High-throughput targeted amplicon screening tool for characterizing intrahost diversity in Staphylococcus aureus...

Area of Science:

• Microbiology and Infectious Diseases
• Genomics and Molecular Biology
• Epidemiology

Background:

• Asymptomatic Staphylococcus aureus (SA) carriage is a significant risk factor for opportunistic infections.
• SA colonization dynamics, strain evolution, and transmission between body sites and individuals complicate detection and control.
• Whole-genome sequencing (WGS) is accurate but resource-intensive for large-scale, longitudinal studies.

Purpose of the Study:

• To develop and validate a low-cost, direct-from-sample amplicon sequencing (AmpSeq) assay for high-resolution SA genotyping.
• To characterize SA colonization patterns and transmission dynamics in a longitudinal study.
• To provide a cost-effective alternative to WGS for initial transmission assessments.

Main Methods:

• Development of a custom, species-specific amplicon sequencing (AmpSeq) assay for SA.
• Longitudinal collection of oral and nasal samples from nine participants over 18 weeks.
• Direct analysis of qPCR-positive samples using AmpSeq without prior culturing.

Main Results:

• AmpSeq successfully discriminated SA genotypes directly from samples, enabling strain typing.
• Longitudinal data revealed within-person spread, with nasal SA populations likely seeding oral colonization.
• The assay rapidly ruled out inter-person transmission among sampled participants.

Conclusions:

• The developed AmpSeq assay is a rapid, cost-effective, direct-from-sample method for SA screening and transmission analysis.
• AmpSeq facilitates population-level characterization, strain typing, and identification of potential reservoirs.
• This approach serves as a valuable precursor to more resource-intensive WGS for detailed colonization pattern validation.