coasts of the Mediterranean Sea. Despite numerous studies on the rich macrofauna and flora associated with Cystoseira spp., there is little knowledge about the epiphytic bacteria. We analyzed bacterial populations associated with canopies of Cystoseira compressa, over an annual vegetative cycle (May-October), and their relationships with the bacterial populations in the surrounding seawater, at intertidal rocky shores in Vasto (Chieti-Italy). The bacterial diversity was assessed using Illumina Miseq sequences of V1-V3 hypervariable regions of 16S rRNA gene. C. compressa bacterial community was dominated by sequences of Proteobacteria and Bacteroidetes, Verrucomicrobia, Actinobacteria, and Cyanobacteria especially of the Rhodobacteriaceae, Flavobacteriaceae, Sapropiraceae, Verrucomicrobiaceae, and Phyllobacteriaceae families. Seawater libraries were also dominated by Proteobacteria and Bacteroidetes sequences, especially of the Candidatus Pelagibacter (SAR11) and Rhodobacteriaceae families, but were shown to be clearly distinct from C. compressa libraries with only few species in common between the two habitats. We observed a clear successional pattern in the epiphytic bacteria of C. compressa over time. These variations were characterized by gradual addition of OTUs (Verrucomicrobia, Actinobacteria and SR1) to the community over a growing season, indicative of a temporal gradient, rather than a radical reorganization of the bacterial community. Moreover, we also found an increase in abundance over time of Rhodobacteraceae, comprising six potential pathogenic genera, Ruegeria, Nautella, Aquimarina, Loktanella, Saprospira, and Phaeobacter which seemed to be associated to aged thalli of C. compressa. These bacteria could have the potential to affect the health and ecology of the algae, suggesting the hypothesis of a possible, but still unexplored, role of the microbial communities in contributing to the extensive ongoing declines of populations of Cystoseira spp. in the Mediterranean Sea. PMID:27092130

  11. Characterization of bacterial communities associated with the pine sawyer beetle Monochamus galloprovincialis, the insect vector of the pinewood nematode Bursaphelenchus xylophilus.

    PubMed

    Vicente, Cláudia S L; Nascimento, Francisco X; Espada, Margarida; Barbosa, Pedro; Hasegawa, Koichi; Mota, Manuel; Oliveira, Solange

    2013-10-01

    Pine wilt disease (PWD) has a tremendous impact on worldwide forestlands, both from the environmental and economical viewpoints. Monochamus sp., a xylophagous insect from the Cerambycidae family, plays an important role in dissemination of the pinewood nematode, Bursaphelenchus xylophilus, the primary pathogenic agent of PWD. This study investigates, for the first time, the bacterial communities of Monochamus galloprovincialis collected from Portuguese Pinus pinaster trees and B. xylophilus free, using a metagenomics approach. Overall, our results show that natural bacterial communities of M. galloprovincialis are mainly composed by γ-proteobacteria, Firmicutes and Bacteroidetes, which may be a reflection of insects' feeding diet and habitat characteristics. We also report different bacterial communities' composition in the thorax and abdomen of M. galloprovincialis, with high abundance of Serratia sp. in both. Our results encourage further studies in the possible relationship between bacteria from the insect vector and B. xylophilus.

  12. Aspergillus parasiticus communities associated with sugarcane in the Rio Grande Valley of Texas: implications of global transport and host association within Aspergillus section Flavi.

    PubMed

    Garber, N P; Cotty, P J

    2014-05-01

    In the Rio Grande Valley of Texas (RGV), values of maize and cottonseed crops are significantly reduced by aflatoxin contamination. Aflatoxin contamination of susceptible crops is the product of communities of aflatoxin producers and the average aflatoxin-producing potentials of these communities influence aflatoxin contamination risk. Cropping pattern influences community composition and, thereby, the epidemiology of aflatoxin contamination. In 2004, Aspergillus parasiticus was isolated from two fields previously cropped to sugarcane but not from 23 fields without recent history of sugarcane cultivation. In 2004 and 2005, A. parasiticus composed 18 to 36% of Aspergillus section Flavi resident in agricultural soils within sugarcane-producing counties. A. parasiticus was not detected in counties that do not produce sugarcane. Aspergillus section Flavi soil communities within sugarcane-producing counties differed significantly dependent on sugarcane cropping history. Fields cropped to sugarcane within the previous 5 years had greater quantities of A. parasiticus (mean = 16 CFU/g) than fields not cropped to sugarcane (mean = 0.1 CFU/g). The percentage of Aspergillus section Flavi composed of A. parasiticus increased to 65% under continuous sugarcane cultivation and remained high the first season of rotation out of sugarcane. Section Flavi communities in fields rotated to non-sugarcane crops for 3 to 5 years were composed of <5% A. parasiticus, and fields with no sugarcane history averaged only 0.2% A. parasiticus. The section Flavi community infecting RGV sugarcane stems ranged from 95% A. parasiticus in billets prepared for commercial planting to 52% A. parasiticus in hand-collected sugarcane stems. Vegetative compatibility assays and multilocus phylogenies verified that aflatoxin contamination of raw sugar was previously attributed to similar A. parasiticus in Japan. Association of closely related A. parasiticus genotypes with sugarcane produced in Japan and RGV, frequent infection of billets by these genotypes, and the ephemeral nature of A. parasiticus in RGV soils suggests global transport with sugarcane planting material.

