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Microbial Genomics logo Microbial Genomics

Volume 11, Issue 3

Multi-strain carriage and intrahost diversity of among Indigenous adults in the USA Open Access

Abstract

(SA) is an opportunistic pathogen and human commensal that is frequently present in the upper respiratory tract, gastrointestinal tract and skin. While SA can cause diseases ranging from minor skin infections to life-threatening bacteraemia, it can also be carried asymptomatically. Indigenous individuals in the Southwest USA 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 sampling several colonies 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 differences in multilocus sequence type, core-genome SNPs and genome content. Using WGS data, we identified 95 distinct SA intra-subject lineages (ISLs) among 60 participants; co-carriage was detected in 42% (25/60). Notably, two participants each carried four distinct SA ISLs. 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.

  • Received:
  • Accepted:
  • Published Online:
Keyword(s): carriage , genomics , Indigenous health and Staphylococcus aureus
Funding
This study was supported by the:
  • National Institute of Allergy and Infectious Diseases (Award K22 AI141582)
    • Principal Award Recipient: TajAzarian
  • Johns Hopkins Bloomberg School of Public Health (Award Internal funds)
    • Principal Award Recipient: LauraL. Hammitt
© 2025 The Authors
  • This is an open-access article distributed under the terms of the Creative Commons Attribution License. This article was made open access via a Publish and Read agreement between the Microbiology Society and the corresponding author’s institution.
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2025-03-14
2026-02-09

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Multi-strain carriage and intrahost diversity of Staphylococcus aureus among Indigenous adults in the USA
M Gen 11, 001367 (2025); https://doi.org/10.1099/mgen.0.001367
/content/journal/mgen/10.1099/mgen.0.001367
/content/journal/mgen/10.1099/mgen.0.001367
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