Genomics and Proteomics Provide New Insight into the Commensal and Pathogenic Lifestyles of Bovine- and Human-Associated Staphylococcus epidermidis Strains Kirsi Savijoki, †,‡ Antti Iivanainen,* ,§,○ Pia Siljama ̈ ki, †,‡,○ Pia K. Laine, ∥ Lars Paulin, ∥ Taru Karonen, § Satu Pyö ra ̈ la ̈ , ⊥ Matti Kankainen, # Tuula A. Nyman, ‡ Tiina Saloma ̈ ki, § Patrik Koskinen, ∇ Liisa Holm, ∇ Heli Simojoki, ⊥ Suvi Taponen, ⊥ Antti Sukura, § Nisse Kalkkinen, ‡ Petri Auvinen,* ,∥ and Pekka Varmanen* ,† † Department of Food and Environmental Sciences, ‡ Institute of Biotechnology, Proteomics Unit, § Department of Veterinary Biosciences, ∥ Institute of Biotechnology, DNA Sequencing and Genomics Laboratory, ⊥ Department of Production Animal Medicine, and ∇ Institute of Biotechnology, Bioinformatics Group, University of Helsinki, FI-00014 Helsinki, Finland # CSC − IT Center for Science Ltd., FI-02101 Espoo, Finland *S Supporting Information ABSTRACT: The present study reports comparative genomics and proteomics of Staphylococcus epidermidis (SE) strains isolated from bovine intramammary infection (PM221) and human hosts (ATCC12228 and RP62A). Genome-level profiling and protein expression analyses revealed that the bovine strain and the mildly infectious ATCC12228 strain are highly similar. Their genomes share high sequence identity and synteny, and both were predicted to encode the commensal-associated fdr marker gene. In contrast, PM221 was judged to differ from the sepsis-associated virulent human RP62A strain on the basis of distinct protein expression patterns and overall lack of genome synteny. The 2D DIGE and phenotypic analyses suggest that PM221 and ATCC12228 coordinate the TCA cycle activity and the formation of small colony variants in a way that could result in increased viability. Pilot experimental infection studies indicated that although ATCC12228 was able to infect a bovine host, the PM221 strain caused more severe clinical signs. Further investigation revealed strain- and condition-specific differences among surface bound proteins with likely roles in adhesion, biofilm formation, and immunomodulatory functions. Thus, our findings revealed a close link between the bovine and commensal-type human strains and suggest that humans could act as a reservoir of bovine mastitis-causing SE strains. KEYWORDS: Genomics, 2D DIGE, surfacome shaving, Staphylococcus epidermidis, intramammary infection, adaptation, virulence ■ INTRODUCTION Coagulase-negative Staphylococcus (CoNS) species including Staphylococcus epidermidis (SE) are important causative species of intramammary infection (IMI) in dairy cattle and are a known cause of persistent IMIs. 1−4 SE is rarely found in the normal microbiota of the bovine skin or on mucous membranes, 5,6 whereas it is common in the barn environment. 7 SE strains isolated from bovine IMI share the same genotype with those isolated from the milker’s skin, which has led to the hypothesis that SE isolated from the bovine host may originate from humans. 5,6 Multigenome screening analyses of commensal and clinical SE human strains suggest that the ability of this species to generate subpopulation variants may be an additional factor affecting commensal and pathogenic characteristics of this species. 8 The mechanisms modulating this interplay are not known. In humans, SE is part of the normal and balanced skin microbiota, which may block the colonization of potentially harmful microbes such as Staphylococcus aureus (SA). 9 Although SE is generally considered to be an indolent and benign inhabitant of the healthy host, in immune-compromised people, neonates, and patients with internal prosthetic devices, it can act as an opportunistic pathogen 10 and cause chronic infections, indicating the capacity of this species to evade host defenses. Biofilm formation, involving the synthesis of protective matrix polymers or other surface and secreted components, is one of the important factors contributing to immune evasion. 11 In SE, biofilms can be generated by various mechanisms, but the polysaccharide intercellular adhesin/poly-N-acetylglucosamine (PIA/PNAG)-mediated biofilm formation is most common and seems to be present in many disease-associated human strains. 12 In addition to PIA/PNAG, SE can also produce an exopolymer, poly-γ-glutamic acid (PGA), which is an essential compound of biofilm matrix and functions as a key player in promoting immune evasion during commensal and infectious states of the bacterium. 12 Instead of producing destructive toxins, SE is suggested to exploit passive strategies involving, Received: March 29, 2014 Published: July 11, 2014 Article pubs.acs.org/jpr © 2014 American Chemical Society 3748 dx.doi.org/10.1021/pr500322d | J. Proteome Res. 2014, 13, 3748−3762