Pangenomic analysis ofHelcococcus ovisreveals widespread tetracycline resistance and a novel bacterial species,Helcococcus bovis

Abstract

AbstractHelcococcus ovis(H. ovis) is an opportunistic bacterial pathogen of a wide range of animal hosts including domestic ruminants, swine, avians, and humans. In this study, we sequenced the genomes of 35Helcococcus sp.clinical isolates from the uterus of dairy cows and explored their antimicrobial resistance and biochemical phenotypes. Phylogenetic and average nucleotide identity analyses placed fourHelcococcusisolates within a cryptic clade-representing an undescribed species, for which we propose the nameHelcococcus bovissp. nov. We applied whole genome comparative analyses to explore the pangenome, resistome, virulome, and taxonomic diversity of the remaining 31H. ovisisolates. H. oviswas more often isolated from cows with metritis, however, there was no associations betweenH. ovisgene clusters and uterine infection. The phylogenetic distribution of high-virulence determinants ofH. ovisis consistent with convergent gene loss in the species. The majority ofH. ovisstrains (30/31) contain mobile tetracycline resistance genes, leading to higher minimum inhibitory concentrations of tetracyclines in vitro. In summary, this study showed that the presence ofH. ovisis associated with uterine infection in dairy cows, that mobile genetic element-mediated tetracycline resistance is widespread inH. ovis, and that there is evidence of co-occurring virulence factors across clades suggesting convergent gene loss in the species. Finally, we introduced a novelHelcococcusspecies closely related toH. ovis, calledH. bovissp. nov.HighlightsThe presence ofHelcococcus ovisis associated with uterine infection in dairy cowsMobile genetic element-mediated tetracycline resistance is widespread inH. ovisCo-occurring virulence factors across clades suggest convergent gene loss in the speciesHelcococcus bovisis a novel species closely related toHelcococcus ovis