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

Abstract

Aims:To investigate if Clostridium (Clostridioides) difficile infection (CDI), traditionally thought of as hospital-acquired, can be genomically linked to hospital or community environmental sources, and to define possible importation routes from the community to the hospital. Methods and Results:In 2019, C. difficile was isolated from 89/300 (29.7%) floor and 96/300 (32.0%) shoe sole samples at a tertiary hospital in Western Australia.Non-toxigenic C. difficile ribotype (RT) 010 predominated among floor (96.6%) and shoe sole (73.2%) isolates, while toxigenic RT 014/020 was most prevalent among contemporaneous clinical cases (33.0%) at the hospital. Whole-genome sequencing and high-resolution core genome single nucleotide polymorphism (cgSNP) analysis on C. difficile strains from hospital and community sources showed no clinical C. difficile RT 014/020 strains were genetically related, and evidence of frequent longdistance, multi-directional spread between humans, animals and the environment.In addition, cgSNP analysis of environmental RT 010 strains suggested transportation of C. difficile via shoe soles. Conclusions: While C. difficile RT 014/020 appears to spread via routes outside the healthcare system, RT 010 displayed a pattern of possible importation from the community into the hospital.Significance and Impact of Study: These findings suggest developing communitybased infection prevention and control strategies could significantly lower rates of CDI in the hospital setting.

Persistence of spore-formingClostridium(Clostridioides)difficilethrough wastewater treatment plants in Western Australia

“…Although the zoonotic and environmental transmission of C. difficile is still being debated, recent data suggest long-distance transmission of C. difficile between animals, environmental reservoirs and humans (18, 19, 39, 42, 49, 50). In our recent study where 142 C. difficile RT014 strains from humans, animals, compost, hospital gardens, lawns, root vegetables, shoes and water bodies were sequenced and analysed, extensive co-clustering of human, animal and environmental strains was found, with 9% of the human strains having a clonal relationship (≤2 SNP) indicative of direct transmission and 60% closely related (≤9 SNP) to at least one animal or environmental strains (22). We suspect the land application of biosolids and animal manure has aided in the dissemination of C. difficile in the environment and may have contributed to a rise in CA-CDI.…”

“…These are likely to be community-based, such as foodborne and/or environmental acquisition, as clinically important C. difficile strains have been isolated from animals, meat, vegetables, compost, gardens, lawns, rivers and lakes (15)(16)(17). This is in agreement with genomic studies in Europe and Australia that show (i) long-distance or cross-continental clonal transmission of C. difficile between humans and animals with ≤2 single nucleotide polymorphism (SNP) differences in their core-genome (18,19), and (ii) genetically closely related C. difficile strains isolated from humans, food and the environment (retail potatoes, ready-to-eat salads, meat, compost, rivers, lakes, lawns and the end-products of wastewater treatment plants) (20)(21)(22). Taken together, this suggests a complex dissemination pathway of C. difficile between animals, humans and the environment.…”

Make It Less difficile: Understanding Genetic Evolution and Global Spread of Clostridioides difficile

“…On the other hand, a study conducted in the earlier period 2013–2018 in a geographically larger area covering 10 diagnostic laboratories from five states in Australia (Western Australia, New South Wales, Victoria, South Australia, and Queensland), reported 203 different RTs in predominantly elderly subjects, with RT014/020 being the most common, while RT027 and RT078 only rarely found [ 145 ]. Additionally, toxigenic RT014/020 was found to be more common among clinical cases in a tertiary hospital in Perth, while non-toxigenic RT010 was prevalent among floor samples and shoe soles of hospital staff, visitors and patients [ 146 ]. Outside of Australia, few research works are available.…”

Spore-Forming Clostridium ( Clostridioides ) difficile in Wastewater Treatment Plants in Western Australia

“…These are likely to be community based, such as foodborne and/or environmental acquisition, as clinically important C. difficile strains have been isolated from animals, meat, vegetables, compost, gardens, lawns, rivers, and lakes ( 15 – 17 ). This is in agreement with genomic studies in Europe and Australia that show (i) long-distance or cross-continental clonal transmission of C. difficile between humans and animals with ≤2 single nucleotide polymorphism (SNP) differences in their core genome ( 18 , 19 ) and (ii) genetically closely related C. difficile strains isolated from humans, food, and the environment (retail potatoes, ready-to-eat salads, meat, compost, rivers, lakes, lawns, and the end products of wastewater treatment plants) ( 20 – 22 ). Taken together, this suggests a complex dissemination pathway of C. difficile between animals, humans, and the environment.…”