Genus-wide genomic characterization of : insights into evolution, population structure, and functional potential.

Introduction: species have been isolated from a range of mammals and mammal-derived food products. While they are largely considered to be animal commensals, spp. can be opportunistic pathogens in both veterinary and human clinical settings. This study aimed to provide insight into the evolution, population structure, and functional potential of the genus, with an emphasis on antimicrobial resistance (AMR) and virulence potential.

Methods: All high-quality, publicly available genomes ( = 104, accessed 27 August 2022), plus six South African genomes sequenced here (two strains from bovine clinical mastitis cases and four strains from beef products), underwent taxonomic assignment (using four different approaches), AMR determinant detection (via AMRFinderPlus), and virulence factor detection (using DIAMOND and the core Virulence Factor Database).

Results: Overall, the 110 genomes were of animal commensal, veterinary clinical, food-associated (including food spoilage), and environmental origins; five genomes (4.5%) originated from human clinical cases. Notably, none of the taxonomic assignment methods produced identical results, highlighting the potential for species misidentifications. The most common predicted antimicrobial classes associated with AMR determinants identified across included macrolides, beta-lactams, and aminoglycosides ( = 81, 61, and 44 of 110 genomes; 73.6, 55.5, and 40.0%, respectively). Genes showing homology to exoenzyme aureolysin were detected across multiple species (using 90% coverage,  = 40 and 77 genomes harboring aureolysin-like genes at 60 and 40% amino acid [AA] identity, respectively). Panton-Valentine leucocidin toxin-associated and homologs were identified in eight genomes (≥40% AA identity, >85% coverage). Using a method that delineates populations using recent gene flow (PopCOGenT), two species ( and ) were composed of multiple within-species populations. Notably, was partitioned into two populations, which differed in functional potential (e.g., one harbored beta-lactamase family, type II toxin-antitoxin system, and stress response proteins, while the other possessed a Type VII secretion system; PopCOGenT  < 0.05).

Discussion: Overall, this study leverages all publicly available genomes in addition to newly sequenced genomes from South Africa to identify genomic elements associated with AMR or virulence potential, which can be queried in future experiments.