Hospital MRSA outbreaks: Binary typing as a screening method for WGS, and the role of the environment in transmission

BackgroundWhole-genome sequencing (WGS) of MRSA has greater accuracy than other typing methods. However its cost (~$AUD80/isolate, excluding bioinformatic analysis) is a barrier for routine use in hospital infection control. Multiplex PCR-reverse line blot binary typing (BT) is a rapid, inexpensive (~$AUD2/isolate), high-throughput laboratory-developed technique producing rapidly interpretable results, with comparable discriminatory power to PFGE and spa typing. We noted ongoing MRSA transmission in the Burns Unit (BU) and Intensive Care Unit (ICU), requiring outbreak control despite intensive interventions. Environmental surveillance of the BU generated large numbers of isolates.AimThe strategy of using BT and epidemiological information (BT-EPI) to determine transmission and thus select isolates for WGS was assessed in these high-burden units.MethodsBT was performed for 94 MRSA BU and ICU patient strains and 170 BU environmental strains. BT-EPI linked 97 of the 264 isolates, which were selected for WGS. Transmission was inferred by a variant distance of less than 6 single nucleotide variants.FindingsMost transmissions determined by BT-EPI were confirmed by WGS, including most environmental sources. Importantly, WGS was able to confirm outbreaks of intense environmental transmission, including the operating theatre, and provide actionable information on environmental reservoirs, including persistence for >6 months. The number of environmental transmissions reduced after aerosolized hydrogen peroxide (aHP) cleaning was introduced.ConclusionBT-EPI can reduce costs ($AUD20,592 wet-laboratory costs alone) of MRSA genomic surveillance. This strategy was successful in confirming outbreaks involving intense environmental transmission, prolonged environmental persistence, and reductions in transmission after the introduction of aHP cleaning.