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Ziaei Chamgordani S, Yadegar A, Ghourchian H. C. difficile biomarkers, pathogenicity and detection. Clin Chim Acta 2024; 558:119674. [PMID: 38621586 DOI: 10.1016/j.cca.2024.119674] [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: 02/04/2024] [Revised: 04/12/2024] [Accepted: 04/12/2024] [Indexed: 04/17/2024]
Abstract
BACKGROUND Clostridioides difficile infection (CDI) is the main etiologic agent of antibiotic-associated diarrhea. CDI contributes to gut inflammation and can lead to disruption of the intestinal epithelial barrier. Recently, the rate of CDI cases has been increased. Thus, early diagnosis of C. difficile is critical for controlling the infection and guiding efficacious therapy. APPROACH A search strategy was set up using the terms C. difficile biomarkers and diagnosis. The found references were classified into two general categories; conventional and advanced methods. RESULTS The pathogenicity and biomarkers of C. difficile, and the collection manners for CDI-suspected specimens were briefly explained. Then, the conventional CDI diagnostic methods were subtly compared in terms of duration, level of difficulty, sensitivity, advantages, and disadvantages. Thereafter, an extensive review of the various newly proposed techniques available for CDI detection was conducted including nucleic acid isothermal amplification-based methods, biosensors, and gene/single-molecule microarrays. Also, the detection mechanisms, pros and cons of these methods were highlighted and compared with each other. In addition, approximately complete information on FDA-approved platforms for CDI diagnosis was collected. CONCLUSION To overcome the deficiencies of conventional methods, the potential of advanced methods for C. difficile diagnosis, their direction, perspective, and challenges ahead were discussed.
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Affiliation(s)
- Sepideh Ziaei Chamgordani
- Laboratory of Bioanalysis, Institute of Biochemistry & Biophysics, University of Tehran, Tehran, Iran
| | - Abbas Yadegar
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Hedayatollah Ghourchian
- Laboratory of Bioanalysis, Institute of Biochemistry & Biophysics, University of Tehran, Tehran, Iran.
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2
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Dong Q, Lin H, Allen MM, Garneau JR, Sia JK, Smith RC, Haro F, McMillen T, Pope RL, Metcalfe C, Burgo V, Woodson C, Dylla N, Kohout C, Sundararajan A, Snitkin ES, Young VB, Fortier LC, Kamboj M, Pamer EG. Virulence and genomic diversity among clinical isolates of ST1 (BI/NAP1/027) Clostridioides difficile. Cell Rep 2023; 42:112861. [PMID: 37523264 PMCID: PMC10627504 DOI: 10.1016/j.celrep.2023.112861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 05/01/2023] [Accepted: 07/07/2023] [Indexed: 08/02/2023] Open
Abstract
Clostridioides difficile produces toxins that damage the colonic epithelium, causing colitis. Variation in disease severity is poorly understood and has been attributed to host factors and virulence differences between C. difficile strains. We test 23 epidemic ST1 C. difficile clinical isolates for their virulence in mice. All isolates encode a complete Tcd pathogenicity locus and achieve similar colonization densities. However, disease severity varies from lethal to avirulent infections. Genomic analysis of avirulent isolates reveals a 69-bp deletion in the cdtR gene, which encodes a response regulator for binary toxin expression. Deleting the 69-bp sequence in virulent R20291 strain renders it avirulent in mice with reduced toxin gene transcription. Our study demonstrates that a natural deletion within cdtR attenuates virulence in the epidemic ST1 C. difficile isolates without reducing colonization and persistence. Distinguishing strains on the basis of cdtR may enhance the specificity of diagnostic tests for C. difficile colitis.
