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Prosty C, Hanula R, Katergi K, Longtin Y, McDonald EG, Lee TC. Clinical Outcomes and Management of NAAT-Positive/Toxin-Negative Clostridioides difficile Infection: A Systematic Review and Meta-Analysis. Clin Infect Dis 2024; 78:430-438. [PMID: 37648251 DOI: 10.1093/cid/ciad523] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Revised: 08/15/2023] [Accepted: 08/29/2023] [Indexed: 09/01/2023] Open
Abstract
BACKGROUND Standalone nucleic acid amplification tests (NAATs) are frequently used to diagnose Clostridioides difficile infections (CDI), although they may be unable to distinguish colonization from disease. A 2-stage algorithm pairing NAATs with toxin immunoassays (Toxin) may improve specificity. We evaluated clinical outcomes of patients who were NAAT+/Toxin+ versus NAAT+/Toxin- and treated versus untreated NAAT+/Toxin- cases through systematic review and meta-analysis. METHODS We searched EMBASE and MEDLINE from inception to April 1, 2023 for articles comparing CDI outcomes among symptomatic patients tested by NAAT and Toxin tests. The risk differences (RD) of all-cause mortality and CDI recurrence were computed by random effects meta-analysis between patients who were NAAT+/Toxin+ and NAAT+/Toxin-, as well as between patients who were NAAT+/Toxin- and treated or untreated. RESULTS Twenty-six observational studies comprising 12 737 patients were included. The 30-day all-cause mortality was not significantly different between those who were NAAT+/Toxin+ (8.4%) and NAAT+/Toxin- (6.7%) (RD = 0.41%, 95% confidence interval [CI] = -.67, 1.49). Recurrence at 60 days was significantly higher among patients who were NAAT+/Toxin+ (19.8%) versus NAAT+/Toxin- (11.0%) (RD = 7.65%, 95% CI = 4.60, 10.71). Among treated compared to untreated NAAT+/Toxin- cases, the all-cause 30-day mortalities were 5.0% and 12.7%, respectively (RD = -7.45%, 95% CI = -12.29, -2.60), but 60-day recurrence was not significantly different (11.6% vs 7.0%, respectively; RD = 5.25%, 95% CI -1.71, 12.22). CONCLUSIONS Treatment of patients who were NAAT+/Toxin- was associated with reduced all-cause mortality but not recurrence. Although subject to the inherent limitations of observational studies, these results suggest that some patients who are NAAT+/Toxin- may benefit from treatment.
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Affiliation(s)
- Connor Prosty
- Faculty of Medicine, McGill University, Montréal, QC, Canada
| | - Ryan Hanula
- Division of Experimental Medicine, Department of Medicine, McGill University, Montréal, QC, Canada
| | - Khaled Katergi
- Faculty of Medicine, Université de Montréal, Montréal, QC, Canada
| | - Yves Longtin
- Division of Infectious Diseases, Department of Medicine, Jewish General Hospital Sir Mortimer B. Davis, Montréal, QC, Canada
| | - Emily G McDonald
- Division of Experimental Medicine, Department of Medicine, McGill University, Montréal, QC, Canada
- Division of General Internal Medicine, Department of Medicine, McGill University Health Centre, Montréal, QC, Canada
- Clinical Practice Assessment Unit, Department of Medicine, McGill University Health Centre, Montréal, QC, Canada
| | - Todd C Lee
- Division of Experimental Medicine, Department of Medicine, McGill University, Montréal, QC, Canada
- Clinical Practice Assessment Unit, Department of Medicine, McGill University Health Centre, Montréal, QC, Canada
- Division of Infectious Diseases, Department of Medicine, McGill University Health Centre, QC, Montréal, Canada
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Skjøt-Arkil H, Rune Nanthan K, Chen M, Rosenvinge FS. Carrier prevalence of Clostridioides difficile in emergency departments and the association of prior antibiotic consumption: a combined cross-sectional and nested case-control study. J Antimicrob Chemother 2023:dkad213. [PMID: 37409612 DOI: 10.1093/jac/dkad213] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2023] [Accepted: 06/25/2023] [Indexed: 07/07/2023] Open
Abstract
INTRODUCTION Clostridioides difficile infection is an urgent public health threat, and the incidence has been increasing over the last decades. Knowledge of the prevalence of C. difficile in acutely admitted patients and risk factors for colonization with C. difficile assists emergency departments (EDs) in prioritizing preventive initiatives. This national study aimed to describe prevalence and risk factors for C. difficile carriers acutely admitted to EDs, focusing on the impact of earlier antibiotic prescription. METHODS We conducted a nationwide analytic cross-sectional study with prospective data collection combined with a nested case-control study with retrospective data collection. All adults visiting one of eight Danish EDs were interviewed and examined for C. difficile. Using a national register, we collected the antibiotic history within the 2 years prior to enrolment. The primary outcome was the prevalence of C. difficile colonization, and secondary outcomes were related to risk factors and prior antibiotic prescription. Multivariate analyses examined the association between earlier antibiotic prescription and C. difficile colonization. RESULTS Of 5019 participants, 89 were colonized with C. difficile (prevalence of 1.8%). A significant and exposure-dependent association was found for penicillins [DDD/person-year(PY) > 20; OR 4.93 (95% CI 2.22-10.97)] and fluoroquinolones [DDD/PY > 20; OR 8.81 (95% CI 2.54-30.55)], but not macrolides. Timing of the prescription did not affect the association. CONCLUSIONS One out of 55 patients visiting a Danish ED were colonized with C. difficile. Risk factors for colonization included high age, comorbidity and prior prescription of fluoroquinolones and penicillins.
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Affiliation(s)
- Helene Skjøt-Arkil
- Department of Regional Health Research at University of Southern Denmark, Aabenraa, Denmark
- Emergency Department at University Hospital of Southern Denmark, Aabenraa, Denmark
| | - Kumanan Rune Nanthan
- Emergency Department at University Hospital of Southern Denmark, Aabenraa, Denmark
| | - Ming Chen
- Department of Microbiology at University Hospital of Southern Denmark, Aabenraa, Denmark
| | - Flemming S Rosenvinge
- Department of Clinical Microbiology at Odense University Hospital, and Research Unit of Clinical Microbiology at University of Southern Denmark, Odense, Denmark
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Bocchetti M, Ferraro MG, Melisi F, Grisolia P, Scrima M, Cossu AM, Yau TO. Overview of current detection methods and microRNA potential in Clostridioides difficile infection screening. World J Gastroenterol 2023; 29:3385-3399. [PMID: 37389232 PMCID: PMC10303512 DOI: 10.3748/wjg.v29.i22.3385] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/25/2023] [Revised: 03/23/2023] [Accepted: 05/04/2023] [Indexed: 06/06/2023] Open
Abstract
Clostridioides difficile (formerly called Clostridium difficile, C. difficile) infection (CDI) is listed as an urgent threat on the 2019 antibiotic resistance threats report in the United States by the Centers for Disease Control and Prevention. Early detection and appropriate disease management appear to be essential. Meanwhile, although the majority of cases are hospital-acquired CDI, community-acquired CDI cases are also on the rise, and this vulnerability is not limited to immunocompromised patients. Gastrointestinal treatments and/or gastrointestinal tract surgeries may be required for patients diagnosed with digestive diseases. Such treatments could suppress or interfere with the patient’s immune system and disrupt gut flora homeostasis, creating a suitable microecosystem for C. difficile overgrowth. Currently, stool-based non-invasive screening is the first-line approach to CDI diagnosis, but the accuracy is varied due to different clinical microbiology detection methods; therefore, improving reliability is clearly required. In this review, we briefly summarised the life cycle and toxicity of C. difficile, and we examined existing diagnostic approaches with an emphasis on novel biomarkers such as microRNAs. These biomarkers can be easily detected through non-invasive liquid biopsy and can yield crucial information about ongoing pathological phenomena, particularly in CDI.
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Affiliation(s)
- Marco Bocchetti
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli,” Naples 80138, Italy
- Department of Molecular Oncology, Precision Medicine Laboratory and COVID19 Laboratory, Biogem Scarl, Ariano Irpino 83031, Italy
| | - Maria Grazia Ferraro
- School of Infection and Immunity, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow G12 8QQ, United Kingdom
- Department of Pharmacy, School of Medicine and Surgery, University of Naples “Federico II,” Naples 80131, Italy
| | - Federica Melisi
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli,” Naples 80138, Italy
- Department of Molecular Oncology, Precision Medicine Laboratory and COVID19 Laboratory, Biogem Scarl, Ariano Irpino 83031, Italy
| | - Piera Grisolia
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli,” Naples 80138, Italy
- Department of Molecular Oncology, Precision Medicine Laboratory and COVID19 Laboratory, Biogem Scarl, Ariano Irpino 83031, Italy
| | - Marianna Scrima
- Department of Molecular Oncology, Precision Medicine Laboratory and COVID19 Laboratory, Biogem Scarl, Ariano Irpino 83031, Italy
| | - Alessia Maria Cossu
- Department of Precision Medicine, University of Campania “Luigi Vanvitelli,” Naples 80138, Italy
- Department of Molecular Oncology, Precision Medicine Laboratory and COVID19 Laboratory, Biogem Scarl, Ariano Irpino 83031, Italy
| | - Tung On Yau
- School of Science and Technology, Nottingham Trent University, Nottingham NG11 8NS, United Kingdom
- Department of Rural Land Use, Scotland’s Rural College, Aberdeen AB21 9YA, Scotland, United Kingdom
- Department of Health Science, University of the People, Pasadena, CA 9110112, United States
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Azzini AM, Be G, Naso L, Lambertenghi L, Salerno ND, Coledan I, Bazaj A, Mirandola M, Miotti J, Mazzaferri F, Accordini S, Lo Cascio G, Tacconelli E. Risk factors for colonization with multidrug-resistant Gram-negative bacteria and Clostridioides difficile in Long Term Care Facilities (LTCFs) residents: the evidence from 27 facilities in a high endemic setting. Front Cell Infect Microbiol 2023; 13:1155320. [PMID: 37377644 PMCID: PMC10292821 DOI: 10.3389/fcimb.2023.1155320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Accepted: 05/19/2023] [Indexed: 06/29/2023] Open
Abstract
Introduction Residency in LTCFs increases the likelihood of colonization with multidrug resistant Gram-negative bacteria (MDR-GNB). We assessed the prevalence and risk factors for enteric colonization by III-generation cephalosporins-resistant and carbapenem-resistant (CR) GNB in a large group of LTCFs in a high endemic setting. We also assessed the prevalence and risk factors for C. difficile colonization. Methods A point prevalence survey with rectal screening (RS) was conducted in 27 LTCFs in north Italy. Epidemiological and clinical variables on the survey day, history of hospitalization and surgery within one year, and antibiotics within three months, were collected. The presence of III-generation cephalosporin resistant and CR GNB was assessed using a selective culture on chromogenic medium and PCR for carbapenemase detection. The presence of C. difficile was assessed using ELISA for GDH and RT-PCR to identify toxigenic strains. Multi-variable analyses were performed using two-level logistic regression models. Results In the study period 1947 RSs were performed. The prevalence of colonization by at least one GNB resistant to III-generation cephalosporin was 51% (E. coli 65%, K. pneumoniae 14% of isolates). The prevalence of colonization by CR GNB was 6%. 6% of all isolates (1150 strains) resulted in a carbapenem-resistant K. pneumoniae, and 3% in a carbapenem-resistant E. coli. KPC was the most frequent carbapenemase (73%) identified by PCR, followed by VIM (23%). The prevalence of colonization by C. difficile was 11.7%. The presence of a medical device (OR 2.67) and previous antibiotic use (OR 1.48) were significantly associated with III-generation cephalosporin resistant GNB colonization. The presence of a medical device (OR 2.67) and previous hospitalization (OR 1.80) were significantly associated with CR GNB. The presence of a medical device (OR 2.30) was significantly associated with C. difficile colonization. Main previously used antibiotic classes were fluoroquinolones (32% of previously treated subjects), III-generation cephalosporins (21%), and penicillins (19%). Conclusion Antimicrobial stewardship in LTCFs is a critical issue, being previous antibiotic treatment a risk factor for colonization by MDR-GNB. The prevalence of colonization by III-generation cephalosporin and CR GNB among LTCF residents also underlines the importance to adhere to hand hygiene indications, infection prevention and control measures, and environmental hygiene protocols, more achievable than rigorous contact precautions in this type of social setting.
