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Coates-Brown R, Moran JC, Pongchaikul P, Darby AC, Horsburgh MJ. Comparative Genomics of Staphylococcus Reveals Determinants of Speciation and Diversification of Antimicrobial Defense. Front Microbiol 2018; 9:2753. [PMID: 30510546 PMCID: PMC6252332 DOI: 10.3389/fmicb.2018.02753] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 10/29/2018] [Indexed: 11/18/2022] Open
Abstract
The bacterial genus Staphylococcus comprises diverse species with most being described as colonizers of human and animal skin. A relational analysis of features that discriminate its species and contribute to niche adaptation and survival remains to be fully described. In this study, an interspecies, whole-genome comparative analysis of 21 Staphylococcus species was performed based on their orthologues. Three well-defined multi-species groups were identified: group A (including aureus/epidermidis); group B (including saprophyticus/xylosus) and group C (including pseudintermedius/delphini). The machine learning algorithm Random Forest was applied to prioritize orthologs that drive formation of the Staphylococcus species groups A-C. Orthologues driving staphylococcal intrageneric diversity comprised regulatory, metabolic and antimicrobial resistance proteins. Notably, the BraSR (NsaRS) two-component system (TCS) and its associated BraDE transporters that regulate antimicrobial resistance showed limited distribution in the genus and their presence was most closely associated with a subset of Staphylococcus species dominated by those that colonize human skin. Divergence of BraSR and GraSR antimicrobial peptide survival TCS and their associated transporters was observed across the staphylococci, likely reflecting niche specific evolution of these TCS/transporters and their specificities for AMPs. Experimental evolution, with selection for resistance to the lantibiotic nisin, revealed multiple routes to resistance and differences in the selection outcomes of the BraSR-positive species S. hominis and S. aureus. Selection supported a role for GraSR in nisin survival responses of the BraSR-negative species S. saprophyticus. Our study reveals diversification of antimicrobial-sensing TCS across the staphylococci and hints at differential relationships between GraSR and BraSR in those species positive for both TCS.
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Affiliation(s)
| | | | | | | | - Malcolm J. Horsburgh
- Institute of Integrative Biology, University of Liverpool, Liverpool, United Kingdom
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Christo-Foroux E, Vallaeys T, Loux V, Dassa E, Deutscher J, Wandersman C, Livernois A, Hot C, Criscuolo A, Dauga C, Clermont D, Chesneau O. Manual and expert annotation of the nearly complete genome sequence of Staphylococcus sciuri strain ATCC 29059: A reference for the oxidase-positive staphylococci that supports the atypical phenotypic features of the species group. Syst Appl Microbiol 2017; 40:401-410. [PMID: 28890241 DOI: 10.1016/j.syapm.2017.07.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2017] [Revised: 06/30/2017] [Accepted: 07/03/2017] [Indexed: 11/30/2022]
Abstract
Staphylococcus sciuri is considered to be one of the most ancestral species in the natural history of the Staphylococcus genus that consists of 48 validly described species. It belongs to the basal group of oxidase-positive and novobiocin-resistant staphylococci that diverged from macrococci approximately 250 million years ago. Contrary to other groups, the S. sciuri species group has not developed host-specific colonization strategies. Genome analysis of S. sciuri ATCC 29059 provides here the first genetic basis for atypical traits that would support the switch between the free-living style and the infective state in animals and humans. From among the most remarkable features, it was noticed in this extensive study that there were a number of phosphoenolpyruvate:carbohydrate phosphotransferase systems (PTS), almost twice as many as any other staphylococci, and the co-occurrence of mevalonate and non-mevalonate pathways for isoprenoid synthesis. The sequenced strain was devoid of the main virulence factors present in Staphylococcus aureus, although it exhibited numerous heme and iron acquisition systems, as well as crt and aldH genes necessary for gold pigment synthesis. The sensing and signaling networks, exemplified by a large and typical repertoire of two-component regulatory systems and a complete panel of master regulators, such as agr, rex, mgrA, rot, sarA and sarR genes, depict the background in which S. aureus virulence genes were later acquired. An additional sigma factor, a distinct set of electron transducer elements and many gene operons similar to those found in Bacillus spp. would constitute the most visible remnant links with Bacillaceae organisms.
