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Heilmann C, Ziebuhr W, Becker K. Are coagulase-negative staphylococci virulent? Clin Microbiol Infect 2018; 25:1071-1080. [PMID: 30502487 DOI: 10.1016/j.cmi.2018.11.012] [Citation(s) in RCA: 161] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 11/06/2018] [Accepted: 11/11/2018] [Indexed: 02/06/2023]
Abstract
BACKGROUND Progress in contemporary medicine is associated with an increasing number of immunocompromised individuals. In this vulnerable group, the underlying disease together with long-term hospitalization and the use of medical devices facilitate infections by opportunistic pathogens, of which coagulase-negative staphylococci (CoNS) represent a prime example. OBJECTIVES The diversity of CoNS with species- and strain-specific differences concerning virulence and clinical impact is highlighted. A focus is on the ability of CoNS to generate biofilms on biotic and abiotic surfaces, which enables skin and mucosa colonization as well as establishment of CoNS on indwelling foreign bodies. SOURCES Literature about the virulence of CoNS listed in PubMed was reviewed. CONTENT Most catheter-related and prosthetic joint infections as well as most other device-related infections are caused by CoNS, specifically by Staphylococcus epidermidis and Staphylococcus haemolyticus. A common theme of CoNS infections is a high antibiotic resistance rate, which often limits treatment options and contributes to the significant health and economic burden imposed by CoNS. IMPLICATIONS Breaching the skin barrier along with the insertion of medical devices offers CoNS opportunities to gain access to host tissues and to sustain there by forming biofilms on foreign body surfaces. Biofilms represent the perfect niche to protect CoNS from both the host immune response and the action of antibiotics. Their particular lifestyle, combined with conditions that facilitate host colonization and infection, has led to the growing impact of CoNS as pathogens. Moreover, CoNS may serve as hidden reservoirs for antibiotic resistance and virulence traits.
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Affiliation(s)
- C Heilmann
- Institute of Medical Microbiology, University Hospital Münster, Münster, Germany
| | - W Ziebuhr
- Institute for Molecular Infection Biology, University of Würzburg, Würzburg, Germany
| | - K Becker
- Institute of Medical Microbiology, University Hospital Münster, Münster, Germany.
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102
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Emiola A, Oh J. High throughput in situ metagenomic measurement of bacterial replication at ultra-low sequencing coverage. Nat Commun 2018; 9:4956. [PMID: 30470746 PMCID: PMC6251912 DOI: 10.1038/s41467-018-07240-8] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Accepted: 10/22/2018] [Indexed: 01/04/2023] Open
Abstract
We developed Growth Rate InDex (GRiD) for estimating in situ growth rates of ultra-low coverage (>0.2×) and de novo-assembled metagenomes. Applying GRiD to human and environmental metagenomic datasets to demonstrate its versatility, we uncovered new associations with previously uncharacterized bacteria whose growth rates were associated with several disease characteristics or environmental interactions. In addition, with GRiD-MG (metagenomic), a high-throughput implementation of GRiD, we estimated growth dynamics of 1756 bacteria species from a healthy skin metagenomic dataset and identified a new Staphylococcus-Corynebacterium antagonism likely mediated by antimicrobial production in the skin. GRiD-MG significantly increases the ability to extract growth rate inferences from complex metagenomic data with minimal input from the user.
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Affiliation(s)
- Akintunde Emiola
- The Jackson Laboratory for Genomic Medicine, Farmington, 06032, CT, USA
| | - Julia Oh
- The Jackson Laboratory for Genomic Medicine, Farmington, 06032, CT, USA.
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103
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Chaudhari NM, Gautam A, Gupta VK, Kaur G, Dutta C, Paul S. PanGFR-HM: A Dynamic Web Resource for Pan-Genomic and Functional Profiling of Human Microbiome With Comparative Features. Front Microbiol 2018; 9:2322. [PMID: 30349509 PMCID: PMC6187978 DOI: 10.3389/fmicb.2018.02322] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Accepted: 09/11/2018] [Indexed: 01/07/2023] Open
Abstract
The conglomerate of microorganisms inhabiting various body-sites of human, known as the human microbiome, is one of the key determinants of human health and disease. Comprehensive pan-genomic and functional analysis approach for human microbiome components can enrich our understanding about impact of microbiome on human health. By utilizing this approach we developed PanGFR-HM (http://www.bioinfo.iicb.res.in/pangfr-hm/) – a novel dynamic web-resource that integrates genomic and functional characteristics of 1293 complete microbial genomes available from Human Microbiome Project. The resource allows users to explore genomic/functional diversity and genome-based phylogenetic relationships between human associated microbial genomes, not provided by any other resource. The key features implemented here include pan-genome and functional analysis of organisms based on taxonomy or body-site, and comparative analysis between groups of organisms. The first feature can also identify probable gene-loss events and significantly over/under represented KEGG/COG categories within pan-genome. The unique second feature can perform comparative genomic, functional and pathways analysis between 4 groups of microbes. The dynamic nature of this resource enables users to define parameters for orthologous clustering and to select any set of organisms for analysis. As an application for comparative feature of PanGFR-HM, we performed a comparative analysis with 67 Lactobacillus genomes isolated from human gut, oral cavity and urogenital tract, and therefore characterized the body-site specific genes, enzymes and pathways. Altogether, PanGFR-HM, being unique in its content and functionality, is expected to provide a platform for microbiome-based comparative functional and evolutionary genomics.
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Affiliation(s)
- Narendrakumar M Chaudhari
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Anupam Gautam
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India.,Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, Kolkata, India
| | - Vinod Kumar Gupta
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Gagneet Kaur
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India.,Department of Pharmacoinformatics, National Institute of Pharmaceutical Education and Research, Kolkata, India
| | - Chitra Dutta
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
| | - Sandip Paul
- Structural Biology and Bioinformatics Division, CSIR-Indian Institute of Chemical Biology, Kolkata, India
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104
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Lee JYH, Monk IR, Gonçalves da Silva A, Seemann T, Chua KYL, Kearns A, Hill R, Woodford N, Bartels MD, Strommenger B, Laurent F, Dodémont M, Deplano A, Patel R, Larsen AR, Korman TM, Stinear TP, Howden BP. Global spread of three multidrug-resistant lineages of Staphylococcus epidermidis. Nat Microbiol 2018; 3:1175-1185. [PMID: 30177740 PMCID: PMC6660648 DOI: 10.1038/s41564-018-0230-7] [Citation(s) in RCA: 179] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 07/27/2018] [Indexed: 01/19/2023]
Abstract
Staphylococcus epidermidis is a conspicuous member of the human microbiome, widely present on healthy skin. Here we show that S. epidermidis has also evolved to become a formidable nosocomial pathogen. Using genomics, we reveal that three multidrug-resistant, hospital-adapted lineages of S. epidermidis (two ST2 and one ST23) have emerged in recent decades and spread globally. These lineages are resistant to rifampicin through acquisition of specific rpoB mutations that have become fixed in the populations. Analysis of isolates from 96 institutions in 24 countries identified dual D471E and I527M RpoB substitutions to be the most common cause of rifampicin resistance in S. epidermidis, accounting for 86.6% of mutations. Furthermore, we reveal that the D471E and I527M combination occurs almost exclusively in isolates from the ST2 and ST23 lineages. By breaching lineage-specific DNA methylation restriction modification barriers and then performing site-specific mutagenesis, we show that these rpoB mutations not only confer rifampicin resistance, but also reduce susceptibility to the last-line glycopeptide antibiotics, vancomycin and teicoplanin. Our study has uncovered the previously unrecognized international spread of a near pan-drug-resistant opportunistic pathogen, identifiable by a rifampicin-resistant phenotype. It is possible that hospital practices, such as antibiotic monotherapy utilizing rifampicin-impregnated medical devices, have driven the evolution of this organism, once trivialized as a contaminant, towards potentially incurable infections.
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Affiliation(s)
- Jean Y H Lee
- Department of Microbiology and Immunology, The University of Melbourne at The Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Ian R Monk
- Department of Microbiology and Immunology, The University of Melbourne at The Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Anders Gonçalves da Silva
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Doherty Institute for Infection and Immunity, Melbourne, Australia
- Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, The University of Melbourne at The Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Torsten Seemann
- Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, The University of Melbourne at The Doherty Institute for Infection and Immunity, Melbourne, Australia
- Melbourne Bioinformatics, The University of Melbourne, Melbourne, Australia
| | - Kyra Y L Chua
- Department of Microbiology, Austin Health, Melbourne, Australia
| | - Angela Kearns
- AMRHAI Reference Unit, National Infection Service, Public Health England, London, UK
| | - Robert Hill
- AMRHAI Reference Unit, National Infection Service, Public Health England, London, UK
| | - Neil Woodford
- AMRHAI Reference Unit, National Infection Service, Public Health England, London, UK
| | - Mette D Bartels
- Department of Clinical Microbiology, Hvidovre University Hospital, Hvidovre, Denmark
| | - Birgit Strommenger
- National Reference Centre for Staphylococci and Enterococci, Division Nosocomial Pathogens and Antibiotic Resistances, Department of Infectious Diseases, Robert Koch Institute, Wernigerode Branch, Wernigerode, Germany
| | - Frederic Laurent
- Department of Bacteriology, Institute for Infectious Agents, French National Reference Centre for Staphylococci, International Centre for Infectiology Research, Institute for Pharmaceutical and Biological Sciences Of Lyon, University of Lyon, Lyon, France
| | - Magali Dodémont
- National Reference Centre for Staphylococci, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Ariane Deplano
- National Reference Centre for Staphylococci, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, and Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, USA
| | - Anders R Larsen
- Reference Laboratory for Antimicrobial Resistance and Staphylococci, Statens Serum Institut, Copenhagen, Denmark
| | - Tony M Korman
- Monash Infectious Diseases, Centre for Inflammatory Diseases, Monash University, Melbourne, Australia
| | - Timothy P Stinear
- Department of Microbiology and Immunology, The University of Melbourne at The Doherty Institute for Infection and Immunity, Melbourne, Australia
- Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, The University of Melbourne at The Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Benjamin P Howden
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, The University of Melbourne at The Doherty Institute for Infection and Immunity, Melbourne, Australia.
- Doherty Applied Microbial Genomics, Department of Microbiology and Immunology, The University of Melbourne at The Doherty Institute for Infection and Immunity, Melbourne, Australia.
- Infectious Diseases Department, Austin Health, Melbourne, Australia.
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105
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Månsson E, Söderquist B, Nilsdotter-Augustinsson Å, Särndahl E, Demirel I. Staphylococcus epidermidis from prosthetic joint infections induces lower IL-1β release from human neutrophils than isolates from normal flora. APMIS 2018; 126:678-684. [PMID: 30168623 DOI: 10.1111/apm.12861] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2017] [Accepted: 05/22/2018] [Indexed: 11/27/2022]
Abstract
The aim of this study was to test the hypothesis that Staphylococcus epidermidis isolated from prosthetic joint infections (PJIs) differs from S. epidermidis isolated from normal flora in terms of its capacity to induce activation of caspase-1 and release of IL-1β in human neutrophils. The amount of active caspase-1 was determined over 6 h by detecting Ac-YVAD-AMC fluorescence in human neutrophils incubated with S. epidermidis isolates from PJIs (ST2) or normal flora. The amount of IL-1β was detected by ELISA in neutrophil supernatants after 6 h of incubation. Mean IL-1β release was lower after incubation with S. epidermidis from PJIs compared to isolates from normal flora, but no statistically significant difference was found in active caspase-1. Substantial inter-individual differences in both active caspase-1 and IL-1β were noted. These results suggest that evasion of innate immune response, measured as reduced capacity to induce release of IL-1β from human neutrophils, might be involved in the predominance of ST2 in S. epidermidis PJIs, but that other microbe-related factors are probably also important.
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Affiliation(s)
- Emeli Månsson
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden.,iRiSC - Inflammatory Response and Infection Susceptibility Centre, Faculty of Medicine and Health, Örebro University, Örebro, Sweden.,Region Västmanland - Uppsala University, Centre for Clinical Research, Hospital of Västmanland, Västerås, Sweden
| | - Bo Söderquist
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden.,iRiSC - Inflammatory Response and Infection Susceptibility Centre, Faculty of Medicine and Health, Örebro University, Örebro, Sweden.,Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Åsa Nilsdotter-Augustinsson
- Department of Infectious Diseases, Department of Clinical and Experimental Medicine, Linköping University, Norrköping, Sweden
| | - Eva Särndahl
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden.,iRiSC - Inflammatory Response and Infection Susceptibility Centre, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | - Isak Demirel
- School of Medical Sciences, Faculty of Medicine and Health, Örebro University, Örebro, Sweden.,iRiSC - Inflammatory Response and Infection Susceptibility Centre, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
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106
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Argemi X, Matelska D, Ginalski K, Riegel P, Hansmann Y, Bloom J, Pestel-Caron M, Dahyot S, Lebeurre J, Prévost G. Comparative genomic analysis of Staphylococcus lugdunensis shows a closed pan-genome and multiple barriers to horizontal gene transfer. BMC Genomics 2018; 19:621. [PMID: 30126366 PMCID: PMC6102843 DOI: 10.1186/s12864-018-4978-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 07/31/2018] [Indexed: 02/07/2023] Open
Abstract
Background Coagulase negative staphylococci (CoNS) are commensal bacteria on human skin. Staphylococcus lugdunensis is a unique CoNS which produces various virulence factors and may, like S. aureus, cause severe infections, particularly in hospital settings. Unlike other staphylococci, it remains highly susceptible to antimicrobials, and genome-based phylogenetic studies have evidenced a highly conserved genome that distinguishes it from all other staphylococci. Results We demonstrate that S. lugdunensis possesses a closed pan-genome with a very limited number of new genes, in contrast to other staphylococci that have an open pan-genome. Whole-genome nucleotide and amino acid identity levels are also higher than in other staphylococci. We identified numerous genetic barriers to horizontal gene transfer that might explain this result. The S. lugdunensis genome has multiple operons encoding for restriction-modification, CRISPR/Cas and toxin/antitoxin systems. We also identified a new PIN-like domain-associated protein that might belong to a larger operon, comprising a metalloprotease, that could function as a new toxin/antitoxin or detoxification system. Conclusion We show that S. lugdunensis has a unique genome profile within staphylococci, with a closed pan-genome and several systems to prevent horizontal gene transfer. Its virulence in clinical settings does not rely on its ability to acquire and exchange antibiotic resistance genes or other virulence factors as shown for other staphylococci. Electronic supplementary material The online version of this article (10.1186/s12864-018-4978-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xavier Argemi
- Service des Maladies Infectieuses et Tropicales, Hôpitaux Universitaires, Nouvel Hôpital Civil, 1 Place de l'Hôpital, 67000, Strasbourg, France. .,Université de Strasbourg, CHRU Strasbourg, Fédération de Médecine Translationnelle de Strasbourg, EA 7290, Virulence Bactérienne Précoce, F-67000, Strasbourg, France.
