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

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.

Keywords: Staphylococcus rostri; antibiotic resistance; bovine mastitis; non-aureus Staphylococci (NAS); phylogeny; virulence factors; whole genome-sequencing (WGS).

Figure 1

Maximum-likelihood phylogenetic tree based on the core genome of 81 S. rostri isolates from bovine mastitis and S. rostri DSM 21968 (GenBank Accession no. GCF002902145) as a reference (tree re-rooted from the reference). The test isolates were labeled from SR1-SR81 (S for “Staphylococcus”, R for “rostri”) and assigned a herd and cow number. In cows with S. rostri in >1 quarters, the isolates were additionally named a–d depending on the number of S. rostri-positive quarters as follows: “a” for the isolate from the S. rostri-positive quarter number 1; “b” for the positive quarter number 2; and so forth.

Figure 2

Network of viral clusters (VCs) representing the predicted phages among the S. rostri isolates. “Overlap”: phages sharing overlap with other phages from multiple VCs; “Other”: phages classified as singletons or outliers; “singletons”: phages with only a few or no gene similarity against other phages; “outliers”: phages with some genes shared with other phages, but not enough to be placed within a VC [28]. Reference strain*: the S. rostri DSM 21968.