{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T20:55:18Z","timestamp":1792788918997,"version":"4.5.0"},"reference-count":69,"publisher":"MDPI AG","issue":"9","license":[{"start":{"date-parts":[[2026,9,21]],"date-time":"2026-09-21T00:00:00Z","timestamp":1789948800000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Fundaci\u00f3n Canaria de Investigaci\u00f3n Sanitaria de Canarias","award":["PIFIISC24\/03"],"award-info":[{"award-number":["PIFIISC24\/03"]}],"id":[{"id":"https:\/\/ror.org\/03vhx9d88","id-type":"ROR","asserted-by":"crossref"}]},{"award":["PIFIISC24\/03"],"award-info":[{"award-number":["PIFIISC24\/03"]}],"id":[{"id":"https:\/\/ror.org\/03vhx9d88","id-type":"ROR","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Antibiotics"],"abstract":"<jats:p>Background\/Objectives:\u00a0Clostridioides difficile colonization is common among hospitalized onco-hematological patients, yet its clinical significance and risk factors in this population remain incompletely characterized. This study aimed to determine the prevalence, risk factors, and genomic characteristics of C. difficile colonization among oncology and hematology inpatients, and to assess its relationship with progression to symptomatic infection. Methods: We conducted a prospective cohort study of patients admitted to the oncology and hematology departments of a tertiary-care hospital in the Canary Islands, Spain, between March and October 2025. Weekly active screening for C. difficile colonization was performed on stool samples throughout hospitalization. Risk factors were assessed using multivariable logistic regression, and whole-genome sequencing was performed on 16 of the 23 recovered isolates (after excluding 3 non-recoverable and 4 contaminated isolates) to characterize sequence types, ribotypes, and antimicrobial resistance determinants. Results: Among 215 patients (262 admission episodes), colonization was detected in 23 episodes (8.8%), with higher rates in oncology (10.9%) than hematology (7.2%; adjusted OR 0.37, 95% CI 0.14\u20130.96, p = 0.042). Chemotherapy administered during hospitalization was the strongest independent risk factor for colonization (adjusted OR 4.16, 95% CI 1.56\u201311.10, p = 0.004). Only 4.3% of colonizations were classified as truly community-associated, with 95.7% of patients showing documented healthcare contact. Sequencing of 16 isolates identified nine sequence types, including ST11 (ribotype 078, of zoonotic origin) and rare ribotypes (RT010, RT451); four isolates (36%) exhibited moxifloxacin resistance linked to gyrA\/gyrB mutations, while all remained susceptible to vancomycin and metronidazole. No colonized patient progressed to symptomatic infection; the single CDI case in the cohort occurred in a non-colonized patient. Conclusions: These findings support current recommendations against isolating or treating asymptomatically colonized patients, while underscoring the need for continued genomic surveillance and reinforced environmental hygiene and antimicrobial stewardship in this high-risk population.<\/jats:p>","DOI":"10.3390\/antibiotics15090939","type":"journal-article","created":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T15:28:43Z","timestamp":1790090923000},"page":"939","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Clostridioides difficile Among Asymptomatic Onco-Hematological Carriers: Risk Factors, Molecular Characterization, and Antibiotic Resistance"],"prefix":"10.3390","volume":"15","author":[{"given":"Ana","family":"Mart\u00edn Berm\u00fadez","sequence":"first","affiliation":[{"name":"Department of Microbiology, Hospital Universitario de Canarias, 38320 San Cristobal de La Laguna, Tenerife, Spain"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"conceptualization","vocabulary":"credit"},{"role":"methodology","vocabulary":"credit"},{"role":"validation","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"visualization","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0009-0008-8214-2008","authenticated-orcid":false,"given":"Sara","family":"Milosevic","sequence":"additional","affiliation":[{"name":"Center for Rare