Evolutionary Relationships and Antimicrobial Resistance of Staphylococcus aureus in Humans, Ruminants and Companion Animals

Staphylococcus aureus is a bacterial pathogen with broad host range, which has been associated with a wide spectrum of diseases both in humans and animals. The domestication of animals and the recent intensification of livestock farming have provided increased opportunities for the transfer of pathogens between humans and animals. Also, the overuse and misuse of antibiotics in human medicine, veterinary medicine and livestock production have led to the emergence of several antibiotic resistant strains. Based on a previous study by Richardson et al. (2018), this project aims to explore the dynamics of Staphylococcus aureus at the human-ruminant-companion animal interface, and to specifically provide answers to questions pertaining to the evolutionary relationships, host jumps and antimicrobial resistance of isolates across selected host groups. Using bioinformatics tools, the genomes of 513 Staphylococcus aureus isolates across 5 continents were downloaded from the NCBI repository, assembled, annotated, aligned, and built into a phylogenetic tree. The data were subsequently imported into R for further statistical analyses and visualization. The study provided evidence for S. aureus transmission among humans, companion animals and ruminants, identifying humans as the major reservoirs for S. aureus transmission, and as the host with the most abundant antimicrobial genes. The findings also reveals Tet38, a gene conferring resistance to tetracycline as the most common AMR gene, and the presence of significant resistance to fosfomycin and penicillins across host groups. Overall, this study establishes the existence of zoonosis as well as reverse-zoonosis, and underscores the need for antimicrobial stewardship in human and veterinary medicine. It also highlights the indication for surveillance in the early detection of emerging clones of pathogens and spill-over among human and animal hosts.