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Affiliation(s)
- Anna Maria Azzini
- Infectious Diseases Division, Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Giorgia Be
- Infectious Diseases Division, Department of Diagnostics and Public Health, University of Verona, Verona, Italy
- Infectious Disease Unit, Mater Salutis Hospital - ULSS 9 Scaligera, Legnago, Italy
| | - Laura Naso
- Microbiology and Virology Unit, AOUI Verona, Verona, Italy
| | - Lorenza Lambertenghi
- Infectious Diseases Division, Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Nicola Duccio Salerno
- Infectious Diseases Division, Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Ilaria Coledan
- Infectious Diseases Division, Department of Diagnostics and Public Health, University of Verona, Verona, Italy
- SerT Suzzara, SC Ser.D. Mantova, ASST Mantova, Suzzara, Italy
| | - Alda Bazaj
- Microbiology Division, Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Massimo Mirandola
- Infectious Diseases Division, Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Jessica Miotti
- Unit of Epidemiology and Medical Statistics, Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Fulvia Mazzaferri
- Infectious Diseases Division, Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Simone Accordini
- Unit of Epidemiology and Medical Statistics, Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Giuliana Lo Cascio
- Microbiology and Virology Unit, AOUI Verona, Verona, Italy
- Microbiology Unit, AUSL Piacenza, Piacenza, Italy
| | - Evelina Tacconelli
- Infectious Diseases Division, Department of Diagnostics and Public Health, University of Verona, Verona, Italy
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Zangiabadian M, Ghorbani A, Nojookambari NY, Ahmadbeigi Y, Hosseini SS, Karimi-Yazdi M, Goudarzi M, Chirani AS, Nasiri MJ. Accuracy of diagnostic assays for the detection of Clostridioides difficile: A systematic review and meta-analysis. J Microbiol Methods 2023; 204:106657. [PMID: 36528183 DOI: 10.1016/j.mimet.2022.106657] [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: 10/06/2022] [Revised: 12/13/2022] [Accepted: 12/13/2022] [Indexed: 12/24/2022]
Abstract
INTRODUCTION Clostridioides difficile Infection (CDI) has been identified as one of the main causes of nosocomial infection all across the world. Rapid diagnosis of CDI is difficult and poses a significant challenge to physicians worldwide. We undertook a systematic review and meta-analysis to evaluate rapid tests' diagnostic accuracy against toxigenic culture as the reference standard for CDI. METHOD We searched the PubMed/MEDLINE and EMBASE databases for the relevant records. The QUADAS-2 tool was used to assess the quality of the studies. Diagnostic accuracy measures [i.e., sensitivity, specificity, diagnostic odds ratio (DOR), positive likelihood ratios (PLR), negative likelihood ratios (NLR), and the area under the curve (AUC)] were pooled with a random-effects model. All statistical analyses were performed with Meta-DiSc (Version 1.4, Cochrane Colloquium, Barcelona, Spain) and RevMan (version 5.3; The Nordic Cochrane Centre, the Cochrane Collaboration, Copenhagen, Denmark). RESULTS We reviewed retrieved records and identified 63 studies that met the inclusion criteria. 26 were about enzyme immunoassay (EIA) (our main index test). The sensitivity of GDH and Tox A/B EIAs were 82% (95% CI: 79-84) and 75% (95% CI: 70-79), respectively. On the other hand, the specificity of GDH EIA was 91% (95% CI: 90-92) and the specificity of Tox A/B EIA was 95% (95% CI: 94-96). Among other index tests, BD Max with 92% has the most sensitivity and cell cytotoxicity neutralization assay (CCNA) has the most specificity (100%). CONCLUSION This meta-analysis demonstrated that EIAs could be reliable methods for detecting CDI based on their sensitivity, specificity, time and cost-effectiveness, and simplicity in the procedure. Further work to improve rapid tests would benefit from improvements to the methodology.
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Affiliation(s)
- Moein Zangiabadian
- Endocrinology and Metabolism Research Center, Institute of Basic and Clinical Physiology Sciences, Kerman University of Medical Sciences, Kerman, Iran
| | - Alireza Ghorbani
- Department of Microbiology, school of medicine, Shahid Beheshti University of medical sciences, Tehran, Iran
| | - Neda Yousefi Nojookambari
- Department of Microbiology, school of medicine, Shahid Beheshti University of medical sciences, Tehran, Iran
| | - Yasaman Ahmadbeigi
- Department of Microbiology and Microbial Biotechnology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
| | - Sareh Sadat Hosseini
- Department of Microbiology, school of medicine, Shahid Beheshti University of medical sciences, Tehran, Iran
| | | | - Mehdi Goudarzi
- Department of Microbiology, school of medicine, Shahid Beheshti University of medical sciences, Tehran, Iran.
| | | | - Mohammad Javad Nasiri
- Department of Microbiology, school of medicine, Shahid Beheshti University of medical sciences, Tehran, Iran.
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Towards Development of a Non-Toxigenic Clostridioides difficile Oral Spore Vaccine against Toxigenic C. difficile. Pharmaceutics 2022; 14:pharmaceutics14051086. [PMID: 35631671 PMCID: PMC9146386 DOI: 10.3390/pharmaceutics14051086] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2022] [Revised: 05/12/2022] [Accepted: 05/16/2022] [Indexed: 11/24/2022] Open
Abstract
Clostridioides difficile is an opportunistic gut pathogen which causes severe colitis, leading to significant morbidity and mortality due to its toxins, TcdA and TcdB. Two intra-muscular toxoid vaccines entered Phase III trials and strongly induced toxin-neutralising antibodies systemically but failed to provide local protection in the colon from primary C. difficile infection (CDI). Alternatively, by immunising orally, the ileum (main immune inductive site) can be directly targeted to confer protection in the large intestine. The gut commensal, non-toxigenic C. difficile (NTCD) was previously tested in animal models as an oral vaccine for natural delivery of an engineered toxin chimera to the small intestine and successfully induced toxin-neutralising antibodies. We investigated whether NTCD could be further exploited to induce antibodies that block the adherence of C. difficile to epithelial cells to target the first stage of pathogenesis. In NTCD strain T7, the colonisation factor, CD0873, and a domain of TcdB were overexpressed. Following oral immunisation of hamsters with spores of recombinant strain, T7-0873 or T7-TcdB, intestinal and systemic responses were investigated. Vaccination with T7-0873 successfully induced intestinal antibodies that significantly reduced adhesion of toxigenic C. difficile to Caco-2 cells, and these responses were mirrored in sera. Additional engineering of NTCD is now warranted to further develop this vaccine.
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Faecal carriage of Clostridioides difficile is low among veterinary healthcare workers in the Netherlands. Epidemiol Infect 2022; 150:e63. [PMID: 35296372 PMCID: PMC8931804 DOI: 10.1017/s0950268822000383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
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Harrison MA, Strahl H, Dawson LF. Regulation of para-cresol production in Clostridioides difficile. Curr Opin Microbiol 2021; 65:131-137. [PMID: 34856509 DOI: 10.1016/j.mib.2021.11.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Revised: 11/08/2021] [Accepted: 11/09/2021] [Indexed: 11/03/2022]
Abstract
The human pathogen Clostridioides difficile colonises the gastrointestinal tract following antibiotic exposure, which causes perturbations in the beneficial microbiome. An unusual feature of C. difficile among the gut microbiota is its ability to produce high concentrations of the antimicrobial compound para-cresol, which selectively targets Gram-negative bacteria. Production of p-cresol occurs either by: (a) tyrosine fermentation via the intermediate para-hydroxyphenylacetate (p-HPA), or (b) direct turnover of exogenous p-HPA in the human gut. p-HPA is decarboxylated to produce p-cresol, by the action of HpdBCA decarboxylase encoded by the hpdBCA operon. HpdBCA decarboxylase production is induced at the transcriptional level by elevated p-HPA, which causes elevated p-cresol production, that significantly reduces microbiome diversity and richness. This deleterious effect of p-cresol on the beneficial gut microbiome is advantageous for C. difficile pathogenesis and infection relapse. Inhibiting this pathway would provide a highly specific therapeutic.