Diseases (CIBERER), Universidad de La Laguna, 38320 San Cristobal de La Laguna, Tenerife, Spain"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"methodology","vocabulary":"credit"},{"role":"software","vocabulary":"credit"},{"role":"validation","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"},{"role":"visualization","vocabulary":"credit"}]},{"given":"Maria Jose","family":"Ramos-Real","sequence":"additional","affiliation":[{"name":"Department of Microbiology, Hospital Universitario de Canarias, 38320 San Cristobal de La Laguna, Tenerife, Spain"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"conceptualization","vocabulary":"credit"},{"role":"validation","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"},{"role":"project-administration","vocabulary":"credit"}]},{"given":"Eduardo","family":"Salido","sequence":"additional","affiliation":[{"name":"Department of Pathology, Hospital Universitario de Canarias, 38320 San Cristobal de La Laguna, Tenerife, Spain"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"conceptualization","vocabulary":"credit"},{"role":"validation","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"},{"role":"resources","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"},{"role":"project-administration","vocabulary":"credit"}]},{"given":"Jose Luis","family":"Irribarren","sequence":"additional","affiliation":[{"name":"Department of Critical Care, Hospital Universitario de Canarias, 38320 San Cristobal de La Laguna, Tenerife, Spain"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"investigation","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7388-4842","authenticated-orcid":false,"given":"Maria","family":"Lecuona","sequence":"additional","affiliation":[{"name":"Department of Microbiology, Hospital Universitario de Canarias, 38320 San Cristobal de La Laguna, Tenerife, Spain"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ana","family":"L\u00f3pez-Lirola","sequence":"additional","affiliation":[{"name":"Infectious Diseases Department, Hospital Universitario de Canarias, 38320 San Cristobal de La Laguna, Tenerife, Spain"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"writing-review-editing","vocabulary":"credit"},{"role":"investigation","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0781-9161","authenticated-orcid":false,"given":"Enrique","family":"Gonz\u00e1lez D\u00e1vila","sequence":"additional","affiliation":[{"name":"Mathematics, Statistics and Operations Research Department, IMAULL Institute, Universidad de La Laguna, 38206 San Cristobal de La Laguna, Tenerife, Spain"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"software","vocabulary":"credit"},{"role":"formal-analysis","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-8488-7723","authenticated-orcid":false,"given":"Bernardo","family":"Gonzalez","sequence":"additional","affiliation":[{"name":"Hematology Department, Hospital Universitario de Canarias, 38320 San Cristobal de La Laguna, Tenerife, Spain"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"writing-review-editing","vocabulary":"credit"},{"role":"resources","vocabulary":"credit"}]},{"given":"Rosa","family":"Garcia","sequence":"additional","affiliation":[{"name":"Oncology Department, Hospital Universitario de Canarias, 38320 San Cristobal de La Laguna, Tenerife, Spain"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"resources","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-9024-0803","authenticated-orcid":false,"given":"Miriam","family":"Hern\u00e1ndez-Porto","sequence":"additional","affiliation":[{"name":"Department of Microbiology, Hospital Universitario de Canarias, 38320 San Cristobal de La Laguna, Tenerife, Spain"},{"name":"Department of Obstetrics, Gynecology, Pediatrics, Preventive Medicine and Public Health, Facultad de Ciencias de la Salud, Universidad de La Laguna, 38200 San Cristobal de La