  13. The bacterial community associated with the marine polychaete Ophelina sp.1 (Annelida: Opheliidae) is altered by copper and zinc contamination in sediments.

    PubMed

    Neave, Matthew J; Streten-Joyce, Claire; Glasby, Chris J; McGuinness, Keith A; Parry, David L; Gibb, Karen S

    2012-04-01

    Tolerant species of polychaete worms can survive in polluted environments using various resistance mechanisms. One aspect of resistance not often studied in polychaetes is their association with symbiotic bacteria, some of which have resistance to metals and may help the organism to survive. We used "next generation" 454 sequencing of bacterial 16S rRNA sequences associated with polychaetes from a copper- and zinc-polluted harbor and from a reference site to determine bacterial community structure. We found changes in the bacteria at the polluted site, including increases in the abundance of bacteria from the order Alteromonadales. These changes in the bacteria associated with polychaetes may be relatively easy to detect and could be a useful indicator of metal pollution.

  14. Diversity of bacterial communities associated with the Indian Ocean sponge Tsitsikamma favus that contains the bioactive pyrroloiminoquinones, tsitsikammamine A and B.

    PubMed

    Walmsley, Tara A; Matcher, Gwynneth F; Zhang, Fan; Hill, Russell T; Davies-Coleman, Michael T; Dorrington, Rosemary A

    2012-12-01

    Tsitsikamma favus is a latrunculid sponge endemic to the coast of South Africa that produces unique pyrroloiminoquinones known as tsitsikammamines. Wakayin and makaluvamine A are structurally similar to the tsitsikammamines and are the only pyrroloiminoquinones isolated from a source other than Porifera (namely a Fijian ascidian Clavelina sp. and a laboratory culture of the myxomycete Didymium bahiense, respectively). The source of the tsitsikammamines is hypothesised to be microbial, which could provide a means of overcoming the current supply problem. This study focuses on characterising the microbial diversity associated with T. favus. We have used denaturing gradient gel electrophoresis together with clonal and deep sequencing of microbial 16S rRNA gene amplicons to show that specimens of this sponge species contain a distinct and conserved microbial population, which is stable over time and is dominated by a unique Betaproteobacterium species.

  15. Application of the Random Amplified Polymorphic DNA (RAPD) Fingerprinting to Analyze Genetic Variation in Community Associated-Methicillin Resistant Staphylococcus Aureus (CA-MRSA) Isolates in Iran

    PubMed Central

    Mobasherizadeh, Sina; Shojaei, Hasan; Havaei, Seyed Asghar; Mostafavizadeh, Kamyar; Davoodabadi, Fazollah; Khorvash, Farzin; Ataei, Behrooz; Daei-Naser, Abbas

    2016-01-01

    The aim of this study was to apply RAPD technique to analyze the genetic variability among the Iranian CA-MRSA isolates. The RAPD amplification was implemented on 25 strains isolated from the anterior nares of 410 healthy children using four randomly selected oligonucleotide primers from the stocks available in our laboratory, including the primers 1254, GE6, OLP6 and OLP13 from our stock. The amplified PCR products were detected on a 1.5% agarose gel and subjected to further analysis to establish the band profiles and genetic relationships using the Gel Compar® program. The Iranian CA-MRSA isolates produced distinct RAPD patterns which varied based on the primer used, however, the primer 1254 revealed highly polymorphic patterns consisting 5 discernable RAPD types (RT), “RT1” (12, 48%), “RT2” (8, 32%), “RT3” (3, 12%), and “RT4 and RT5”, (a single RAPD type each, 4%). Phylogenetic analysis based on RAPD profiles divided most of the CA-MRSA isolates into 2 distinct but related RAPD clusters, a small group and two single unrelated RAPD types. This study shows that the simple and cost-effective but rather difficult to optimize RAPD fingerprinting could be used to evaluate genetic and epidemiological relationships of CA-MRSA isolates on condition that the patterns are obtained from carefully optimized laboratory tests. PMID:27045409

  16. Illumina-based analysis of the rhizosphere microbial communities associated with healthy and wilted Lanzhou lily (Lilium davidii var. unicolor) plants grown in the field.

