Clostridioides difficile cgMLST to investigate nosocomial transmission

Transmission of Clostridioides difficile infection (CDI) still represents a substantial burden in healthcare facilities, despite the optimization of infection control measures. Traditional epidemiological investigations alone are often insufficient highlighting the need for new strategies to investigate nosocomial transmission. This study aimed to evaluate a procedure that includes secondary isolation and genomic typing of single toxigenic colonies using core genome multilocus sequence typing (cgMLST) for the investigation of C. difficile nosocomial transmissions. We analyzed all toxigenic C. difficile-positive stool samples that have been systematically stored at the Lausanne University hospital during six consecutive months. All isolates were initially typed and classified using a modified double locus sequence typing (DLST) method. Genome comparison of isolates with the same DLST and clustering was subsequently performed using cgMLST. The electronic administrative records of patients with CDI were investigated for epidemiological links supporting hospital transmission. Three levels of epidemiological links were defined: type A (patient-to-patient), type B (ward-to-patient) and type C (overlapping hospital stays in different wards). A comparative descriptive analysis between genomic and epidemiological data was then performed. From January to June 2021, we were able to culture C. difficile from 87 thawed samples from 72 different patients. Fourteen different DLST types were shared within groups of two or more patients and 14 were observed in single patients. A genomic cluster was arbitrary defined as a set of isolates from different patients with differences of 20 loci or less, as determined by cgMLST. Twelve genomic clusters (2 to 8 patients per cluster, total 42) were identified. Among these clusters, epidemiological links between patients were of type A in 3/12 (25%), type B in 3/12 (25%), type C in 3/12 (25%) and absence of links in 3/12 (25%). Among cases with type A links, the median interpatient exposure was 8 days (IQR: 4-12). Among cases with type B links, the median minimum potential ward contamination period was 14 days (IQR: 5-17). The median maximum incubation period was 15.5 days (IQR: 8-28) for cases with both type A and B links. Among clusters determined by cgMLST analysis, half included unexplained nosocomial CDI acquisitions, which may be explained by unidentified epidemiological links and/or asymptomatic colonization. The use of DLST for the initial cluster analysis, followed by whole genome sequencing analysis for isolates sharing the same DLST, is a promising and cost-effective stepwise approach for the investigation of nosocomial transmission of CDI.