| | - Dorota Matelska
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, 02-089, Warsaw, Poland
| | - Krzysztof Ginalski
- Laboratory of Bioinformatics and Systems Biology, Centre of New Technologies, University of Warsaw, Zwirki i Wigury 93, 02-089, Warsaw, Poland
| | - Philippe Riegel
- Université de Strasbourg, CHRU Strasbourg, Fédération de Médecine Translationnelle de Strasbourg, EA 7290, Virulence Bactérienne Précoce, F-67000, Strasbourg, France
| | - Yves Hansmann
- Service des Maladies Infectieuses et Tropicales, Hôpitaux Universitaires, Nouvel Hôpital Civil, 1 Place de l'Hôpital, 67000, Strasbourg, France.,Université de Strasbourg, CHRU Strasbourg, Fédération de Médecine Translationnelle de Strasbourg, EA 7290, Virulence Bactérienne Précoce, F-67000, Strasbourg, France
| | - Jochen Bloom
- Bioinformatics & Systems Biology, Justus-Liebig-University Gießen, 35392, Gießen, Germany
| | - Martine Pestel-Caron
- Normandie Univ, UNIROUEN, GRAM EA2656, Rouen University Hospital, F-76000, Rouen, France
| | - Sandrine Dahyot
- Normandie Univ, UNIROUEN, GRAM EA2656, Rouen University Hospital, F-76000, Rouen, France
| | - Jérémie Lebeurre
- Normandie Univ, UNIROUEN, GRAM EA2656, Rouen University Hospital, F-76000, Rouen, France
| | - Gilles Prévost
- Université de Strasbourg, CHRU Strasbourg, Fédération de Médecine Translationnelle de Strasbourg, EA 7290, Virulence Bactérienne Précoce, F-67000, Strasbourg, France
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107
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Yang T, Zhong J, Zhang J, Li C, Yu X, Xiao J, Jia X, Ding N, Ma G, Wang G, Yue L, Liang Q, Sheng Y, Sun Y, Huang H, Chen F. Pan-Genomic Study of Mycobacterium tuberculosis Reflecting the Primary/Secondary Genes, Generality/Individuality, and the Interconversion Through Copy Number Variations. Front Microbiol 2018; 9:1886. [PMID: 30177918 PMCID: PMC6109687 DOI: 10.3389/fmicb.2018.01886] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 07/27/2018] [Indexed: 11/13/2022] Open
Abstract
Tuberculosis (TB) has surpassed HIV as the leading infectious disease killer worldwide since 2014. The main pathogen, Mycobacterium tuberculosis (Mtb), contains ~4,000 genes that account for ~90% of the genome. However, it is still unclear which of these genes are primary/secondary, which are responsible for generality/individuality, and which interconvert during evolution. Here we utilized a pan-genomic analysis of 36 Mtb genomes to address these questions. We identified 3,679 Mtb core (i.e., primary) genes, determining their phenotypic generality (e.g., virulence, slow growth, dormancy). We also observed 1,122 dispensable and 964 strain-specific secondary genes, reflecting partially shared and lineage-/strain-specific individualities. Among which, five L2 lineage-specific genes might be related to the increased virulence of the L2 lineage. Notably, we discovered 28 Mtb “Super Core Genes” (SCGs: more than a copy in at least 90% strains), which might be of increased importance, and reflected the “super phenotype generality.” Most SCGs encode PE/PPE, virulence factors, antigens, and transposases, and have been verified as playing crucial roles in Mtb pathogenicity. Further investigation of the 28 SCGs demonstrated the interconversion among SCGs, single-copy core, dispensable, and strain-specific genes through copy number variations (CNVs) during evolution; different mutations on different copies highlight the delicate adaptive-evolution regulation amongst Mtb lineages. This reflects that the importance of genes varied through CNVs, which might be driven by selective pressure from environment/host-adaptation. In addition, compared with Mycobacterium bovis (Mbo), Mtb possesses 48 specific single core genes that partially reflect the differences between Mtb and Mbo individuality.
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Affiliation(s)
- Tingting Yang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jun Zhong
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Ju Zhang
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Cuidan Li
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Xia Yu
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, China
| | - Jingfa Xiao
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,BIG Data Center, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Xinmiao Jia
- Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Nan Ding
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Guannan Ma
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Guirong Wang
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, China
| | - Liya Yue
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Qian Liang
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, China
| | - Yongjie Sheng
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, Jilin University, Changchun, China
| | - Yanhong Sun
- Key Laboratory for Molecular Enzymology and Engineering of Ministry of Education, Jilin University, Changchun, China
| | - Hairong Huang
- National Clinical Laboratory on Tuberculosis, Beijing Key Laboratory on Drug-Resistant Tuberculosis Research, Beijing Chest Hospital, Capital Medical University, Beijing Tuberculosis and Thoracic Tumor Institute, Beijing, China
| | - Fei Chen
- CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.,University of Chinese Academy of Sciences, Beijing, China.,Collaborative Innovation Center for Genetics and Development, Beijing, China
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108
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Ardon CB, Prens EP, Fuursted K, Ejaz RN, Shailes J, Jenssen H, Jemec GBE. Biofilm production and antibiotic susceptibility of Staphylococcus epidermidis strains from Hidradenitis Suppurativa lesions. J Eur Acad Dermatol Venereol 2018; 33:170-177. [PMID: 30022542 DOI: 10.1111/jdv.15183] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2018] [Accepted: 07/10/2018] [Indexed: 12/22/2022]
Abstract
BACKGROUND An aberrant interaction between commensal skin bacteria and the host skin immune system is considered important in the pathogenesis of hidradenitis suppurativa (HS). OBJECTIVE In this study, we investigated the antibiotic susceptibility and biofilm-forming capabilities of S. epidermidis strains isolated from HS patients. METHODS Skin biopsies were taken from active HS lesions such as inflammatory nodules and/or sinuses and non-involved skin from 26 patients and cultured under optimal microbiological conditions for 24 h. Planktonic growth, biofilm production, antibiotic susceptibility and biofilm eradication by clindamycin, doxycycline, rifampicin and tetracycline were tested including a laboratory control strain of S. epidermidis for reference. RESULTS Staphylococcus epidermidis was cultured in 16 of 26 HS patients (62%). In total 27 different S. epidermidis isolates were identified; 16 (59%) from non-involved skin and 11 (41%) from HS lesions. All bacterial strains showed planktonic growth. Twenty-four of 27 (89%) isolates were strong biofilm producers in vitro. The biofilm-forming capability varied amongst the strains from non-involved skin and lesional skin. Twenty-four strains had an intermediate to resistant antibiotic susceptibility to clindamycin (89%). Rifampicin was the most effective antibiotic at inhibiting planktonic growth and at eradication of biofilm (P < 0.05). CONCLUSION We observed a slight increase in S. epidermidis virulence, characterized by resistance to commonly used antibiotics, increased biofilm production and resistance to biofilm eradication. In particular, the reduced sensitivity to tetracycline and clindamycin, two standard antibiotics in the treatment of HS, is alarming. Rifampicin, also important in HS treatment, showed the greatest efficacy at eradicating the biofilm at low MIC concentrations.
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Affiliation(s)
- C B Ardon
- Department of Dermatology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands.,Department of Science and Environment, Roskilde University, Roskilde, Denmark
| | - E P Prens
- Department of Dermatology, Erasmus MC, University Medical Center Rotterdam, Rotterdam, The Netherlands
| | - K Fuursted
- Department of Microbiology and Infection Control, Staten Serum Institute, Copenhagen, Denmark
| | - R N Ejaz
- Department of Science and Environment, Roskilde University, Roskilde, Denmark
| | - J Shailes
- Department of Science and Environment, Roskilde University, Roskilde, Denmark
| | - H Jenssen
- Department of Science and Environment, Roskilde University, Roskilde, Denmark
| | - G B E Jemec
- Department of Dermatology, University Hospital Zealand, Roskilde, Denmark
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109
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Li X, Arias CA, Aitken SL, Galloway Peña J, Panesso D, Chang M, Diaz L, Rios R, Numan Y, Ghaoui S, DebRoy S, Bhatti MM, Simmons DE, Raad I, Hachem R, Folan SA, Sahasarabhojane P, Kalia A, Shelburne SA. Clonal Emergence of Invasive Multidrug-Resistant Staphylococcus epidermidis Deconvoluted via a Combination of Whole-Genome Sequencing and Microbiome Analyses. Clin Infect Dis 2018; 67:398-406. [PMID: 29546356 PMCID: PMC6051468 DOI: 10.1093/cid/ciy089] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 02/03/2018] [Indexed: 01/05/2023] Open
Abstract
Background Pathobionts, bacteria that are typically human commensals but can cause disease, contribute significantly to antimicrobial resistance. Staphylococcus epidermidis is a prototypical pathobiont as it is a ubiquitous human commensal but also a leading cause of healthcare-associated bacteremia. We sought to determine the etiology of a recent increase in invasive S. epidermidis isolates resistant to linezolid. Methods Whole-genome sequencing (WGS) was performed on 176 S. epidermidis bloodstream isolates collected at the MD Anderson Cancer Center in Houston, Texas, between 2013 and 2016. Molecular relationships were assessed via complementary phylogenomic approaches. Abundance of the linezolid resistance determinant cfr was determined in stool samples via reverse-transcription quantitative polymerase chain reaction. Results Thirty-nine of the 176 strains were linezolid resistant (22%). Thirty-one of the 39 linezolid-resistant S. epidermidis infections were caused by a particular clone resistant to multiple antimicrobials that spread among leukemia patients and carried cfr on a 49-kb plasmid (herein called pMB151a). The 6 kb of pMB151a surrounding the cfr gene was nearly 100% identical to a cfr-containing plasmid isolated from livestock-associated staphylococci in China. Analysis of serial stool samples from leukemia patients revealed progressive staphylococcal domination of the intestinal microflora and an increase in cfr abundance following linezolid use. Conclusions The combination of linezolid use plus transmission of a multidrug-resistant clone drove expansion of invasive, linezolid-resistant S. epidermidis. Our results lend support to the notion that a combination of antibiotic stewardship plus infection control measures may help to control the spread of a multidrug-resistant pathobiont.
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Affiliation(s)
- Xiqi Li
- Graduate Program in Diagnostic Genetics, School of Health Professions, University of Texas MD Anderson Cancer Center, Bogota, Colombia
| | - Cesar A Arias
- Center for Antimicrobial Resistance and Microbial Genomics, Bogota, Colombia
- Division of Infectious Diseases, University of Texas McGovern Medical School at Houston, Bogota, Colombia
- Molecular Genetics and Antimicrobial Resistance Unit and International Center for Microbial Genomics, Universidad El Bosque, Bogota, Colombia
| | - Samuel L Aitken
- Division of Pharmacy, University of Texas MD Anderson Cancer Center, Houston
| | - Jessica Galloway Peña
- Department of Infectious Diseases, University of Texas MD Anderson Cancer Center, Houston
| | - Diana Panesso
- Center for Antimicrobial Resistance and Microbial Genomics, Bogota, Colombia
| | - Michael Chang
- Center for Antimicrobial Resistance and Microbial Genomics, Bogota, Colombia
| | - Lorena Diaz
- Molecular Genetics and Antimicrobial Resistance Unit and International Center for Microbial Genomics, Universidad El Bosque, Bogota, Colombia
| | - Rafael Rios
- Molecular Genetics and Antimicrobial Resistance Unit and International Center for Microbial Genomics, Universidad El Bosque, Bogota, Colombia
| | - Yazan Numan
- Department of Infectious Diseases, University of Texas MD Anderson Cancer Center, Houston
| | - Sammi Ghaoui
- Department of Infectious Diseases, University of Texas MD Anderson Cancer Center, Houston
| | - Sruti DebRoy
- Department of Infectious Diseases, University of Texas MD Anderson Cancer Center, Houston
| | - Micah M Bhatti
- Department of Laboratory Medicine, University of Texas MD Anderson Cancer Center, Houston
| | - Dawn E Simmons
- Department of Laboratory Medicine, University of Texas MD Anderson Cancer Center, Houston
| | - Isaam Raad
- Department of Infectious Diseases, University of Texas MD Anderson Cancer Center, Houston
| | - Ray Hachem
- Department of Infectious Diseases, University of Texas MD Anderson Cancer Center, Houston
| | - Stephanie A Folan
- Division of Pharmacy, University of Texas MD Anderson Cancer Center, Houston
| | | | - Awdhesh Kalia
- Graduate Program in Diagnostic Genetics, School of Health Professions, University of Texas MD Anderson Cancer Center, Bogota, Colombia
| | - Samuel A Shelburne
- Center for Antimicrobial Resistance and Microbial Genomics, Bogota, Colombia
- Department of Infectious Diseases, University of Texas MD Anderson Cancer Center, Houston
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston
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110
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Byrd AL, Deming C, Cassidy SKB, Harrison OJ, Ng WI, Conlan S, Belkaid Y, Segre JA, Kong HH. Staphylococcus aureus and Staphylococcus epidermidis strain diversity underlying pediatric atopic dermatitis. Sci Transl Med 2018; 9:9/397/eaal4651. [PMID: 28679656 DOI: 10.1126/scitranslmed.aal4651] [Citation(s) in RCA: 347] [Impact Index Per Article: 57.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 04/22/2017] [Indexed: 12/13/2022]
Abstract
The heterogeneous course, severity, and treatment responses among patients with atopic dermatitis (AD; eczema) highlight the complexity of this multifactorial disease. Prior studies have used traditional typing methods on cultivated isolates or sequenced a bacterial marker gene to study the skin microbial communities of AD patients. Shotgun metagenomic sequence analysis provides much greater resolution, elucidating multiple levels of microbial community assembly ranging from kingdom to species and strain-level diversification. We analyzed microbial temporal dynamics from a cohort of pediatric AD patients sampled throughout the disease course. Species-level investigation of AD flares showed greater Staphylococcus aureus predominance in patients with more severe disease and Staphylococcus epidermidis predominance in patients with less severe disease. At the strain level, metagenomic sequencing analyses demonstrated clonal S. aureus strains in more severe patients and heterogeneous S. epidermidis strain communities in all patients. To investigate strain-level biological effects of S. aureus, we topically colonized mice with human strains isolated from AD patients and controls. This cutaneous colonization model demonstrated S. aureus strain-specific differences in eliciting skin inflammation and immune signatures characteristic of AD patients. Specifically, S. aureus isolates from AD patients with more severe flares induced epidermal thickening and expansion of cutaneous T helper 2 (TH2) and TH17 cells. Integrating high-resolution sequencing, culturing, and animal models demonstrated how functional differences of staphylococcal strains may contribute to the complexity of AD disease.