    PubMed

    Shang, Qianhan; Yang, Guo; Wang, Yun; Wu, Xiukun; Zhao, Xia; Hao, Haiting; Li, Yuyao; Xie, Zhongkui; Zhang, Yubao; Wang, Ruoyu

    2016-06-01

    Lanzhou lily (Liliumdavidii var. unicolor) is the best edible lily as well as a traditional medicinal plant in China. The microbes associated with plant roots play crucial roles in plant growth and health. However, little is known about the differences of rhizosphere microbes between healthy and wilted Lanzhou lily (Lilium davidii var. unicolor) plants. The objective of this study was to compare the rhizosphere microbial community and functional diversity of healthy and wilted plants, and to identify potential biocontrol agents with significant effect. Paired end Illumina Mi-Seq sequencing of 16S rRNA and ITS gene amplicons was employed to study the bacterial and fungal communities in the rhizosphere soil of Lanzhou lily plants. BIOLOG technology was adopted to investigate the microbial functional diversity. Our results indicated that there were major differences in the rhizosphere microbial composition and functional diversity of wilted samples compared with healthy samples. Healthy Lanzhou lily plants exhibited lower rhizosphere-associated bacterial diversity than diseased plants, whereas fungi exhibited the opposite trend. The dominant phyla in both the healthy and wilted samples were Proteobacteria and Ascomycota, i.e., 34.45 and 64.01 %, respectively. The microbial functional diversity was suppressed in wilted soil samples. Besides Fusarium, the higher relative abundances of Rhizoctonia, Verticillium, Penicillium, and Ilyonectria (Neonectria) in the wilted samples suggest they may pathogenetic root rot fungi. The high relative abundances of Bacillus in Firmicutes in healthy samples may have significant roles as biological control agents against soilborne pathogens. This is the first study to find evidence of major differences between the microbial communities in the rhizospheric soil of healthy and wilted Lanzhou lily, which may be linked to the health status of plants. PMID:27116961

  17. Diversity and Temporal Dynamics of the Epiphytic Bacterial Communities Associated with the Canopy-Forming Seaweed Cystoseira compressa (Esper) Gerloff and Nizamuddin.

    PubMed

    Mancuso, Francesco P; D'Hondt, Sofie; Willems, Anne; Airoldi, Laura; De Clerck, Olivier

    2016-01-01

    Canopy-forming seaweed species of the genus Cystoseira form diverse and productive habitats along temperate rocky coasts of the Mediterranean Sea. Despite numerous studies on the rich macrofauna and flora associated with Cystoseira spp., there is little knowledge about the epiphytic bacteria. We analyzed bacterial populations associated with canopies of Cystoseira compressa, over an annual vegetative cycle (May-October), and their relationships with the bacterial populations in the surrounding seawater, at intertidal rocky shores in Vasto (Chieti-Italy). The bacterial diversity was assessed using Illumina Miseq sequences of V1-V3 hypervariable regions of 16S rRNA gene. C. compressa bacterial community was dominated by sequences of Proteobacteria and Bacteroidetes, Verrucomicrobia, Actinobacteria, and Cyanobacteria especially of the Rhodobacteriaceae, Flavobacteriaceae, Sapropiraceae, Verrucomicrobiaceae, and Phyllobacteriaceae families. Seawater libraries were also dominated by Proteobacteria and Bacteroidetes sequences, especially of the Candidatus Pelagibacter (SAR11) and Rhodobacteriaceae families, but were shown to be clearly distinct from C. compressa libraries with only few species in common between the two habitats. We observed a clear successional pattern in the epiphytic bacteria of C. compressa over time. These variations were characterized by gradual addition of OTUs (Verrucomicrobia, Actinobacteria and SR1) to the community over a growing season, indicative of a temporal gradient, rather than a radical reorganization of the bacterial community. Moreover, we also found an increase in abundance over time of Rhodobacteraceae, comprising six potential pathogenic genera, Ruegeria, Nautella, Aquimarina, Loktanella, Saprospira, and Phaeobacter which seemed to be associated to aged thalli of C. compressa. These bacteria could have the potential to affect the health and ecology of the algae, suggesting the hypothesis of a possible, but still unexplored, role of the microbial communities in contributing to the extensive ongoing declines of populations of Cystoseira spp. in the Mediterranean Sea.

  18. Novel Bacterial Community Associated with 500-Year-Old Unpreserved Archaeological Wood from King Henry VIII's Tudor Warship the Mary Rose

    PubMed Central

    Watts, Joy E. M.; Jones, Mark

    2012-01-01

    A 500-year-old unpreserved Mary Rose sample, historically containing an iron bolt, was analyzed using enrichment cultures and 16S sequencing. The novel community of bacteria present demonstrates a biological pathway of Fe and S oxidation and a range of acid-generating metabolisms, with implications for preservation and biogeochemical cycling. PMID:23023757

  19. Ectomycorrhizal fungal communities associated with Populus simonii and Pinus tabuliformis in the hilly-gully region of the Loess Plateau, China.