Laguna, Tenerife, Spain"}],"role":[{"vocabulary":"crossref","role":"author"},{"role":"conceptualization","vocabulary":"credit"},{"role":"methodology","vocabulary":"credit"},{"role":"data-curation","vocabulary":"credit"},{"role":"writing-original-draft","vocabulary":"credit"},{"role":"writing-review-editing","vocabulary":"credit"},{"role":"supervision","vocabulary":"credit"},{"role":"funding-acquisition","vocabulary":"credit"},{"role":"project-administration","vocabulary":"credit"}]}],"member":"1968","published-online":{"date-parts":[[2026,9,21]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"2150452","DOI":"10.1080\/21505594.2022.2150452","article-title":"Pathogenicity and Virulence of Clostridioides difficile","volume":"14","author":"Buddle","year":"2023","journal-title":"Virulence"},{"key":"ref_2","doi-asserted-by":"crossref","first-page":"1800516","DOI":"10.2807\/1560-7917.ES.2018.23.46.1800516","article-title":"Prevalence of Healthcare-Associated Infections, Estimated Incidence and Composite Antimicrobial Resistance Index in Acute Care Hospitals and Long-Term Care Facilities: Results from Two European Point Prevalence Surveys, 2016 to 2017","volume":"23","author":"Suetens","year":"2018","journal-title":"Eurosurveillance"},{"key":"ref_3","unstructured":"Kinross, P. (2019). European Surveillance of Clostridioides (Clostridium) difficile Infections: Surveillance Protocol Version 2.4, European Centre for Disease Prevention and Control."},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"604","DOI":"10.1128\/CMR.00016-13","article-title":"Diagnosis of Clostridium difficile Infection: An Ongoing Conundrum for Clinicians and for Clinical Laboratories","volume":"26","author":"Burnham","year":"2013","journal-title":"Clin. Microbiol. Rev."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"4182","DOI":"10.1172\/JCI72336","article-title":"Clostridium difficile and the Microbiota","volume":"124","author":"Seekatz","year":"2014","journal-title":"J. Clin. Investig."},{"key":"ref_6","doi-asserted-by":"crossref","first-page":"110","DOI":"10.1186\/s13756-024-01461-x","article-title":"Hand and Environmental Hygiene: Respective Roles for MRSA, Multi-Resistant Gram Negatives, Clostridioides difficile, and Candida spp.","volume":"13","author":"Boyce","year":"2024","journal-title":"Antimicrob. Resist. Infect. Control"},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"743","DOI":"10.1007\/s41999-024-00942-x","article-title":"Recurrence of Clostridioides difficile Infection and Mortality in Older Inpatients","volume":"15","author":"Remelli","year":"2024","journal-title":"Eur. Geriatr. Med."},{"key":"ref_8","unstructured":"European Centre for Disease Prevention and Control (2024). Clostridium difficile Infections\u2014Annual Epidemiological Report 2018\u20132020, European Centre for Disease Prevention and Control."},{"key":"ref_9","doi-asserted-by":"crossref","first-page":"1031","DOI":"10.1053\/j.gastro.2016.12.035","article-title":"Asymptomatic Carriers Contribute to Nosocomial Clostridium difficile Infection: A Cohort Study of 4508 Patients","volume":"152","author":"Blixt","year":"2017","journal-title":"Gastroenterology"},{"key":"ref_10","doi-asserted-by":"crossref","unstructured":"Mastrantonio, P., and Rupnik, M. (2024). Updates on Clostridioides difficile in Europe, Springer. [2nd ed.].","DOI":"10.1007\/978-3-031-42108-2"},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"237","DOI":"10.1016\/j.femsim.2004.03.007","article-title":"Human Antibody Response to Surface Layer Proteins in Clostridium difficile Infection","volume":"41","author":"Drudy","year":"2004","journal-title":"FEMS Immunol. Med. Microbiol."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"750","DOI":"10.1099\/jmm.0.47532-0","article-title":"Immunoreactive Cell Wall Proteins of Clostridium difficile Identified by Human Sera","volume":"57","author":"Wright","year":"2008","journal-title":"J. Med. Microbiol."},{"key":"ref_13","first-page":"1017","article-title":"Gender Differences in Non-Toxigenic Clostridium difficile Colonization and Risk of Subsequent C. difficile Infection","volume":"2","author":"Natarajan","year":"2015","journal-title":"Clin. Res. Infect. Dis."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"e00021-17","DOI":"10.1128\/CMR.00021-17","article-title":"Understanding Clostridium difficile colonization","volume":"31","author":"Crobach","year":"2018","journal-title":"Clin. Microbiol. Rev."