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Guh, A. Y. et al. Trends in U.S. Burden of Clostridioides difficile infection and outcomes. N. Engl. J. Med. 382, 13201330 (2020).

Article CAS PubMed PubMed Central Google Scholar

Antibiotic Resistance Threats in the United States (Centers for Disease Control and Prevention, 2019); https://doi.org/10.15620/cdc:82532

Evans, C. T. & Safdar, N. Current trends in the epidemiology and outcomes of Clostridium difficile infection. Clin. Infect. Dis. 60, S66S71 (2015).

Article PubMed Google Scholar

Eyre, D. W. et al. Diverse sources of C. difficile infection identified on whole-genome sequencing. N. Engl. J. Med. 369, 11951205 (2013).

Article CAS PubMed Google Scholar

Walker, A. S. et al. Characterisation of Clostridium difficile hospital ward-based transmission using extensive epidemiological data and molecular typing.PLoS Med. 9, e1001172 (2012).

Article PubMed PubMed Central Google Scholar

Blixt, T. et al. Asymptomatic carriers contribute to nosocomial Clostridium difficile infection: a cohort study of 4508 patients. Gastroenterology 152, 10311041 (2017).

Article PubMed Google Scholar

Galdys, A. L., Curry, S. R. & Harrison, L. H. Asymptomatic Clostridium difficile colonization as a reservoir for Clostridium difficile infection. Expert Rev. Anti Infect. Ther. 12, 967980 (2014).

Article CAS PubMed Google Scholar

Furuya-Kanamori, L. et al. Asymptomatic Clostridium difficile colonization: epidemiology and clinical implications. BMC Infect. Dis. 15, 516 (2015).

Article PubMed PubMed Central Google Scholar

Sethi, A. K., Al-Nassir, W. N., Nerandzic, M. M., Bobulsky, G. S. & Donskey, C. J. Persistence of skin contamination and environmental shedding of Clostridium difficile during and after treatment of C. difficile infection. Infect. Control Hosp. Epidemiol. 31, 2127 (2010).

Article PubMed Google Scholar

McDonald, L. C. & Diekema, D. J. Point-counterpoint: active surveillance for carriers of toxigenic Clostridium difficile should be performed to guide prevention efforts. J. Clin. Microbiol. 56, e00782-18 (2018).

Article PubMed PubMed Central Google Scholar

Baron, S. W. et al. Screening of Clostridioides difficile carriers in an urban academic medical center: understanding implications of disease.Infect. Control Hosp. Epidemiol. 41, 149153 (2020).

PubMed PubMed Central Google Scholar

McDonald, L. C. et al. Clinical practice guidelines for Clostridium difficile infection in adults and children: 2017 update by the Infectious Diseases Society of America (IDSA) and Society for Healthcare Epidemiology of America (SHEA). Clin. Infect. Dis. 66, 987994 (2018).

Article CAS PubMed Google Scholar

Didelot, X. et al. Microevolutionary analysis of Clostridium difficile genomes to investigate transmission. Genome Biol. 13, R118 (2012).

Article PubMed PubMed Central Google Scholar

Surveillance for C. difficile, MRSA, and Other Drug-resistant Infections (Centers for Disease Control and Prevention, 2018); https://www.cdc.gov/nhsn/acute-care-hospital/cdiff-mrsa/index.html

Magill, S. S. et al. Multistate point-prevalence survey of health careassociated infections. N. Engl. J. Med. 370, 11981208 (2014).

Article CAS PubMed PubMed Central Google Scholar

Ponnada, S. et al. Acquisition of Clostridium difficile colonization and infection after transfer from a Veterans Affairs hospital to an affiliated long-term care facility. Infect. Control Hosp. Epidemiol. 38, 10701076 (2017).

Article PubMed Google Scholar

Curry, S. R. et al. Use of multilocus variable number of tandem repeats analysis genotyping to determine the role of asymptomatic carriers in Clostridium difficile transmission. Clin. Infect. Dis. 57, 10941102 (2013).