    PubMed

    Long, Dongfeng; Liu, Jianjun; Han, Qisheng; Wang, Xiaobing; Huang, Jian

    2016-04-11

    The Loess Plateau region of northwestern China has unique geological and dry/semi-dry climate characteristics. However, knowledge about ectomycorrhizal fungal (EMF) communities in the Loess Plateau is limited. In this study, we investigated EMF communities in Populus simonii and Pinus tabuliformis patches within the forest-steppe zone, in pine forests within the forest zone, and the transitional zone between them. We revealed high species richness (115 operational taxonomic units [OTUs]) of indigenous EMF resources at the Loess Plateau, of which Tomentella (35 OTUs), Inocybe (16), Sebacina (16), and Geopora (7) were the most OTU-rich lineages. EMF richness within the forest-steppe zone and the transitional zone was limited, while the natural pine forest maintained diverse EMF communities in the forest zone. The changes of EMF community richness and composition along arid eco-zones were highlighted for the complex factors including precipitation, soil factors, host, DBH, and altitude. Indicator analysis revealed that some EMF showed clear host preference and some taxa, i.e., genera Geopora and Inocybe, were dominant in drought and alkaline-saline conditions attributed to their environmental preference. This study revealed that EMF communities were quite limited in the forest-steppe zone, while the forest region contained diverse EMF communities in the Loess Plateau.

  20. Ectomycorrhizal fungal communities associated with Populus simonii and Pinus tabuliformis in the hilly-gully region of the Loess Plateau, China

    PubMed Central

    Long, Dongfeng; Liu, Jianjun; Han, Qisheng; Wang, Xiaobing; Huang, Jian

    2016-01-01

    The Loess Plateau region of northwestern China has unique geological and dry/semi-dry climate characteristics. However, knowledge about ectomycorrhizal fungal (EMF) communities in the Loess Plateau is limited. In this study, we investigated EMF communities in Populus simonii and Pinus tabuliformis patches within the forest-steppe zone, in pine forests within the forest zone, and the transitional zone between them. We revealed high species richness (115 operational taxonomic units [OTUs]) of indigenous EMF resources at the Loess Plateau, of which Tomentella (35 OTUs), Inocybe (16), Sebacina (16), and Geopora (7) were the most OTU-rich lineages. EMF richness within the forest-steppe zone and the transitional zone was limited, while the natural pine forest maintained diverse EMF communities in the forest zone. The changes of EMF community richness and composition along arid eco-zones were highlighted for the complex factors including precipitation, soil factors, host, DBH, and altitude. Indicator analysis revealed that some EMF showed clear host preference and some taxa, i.e., genera Geopora and Inocybe, were dominant in drought and alkaline-saline conditions attributed to their environmental preference. This study revealed that EMF communities were quite limited in the forest-steppe zone, while the forest region contained diverse EMF communities in the Loess Plateau. PMID:27063338

  1. Free-living bacterial communities associated with tubeworm (Ridgeia piscesae) aggregations in contrasting diffuse flow hydrothermal vent habitats at the Main Endeavour Field, Juan de Fuca Ridge

    PubMed Central

    Forget, Nathalie L; Kim Juniper, S

    2013-01-01

    We systematically studied free-living bacterial diversity within aggregations of the vestimentiferan tubeworm Ridgeia piscesae sampled from two contrasting flow regimes (High Flow and Low Flow) in the Endeavour Hydrothermal Vents Marine Protected Area (MPA) on the Juan de Fuca Ridge (Northeast Pacific). Eight samples of particulate detritus were recovered from paired tubeworm grabs from four vent sites. Most sequences (454 tag and Sanger methods) were affiliated to the Epsilonproteobacteria, and the sulfur-oxidizing genus Sulfurovum was dominant in all samples. Gammaproteobacteria were also detected, mainly in Low Flow sequence libraries, and were affiliated with known methanotrophs and decomposers. The cooccurrence of sulfur reducers from the Deltaproteobacteria and the Epsilonproteobacteria suggests internal sulfur cycling within these habitats. Other phyla detected included Bacteroidetes, Actinobacteria, Chloroflexi, Firmicutes, Planctomycetes, Verrucomicrobia, and Deinococcus–Thermus. Statistically significant relationships between sequence library composition and habitat type suggest a predictable pattern for High Flow and Low Flow environments. Most sequences significantly more represented in High Flow libraries were related to sulfur and hydrogen oxidizers, while mainly heterotrophic groups were more represented in Low Flow libraries. Differences in temperature, available energy for metabolism, and stability between High Flow and Low Flow habitats potentially explain their distinct bacterial communities. PMID:23401293

  2. Influence of host species on ectomycorrhizal communities associated with two co-occurring oaks (Quercus spp.) in a tropical cloud forest.