},{"key":"ref_15","doi-asserted-by":"crossref","first-page":"1683","DOI":"10.3201\/eid2509.181142","article-title":"Risk for Clostridioides difficile Infection among Older Adults with Cancer","volume":"25","author":"Kamboj","year":"2019","journal-title":"Emerg. Infect. Dis."},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"102106","DOI":"10.1016\/j.anaerobe.2019.102106","article-title":"A Nationwide Study of Molecular Epidemiology and Antimicrobial Susceptibility of Clostridioides difficile in South Korea","volume":"60","author":"Byun","year":"2019","journal-title":"Anaerobe"},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"22135","DOI":"10.1038\/s41598-020-79123-2","article-title":"Phylogenomic Analysis of Clostridioides difficile Ribotype 106 Strains Reveals Novel Genetic Islands and Emergent Phenotypes","volume":"10","author":"Roxas","year":"2020","journal-title":"Sci. Rep."},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"e00923-17","DOI":"10.1128\/genomeA.00923-17","article-title":"Complete Genome Sequence of Clostridioides difficile Epidemic Strain DH\/NAP11\/106\/ST-42, Isolated from Stool from a Pediatric Patient with Diarrhea","volume":"5","author":"Ozer","year":"2017","journal-title":"Genome Announc."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"718","DOI":"10.1017\/ice.2017.48","article-title":"Risk of Clostridium difficile Infection in Hematology-Oncology Patients Colonized with Toxigenic C. difficile","volume":"38","author":"Cannon","year":"2017","journal-title":"Infect. Control Hosp. Epidemiol."},{"key":"ref_20","first-page":"001748","article-title":"Molecular Characterization and Genotyping of Isolates from Cancer Patients with Clostridioides difficile Infection or Asymptomatic Colonization","volume":"72","author":"Peniche","year":"2023","journal-title":"J. Med. Microbiol."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"6","DOI":"10.1186\/s13099-024-00674-0","article-title":"Heterogeneity of Clostridioides difficile Asymptomatic Colonization Prevalence: A Systematic Review and Meta-Analysis","volume":"17","author":"Blumberg","year":"2025","journal-title":"Gut Pathog."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"209","DOI":"10.1007\/s40121-022-00722-9","article-title":"Risk Factors Associated with Severe Clostridioides difficile Infection in Patients with Cancer","volume":"12","author":"Francisco","year":"2023","journal-title":"Infect. Dis. Ther."},{"key":"ref_23","doi-asserted-by":"crossref","first-page":"102993","DOI":"10.1016\/j.anaerobe.2025.102993","article-title":"Detection and Risk Factor Analysis of Clostridioides difficile Infection in Patients with Malignant Tumours","volume":"96","author":"Guo","year":"2025","journal-title":"Anaerobe"},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"565","DOI":"10.1017\/ice.2020.1236","article-title":"Risk Factors for Clostridioides difficile Colonization among Hospitalized Adults: A Meta-Analysis and Systematic Review","volume":"42","author":"Anjewierden","year":"2021","journal-title":"Infect. Control Hosp. Epidemiol."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"37","DOI":"10.1093\/cid\/ciae429","article-title":"Diverse Sources and Latent Reservoirs of Community-Associated Clostridioides difficile Infection","volume":"80","author":"Alshannaq","year":"2025","journal-title":"Clin. Infect. Dis."},{"key":"ref_26","doi-asserted-by":"crossref","unstructured":"Stoesser, N., Eyre, D.W., Quan, T.P., Godwin, H., Pill, G., Mbuvi, E., Vaughan, A., Griffiths, D., Martin, J., and Fawley, W. (2017). Epidemiology of Clostridium difficile in Infants in Oxfordshire, UK: Risk Factors for Colonization and Carriage, and Genetic Overlap with Regional C. difficile Infection Strains. PLoS ONE, 12.","DOI":"10.1371\/journal.pone.0182307"},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"204","DOI":"10.1056\/NEJM198901263200402","article-title":"Nosocomial Acquisition of Clostridium difficile Infection","volume":"320","author":"McFarland","year":"1989","journal-title":"N. Engl. J. Med."