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Fishbein SRS, DeVeaux AL, Khanna S, Ferreiro AL, Liao J, Agee W, Ning J, Mahmud B, Wallace MJ, Hink T, Reske KA, Guruge J, Leekha S, Dubberke ER, Dantas G. Commensal-pathogen dynamics structure disease outcomes during Clostridioides difficile colonization. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.11.603094. [PMID: 39026847 PMCID: PMC11257545 DOI: 10.1101/2024.07.11.603094] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
Abstract
Gastrointestinal colonization by Clostridioides difficile is common in healthcare settings and ranges in clinical presentation from asymptomatic carriage to lethal C. difficile infection (CDI). We used a systems biology approach to investigate why patients colonized with C. difficile have a range of outcomes. Microbiota-humanization of germ-free mice with fecal samples from toxigenic C. difficile carriers revealed a spectrum of virulence among clade 1 lineages and identified commensal Blautia associated with markers of non-pathogenic colonization. Using gnotobiotic mice engrafted with defined human microbiota, we observed strain-specific CDI severity across clade 1 strains. Yet, mice engrafted with a higher diversity community were protected from severe disease across all strains without suppression of C. difficile colonization. These results indicate that when colonization resistance has been breached without overt infection, commensals can attenuate a diversity of virulent strains without inhibiting pathogen colonization, providing insight into determinants of stable C. difficile carriage.
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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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Morgan DJ, Dubberke ER, Hink T, Paszkiewicz G, Burnham CAD, Pineles L, Magder L, Johnson JK, Leekha S, Harris AD. The Impact of Universal Glove and Gown Use on Clostridioides Difficile Acquisition: A Cluster-Randomized Trial. Clin Infect Dis 2023; 76:e1202-e1207. [PMID: 35776131 DOI: 10.1093/cid/ciac519] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Revised: 06/15/2022] [Accepted: 06/22/2022] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Clostridioides difficile is the most common cause of healthcare-associated infections in the United States. It is unknown whether universal gown and glove use in intensive care units (ICUs) decreases acquisition of C. difficile. METHODS This was a secondary analysis of a cluster-randomized trial in 20 medical and surgical ICUs in 20 US hospitals from 4 January 2012 to 4 October 2012. After a baseline period, ICUs were randomized to standard practice for glove and gown use versus the intervention of all healthcare workers being required to wear gloves and gowns for all patient contact and when entering any patient room (contact precautions). The primary outcome was acquisition of toxigenic C. difficile determined by surveillance cultures collected on admission and discharge from the ICU. RESULTS A total of 21 845 patients had both admission and discharge perianal swabs cultured for toxigenic C. difficile. On admission, 9.43% (2060/21 845) of patients were colonized with toxigenic C. difficile. No significant difference was observed in the rate of toxigenic C. difficile acquisition with universal gown and glove use. Differences in acquisition rates in the study period compared with the baseline period in control ICUs were 1.49 per 100 patient-days versus 1.68 per 100 patient-days in universal gown and glove ICUs (rate difference, -0.28; generalized linear mixed model, P = .091). CONCLUSIONS Glove and gown use for all patient contact in medical and surgical ICUs did not result in a reduction in the acquisition of C. difficile compared with usual care. CLINICAL TRIALS REGISTRATION NCT01318213.