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Affiliation(s)
- Qiwen Dong
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA; Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA.
| | - Huaiying Lin
- Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA
| | - Marie-Maude Allen
- Department of Microbiology and Infectious Diseases, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - Julian R Garneau
- Department of Microbiology and Infectious Diseases, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - Jonathan K Sia
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Rita C Smith
- Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA
| | - Fidel Haro
- Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA
| | - Tracy McMillen
- Infection Control, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Rosemary L Pope
- Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA; Committee on Immunology, University of Chicago, Chicago, IL 60637, USA
| | - Carolyn Metcalfe
- Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA
| | - Victoria Burgo
- Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA
| | - Che Woodson
- Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA
| | - Nicholas Dylla
- Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA
| | - Claire Kohout
- Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA
| | | | - Evan S Snitkin
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA
| | - Vincent B Young
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, MI 48109, USA; Department of Microbiology & Immunology, University of Michigan, Ann Arbor, MI 48109, USA
| | - Louis-Charles Fortier
- Department of Microbiology and Infectious Diseases, Université de Sherbrooke, Sherbrooke, QC J1E 4K8, Canada
| | - Mini Kamboj
- Infection Control, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Eric G Pamer
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA; Duchossois Family Institute, University of Chicago, Chicago, IL 60637, USA; Committee on Immunology, University of Chicago, Chicago, IL 60637, USA
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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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4
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Dong Q, Lin H, Allen MM, Garneau JR, Sia JK, Smith RC, Haro F, McMillen T, Pope RL, Metcalfe C, Burgo V, Woodson C, Dylla N, Kohout C, Sundararajan A, Snitkin ES, Young VB, Fortier LC, Kamboj M, Pamer EG. Virulence and genomic diversity among clinical isolates of ST1 (BI/NAP1/027) Clostridioides difficile. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.01.12.523823. [PMID: 36711955 PMCID: PMC9882218 DOI: 10.1101/2023.01.12.523823] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Clostridioides difficile (C. difficile) , a leading cause of nosocomial infection, produces toxins that damage the colonic epithelium and results in colitis that varies from mild to fulminant. Variation in disease severity is poorly understood and has been attributed to host factors (age, immune competence and intestinal microbiome composition) and/or virulence differences between C. difficile strains, with some, such as the epidemic BI/NAP1/027 (MLST1) strain, being associated with greater virulence. We tested 23 MLST1(ST1) C. difficile clinical isolates for virulence in antibiotic-treated C57BL/6 mice. All isolates encoded a complete Tcd pathogenicity locus and achieved similar colonization densities in mice. Disease severity varied, however, with 5 isolates causing lethal infections, 16 isolates causing a range of moderate infections and 2 isolates resulting in no detectable disease. The avirulent ST1 isolates did not cause disease in highly susceptible Myd88 -/- or germ-free mice. Genomic analysis of the avirulent isolates revealed a 69 base-pair deletion in the N-terminus of the cdtR gene, which encodes a response regulator for binary toxin (CDT) expression. Genetic deletion of the 69 base-pair cdtR sequence in the highly virulent ST1 R20291 C. difficile strain rendered it avirulent and reduced toxin gene transcription in cecal contents. Our study demonstrates that a natural deletion within cdtR attenuates virulence in the epidemic ST1 C. difficile strain without reducing colonization and persistence in the gut. Distinguishing strains on the basis of cdtR may enhance the specificity of diagnostic tests for C. difficile colitis.