    PubMed

    Morris, Melissa H; Pérez-Pérez, Miguel A; Smith, Matthew E; Bledsoe, Caroline S

    2009-08-01

    Interactions between host tree species and ectomycorrhizal fungi are important in structuring ectomycorrhizal communities, but there are only a few studies on host influence of congeneric trees. We investigated ectomycorrhizal community assemblages on roots of deciduous Quercus crassifolia and evergreen Quercus laurina in a tropical montane cloud forest, one of the most endangered tropical forest ecosystems. Ectomycorrhizal fungi were identified by sequencing internal transcribed spacer and partial 28S rRNA gene. We sampled 80 soil cores and documented high ectomycorrhizal diversity with a total of 154 taxa. Canonical correspondence analysis indicated that oak host was significant in explaining some of the variation in ectomycorrhizal communities, despite the fact that the two Quercus species belong to the same red oak lineage (section Lobatae). A Tuber species, found in 23% of the soil cores, was the most frequent taxon. Similar to oak-dominated ectomycorrhizal communities in temperate forests, Thelephoraceae, Russulaceae and Sebacinales were diverse and dominant.

  3. ABCC8 R1420H Loss-of-Function Variant in a Southwest American Indian Community: Association With Increased Birth Weight and Doubled Risk of Type 2 Diabetes.

    PubMed

    Baier, Leslie J; Muller, Yunhua Li; Remedi, Maria Sara; Traurig, Michael; Piaggi, Paolo; Wiessner, Gregory; Huang, Ke; Stacy, Alyssa; Kobes, Sayuko; Krakoff, Jonathan; Bennett, Peter H; Nelson, Robert G; Knowler, William C; Hanson, Robert L; Nichols, Colin G; Bogardus, Clifton

    2015-12-01

    Missense variants in KCNJ11 and ABCC8, which encode the KIR6.2 and SUR1 subunits of the β-cell KATP channel, have previously been implicated in type 2 diabetes, neonatal diabetes, and hyperinsulinemic hypoglycemia of infancy (HHI). To determine whether variation in these genes affects risk for type 2 diabetes or increased birth weight as a consequence of fetal hyperinsulinemia in Pima Indians, missense and common noncoding variants were analyzed in individuals living in the Gila River Indian Community. A R1420H variant in SUR1 (ABCC8) was identified in 3.3% of the population (N = 7,710). R1420H carriers had higher mean birth weights and a twofold increased risk for type 2 diabetes with a 7-year earlier onset age despite being leaner than noncarriers. One individual homozygous for R1420H was identified; retrospective review of his medical records was consistent with HHI and a diagnosis of diabetes at age 3.5 years. In vitro studies showed that the R1420H substitution decreases KATP channel activity. Identification of this loss-of-function variant in ABCC8 with a carrier frequency of 3.3% affects clinical care as homozygous inheritance and potential HHI will occur in 1/3,600 births in this American Indian population. PMID:26246406

  4. Guadalupian (Middle Permian) giant bivalve Alatoconchidae from a mid-Panthalassan paleo-atoll complex in Kyushu, Japan: A unique community associated with Tethyan fusulines and corals.

    PubMed

    Isozaki, Yukio

    2006-03-01

    Unique new fossil assemblages containing the large bivalve family Alatoconchidae are recorded from the Guadalupian (Middle Permian) shallow marine limestone in Kamura, Kyushu. The large bivalves occur in the Neoschwagerina Zone and Lepidolina Zone. This discovery establishes that the biostratigraphic range of the family Alatoconchidae extends up to the top of the Lepidolina Zone (upper Capitanian of upper Guadalupian) i.e., to the end-Guadalupian extinction level. The largest Alatoconchidae in Kamura occurs in the Neoschwagerina Zone, the size of which is up to 50 cm long and 5 cm thick. Although details are still unknown, their morphology with a wing-like side projection of their valves appears very similar to that of Alatoconchidae that includes the well-known genus Shikamaia Ozaki. The bivalve-bearing Iwato Formation was derived from a mid-oceanic shallow marine carbonate build-up formed on a mid-oceanic paleo-seamount. The close association among the Alatoconchidae, typical Tethyan fusulines (Verbeekinidae) and rugose corals (Waagenophyllidae), plus their common extinction pattern suggests that the Alatoconchidae flourished in warm, shallow (photic) marine environments in low latitude areas in Panthalassa as well as Tethys. The extra-large size and double-layered shell with a translucent outer layer composed of prismatic calcite suggests that these bivalves may have hosted abundant photosynthetic algal symbionts to support their large-body metabolism. PMID:25792767

  5. Culture-independent characterization of bacterial communities associated with the cold-water coral Lophelia pertusa in the northeastern Gulf of Mexico

    USGS Publications Warehouse

    Kellogg, C.A.; Lisle, J.T.; Galkiewicz, J.P.

