Whole-genome sequencing shows that patient-to-patient transmission rarely accounts for acquisition of Staphylococcus aureus in an intensive care unit

This study indicates that only 20% of patients who acquired S. aureus appeared to acquire it through horizontal spread from other patients. All patients admitted to a 16 bed ICU in Brighton were screened on admission and weekly to detect S. aureus colonization and acquisition. Each isolate was typed by spa and whole genome sequencing (WGS). The number of acquisitions that could be linked using conventional methods (spa typing combined with an analysis of overlapping stays) vs. WGS was evaluated. Overall, 185 (16.7%) of 1109 admissions carried S. aureus; 59 carried MRSA (5.3%). 680 patients were on the unit for long enough to have a weekly screen and hence were eligible for assessing acquisition. Of these, 44 S. aureus (22 MRSA) acquisitions were detected in 41 patients.
Thirty-five of these acquisitions were in patients who were screen-negative on admission and nine were acquisitions of different strains in patients who were already colonized on admission. Only 14% (5/36) of the acquisitions available for typing were of the same spa type as another patient on the unit at the same time. All of these were MRSA. WGS discounted three of these apparent occurrences of patient-to-patient transmission, confirmed two and identified a further five (3 MRSA, 2 MSSA). So, in total, 7/36 (19%) of acquired isolates (5 MRSA and 2 MSSA) were linked to isolates from other patients. The study shows that use of an aconventional approach to investigate transmission (spa typing and epidemiological association) falsely suggests transmission links between patients but also fails to identify transmission links particularly where patient stays do not overlap, and that transmission might have occurred indirectly such as via healthcare workers or environmental contamination.