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Affiliation(s)
- Allyson L Byrd
- Microbial Genomics Section, National Human Genome Research Institute, National Institutes of Health (NIH), Bethesda, MD 20892, USA.,Department of Bioinformatics, Boston University, Boston, MA 02215, USA.,Mucosal Immunology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD 20892, USA
| | - Clay Deming
- Microbial Genomics Section, National Human Genome Research Institute, National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Sara K B Cassidy
- Microbial Genomics Section, National Human Genome Research Institute, National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Oliver J Harrison
- Mucosal Immunology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD 20892, USA
| | - Weng-Ian Ng
- Microbial Genomics Section, National Human Genome Research Institute, National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | - Sean Conlan
- Microbial Genomics Section, National Human Genome Research Institute, National Institutes of Health (NIH), Bethesda, MD 20892, USA
| | | | - Yasmine Belkaid
- Mucosal Immunology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases (NIAID), NIH, Bethesda, MD 20892, USA.,NIAID Microbiome Program, Department of Intramural Research, NIAID, NIH, Bethesda, MD 20892, USA
| | - Julia A Segre
- Microbial Genomics Section, National Human Genome Research Institute, National Institutes of Health (NIH), Bethesda, MD 20892, USA.
| | - Heidi H Kong
- Dermatology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
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111
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Sharma S, Chaudhry V, Kumar S, Patil PB. Phylogenomic Based Comparative Studies on Indian and American Commensal Staphylococcus epidermidis Isolates. Front Microbiol 2018. [PMID: 29535698 PMCID: PMC5835047 DOI: 10.3389/fmicb.2018.00333] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Staphylococcus epidermidis is a prominent commensal member of human skin microbiome and an emerging nosocomial pathogen, making it a good model organism to provide genomic insights, correlating its transition between commensalism and pathogenicity. While there are numerous studies to understand differences in commensal and pathogenic isolates, systematic efforts to understand variation and evolutionary pattern in multiple strains isolated from healthy individuals are lacking. In the present study, using whole genome sequencing and analysis, we report presence of diverse lineages of S. epidermidis isolates in healthy individuals from two geographically diverse locations of India and North America. Further, there is distinct pattern in the distribution of candidate gene(s) for pathogenicity and commensalism. The pattern is not only reflected in lineages but is also based on geographic origin of the isolates. This is evident by the fact that North American isolates under this study are more genomically dynamic and harbor pathogenicity markers in higher frequency. On the other hand, isolates of Indian origin are less genomically dynamic, harbor less pathogenicity marker genes and possess two unique antimicrobial peptide gene clusters. This study provides a basis to understand the nature of selection pressure in a key human skin commensal bacterium with implications in its management as an opportunistic pathogen.
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Affiliation(s)
- Shikha Sharma
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Vasvi Chaudhry
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Sanjeet Kumar
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
| | - Prabhu B Patil
- Bacterial Genomics and Evolution Laboratory, CSIR-Institute of Microbial Technology, Chandigarh, India
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112
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Pinheiro L, Mello PL, Abraão LM, Corrente JE, Lourdes Rs Cunha MD. Evaluation of reference values for phenotypic tests to detect oxacillin resistance in coagulase-negative staphylococci. Future Microbiol 2018. [PMID: 29521121 DOI: 10.2217/fmb-2017-0221] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
AIM To evaluate the adequacy of the disc-diffusion test and E-test® compared with detection of mecA for coagulase-negative staphylococci isolated from blood cultures, nasal swabs and wounds. RESULTS Agreement between all techniques was observed in 65.7% of cases. The greatest discrepancy between mecA/susceptible E-test was observed for non-epidermidis species. A resistance breakpoint ≤19 mm using the oxacillin disc was found to best classify all coagulase-negative staphylococci isolates; Staphylococcus epidermidis, ≤19 mm (oxacillin) and ≤27 mm (cefoxitin); Staphylococcus haemolyticus and Staphylococcus capitis, ≤21 mm (oxacillin) and ≤18 mm (cefoxitin); Staphylococcus warneri, MICs ≥0.75 mg/l. CONCLUSION Although no longer recommended by the Clinical Laboratory Standards Institute, we observed some cases in which only the oxacillin disc-diffusion test detected resistance. The discrepancy between phenotypic tests and mecA is probably due to heterogeneity and borderline resistance.
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Affiliation(s)
- Luiza Pinheiro
- Department of Microbiology & Immunology, Institute of Biosciences of Botucatu, Universidade Estadual Paulista - UNESP, Botucatu 18618-970, Brazil.,Departament of Anatomic Pathology, Instituto Lauro de Souza Lima, Bauru 17034-971, Brazil
| | - Priscila L Mello
- Department of Microbiology & Immunology, Institute of Biosciences of Botucatu, Universidade Estadual Paulista - UNESP, Botucatu 18618-970, Brazil
| | - Ligia M Abraão
- Department of Microbiology & Immunology, Institute of Biosciences of Botucatu, Universidade Estadual Paulista - UNESP, Botucatu 18618-970, Brazil
| | - José Eduardo Corrente
- Department of Biostatistics, Institute of Biosciences of Botucatu, Universidade Estadual Paulista - UNESP, Botucatu 18618-970, Brazil
| | - Maria de Lourdes Rs Cunha
- Department of Microbiology & Immunology, Institute of Biosciences of Botucatu, Universidade Estadual Paulista - UNESP, Botucatu 18618-970, Brazil
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113
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Comparative Genomics and Identification of an Enterotoxin-Bearing Pathogenicity Island, SEPI-1/SECI-1, in Staphylococcus epidermidis Pathogenic Strains. Toxins (Basel) 2018; 10:toxins10030093. [PMID: 29495323 PMCID: PMC5869381 DOI: 10.3390/toxins10030093] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2018] [Revised: 02/22/2018] [Accepted: 02/22/2018] [Indexed: 02/08/2023] Open
Abstract
Staphylococcus epidermidis is a leading cause of nosocomial infections, majorly resistant to beta-lactam antibiotics, and may transfer several mobile genetic elements among the members of its own species, as well as to Staphylococcus aureus; however, a genetic exchange from S. aureus to S. epidermidis remains controversial. We recently identified two pathogenic clinical strains of S. epidermidis that produce a staphylococcal enterotoxin C3-like (SEC) similar to that by S. aureus pathogenicity islands. This study aimed to determine the genetic environment of the SEC-coding sequence and to identify the mobile genetic elements. Whole-genome sequencing and annotation of the S. epidermidis strains were performed using Illumina technology and a bioinformatics pipeline for assembly, which provided evidence that the SEC-coding sequences were located in a composite pathogenicity island that was previously described in the S. epidermidis strain FRI909, called SePI-1/SeCI-1, with 83.8–89.7% nucleotide similarity. Various other plasmids were identified, particularly p_3_95 and p_4_95, which carry antibiotic resistance genes (hsrA and dfrG, respectively), and share homologies with SAP085A and pUSA04-2-SUR11, two plasmids described in S. aureus. Eventually, one complete prophage was identified, ΦSE90, sharing 30 out of 52 coding sequences with the Acinetobacter phage vB_AbaM_IME200. Thus, the SePI-1/SeCI-1 pathogenicity island was identified in two pathogenic strains of S. epidermidis that produced a SEC enterotoxin causing septic shock. These findings suggest the existence of in vivo genetic exchange from S. aureus to S. epidermidis.
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114
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Ridaura VK, Bouladoux N, Claesen J, Chen YE, Byrd AL, Constantinides MG, Merrill ED, Tamoutounour S, Fischbach MA, Belkaid Y. Contextual control of skin immunity and inflammation by Corynebacterium. J Exp Med 2018; 215:785-799. [PMID: 29382696 PMCID: PMC5839758 DOI: 10.1084/jem.20171079] [Citation(s) in RCA: 128] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Revised: 11/03/2017] [Accepted: 12/21/2017] [Indexed: 12/23/2022] Open
Abstract
Belkaid et al. show that Corynebacterium, a dominant skin microbe, promotes activation of γδ T cells in a mycolic acid–dependent manner without altering skin homeostasis. Such effect promotes inflammation in the context of high-fat-diet and psoriasis-like settings. How defined microbes influence the skin immune system remains poorly understood. Here we demonstrate that Corynebacteria, dominant members of the skin microbiota, promote a dramatic increase in the number and activation of a defined subset of γδ T cells. This effect is long-lasting, occurs independently of other microbes, and is, in part, mediated by interleukin (IL)-23. Under steady-state conditions, the impact of Corynebacterium is discrete and noninflammatory. However, when applied to the skin of a host fed a high-fat diet, Corynebacterium accolens alone promotes inflammation in an IL-23–dependent manner. Such effect is highly conserved among species of Corynebacterium and dependent on the expression of a dominant component of the cell envelope, mycolic acid. Our data uncover a mode of communication between the immune system and a dominant genus of the skin microbiota and reveal that the functional impact of canonical skin microbial determinants is contextually controlled by the inflammatory and metabolic state of the host.
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Affiliation(s)
- Vanessa K Ridaura
- Mucosal Immunology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Nicolas Bouladoux
- Mucosal Immunology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,Microbiome Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Jan Claesen
- Department of Bioengineering, Stanford University, Stanford, CA
| | - Y Erin Chen
- Department of Bioengineering, Stanford University, Stanford, CA
| | - Allyson L Byrd
- Mucosal Immunology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD.,Translational and Functional Genomics Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, MD.,Department of Bioinformatics, Boston University, Boston, MA
| | - Michael G Constantinides
- Mucosal Immunology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Eric D Merrill
- Mucosal Immunology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Samira Tamoutounour
- Mucosal Immunology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | | | - Yasmine Belkaid
- Mucosal Immunology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD .,Microbiome Program, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
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115
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Zhou W, Gay N, Oh J. ReprDB and panDB: minimalist databases with maximal microbial representation. MICROBIOME 2018; 6:15. [PMID: 29347966 PMCID: PMC5774170 DOI: 10.1186/s40168-018-0399-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2017] [Accepted: 01/10/2018] [Indexed: 05/11/2023]
Abstract
BACKGROUND Profiling of shotgun metagenomic samples is hindered by a lack of unified microbial reference genome databases that (i) assemble genomic information from all open access microbial genomes, (ii) have relatively small sizes, and (iii) are compatible to various metagenomic read mapping tools. Moreover, computational tools to rapidly compile and update such databases to accommodate the rapid increase in new reference genomes do not exist. As a result, database-guided analyses often fail to profile a substantial fraction of metagenomic shotgun sequencing reads from complex microbiomes. RESULTS We report pipelines that efficiently traverse all open access microbial genomes and assemble non-redundant genomic information. The pipelines result in two species-resolution microbial reference databases of relatively small sizes: reprDB, which assembles microbial representative or reference genomes, and panDB, for which we developed a novel iterative alignment algorithm to identify and assemble non-redundant genomic regions in multiple sequenced strains. With the databases, we managed to assign taxonomic labels and genome positions to the majority of metagenomic reads from human skin and gut microbiomes, demonstrating a significant improvement over a previous database-guided analysis on the same datasets. CONCLUSIONS reprDB and panDB leverage the rapid increases in the number of open access microbial genomes to more fully profile metagenomic samples. Additionally, the databases exclude redundant sequence information to avoid inflated storage or memory space and indexing or analyzing time. Finally, the novel iterative alignment algorithm significantly increases efficiency in pan-genome identification and can be useful in comparative genomic analyses.
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Affiliation(s)
- Wei Zhou
- The Jackson Laboratory for Genomic Medicine, Farmington, CT USA
| | - Nicole Gay
- The Jackson Laboratory for Genomic Medicine, Farmington, CT USA
- Stanford University, Stanford, CA USA
| | - Julia Oh
- The Jackson Laboratory for Genomic Medicine, Farmington, CT USA
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116
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Linehan JL, Harrison OJ, Han SJ, Byrd AL, Vujkovic-Cvijin I, Villarino AV, Sen SK, Shaik J, Smelkinson M, Tamoutounour S, Collins N, Bouladoux N, Dzutsev A, Rosshart SP, Arbuckle JH, Wang CR, Kristie TM, Rehermann B, Trinchieri G, Brenchley JM, O'Shea JJ, Belkaid Y. Non-classical Immunity Controls Microbiota Impact on Skin Immunity and Tissue Repair. Cell 2018; 172:784-796.e18. [PMID: 29358051 DOI: 10.1016/j.cell.2017.12.033] [Citation(s) in RCA: 295] [Impact Index Per Article: 49.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Revised: 10/17/2017] [Accepted: 12/21/2017] [Indexed: 02/02/2023]
Abstract
Mammalian barrier surfaces are constitutively colonized by numerous microorganisms. We explored how the microbiota was sensed by the immune system and the defining properties of such responses. Here, we show that a skin commensal can induce T cell responses in a manner that is restricted to non-classical MHC class I molecules. These responses are uncoupled from inflammation and highly distinct from pathogen-induced cells. Commensal-specific T cells express a defined gene signature that is characterized by expression of effector genes together with immunoregulatory and tissue-repair signatures. As such, non-classical MHCI-restricted commensal-specific immune responses not only promoted protection to pathogens, but also accelerated skin wound closure. Thus, the microbiota can induce a highly physiological and pleiotropic form of adaptive immunity that couples antimicrobial function with tissue repair. Our work also reveals that non-classical MHC class I molecules, an evolutionarily ancient arm of the immune system, can promote homeostatic immunity to the microbiota.
