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Newcomer EP, Fishbein SRS, Zhang K, Hink T, Reske KA, Cass C, Iqbal ZH, Struttmann EL, Burnham CAD, Dubberke ER, Dantas G. Genomic surveillance of Clostridioides difficile transmission and virulence in a healthcare setting. mBio 2024; 15:e0330023. [PMID: 38329369 PMCID: PMC10936198 DOI: 10.1128/mbio.03300-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Accepted: 01/16/2024] [Indexed: 02/09/2024] Open
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 the genomic determinants of disease outcomes. Across two wards over 6 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%) patients were colonized with toxigenic C. difficile on admission to the hospital. We defined 25 strain networks at ≤2 core gene single nucleotide polymorphisms; two of these networks contain strains from different patients. Strain networks were temporally linked (P < 0.0001). To understand the genomic correlates of the 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 that toxigenic and nontoxigenic C. difficile contamination persist in a hospital setting and highlight further investigation into how accessory genomic repertoires contribute to C. difficile colonization and disease. IMPORTANCE Clostridioides difficile infection remains a leading cause of hospital-associated diarrhea, despite increased antibiotic stewardship and transmission prevention strategies. This suggests a changing genomic landscape of C. difficile. Our study provides insight into the nature of prevalent C. difficile strains in a hospital setting and transmission patterns among carriers. Longitudinal sampling of surfaces and patient stool revealed that both toxigenic and nontoxigenic strains of C. difficile clade 1 dominate these two wards. Moreover, quantification of transmission in carriers of these clade 1 isolates underscores the need to revisit infection prevention measures in this patient group. We identified unique genetic signatures associated with virulence in this clade. Our data highlight the complexities of preventing transmission of this pathogen in a hospital setting and the need to investigate the mechanisms of in vivo persistence and virulence of prevalent lineages in the host gut microbiome.
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Affiliation(s)
- Erin P. Newcomer
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Skye R. S. Fishbein
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
- Division of Laboratory and Genomic Medicine, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Kailun Zhang
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
- Division of Laboratory and Genomic Medicine, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Tiffany Hink
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Kimberly A. Reske
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Candice Cass
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Zainab H. Iqbal
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Emily L. Struttmann
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Carey-Ann D. Burnham
- Division of Laboratory and Genomic Medicine, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Erik R. Dubberke
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
- Division of Laboratory and Genomic Medicine, Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, Missouri, USA
- Department of Pediatrics, Washington University School of Medicine, St. Louis, Missouri, USA
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Newcomer EP, Fishbein SRS, Zhang K, Hink T, Reske KA, Cass C, Iqbal ZH, Struttmann EL, Dubberke ER, Dantas G. Genomic surveillance of Clostridioides difficile transmission and virulence in a healthcare setting. MEDRXIV : THE PREPRINT SERVER FOR HEALTH SCIENCES 2023:2023.09.26.23295023. [PMID: 38105952 PMCID: PMC10723495 DOI: 10.1101/2023.09.26.23295023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2023]
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<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.
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Yetmar ZA, Miller VL, Sampathkumar P, Beam E. Impact of a change in universal gloving protocol on rates of central line-related bloodstream infection, Clostridioides difficile, and vancomycin-resistant Enterococcus. Am J Infect Control 2023; 51:720-722. [PMID: 36244572 PMCID: PMC10097826 DOI: 10.1016/j.ajic.2022.10.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2022] [Revised: 09/30/2022] [Accepted: 10/01/2022] [Indexed: 11/25/2022]
Abstract
In this retrospective cohort of adult hematology-oncology and transplant patients, discontinuation of universal gloving did not result in significant changes in rates of central line-associated bloodstream infection, Clostridioides difficile infection, or vancomycin-resistant Enterococcus colonization. Active surveillance and subsequent isolation may be a viable alternative strategy to universal precautions.
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Affiliation(s)
- Zachary A Yetmar
- Division of Public Health, Infectious Diseases, and Occupational Medicine, Mayo Clinic, Rochester, MN.
| | - Vickie L Miller
- Infection Prevention and Control, Mayo Clinic, Rochester, MN
| | - Priya Sampathkumar
- Division of Public Health, Infectious Diseases, and Occupational Medicine, Mayo Clinic, Rochester, MN
| | - Elena Beam
- Division of Public Health, Infectious Diseases, and Occupational Medicine, Mayo Clinic, Rochester, MN
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