Absence of patient-to-patient intrahospital transmission of Staphylococcus aureus as determined by whole-genome sequencing.
Bottom Line: To identify patient-to-patient intrahospital transmission using high-resolution genetic analysis, we sequenced the genomes of a consecutive set of 398 S. aureus isolates from sterile-site infections.The S. aureus strains were collected from four hospitals in the Houston Methodist Hospital System over a 6-month period.In addition, our data demonstrate that highly related pools of S. aureus strains exist in the community which may complicate outbreak investigations.
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Mentions: Within-host evolution of asymptomatic S. aureus carriage strains has been recently studied using whole-genome sequencing (45), but there are currently no data that define within-host microevolution over time in the setting of sterile-site infections. The distinction is important as there are potentially very different selective pressures exerted on sterile-site isolates versus strains isolated from asymptomatic carriers. It has also been observed that ST8 isolates tend to be more clonal and less variable than other ST types (35). We examined genomic variation among strains collected over time from the same patient. In this set of isolates (n = 30), the average time between the two isolates for ST8 strains (n = 15) was 24.6 days (range, 1 to 144 days; SD, 38.9 days) and 20.2 days for ST5 strains (n = 15) (range, 1 to 83 days; SD, 23.9 days). By considering SNP accumulation between the two isolates, and the time interval, we determined that ST8 strains accrued an average of 2.2 SNPs per day (range, 0 to 12 SNPs; SD, 3.0SNPs) compared to ST5 strains that accrued an average of 17.7 SNPs per day (range, 0.6 to 80.5 SNPs; SD, 24.6 SNPs). This difference was statistically significant (P = 0.031, unpaired t test with Welch’s correction) and is shown in Fig. 4. Although two outlier strains exist in the ST5 population that inflate the mean rate, when these outliers are removed from the analysis, the increased ST5 SNP accumulation rate remains statistically significant compared to that of ST8 organisms (P = 0.0005, unpaired t test with Welch’s correction). Taken together, our findings are consistent with the clonal nature of the ST8 population (35).