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Affiliation(s)
- Mark A Harrison
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Henrik Strahl
- Centre for Bacterial Cell Biology, Biosciences Institute, Newcastle University, Baddiley-Clark Building, Richardson Road, Newcastle upon Tyne, NE2 4AX, UK
| | - Lisa F Dawson
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
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Worley J, Delaney ML, Cummins CK, DuBois A, Klompas M, Bry L. Genomic Determination of Relative Risks for Clostridioides difficile Infection From Asymptomatic Carriage in Intensive Care Unit Patients. Clin Infect Dis 2021; 73:e1727-e1736. [PMID: 32676661 PMCID: PMC8678446 DOI: 10.1093/cid/ciaa894] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 06/24/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Clostridioides difficile infections (CDIs) are among the most prevalent hospital-associated infections (HAIs), particularly for intensive care unit (ICU) patients. The risks for developing active CDI from asymptomatic carriage of C. difficile are not well understood. METHODS We identified asymptomatic C. difficile carriage among 1897 ICU patients using rectal swabs from an existing ICU vancomycin-resistant enterococci (VRE) surveillance program. C. difficile isolates from VRE swabs, and from C. difficile-positive stool samples, were genome sequenced. Spatial-temporal data from hospital records assessed genomically identified clusters for potential transmission events. RESULTS Genomic analyses identified a diverse set of strains in infected patients and asymptomatic carriers. A total of 7.4% of ICU patients asymptomatically carried C. difficile; 69% of isolates carried an intact toxin locus. In contrast, 96% of C. difficile stool isolates were toxin encoding. CDI rates in asymptomatic carriers of toxin-encoding strains were 5.3% versus 0.57% in noncarriers. The relative risk for CDI with asymptomatic carriage of a toxin-encoding strain was 9.32 (95% confidence interval, 3.25-26.7). Genomic identification of clonal clusters supported analyses for asymptomatic transmission events, with spatial-temporal overlaps identified in 13 of 28 cases. CONCLUSIONS Our studies provide the first genomically confirmed assessments of CDI relative risk from asymptomatic carriage of toxin-encoding strains and highlight the complex dynamics of asymptomatic transmission in ICUs. Asymptomatic carriers are an active reservoir of C. difficile in the nosocomial environment. C. difficile screening can be implemented within existing HAI surveillance programs and has the potential to support infection-control efforts against this pathogen.
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Affiliation(s)
- Jay Worley
- Massachusetts Host-Microbiome Center, Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Mary L Delaney
- Massachusetts Host-Microbiome Center, Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Clinical Microbiology Laboratory, Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Christopher K Cummins
- Massachusetts Host-Microbiome Center, Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Andrea DuBois
- Massachusetts Host-Microbiome Center, Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Clinical Microbiology Laboratory, Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Michael Klompas
- Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, Massachusetts, USA
- Division of Infectious Diseases, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Lynn Bry
- Massachusetts Host-Microbiome Center, Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Clinical Microbiology Laboratory, Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
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Novakova E, Stofkova Z, Sadlonova V, Hleba L. Diagnostic Methods of Clostridioides difficile Infection and Clostridioides difficile Ribotypes in Studied Sample. Antibiotics (Basel) 2021; 10:antibiotics10091035. [PMID: 34572617 PMCID: PMC8466394 DOI: 10.3390/antibiotics10091035] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 07/26/2021] [Accepted: 08/19/2021] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Clostridioides (Clostridium) difficile is the most common nosocomial pathogen and antibiotic-related diarrhea in health-care facilities. Over the last few years, there was an increase in the incidence rate of C. difficile infection cases in Slovakia. In this study, the phenotypic (toxigenicity, antimicrobial susceptibility) and genotypic (PCR ribotypes, genes for binary toxins) patterns of C. difficile isolates from patients with CDI were analyzed, from July to August 2016, taken from hospitals in the Horne Povazie region of northern Slovakia. The aim of the study was also to identify hypervirulent strains (e.g., the presence of RT027 or RT176). METHODS The retrospective analysis of biological samples suspected of CDI were analyzed by GDH, anaerobic culture, enzyme immunoassay on toxins A/B, multiplex "real-time" PCR and PCR capillary-based electrophoresis ribotyping, and by MALDI TOF MS. RESULTS C. difficile isolates (n = 44) were identified by PCR ribotyping, which revealed five different ribotypes (RT001, 011, 017, 081, 176). The presence of hypervirulent RT027 was not identified. The C. difficile isolates (RT001, 011, 081, 176) were susceptible to metronidazole and vancomycin. One isolate RT017 had reduced susceptibility to vancomycin. A statistically significant difference between the most prevalent PCR ribotypes, RT001 and RT176, regarding variables such as albumin, CRP, creatinine, the length of hospitalization (p = 0.175), and glomerular filtration (p = 0.05) was not found. CONCLUSION The results of PCR capillary-based electrophoresis ribotyping in the studied samples showed a high prevalence of RT176 and 001.
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Affiliation(s)
- Elena Novakova
- Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Mala Hora 4A, 03601 Martin, Slovakia; (E.N.); (V.S.)
| | - Zuzana Stofkova
- Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Mala Hora 4A, 03601 Martin, Slovakia; (E.N.); (V.S.)
- Correspondence:
| | - Vladimira Sadlonova
- Jessenius Faculty of Medicine in Martin, Comenius University in Bratislava, Mala Hora 4A, 03601 Martin, Slovakia; (E.N.); (V.S.)
| | - Lukas Hleba
- Faculty of Biotechnology and Food Sciences, Slovak University of Agriculture in Nitra, A. Hlinku 610/4, 94901 Nitra, Slovakia;
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Ducarmon QR, Terveer EM, Nooij S, Bloem MN, Vendrik KEW, Caljouw MAA, Sanders IMJG, van Dorp SM, Wong MC, Zwittink RD, Kuijper EJ. Microbiota-associated risk factors for asymptomatic gut colonisation with multi-drug-resistant organisms in a Dutch nursing home. Genome Med 2021; 13:54. [PMID: 33827686 PMCID: PMC8028076 DOI: 10.1186/s13073-021-00869-z] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2020] [Accepted: 03/16/2021] [Indexed: 11/25/2022] Open
Abstract
Background Nursing home residents have increased rates of intestinal colonisation with multidrug-resistant organisms (MDROs). We assessed the colonisation and spread of MDROs among this population, determined clinical risk factors for MDRO colonisation and investigated the role of the gut microbiota in providing colonisation resistance against MDROs. Methods We conducted a prospective cohort study in a Dutch nursing home. Demographical, epidemiological and clinical data were collected at four time points with 2-month intervals (October 2016–April 2017). To obtain longitudinal data, faecal samples from residents were collected for at least two time points. Ultimately, twenty-seven residents were included in the study and 93 faecal samples were analysed, of which 27 (29.0%) were MDRO-positive. Twelve residents (44.4%) were colonised with an MDRO at at least one time point throughout the 6-month study. Results Univariable generalised estimating equation logistic regression indicated that antibiotic use in the previous 2 months and hospital admittance in the previous year were associated with MDRO colonisation. Characterisation of MDRO isolates through whole-genome sequencing revealed Escherichia coli sequence type (ST)131 to be the most prevalent MDRO and ward-specific clusters of E. coli ST131 were identified. Microbiota analysis by 16S rRNA gene amplicon sequencing revealed no differences in alpha or beta diversity between MDRO-positive and negative samples, nor between residents who were ever or never colonised. Three bacterial taxa (Dorea, Atopobiaceae and Lachnospiraceae ND3007 group) were more abundant in residents never colonised with an MDRO throughout the 6-month study. An unexpectedly high abundance of Bifidobacterium was observed in several residents. Further investigation of a subset of samples with metagenomics showed that various Bifidobacterium species were highly abundant, of which B. longum strains remained identical within residents over time, but were different between residents. Conclusions Our study provides new evidence for the role of the gut microbiota in colonisation resistance against MDROs in the elderly living in a nursing home setting. Dorea, Atopobiaceae and Lachnospiraceae ND3007 group may be associated with protection against MDRO colonisation. Furthermore, we report a uniquely high abundance of several Bifidobacterium species in multiple residents and excluded the possibility that this was due to probiotic supplementation. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-021-00869-z.
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Affiliation(s)
- Quinten R Ducarmon
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands. .,Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, The Netherlands.
| | - Elisabeth M Terveer
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands.,Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, The Netherlands
| | - Sam Nooij
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands.,Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, The Netherlands
| | - Michelle N Bloem
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands.,Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, The Netherlands
| | - Karuna E W Vendrik
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands.,Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Monique A A Caljouw
- Department of Public Health and Primary Care, Leiden University Medical Center, Leiden, The Netherlands
| | - Ingrid M J G Sanders
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Sofie M van Dorp
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands.,Department of Internal Medicine and Geriatrics, Onze Lieve Vrouwe Gasthuis (OLVG Hospital), Amsterdam, The Netherlands
| | - Man C Wong
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands
| | - Romy D Zwittink
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands.,Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, The Netherlands
| | - Ed J Kuijper
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, The Netherlands.,Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, The Netherlands.,Center for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
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12
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Henson MA. Computational modeling of the gut microbiota reveals putative metabolic mechanisms of recurrent Clostridioides difficile infection. PLoS Comput Biol 2021; 17:e1008782. [PMID: 33617526 PMCID: PMC7932513 DOI: 10.1371/journal.pcbi.1008782] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 03/04/2021] [Accepted: 02/05/2021] [Indexed: 12/16/2022] Open
Abstract
Approximately 30% of patients who have Clostridioides difficile infection (CDI) will suffer at least one incident of reinfection. While the underlying causes of CDI recurrence are poorly understood, interactions between C. difficile and commensal gut bacteria are thought to play an important role. In this study, an in silico pipeline was used to process 16S rRNA gene amplicon sequence data of 225 stool samples from 93 CDI patients into sample-specific models of bacterial community metabolism. Clustered metabolite production rates generated from post-diagnosis samples generated a high Enterobacteriaceae abundance cluster containing disproportionately large numbers of recurrent samples and patients. This cluster was predicted to have significantly reduced capabilities for secondary bile acid synthesis but elevated capabilities for aromatic amino acid catabolism. When applied to 16S sequence data of 40 samples from fecal microbiota transplantation (FMT) patients suffering from recurrent CDI and their stool donors, the community modeling method generated a high Enterobacteriaceae abundance cluster with a disproportionate large number of pre-FMT samples. This cluster also was predicted to exhibit reduced secondary bile acid synthesis and elevated aromatic amino acid catabolism. Collectively, these in silico predictions suggest that Enterobacteriaceae may create a gut environment favorable for C. difficile spore germination and/or toxin synthesis.
