Population and pan-genomic analyses of <i>Staphylococcus pseudintermedius</i> identify geographic distinctions in accessory gene content and novel loci associated with AMR

<i>Staphylococcus pseudintermedius</i> is a common representative of the normal skin microbiota of dogs and cats but is also a causative agent of a variety of infections. Although primarily a canine/feline bacterium, recent studies suggest an expanded host range including humans. This paper details population genomic analyses of the largest yet assembled and sequenced collection of <i>S. pseudintermedius</i> isolates from across the USA and Canada and assesses these isolates within a larger global population genetic context. We then employ a pan-genome-wide association study analysis of over 1,700 <i>S</i>. <i>pseudintermedius</i> isolates from sick dogs and cats, covering the period 2017-2020, correlating loci at a genome-wide level, with <i>in vitro</i> susceptibility data for 23 different antibiotics. We find no evidence from either core genome phylogenies or accessory genome content for separate lineages colonizing cats or dogs. Some core genome geographic clustering was evident on a global scale, and accessory gene content was noticeably different between various regions, some of which could be linked to known antimicrobial resistance (AMR) loci for certain classes of antibiotics (e.g., aminoglycosides). Analysis of genes correlated with AMR was divided into different categories, depending on whether they were known resistance mechanisms, on a plasmid, or a putatively novel resistance mechanism on the chromosome. We discuss several novel chromosomal candidates for follow-up laboratory experimentation, including, for example, a bacteriocin (subtilosin), for which the same protein from <i>Bacillus subtilis</i> has been shown to be active against <i>Staphylococcus aureus</i> infections, and for which the operon, present in closely related <i>Staphylococcus</i> species, is absent in <i>S. aureus</i>.IMPORTANCE<i>Staphylococcus pseudintermedius</i> is an important causative agent of a variety of canine and feline infections, with recent studies suggesting an expanded host range, including humans. This paper presents global population genomic data and analysis of the largest set yet sequenced for this organism, covering the USA and Canada as well as more globally. It also presents analysis of <i>in vitro</i> antibiotic susceptibility testing results for the North American (NA) isolates, as well as genetic analysis for the global set. We conduct a pan-genome-wide association study analysis of over 1,700 S. <i>pseudintermedius</i> isolates from sick dogs and cats from NA to correlate loci at a genome-wide level with the <i>in vitro</i> susceptibility data for 23 different antibiotics. We discuss several chromosomal loci arising from this analysis for follow-up laboratory experimentation. This study should provide insight regarding the development of novel molecular treatments for an organism of both veterinary and, increasingly, human medical concern.