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Affiliation(s)
- Daniel J Morgan
- Department of Epidemiology and Public Health, University of Maryland School of Medicine and VA Maryland Healthcare System, Baltimore, Maryland, USA
| | - Erik R Dubberke
- Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri, USA
| | - Tiffany Hink
- Department of Medicine, Washington University in St. Louis School of Medicine, St. Louis, Missouri, USA
| | - Gwen Paszkiewicz
- Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Carey-Ann D Burnham
- Departments of Pathology and Immunology, Medicine, Molecular Microbiology, and Pediatrics, Washington University in St. Louis School of Medicine, St. Louis, Missouri, USA
| | - Lisa Pineles
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Larry Magder
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - J Kristie Johnson
- Department of Pathology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Surbhi Leekha
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Anthony D Harris
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
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Fishbein SR, Robinson JI, Hink T, Reske KA, Newcomer EP, Burnham CAD, Henderson JP, Dubberke ER, Dantas G. Multi-omics investigation of Clostridioides difficile-colonized patients reveals pathogen and commensal correlates of C. difficile pathogenesis. eLife 2022; 11:72801. [PMID: 35083969 PMCID: PMC8794467 DOI: 10.7554/elife.72801] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 01/17/2022] [Indexed: 02/06/2023] Open
Abstract
Clostridioides difficile infection (CDI) imposes a substantial burden on the health care system in the United States. Understanding the biological basis for the spectrum of C. difficile-related disease manifestations is imperative to improving treatment and prevention of CDI. Here, we investigate the correlates of asymptomatic C. difficile colonization using a multi-omics approach. We compared the fecal microbiome and metabolome profiles of patients with CDI versus asymptomatically colonized patients, integrating clinical and pathogen factors into our analysis. We found that CDI patients were more likely to be colonized by strains with the binary toxin (CDT) locus or strains of ribotype 027, which are often hypervirulent. We find that microbiomes of asymptomatically colonized patients are significantly enriched for species in the class Clostridia relative to those of symptomatic patients. Relative to CDI microbiomes, asymptomatically colonized patient microbiomes were enriched with sucrose degradation pathways encoded by commensal Clostridia, in addition to glycoside hydrolases putatively involved in starch and sucrose degradation. Fecal metabolomics corroborates the carbohydrate degradation signature: we identify carbohydrate compounds enriched in asymptomatically colonized patients relative to CDI patients. Further, we reveal that across C. difficile isolates, the carbohydrates sucrose, rhamnose, and lactulose do not serve as robust growth substrates in vitro, consistent with their enriched detection in our metagenomic and metabolite profiling of asymptomatically colonized individuals. We conclude that pathogen genetic variation may be strongly related to disease outcome. More interestingly, we hypothesize that in asymptomatically colonized individuals, carbohydrate metabolism by other commensal Clostridia may prevent CDI by inhibiting C. difficile proliferation. These insights into C. difficile colonization and putative commensal competition suggest novel avenues to develop probiotic or prebiotic therapeutics against CDI.
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Affiliation(s)
- Skye Rs Fishbein
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, United States.,Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, United States
| | - John I Robinson
- Center for Women's Infectious Disease Research, Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, St Louis, United States
| | - Tiffany Hink
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, United States
| | - Kimberly A Reske
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, United States
| | - Erin P Newcomer
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, United States.,Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, United States
| | - Carey-Ann D Burnham
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, United States.,Department of Molecular Microbiology, Washington University School of Medicine, St Louis, United States.,Department of Pediatrics, Washington University School of Medicine, St. Louis, United States
| | - Jeffrey P Henderson
- Center for Women's Infectious Disease Research, Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, St Louis, United States
