Staphylococcus aureus CC398 in humans and livestock

Staphylococcus aureus clonal complex 398 (CC398) is an important bacterial pathogen found in humans and livestock, and its origins and spread have generated considerable interest. We perform the first time-scaled phylogenetic study of CC398, using the largest dataset to-date and including newly sequenced isolates from Scotland. We find distinct human- and livestock-associated clades, but observe clustering of CC398 sequences from hospital environments and patients within the livestock-associated clade, consistent with human-to-human transmission of livestock-associated CC398. This is the first phylogenetic study to include CC398 genomes from the UK, and we investigate the spread of CC398 between countries. Using state-of-the-art methods for mapping traits onto phylogenies, we quantify transition between host species to identify sink and source populations for CC398, and also take a novel approach to investigate the gain and loss of antibiotic resistance in CC398 over time. We demonstrate significant differences in the dynamics of resistance to methicillin and tetracycline, which may be due to contrasts in historical patterns of antibiotic usage in the livestock industry and human medicine, and/or the mode of inheritance of the resistance determinants.