Comparative Genomics of Staphylococcus rostri, an Undescribed Bacterium Isolated from Dairy Mastitis

SIMPLE SUMMARY: Mastitis is one of the most common diseases in dairy cows. To control mastitis in dairy cows, it is vital to understand the causative agents including their respective mode of action. Several bacterial species may cause bovine mastitis although non-aureus Staphylococci (NAS) are often reported as the most frequently observed cause of subclinical mastitis in dairy cows. As species of NAS may differ in their epidemiology and pathogenicity, performing diagnostics at the species level is crucial. This study is about Staphylococcus rostri, which is a newly identified NAS. Staphylococcus rostri is rarely reported or characterized in domestic animals, and, to our knowledge, never as a causative agent of dairy mastitis. With the present study, we report the finding of 81 Staphylococcus rostri isolates from nine dairy herds and mainly from subclinical mastitis. We characterized these S. rostri isolates with whole genome sequencing analysis. The results showed a limited distribution of known genes associated with virulence (clpP and clpC, n = 81 isolates) and antibiotic resistance (str, n = 1 isolate and lnuA n = 2 isolates). However, we found that the S. rostri isolates consisted of herd-specific clones, indicating that each herd had separate introduction source(s). Overall, this study suggests that S. rostri acts as a mastitis pathogen, despite the exact pathogenetic mechanisms of S. rostri still requiring full characterization and remaining unknown. ABSTRACT: This study characterizes 81 S. rostri isolates from bovine mastitis (of which 80 were subclinical). The isolates were first identified as S. microti by MALDI-TOF MS, but later whole genome sequencing analysis allowed reclassification as S. rostri. The isolates were derived from 52 cows and nine dairy herds in Denmark. To describe the pathogenicity of S. rostri, we used whole genome sequencing to infer the distribution of genes associated with virulence, antibiotic resistance, and mobile genetic elements. Also, we performed a core-genome phylogeny analysis to study the genetic relatedness among the isolates. All 81 isolates expressed the same virulence profile comprising two putative virulence genes, clpP and clpC. Three isolates carried a resistance gene encoding streptomycin (str) or lincomycin (lnuA) resistance. The distribution of plasmids suggested the detected antibiotic resistance genes to be plasmid-mediated. Phages were abundant among the isolates, and the single isolate from clinical mastitis acquired a phage disparate from the rest, which potentially could be involved with virulence in S. rostri. The core genome phylogeny revealed a strong genetic intra-herd conservation, which indicates the source of introduction being herd-specific and might further imply the ability of S. rostri to adapt to the bovine niche and spread from cow-to-cow in a contagious manner. With this study, we aim to acquaint clinicians and professionals with the existence of S. rostri which might have been overlooked so far.