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Affiliation(s)
- Jonathan L Linehan
- Mucosal Immunology Section, Laboratory of Parasitic Diseases, NIAID, NIH, Bethesda, MD 20892, USA
| | - Oliver J Harrison
- Mucosal Immunology Section, Laboratory of Parasitic Diseases, NIAID, NIH, Bethesda, MD 20892, USA
| | - Seong-Ji Han
- Mucosal Immunology Section, Laboratory of Parasitic Diseases, NIAID, NIH, Bethesda, MD 20892, USA
| | - Allyson L Byrd
- Mucosal Immunology Section, Laboratory of Parasitic Diseases, NIAID, NIH, Bethesda, MD 20892, USA; Translational and Functional Genomics Branch, NHGRI, NIH, Bethesda, MD 20892, USA; Department of Bioinformatics, Boston University, Boston, MA 02215, USA
| | - Ivan Vujkovic-Cvijin
- Mucosal Immunology Section, Laboratory of Parasitic Diseases, NIAID, NIH, Bethesda, MD 20892, USA
| | | | - Shurjo K Sen
- Cancer and Inflammation Program, NCI, NIH, Bethesda, MD 20892, USA
| | - Jahangheer Shaik
- Laboratory of Parasitic Diseases, NIAID, NIH, Bethesda, MD 20892, USA
| | - Margery Smelkinson
- Biological Imaging, Research Technology Branch, NIAID, NIH, Bethesda, MD 20892, USA
| | - Samira Tamoutounour
- Mucosal Immunology Section, Laboratory of Parasitic Diseases, NIAID, NIH, Bethesda, MD 20892, USA
| | - Nicholas Collins
- Mucosal Immunology Section, Laboratory of Parasitic Diseases, NIAID, NIH, Bethesda, MD 20892, USA
| | - Nicolas Bouladoux
- Mucosal Immunology Section, Laboratory of Parasitic Diseases, NIAID, NIH, Bethesda, MD 20892, USA; NIAID Microbiome Program, NIH, Bethesda, MD 20892, USA
| | - Amiran Dzutsev
- Cancer and Inflammation Program, NCI, NIH, Bethesda, MD 20892, USA
| | - Stephan P Rosshart
- Immunology Section, Liver Diseases Branch, NIDDK, NIH, Bethesda, MD 20892, USA
| | | | - Chyung-Ru Wang
- Department of Microbiology and Immunology, Northwestern University, Chicago, IL 60611, USA
| | | | - Barbara Rehermann
- Immunology Section, Liver Diseases Branch, NIDDK, NIH, Bethesda, MD 20892, USA
| | | | - Jason M Brenchley
- Barrier Immunity Section, Laboratory of Parasitic Diseases, NIAID, NIH, Bethesda, MD 20892, USA
| | - John J O'Shea
- Molecular Immunology and Inflammation Branch, NIAMS, NIH, Bethesda, MD 20892, USA
| | - Yasmine Belkaid
- Mucosal Immunology Section, Laboratory of Parasitic Diseases, NIAID, NIH, Bethesda, MD 20892, USA.
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117
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Abstract
Functioning as the exterior interface of the human body with the environment, skin acts as a physical barrier to prevent the invasion of foreign pathogens while providing a home to the commensal microbiota. The harsh physical landscape of skin, particularly the desiccated, nutrient-poor, acidic environment, also contributes to the adversity that pathogens face when colonizing human skin. Despite this, the skin is colonized by a diverse microbiota. In this Review, we describe amplicon and shotgun metagenomic DNA sequencing studies that have been used to assess the taxonomic diversity of microorganisms that are associated with skin from the kingdom to the strain level. We discuss recent insights into skin microbial communities, including their composition in health and disease, the dynamics between species and interactions with the immune system, with a focus on Propionibacterium acnes, Staphylococcus epidermidis and Staphylococcus aureus.
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Affiliation(s)
- Allyson L Byrd
- Microbial Genomics Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA.,Department of Bioinformatics, Boston University, Boston, Massachusetts 02215, USA.,Mucosal Immunology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA.,Department of Cancer Immunology, Genentech, South San Francisco, California 94080, USA
| | - Yasmine Belkaid
- Mucosal Immunology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA.,National Institute of Allergy and Infectious Diseases Microbiome Program, Department of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, Maryland 20892, USA
| | - Julia A Segre
- Microbial Genomics Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland 20892, USA
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118
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Larssen KW, Nor A, Bergh K. Rapid discrimination of Staphylococcus epidermidis genotypes in a routine clinical microbiological laboratory using single nucleotide polymorphisms in housekeeping genes. J Med Microbiol 2018; 67:169-182. [PMID: 29293080 DOI: 10.1099/jmm.0.000663] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
PURPOSE Staphylococcus epidermidis colonies often display several morphologies and antimicrobial susceptibility patterns when cultured from device-related infections, and may represent one or multiple genotypes. Genotyping may be helpful in the clinical interpretation, but is time consuming and expensive. We wanted to establish a method for rapid discrimination of S. epidermidis genotypes for use in a routine microbiology laboratory. METHODOLOGY A real-time PCR targeting eight discriminatory class I or II single-nucleotide polymorphisms (SNPs) in six of the seven housekeeping genes was constructed. Post PCR, high-resolution melt (HRM) analysis using EvaGreen as fluorophore discriminated amplicons based on their percentage GC content. RESULTS In silico, 42 representative sequence types (STs), including all major MLST group and subgroup founders, were separated into 23 different cluster profiles with a Simpson's index of diversity of 0.97. By HRM-PCR, 11 commonly encountered hospital and outbreak STs were separated into eight HRM patterns. CONCLUSION This method can rapidly establish whether S. epidermidis strains belong to different genotypes. It can be used in patients with S. epidermidis infections, as an aid in outbreak investigations and to select strains for investigation with more discriminatory methods, saving workload and costs. Results may be obtained the same day as culture results. Its strength lies mainly in indicating differences, as some STs may have the same melt profile. Changes in S. epidermidis epidemiology may warrant alterations in the inclusion of SNPs. We believe this method can reduce the threshold for performing genotyping analysis on an increasingly important nosocomial pathogen.
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Affiliation(s)
- Kjersti Wik Larssen
- Department of Medical Microbiology, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
| | - Anne Nor
- Department of Laboratory medicine, Children's and Women's health, Faculty of Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Kåre Bergh
- Department of Medical Microbiology, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
- Department of Laboratory medicine, Children's and Women's health, Faculty of Medicine, Norwegian University of Science and Technology, Trondheim, Norway
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119
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Cesur MF, Abdik E, Güven-Gülhan Ü, Durmuş S, Çakır T. Computational Systems Biology of Metabolism in Infection. EXPERIENTIA SUPPLEMENTUM (2012) 2018; 109:235-282. [PMID: 30535602 DOI: 10.1007/978-3-319-74932-7_6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
A systems approach to elucidate the effect of infection on cell metabolism provides several opportunities from a better understanding of molecular mechanisms to the identification of potential biomarkers and drug targets. This is obvious from the fact that we have witnessed the accelerated use of computational systems biology in the last five years to study metabolic changes in pathogen and/or host cells in response to infection. In this chapter, we aim to present a comprehensive review of the recent research by focusing on genome-scale metabolic network models of pathogen-host systems and genome-wide metabolomics and fluxomics analysis of infected cells.
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Affiliation(s)
- Müberra Fatma Cesur
- Computational Systems Biology Group, Department of Bioengineering, Gebze Technical University, Gebze, Kocaeli, Turkey
| | - Ecehan Abdik
- Computational Systems Biology Group, Department of Bioengineering, Gebze Technical University, Gebze, Kocaeli, Turkey
| | - Ünzile Güven-Gülhan
- Computational Systems Biology Group, Department of Bioengineering, Gebze Technical University, Gebze, Kocaeli, Turkey
| | - Saliha Durmuş
- Computational Systems Biology Group, Department of Bioengineering, Gebze Technical University, Gebze, Kocaeli, Turkey
| | - Tunahan Çakır
- Computational Systems Biology Group, Department of Bioengineering, Gebze Technical University, Gebze, Kocaeli, Turkey.
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120
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Comparative Genomics Study of Staphylococcus epidermidis Isolates from Orthopedic-Device-Related Infections Correlated with Patient Outcome. J Clin Microbiol 2017; 55:3089-3103. [PMID: 28794175 DOI: 10.1128/jcm.00881-17] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2017] [Accepted: 07/18/2017] [Indexed: 12/16/2022] Open
Abstract
Staphylococcus epidermidis has emerged as an important opportunistic pathogen causing orthopedic-device-related infections (ODRI). This study investigated the association of genome variation and phenotypic features of the infecting S. epidermidis isolate with the clinical outcome for the infected patient. S. epidermidis isolates were collected from 104 patients with ODRI. Their clinical outcomes were evaluated, after an average of 26 months, as either "cured" or "not cured." The isolates were tested for antibiotic susceptibility and biofilm formation. Whole-genome sequencing was performed on all isolates, and genomic variation was related to features associated with "cured" and "not cured." Strong biofilm formation and aminoglycoside resistance were associated with a "not-cured" outcome (P = 0.031 and P < 0.001, respectively). Based on gene-by-gene analysis, some accessory genes were more prevalent in isolates from the "not-cured" group. These included the biofilm-associated bhp gene, the antiseptic resistance qacA gene, the cassette chromosome recombinase-encoding genes ccrA and ccrB, and the IS256-like transposase gene. This study identifies biofilm formation and antibiotic resistance as associated with poor outcome in S. epidermidis ODRI. Whole-genome sequencing identified specific genes associated with a "not-cured" outcome that should be validated in future studies. (The study has been registered at ClinicalTrials.gov with identifier NCT02640937.).
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Bypassing the Restriction System To Improve Transformation of Staphylococcus epidermidis. J Bacteriol 2017; 199:JB.00271-17. [PMID: 28559294 DOI: 10.1128/jb.00271-17] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2017] [Accepted: 05/21/2017] [Indexed: 12/23/2022] Open
Abstract
Staphylococcus epidermidis is the leading cause of infections on indwelling medical devices worldwide. Intrinsic antibiotic resistance and vigorous biofilm production have rendered these infections difficult to treat and, in some cases, require the removal of the offending medical prosthesis. With the exception of two widely passaged isolates, RP62A and 1457, the pathogenesis of infections caused by clinical S. epidermidis strains is poorly understood due to the strong genetic barrier that precludes the efficient transformation of foreign DNA into clinical isolates. The difficulty in transforming clinical S. epidermidis isolates is primarily due to the type I and IV restriction-modification systems, which act as genetic barriers. Here, we show that efficient plasmid transformation of clinical S. epidermidis isolates from clonal complexes 2, 10, and 89 can be realized by employing a plasmid artificial modification (PAM) in Escherichia coli DC10B containing a Δdcm mutation. This transformative technique should facilitate our ability to genetically modify clinical isolates of S. epidermidis and hence improve our understanding of their pathogenesis in human infections.IMPORTANCE Staphylococcus epidermidis is a source of considerable morbidity worldwide. The underlying mechanisms contributing to the commensal and pathogenic lifestyles of S. epidermidis are poorly understood. Genetic manipulations of clinically relevant strains of S. epidermidis are largely prohibited due to the presence of a strong restriction barrier. With the introductions of the tools presented here, genetic manipulation of clinically relevant S. epidermidis isolates has now become possible, thus improving our understanding of S. epidermidis as a pathogen.
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García-Gómez E, Miranda-Ozuna JFT, Díaz-Cedillo F, Vázquez-Sánchez EA, Rodríguez-Martínez S, Jan-Roblero J, Cancino-Diaz ME, Cancino-Diaz JC. Staphylococcus epidermidis lipoteichoic acid: exocellular release and ltaS gene expression in clinical and commensal isolates. J Med Microbiol 2017. [PMID: 28639932 DOI: 10.1099/jmm.0.000502] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
PURPOSE Staphylococcus epidermidis ATCC12228 lipoteichoic acid (LTA) inhibits TNFα production from keratinocytes that are activated with poly I:C. However, this effect has not been proven in clinical or commensal isolates. METHODOLOGY The <10 kDa fractions of S. epidermidis isolates from ocular infections (n=56), healthy skin (n=35) and healthy conjunctiva (n=32) were obtained. TNFα production was determined by elisa in HaCaT keratinocytes stimulated with poly I:C and with the <10 kDa fractions. LTA in the cytoplasmic membrane and in the <10 kDa fractions of the isolates was determined during bacterial growth by flow cytometry, Western blot and electrospray ionization mass spectrometry. The expression levels of ugtP, ltaA and ltaS were evaluated. RESULTS Two populations of isolates were found: a population that inhibited TNFα production (TNFα-inhibitor isolates) and a population that did not inhibit it (TNFα non-inhibitor isolates). The cells from the TNFα-inhibitor isolates had less LTA in the cytoplasmic membrane compared to the cells from the TNFα non-inhibitor isolates (P<0.05). Similarly, LTA was detected in the supernatants of TNFα-inhibitor isolates, and it was absent in TNFα non-inhibitor isolates. High expression levels of the ugtP and ltaA genes in the 1850I (TNFα-inhibitor isolate) and 37HS (TNFα non-inhibitor isolate) isolates were found during bacterial growth. However, the ltaS gene had a low expression level (P<0.05) in the 37HS isolate. CONCLUSION The TNFα-inhibitor isolates release LTA due to high expression of the LTA synthesis genes. By contrast, TNFα non-inhibitor isolates do not release LTA due to low expression level of the ltaS gene.
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Affiliation(s)
- Elizabeth García-Gómez
- Departments of Microbiology, Escuela Nacional de Ciencias Biológicas-Instituto Politécnico Nacional, Carpio y Plan de Ayala S/N Col, Santo Tomas, Deleg, Miguel Hidalgo, Mexico City, Mexico.,Unidad de Investigación en Reproducción Humana, CONACyT-Instituto Nacional de Perinatología, Montes Urales 800, Col, Lomas Virreyes Deleg, Miguel Hidalgo, Mexico City, Mexico
| | - Jesús F T Miranda-Ozuna
- Departments of Microbiology, Escuela Nacional de Ciencias Biológicas-Instituto Politécnico Nacional, Carpio y Plan de Ayala S/N Col, Santo Tomas, Deleg, Miguel Hidalgo, Mexico City, Mexico
| | - Francisco Díaz-Cedillo
- Departments of Organic Chemistry, Escuela Nacional de Ciencias Biológicas-Instituto Politécnico Nacional, Carpio y Plan de Ayala S/N Col, Santo Tomas, Deleg, Miguel Hidalgo, Mexico City, Mexico
| | - Ernesto A Vázquez-Sánchez
- Departments of Immunology, Escuela Nacional de Ciencias Biológicas-Instituto Politécnico Nacional, Carpio y Plan de Ayala S/N, Col, Santo Tomas, Deleg, Miguel Hidalgo, Mexico City, Mexico
| | - Sandra Rodríguez-Martínez
- Departments of Immunology, Escuela Nacional de Ciencias Biológicas-Instituto Politécnico Nacional, Carpio y Plan de Ayala S/N, Col, Santo Tomas, Deleg, Miguel Hidalgo, Mexico City, Mexico
| | - Janet Jan-Roblero
- Departments of Microbiology, Escuela Nacional de Ciencias Biológicas-Instituto Politécnico Nacional, Carpio y Plan de Ayala S/N Col, Santo Tomas, Deleg, Miguel Hidalgo, Mexico City, Mexico
| | - Mario E Cancino-Diaz
- Departments of Immunology, Escuela Nacional de Ciencias Biológicas-Instituto Politécnico Nacional, Carpio y Plan de Ayala S/N, Col, Santo Tomas, Deleg, Miguel Hidalgo, Mexico City, Mexico
| | - Juan Carlos Cancino-Diaz
- Departments of Microbiology, Escuela Nacional de Ciencias Biológicas-Instituto Politécnico Nacional, Carpio y Plan de Ayala S/N Col, Santo Tomas, Deleg, Miguel Hidalgo, Mexico City, Mexico
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Tett A, Pasolli E, Farina S, Truong DT, Asnicar F, Zolfo M, Beghini F, Armanini F, Jousson O, De Sanctis V, Bertorelli R, Girolomoni G, Cristofolini M, Segata N. Unexplored diversity and strain-level structure of the skin microbiome associated with psoriasis. NPJ Biofilms Microbiomes 2017; 3:14. [PMID: 28649415 PMCID: PMC5481418 DOI: 10.1038/s41522-017-0022-5] [Citation(s) in RCA: 116] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Revised: 03/22/2017] [Accepted: 05/22/2017] [Indexed: 12/20/2022] Open
Abstract
Psoriasis is an immune-mediated inflammatory skin disease that has been associated with cutaneous microbial dysbiosis by culture-dependent investigations and rRNA community profiling. We applied, for the first time, high-resolution shotgun metagenomics to characterise the microbiome of psoriatic and unaffected skin from 28 individuals. We demonstrate psoriatic ear sites have a decreased diversity and psoriasis is associated with an increase in Staphylococcus, but overall the microbiomes of psoriatic and unaffected sites display few discriminative features at the species level. Finer strain-level analysis reveals strain heterogeneity colonisation and functional variability providing the intriguing hypothesis of psoriatic niche-specific strain adaptation or selection. Furthermore, we accessed the poorly characterised, but abundant, clades with limited sequence information in public databases, including uncharacterised Malassezia spp. These results highlight the skins hidden diversity and suggests strain-level variations could be key determinants of the psoriatic microbiome. This illustrates the need for high-resolution analyses, particularly when identifying therapeutic targets. This work provides a baseline for microbiome studies in relation to the pathogenesis of psoriasis.