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Affiliation(s)
- Eugene Christo-Foroux
- Département de Microbiologie, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris Cedex 15, France.
| | - Tatiana Vallaeys
- Département de Biologie Ecologie, Université de Montpellier, CC 13002, Place Eugène Bataillon, 34095 Montpellier, France.
| | - Valentin Loux
- MaIAGE, INRA, Université Paris-Saclay, Domaine de Vilvert, 78352 Jouy-en-Josas, France.
| | - Elie Dassa
- Département de Microbiologie, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris Cedex 15, France
| | - Josef Deutscher
- CNRS, UMR 8261 Expression Génétique Microbienne, Institut de Biologie Physico-Chimique, Université Paris Diderot, Sorbonne-Paris-Cité, 13 rue Pierre et Marie Curie, Paris, France.
| | - Cécile Wandersman
- Département de Microbiologie, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris Cedex 15, France
| | - Aurélien Livernois
- Département de Microbiologie, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris Cedex 15, France; Département de Biologie Ecologie, Université de Montpellier, CC 13002, Place Eugène Bataillon, 34095 Montpellier, France
| | - Chloe Hot
- Département de Microbiologie, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris Cedex 15, France
| | - Alexis Criscuolo
- Hub, Center for Bioinformatics, Biostatistics and Integrative Biology (C3BI), Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris Cedex 15, France.
| | - Catherine Dauga
- International Group of Data Analysis (IGDA), Center for Bioinformatics, Biostatistics and Integrative Biology (C3BI), Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris Cedex 15, France.
| | - Dominique Clermont
- Collection de l'Institut Pasteur (CIP), Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris Cedex 15, France.
| | - Olivier Chesneau
- Département de Microbiologie, Institut Pasteur, 28 rue du Dr. Roux, 75724 Paris Cedex 15, France.
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Jeong DW, Kim HR, Lee JH. Genetic diversity of Staphylococcus equorum isolates from Saeu-jeotgal evaluated by multilocus sequence typing. Antonie Van Leeuwenhoek 2014; 106:795-808. [PMID: 25103946 DOI: 10.1007/s10482-014-0249-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2014] [Accepted: 07/29/2014] [Indexed: 10/24/2022]
Abstract
Staphylococcus equorum, the predominant bacterial species detected in Saeu-jeotgal, a Korean high-salt fermented seafood, is a candidate starter bacterium for Saeu-jeotgal fermentation. A multilocus sequence typing (MLST) scheme was developed to evaluate the genetic diversity and background of S. equorum strains isolated from Saeu-jeotgal. A total of 135 strains, including 117 isolates from Saeu-jeotgal, and others from Myeolchi-jeotgal, sausage, cheese and horse skin, were subjected to MLST, and the internal fragments of seven housekeeping genes, aroE, dnaJ, glpF, gmk, hsp60, mutS, and pta, were compared. This MLST scheme produced 45 sequence types (STs) and the eBURST algorithm clustered the STs into nine clonal groups and seven singletons. Clonal group 1, the major group, consisted of 30 isolates from cheese, Saeu-jeotgal and sausages, which were classified into 12 STs. The predominant ST, ST26, comprised 25 isolates and presented as a singleton. Most of the isolates from Myeolchi-jeotgal and sausages clustered on two different branches of a phylogenetic tree generated with a cluster analysis using the maximum likelihood algorithm. This MLST scheme established the genetic backgrounds of S. equorum strains isolated from different types of food. Among the housekeeping genes used for MLST, gmk had the fewest allele types and fairly low sequence identities (74.0-90.0%) within the Staphylococcus species. Therefore, sequence analyses of the gmk gene and 16S rRNA gene can be used for the accurate and rapid identification of S. equorum.
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Affiliation(s)
- Do-Won Jeong
- Department of Food Science and Biotechnology, Kyonggi University, Suwon, 443-760, Republic of Korea
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Genome Sequence Analysis of Staphylococcus equorum Bovine Mastitis Isolate UMC-CNS-924. GENOME ANNOUNCEMENTS 2013; 1:1/5/e00840-13. [PMID: 24136848 PMCID: PMC3798454 DOI: 10.1128/genomea.00840-13] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Intramammary infections in dairy cattle are frequently caused by staphylococci, resulting in mastitis and associated economic losses. A draft genome sequence was determined for Staphylococcus equorum UMC-CNS-924, isolated from the milk of a Holstein cow, to better understand the genetic basis of its pathogenesis and adaptation to the bovine mammary gland.
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