| | - Erik R Dubberke
- Division of Infectious Diseases, Washington University School of Medicine, St. Louis, United States
| | - Gautam Dantas
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St Louis, United States.,Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, United States.,Department of Molecular Microbiology, Washington University School of Medicine, St Louis, United States.,Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, United States
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Kwon JH, O'Neil CA, Hink T, Reske KA, Bosserman RE, Dubberke ER, Burnham CAD. Alternative Causes of Infectious Diarrhea in Patients with Negative Tests for Clostridoides Difficile. J Appl Lab Med 2021; 7:437-443. [PMID: 34609483 DOI: 10.1093/jalm/jfab110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 08/09/2021] [Indexed: 11/12/2022]
Abstract
BACKGROUND Hospitalized patients with diarrhea who have a negative Clostridoides difficile (C. difficile) test are not routinely evaluated for alternative causes of infectious diarrhea. This study assessed for potential infectious causes of diarrhea in hospitalized patients with an order for repeat C. difficile toxin enzyme immunoassay (tEIA) testing after an initial tEIA test was negative. METHODS For patients age ≥18 years who had a second C. difficile tEIA test ordered within 96 h after a negative tEIA test, remnant fecal specimens from the first (negative) tEIA test were evaluated using the BioFire FilmArray Gastrointestinal Panel PCR, C. difficile toxigenic culture, and culture on a blood agar plate (BAP) to identify other potential causes of infectious diarrhea. Growth of organisms on the BAP was also used to assess potential disruptions in the gastrointestinal microbiota. RESULTS Among 84 remnant specimens, toxigenic C. difficile was identified in 9 (11%) by culture or PCR, while potential alternative causes of infectious diarrhea, including norovirus, rotavirus, enteropathogenic Escherichia coli, and Salmonella, were identified in 11 specimens (13%) by PCR. For the majority of patients, no infectious cause of diarrhea was identified, but 84% exhibited disrupted gastrointestinal microbiota, which may contribute to diarrhea. CONCLUSIONS When a hospitalized patient has a negative C. difficile tEIA test but continues to have diarrhea, alternative infectious and noninfectious causes of diarrhea should be considered. If the patient has clinical signs and symptoms suggestive of infection or risk factors for gastrointestinal infection, laboratory testing for other etiologic agents may be appropriate.
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Affiliation(s)
- Jennie H Kwon
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - Caroline A O'Neil
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - Tiffany Hink
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - Kimberly A Reske
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - Rachel E Bosserman
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - Erik R Dubberke
- Department of Medicine, Division of Infectious Diseases, Washington University School of Medicine, St. Louis, MO, USA
| | - Carey-Ann D Burnham
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, USA
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Diagnostic stewardship of Clostridioides difficile polymerase chain reaction results from syndromic diarrhea panel and implications for patient outcomes. Diagn Microbiol Infect Dis 2020; 97:115032. [PMID: 32299633 DOI: 10.1016/j.diagmicrobio.2020.115032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2019] [Revised: 02/27/2020] [Accepted: 02/28/2020] [Indexed: 11/23/2022]
Abstract
BACKGROUND A syndromic gastrointestinal pathogen panel (GIP) was implemented in May 2018. All positive (+) GIP and standard-of-care (SOC) C. difficile results were reviewed. METHODS A single-center audit of adult patients with GIP results was conducted May-December 2018. We reviewed GIP(+)/SOC(+/-) and GIP(-)/SOC(-) tests (control group) for clinical outcomes. RESULTS We reviewed 269 GIP(+) patients. Of 119 GIP(+)/SOC(+) patients, 44 (37%) were positive by toxin A/B enzyme immunoassay, and 75 (63%) by PCR only. Thirty-day mortality and re-admission were not significantly different between groups. CDI rates within 6 months were not significantly different between GIP(+)/SOC(-) and controls (p-value = 0.39). Those with initial SOC(+) tests had more true CDI events within 6 months, compared to controls (p-values < 0.001). CONCLUSIONS Forty percent of patients with GIP(+) C. difficile were (-) by SOC test, suggesting that true CDI was not present. Additional PCR-based testing may not impact outcomes.