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Affiliation(s)
- Michael A. Henson
- Department of Chemical Engineering and Institute for Applied Life Sciences, University of Massachusetts, Amherst, Massachusetts, United States of America
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13
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Sehgal K, Khanna S. Immune response against Clostridioides difficile and translation to therapy. Therap Adv Gastroenterol 2021; 14:17562848211014817. [PMID: 33995585 PMCID: PMC8111532 DOI: 10.1177/17562848211014817] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 04/12/2021] [Indexed: 02/04/2023] Open
Abstract
The pathogenesis of Clostridioides difficile infection (CDI) has largely been attributed to the action of two major toxins - A and B. An enhanced systemic humoral immune response against these toxins has been shown to be protective against recurrent CDI. Over the years, fully human monoclonal antibodies against both of these toxins have been developed in an attempt to counter the increasing incidence of recurrent CDI. Clinical trials conducted to evaluate the efficacy of anti-toxin A monoclonal antibody, actoxumab, and anti-toxin B monoclonal antibody, bezlotoxumab, demonstrated that bezlotoxumab substantially lowered the rate of recurrent infection, while actoxumab did not. A significant therapeutic benefit was appreciated in patients with at least one high-risk factor for recurrence, including, age ⩾65 years, immunocompromised state, prior CDI and severe CDI. In light of toxins A and B being immunogenic, vaccine trials are underway with the aim to prevent primary infection.
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Affiliation(s)
- Kanika Sehgal
- Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
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14
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McLean K, Balada-Llasat JM, Waalkes A, Pancholi P, Salipante SJ. Whole-genome sequencing of clinical Clostridioides difficile isolates reveals molecular epidemiology and discrepancies with conventional laboratory diagnostic testing. J Hosp Infect 2020; 108:64-71. [PMID: 33227298 DOI: 10.1016/j.jhin.2020.11.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 10/06/2020] [Accepted: 11/16/2020] [Indexed: 12/29/2022]
Abstract
BACKGROUND The high clinical burden of Clostridioides difficile infections merits rapid and sensitive identification of affected individuals. However, effective diagnosis remains challenging. Current best practice guidelines recommend molecular and/or direct toxin detection-based screening for symptomatic individuals, but previous work has called into question the concordance and performance of extant clinical assays. AIM To better correlate the genomic and phenotypic properties of clinical C. difficile isolates with laboratory testing outcomes in both C. difficile-infected patients and asymptomatic carriers. METHODS Whole-genome sequencing of clinical C. difficile isolates collected from an inpatient population at a single healthcare institution was performed, enabling examination of their molecular epidemiology and toxigenic gene content. Genomic findings were compared with clinical testing outcomes, identifying multiple diagnostic discrepancies. FINDINGS Toxigenic culture, considered a 'reference standard', provided perfect sensitivity and specificity in predicting toxigenic gene content, whereas reduced performance was observed for Simplexa C. difficile Direct Assay (100% specificity, 88% sensitivity), Gene Xpert CD/Epi Assay (86% specificity, 83% sensitivity), and Quick Check Complete Tox A/B (100% specificity, 30% sensitivity). Genomic analysis additionally revealed variability in toxin gene sequences among C. difficile strains, phylogenomic equivalency between isolates from affected patients and carriers, and patient carriage with uncommon environmentally derived C. difficile lineages, as well as presenting opportunities for tracing pathogen transmission events. CONCLUSION These results highlight the variable performance of clinical stool-based testing approaches as well as the potential diagnostic utility of whole-genome sequencing as an alternative to conventional testing algorithms.
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Affiliation(s)
- K McLean
- University of Washington Department of Laboratory Medicine, Seattle, WA, USA
| | - J-M Balada-Llasat
- Ohio State University Wexner Medical Center, Department of Pathology, Columbus, OH, USA
| | - A Waalkes
- University of Washington Department of Laboratory Medicine, Seattle, WA, USA
| | - P Pancholi
- Ohio State University Wexner Medical Center, Department of Pathology, Columbus, OH, USA.
| | - S J Salipante
- University of Washington Department of Laboratory Medicine, Seattle, WA, USA.
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15
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Terra DADA, Vilela EG, Silva ROS, LeÃo LA, Lima KS, Passos RIFÂ, Diniz AN, Coelho LGV. STRUCTURING A FECAL MICROBIOTA TRANSPLANTATION CENTER IN A UNIVERSITY HOSPITAL IN BRAZIL. ARQUIVOS DE GASTROENTEROLOGIA 2020; 57:434-458. [PMID: 33331486 DOI: 10.1590/s0004-2803.202000000-79] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Accepted: 06/30/2020] [Indexed: 12/15/2022]
Abstract
BACKGROUND Fecal microbiota transplantation (FMT) is an important therapeutic option for recurrent or refractory Clostridioides difficile infection, being a safe and effective method. Initial results suggest that FMT also plays an important role in other conditions whose pathogenesis involves alteration of the intestinal microbiota. However, its systematized use is not widespread, especially in Brazil. In the last decade, multiple reports and several cases emerged using different protocols for FMT, without standardization of methods and with variable response rates. In Brazil, few isolated cases of FMT have been reported without the implantation of a Fecal Microbiota Transplantation Center (FMTC). OBJECTIVE The main objective of this study is to describe the process of implanting a FMTC with a stool bank, in a Brazilian university hospital for treatment of recurrent and refractory C. difficile infection. METHODS The center was structured within the criteria required by international organizations such as the Food and Drug Administration, the European Fecal Microbiota Transplant Group and in line with national epidemiological and regulatory aspects. RESULTS A whole platform involved in structuring a transplant center with stool bank was established. The criteria for donor selection, processing and storage of samples, handling of recipients before and after the procedure, routes of administration, short and long-term follow-up of transplant patients were determined. Donor selection was conducted in three stages: pre-screening, clinical evaluation and laboratory screening. Most of the candidates were excluded in the first (75.4%) and second stage (72.7%). The main clinical exclusion criteria were: recent acute diarrhea, overweight (body mass index ≥25 kg/m2) and chronic gastrointestinal disorders. Four of the 134 candidates were selected after full screening, with a donor detection rate of 3%. CONCLUSION The implantation of a transplant center, unprecedented in our country, allows the access of patients with recurrent or refractory C. difficile infection to innovative, safe treatment, with a high success rate and little available in Brazil. Proper selection of qualified donors is vital in the process of implementing a FMTC. The rigorous clinical evaluation of donors allowed the rational use of resources. A transplant center enables treatment on demand, on a larger scale, less personalized, with more security and traceability. This protocol provides subsidies for conducting FMT in emerging countries.
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Affiliation(s)
| | - Eduardo Garcia Vilela
- Instituto Alfa de Gastroenterologia, Hospital das Clínicas / EBSERH, Universidade Federal de Mina Gerais, Belo Horizonte, MG, Brasil
| | | | - Laiane Alves LeÃo
- Instituto Alfa de Gastroenterologia, Hospital das Clínicas / EBSERH, Universidade Federal de Mina Gerais, Belo Horizonte, MG, Brasil
| | - Karine Sampaio Lima
- Instituto Alfa de Gastroenterologia, Hospital das Clínicas / EBSERH, Universidade Federal de Mina Gerais, Belo Horizonte, MG, Brasil
| | | | - Amanda Nádia Diniz
- Universidade Federal de Minas Gerais, Escola de Veterinária, Belo Horizonte, MG, Brasil
| | - Luiz Gonzaga Vaz Coelho
- Instituto Alfa de Gastroenterologia, Hospital das Clínicas / EBSERH, Universidade Federal de Mina Gerais, Belo Horizonte, MG, Brasil
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16
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A 2-step algorithm combining glutamate dehydrogenase and nucleic acid amplification tests for the detection of Clostridioides difficile in stool specimens. Eur J Clin Microbiol Infect Dis 2020; 40:345-351. [PMID: 32944896 DOI: 10.1007/s10096-020-04027-y] [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: 06/22/2020] [Accepted: 08/26/2020] [Indexed: 10/23/2022]
Abstract
The optimized diagnosis algorithm of Clostridioides difficile infection (CDI) is worldwide concerns. The purpose of this study was to assess the toxigenic C. difficile test performance and propose an optimal laboratory workflow for the diagnosis of CDI in mild virulent epidemic areas. Diarrhea samples collected from patients were analyzed by glutamate dehydrogenase (GDH), toxin AB (CDAB), and nucleic acid amplification test (NAAT). We assessed the performance of GDH, the GDH-CDAB algorithm, and the GDH-NAAT algorithm using toxigenic culture (TC) as a reference method. In this study, 186 diarrhea samples were collected. The numbers of TC-positive and TC-negative samples were 39 and 147, respectively. The sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and kappa of the GDH assay were 100%, 80.3%, 57.4%, 100%, and 0.63; of the GDH-CDAB algorithm were 48.7%, 97.3%, 82.6%, 87.7%, and 0.54; and of the GDH-NAAT algorithm were 74.4%, 100%, 100%, 93.6%, and 0.82, respectively. The GDH-NAAT algorithm has great concordance with TC in detecting toxigenic C. difficile (kappa = 0.82), while the sensitivity of the GDH-CDAB algorithm was too low to meet the demand of CDI diagnosis clinically. GDH-NAAT algorithm is recommended for the detection of toxigenic C. difficile with high specificity, increased sensitivity, and cost-effective.