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Affiliation(s)
- Adrian Tett
- Centre for Integrative Biology, University of Trento, Trento, Italy
| | - Edoardo Pasolli
- Centre for Integrative Biology, University of Trento, Trento, Italy
| | | | - Duy Tin Truong
- Centre for Integrative Biology, University of Trento, Trento, Italy
| | | | - Moreno Zolfo
- Centre for Integrative Biology, University of Trento, Trento, Italy
| | | | | | - Olivier Jousson
- Centre for Integrative Biology, University of Trento, Trento, Italy
| | - Veronica De Sanctis
- NGS Facility, Laboratory of Biomolecular Sequence and Structure Analysis for Health, Centre for Integrative Biology, University of Trento, Trento, Italy
| | - Roberto Bertorelli
- NGS Facility, Laboratory of Biomolecular Sequence and Structure Analysis for Health, Centre for Integrative Biology, University of Trento, Trento, Italy
| | - Giampiero Girolomoni
- Department of Medicine, Section of Dermatology, University of Verona, Verona, Italy
| | | | - Nicola Segata
- Centre for Integrative Biology, University of Trento, Trento, Italy
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McGuire AL, Mulroney KT, Carson CF, Ram R, Morahan G, Chakera A. Analysis of early mesothelial cell responses to Staphylococcus epidermidis isolated from patients with peritoneal dialysis-associated peritonitis. PLoS One 2017; 12:e0178151. [PMID: 28542390 PMCID: PMC5443531 DOI: 10.1371/journal.pone.0178151] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2016] [Accepted: 05/08/2017] [Indexed: 02/06/2023] Open
Abstract
The major complication of peritoneal dialysis (PD) is the development of peritonitis, an infection within the abdominal cavity, primarily caused by bacteria. PD peritonitis is associated with significant morbidity, mortality and health care costs. Staphylococcus epidermidis is the most frequently isolated cause of PD-associated peritonitis. Mesothelial cells are integral to the host response to peritonitis, and subsequent clinical outcomes, yet the effects of infection on mesothelial cells are not well characterised. We systematically investigated the early mesothelial cell response to clinical and reference isolates of S. epidermidis using primary mesothelial cells and the mesothelial cell line Met-5A. Using an unbiased whole genome microarray, followed by a targeted panel of genes known to be involved in the human antibacterial response, we identified 38 differentially regulated genes (adj. p-value < 0.05) representing 35 canonical pathways after 1 hour exposure to S. epidermidis. The top 3 canonical pathways were TNFR2 signaling, IL-17A signaling, and TNFR1 signaling (adj. p-values of 0.0012, 0.0012 and 0.0019, respectively). Subsequent qPCR validation confirmed significant differences in gene expression in a number of genes not previously described in mesothelial cell responses to infection, with heterogeneity observed between clinical isolates of S. epidermidis, and between Met-5A and primary mesothelial cells. Heterogeneity between different S. epidermidis isolates suggests that specific virulence factors may play critical roles in influencing outcomes from peritonitis. This study provides new insights into early mesothelial cell responses to infection with S. epidermidis, and confirms the importance of validating findings in primary mesothelial cells.
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Affiliation(s)
- Amanda L. McGuire
- Translational Renal Research Group, Harry Perkins Institute of Medical Research, Nedlands, Western Australia, Australia
- School of Medicine and Pharmacology, University of Western Australia, Crawley, Western Australia, Australia
- * E-mail:
| | - Kieran T. Mulroney
- Translational Renal Research Group, Harry Perkins Institute of Medical Research, Nedlands, Western Australia, Australia
- School of Medicine and Pharmacology, University of Western Australia, Crawley, Western Australia, Australia
| | - Christine F. Carson
- Translational Renal Research Group, Harry Perkins Institute of Medical Research, Nedlands, Western Australia, Australia
- School of Medicine and Pharmacology, University of Western Australia, Crawley, Western Australia, Australia
| | - Ramesh Ram
- Centre for Diabetes Research, Harry Perkins Institute of Medical Research, Nedlands, Western Australia, Australia
| | - Grant Morahan
- Centre for Diabetes Research, Harry Perkins Institute of Medical Research, Nedlands, Western Australia, Australia
| | - Aron Chakera
- Translational Renal Research Group, Harry Perkins Institute of Medical Research, Nedlands, Western Australia, Australia
- School of Medicine and Pharmacology, University of Western Australia, Crawley, Western Australia, Australia
- Department of Renal Medicine, Sir Charles Gairdner Hospital, Nedlands, Western Australia, Australia
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Costa EM, Silva S, Vicente S, Neto C, Castro PM, Veiga M, Madureira R, Tavaria F, Pintado MM. Chitosan nanoparticles as alternative anti-staphylococci agents: Bactericidal, antibiofilm and antiadhesive effects. MATERIALS SCIENCE & ENGINEERING. C, MATERIALS FOR BIOLOGICAL APPLICATIONS 2017. [PMID: 28629011 DOI: 10.1016/j.msec.2017.05.047] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
Chitosan is a biocompatible, bioactive, non-toxic polymer that due to these characteristics has been widely used as a carrier for targeted delivery of bioactive molecules. In recent years, and considering that chitosan has a strong antimicrobial potential, the scientific community's focus has shifted onto the possible antimicrobial activity of chitosan nanoparticles. With this in mind, the aim of this work was to produce low molecular weight chitosan nanoparticles, through the ionic gelation method and characterize their potential biological activity against three staphylococci (MSSA, MRSA and MRSE) in planktonic and sessile environments. The chitosan nanoparticles produced had an average size of 244±12nm, an average charge of 17.3±1.4mV and had a MIC of 1.25mg/mL for all tested microorganisms. Bactericidal activity was only registered for MSSA and MRSA with the time-inhibition curves showing bactericidal activity within 1h. Assays regarding chitosan nanoparticles' impact upon sessile populations showed that they were effective in preventing MRSE adhesion and highly effective in reducing MRSA and MSSA biofilm formation.
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Affiliation(s)
- E M Costa
- CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa/Porto, Rua Arquiteto Lobão Vital, Apartado 2511, 4202-401 Porto, Portugal
| | - S Silva
- CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa/Porto, Rua Arquiteto Lobão Vital, Apartado 2511, 4202-401 Porto, Portugal
| | - S Vicente
- CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa/Porto, Rua Arquiteto Lobão Vital, Apartado 2511, 4202-401 Porto, Portugal
| | - C Neto
- CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa/Porto, Rua Arquiteto Lobão Vital, Apartado 2511, 4202-401 Porto, Portugal
| | - P M Castro
- CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa/Porto, Rua Arquiteto Lobão Vital, Apartado 2511, 4202-401 Porto, Portugal
| | - M Veiga
- CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa/Porto, Rua Arquiteto Lobão Vital, Apartado 2511, 4202-401 Porto, Portugal
| | - R Madureira
- CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa/Porto, Rua Arquiteto Lobão Vital, Apartado 2511, 4202-401 Porto, Portugal
| | - F Tavaria
- CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa/Porto, Rua Arquiteto Lobão Vital, Apartado 2511, 4202-401 Porto, Portugal
| | - M M Pintado
- CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Universidade Católica Portuguesa/Porto, Rua Arquiteto Lobão Vital, Apartado 2511, 4202-401 Porto, Portugal.
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Complete Genome Sequence of a Staphylococcus epidermidis Strain with Exceptional Antimicrobial Activity. GENOME ANNOUNCEMENTS 2017; 5:5/10/e00004-17. [PMID: 28280007 PMCID: PMC5347227 DOI: 10.1128/genomea.00004-17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
Staphylococcus epidermidis is a Gram-positive bacterium that is prevalent on human skin. The species is associated with skin health, as well as with opportunistic infections. Here, we report the complete genome sequence of S. epidermidis 14.1.R1, isolated from human skin. In bacterial interference assays, the strain showed exceptional antimicrobial activity.
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Salgueiro VC, Iorio NLP, Ferreira MC, Chamon RC, Dos Santos KRN. Methicillin resistance and virulence genes in invasive and nasal Staphylococcus epidermidis isolates from neonates. BMC Microbiol 2017; 17:15. [PMID: 28086793 PMCID: PMC5237318 DOI: 10.1186/s12866-017-0930-9] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 01/09/2017] [Indexed: 01/04/2023] Open
Abstract
Background Staphylococcus epidermidis is an opportunistic pathogen involved in hospital-acquired infections, particularly in those related to medical devices. This study characterized 50 genetically unrelated S. epidermidis isolates from bloodstream infections (BSIs, n = 31) and nares (n = 19) of neonates in relation to staphylococcal chromosomal cassette mec (SCCmec) type, biofilm production and associated genes, and the arginine catabolic mobile elements (ACME), in order to detect virulence factors that could discriminate a potential invasiveness isolate or predict an increasing pathogenicity. Results Isolates from both groups showed no difference for biofilm production and ACME genes detection. However, BSI isolates harbored more frequently the sdrF and sesI genes (p < 0.05), whereas biofilm producer isolates were associated with presence of the aap gene. The sdrF gene was also significantly more in the biofilm producer isolates from BSI. The SCCmec type IV and the ccr2 complex were related to BSI isolates (p < 0.05), while 83% of the nasal isolates were non-typeable for the SCCmec elements, with the mec complex and ccr undetectable as the most frequent profile. Conclusions Despite the great clonal diversity displayed by S. epidermidis isolates from neonates, BSI isolates harbored more frequently the sdrF and sesI adhesin genes, while nasal isolates were very variable in SCCmec composition. These aspects could be advantageous to improve colonization in the host increasing its pathogenicity.
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Affiliation(s)
- Vivian Carolina Salgueiro
- Departamento de Microbiologia Médica, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Av Carlos Chagas Filho, no 373, CCS, Bloco I, Sala 010, Cidade Universitária, Rio de Janeiro, Brazil
| | - Natalia Lopes Pontes Iorio
- Departamento de Ciências Básicas, Universidade Federal Fluminense, R. Dr. Silvio Henrique Braune, no 22, Nova Friburgo, Rio de Janeiro, Brazil
| | - Marcelle Cristina Ferreira
- Departamento de Microbiologia Médica, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Av Carlos Chagas Filho, no 373, CCS, Bloco I, Sala 010, Cidade Universitária, Rio de Janeiro, Brazil
| | - Raiane Cardoso Chamon
- Departamento de Microbiologia Médica, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Av Carlos Chagas Filho, no 373, CCS, Bloco I, Sala 010, Cidade Universitária, Rio de Janeiro, Brazil
| | - Kátia Regina Netto Dos Santos
- Departamento de Microbiologia Médica, Instituto de Microbiologia Paulo de Góes, Universidade Federal do Rio de Janeiro, Av Carlos Chagas Filho, no 373, CCS, Bloco I, Sala 010, Cidade Universitária, Rio de Janeiro, Brazil.
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128
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Oh J, Byrd AL, Park M, Kong HH, Segre JA. Temporal Stability of the Human Skin Microbiome. Cell 2017; 165:854-66. [PMID: 27153496 DOI: 10.1016/j.cell.2016.04.008] [Citation(s) in RCA: 597] [Impact Index Per Article: 85.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Revised: 01/21/2016] [Accepted: 03/31/2016] [Indexed: 12/16/2022]
Abstract
Biogeography and individuality shape the structural and functional composition of the human skin microbiome. To explore these factors' contribution to skin microbial community stability, we generated metagenomic sequence data from longitudinal samples collected over months and years. Analyzing these samples using a multi-kingdom, reference-based approach, we found that despite the skin's exposure to the external environment, its bacterial, fungal, and viral communities were largely stable over time. Site, individuality, and phylogeny were all determinants of stability. Foot sites exhibited the most variability; individuals differed in stability; and transience was a particular characteristic of eukaryotic viruses, which showed little site-specificity in colonization. Strain and single-nucleotide variant-level analysis showed that individuals maintain, rather than reacquire, prevalent microbes from the environment. Longitudinal stability of skin microbial communities generates hypotheses about colonization resistance and empowers clinical studies exploring alterations observed in disease states.
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Affiliation(s)
- Julia Oh
- Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA
| | - Allyson L Byrd
- Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA; Department of Bioinformatics, Boston University, Boston, MA 02215, USA
| | - Morgan Park
- NIH Intramural Sequencing Center, National Human Genome Research Institute, Bethesda, MD 20892, USA
| | | | - Heidi H Kong
- Dermatology Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA.
| | - Julia A Segre
- Translational and Functional Genomics Branch, National Human Genome Research Institute, NIH, Bethesda, MD 20892, USA.
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Lee JYH, Monk IR, Pidot SJ, Singh S, Chua KYL, Seemann T, Stinear TP, Howden BP. Functional analysis of the first complete genome sequence of a multidrug resistant sequence type 2 Staphylococcus epidermidis. Microb Genom 2016; 2:e000077. [PMID: 28785416 PMCID: PMC5537629 DOI: 10.1099/mgen.0.000077] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 07/05/2016] [Indexed: 12/31/2022] Open
Abstract
Staphylococcus epidermidis is a significant opportunistic pathogen of humans. The ST2 lineage is frequently multidrug-resistant and accounts for most of the clinical disease worldwide. However, there are no publically available, closed ST2 genomes and pathogenesis studies have not focused on these strains. We report the complete genome and methylome of BPH0662, a multidrug-resistant, hospital-adapted, ST2 S. epidermidis, and describe the correlation between resistome and phenotype, as well as demonstrate its relationship to publically available, international ST2 isolates. Furthermore, we delineate the methylome determined by the two type I restriction modification systems present in BPH0662 through heterologous expression in Escherichia coli, allowing the assignment of each system to its corresponding target recognition motif. As the first, to our knowledge, complete ST2 S. epidermidis genome, BPH0662 provides a valuable reference for future genomic studies of this clinically relevant lineage. Defining the methylome and the construction of these E. coli hosts provides the foundation for the development of molecular tools to bypass restriction modification systems in this lineage that has hitherto proven intractable.
