Whole Genome Sequencing Identifies Enterotoxigenic and Antimicrobial Resistance Potential of Staphylococcus aureus from Maine Dairy Farms

Abstract Background Staphylococcus aureus is a leading cause of mastitis in dairy livestock and is a pathogen with unknown but potentially substantial impact on public and herd health in Maine. The primary objective of this study was to describe retrospective trends in S. aureus detection at the University of Maine Cooperative Extension Veterinary Diagnostic Laboratory (UMVDL) for milk samples from mastitis cases submitted between July 2017 and June 2022. The second objective was to assess the genetic profiles of 29 S. aureus isolates collected from dairy farms in Maine in 2017 and 2022. Results Overall, 7.8% of milk samples from mastitis cases submitted to UMVDL between July 2017 and June 2022 were positive for S. aureus, and the percentage of S. aureus-positive samples increased annually. The 29 isolates collected in 2017 (2 isolates) and between May and July of 2022 (27 isolates) and analyzed by whole genome sequencing belonged to 8 strain types and 5 clonal complexes typically associated with ruminant species. Across the genomes of the 29 isolates, 14 antimicrobial resistance genes were detected, with antibiotic efflux as the primary resistance mechanism. Each isolate contained 2 to 10 staphylococcal enterotoxin genes representing 15 unique genes. Antimicrobial resistance and staphylococcal enterotoxin gene presence/absence clustered with clonal complex and host species of origin. Conclusions Whole genome sequencing identified ruminant-associated sequence types and antimicrobial susceptibility profiles consistent with other regional reports. Staphylococcal enterotoxins genes of potential public health concern were also identified. This study provides insight into future opportunities to study S. aureus epidemiology and to survey dairy production in animal and public health contexts in Maine.