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17
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Crobach MJT, Ducarmon QR, Terveer EM, Harmanus C, Sanders IMJG, Verduin KM, Kuijper EJ, Zwittink RD. The Bacterial Gut Microbiota of Adult Patients Infected, Colonized or Noncolonized by Clostridioides difficile. Microorganisms 2020; 8:microorganisms8050677. [PMID: 32384826 PMCID: PMC7284656 DOI: 10.3390/microorganisms8050677] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 05/01/2020] [Accepted: 05/04/2020] [Indexed: 12/15/2022] Open
Abstract
: Gut microbiota composition in patients with Clostridioides difficile colonization is not well investigated. We aimed to identify bacterial signatures associated with resistance and susceptibility to C. difficile colonization (CDC) and infection (CDI). Therefore, gut microbiota composition from patients with CDC (n = 41), with CDI (n = 41), and without CDC (controls, n = 43) was determined through 16S rRNA gene amplicon sequencing. Bacterial diversity was decreased in CDC and CDI patients (p<0.01). Overall microbiota composition was significantly different between control, CDC, and CDI patients (p = 0.001). Relative abundance of Clostridioides (most likely C. difficile) increased stepwise from controls to CDC and CDI patients. In addition, differential abundance analysis revealed that CDI patients' gut microbiota was characterized by significantly higher relative abundance of Bacteroides and Veillonella than CDC patients and controls. Control patients had significantly higher Eubacterium hallii and Fusicatenibacter abundance than colonized patients. Network analysis indicated that Fusicatenibacter was negatively associated with Clostridioides in CDI patients, while Veillonella was positively associated with Clostridioides in CDC patients. Bacterial microbiota diversity decreased in both CDC and CDI patients, but harbored a distinct microbiota. Eubacterium hallii and Fusicatenibacter may indicate resistance against C. difficile colonization and subsequent infection, while Veillonella may indicate susceptibility to colonization and infection by C. difficile.
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Affiliation(s)
- Monique J. T. Crobach
- Experimental Bacteriology, Department of Medical Microbiology, Center for Infectious Diseases, Leiden University Medical Center, 2333ZA Leiden, The Netherlands; (M.J.T.C.); (Q.R.D.); (E.M.T.); (C.H.); (I.M.J.G.S.); (E.J.K.)
| | - Quinten R. Ducarmon
- Experimental Bacteriology, Department of Medical Microbiology, Center for Infectious Diseases, Leiden University Medical Center, 2333ZA Leiden, The Netherlands; (M.J.T.C.); (Q.R.D.); (E.M.T.); (C.H.); (I.M.J.G.S.); (E.J.K.)
- Center for Microbiome Analyses and Therapeutics, Department of Medical Microbiology, Center for Infectious Diseases, Leiden University Medical Center, 2333ZA Leiden, The Netherlands
| | - Elisabeth M. Terveer
- Experimental Bacteriology, Department of Medical Microbiology, Center for Infectious Diseases, Leiden University Medical Center, 2333ZA Leiden, The Netherlands; (M.J.T.C.); (Q.R.D.); (E.M.T.); (C.H.); (I.M.J.G.S.); (E.J.K.)
- Center for Microbiome Analyses and Therapeutics, Department of Medical Microbiology, Center for Infectious Diseases, Leiden University Medical Center, 2333ZA Leiden, The Netherlands
- Netherlands Donor Feces Bank, 2333ZA Leiden, The Netherlands
| | - Celine Harmanus
- Experimental Bacteriology, Department of Medical Microbiology, Center for Infectious Diseases, Leiden University Medical Center, 2333ZA Leiden, The Netherlands; (M.J.T.C.); (Q.R.D.); (E.M.T.); (C.H.); (I.M.J.G.S.); (E.J.K.)
| | - Ingrid M. J. G. Sanders
- Experimental Bacteriology, Department of Medical Microbiology, Center for Infectious Diseases, Leiden University Medical Center, 2333ZA Leiden, The Netherlands; (M.J.T.C.); (Q.R.D.); (E.M.T.); (C.H.); (I.M.J.G.S.); (E.J.K.)
| | - Kees M. Verduin
- Department of Microbiology and Infection Prevention, Amphia Hospital, 4818CK Breda, The Netherlands;
| | - Ed J. Kuijper
- Experimental Bacteriology, Department of Medical Microbiology, Center for Infectious Diseases, Leiden University Medical Center, 2333ZA Leiden, The Netherlands; (M.J.T.C.); (Q.R.D.); (E.M.T.); (C.H.); (I.M.J.G.S.); (E.J.K.)
- Center for Microbiome Analyses and Therapeutics, Department of Medical Microbiology, Center for Infectious Diseases, Leiden University Medical Center, 2333ZA Leiden, The Netherlands
- Netherlands Donor Feces Bank, 2333ZA Leiden, The Netherlands
| | - Romy D. Zwittink
- Experimental Bacteriology, Department of Medical Microbiology, Center for Infectious Diseases, Leiden University Medical Center, 2333ZA Leiden, The Netherlands; (M.J.T.C.); (Q.R.D.); (E.M.T.); (C.H.); (I.M.J.G.S.); (E.J.K.)
- Center for Microbiome Analyses and Therapeutics, Department of Medical Microbiology, Center for Infectious Diseases, Leiden University Medical Center, 2333ZA Leiden, The Netherlands
- Correspondence: ; Tel.: +31-(0)71-526-4830
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Guerrero-Araya E, Meneses C, Castro-Nallar E, Guzmán D. AM, Álvarez-Lobos M, Quesada-Gómez C, Paredes-Sabja D, Rodríguez C. Origin, genomic diversity and microevolution of the Clostridium difficile B1/NAP1/RT027/ST01 strain in Costa Rica, Chile, Honduras and Mexico. Microb Genom 2020; 6:e000355. [PMID: 32176604 PMCID: PMC7371124 DOI: 10.1099/mgen.0.000355] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 02/28/2020] [Indexed: 12/18/2022] Open
Abstract
Clostridium difficile B1/NAP1/RT027/ST01 has been responsible for outbreaks of antibiotic-associated diarrhoea in clinical settings worldwide and is associated with severe disease presentations and increased mortality rates. Two fluoroquinolone-resistant (FQR) lineages of the epidemic B1/NAP1/RT027/ST01 strain emerged in the USA in the early 1990s and disseminated trans continentally (FQR1 and FQR2). However, it is unclear when and from where they entered Latin America (LA) and whether isolates from LA exhibit unique genomic features when compared to B1/NAP1/RT027/ST01 isolates from other regions of the world. To answer the first issue we compared whole-genome sequences (WGS) of 25 clinical isolates typed as NAP1, RT027 or ST01 in Costa Rica (n=16), Chile (n=5), Honduras (n=3) and Mexico (n=1) to WGS of 129 global isolates from the same genotype using Bayesian phylogenomics. The second question was addressed through a detailed analysis of the number and type of mutations of the LA isolates and their mobile resistome. All but two B1/NAP1/RT027/ST01 isolates from LA belong to the FQR2 lineage (n=23, 92 %), confirming its widespread distribution. As indicated by analysis of a dataset composed of 154 WGS, the B1/NAP1/RT027/ST01 strain was introduced into the four LA countries analysed between 1998 and 2005 from North America (twice) and Europe (at least four times). These events occurred soon after the emergence of the FQR lineages and more than one decade before the first report of the detection of the B1/NAP1/RT027/ST01 in LA. A total of 552 SNPs were identified across all genomes examined (3.8-4.3 Mb) in pairwise comparisons to the R20291 reference genome. Moreover, pairwise SNP distances were among the smallest distances determined in this species so far (0 to 55). Despite this high level of genomic conservation, 39 unique SNPs (7 %) in genes that play roles in the infection process (i.e. slpA) or antibiotic resistance (i.e. rpoB, fusA) distinguished the LA isolates. In addition, isolates from Chile, Honduras and Mexico had twice as many antibiotic resistance genes (ARGs, n=4) than related isolates from other regions. Their unique set of ARGs includes a cfr-like gene and tetM, which were found as part of putative mobile genetic elements whose sequences resemble undescribed integrative and conjugative elements. These results show multiple, independent introductions of B1/NAP1/RT027/ST01 isolates from the FQR1 and FQR2 lineages from different geographical sources into LA and a rather rapid accumulation of distinct mutations and acquired ARG by the LA isolates.
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Affiliation(s)
- Enzo Guerrero-Araya
- Millennium Nucleus in the Biology of Intestinal Microbiota, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
- Microbiota-Host Interactions & Clostridia Research Group, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Claudio Meneses
- Centro de Biotecnología Vegetal, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
- FONDAP Center for Genome Regulation, Universidad Andrés Bello, Santiago, Chile
| | - Eduardo Castro-Nallar
- Center for Bioinformatics and Integrative Biology, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - Ana M. Guzmán D.
- Department of Clinical Laboratory, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Manuel Álvarez-Lobos
- Department of Gastroenterology, Faculty of Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile
| | - Carlos Quesada-Gómez
- Facultad de Microbiología & Centro de Investigación en Enfermedades Tropicales (CIET), Universidad de Costa Rica, San José, Costa Rica
| | - Daniel Paredes-Sabja
- Millennium Nucleus in the Biology of Intestinal Microbiota, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
- Microbiota-Host Interactions & Clostridia Research Group, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile
| | - César Rodríguez
- Facultad de Microbiología & Centro de Investigación en Enfermedades Tropicales (CIET), Universidad de Costa Rica, San José, Costa Rica
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Carroll KC, Mizusawa M. Laboratory Tests for the Diagnosis of Clostridium difficile. Clin Colon Rectal Surg 2020; 33:73-81. [PMID: 32104159 PMCID: PMC7042017 DOI: 10.1055/s-0039-3400476] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Clostridium (reclassified as " Clostridioides ") difficile is an anaerobic, gram-positive bacterium that causes significant disease through elaboration of two potent toxins in patients whose normal gut microbiota has been altered through antimicrobial or chemotherapeutic agents (dysbiosis). The optimum method of laboratory diagnosis is still somewhat controversial. Recent practice guidelines published by professional societies recommend a two-step approach beginning with a test for glutamate dehydrogenase (GDH), followed by a toxin test and/or a nucleic acid test. Alternatively, in institutions where established clinical algorithms guide testing, a nucleic acid test alone is acceptable. Nucleic acid tests are the methods of choice in approximately 50% of laboratories in the United States. These tests are considered as the most sensitive methods for detection of C. difficile in stool and are the least specific. Because of the lower specificity with nucleic acid tests, some clinicians believe that toxin enzyme immunoassays are better predictors of disease, despite their known poor performance in certain patient populations. This review will discuss the advantages and disadvantages of the currently available test methods for the diagnosis of C. difficile with a brief mention of some novel assays that are currently in clinical trials.