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Affiliation(s)
- Jean Y. H. Lee
- Department of Microbiology & Immunology at The Doherty Institute for Infection & Immunity, University of Melbourne, Melbourne, Australia
| | - Ian R. Monk
- Department of Microbiology & Immunology at The Doherty Institute for Infection & Immunity, University of Melbourne, Melbourne, Australia
| | - Sacha J. Pidot
- Department of Microbiology & Immunology at The Doherty Institute for Infection & Immunity, University of Melbourne, Melbourne, Australia
| | | | - Kyra Y. L. Chua
- Microbiology Department, Austin Health, Melbourne, Australia
| | - Torsten Seemann
- Doherty Applied Microbial Genomics, Department of Microbiology & Immunology at The Doherty Institute for Infection & Immunity, University of Melbourne, Melbourne, Australia
- Victorian Life Sciences Computation Inititative, University of Melbourne, Melbourne, Victoria, Australia
| | - Timothy P. Stinear
- Department of Microbiology & Immunology at The Doherty Institute for Infection & Immunity, University of Melbourne, Melbourne, Australia
- Doherty Applied Microbial Genomics, Department of Microbiology & Immunology at The Doherty Institute for Infection & Immunity, University of Melbourne, Melbourne, Australia
| | - Benjamin P. Howden
- Doherty Applied Microbial Genomics, Department of Microbiology & Immunology at The Doherty Institute for Infection & Immunity, University of Melbourne, Melbourne, Australia
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology & Immunology at The Doherty Institute for Infection & Immunity, University of Melbourne, Melbourne, Australia
- Infectious Diseases Department, Austin Health, Melbourne, Australia
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130
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Chng KR, Tay ASL, Li C, Ng AHQ, Wang J, Suri BK, Matta SA, McGovern N, Janela B, Wong XFCC, Sio YY, Au BV, Wilm A, De Sessions PF, Lim TC, Tang MBY, Ginhoux F, Connolly JE, Lane EB, Chew FT, Common JEA, Nagarajan N. Whole metagenome profiling reveals skin microbiome-dependent susceptibility to atopic dermatitis flare. Nat Microbiol 2016; 1:16106. [PMID: 27562258 DOI: 10.1038/nmicrobiol.2016.106] [Citation(s) in RCA: 236] [Impact Index Per Article: 29.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2015] [Accepted: 06/01/2016] [Indexed: 12/19/2022]
Abstract
Whole metagenome analysis has the potential to reveal functional triggers of skin diseases, but issues of cost, robustness and sampling efficacy have limited its application. Here, we have established an alternative, clinically practical and robust metagenomic analysis protocol and applied it to 80 skin microbiome samples epidemiologically stratified for atopic dermatitis (AD). We have identified distinct non-flare, baseline skin microbiome signatures enriched for Streptococcus and Gemella but depleted for Dermacoccus in AD-prone versus normal healthy skin. Bacterial challenge assays using keratinocytes and monocyte-derived dendritic cells established distinct IL-1-mediated, innate and Th1-mediated adaptive immune responses with Staphylococcus aureus and Staphylococcus epidermidis. Bacterial differences were complemented by perturbations in the eukaryotic community and functional shifts in the microbiome-wide gene repertoire, which could exacerbate a dry and alkaline phenotype primed for pathogen growth and inflammation in AD-susceptible skin. These findings provide insights into how the skin microbial community, skin surface microenvironment and immune system cross-modulate each other, escalating the destructive feedback cycle between them that leads to AD flare.
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Affiliation(s)
- Kern Rei Chng
- Genome Institute of Singapore, Singapore 138672, Singapore
| | | | - Chenhao Li
- Genome Institute of Singapore, Singapore 138672, Singapore
| | | | - Jingjing Wang
- Institute of Molecular and Cell Biology, Singapore 138673, Singapore.,Department of Neurology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan 450001, China.,Institute of Biomedical Studies, Baylor University, Waco, Texas 76798, USA
| | - Bani Kaur Suri
- Department of Biological Sciences, National University of Singapore, Singapore 117543
| | - Sri Anusha Matta
- Department of Biological Sciences, National University of Singapore, Singapore 117543
| | - Naomi McGovern
- Singapore Immunology Network, Singapore 138648, Singapore
| | | | | | - Yang Yie Sio
- Department of Biological Sciences, National University of Singapore, Singapore 117543
| | - Bijin Veonice Au
- Institute of Molecular and Cell Biology, Singapore 138673, Singapore
| | - Andreas Wilm
- Genome Institute of Singapore, Singapore 138672, Singapore
| | | | - Thiam Chye Lim
- Division of Plastic, Reconstructive &Aesthetic Surgery, National University Health System, Singapore 119074, Singapore
| | | | | | - John E Connolly
- Institute of Molecular and Cell Biology, Singapore 138673, Singapore.,Institute of Biomedical Studies, Baylor University, Waco, Texas 76798, USA.,Department of Microbiology and Immunology, National University of Singapore, Singapore 117545, Singapore
| | | | - Fook Tim Chew
- Department of Biological Sciences, National University of Singapore, Singapore 117543
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Susceptibility to chlorhexidine amongst multidrug-resistant clinical isolates of Staphylococcus epidermidis from bloodstream infections. Int J Antimicrob Agents 2016; 48:86-90. [DOI: 10.1016/j.ijantimicag.2016.04.015] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2015] [Revised: 04/06/2016] [Accepted: 04/16/2016] [Indexed: 11/18/2022]
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132
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Tolo I, Thomas JC, Fischer RSB, Brown EL, Gray BM, Robinson DA. Do Staphylococcus epidermidis Genetic Clusters Predict Isolation Sources? J Clin Microbiol 2016; 54:1711-1719. [PMID: 27076664 PMCID: PMC4922092 DOI: 10.1128/jcm.03345-15] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 04/07/2016] [Indexed: 12/24/2022] Open
Abstract
Staphylococcus epidermidis is a ubiquitous colonizer of human skin and a common cause of medical device-associated infections. The extent to which the population genetic structure of S. epidermidis distinguishes commensal from pathogenic isolates is unclear. Previously, Bayesian clustering of 437 multilocus sequence types (STs) in the international database revealed a population structure of six genetic clusters (GCs) that may reflect the species' ecology. Here, we first verified the presence of six GCs, including two (GC3 and GC5) with significant admixture, in an updated database of 578 STs. Next, a single nucleotide polymorphism (SNP) assay was developed that accurately assigned 545 (94%) of 578 STs to GCs. Finally, the hypothesis that GCs could distinguish isolation sources was tested by SNP typing and GC assignment of 154 isolates from hospital patients with bacteremia and those with blood culture contaminants and from nonhospital carriage. GC5 was isolated almost exclusively from hospital sources. GC1 and GC6 were isolated from all sources but were overrepresented in isolates from nonhospital and infection sources, respectively. GC2, GC3, and GC4 were relatively rare in this collection. No association was detected between fdh-positive isolates (GC2 and GC4) and nonhospital sources. Using a machine learning algorithm, GCs predicted hospital and nonhospital sources with 80% accuracy and predicted infection and contaminant sources with 45% accuracy, which was comparable to the results seen with a combination of five genetic markers (icaA, IS256, sesD [bhp], mecA, and arginine catabolic mobile element [ACME]). Thus, analysis of population structure with subgenomic data shows the distinction of hospital and nonhospital sources and the near-inseparability of sources within a hospital.
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Affiliation(s)
- Isaiah Tolo
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, Mississippi, USA
| | | | - Rebecca S B Fischer
- Center for Infectious Disease, University of Texas Health Science Center, Houston, Texas, USA
| | - Eric L Brown
- Center for Infectious Disease, University of Texas Health Science Center, Houston, Texas, USA
| | - Barry M Gray
- Department of Pediatrics, University of Illinois College of Medicine at Peoria, Peoria, Illinois, USA
| | - D Ashley Robinson
- Department of Microbiology and Immunology, University of Mississippi Medical Center, Jackson, Mississippi, USA
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134
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135
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Significance of Staphylococcus epidermidis in Health Care-Associated Infections, from Contaminant to Clinically Relevant Pathogen: This Is a Wake-Up Call! J Clin Microbiol 2016; 54:1679-1681. [PMID: 27170016 DOI: 10.1128/jcm.00743-16] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Coagulase-negative staphylococci, particularly Staphylococcus epidermidis, have been recognized as an important cause of health care-associated infections. Concurrently, S. epidermidis is a common contaminant in clinical cultures, which poses a diagnostic challenge. An article in this issue of Journal of Clinical Microbiology (I. Tolo, J. C. Thomas, R. S. B. Fischer, E. L. Brown, B. M. Gray, and D. A. Robinson, J Clin Microbiol 54:1711-1719, 2015, http://dx.doi.org/10.1128/JCM.03345-15) describes a rapid single nucleotide polymorphism-based assay for distinguishing between S. epidermidis isolates from hospital and nonhospital sources, which represents an important contribution to the characterization and understanding of S. epidermidis health care-associated infections.
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136
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Christensen GJM, Scholz CFP, Enghild J, Rohde H, Kilian M, Thürmer A, Brzuszkiewicz E, Lomholt HB, Brüggemann H. Antagonism between Staphylococcus epidermidis and Propionibacterium acnes and its genomic basis. BMC Genomics 2016; 17:152. [PMID: 26924200 PMCID: PMC4770681 DOI: 10.1186/s12864-016-2489-5] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2015] [Accepted: 02/17/2016] [Indexed: 01/09/2023] Open
Abstract
Background Propionibacterium acnes and Staphylococcus epidermidis live in close proximity on human skin, and both bacterial species can be isolated from normal and acne vulgaris-affected skin sites. The antagonistic interactions between the two species are poorly understood, as well as the potential significance of bacterial interferences for the skin microbiota. Here, we performed simultaneous antagonism assays to detect inhibitory activities between multiple isolates of the two species. Selected strains were sequenced to identify the genomic basis of their antimicrobial phenotypes. Results First, we screened 77 P. acnes strains isolated from healthy and acne-affected skin, and representing all known phylogenetic clades (I, II, and III), for their antimicrobial activities against 12 S. epidermidis isolates. One particular phylogroup (I-2) exhibited a higher antimicrobial activity than other P. acnes phylogroups. All genomes of type I-2 strains carry an island encoding the biosynthesis of a thiopeptide with possible antimicrobial activity against S. epidermidis. Second, 20 S. epidermidis isolates were examined for inhibitory activity against 25 P. acnes strains. The majority of S. epidermidis strains were able to inhibit P. acnes. Genomes of S. epidermidis strains with strong, medium and no inhibitory activities against P. acnes were sequenced. Genome comparison underlined the diversity of S. epidermidis and detected multiple clade- or strain-specific mobile genetic elements encoding a variety of functions important in antibiotic and stress resistance, biofilm formation and interbacterial competition, including bacteriocins such as epidermin. One isolate with an extraordinary antimicrobial activity against P. acnes harbors a functional ESAT-6 secretion system that might be involved in the antimicrobial activity against P. acnes via the secretion of polymorphic toxins. Conclusions Taken together, our study suggests that interspecies interactions could potentially jeopardize balances in the skin microbiota. In particular, S. epidermidis strains possess an arsenal of different mechanisms to inhibit P. acnes. However, if such interactions are relevant in skin disorders such as acne vulgaris remains questionable, since no difference in the antimicrobial activity against, or the sensitivity towards S. epidermidis could be detected between health- and acne-associated strains of P. acnes. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-2489-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | - Jan Enghild
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus, Denmark.
| | - Holger Rohde
- Institute of Medical Microbiology, University Hospital Hamburg-Eppendorf, Hamburg, Germany.
| | - Mogens Kilian
- Department of Biomedicine, Aarhus University, Aarhus, Denmark.
| | - Andrea Thürmer
- Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, Georg-August University Göttingen, Göttingen, Germany.
| | - Elzbieta Brzuszkiewicz
- Department of Genomic and Applied Microbiology, Institute of Microbiology and Genetics, Georg-August University Göttingen, Göttingen, Germany.
| | - Hans B Lomholt
- Department of Biomedicine, Aarhus University, Aarhus, Denmark.
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Chaudhry V, Patil PB. Genomic investigation reveals evolution and lifestyle adaptation of endophytic Staphylococcus epidermidis. Sci Rep 2016; 6:19263. [PMID: 26758912 PMCID: PMC4713051 DOI: 10.1038/srep19263] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Accepted: 12/10/2015] [Indexed: 12/12/2022] Open
Abstract
Staphylococcus epidermidis is a major human associated bacterium and also an emerging nosocomial pathogen. There are reports of its association to rodents, sheep and plants. However, comparative and evolutionary studies of ecologically diverse strains of S. epidermidis are lacking. Here, we report the whole genome sequences of four S. epidermidis strains isolated from surface sterilized rice seeds along with genome sequence of type strain. Phylogenomic analysis of rice endophytic S. epidermidis (RESE) with “type strain” unequivocally established their species identity. Whole genome based tree of 93 strains of S. epidermidis revealed RESE as distinct sub-lineage which is more related to rodent sub-lineage than to majority of human lineage strains. Furthermore, comparative genomics revealed 20% variable gene-pool in S. epidermidis, suggesting that genomes of ecologically diverse strains are under flux. Interestingly, we were also able to map several genomic regions that are under flux and gave rise to RESE strains. The largest of these genomic regions encodes a cluster of genes unique to RESE that are known to be required for survival and stress tolerance, apart from those required for adaptation to plant habitat. The genomes and genes of RESE represent distinct ecological resource/sequences and provided first evolutionary insights into adaptation of S. epidermidis to plants.
