Whole genome sequencing links Clostridium (Clostridioides) difficile in the hospital to diverse sources in the community

Aims: To investigate if C. difficile is being imported into the hospital setting from the community via contaminated shoe soles, and if clinical CDI cases could be genomically linked to hospital and/or community environmental sources.Methods and Results: From January to December 2019, 300 floor and 300 shoe samples were sampled at a tertiary hospital in Western Australia. Non-toxigenic C. difficile RT 010 predominated in both the floor (96.6%) and shoe (73.2%) isolates, while RT 014/020 was the most prevalent RT among clinical cases (33.0%) at our hospital. Whole genome sequencing and high-resolution core genome single nucleotide variant analysis were performed on 142 C. difficile RT 014/020 and 66 C. difficile RT 010 strains from hospital and community sources. Our results reveal that none of the C. difficile RT 014/020 strains from CDI cases isolated at our hospital in 2019 were not genetically related — a finding that completely refutes the longstanding notion that CDI is a hospital-acquired infection. Our analysis on a larger population of C. difficile RT 014/020 provided evidence for frequent spread between humans, animals and the environment. While C. difficile RT 014/020 appear to spread via routes outside of the healthcare system, RT 010 displayed a pattern of possible importation from the community into the hospital.Conclusions: This study enhanced our understanding of the complex transmission dynamics of C. difficile by providing strong evidence for frequent long-range bidirectional spreads between humans and community reservoirs. We demonstrated the potential of importing C. difficile into a hospital from sources/reservoirs such as lawn, compost and gardens, through contaminated shoe soles. These findings highlight the importance of starting a conversation with stakeholders about developing a set of community-based infection control strategies which could significantly lower the infection rate of CDI.