},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"e0330023","DOI":"10.1128\/mbio.03300-23","article-title":"Genomic Surveillance of Clostridioides difficile Transmission and Virulence in a Healthcare Setting","volume":"15","author":"Newcomer","year":"2024","journal-title":"mBio"},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"ofag121","DOI":"10.1093\/ofid\/ofag121","article-title":"Relationship Between Clostridioides difficile Stool Concentration, Nucleic Acid Amplification Test Results, and Environmental Contamination","volume":"13","author":"Lee","year":"2026","journal-title":"Open Forum Infect. Dis."},{"key":"ref_30","unstructured":"European Centre for Disease Prevention and Control (2024). Survey Protocol for Whole Genome Sequencing of Clostridioides difficile Isolates from Tertiary Acute Care Hospitals, EU\/EEA, 2022\u20132023, European Centre for Disease Prevention and Control."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"479","DOI":"10.1016\/j.ijmm.2016.07.003","article-title":"Molecular Characterisation of Czech Clostridium difficile Isolates Collected in 2013\u20132015","volume":"306","author":"Krutova","year":"2016","journal-title":"Int. J. Med. Microbiol."},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"2200244","DOI":"10.2807\/1560-7917.ES.2022.27.49.2200244","article-title":"Sentinel Surveillance and Epidemiology of Clostridioides difficile in Denmark, 2016 to 2019","volume":"27","author":"Persson","year":"2022","journal-title":"Eurosurveillance"},{"key":"ref_33","doi-asserted-by":"crossref","unstructured":"Marcos, P., Whyte, P., Burgess, C., Ekhlas, D., and Bolton, D. (2022). Detection and Genomic Characterisation of Clostridioides difficile from Spinach Fields. Pathogens, 11.","DOI":"10.3390\/pathogens11111310"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"329","DOI":"10.1099\/jmm.0.46931-0","article-title":"Variant Forms of the Binary Toxin CDT Locus and TcdC Gene in Clostridium difficile Strains","volume":"56","author":"Stare","year":"2007","journal-title":"J. Med. Microbiol."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"215","DOI":"10.1128\/JCM.01599-06","article-title":"TcdC Genotypes Associated with Severe TcdC Truncation in an Epidemic Clone and Other Strains of Clostridium difficile","volume":"45","author":"Curry","year":"2007","journal-title":"J. Clin. Microbiol."},{"key":"ref_36","doi-asserted-by":"crossref","unstructured":"Lyon, S.A., Hutton, M.L., Rood, J.I., Cheung, J.K., and Lyras, D. (2016). CdtR Regulates TcdA and TcdB Production in Clostridium difficile. PLoS Pathog., 12.","DOI":"10.1371\/journal.ppat.1005758"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"1632","DOI":"10.1016\/j.str.2015.06.018","article-title":"Structural Basis of Proline-Proline Peptide Bond Specificity of the Metalloprotease Zmp1 Implicated in Motility of Clostridium difficile","volume":"23","author":"Schacherl","year":"2015","journal-title":"Structure"},{"key":"ref_38","first-page":"23","article-title":"Recent Advances in the Understanding of Antibiotic Resistance in Clostridium difficile Infection","volume":"3","author":"Spigaglia","year":"2016","journal-title":"Ther. Adv. Infect. Dis."},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"612","DOI":"10.1111\/mmi.12299","article-title":"The Functional VanGCd Cluster of Clostridium difficile Does Not Confer Vancomycin Resistance","volume":"89","author":"Ammam","year":"2013","journal-title":"Mol. Microbiol."},{"key":"ref_40","doi-asserted-by":"crossref","first-page":"e64325","DOI":"10.7554\/eLife.64325","article-title":"Major Genetic Discontinuity and Novel Toxigenic Species in Clostridioides difficile Taxonomy","volume":"10","author":"Knight","year":"2021","journal-title":"eLife"},{"key":"ref_41","doi-asserted-by":"crossref","first-page":"859","DOI":"10.1093\/jac\/dkz513","article-title":"Constitutive Expression of the Cryptic VanGCd Operon Promotes Vancomycin Resistance in Clostridioides difficile Clinical Isolates","volume":"75","author":"Shen","year":"2020","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_42","doi-asserted-by":"crossref","unstructured":"Sholeh, M., Beig, M., Kouhsari, E., Rohani, M., Katouli, M., and Badmasti, F. (2024). Global Insights into the Genome Dynamics of Clostridioides difficile Associated with Antimicrobial Resistance, Virulence, and Genomic Adaptations among Clonal Lineages. Front. Cell. Infect. Microbiol., 14.","DOI":"10.3389\/fcimb.2024.1493225"},{"key":"ref_43","doi-asserted-by":"crossref","first-page":"109","DOI":"10.1038\/ng.2478","article-title":"Emergence and Global Spread of Epidemic Healthcare-Associated Clostridium difficile","volume":"45","author":"He","year":"2013","journal-title":"Nat. Genet."