Article PubMed PubMed Central Google Scholar

Riggs, M. M. et al. Asymptomatic carriers are a potential source for transmission of epidemic and nonepidemic Clostridium difficile strains among long-term care facility residents. Clin. Infect. Dis. 45, 992998 (2007).

Article PubMed Google Scholar

Sheth, P. M. et al. Evidence of transmission of Clostridium difficile in asymptomatic patients following admission screening in a tertiary care hospital. PLoS ONE 14, e0207138 (2019).

Article CAS PubMed PubMed Central Google Scholar

Kong, L. Y. et al. Clostridium difficile: investigating transmission patterns between infected and colonized patients using whole genome sequencing. Clin. Infect. Dis. 68, 204209 (2019).

Article PubMed Google Scholar

Zacharioudakis, I. M., Zervou, F. N., Pliakos, E. E., Ziakas, P. D. & Mylonakis, E. Colonization with toxinogenic C. difficile upon hospital admission, and risk of infection: a systematic review and meta-analysis. Am. J. Gastroenterol. 110, 381390 (2015).

Article PubMed Google Scholar

Eyre, D. W. et al. Asymptomatic Clostridium difficile colonisation and onward transmission. PLoS ONE 8, e78445 (2013).

Article CAS PubMed PubMed Central Google Scholar

Truong, C. et al. Clostridium difficile rates in asymptomatic and symptomatic hospitalized patients using nucleic acid testing. Diagn. Microbiol. Infect. Dis. 87, 365370 (2017).

Article CAS PubMed Google Scholar

Clabots, C. R., Johnson, S., Olson, M. M., Peterson, L. R. & Gerding, D. N. Acquisition of Clostridium difficile by hospitalized patients: evidence for colonized new admissions as a source of infection. J. Infect. Dis. 166, 561567 (1992).

Article CAS PubMed Google Scholar

Worley, J. et al. Genomic determination of relative risks for Clostridioides difficile infection from asymptomatic carriage in intensive care unit patients.Clin. Infect. Dis. 73, e1727e1736 (2021).

Article CAS PubMed Google Scholar

Brazier, J. S. et al. Screening for carriage and nosocomial acquisition of Clostridium difficile by culture: a study of 284 admissions of elderly patients to six general hospitals in Wales. J. Hosp. Infect. 43, 317319 (1999).

Article CAS PubMed Google Scholar

Lanzas, C. & Dubberke, E. R. Effectiveness of screening hospital admissions to detect asymptomatic carriers of Clostridium difficile: a modeling evaluation. Infect. Control Hosp. Epidemiol. 35, 10431050 (2014).

Article PubMed Google Scholar

Longtin, Y. et al. Effect of detecting and isolating Clostridium difficile carriers at hospital admission on the incidence of C. difficile infections: a quasi-experimental controlled study. JAMA Intern. Med. 176, 796804 (2016).

Article PubMed Google Scholar

Tickler, I. A. et al. Strain types and antimicrobial resistance patterns of Clostridium difficile isolates from the United States, 2011 to 2013. Antimicrob. Agents Chemother. 58, 42144218 (2014).

Article PubMed PubMed Central Google Scholar

Keegan, J. et al. Toxigenic Clostridioides difficile colonization as a risk factor for development of C. difficile infection in solid-organ transplant patients. Infect. Control Hosp. Epidemiol. 42, 287291 (2021).

Article PubMed Google Scholar

Shim, J. K., Johnson, S., Samore, M. H., Bliss, D. Z. & Gerding, D. N. Primary symptomless colonisation by Clostridium difficile and decreased risk of subsequent diarrhoea. Lancet 351, 633636 (1998).

Article CAS PubMed Google Scholar

Goldenberg, J. Z. et al. Probiotics for the prevention of Clostridium difficile-associated diarrhea in adults and children.Cochrane Database Syst. Rev. 12, CD006095 (2017).

PubMed Google Scholar

Mullane, K. M. et al. A randomized, placebo-controlled trial of fidaxomicin for prophylaxis of Clostridium difficile-associated diarrhea in adults undergoing hematopoietic stem cell transplantation. Clin. Infect. Dis. 68, 196203 (2019).

