Genomic analysis of a porcine exudative epidermitis outbreak caused by Staphylococcus hyicus

Exudative epidermitis (EE) causes substantial morbidity and mortality in piglets. This study investigated the microbial ecology, antimicrobial resistance (AMR), and genomic diversity of Staphylococcus hyicus associated with an EE outbreak in an Australian piggery. Lesion swabs from 20 affected piglets yielded 160 bacterial isolates (including S. hyicus and cohabiting species). Isolates underwent species identification, antimicrobial susceptibility testing, and whole-genome sequencing (WGS) of S. hyicus for AMR/virulence gene profiling and core-genome SNP analysis to assess genomic relatedness. S. hyicus predominated among lesion isolates. Phenotypic testing showed varied AMR, with frequent resistance to erythromycin and tetracycline. WGS of 27 S. hyicus isolates identified five distinct genotypic AMR profiles, including combinations spanning multiple drug classes. All S. hyicus carried the exfoliative toxin gene shetA, and 24 also carried exhD. Core-genome analysis indicated a highly clonal outbreak: 24/27 genomes differed by 0 core SNPs, with the remaining three closely related. Despite this clonality, resistance gene carriage varied across isolates. Consequently, reliance on a single colony to represent an outbreak could understate resistance and overstate treatability. These findings support routine multi-isolate sampling to capture within-clone AMR variability, bolster antimicrobial selection during EE management, and inform consideration of autogenous vaccines targeting dominant outbreak clones.