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Okada Y, Yagihara Y, Wakabayashi Y, Igawa G, Saito R, Higurashi Y, Ikeda M, Tatsuno K, Okugawa S, Moriya K. Epidemiology and virulence-associated genes of Clostridioides difficile isolates and factors associated with toxin EIA results at a university hospital in Japan. Access Microbiol 2019; 2:acmi000086. [PMID: 34568752 PMCID: PMC8459100 DOI: 10.1099/acmi.0.000086] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 11/28/2019] [Indexed: 12/19/2022] Open
Abstract
Introduction Clostridioides difficile is one of the most important nosocomial pathogens; however, reports regarding its clinical and molecular characteristics from Japan are scarce. Aims We studied the multilocus sequence typing (MLST)-based epidemiology and virulence-associated genes of isolates and the clinical backgrounds of patients from whom the isolates had been recovered. Methods A total of 105 stool samples tested in a C. difficile toxin enzyme immune assay (EIA) were analysed at the University of Tokyo Hospital from March 2013 to July 2014. PCR for MLST and the virulence-associated genes tcdA, tcdB, cdtA, cdtB and tcdC was performed on C. difficile isolates meeting our inclusion criteria following retrospective review of medical records. EIA-positive and EIA-negative groups with toxigenic strains underwent clinical and molecular background comparison. Results The toxigenic strains ST17, ST81, ST2, ST54, ST8, ST3, ST37 and ST53 and the non-toxigenic strains ST109, ST15 and ST100 were frequently recovered. The prevalence rate of tcdA-negative ST81 and ST37, endemic in China and Korea, was higher (11.4%) than that reported in North America and Europe, and hypervirulent ST1(RT027) and ST11(RT078) strains that occur in North America and Europe were not recovered. The linkage between the EIA results and cdt A/B positivity, tcdC deletion, or tcdA variation was absent among toxigenic strains. Compared with the 38 EIA-negative cases, the 36 EIA-positive cases showed that the patients in EIA-positive cases were older and more frequently had chronic kidney disease, as well as a history of beta-lactam use and proton pump inhibitor therapy. Conclusion In Japan, the prevalence rates for tcdA-negative strains are high, whereas the cdtA/B-positive strains are rare. EIA positivity is linked to older age, chronic kidney disease and the use of beta-lactams and proton pump inhibitors.
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Affiliation(s)
- Yuta Okada
- Department of Infectious Diseases, The University of Tokyo Hospital, Bunkyo-ku, Tokyo, Japan
| | - Yuka Yagihara
- Department of Infection Control and Prevention, The University of Tokyo Hospital, Bunkyo-ku, Tokyo, Japan
| | - Yoshitaka Wakabayashi
- Department of Infectious Diseases, The University of Tokyo Hospital, Bunkyo-ku, Tokyo, Japan
| | - Gene Igawa
- Department of Molecular Microbiology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo, Japan
| | - Ryoichi Saito
- Department of Molecular Microbiology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo, Japan
| | - Yoshimi Higurashi
- Department of Infection Control and Prevention, The University of Tokyo Hospital, Bunkyo-ku, Tokyo, Japan
| | - Mahoko Ikeda
- Department of Infection Control and Prevention, The University of Tokyo Hospital, Bunkyo-ku, Tokyo, Japan
| | - Keita Tatsuno
- Department of Infection Control and Prevention, The University of Tokyo Hospital, Bunkyo-ku, Tokyo, Japan
| | - Shu Okugawa
- Department of Infectious Diseases, The University of Tokyo Hospital, Bunkyo-ku, Tokyo, Japan
- *Correspondence: Shu Okugawa,
| | - Kyoji Moriya
- Department of Infectious Diseases, The University of Tokyo Hospital, Bunkyo-ku, Tokyo, Japan
- Department of Infection Control and Prevention, The University of Tokyo Hospital, Bunkyo-ku, Tokyo, Japan
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Jonica ER, Sulis CA, Soni K, Hughes M, Jones E, Weinberg J, Miller NS, Farraye FA. Role of Cycle Threshold in Clostridioides difficile Polymerase Chain Reaction Testing as a Predictor of Clinical Outcomes in Patients With Inflammatory Bowel Disease. CROHN'S & COLITIS 360 2019. [DOI: 10.1093/crocol/otz036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Abstract
Background
Distinguishing Clostridioides difficile infection from colonization is challenging in patients with Inflammatory Bowel Disease (IBD). Cycle threshold (Ct), the cutoff for PCR positivity, has been investigated in non-IBD patients.
Methods
Patients with positive C. difficile PCR (25 IBD, 51 non-IBD) were identified retrospectively. Fifteen-day outcomes were assessed.