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Affiliation(s)
- Karen C. Carroll
- Division of Medical Microbiology, Department of Pathology, the Johns Hopkins University School of Medicine, Baltimore, Maryland
- Address for correspondence Karen C. Carroll, MD Division of Medical Microbiology, Department of Pathology, the Johns Hopkins University School of MedicineMeyer B1-193, 600 North Wolfe Street, Baltimore MD 21287
| | - Masako Mizusawa
- Section of Infectious Diseases, Department of Internal Medicine, University of Missouri, Kansas City, Missouri
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20
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Vaughn JL, Balada-Llasat JM, Lamprecht M, Huang Y, Anghelina M, El Boghdadly Z, Bishop-Hill K, Childs R, Pancholi P, Andritsos LA. Detection of toxigenic Clostridium difficile colonization in patients admitted to the hospital for chemotherapy or haematopoietic cell transplantation. J Med Microbiol 2020; 67:976-981. [PMID: 29863458 PMCID: PMC6152365 DOI: 10.1099/jmm.0.000774] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Increasing evidence suggests that asymptomatic carriers are an important source of healthcare-associated Clostridium difficile infection. However, it is not known which test for the detection of C. difficile colonization is most sensitive in patients with haematological malignancies. We performed a prospective cohort study of 101 patients with haematological malignancies who had been admitted to the hospital for scheduled chemotherapy or haematopoietic cell transplantation. Each patient provided a formed stool sample. We compared the performance of five different commercially available assays, using toxigenic culture as the reference method. The prevalence of toxigenic C. difficile colonization as determined by toxigenic culture was 14/101 (14 %). The Cepheid Xpert PCR C. difficile/Epi was the most sensitive test for the detection of toxigenic C. difficile colonization, with 93 % sensitivity and 99 % negative predictive value. Our findings suggest that the Xpert PCR C. difficile/Epi could be used to rule out toxigenic C. difficile colonization in this population.
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Affiliation(s)
- John L Vaughn
- Division of Hematology, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | | | - Misty Lamprecht
- Comprehensive Cancer Center, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Ying Huang
- Division of Hematology, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Mirela Anghelina
- Comprehensive Cancer Center, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Zeinab El Boghdadly
- Division of Infectious Diseases, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Karen Bishop-Hill
- Division of Infectious Diseases, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Rachel Childs
- Nursing Research, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Preeti Pancholi
- Department of Pathology, The Ohio State University Wexner Medical Center, Columbus, OH, USA
| | - Leslie A Andritsos
- Division of Hematology, The Ohio State University Wexner Medical Center, Columbus, OH, USA
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Khodaparast S, Mohabati Mobarez A, Saberifiroozi M. A Two-Step Approach for Diagnosing Glutamate Dehydrogenase Genes by Conventional Polymerase Chain Reaction from Clostridium difficile Isolates. Middle East J Dig Dis 2019; 11:135-140. [PMID: 31687111 PMCID: PMC6819966 DOI: 10.15171/mejdd.2019.139] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/09/2019] [Accepted: 05/10/2019] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Clostridium difficile is the major causative agent of nosocomial antibiotic-associated colitis. The gold standard for C. difficile detection is stool culture followed by cytotoxic assay, although it is laborious and time-consuming. We developed a screening test based on a two-step conventional polymerase chain reaction (PCR) approach to detect gluD, the glutamate dehydrogenase (GDH) enzyme gene, which is a marker for screening of C. difficile. Targeting gluD comparing to the conserved stable genetic element of pathogenicity locus (PaLoc), with an accessory gene of Cdd3, was an effective method for the detection of this pathogen from patients with enterocolitis.
METHODS
Fresh fecal samples of the patients who were clinically suspicious for antibiotic-associated colitis were collected. Stool specimens were cultured on the cycloserine-cefoxitin fructose agar (CCFA) in an anaerobic condition, following alcohol shock treatment and enrichment in Clostridium difficile Brucella broth (CDBB). On confirmed colonies, PCR was carried out for detection of PaLoc subsidiary gene, Cdd3, and toxicogenic genes, tcdA and tcdB. The gluD that is GDH gene detection was performed by conventional PCR on the extracted DNA from 578 fresh stool samples.
RESULTS
57 (9.8%) strains of C. difficile were approved by conventional PCR for gluD and Cdd3 genes, in which 37 (6.4%) colonies had tcdA+/tcdB+ genotype, 2 (0.3%) tcdA+/tcdB-, 4 (0.7%) tcdA-/ tcdB+ and the remaining 14 (2.4%) colonies were tcdA and tcdB negative.
CONCLUSION
These results demonstrate that targeting gluD by PCR is quite promising for rapid detection of C. difficile from fresh fecal samples. Furthermore, the multiple-gene analysis for tcdA and tcdB assay proved a reliable approach for diagnosing of toxigenic strains among clinical samples.
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Affiliation(s)
- Sepideh Khodaparast
- Department of Bacteriology, Faculty of Medical Sciences, Tarbiat Modares University. Tehran, Iran
| | - Ashraf Mohabati Mobarez
- Department of Bacteriology, Faculty of Medical Sciences, Tarbiat Modares University. Tehran, Iran
| | - Mehdi Saberifiroozi
- Digestive Disease Research Institute, Tehran University of Medical Sciences, Tehran, Iran
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22
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Mullane KM, Dubberke ER. Management of Clostridioides (formerly Clostridium) difficile infection (CDI) in solid organ transplant recipients: Guidelines from the American Society of Transplantation Community of Practice. Clin Transplant 2019; 33:e13564. [PMID: 31002420 DOI: 10.1111/ctr.13564] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 04/09/2019] [Indexed: 02/06/2023]
Abstract
These updated guidelines from the American Society of Transplantation Infectious Diseases Community of Practice address the prevention and management of Clostridium difficile infection in solid organ transplant (SOT) recipients. Clostridioides (formerly Clostridium) difficile infection (CDI) is among the most common hospital acquired infections. In SOT recipients, the incidence of CDI varies by type and number or organs transplanted. While a meta-analysis of published literature found the prevalence of postoperative CDI in the general surgical population to be approximately 0.51%, the prevalence of CDI that is seen in the solid organ transplant population ranges from a low of 3.2% in the pancreatic transplant population to 12.7% in those receiving multiple organ transplants. There are no randomized, controlled trials evaluating the management of CDI in the SOT population. Herein is a review and summary of the currently available literature that has been synthesized into updated treatment guidelines for the management of CDI in the SOT population.
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Affiliation(s)
- Kathleen M Mullane
- Department of Medicine, Section of Infectious Diseases & Global Health, University of Chicago, Chicago, Illinois
| | - Erik R Dubberke
- Department of Medicine, Division of Infectious Diseases, School of Medicine, Washington University, St. Louis, Missouri
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23
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Boyanova L, Kalvatchev N, Yordanov D, Hadzhiyski P, Markovska R, Gergova G, Mitov I. Clostridioides (Clostridium) difficile carriage in asymptomatic children since 2010: a narrative review. BIOTECHNOL BIOTEC EQ 2019. [DOI: 10.1080/13102818.2019.1650666] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Affiliation(s)
- Lyudmila Boyanova
- Department of Medical Microbiology, Faculty of Medicine, Medical University of Sofia, Sofia, Bulgaria
| | - Nikolay Kalvatchev
- Department of Medical Microbiology, Faculty of Medicine, Medical University of Sofia, Sofia, Bulgaria
| | - Daniel Yordanov
- Department of Medical Microbiology, Faculty of Medicine, Medical University of Sofia, Sofia, Bulgaria
| | - Petyo Hadzhiyski
- Specialized Hospital for Active Pediatric Treatment, Medical University of Sofia, Sofia, Bulgaria
| | - Rumyana Markovska
- Department of Medical Microbiology, Faculty of Medicine, Medical University of Sofia, Sofia, Bulgaria
| | - Galina Gergova
- Department of Medical Microbiology, Faculty of Medicine, Medical University of Sofia, Sofia, Bulgaria
| | - Ivan Mitov
- Department of Medical Microbiology, Faculty of Medicine, Medical University of Sofia, Sofia, Bulgaria
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24
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Terveer EM, Fallon M, Kraakman MEM, Ormond A, Fitzpatrick M, Caljouw MAA, Martin A, van Dorp SM, Wong MC, Kuijper EJ, Fitzpatrick F. Spread of ESBL-producing Escherichia coli in nursing home residents in Ireland and the Netherlands may reflect infrastructural differences. J Hosp Infect 2019; 103:160-164. [PMID: 31077778 DOI: 10.1016/j.jhin.2019.05.003] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 05/01/2019] [Indexed: 12/29/2022]
Abstract
A prevalence study in two nursing homes (one each in the Netherlands and Ireland) found four (11%) Dutch and six (9%) Irish residents colonized with 11 extended-spectrum beta-lactamase-producing Escherichia coli, 10 of which contained CTX-M-15. Four Dutch isolates, from three residents of the same ward, belonged to E. coli O25:H4, sequence type (ST) 131 and were part of the same cluster type by whole-genome sequencing. Four Irish residents on three different wards were colonized with an identical E. coli O89:H9, ST131, complex type 1478. Cross-transmission between three Irish wards may reflect differences in nursing home infrastructure, specifically communal areas and multi-bedded resident rooms.
