Multi-strain carriage and intrahost diversity of Staphylococcus aureus among Indigenous adults in the US

Staphylococcus aureus (SA) is an opportunistic pathogen and human commensal that is frequently present in the upper respiratory tract, gastrointestinal tract, and on the skin. While SA can cause disease ranging from minor skin infections to life-threatening bacteremia, it can also be carried asymptomatically. Indigenous individuals in the Southwest United States experience high rates of invasive SA disease. As carriage is the most significant risk factor for disease, understanding the dynamics of SA carriage, and in particular co-carriage of multiple strains, is important to develop strategies to prevent transmission in vulnerable communities. Here we investigated SA co-carriage and intrahost evolution by performing high density sampling from multiple anatomical sites and whole-genome sequencing (WGS) on 310 SA isolates collected from 60 Indigenous adults participating in a cross-sectional carriage study. We assessed the richness and diversity of SA isolates via differences in multi-locus sequence type (MLST), core-genome single-nucleotide-polymorphisms (SNPs), and genome content. Using WGS data, we identified 95 distinct SA populations among 60 participants; co-carriage was detected in 42% (25/60). Notably, two participants each carried four distinct SA strains. Variation in antibiotic resistance determinants among carried strains was identified among 42% (25/60) of participants. Lastly, we found unequal distribution of clonal complex by body site, suggesting that certain lineages may be adapted to specific anatomical sites. Together, these findings suggest that co-carriage may occur more frequently than previously appreciated and further our understanding of SA intrahost diversity during carriage, which has implications for surveillance activities and epidemiological investigations.