Article CAS PubMed Google Scholar

Baunwall, S. M. D. et al. Faecal microbiota transplantation for recurrent Clostridioides difficile infection: an updated systematic review and meta-analysis. EClinicalMedicine 2930, 100642 (2020).

Article PubMed PubMed Central Google Scholar

Tamma, P. D. et al. Association of a safety program for improving antibiotic use with antibiotic use and hospital-onset Clostridioides difficile infection rates among US hospitals. JAMA Netw. Open 4, e210235 (2021).

Article PubMed PubMed Central Google Scholar

Baur, D. et al. Effect of antibiotic stewardship on the incidence of infection and colonisation with antibiotic-resistant bacteria and Clostridium difficile infection: a systematic review and meta-analysis. Lancet Infect. Dis. 17, 9901001 (2017).

Article PubMed Google Scholar

Caroff, D. A., Yokoe, D. S. & Klompas, M. Evolving insights into the epidemiology and control of Clostridium difficile in hospitals. Clin. Infect. Dis. 65, 12321238 (2017).

Article CAS PubMed Google Scholar

Crobach, M. J. T. et al. Understanding Clostridium difficile colonization. Clin. Microbiol. Rev. 31, e00021-17 (2018).

Article CAS PubMed PubMed Central Google Scholar

Behroozian, A. A. et al. Detection of mixed populations of Clostridium difficile from symptomatic patients using capillary-based polymerase chain reaction ribotyping. Infect. Control Hosp. Epidemiol. 34, 961966 (2013).

Article PubMed PubMed Central Google Scholar

Dayananda, P. & Wilcox, M. H. A review of mixed strain clostridium difficile colonization and infection. Front. Microbiol. 10, 692 (2019).

Article PubMed PubMed Central Google Scholar

Sun, J., Mc Millen, T., Babady, N. E. & Kamboj, M. Role of coinfecting strains in recurrent Clostridium difficile infection. Infect. Control Hosp. Epidemiol. 37, 14811484 (2016).

Article PubMed PubMed Central Google Scholar

Seekatz, A. M. et al. Presence of multiple Clostridium difficile strains at primary infection is associated with development of recurrent disease. Anaerobe 53, 7481 (2018).

Article PubMed PubMed Central Google Scholar

Gonzalez-Orta, M. et al. Are many patients diagnosed with healthcare-associated Clostridioides difficile infections colonized with the infecting strain on admission? Clin. Infect. Dis. 69, 18011804 (2019).

Article PubMed Google Scholar

Lin, M. Y. et al. Impact of mandatory infectious disease specialist approval on hospital-onset Clostridioides difficile infection rates and testing appropriateness.Clin. Infect. Dis. 77, 346350 (2023).

Article PubMed Google Scholar

Bolger, A. M., Lohse, M. & Usadel, B. Trimmomatic: a flexible trimmer for Illumina sequence data. Bioinformatics 30, 21142120 (2014).

Article CAS PubMed PubMed Central Google Scholar

Hunt, M. et al. ARIBA: rapid antimicrobial resistance genotyping directly from sequencing reads. Microb. Genom. 3, e000131 (2017).

PubMed PubMed Central Google Scholar

Bankevich, A. et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J. Comput. Biol. 19, 455477 (2012).

Article CAS PubMed PubMed Central Google Scholar

Seemann, T. Prokka: rapid prokaryotic genome annotation. Bioinformatics 30, 20682069 (2014).

Article CAS PubMed Google Scholar

Crawford, R. D. & Snitkin, E. S. cognac: rapid generation of concatenated gene alignments for phylogenetic inference from large, bacterial whole genome sequencing datasets. BMC Bioinformatics 22, 70 (2021).

Article CAS PubMed PubMed Central Google Scholar

Elliott, B., Androga, G. O., Knight, D. R. & Riley, T. V. Clostridium difficile infection: evolution, phylogeny and molecular epidemiology. Infect. Genet. Evol. 49, 111 (2017).

Article PubMed Google Scholar

Li, H. Aligning sequence reads, clone sequences and assembly contigs with BWAMEM. Preprint at https://doi.org/10.48550/arXiv.1303.3997 (2013).

Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 20782079 (2009).

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