Comparative Genome Analysis of Staphylococcus lugdunensis Shows Clonal Complex-Dependent Diversity of the Putative Virulence Factor, ess/Type VII Locus

Jérémie Lebeurre (1) , Sandrine Dahyot (1) , Seydina Diene (2) , Amandine Paulay (1) , Marion Aubourg (3) , Xavier Argemi (4) , Jean-Christophe Giard (5) , Isabelle Tournier (6) , Patrice François (7) , Martine Pestel-Caron (1)

1 GRAM 2.0 - Groupe de Recherche sur l'Adaptation Microbienne
2 MEPHI - Microbes évolution phylogénie et infections
3 CHU Trousseau [Tours]
4 Virulence bactérienne précoce : fonctions cellulaires et contrôle de l'infection aiguë et subaiguë
5 U2RM - Unité de Recherche Risques Microbiens
6 GPMCND - Génomique et Médecine Personnalisée du Cancer et des Maladies Neuropsychiatriques
7 HUG - Hôpitaux Universitaires de Genève

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 putative virulence-associated loci, especially in CC3 strains. For a clonal population, high variability and eight CC-dependent genetic organizations were observed for the ess locus, which encodes a putative type VII secretion system (T7SS) homologous to that of S. aureus. Further phenotypic and functional studies are needed to characterize this particular CC3 and to evaluate the role of T7SS in the virulence of S. lugdunensis.

Mots clés: virulence; genomic comparative analysis; Staphylococcus lugdunensis; ess/type VII locus; clonal complexes

Domaines: Bactériologie; Génomique, Transcriptomique et Protéomique [q-bio.GN]

Jérémie Lebeurre, Sandrine Dahyot, Seydina Diene, Amandine Paulay, Marion Aubourg, 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, 10, pp.2479. ⟨10.3389/fmicb.2019.02479⟩. ⟨hal-02375679⟩