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Affiliation(s)
- Vasvi Chaudhry
- CSIR- Institute of Microbial Technology, Sector 39A, Chandigarh-160036 (India)
| | - Prabhu B Patil
- CSIR- Institute of Microbial Technology, Sector 39A, Chandigarh-160036 (India)
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138
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Arora S, Uhlemann AC, Lowy FD, Hook M. A Novel MSCRAMM Subfamily in Coagulase Negative Staphylococcal Species. Front Microbiol 2016; 7:540. [PMID: 27199900 PMCID: PMC4850167 DOI: 10.3389/fmicb.2016.00540] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 04/01/2016] [Indexed: 12/14/2022] Open
Abstract
Coagulase negative staphylococci (CoNS) are important opportunistic pathogens. Staphylococcus epidermidis, a coagulase negative staphylococcus, is the third leading cause of nosocomial infections in the US. Surface proteins like Microbial Surface Components Recognizing Adhesive Matrix Molecules (MSCRAMMs) are major virulence factors of pathogenic gram positive bacteria. Here, we identified a new chimeric protein in S. epidermidis, that we call SesJ. SesJ represents a prototype of a new subfamily of MSCRAMMs. Structural predictions show that SesJ has structural features characteristic of a MSCRAMM along with a N-terminal repeat region and an aspartic acid containing C-terminal repeat region, features that have not been previously observed in staphylococcal MSCRAMMs but have been found in other surface proteins from gram positive bacteria. We identified and analyzed structural homologs of SesJ in three other CoNS. These homologs of SesJ have an identical structural organization but varying sequence identities within the domains. Using flow cytometry, we also show that SesJ is expressed constitutively on the surface of a representative S. epidermidis strain, from early exponential to stationary growth phase. Thus, SesJ is positioned to interact with protein targets in the environment and plays a role in S. epidermidis virulence.
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Affiliation(s)
- Srishtee Arora
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M University Health Science Center, HoustonTX, USA
| | - Anne-Catrin Uhlemann
- Division of Infectious Diseases, Department of Medicine, College of Physicians and Surgeons, Columbia University in the City of New York, New YorkNY, USA
| | - Franklin D. Lowy
- Division of Infectious Diseases, Department of Medicine, College of Physicians and Surgeons, Columbia University in the City of New York, New YorkNY, USA
| | - Magnus Hook
- Center for Infectious and Inflammatory Diseases, Institute of Biosciences and Technology, Texas A&M University Health Science Center, HoustonTX, USA
- *Correspondence: Magnus Hook,
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139
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Watanabe K, Nakaminami H, Azuma C, Tanaka I, Nakase K, Matsunaga N, Okuyama K, Yamada K, Utsumi K, Fujii T, Noguchi N. Methicillin-Resistant Staphylococcus epidermidis Is Part of the Skin Flora on the Hands of Both Healthy Individuals and Hospital Workers. Biol Pharm Bull 2016; 39:1868-1875. [DOI: 10.1248/bpb.b16-00528] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
| | - Hidemasa Nakaminami
- Department of Microbiology, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences
| | - Chihiro Azuma
- Department of Microbiology, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences
| | - Ippei Tanaka
- Department of Microbiology, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences
| | - Keisuke Nakase
- Department of Microbiology, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences
| | - Norifumi Matsunaga
- Department of Pharmacy, Tokyo Medical University Hachioji Medical Center
| | - Kiyoshi Okuyama
- Department of Pharmacy, Tokyo Medical University Hachioji Medical Center
| | - Kanako Yamada
- Department of Infectious Diseases, Tokyo Medical University Hachioji Medical Center
| | - Kenta Utsumi
- Department of Respiratory Medicine, Tokyo Medical University Hachioji Medical Center
| | - Takeshi Fujii
- Department of Infectious Diseases, Tokyo Medical University Hachioji Medical Center
| | - Norihisa Noguchi
- Department of Microbiology, School of Pharmacy, Tokyo University of Pharmacy and Life Sciences
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140
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Kleinschmidt S, Huygens F, Faoagali J, Rathnayake IU, Hafner LM. Staphylococcus epidermidis as a cause of bacteremia. Future Microbiol 2015; 10:1859-79. [DOI: 10.2217/fmb.15.98] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Staphylococcus epidermidis is a biofilm-producing commensal organism found ubiquitously on human skin and mucous membranes, as well as on animals and in the environment. Biofilm formation enables this organism to evade the host immune system. Colonization of percutaneous devices or implanted medical devices allows bacteria access to the bloodstream. Isolation of this organism from blood cultures may represent either contamination during the blood collection procedure or true bacteremia. S. epidermidis bloodstream infections may be indolent compared with other bacteria. Isolation of S. epidermidis from a blood culture may present a management quandary for clinicians. Over-treatment may lead to patient harm and increases in healthcare costs. There are numerous reports indicating the difficulty of predicting clinical infection in patients with positive blood cultures with this organism. No reliable phenotypic or genotypic algorithms currently exist to predict the pathogenicity of a S. epidermidis bloodstream infection. This review will discuss the latest advances in identification methods, global population structure, pathogenicity, biofilm formation, antimicrobial resistance and clinical significance of the detection of S. epidermidis in blood cultures. Previous studies that have attempted to discriminate between invasive and contaminating strains of S. epidermidis in blood cultures will be analyzed.
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Affiliation(s)
- Sharon Kleinschmidt
- School of Biomedical Sciences, Institute of Health & Biomedical Innovation, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
- Microbiology Department, Pathology Queensland, Princess Alexandra Hospital, Woolloongabba, QLD, Australia
| | - Flavia Huygens
- School of Biomedical Sciences, Institute of Health & Biomedical Innovation, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
| | - Joan Faoagali
- School of Biomedical Sciences, Institute of Health & Biomedical Innovation, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
| | - Irani U Rathnayake
- School of Biomedical Sciences, Institute of Health & Biomedical Innovation, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
| | - Louise M Hafner
- School of Biomedical Sciences, Institute of Health & Biomedical Innovation, Faculty of Health, Queensland University of Technology, Brisbane, QLD, Australia
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Flores-Páez LA, Zenteno JC, Alcántar-Curiel MD, Vargas-Mendoza CF, Rodríguez-Martínez S, Cancino-Diaz ME, Jan-Roblero J, Cancino-Diaz JC. Molecular and Phenotypic Characterization of Staphylococcus epidermidis Isolates from Healthy Conjunctiva and a Comparative Analysis with Isolates from Ocular Infection. PLoS One 2015; 10:e0135964. [PMID: 26275056 PMCID: PMC4537226 DOI: 10.1371/journal.pone.0135964] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2015] [Accepted: 07/29/2015] [Indexed: 11/26/2022] Open
Abstract
Staphylococcus epidermidis is a common commensal of healthy conjunctiva and it can cause endophthalmitis, however its presence in conjunctivitis, keratitis and blepharitis is unknown. Molecular genotyping of S. epidermidis from healthy conjunctiva could provide information about the origin of the strains that infect the eye. In this paper two collections of S. epidermidis were used: one from ocular infection (n = 62), and another from healthy conjunctiva (n = 45). All isolates were genotyped by pulsed field gel electrophoresis (PFGE), multilocus sequence typing (MLST), staphylococcal cassette chromosome mec (SCCmec), detection of the genes icaA, icaD, IS256 and polymorphism type of agr locus. The phenotypic data included biofilm production and antibiotic resistance. The results displayed 61 PFGE types from 107 isolates and they were highly discriminatory. MLST analysis generated a total of 25 STs, of which 11 STs were distributed among the ocular infection isolates and lineage ST2 was the most frequent (48.4%), while 14 STs were present in the healthy conjunctiva isolates and lineage ST5 was the most abundant (24.4%). By means of a principal coordinates analysis (PCoA) and a discriminant analysis (DA) it was found that ocular infection isolates had as discriminant markers agr III or agr II, SCCmec V or SCCmec I, mecA gene, resistance to tobramycin, positive biofilm, and IS256+. In contrast to the healthy conjunctiva isolates, the discriminating markers were agr I, and resistance to chloramphenicol, ciprofloxacin, gatifloxacin and oxacillin. The discriminant biomarkers of ocular infection were examined in healthy conjunctiva isolates, and it was found that 3 healthy conjunctiva isolates [two with ST2 and another with ST9] (3/45, 6.66%) had similar genotypic and phenotypic characteristics to ocular infection isolates, therefore a small population from healthy conjunctiva could cause an ocular infection. These data suggest that the healthy conjunctiva isolates do not, in almost all cases, infect the eye due to their large genotypic and phenotypic difference with the ocular infection isolates.
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Affiliation(s)
- Luis A. Flores-Páez
- Department of Microbiology, Escuela Nacional de Ciencias Biológicas-Instituto Politécnico Nacional, Mexico City, Mexico
| | - Juan C. Zenteno
- Instituto de Oftalmología Fundación Conde de Valenciana, Mexico City, Mexico
| | | | - Carlos F. Vargas-Mendoza
- Department of Zoology, Escuela Nacional de Ciencias Biológicas-Instituto Politécnico Nacional, Mexico City, Mexico
| | - Sandra Rodríguez-Martínez
- Department of Immunology, Escuela Nacional de Ciencias Biológicas-Instituto Politécnico Nacional, Mexico City, Mexico
| | - Mario E. Cancino-Diaz
- Department of Immunology, Escuela Nacional de Ciencias Biológicas-Instituto Politécnico Nacional, Mexico City, Mexico
| | - Janet Jan-Roblero
- Department of Microbiology, Escuela Nacional de Ciencias Biológicas-Instituto Politécnico Nacional, Mexico City, Mexico
| | - Juan C. Cancino-Diaz
- Department of Microbiology, Escuela Nacional de Ciencias Biológicas-Instituto Politécnico Nacional, Mexico City, Mexico
- * E-mail:
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142
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Roach DJ, Burton JN, Lee C, Stackhouse B, Butler-Wu SM, Cookson BT, Shendure J, Salipante SJ. A Year of Infection in the Intensive Care Unit: Prospective Whole Genome Sequencing of Bacterial Clinical Isolates Reveals Cryptic Transmissions and Novel Microbiota. PLoS Genet 2015; 11:e1005413. [PMID: 26230489 PMCID: PMC4521703 DOI: 10.1371/journal.pgen.1005413] [Citation(s) in RCA: 135] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 07/02/2015] [Indexed: 01/05/2023] Open
Abstract
Bacterial whole genome sequencing holds promise as a disruptive technology in clinical microbiology, but it has not yet been applied systematically or comprehensively within a clinical context. Here, over the course of one year, we performed prospective collection and whole genome sequencing of nearly all bacterial isolates obtained from a tertiary care hospital's intensive care units (ICUs). This unbiased collection of 1,229 bacterial genomes from 391 patients enables detailed exploration of several features of clinical pathogens. A sizable fraction of isolates identified as clinically relevant corresponded to previously undescribed species: 12% of isolates assigned a species-level classification by conventional methods actually qualified as distinct, novel genomospecies on the basis of genomic similarity. Pan-genome analysis of the most frequently encountered pathogens in the collection revealed substantial variation in pan-genome size (1,420 to 20,432 genes) and the rate of gene discovery (1 to 152 genes per isolate sequenced). Surprisingly, although potential nosocomial transmission of actively surveilled pathogens was rare, 8.7% of isolates belonged to genomically related clonal lineages that were present among multiple patients, usually with overlapping hospital admissions, and were associated with clinically significant infection in 62% of patients from which they were recovered. Multi-patient clonal lineages were particularly evident in the neonatal care unit, where seven separate Staphylococcus epidermidis clonal lineages were identified, including one lineage associated with bacteremia in 5/9 neonates. Our study highlights key differences in the information made available by conventional microbiological practices versus whole genome sequencing, and motivates the further integration of microbial genome sequencing into routine clinical care.
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Affiliation(s)
- David J. Roach
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Joshua N. Burton
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Choli Lee
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Bethany Stackhouse
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Susan M. Butler-Wu
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, United States of America
| | - Brad T. Cookson
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, United States of America
- Department of Microbiology, University of Washington, Seattle, Washington, United States of America
| | - Jay Shendure
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
| | - Stephen J. Salipante
- Department of Genome Sciences, University of Washington, Seattle, Washington, United States of America
- Department of Laboratory Medicine, University of Washington, Seattle, Washington, United States of America
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143
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Rouli L, Merhej V, Fournier PE, Raoult D. The bacterial pangenome as a new tool for analysing pathogenic bacteria. New Microbes New Infect 2015; 7:72-85. [PMID: 26442149 PMCID: PMC4552756 DOI: 10.1016/j.nmni.2015.06.005] [Citation(s) in RCA: 155] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2015] [Accepted: 06/16/2015] [Indexed: 01/18/2023] Open
Abstract
The bacterial pangenome was introduced in 2005 and, in recent years, has been the subject of many studies. Thanks to progress in next-generation sequencing methods, the pangenome can be divided into two parts, the core (common to the studied strains) and the accessory genome, offering a large panel of uses. In this review, we have presented the analysis methods, the pangenome composition and its application as a study of lifestyle. We have also shown that the pangenome may be used as a new tool for redefining the pathogenic species. We applied this to the Escherichia coli and Shigella species, which have been a subject of controversy regarding their taxonomic and pathogenic position. Pangenome is a new way of studying pathogenic bacteria. Pangenome can be used as a taxonomic tool. This review describes pangenome in the world of pathogenic bacteria.
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Affiliation(s)
- L Rouli
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095, 13005 Marseille, France
| | - V Merhej
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095, 13005 Marseille, France
| | - P-E Fournier
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095, 13005 Marseille, France
| | - D Raoult
- Aix Marseille Université, URMITE, UM63, CNRS 7278, IRD 198, Inserm 1095, 13005 Marseille, France
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144
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Inter-individual differences in the gene content of human gut bacterial species. Genome Biol 2015; 16:82. [PMID: 25896518 PMCID: PMC4428241 DOI: 10.1186/s13059-015-0646-9] [Citation(s) in RCA: 116] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2014] [Accepted: 04/01/2015] [Indexed: 01/15/2023] Open
Abstract
BACKGROUND Gene content differences in human gut microbes can lead to inter-individual phenotypic variations such as digestive capacity. It is unclear whether gene content variation is caused by differences in microbial species composition or by the presence of different strains of the same species; the extent of gene content variation in the latter is unknown. Unlike pan-genome studies of cultivable strains, the use of metagenomic data can provide an unbiased view of structural variation of gut bacterial strains by measuring them in their natural habitats, the gut of each individual in this case, representing native boundaries between gut bacterial populations. We analyzed publicly available metagenomic data from fecal samples to characterize inter-individual variation in gut bacterial species. RESULTS A comparison of 11 abundant gut bacterial species showed that the gene content of strains from the same species differed, on average, by 13% between individuals. This number is based on gene deletions only and represents a lower limit, yet the variation is already in a similar range as observed between completely sequenced strains of cultivable species. We show that accessory genes that differ considerably between individuals can encode important functions, such as polysaccharide utilization and capsular polysaccharide synthesis loci. CONCLUSION Metagenomics can yield insights into gene content variation of strains in complex communities, which cannot be predicted by phylogenetic marker genes alone. The large degree of inter-individual variability in gene content implies that strain resolution must be considered in order to fully assess the functional potential of an individual's human gut microbiome.
