{"doi":"10.1101/2023.09.26.23295023","title":"Genomic surveillance of <i>Clostridioides difficile</i> transmission and virulence in a healthcare setting","abstract":"Abstract Clostridioides difficile infection (CDI) is a major cause of healthcare-associated diarrhea, despite the widespread implementation of contact precautions for patients with CDI. Here, we investigate strain contamination in a hospital setting and genomic determinants of disease outcomes. Across two wards over six months, we selectively cultured C. difficile from patients (n=384) and their environments. Whole-genome sequencing (WGS) of 146 isolates revealed that most C. difficile isolates were from clade 1 (131/146, 89.7%), while only one isolate of the hypervirulent ST1 was recovered. Of culture-positive admissions (n=79), 19 (24%) of patients were colonized with toxigenic C. difficile on admission to the hospital. We defined 25 strain networks at ≤ 2 core gene SNPs; 2 of these networks contain strains from different patients. Strain networks were temporally linked (p&lt;0.0001). To understand genomic correlates of disease, we conducted WGS on an additional cohort of C. difficile (n=102 isolates) from the same hospital and confirmed that clade 1 isolates are responsible for most CDI cases. We found that while toxigenic C. difficile isolates are associated with the presence of cdtR , nontoxigenic isolates have an increased abundance of prophages. Our pangenomic analysis of clade 1 isolates suggests that while toxin genes ( tcdABER and cdtR ) were associated with CDI symptoms, they are dispensable for patient colonization. These data indicate toxigenic and nontoxigenic C. difficile contamination persists in a hospital setting and highlight further investigation into how accessory genomic repertoires contribute to C. difficile colonization and disease.","journal":"medRxiv","year":2023,"id":395138,"datarank":0.20794415416798362,"base_score":1.3862943611198906,"endowment":1.3862943611198906,"self_citation_contribution":0.20794415416798362,"citation_network_contribution":0.0,"self_endowment_contribution":0.20794415416798362,"citer_contribution":0.0,"corpus_percentile":null,"corpus_rank":null,"citation_count":3,"citer_count":0,"citers_with_citation_signal":0,"citers_with_endowment":0,"datacite_reuse_total":0,"is_dataset":false,"is_dataset_confidence":0.9518,"is_data_producer":false,"deposit_databanks":null,"is_oa":true,"file_count":0,"downloads":0,"has_version_chain":false,"published_date":"2023-01-01","fair_score":null,"fair_percentile":null,"algorithm_id":"datarank_citation_only_1hop_v6","ranking_scope":"data_only","authors":[{"id":304642,"name":"Skye R. S. Fishbein","orcid":"0000-0002-9554-1170","position":1,"is_corresponding":false},{"id":440237,"name":"Kailun Zhang","orcid":"0000-0002-6994-9033","position":2,"is_corresponding":false},{"id":436911,"name":"Tiffany Hink","orcid":null,"position":3,"is_corresponding":false},{"id":435923,"name":"Kimberly A. Reske","orcid":"0000-0003-4752-8796","position":4,"is_corresponding":false},{"id":843151,"name":"Candice Cass","orcid":null,"position":5,"is_corresponding":false},{"id":865132,"name":"Zainab Hassan Iqbal","orcid":"0000-0003-4594-3646","position":6,"is_corresponding":false},{"id":865131,"name":"Emily Struttmann","orcid":"0000-0002-9307-4214","position":7,"is_corresponding":false},{"id":396876,"name":"Erik R. Dubberke","orcid":"0000-0003-3779-2796","position":8,"is_corresponding":false},{"id":233597,"name":"Gautam Dantas","orcid":"0000-0003-0455-8370","position":9,"is_corresponding":false},{"id":821450,"name":"Erin Newcomer","orcid":"0000-0002-2028-0359","position":0,"is_corresponding":true}],"reference_count":67,"raw_metadata":{"citation_network_status":"fetched"},"created_at":"2026-07-19T01:19:18.686170Z","pmid":"38105952","pmcid":null,"fwci":null,"citation_percentile":null,"influential_citations":0,"oa_status":null,"license":null,"views":0,"total_file_size_bytes":0,"version_count":0,"fair_f":null,"fair_a":null,"fair_i":null,"fair_r":null,"fair_zscore":null,"fair_rationale":null,"fair_model":null,"fair_agent_version":null,"fair_fulltext_source":null,"fair_has_llm":null,"fair_computed_at":null,"clinical_trials":[],"software_tools":[],"db_accessions":[],"linked_datasets":[],"topics":[]}