Whole-Genome Sequence of Staphylococcus hominis Strain J31 Isolated from Healthy Human Skin

Coates-Brown, Rosanna; Horsburgh, Malcolm J.

doi:10.1128/genomea.01548-16

Cited by 3 publications

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References 14 publications

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“…Annotation was carried out using PROKKA version 1.5.2 ( Seemann, 2014 ). The PacBio assembly of S. hominis strain J31 (Accession FBVO01000000) ( Coates-Brown and Horsburgh, 2017 ) was used as the comparator assembly for this strain. Good quality filtered reads from experimentally evolved pools and single clones were aligned to respective comparator strains using the BWA (version 0.5.9-r16) ( Li and Durbin, 2009 ) packages aln and sampe, and also using BWA (version 0.7.5a-r405) mem package.…”

Section: Methodsmentioning

confidence: 99%

Comparative Genomics of Staphylococcus Reveals Determinants of Speciation and Diversification of Antimicrobial Defense

et al. 2018

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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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Section: Methodsmentioning

confidence: 99%

Comparative Genomics of Staphylococcus Reveals Determinants of Speciation and Diversification of Antimicrobial Defense

et al. 2018

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“…T 0 comparator strains were assembled using VelvetOptimiser (version 2.2.5; Victoria Bioinformatics Consortium) with Kmer sizes from 19 to 99 and Velvet version 1.2.06 (45). Annotation was carried out using PROKKA version 1.5.2 (Seemann 2014).…”

Section: Methodsmentioning

confidence: 99%

Comparative Genomics of Staphylococcus Reveals Determinants of Speciation and Diversification of Antimicrobial Defense

Horsburgh

Coates-Brown

Darby

et al. 2018

Preprint

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26The bacterial genus Staphylococcus comprises diverse species with most being described 27 as colonizers of human and animal skin. A relational analysis of features that 28 discriminate its species and contribute to niche adaptation and survival remains to be fully 29 described. In this study, an interspecies, whole-genome comparative analysis of 21 30Staphylococcus species was performed based on their orthologues. Three well-defined 31 multi-species groups were identified: group A (including aureus/epidermidis); group B 32 (including saprophyticus/xylosus) and group C (including pseudintermedius/delphini). 33The machine learning algorithm Random Forest was applied to identify variable 34 orthologues that drive formation of the Staphylococcus species groups A-C. Orthologues 35 driving staphylococcal infrageneric diversity comprised regulatory, metabolic and 36 antimicrobial resistance proteins. Notably, the BraSR (NsaRS) two-component system 37 (TCS) and its associated BraDE transporters that regulate antimicrobial resistance 38 distinguish group A Staphylococcus species from others in the genus that lack the BraSR 39 TCS. Divergence of BraSR and GraSR antimicrobial peptide survival TCS and their 40 associated transporters was observed across the staphylococci, likely reflecting niche 41 specific evolution of these TCS/transporters and their specificities for AMPs. 42 Experimental evolution, with selection for resistance to the lantibiotic nisin, revealed 43 multiple routes to resistance and differences in the selection outcomes of the BraSR-44 positive species S. hominis and S. aureus. Selection supported a role for GraSR in nisin 45 survival responses of the BraSR-negative group B species S. saprophyticus. Our study 46 reveals diversification of antimicrobial-sensing TCS across the staphylococci and hints at 47 differential relationships between GraSR and BraSR in those species positive for both 48 TCS. 49 50 Importance 51The genus Staphylococcus includes species that are commensals and opportunist 52 pathogens of humans and animals. Identifying the features that discriminate species of 53 staphylococci is relevant to understanding niche selection and the structure of their 54 microbiomes. Moreover, the determinants that structure the community are relevant for 55 strategies to modify the frequency of individual species associated with dysbiosis and 56 disease. In this study, we identify orthologous proteins that discriminate genomes of 57 staphylococci. In particular, species restriction of a major antimicrobial survival system, 58 BraSR (NsaRS), to a group of staphylococci dominated by those that can colonize human 59 skin. The diversity of antimicrobial sensing loci was revealed by comparative analysis 60 3 and experimental evolution with selection for nisin resistance identified the potential for 61 variation in antimicrobial sensing in BraRS-encoding staphylococci. This study provides 62 insights into staphylococcal species diversity. 63 64 Introduction 65 Staphylococcus species and genomics 66The existen...

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The bla and mec families of β-lactam resistance genes in the genera Macrococcus, Mammaliicoccus and Staphylococcus: an in-depth analysis with emphasis on Macrococcus

Schwendener

Perreten

2022

Journal of Antimicrobial Chemotherapy

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β-Lactamases (Bla) and low-affinity penicillin-binding proteins (PBP2A) are responsible for β-lactam resistance in the genera Macrococcus, Mammaliicoccus and Staphylococcus. These resistance mechanisms are in most species acquired through mobile genetic elements that carry a blaZ-like β-lactamase gene for penicillin resistance and/or a mec gene (mecA, mecB, mecC, mecD) encoding a PBP2A for resistance to virtually all classes of β-lactams. The mecA and mecC genes can be acquired through staphylococcal cassette chromosome mec (SCCmec) elements in Staphylococcus and Mammaliicoccus. The mecB and mecD genes are found in Macrococcus on SCCmec elements, as well as on unrelated mecD-carrying Macrococcus resistance islands (McRImecD) and large mecB-carrying plasmids. This review provides a phylogenetic overview of Macrococcus, Mammaliicoccus and Staphylococcus species and an in-depth analysis of the genetic structures carrying bla and mec genes in these genera. Native bla genes were detected in species belonging to the novobiocin-resistant Staphylococcus saprophyticus group and Mammaliicoccus. The evolutionary relatedness between Macrococcus and Mammaliicoccus is illustrated on the basis of a similar set of intrinsic PBPs, especially, the presence of a second class A PBP. The review further focuses on macrococcal elements carrying mecB and mecD, and compares them with structures present in Staphylococcus and Mammaliicoccus. It also discusses the different recombinases (ccr of SCCmec) and integrases (int of McRI) that contribute to the mobility of methicillin resistance genes, revealing Macrococcus as an important source for mobilization of antibiotic resistance genes within the family of Staphylococcaceae.

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Whole-Genome Sequence of Staphylococcus hominis Strain J31 Isolated from Healthy Human Skin

Cited by 3 publications

References 14 publications

Comparative Genomics of Staphylococcus Reveals Determinants of Speciation and Diversification of Antimicrobial Defense

Comparative Genomics of Staphylococcus Reveals Determinants of Speciation and Diversification of Antimicrobial Defense

Comparative Genomics of Staphylococcus Reveals Determinants of Speciation and Diversification of Antimicrobial Defense

The bla and mec families of β-lactam resistance genes in the genera Macrococcus, Mammaliicoccus and Staphylococcus: an in-depth analysis with emphasis on Macrococcus

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