    2009-01-01

    Bacteria are recognized as an important part of the total biology of shallow-water corals. Studies of shallow-water corals suggest that associated bacteria may benefit the corals by cycling carbon, fixing nitrogen, chelating iron, and producing antibiotics that protect the coral from other microbes. Cold-water or deep-sea corals have a fundamentally different ecology due to their adaptation to cold, dark, high-pressure environments and as such have novel microbiota. The goal of this study was to characterize the microbial associates of Lophelia pertusa in the northeastern Gulf of Mexico. This is the first study to collect the coral samples in individual insulated containers and to preserve coral samples at depth in an effort to minimize thermal shock and evaluate the effects of environmental gradients on the microbial diversity of samples. Molecular analysis of bacterial diversity showed a marked difference between the two study sites, Viosca Knoll 906/862 (VK906/862) and Viosca Knoll 826 (VK826). The bacterial communities from VK826 were dominated by a variety of unknown mycoplasmal members of the Tenericutes and Bacteroidetes, whereas the libraries from VK906/862 were dominated by members of the Proteobacteria. In addition to novel sequences, the 16S rRNA gene clone libraries revealed many bacterial sequences in common between Gulf of Mexico Lophelia corals and Norwegian fjord Lophelia corals, as well as shallow-water corals. Two Lophelia-specific bacterial groups were identified: a cluster of gammaproteobacteria related to sulfide-oxidizing gill symbionts of seep clams and a group of Mycoplasma spp. The presence of these groups in both Gulf and Norwegian Lophelia corals indicates that in spite of the geographic heterogeneity observed in Lophelia-associated bacterial communities, there are Lophelia-specific microbes. Copyright ?? 2009, American Society for Microbiology. All Rights Reserved.

  6. Arctic fungal communities associated with roots of Bistorta vivipara do not respond to the same fine-scale edaphic gradients as the aboveground vegetation.

    PubMed

    Mundra, Sunil; Halvorsen, Rune; Kauserud, Håvard; Müller, Eike; Vik, Unni; Eidesen, Pernille B

    2015-03-01

    Soil conditions and microclimate are important determinants of the fine-scale distribution of plant species in the Arctic, creating locally heterogeneous vegetation. We hypothesize that root-associated fungal (RAF) communities respond to the same fine-scale environmental gradients as the aboveground vegetation, creating a coherent pattern between aboveground vegetation and RAF. We explored how RAF communities of the ectomycorrhizal (ECM) plant Bistorta vivipara and aboveground vegetation structure of arctic plants were affected by biotic and abiotic variables at 0.3-3.0-m scales. RAF communities were determined using pyrosequencing. Composition and spatial structure of RAF and aboveground vegetation in relation to collected biotic and abiotic variables were analysed by ordination and semi-variance analyses. The vegetation was spatially structured along soil C and N gradients, whereas RAF lacked significant spatial structure. A weak relationship between RAF community composition and the cover of two ECM plants, B. vivipara and S. polaris, was found, and RAF richness increased with host root length and root weight. Results suggest that the fine-scale spatial structure of RAF communities of B. vivipara and the aboveground vegetation are driven by different factors. At fine spatial scales, neighbouring ECM plants may affect RAF community composition, whereas soil nutrients gradients structure the vegetation.

  7. Bacterial communities associated with Brassica napus L. grown on trace element-contaminated and non-contaminated fields: a genotypic and phenotypic comparison

    PubMed Central

    Croes, S; Weyens, N; Janssen, J; Vercampt, H; Colpaert, JV; Carleer, R; Vangronsveld, J

    2013-01-01

    Summary Cultivable bacterial strains associated with field-grown Brassica napus L. (soil, rhizosphere and roots) from a trace elements (Cd, Zn and Pb) contaminated field and a non-contaminated control field were characterized genotypically and phenotypically. Correspondence analysis of the genotypic data revealed a correlation between soil and rhizosphere communities isolated from the same field, indicating that local conditions play a more important role in influencing the composition of (rhizosphere) soil bacterial communities than root exudates. In contrast, endophytic communities of roots showed a correlation between fields, suggesting that plants on the two fields contain similar obligate endophytes derived from a common seed endophytic community and/or can select bacteria from the rhizosphere. The latter seemed not very likely since, despite the presence of several potential endophytic taxa in the rhizosphere, no significant correlation was found between root and rhizosphere communities. The majority of Cd/Zn tolerant strains capable of phosphorus solubilization, nitrogen fixation, indole-3-acetic acid production and showing 1-aminocyclopropane-1-carboxylate deaminase capacity were found in the rhizosphere and roots of plants growing on the contaminated field. PMID:23594409

  8. [Revelation and phylogenetic analysis of the predominant bacterial community associated with sponges in the South China Sea based on PCR- DGGE fingerprints].

    PubMed

    He, Li-Ming; Li, Zhi-Yong; Wu, Jie; Hu, Ye; Jiang, Qun

    2006-06-01

    The predominant bacterial community structure of Dysidea avara and Craniella australiensis in the South China Sea were revealed by PCR- DGGE fingerprinting in the present study. With further cloning, sequencing and phylogenetic analysis, it was found that Proteobacteria predominated in these two sponges. Alphaproteobacteria, Betaproteobacteria and Gammaproteobacteria were found in Dysidea avara and only Gammaproteobacteria found in Craniella australiensis. Although Bacteroidetes were found in both sponges, they differed in the species. These bacteria were found in sponges firstly. The bacteria in Craniella australiensis show more complex diversity than that in Dysidea avara. Because compared with Dysidea avara, Craniella australiensis include Actinobacteria, Firmicutes, etc. The bacterial community diversity in these two sponges indicates that the sponge-associated bacteria are host-specific even if the hosts are from the same marine location. DGGE fingerprint-based analysis should integrate with band cloning and sequencing, phylogenetic analysis, etc., molecular techniques to get precise results for the microbial community and diversity revelation. The research of studying sponge microbe by DGGE technique is initial work, that will accelerate the development of sponge microorganisms item.