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"4130","DOI":"10.1038\/s41467-023-39429-x","article-title":"Decoding a Cryptic Mechanism of Metronidazole Resistance among Globally Disseminated Fluoroquinolone-Resistant Clostridioides difficile","volume":"14","author":"Olaitan","year":"2023","journal-title":"Nat. Commun."},{"key":"ref_45","doi-asserted-by":"crossref","first-page":"381","DOI":"10.1038\/ajg.2015.22","article-title":"Colonization with Toxinogenic C. difficile upon Hospital Admission, and Risk of Infection: A Systematic Review and Meta-Analysis","volume":"110","author":"Zacharioudakis","year":"2015","journal-title":"Am. J. Gastroenterol."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"77","DOI":"10.1093\/cid\/ciad142","article-title":"Natural History of Clostridioides difficile Colonization and Infection Following New Acquisition of Carriage in Healthcare Settings: A Prospective Cohort Study","volume":"77","author":"Curry","year":"2023","journal-title":"Clin. Infect. Dis."},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"1719","DOI":"10.1001\/jama.2015.3725","article-title":"Administration of Spores of Nontoxigenic Clostridium difficile Strain M3 for Prevention of Recurrent C. difficile Infection: A Randomized Clinical Trial","volume":"313","author":"Gerding","year":"2015","journal-title":"JAMA-J. Am. Med. Assoc."},{"key":"ref_48","doi-asserted-by":"crossref","unstructured":"Hensen, A.D.O., Harmanus, C., Verbeek-Menken, P.H., Koopman, J.P.R., Lamers, O.A.C., Roozen, G.V.T., Janse, J.J., Balke-Buijs, M., van der Stoep, M.Y.E.C., and Meij, P. (2026). Experimental Human Colonisation with Non-Toxigenic Clostridioides difficile: A Placebo-Controlled Randomised Clinical Trial. Nat. Commun.","DOI":"10.1038\/s41467-026-74327-y"},{"key":"ref_49","doi-asserted-by":"crossref","first-page":"1781","DOI":"10.1086\/345676","article-title":"Colonization for the Prevention of Clostridium difficile Disease in Hamsters","volume":"186","author":"Sambol","year":"2002","journal-title":"J. Infect. Dis."},{"key":"ref_50","doi-asserted-by":"crossref","first-page":"e1029","DOI":"10.1093\/cid\/ciab549","article-title":"Clinical Practice Guideline by the Infectious Diseases Society of America (IDSA) and Society for Healthcare Epidemiology of America (SHEA): 2021 Focused Update Guidelines on Management of Clostridioides Difficile Infection in Adults","volume":"73","author":"Johnson","year":"2021","journal-title":"Clin. Infect. Dis."},{"key":"ref_51","doi-asserted-by":"crossref","first-page":"S1","DOI":"10.1016\/j.cmi.2021.09.038","article-title":"2021 Update on the Treatment Guidance Document for Clostridioides Difficile Infection in Adults","volume":"27","author":"Reigadas","year":"2021","journal-title":"Clin. Microbiol. Infect."},{"key":"ref_52","doi-asserted-by":"crossref","first-page":"155","DOI":"10.1016\/j.jhin.2013.07.002","article-title":"Asymptomatic Carriage of Toxigenic Clostridium difficile by Hospitalized Patients","volume":"85","author":"Guerrero","year":"2013","journal-title":"J. Hosp. Infect."},{"key":"ref_53","unstructured":"European Centre for Disease Prevention and Control (2019). European Surveillance of Clostridioides (Clostridium) difficile Infections, European Centre for Disease Prevention and Control."},{"key":"ref_54","unstructured":"Cercenado Mansilla, E., and Cant\u00f3n Moreno, R. (2015). Diagn\u00f3stico Microbiol\u00f3gico de La Infecci\u00f3n Por Clostridium difficile, Sociedad Espa\u00f1ola de Enfermedades Infecciosas y Microbiolog\u00eda Cl\u00ednica (SEIMC), Procedimientos en Microbiolog\u00eda Cl\u00ednica."