Results
Ct correlated with diarrheal days in non-IBD (P = 0.048), but not IBD patients (P = 0.769). IBD patients had shorter LOS and less severe infection, but more diarrheal days (P < 0.05).
Conclusions
IBD patients had a milder course but Ct results were not significant. Larger studies are needed to clarify utility of Ct in IBD.
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Affiliation(s)
- Emily R Jonica
- Section of Gastroenterology, Boston University Medical Center,, Boston, MA
- Division of Gastroenterology and Hepatology, University of Colorado Anschutz Medical Campus, Aurora, CO
| | - Carol A Sulis
- Division of Infectious Diseases, Boston University School of Medicine, Boston, MA
| | - Kanupriya Soni
- Section of Gastroenterology, Boston University Medical Center,, Boston, MA
| | - Michelle Hughes
- Section of Gastroenterology, Boston University Medical Center,, Boston, MA
- Division of Gastroenterology and Hepatology, University of Rochester Medical Center, Rochester, NY
| | - Eric Jones
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
| | - Janice Weinberg
- Department of Biostatistics, Boston University School of Public Health, Boston, MA
| | - Nancy S Miller
- Department of Pathology and Laboratory Medicine, Boston University School of Medicine, Boston, MA
| | - Francis A Farraye
- Section of Gastroenterology, Boston University Medical Center,, Boston, MA
- Division of Gastroenterology and Hepatology, Mayo Clinic, Jacksonville, FL
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10
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Robinson JI, Weir WH, Crowley JR, Hink T, Reske KA, Kwon JH, Burnham CAD, Dubberke ER, Mucha PJ, Henderson JP. Metabolomic networks connect host-microbiome processes to human Clostridioides difficile infections. J Clin Invest 2019; 129:3792-3806. [PMID: 31403473 DOI: 10.1172/jci126905] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2019] [Accepted: 06/11/2019] [Indexed: 12/15/2022] Open
Abstract
Clostridioides difficile infection (CDI) accounts for a substantial proportion of deaths attributable to antibiotic-resistant bacteria in the United States. Although C. difficile can be an asymptomatic colonizer, its pathogenic potential is most commonly manifested in patients with antibiotic-modified intestinal microbiomes. In a cohort of 186 hospitalized patients, we showed that host and microbe-associated shifts in fecal metabolomes had the potential to distinguish patients with CDI from those with non-C. difficile diarrhea and C. difficile colonization. Patients with CDI exhibited a chemical signature of Stickland amino acid fermentation that was distinct from those of uncolonized controls. This signature suggested that C. difficile preferentially catabolizes branched chain amino acids during CDI. Unexpectedly, we also identified a series of noncanonical, unsaturated bile acids that were depleted in patients with CDI. These bile acids may derive from an extended host-microbiome dehydroxylation network in uninfected patients. Bile acid composition and leucine fermentation defined a prototype metabolomic model with potential to distinguish clinical CDI from asymptomatic C. difficile colonization.
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Affiliation(s)
- John I Robinson
- Center for Women's Infectious Disease Research, Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - William H Weir
- Carolina Center for Interdisciplinary Applied Mathematics, Department of Mathematics, and Curriculum in Bioinformatics & Computational Biology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Jan R Crowley
- Center for Women's Infectious Disease Research, Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Tiffany Hink
- Center for Women's Infectious Disease Research, Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Kimberly A Reske
- Center for Women's Infectious Disease Research, Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Jennie H Kwon
- Center for Women's Infectious Disease Research, Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Carey-Ann D Burnham
- Department of Pathology and Immunology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Erik R Dubberke
- Center for Women's Infectious Disease Research, Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
| | - Peter J Mucha
- Carolina Center for Interdisciplinary Applied Mathematics, Department of Mathematics, and Curriculum in Bioinformatics & Computational Biology, University of North Carolina, Chapel Hill, North Carolina, USA
| | - Jeffrey P Henderson
- Center for Women's Infectious Disease Research, Division of Infectious Diseases, Department of Internal Medicine, Washington University School of Medicine, St. Louis, Missouri, USA
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