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Affiliation(s)
- E M Terveer
- Department of Medical Microbiology, Leiden University Medical Centre, Leiden, the Netherlands.
| | - M Fallon
- Department of Clinical Microbiology, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - M E M Kraakman
- Department of Medical Microbiology, Leiden University Medical Centre, Leiden, the Netherlands
| | - A Ormond
- Department of Clinical Microbiology, Beaumont Hospital, Dublin, Ireland
| | - M Fitzpatrick
- Department of Clinical Microbiology, Beaumont Hospital, Dublin, Ireland
| | - M A A Caljouw
- Department of Public Health and Primary Care, Leiden University Medical Centre, Leiden, the Netherlands
| | - A Martin
- Department of Geriatric and Stroke Medicine, Beaumont Hospital, Dublin, Ireland; Department of Geriatric and Stroke Medicine, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - S M van Dorp
- Department of Medical Microbiology, Leiden University Medical Centre, Leiden, the Netherlands
| | - M C Wong
- Department of Medical Microbiology, Leiden University Medical Centre, Leiden, the Netherlands
| | - E J Kuijper
- Department of Medical Microbiology, Leiden University Medical Centre, Leiden, the Netherlands
| | - F Fitzpatrick
- Department of Clinical Microbiology, Royal College of Surgeons in Ireland, Dublin, Ireland; Department of Clinical Microbiology, Beaumont Hospital, Dublin, Ireland
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25
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Al-Rawahi GN, Al-Najjar A, McDonald R, Deyell RJ, Golding GR, Brant R, Tilley P, Thomas E, Rassekh SR, O'Gorman A, Wong P, Turnham L, Dobson S. Pediatric oncology and stem cell transplant patients with healthcare-associated Clostridium difficile infection were already colonized on admission. Pediatr Blood Cancer 2019; 66:e27604. [PMID: 30666782 DOI: 10.1002/pbc.27604] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Revised: 11/22/2018] [Accepted: 12/14/2018] [Indexed: 01/02/2023]
Abstract
UNLABELLED Clostridium difficile is the leading cause of healthcare-associated infections worldwide. The diagnosis of C. difficile infection (CDI) in pediatric oncology patients is complex as diarrhea is common, and there is a high rate of colonization in infants and young children. This study was conducted to assess the accuracy of the surveillance definitions of healthcare-associated CDI (HA-CDI) and to determine the prevalence of toxigenic C. difficile colonization among pediatric oncology and stem cell transplant patients. METHODS A prospective cohort study was conducted over a three-year period in an inpatient pediatric oncology and stem cell transplant setting. Baseline stool samples were collected within three days of admission and were genotypically compared with clinically indicated samples submitted after three days of admission. RESULTS A total of 175 patients were recruited with a total of 536 admissions. The adjusted prevalence of baseline toxigenic C. difficile colonization among admissions was 32.8%. Seventy-eight percent of positive admissions did not have history of CDI. Colonization with a toxigenic strain on admission was predictive of CDI (OR = 28.6; 95% CI, 6.58-124.39; P < 0.001). Nearly all clinical isolates (8/9) shared identical pulsed-field gel electrophoresis patterns with baseline isolates or were closely related (1/9). Only one of the 11 cases that were considered HA-CDI was potentially nosocomially acquired. CONCLUSION The prevalence of colonization with toxigenic C. difficile in our cohort is high. Unfortunately, the current CDI surveillance definitions overestimate the incidence of HA-CDI in pediatric oncology and stem cell transplantation settings.
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Affiliation(s)
- Ghada N Al-Rawahi
- Department of Pathology and Laboratory Medicine, University of British Columbia, British Columbia Children's Hospital, Vancouver, British Columbia, Canada
| | - Abeer Al-Najjar
- Pediatric Infectious Diseases, Faculty of Medicine, King Abdulaziz University Hospital, Jeddah, Saudi Arabia
| | - Rachel McDonald
- Department of Pediatrics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Rebecca J Deyell
- Division of Pediatric Hematology/Oncology/BMT, University of British Columbia, British Columbia Children's Hospital, Vancouver, British Columbia, Canada
| | - George R Golding
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, Manitoba, Canada
| | - Rollin Brant
- Department of Statistics, University of British Columbia, British Columbia Children's Hospital Research Institute, Vancouver, British Columbia, Canada
| | - Peter Tilley
- Department of Pathology and Laboratory Medicine, University of British Columbia, British Columbia Children's Hospital, Vancouver, British Columbia, Canada
| | - Eva Thomas
- Department of Pathology, Sidra Medicine and Weill Cornell Medical College in Qatar, Doha, Qatar
| | - Shahrad R Rassekh
- Division of Pediatric Hematology/Oncology/BMT, University of British Columbia, British Columbia Children's Hospital, Vancouver, British Columbia, Canada
| | - Aisling O'Gorman
- Division of Pediatric Hematology/Oncology/BMT, University of British Columbia, British Columbia Children's Hospital, Vancouver, British Columbia, Canada
| | - Peggy Wong
- Division of Pediatric Hematology/Oncology/BMT, University of British Columbia, British Columbia Children's Hospital, Vancouver, British Columbia, Canada
| | - Lucy Turnham
- Division of Pediatric Hematology/Oncology/BMT, University of British Columbia, British Columbia Children's Hospital, Vancouver, British Columbia, Canada
| | - Simon Dobson
- Department of Pathology, Sidra Medicine and Weill Cornell Medical College in Qatar, Doha, Qatar
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26
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Baktash A, Terveer EM, Zwittink RD, Hornung BVH, Corver J, Kuijper EJ, Smits WK. Mechanistic Insights in the Success of Fecal Microbiota Transplants for the Treatment of Clostridium difficile Infections. Front Microbiol 2018; 9:1242. [PMID: 29946308 PMCID: PMC6005852 DOI: 10.3389/fmicb.2018.01242] [Citation(s) in RCA: 64] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2018] [Accepted: 05/23/2018] [Indexed: 12/12/2022] Open
Abstract
Fecal microbiota transplantation has proven to be an effective treatment for infections with the gram-positive enteropathogen Clostridium difficile. Despite its effectiveness, the exact mechanisms that underlie its success are largely unclear. In this review, we highlight the pleiotropic effectors that are transferred during fecal microbiota transfer and relate this to the C. difficile lifecycle. In doing so, we show that it is likely that multiple factors contribute to the elimination of symptoms of C. difficile infections after fecal microbiota transplantation.
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Affiliation(s)
- Amoe Baktash
- Clinical Microbiology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
| | - Elisabeth M Terveer
- Clinical Microbiology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands.,Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, Netherlands.,Netherlands Donor Feces Bank, Leiden, Netherlands
| | - Romy D Zwittink
- Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, Netherlands.,Experimental Bacteriology, Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
| | - Bastian V H Hornung
- Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, Netherlands.,Experimental Bacteriology, Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
| | - Jeroen Corver
- Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, Netherlands.,Experimental Bacteriology, Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
| | - Ed J Kuijper
- Clinical Microbiology Laboratory, Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands.,Center for Microbiome Analyses and Therapeutics, Leiden University Medical Center, Leiden, Netherlands.,Netherlands Donor Feces Bank, Leiden, Netherlands.,Experimental Bacteriology, Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
| | - Wiep Klaas Smits
- Experimental Bacteriology, Department of Medical Microbiology, Leiden University Medical Center, Leiden, Netherlands
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27
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Schäffler H, Breitrück A. Clostridium difficile - From Colonization to Infection. Front Microbiol 2018; 9:646. [PMID: 29692762 PMCID: PMC5902504 DOI: 10.3389/fmicb.2018.00646] [Citation(s) in RCA: 102] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Accepted: 03/19/2018] [Indexed: 12/19/2022] Open
Abstract
Clostridium difficile is the most frequent cause of nosocomial antibiotic-associated diarrhea. The incidence of C. difficile infection (CDI) has been rising worldwide with subsequent increases in morbidity, mortality, and health care costs. Asymptomatic colonization with C. difficile is common and a high prevalence has been found in specific cohorts, e.g., hospitalized patients, adults in nursing homes and in infants. However, the risk of infection with C. difficile differs significantly between these cohorts. While CDI is a clear indication for therapy, colonization with C. difficile is not believed to be a direct precursor for CDI and therefore does not require treatment. Antibiotic therapy causes alterations of the intestinal microbial composition, enabling C. difficile colonization and consecutive toxin production leading to disruption of the colonic epithelial cells. Clinical symptoms of CDI range from mild diarrhea to potentially life-threatening conditions like pseudomembranous colitis or toxic megacolon. While antibiotics are still the treatment of choice for CDI, new therapies have emerged in recent years such as antibodies against C. difficile toxin B and fecal microbial transfer (FMT). This specific therapy for CDI underscores the role of the indigenous bacterial composition in the prevention of the disease in healthy individuals and its role in the pathogenesis after alteration by antibiotic treatment. In addition to the pathogenesis of CDI, this review focuses on the colonization of C. difficile in the human gut and factors promoting CDI.
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Affiliation(s)
- Holger Schäffler
- Division of Gastroenterology, Department of Medicine II, University of Rostock, Rostock, Germany
| | - Anne Breitrück
- Extracorporeal Immunomodulation Unit, Fraunhofer Institute for Cell Therapy and Immunology, Rostock, Germany.,Institute of Medical Microbiology, Virology and Hygiene, University of Rostock, Rostock, Germany
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28
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Validation of Active Surveillance Testing for Clostridium difficile Colonization Using the cobas Cdiff Test. J Clin Microbiol 2018; 56:JCM.01553-17. [PMID: 29367295 DOI: 10.1128/jcm.01553-17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 01/17/2018] [Indexed: 12/14/2022] Open
Abstract
Clostridium difficile infection (CDI) is not declining in the United States. Nucleic acid amplification tests (NAAT) are used as part of active surveillance testing programs to prevent health care-associated infection. The objective of this study was to validate the cobas Cdiff Test on the cobas 4800 System (cobas) within a four-hospital system using prospectively collected perirectal swabs from asymptomatic patients at admission and during monthly intensive care unit (ICU) screening in an infection control CDI reduction program. Performance of the cobas was compared to that of toxigenic culture. Each positive cobas sample and the next following negative patient swab were cultured. The study design gave 273 samples processed by both cobas (137 positive and 136 negative) and culture (one negative swab was not cultured). Discrepant analysis was performed using a second NAAT, the Xpert C. difficile Epi test (Xpert). This strategy was compared to a medical record review for antibiotic receipt that would inhibit growth of C. difficile in colonic stool. None of the cobas-negative samples were culture positive. The cobas positive predictive value was 75.2% (95% confidence interval [CI], 66.9% to 82%) and positive percent agreement was 100% (95% CI, 96.0% to 100%). Overall agreement between cobas and direct toxigenic culture was 87.6% (95% CI, 83.1% to 91%). For the cobas-positive/culture-negative (discrepant) samples, 7 Xpert-positive samples were from patients receiving inhibitory antimicrobials; only 4 of 23 Xpert-negative samples received these agents (P = 0.00006). Our results support use of the cobas as a reliable assay for an active surveillance testing program to detect asymptomatic carriers of toxigenic C. difficile.