  9. Prevalence of MRSA strains among Staphylococcus aureus isolated from outpatients, 2006.

    PubMed

    Coombs, Geoffrey W; Nimmo, Graeme R; Pearson, Julie C; Christiansen, Keryn J; Bell, Jan M; Collignon, Peter J; McLaws, Mary-Louise

    2009-03-01

    Biennial community-based Staphylococcus aureus antimicrobial surveillance programs have been performed by the Australian Group for Antimicrobial Resistance (AGAR) since 2000. Over this time the percentage of S. aureus identified as methicillin resistant has increased significantly from 10.3% in 2000 to 16% in 2006. This increase has occurred throughout Australia and has been due to the emergence of community-associated MRSA (CA-MRSA) clones. However, healthcare associated MRSA were still predominant in New South Wales/Australian Capital Territory and Victoria/Tasmania. In the 2006 survey CA-MRSA accounted for 8.8% of community-onset S. aureus infections. Although multiple CA-MRSA clones were characterised, the predominate clone identified was Queensland (Qld) MRSA (ST93-MRSA-IV) a Panton-Valentine leukocidin (PVL) positive MRSA that was first reported in Queensland and northern New South Wales in 2003 but has now spread throughout Australia. Several international PVL-positive CA-MRSA clones were also identified including USA300 MRSA (ST8-MRSA-IV). In addition, PVL was detected in an EMRSA-15 (ST22-MRSA-IV) isolate; a hospital associated MRSA clone that is known to be highly transmissible in the healthcare setting. With the introduction of the international clones and the transmission of Qld MRSA throughout the country, over 50% of CA-MRSA in Australia are now PVL positive. This change in the epidemiology of CA-MRSA in the Australian community will potentially result in an increase in skin and soft tissue infections in young Australians. As infections caused by these strains frequently results in hospitalisation their emergence is a major health concern.

  10. Staphylococcus aureus Colonization and Strain Type at Various Body Sites among Patients with a Closed Abscess and Uninfected Controls at U.S. Emergency Departments

    PubMed Central

    Albrecht, Valerie S.; Moran, Gregory J.; Krishnadasan, Anusha; Gorwitz, Rachel J.; McDougal, Linda K.; Talan, David A.

    2015-01-01

    Community-associated methicillin-resistant Staphylococcus aureus (CA-MRSA) is a prevalent cause of skin and soft tissue infections (SSTI), but the association between CA-MRSA colonization and infection remains uncertain. We studied the carriage frequency at several body sites and the diversity of S. aureus strains from patients with and without SSTI. Specimens from the nares, throat, rectum, and groin of case subjects with a closed skin abscess (i.e., without drainage) and matched control subjects without a skin infection (n = 147 each) presenting to 10 U.S. emergency departments were cultured using broth enrichment; wound specimens were cultured from abscess cases. Methicillin resistance testing and spa typing were performed for all S. aureus isolates. S. aureus was found in 85/147 (57.8%) of abscesses; 49 isolates were MRSA, and 36 were methicillin-susceptible S. aureus (MSSA). MRSA colonization was more common among cases (59/147; 40.1%) than among controls (27/147; 18.4%) overall (P < 0.001) and at each body site; no differences were observed for MSSA. S. aureus-infected subjects were usually (75/85) colonized with the infecting strain; among MRSA-infected subjects, this was most common in the groin. The CC8 lineage accounted for most of both infecting and colonizing isolates, although more than 16 distinct strains were identified. Nearly all MRSA infections were inferred to be USA300. There was more diversity among colonizing than infecting isolates and among those isolated from controls versus cases. CC8 S. aureus is a common colonizer of persons with and without skin infections. Detection of S. aureus colonization, and especially MRSA, may be enhanced by extranasal site culture. PMID:26292314

  11. Changing Epidemiology of Methicillin-Resistant Staphylococcus aureus in Iceland from 2000 to 2008: a Challenge to Current Guidelines ▿ †

    PubMed Central

    Holzknecht, Barbara Juliane; Hardardottir, Hjördis; Haraldsson, Gunnsteinn; Westh, Henrik; Valsdottir, Freyja; Boye, Kit; Karlsson, Sigfus; Kristinsson, Karl Gustaf; Gudlaugsson, Olafur

