PRJNA380544
Staphylococcus aureus Raw sequence reads
Whole genome sequencing (WGS) makes it possible to determine the relatedness of bacterial isolates at high resolution, helping to characterise outbreaks. However, for Staphylococcus aureus, accumulation of within-host diversity during carriage might limit interpretation of sequencing data.In this study, we hypothesised the converse: that within-host diversity can in fact be exploited to reveal the involvement of long-term carriers (LTCs) in outbreaks. We analysed WGS data from 20 historical outbreaks, and applied phylogenetic methods to assess genetic relatedness and estimate time to most recent common ancestor (TMRCA). Findings were compared with the routine investigation results and epidemiological evidence.Outbreaks with epidemiological evidence for an LTC source had a mean estimated TMRCA (adjusted for outbreak duration) of 243 days (95% CI 143-343), compared with 55 days (28-81) for outbreaks lacking epidemiological evidence for an LTC (p=0.004). A threshold of 156 days predicted LTC involvement with a sensitivity of 0.875 and a specificity of 1.We also found 6/20 outbreaks included isolates with differing antimicrobial susceptibility profiles, however, these had only modestly increased pairwise diversity (mean 17.5 SNVs (95% CI 17.3-17.8) vs 12.7 (12.5-12.8)) compared with isolates with identical antibiograms (p<0.0001). Additionally, for 2 outbreaks, WGS identified 1 or more isolates which were genetically distinct despite having the outbreak PFGE pulsotype.Duration-adjusted TMRCA allowed the involvement of LTCs in outbreaks to be identified and could be used to decide whether screening for long-term carriage (e.g. in healthcare workers) is warranted. Requiring identical antibiograms to trigger investigation could miss important contributors to outbreaks.