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29
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Nucleic Acid Amplification Test Quantitation as Predictor of Toxin Presence in Clostridium difficile Infection. J Clin Microbiol 2018; 56:JCM.01316-17. [PMID: 29237788 DOI: 10.1128/jcm.01316-17] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2017] [Accepted: 12/05/2017] [Indexed: 01/05/2023] Open
Abstract
Multistep algorithmic testing in which a sensitive nucleic acid amplification test (NAAT) is followed by a specific toxin A and toxin B enzyme immunoassay (EIA) is among the most accurate methods for Clostridium difficile infection (CDI) diagnosis. The obvious shortcoming of this approach is that multiple tests must be performed to establish a CDI diagnosis, which may delay treatment. Therefore, we sought to determine whether a preliminary diagnosis could be made on the basis of the quantitative results of the first test in algorithmic testing, which provide a measure of organism burden. To do so, we retrospectively analyzed two large collections of samples (n = 2,669 and n = 1,718) that were submitted to the laboratories of two Dutch hospitals for CDI testing. Both hospitals apply a two-step testing algorithm in which a NAAT is followed by a toxin A/B EIA. Of all samples, 208 and 113 samples, respectively, tested positive by NAAT. Among these NAAT-positive samples, significantly lower mean quantification cycle (Cq ) values were found for patients whose stool eventually tested positive for toxin, compared with patients who tested negative for toxin (mean Cq values of 24.4 versus 30.4 and 26.8 versus 32.2; P < 0.001 for both cohorts). Receiver operating characteristic curve analysis was performed to investigate the ability of Cq values to predict toxin status and yielded areas under the curve of 0.826 and 0.854. Using the optimal Cq cutoff values, prediction of the eventual toxin A/B EIA results was accurate for 78.9% and 80.5% of samples, respectively. In conclusion, Cq values can serve as predictors of toxin status but, due to the suboptimal correlation between the two tests, additional toxin testing is still needed.
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30
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Abstract
Clostridium difficile is the most frequent cause of nosocomial antibiotic-associated diarrhea. The incidence of C. difficile infection (CDI) has been rising worldwide with subsequent increases in morbidity, mortality, and health care costs. Asymptomatic colonization with C. difficile is common and a high prevalence has been found in specific cohorts, e.g., hospitalized patients, adults in nursing homes and in infants. However, the risk of infection with C. difficile differs significantly between these cohorts. While CDI is a clear indication for therapy, colonization with C. difficile is not believed to be a direct precursor for CDI and therefore does not require treatment. Antibiotic therapy causes alterations of the intestinal microbial composition, enabling C. difficile colonization and consecutive toxin production leading to disruption of the colonic epithelial cells. Clinical symptoms of CDI range from mild diarrhea to potentially life-threatening conditions like pseudomembranous colitis or toxic megacolon. While antibiotics are still the treatment of choice for CDI, new therapies have emerged in recent years such as antibodies against C. difficile toxin B and fecal microbial transfer (FMT). This specific therapy for CDI underscores the role of the indigenous bacterial composition in the prevention of the disease in healthy individuals and its role in the pathogenesis after alteration by antibiotic treatment. In addition to the pathogenesis of CDI, this review focuses on the colonization of C. difficile in the human gut and factors promoting CDI.
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Affiliation(s)
- Holger Schäffler
- Division of Gastroenterology, Department of Medicine II, University of Rostock, Rostock, Germany
| | - Anne Breitrück
- Extracorporeal Immunomodulation Unit, Fraunhofer Institute for Cell Therapy and Immunology, Rostock, Germany
- Institute of Medical Microbiology, Virology and Hygiene, University of Rostock, Rostock, Germany
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31
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van Dorp SM, de Greeff SC, Harmanus C, Sanders IMJG, Dekkers OM, Knetsch CW, Kampinga GA, Notermans DW, Kuijper EJ. Ribotype 078 Clostridium difficile infection incidence in Dutch hospitals is not associated with provincial pig farming: Results from a national sentinel surveillance, 2009-2015. PLoS One 2017; 12:e0189183. [PMID: 29287077 PMCID: PMC5747436 DOI: 10.1371/journal.pone.0189183] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2017] [Accepted: 11/21/2017] [Indexed: 02/04/2023] Open
Abstract
Background It has been suggested that the high incidence of ribotype 078 Clostridium difficile infections (CDI) in the Netherlands is related to pig farming. Methods We used data of hospitalised CDI patients (>2yrs of age) diagnosed between May 2009 and May 2015 in 26 hospitals participating in a national sentinel surveillance. We compared clinical and geographical characteristics of 078 CDI to other CDI. We investigated the association between 078 CDI incidence and four indicators of pig farming (piglet, pig, piglet farm and pig farm density) by mixed-effects Poisson regression. We used a space-time permutation model to search for community-onset 078 CDI clusters (using SaTScan). Results A total of 4,691 CDI were identified. Ribotype 078 was isolated in 493 of 3,756 patients (13.1%) including a typing result. These patients had slightly higher community-onset disease and a 35% increase of 30-day mortality compared to non-078 CDI patients. The pooled overall and 078 incidence rates were 2.82 (95% CI, 2.42–3.29) and 0.26 (95% CI, 0.21–0.31) CDI per 10,000 patients-days respectively. Hospital 078 CDI incidence was not associated with provincial pig (IRR, 0.98; 95% CI, 0.89–1.08), piglet (IRR, 0.95; 95% CI, 0.75–1.19), pig farm (IRR, 1.08; 95% CI, 0.84–1.39), or piglet farm density (IRR, 1.00; 95% CI, 0.56–1.79). No clusters of community-onset ribotype 078 CDI were found. Conclusions Our results do not indicate that the ribotype 078 CDI incidence in hospitals is related to pig (farm) or piglet (farm) density. However, transmission beyond provincial borders or in non-hospitalised patients cannot be excluded.
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Affiliation(s)
- Sofie M. van Dorp
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
- * E-mail:
| | - Sabine C. de Greeff
- Centre for Infectious Disease Control, the National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Céline Harmanus
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Ingrid M. J. G. Sanders
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Olaf M. Dekkers
- Department of Clinical Epidemiology and Endocrinology and Metabolic Diseases, Leiden University Medical Center, Leiden, the Netherlands
| | - Cornelis W. Knetsch
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Greetje A. Kampinga
- Department of Medical Microbiology, University of Groningen, University Medical Center Groningen, Groningen, the Netherlands
| | - Daan W. Notermans
- Centre for Infectious Disease Control, the National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Ed J. Kuijper
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
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Nagy E. What do we know about the diagnostics, treatment and epidemiology of Clostridioides (Clostridium) difficile infection in Europe? J Infect Chemother 2017; 24:164-170. [PMID: 29289484 DOI: 10.1016/j.jiac.2017.12.003] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2017] [Revised: 11/28/2017] [Accepted: 12/05/2017] [Indexed: 12/17/2022]
Abstract
Clostridium difficile, recently reclassified as Clostridioides difficile is responsible for a significant part of diarrheal diseases in the hospitals and in the community. Besides the main pathogenic factors, toxin A, toxin B and the binary toxin, several other putative virulence factors have been investigated. This manuscript summarize recent findings in Europe concerning source of infection, epidemiology of CDI, the changing pattern of PCR ribotypes of C. difficile strains in different European countries, recommendations for diagnosis and treatment of CDI.
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Affiliation(s)
- Elisabeth Nagy
- Institute of Clinical Microbiology, University of Szeged, Szeged, Hungary.
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Xiao Y, Paquet-Bolduc B, Garenc C, Gervais P, Trottier S, Roussy JF, Longtin J, Loo VG, Longtin Y. Impact of Isolating Clostridium difficile Carriers on the Burden of Isolation Precautions: A Time Series Analysis. Clin Infect Dis 2017; 66:1377-1382. [DOI: 10.1093/cid/cix1024] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2017] [Accepted: 11/13/2017] [Indexed: 01/09/2023] Open
Affiliation(s)
- Yasi Xiao
- McGill University Faculty of Medicine, Montreal
| | | | - Christophe Garenc
- Institut National de Santé Publique du Québec, Quebec City
- Centre Hospitalier Universitaire de Québec
| | - Philippe Gervais
- Quebec Heart and Lung Institute, Publique du Québec, Quebec City
- Centre Hospitalier Universitaire de Québec
| | - Sylvie Trottier
- Quebec Heart and Lung Institute, Publique du Québec, Quebec City
- Centre Hospitalier Universitaire de Québec
| | - Jean-François Roussy
- Quebec Heart and Lung Institute, Publique du Québec, Quebec City
- Centre Hospitalier Universitaire de Québec
| | - Jean Longtin
- Centre Hospitalier Universitaire de Québec
- Laboratoire de santé publique du Québec, Sainte-Anne-de-Bellevue
| | - Vivian G Loo
- McGill University Faculty of Medicine, Montreal
- McGill University Health Centre
| | - Yves Longtin
- McGill University Health Centre
- Jewish General Hospital Sir Mortimer B. Davis, Montreal, Québec, Canada
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Laboratory Testing of Donors and Stool Samples for Fecal Microbiota Transplantation for Recurrent Clostridium difficile Infection. J Clin Microbiol 2017; 55:1002-1010. [PMID: 28077694 DOI: 10.1128/jcm.02327-16] [Citation(s) in RCA: 52] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Fecal microbiota transplantation is an efficacious and inexpensive therapy for recurrent Clostridium difficile infection, yet its safety is thought to depend on appropriate fecal donor screening. FDA guidance for regulation of this procedure is in flux, but screening and manufacture of fecal material from asymptomatic donors present many challenges to clinical laboratories. This minireview summarizes FDA regulatory changes, principles of donor selection, and recommended laboratory screening practices for fecal microbiota transplantation.
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