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145
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Méric G, Miragaia M, de Been M, Yahara K, Pascoe B, Mageiros L, Mikhail J, Harris LG, Wilkinson TS, Rolo J, Lamble S, Bray JE, Jolley KA, Hanage WP, Bowden R, Maiden MCJ, Mack D, de Lencastre H, Feil EJ, Corander J, Sheppard SK. Ecological Overlap and Horizontal Gene Transfer in Staphylococcus aureus and Staphylococcus epidermidis. Genome Biol Evol 2015; 7:1313-28. [PMID: 25888688 PMCID: PMC4453061 DOI: 10.1093/gbe/evv066] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The opportunistic pathogens Staphylococcus aureus and Staphylococcus epidermidis represent major causes of severe nosocomial infection, and are associated with high levels of mortality and morbidity worldwide. These species are both common commensals on the human skin and in the nasal pharynx, but are genetically distinct, differing at 24% average nucleotide divergence in 1,478 core genes. To better understand the genome dynamics of these ecologically similar staphylococcal species, we carried out a comparative analysis of 324 S. aureus and S. epidermidis genomes, including 83 novel S. epidermidis sequences. A reference pan-genome approach and whole genome multilocus-sequence typing revealed that around half of the genome was shared between the species. Based on a BratNextGen analysis, homologous recombination was found to have impacted on 40% of the core genes in S. epidermidis, but on only 24% of the core genes in S. aureus. Homologous recombination between the species is rare, with a maximum of nine gene alleles shared between any two S. epidermidis and S. aureus isolates. In contrast, there was considerable interspecies admixture of mobile elements, in particular genes associated with the SaPIn1 pathogenicity island, metal detoxification, and the methicillin-resistance island SCCmec. Our data and analysis provide a context for considering the nature of recombinational boundaries between S. aureus and S. epidermidis and, the selective forces that influence realized recombination between these species.
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Affiliation(s)
- Guillaume Méric
- College of Medicine, Institute of Life Science, Swansea University, United Kingdom
| | - Maria Miragaia
- Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica António Xavier (ITQB), Universidade Nova de Lisboa, Oeiras, Portugal Laboratory of Bacterial Evolution and Molecular Epidemiology, Instituto de Tecnologia Química e Biológica António Xavier (ITQB), Universidade Nova de Lisboa, Oeiras, Portugal
| | - Mark de Been
- Department of Medical Microbiology, University Medical Center Utrecht, The Netherlands
| | - Koji Yahara
- College of Medicine, Institute of Life Science, Swansea University, United Kingdom The Biostatistics Center, Kurume University, Fukuoka, Japan
| | - Ben Pascoe
- College of Medicine, Institute of Life Science, Swansea University, United Kingdom MRC CLIMB Consortium, Institute of Life Science, Swansea University, United Kingdom
| | - Leonardos Mageiros
- College of Medicine, Institute of Life Science, Swansea University, United Kingdom
| | - Jane Mikhail
- College of Medicine, Institute of Life Science, Swansea University, United Kingdom
| | - Llinos G Harris
- College of Medicine, Institute of Life Science, Swansea University, United Kingdom
| | - Thomas S Wilkinson
- College of Medicine, Institute of Life Science, Swansea University, United Kingdom
| | - Joana Rolo
- Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica António Xavier (ITQB), Universidade Nova de Lisboa, Oeiras, Portugal Laboratory of Bacterial Evolution and Molecular Epidemiology, Instituto de Tecnologia Química e Biológica António Xavier (ITQB), Universidade Nova de Lisboa, Oeiras, Portugal
| | - Sarah Lamble
- Wellcome Trust Centre for Human Genetics, University of Oxford, United Kingdom
| | - James E Bray
- Department of Zoology, University of Oxford, United Kingdom
| | - Keith A Jolley
- Department of Zoology, University of Oxford, United Kingdom
| | - William P Hanage
- Center for Communicable Disease Dynamics, Harvard School of Public Health
| | - Rory Bowden
- Wellcome Trust Centre for Human Genetics, University of Oxford, United Kingdom
| | | | - Dietrich Mack
- College of Medicine, Institute of Life Science, Swansea University, United Kingdom College of Medicine, Institute of Life Science, Swansea University, United Kingdom
| | - Hermínia de Lencastre
- Laboratory of Molecular Genetics, Instituto de Tecnologia Química e Biológica António Xavier (ITQB), Universidade Nova de Lisboa, Oeiras, Portugal College of Medicine, Institute of Life Science, Swansea University, United Kingdom
| | - Edward J Feil
- College of Medicine, Institute of Life Science, Swansea University, United Kingdom
| | - Jukka Corander
- College of Medicine, Institute of Life Science, Swansea University, United Kingdom
| | - Samuel K Sheppard
- College of Medicine, Institute of Life Science, Swansea University, United Kingdom MRC CLIMB Consortium, Institute of Life Science, Swansea University, United Kingdom
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146
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Kadam A, Janto B, Eutsey R, Earl JP, Powell E, Dahlgren ME, Hu FZ, Ehrlich GD, Hiller NL. Streptococcus pneumoniae Supragenome Hybridization Arrays for Profiling of Genetic Content and Gene Expression. ACTA ACUST UNITED AC 2015; 36:9D.4.1-9D.4.20. [PMID: 25641101 DOI: 10.1002/9780471729259.mc09d04s36] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
There is extensive genomic diversity among Streptococcus pneumoniae isolates. Approximately half of the comprehensive set of genes in the species (the supragenome or pangenome) is present in all the isolates (core set), and the remaining is unevenly distributed among strains (distributed set). The Streptococcus pneumoniae Supragenome Hybridization (SpSGH) array provides coverage for an extensive set of genes and polymorphisms encountered within this species, capturing this genomic diversity. Further, the capture is quantitative. In this manner, the SpSGH array allows for both genomic and transcriptomic analyses of diverse S. pneumoniae isolates on a single platform. In this unit, we present the SpSGH array, and describe in detail its design and implementation for both genomic and transcriptomic analyses. The methodology can be applied to construction and modification of SpSGH array platforms, as well to other bacterial species as long as multiple whole-genome sequences are available that collectively capture the vast majority of the species supragenome.
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Affiliation(s)
- Anagha Kadam
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania
| | - Benjamin Janto
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania
| | - Rory Eutsey
- Center of Excellence in Biofilm Research, Allegheny Health Network, Pittsburgh, Pennsylvania
| | - Joshua P Earl
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania
| | - Evan Powell
- Center of Excellence in Biofilm Research, Allegheny Health Network, Pittsburgh, Pennsylvania
| | - Margaret E Dahlgren
- Center of Excellence in Biofilm Research, Allegheny Health Network, Pittsburgh, Pennsylvania
| | - Fen Z Hu
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania
| | - Garth D Ehrlich
- Department of Microbiology and Immunology, Drexel University College of Medicine, Philadelphia, Pennsylvania
| | - N Luisa Hiller
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh, Pennsylvania.,Center of Excellence in Biofilm Research, Allegheny Health Network, Pittsburgh, Pennsylvania
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147
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Naik S, Bouladoux N, Linehan JL, Han SJ, Harrison OJ, Wilhelm C, Conlan S, Himmelfarb S, Byrd AL, Deming C, Quinones M, Brenchley JM, Kong HH, Tussiwand R, Murphy KM, Merad M, Segre JA, Belkaid Y. Commensal-dendritic-cell interaction specifies a unique protective skin immune signature. Nature 2015; 520:104-8. [PMID: 25539086 DOI: 10.1038/nature14052] [Citation(s) in RCA: 550] [Impact Index Per Article: 61.1] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Accepted: 11/11/2014] [Indexed: 02/07/2023]
Abstract
The skin represents the primary interface between the host and the environment. This organ is also home to trillions of microorganisms that play an important role in tissue homeostasis and local immunity. Skin microbial communities are highly diverse and can be remodelled over time or in response to environmental challenges. How, in the context of this complexity, individual commensal microorganisms may differentially modulate skin immunity and the consequences of these responses for tissue physiology remains unclear. Here we show that defined commensals dominantly affect skin immunity and identify the cellular mediators involved in this specification. In particular, colonization with Staphylococcus epidermidis induces IL-17A(+) CD8(+) T cells that home to the epidermis, enhance innate barrier immunity and limit pathogen invasion. Commensal-specific T-cell responses result from the coordinated action of skin-resident dendritic cell subsets and are not associated with inflammation, revealing that tissue-resident cells are poised to sense and respond to alterations in microbial communities. This interaction may represent an evolutionary means by which the skin immune system uses fluctuating commensal signals to calibrate barrier immunity and provide heterologous protection against invasive pathogens. These findings reveal that the skin immune landscape is a highly dynamic environment that can be rapidly and specifically remodelled by encounters with defined commensals, findings that have profound implications for our understanding of tissue-specific immunity and pathologies.
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Affiliation(s)
- Shruti Naik
- 1] Immunity at Barrier Sites Initiative, National Institute of Allergy and Infectious Diseases, NIH, Bethesda 20892, USA [2] Mucosal Immunology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland 20892, USA
| | - Nicolas Bouladoux
- 1] Immunity at Barrier Sites Initiative, National Institute of Allergy and Infectious Diseases, NIH, Bethesda 20892, USA [2] Mucosal Immunology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland 20892, USA
| | - Jonathan L Linehan
- 1] Immunity at Barrier Sites Initiative, National Institute of Allergy and Infectious Diseases, NIH, Bethesda 20892, USA [2] Mucosal Immunology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland 20892, USA
| | - Seong-Ji Han
- 1] Immunity at Barrier Sites Initiative, National Institute of Allergy and Infectious Diseases, NIH, Bethesda 20892, USA [2] Mucosal Immunology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland 20892, USA
| | - Oliver J Harrison
- 1] Immunity at Barrier Sites Initiative, National Institute of Allergy and Infectious Diseases, NIH, Bethesda 20892, USA [2] Mucosal Immunology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland 20892, USA
| | - Christoph Wilhelm
- 1] Immunity at Barrier Sites Initiative, National Institute of Allergy and Infectious Diseases, NIH, Bethesda 20892, USA [2] Mucosal Immunology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland 20892, USA
| | - Sean Conlan
- Translational and Functional Genomics Branch, National Human Genome Research Institute, Bethesda, Maryland 20892, USA
| | - Sarah Himmelfarb
- 1] Immunity at Barrier Sites Initiative, National Institute of Allergy and Infectious Diseases, NIH, Bethesda 20892, USA [2] Mucosal Immunology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland 20892, USA
| | - Allyson L Byrd
- 1] Immunity at Barrier Sites Initiative, National Institute of Allergy and Infectious Diseases, NIH, Bethesda 20892, USA [2] Mucosal Immunology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland 20892, USA [3] Translational and Functional Genomics Branch, National Human Genome Research Institute, Bethesda, Maryland 20892, USA
| | - Clayton Deming
- Translational and Functional Genomics Branch, National Human Genome Research Institute, Bethesda, Maryland 20892, USA
| | - Mariam Quinones
- Bioinformatics and Computational Bioscience Branch, National Institute of Allergy and Infectious Diseases, NIH Bethesda, Maryland 20892, USA
| | - Jason M Brenchley
- 1] Immunity at Barrier Sites Initiative, National Institute of Allergy and Infectious Diseases, NIH, Bethesda 20892, USA [2] Immunopathogenesis Section, Laboratory of Molecular Microbiology, National Institute of Allergy and Infectious Diseases, NIH Bethesda, Maryland 20892, USA
| | - Heidi H Kong
- Dermatology Branch, National Cancer Institute, NIH Bethesda, Maryland 20892, USA
| | - Roxanne Tussiwand
- Howard Hughes Medical Institute, Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri 63110, USA
| | - Kenneth M Murphy
- Howard Hughes Medical Institute, Department of Pathology and Immunology, Washington University School of Medicine, St Louis, Missouri 63110, USA
| | - Miriam Merad
- Department of Oncological Sciences, Tisch Cancer Institute and Immunology Institute, Icahn School of Medicine at Mount Sinai, New York, New York 10029, USA
| | - Julia A Segre
- Translational and Functional Genomics Branch, National Human Genome Research Institute, Bethesda, Maryland 20892, USA
| | - Yasmine Belkaid
- 1] Immunity at Barrier Sites Initiative, National Institute of Allergy and Infectious Diseases, NIH, Bethesda 20892, USA [2] Mucosal Immunology Section, Laboratory of Parasitic Diseases, National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland 20892, USA
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149
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RNA sequencing provides evidence for functional variability between naturally co-existing Alteromonas macleodii lineages. BMC Genomics 2014; 15:938. [PMID: 25344729 PMCID: PMC4223743 DOI: 10.1186/1471-2164-15-938] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2014] [Accepted: 10/16/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Alteromonas macleodii is a ubiquitous gammaproteobacterium shown to play a biogeochemical role in marine environments. Two A. macleodii strains (AltDE and AltDE1) isolated from the same sample (i.e., the same place at the same time) show considerable genomic differences. In this study, we investigate the transcriptional response of these two strains to varying growth conditions in order to investigate differences in their ability to adapt to varying environmental parameters. RESULTS RNA sequencing revealed transcriptional changes between all growth conditions examined (e.g., temperature and medium) as well as differences between the two A. macleodii strains within a given condition. The main inter-strain differences were more marked in the adaptation to grow on minimal medium with glucose and, even more so, under starvation. These differences suggested that AltDE1 may have an advantage over AltDE when glucose is the major carbon source, and co-culture experiments confirmed this advantage. Additional differences were observed between the two strains in the expression of ncRNAs and phage-related genes, as well as motility. CONCLUSIONS This study shows that the genomic diversity observed in closely related strains of A. macleodii from a single environment result in different transcriptional responses to changing environmental parameters. This data provides additional support for the idea that greater diversity at the strain level of a microbial community could enhance the community's ability to adapt to environmental shifts.
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150
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Development and validation of an Haemophilus influenzae supragenome hybridization (SGH) array for transcriptomic analyses. PLoS One 2014; 9:e105493. [PMID: 25290153 PMCID: PMC4188559 DOI: 10.1371/journal.pone.0105493] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2013] [Accepted: 07/23/2014] [Indexed: 01/04/2023] Open
Abstract
We previously carried out the design and testing of a custom-built Haemophilus influenzae supragenome hybridization (SGH) array that contains probe sequences to 2,890 gene clusters identified by whole genome sequencing of 24 strains of H. influenzae. The array was originally designed as a tool to interrogate the gene content of large numbers of clinical isolates without the need for sequencing, however, the data obtained is quantitative and is thus suitable for transcriptomic analyses. In the current study RNA was extracted from H. influenzae strain CZ4126/02 (which was not included in the design of the array) converted to cDNA, and labelled and hybridized to the SGH arrays to assess the quality and reproducibility of data obtained from these custom-designed chips to serve as a tool for transcriptomics. Three types of experimental replicates were analyzed with all showing very high degrees of correlation, thus validating both the array and the methods used for RNA profiling. A custom filtering pipeline for two-condition unpaired data using five metrics was developed to minimize variability within replicates and to maximize the identification of the most significant true transcriptional differences between two samples. These methods can be extended to transcriptional analysis of other bacterial species utilizing supragenome-based arrays.
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