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Abstract
Staphylococcus epidermidis is a prominent commensal member of human skin microbiome and an emerging nosocomial pathogen, making it a good model organism to provide genomic insights, correlating its transition between commensalism and pathogenicity. While there are numerous studies to understand differences in commensal and pathogenic isolates, systematic efforts to understand variation and evolutionary pattern in multiple strains isolated from healthy individuals are lacking. In the present study, using whole genome sequencing and analysis, we report presence of diverse lineages of S. epidermidis isolates in healthy individuals from two geographically diverse locations of India and North America. Further, there is distinct pattern in the distribution of candidate gene(s) for pathogenicity and commensalism. The pattern is not only reflected in lineages but is also based on geographic origin of the isolates. This is evident by the fact that North American isolates under this study are more genomically dynamic and harbor pathogenicity markers in higher frequency. On the other hand, isolates of Indian origin are less genomically dynamic, harbor less pathogenicity marker genes and possess two unique antimicrobial peptide gene clusters. This study provides a basis to understand the nature of selection pressure in a key human skin commensal bacterium with implications in its management as an opportunistic pathogen.
Highlights
Staphylococcus epidermidis is coagulase-negative staphylococcus (CONS) commensal member of human skin microbiota inhabiting skin since millions of years (Rogers et al, 2009)
We reported that S. epidermidis isolates from diverse habitats like plants, rodents and human shown remarkable variation suggesting the ongoing selection in this species (Chaudhry and Patil, 2016)
Twenty-eight S. epidermidis (SE) isolates from different body sites of healthy individuals of Indian origin (SEI) were sequenced (Table S1) and high quality data was obtained with coverage >50x and number of contigs in range, 52–176
Summary
Staphylococcus epidermidis is coagulase-negative staphylococcus (CONS) commensal member of human skin microbiota inhabiting skin since millions of years (Rogers et al, 2009). There are many studies showing its role in immune system modulation (Lai et al, 2009, 2010; Belkaid and Tamoutounour, 2016; Egert et al, 2017) It is considered crucial for skin microbiota because of its ability to inhibit the growth of notorious skin pathogen, Staphylococcus aureus (Otto et al, 1999; Heikkilä and Saris, 2003; Iwase et al, 2010). Management of S. epidermidis is further challenged by the presence of antibiotic resistance genes (Archer, 1978; Raad et al, 1998; Gill et al, 2005; Dave et al, 2011; Widerström et al, 2012b), thereby contributing to multi-drug resistance forms of the species (Rabaud and Mauuary, 2001; Miragaia et al, 2005) These strains may transfer them horizontally to its pathogenic relative, S. aureus (Méric et al, 2015). Management of this commensal yet an opportunistic pathogen is crucial in both community and clinical settings
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