Plasmids of co-circulating Staphylococcus aureus serve as vehicles for antimicrobial resistance sharing across diseased host-species at short timescales

The multi-host opportunistic pathogen Staphylococcus aureus causes various superficial and life-threatening diseases. Here, we aim to determine to what extent closely related, co-circulating S. aureus isolates from diseased humans and animals differ in their phenotypic traits, core genomes, and plasmids. We selected 36 phylogenetically matched pairs of S. aureus from diseased humans and animals in New England, USA sampled from 2011 – 2020. These represented 24 sequence types (ST), with ST30 (12/72 genomes), ST5 (12/72 genomes), and ST8 (8/72 genomes) as being the most common. Core genome sequences were highly similar between paired isolates. We found no significant differences between human- and animal-derived isolates in hemolytic activity, growth rate, or biofilm formation under high-glucose conditions. Across all 72 genomes, we detected 24 antimicrobial resistance (AMR) genes, with mepA , tet38 , blaZ , and fosB being most common. We identified a total of 30 complete circular plasmids in 56 hybrid genome assemblies, i.e. , assembled from short- and long-reads data. A total of 19 plasmids (10 from animal isolates and nine from human isolates) carried genes conferring resistance to beta-lactams, aminoglycosides, macrolides, and heavy metals. Plasmids carrying the rep16 + rep19 replicon types exhibited the greatest diversity of genes associated with resistance against various agents, including two plasmids with ant(6)-Ia , aph(3")-IIIa , blaI, blaR1, blaZ , bcrA , bcrR , upp , msr(A), mph(C), sat4, graS, and graR genes. Clustering the plasmids based on sequence similarity calculated using Jaccard distances revealed nearly identical resistance plasmids present in isolates from different host species, including pairs that were not each other's closest phylogenetic relative. Our findings are consistent with plasmids and plasmid-borne AMR genes being shared across co-circulating S. aureus populations from different hosts over short evolutionary timescales, irrespective of their core genome relatedness. These findings can guide public and veterinary health strategies to limit the emergence and dissemination and spread of resistant clones.