    2010-01-01

    The epidemiology of methicillin-resistant Staphylococcus aureus (MRSA) is continuously changing. Iceland has a low incidence of MRSA. A “search and destroy” policy (screening patients with defined risk factors and attempting eradication in carriers) has been implemented since 1991. Clinical and microbiological data of all MRSA patients from the years 2000 to 2008 were collected prospectively. Isolates were characterized by pulsed-field gel electrophoresis (PFGE), sequencing of the repeat region of the Staphylococcus protein A gene (spa typing), staphylococcal cassette chromosome mec (SCCmec) typing, and screening for the Panton-Valentine leukocidin (PVL) gene. Two hundred twenty-six infected (60%) or colonized (40%) individuals were detected (annual incidence 2.5 to 16/100,000). From 2000 to 2003, two health care-associated outbreaks dominated (spa types t037 and t2802), which were successfully controlled with extensive infection control measures. After 2004, an increasing number of community-associated (CA) cases without relation to the health care system occurred. A great variety of clones (40 PFGE types and 49 spa types) were found, reflecting an influx of MRSA from abroad. The USA300 and Southwest Pacific (SWP) clones were common. SCCmec type IV was most common (72%), and 38% of the isolates were PVL positive. The incidence of MRSA in Iceland has increased since 1999 but remains low and has been stable in the last years. The search and destroy policy was effective to control MRSA in the health care setting. However, MRSA in Iceland is now shifting into the community, challenging the current Icelandic guidelines, which are tailored to the health care system. PMID:20844224

  12. Staphylococcus aureus Panton-Valentine Leukocidin Is a Very Potent Cytotoxic Factor for Human Neutrophils

    PubMed Central

    Löffler, Bettina; Hussain, Muzaffar; Grundmeier, Matthias; Brück, Michaela; Holzinger, Dirk; Varga, Georg; Roth, Johannes; Kahl, Barbara C.; Proctor, Richard A.; Peters, Georg

    2010-01-01

    The role of the pore-forming Staphylococcus aureus toxin Panton-Valentine leukocidin (PVL) in severe necrotizing diseases is debated due to conflicting data from epidemiological studies of community-associated methicillin-resistant S. aureus (CA-MRSA) infections and various murine disease-models. In this study, we used neutrophils isolated from different species to evaluate the cytotoxic effect of PVL in comparison to other staphylococcal cytolytic components. Furthermore, to study the impact of PVL we expressed it heterologously in a non-virulent staphylococcal species and examined pvl-positive and pvl-negative clinical isolates as well as the strain USA300 and its pvl-negative mutant. We demonstrate that PVL induces rapid activation and cell death in human and rabbit neutrophils, but not in murine or simian cells. By contrast, the phenol-soluble modulins (PSMs), a newly identified group of cytolytic staphylococcal components, lack species-specificity. In general, after phagocytosis of bacteria different pvl-positive and pvl-negative staphylococcal strains, expressing a variety of other virulence factors (such as surface proteins), induced cell death in neutrophils, which is most likely associated with the physiological clearing function of these cells. However, the release of PVL by staphylococcal strains caused rapid and premature cell death, which is different from the physiological (and programmed) cell death of neutrophils following phagocytosis and degradation of virulent bacteria. Taken together, our results question the value of infection-models in mice and non-human primates to elucidate the impact of PVL. Our data clearly demonstrate that PVL acts differentially on neutrophils of various species and suggests that PVL has an important cytotoxic role in human neutrophils, which has major implications for the pathogenesis of CA-MRSA infections. PMID:20072612

  13. Rapid and high-resolution distinction of community-acquired and nosocomial Staphylococcus aureus isolates with identical pulsed-field gel electrophoresis patterns and spa types.

    PubMed

    Glasner, Corinna; Sabat, Artur J; Dreisbach, Annette; Larsen, Anders R; Friedrich, Alexander W; Skov, Robert L; van Dijl, Jan Maarten

    2013-03-01

    Methicillin-resistant Staphylococcus aureus (MRSA) represent a serious threat for public health worldwide. Of particular concern is the emergence of community-acquired MRSA, which is often difficult to distinguish from nosocomial MRSA due to a lack of suitable typing methods for early detection. For example, the USA300 pulsed-field gel electrophoresis (PFGE) pattern includes both the 'classical' community-acquired USA300 clone with spa type t008 and an epidemiologically unrelated nosocomial clone with spa type t024. Likewise, spa typing cannot distinguish the classic USA300 from nosocomial MRSA with the spa type t008. Since the fast and high-resolution distinction of these S. aureus types is important for infection prevention and surveillance, we investigated whether multiple-locus variable number tandem repeat fingerprinting (MLVF) can be applied to overcome these limitations. Indeed, MLVF correctly grouped 91 MRSA isolates belonging to the classic USA300 lineage, nosocomial MRSA isolates with the USA300 PFGE profile and spa type t024, and nosocomial MRSA isolates with spa type t008 into 3 distinct clusters. Importantly, several sub-clusters were also identified, reflecting epidemiological relationships between the respective isolates. We conclude that MLVF has the discriminatory power needed to rapidly distinguish very similar community-acquired and nosocomial MRSA isolates and that MLVF-based sub-clustering of isolates is highly useful for epidemiological investigations, outbreak prevention, and control.