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Comparative Genome Analysis of Staphylococcus lugdunensis Shows Clonal Complex-Dependent Diversity of the Putative Virulence

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Comparative Genome Analysis of Staphylococcus lugdunensis Shows Clonal Complex-Dependent Diversity of the Putative Virulence

Factor, ess/Type VII Locus

LEBEURRE, Jérémie, et al .

Abstract

Staphylococcus lugdunensis is a commensal bacterium of human skin that has emerged as a virulent Coagulase-Negative Staphylococcus in both community-acquired and healthcare associated infections. Genotyping methods have shown a clonal population structure of this pathogen but failed to identify hypervirulent lineages. Here, complete genomes of three pathogenic and three carriage S. lugdunensis strains were obtained by Single-Molecule sequencing (PacBio) and compared to 15 complete genomes available in GenBank database.

The aim was to identify (i) genetic determinants specific to pathogenic or carriage strains or specific to clonal complexes (CCs) defined by MultiLocus Sequence Typing, and (ii) antibiotic resistance genes and new putative virulence factors encoded or not by mobile genetic elements (MGE). Comparative genomic analysis did not show a strict correlation between gene content and the ability of the six strains to cause infections in humans and in a Galleria mellonella infection model. However, this study identified new MGEs (five prophages, two genomic islands and one plasmid) and genetic variations of some [...]

LEBEURRE, Jérémie, et al . Comparative Genome Analysis of Staphylococcus lugdunensis Shows Clonal Complex-Dependent Diversity of the Putative Virulence Factor, ess/Type VII Locus. Frontiers in Microbiology , 2019, vol. 10, p. 2479

DOI : 10.3389/fmicb.2019.02479 PMID : 31736914

Available at:

http://archive-ouverte.unige.ch/unige:142479

Disclaimer: layout of this document may differ from the published version.

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Supplementary data

Figure S1. Phylogenetic trees based on (A) the agr hypervariable region (agrB to agrD) and (B) the cap hypervariable region (capH to capK) of the 21 genomes of S. lugdunensis.

A B

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Table S1. Clinical and geographical origins of strains with complete genomes available in NCBI.

S. lugdunensis strains NCBI accession numbers Isolation source Country HKU0901 NC_013893 Skin and soft tissue infection Hong Kong N920143 NC_017353 Skin and soft tissue infection France

FDAARGOS141 NZ_CP014022 Bursitis USA

FDAARGOS143 NZ_CP014023 Skin and soft tissue infection USA FDAARGOS222 NZ_CP020406 Skin and soft tissue infection Strasbourg

Klug93G4 NZ_CP017069 Carriage Hong Kong

FDAARGOS377 NZ_CP023539 Abscess USA

FDAARGOS381 NZ_CP023970 Abscess USA

VISLISI_21 NZ_CP020762 Bacteraemia France

VISLISI_22 NZ_CP020764 Infective endocarditis France

VISLISI_25 NZ_CP020763 Material infection France

VISLISI_27 NZ_CP020735 Material infection France

VISLISI_33 NZ_CP020769 Liver abscess France

VISLISI_37 NZ_CP020761 Infective endocarditis France

C33 NZ_CP020768 Carriage France

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