%A Simões,Patrícia Martins %A Lemriss,Hajar %A Dumont,Yann %A Lemriss,Sanâa %A Rasigade,Jean-Philippe %A Assant-Trouillet,Sophie %A Ibrahimi,Azeddine %A El Kabbaj,Saâd %A Butin,Marine %A Laurent,Frédéric %D 2016 %J Frontiers in Microbiology %C %F %G English %K methicillin resistant Staphylococcus capitis,Late-Onset Sepsis,complete genome SMRT,Nisin resistance,Staphylococcal Infections,Comparative genomics,worldwide diffusion CoNS multi resistant clone %Q %R 10.3389/fmicb.2016.01991 %W %L %M %P %7 %8 2016-December-15 %9 Original Research %+ Patrícia Martins Simões,Department of Clinical Microbiology, Northern Hospital Group, Hospices Civils de Lyon,Lyon, France,patricia.martins-simoes01@chu-lyon1.fr %+ Patrícia Martins Simões,International Centre for Research in Infectious Diseases, Institut National de la Santé et de la Recherche Médicale U1111, University of Lyon,Lyon, France,patricia.martins-simoes01@chu-lyon1.fr %+ Patrícia Martins Simões,National Reference Center for Staphylococci, Hospices Civils de Lyon,Lyon, France,patricia.martins-simoes01@chu-lyon1.fr %# %! Genomic characterization of the NRCS-A clone %* %< %T Single-Molecule Sequencing (PacBio) of the Staphylococcus capitis NRCS-A Clone Reveals the Basis of Multidrug Resistance and Adaptation to the Neonatal Intensive Care Unit Environment %U https://www.frontiersin.org/articles/10.3389/fmicb.2016.01991 %V 7 %0 JOURNAL ARTICLE %@ 1664-302X %X The multi-resistant Staphylococcus capitis clone NRCS-A has recently been described as a major pathogen causing nosocomial, late-onset sepsis (LOS) in preterm neonates worldwide. NRCS-A representatives exhibit an atypical antibiotic resistance profile. Here, the complete closed genome (chromosomal and plasmid sequences) of NRCS-A prototype strain CR01 and the draft genomes of three other clinical NRCS-A strains from Australia, Belgium and the United Kingdom are annotated and compared to available non-NRCS-A S. capitis genomes. Our goal was to delineate the uniqueness of the NRCS-A clone with respect to antibiotic resistance, virulence factors and mobile genetic elements. We identified 6 antimicrobial resistance genes, all carried by mobile genetic elements. Previously described virulence genes present in the NRCS-A genomes are shared with the six non-NRCS-A S. capitis genomes. Overall, 63 genes are specific to the NRCS-A lineage, including 28 genes located in the methicillin-resistance cassette SCCmec. Among the 35 remaining genes, 25 are of unknown function, and 9 correspond to an additional type I restriction modification system (n = 3), a cytosine methylation operon (n = 2), and a cluster of genes related to the biosynthesis of teichoic acids (n = 4). Interestingly, a tenth gene corresponds to a resistance determinant for nisin (nsr gene), a bacteriocin secreted by potential NRCS-A strain niche competitors in the gut microbiota. The genomic characteristics presented here emphasize the contribution of mobile genetic elements to the emergence of multidrug resistance in the S. capitis NRCS-A clone. No NRCS-A-specific known virulence determinant was detected, which does not support a role for virulence as a driving force of NRCS-A emergence in NICUs worldwide. However, the presence of a nisin resistance determinant on the NRCS-A chromosome, but not in other S. capitis strains and most coagulase-negative representatives, might confer a competitive advantage to NRCS-A strains during the early steps of gut colonization in neonates. This suggests that the striking adaptation of NRCS-A to the NICU environment might be related to its specific antimicrobial resistance and also to a possible enhanced ability to challenge competing bacteria in its ecological niche.