},{"key":"ref_55","unstructured":"(2018). Methods for Antimicrobial Susceptibility Testing of Anaerobic Bacteria (Standard No. M11)."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"261","DOI":"10.1111\/j.1574-6968.1999.tb13629.x","article-title":"Development of a New PCR-Ribotyping Method for Clostridium difficile Based on Ribosomal RNA Gene Sequencing","volume":"175","author":"Bidet","year":"1999","journal-title":"FEMS Microbiol. Lett."},{"key":"ref_57","unstructured":"European Centre for Disease Prevention and Control (2018). Laboratory Procedures for Diagnosis and Typing of Human Clostridium difficile Infection, European Centre for Disease Prevention and Control."},{"key":"ref_58","unstructured":"(2025, April 01). Austrian Agency for Health and Food Safety (AGES) WebRibo. Available online: https:\/\/webribo.ages.at."},{"key":"ref_59","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: A Flexible Trimmer for Illumina Sequence Data","volume":"30","author":"Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"e102","DOI":"10.1002\/cpbi.102","article-title":"Using SPAdes De Novo Assembler","volume":"70","author":"Prjibelski","year":"2020","journal-title":"Curr. Protoc. Bioinform."},{"key":"ref_61","unstructured":"Seemann, T. (2026, April 25). Mlst: Scan Contig Files Against PubMLST Typing Schemes. Available online: https:\/\/github.com\/tseemann\/mlst."},{"key":"ref_62","doi-asserted-by":"crossref","first-page":"12728","DOI":"10.1038\/s41598-021-91456-0","article-title":"AMRFinderPlus and the Reference Gene Catalog Facilitate Examination of the Genomic Links among Antimicrobial Resistance, Stress Response, and Virulence","volume":"11","author":"Feldgarden","year":"2021","journal-title":"Sci. Rep."},{"key":"ref_63","doi-asserted-by":"crossref","first-page":"3491","DOI":"10.1093\/jac\/dkaa345","article-title":"ResFinder 4.0 for Predictions of Phenotypes from Genotypes","volume":"75","author":"Bortolaia","year":"2020","journal-title":"J. Antimicrob. Chemother."},{"key":"ref_64","unstructured":"Seemann, T. (2026, April 26). Abricate: Mass Screening of Contigs for Antimicrobial and Virulence Genes. Available online: https:\/\/github.com\/tseemann\/abricate."},{"key":"ref_65","doi-asserted-by":"crossref","unstructured":"Camacho, C., Coulouris, G., Avagyan, V., Ma, N., Papadopoulos, J., Bealer, K., and Madden, T.L. (2009). BLAST+: Architecture and Applications. BMC Bioinform., 10.","DOI":"10.1186\/1471-2105-10-421"},{"key":"ref_66","doi-asserted-by":"crossref","first-page":"D912","DOI":"10.1093\/nar\/gkab1107","article-title":"VFDB 2022: A General Classification Scheme for Bacterial Virulence Factors","volume":"50","author":"Liu","year":"2022","journal-title":"Nucleic Acids Res."},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"1422","DOI":"10.1093\/bioinformatics\/btp163","article-title":"Biopython: Freely Available Python Tools for Computational Molecular Biology and Bioinformatics","volume":"25","author":"Cock","year":"2009","journal-title":"Bioinformatics"},{"key":"ref_68","unstructured":"Seemann, T. (2026, April 20). Snippy: Rapid Haploid Variant Calling and Core Genome Alignment. Available online: https:\/\/github.com\/tseemann\/snippy."},{"key":"ref_69","doi-asserted-by":"crossref","first-page":"526","DOI":"10.1093\/bioinformatics\/bty633","article-title":"Ape 5.0: An Environment for Modern Phylogenetics and Evolutionary Analyses in R","volume":"35","author":"Paradis","year":"2019","journal-title":"Bioinformatics"}],"container-title":["Antibiotics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2079-6382\/15\/9\/939\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,9,22]],"date-time":"2026-09-22T16:04:18Z","timestamp":1790093058000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2079-6382\/15\/9\/939"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,21]]},"references-count":69,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2026,9]]}},"alternative-id":["antibiotics15090939"],"URL":"https:\/\/doi.org\/10.3390\/antibiotics15090939","relation":{},"ISSN":["2079-6382"],"issn-type":[{"value":"2079-6382","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,21]]}}}