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Affiliation(s)
- Qiwen Dong
- Department of Medicine, University of Chicago, Chicago, Illinois, USA
- Duchossois Family Institute, University of Chicago, Chicago, Illinois, USA
| | - Huaiying Lin
- Duchossois Family Institute, University of Chicago, Chicago, Illinois, USA
| | - Marie-Maude Allen
- Department of Microbiology and Infectious Diseases, Universite de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Julian R. Garneau
- Department of Microbiology and Infectious Diseases, Universite de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Jonathan K. Sia
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York City, New York, USA
| | - Rita C. Smith
- Duchossois Family Institute, University of Chicago, Chicago, Illinois, USA
| | - Fidel Haro
- Duchossois Family Institute, University of Chicago, Chicago, Illinois, USA
| | - Tracy McMillen
- Infection Control, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Rosemary L. Pope
- Duchossois Family Institute, University of Chicago, Chicago, Illinois, USA
- Committee on Immunology, University of Chicago, Chicago, Illinois, USA
| | - Carolyn Metcalfe
- Duchossois Family Institute, University of Chicago, Chicago, Illinois, USA
| | - Victoria Burgo
- Duchossois Family Institute, University of Chicago, Chicago, Illinois, USA
| | - Che Woodson
- Duchossois Family Institute, University of Chicago, Chicago, Illinois, USA
| | - Nicholas Dylla
- Duchossois Family Institute, University of Chicago, Chicago, Illinois, USA
| | - Claire Kohout
- Duchossois Family Institute, University of Chicago, Chicago, Illinois, USA
| | | | - Evan S Snitkin
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
| | - Vincent B. Young
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan, USA
- Department of Microbiology & Immunology, University of Michigan, Ann Arbor, MI, USA
| | - Louis-Charles Fortier
- Department of Microbiology and Infectious Diseases, Universite de Sherbrooke, Sherbrooke, Quebec, Canada
| | - Mini Kamboj
- Infection Control, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York, USA
| | - Eric G. Pamer
- Department of Medicine, University of Chicago, Chicago, Illinois, USA
- Duchossois Family Institute, University of Chicago, Chicago, Illinois, USA
- Committee on Immunology, University of Chicago, Chicago, Illinois, USA
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5
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Angione SL, Croote D, Leung JW, Mermel LA, Tripathi A. Single fluorophore melting curve analysis for detection of hypervirulent Clostridium difficile. J Med Microbiol 2015; 65:62-70. [PMID: 26516039 DOI: 10.1099/jmm.0.000199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
This study demonstrates a novel detection assay able to identify and subtype strains of Clostridium difficile. Primers carefully designed for melting curve analysis amplify DNA from three C. difficile genes, tcdB, tcdC and cdtB, during quantitative (q)PCR. The tcdB gene allows for confirmation of organism presence, whilst the tcdC and cdtB genes allow for differentiation of virulence status, as deletions in the tcdC gene and the concurrent presence of the cdtB gene, which produces binary toxin, are associated with hypervirulence. Following qPCR, subtyping is then achieved by automated, inline melting curve analysis using only a single intercalating dye and verified by microchip electrophoresis. This assay represents a novel means of distinguishing between toxigenic and hypervirulent C. difficile strains NAP1/027/BI and 078 ribotype, which are highly prevalent hypervirulent strains in humans. This methodology can help rapidly detect and identify C. difficile strains that impose a significant health and economic burden in hospitals and other healthcare settings.
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Affiliation(s)
- Stephanie L Angione
- Center for Biomedical Engineering, School of Engineering, Brown University, Providence, RI, USA
| | - Derek Croote
- Center for Biomedical Engineering, School of Engineering, Brown University, Providence, RI, USA
| | - Joshua W Leung
- Center for Biomedical Engineering, School of Engineering, Brown University, Providence, RI, USA
| | - Leonard A Mermel
- Division of Infectious Diseases, Department of Medicine, Rhode Island Hospital, , Providence, RI, USA.,Warren Alpert Medical School of Brown University, Providence, RI, USA
| | - Anubhav Tripathi
- Center for Biomedical Engineering, School of Engineering, Brown University, Providence, RI, USA
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Abstract
Diagnostic Microbiology is the tool that makes it possible to identify the exact etiology of infectious diseases and the most optimal therapy at the level of individual patients as well as communities. Conventional methods require time to grow the microbes in vitro under specific conditions and not all microbes are easily cultivable. This is followed by biochemical methods for identification which also require hours and sometimes days. Transport of the specimens under less than ideal conditions, prior use of antibiotics and small number of organisms are among the factors that render culture-based methods less reliable. Newer methods depend on amplification of nucleic acids followed by use of probes for identification. This mitigates the need for higher microbial load, presence of metabolically active viable organisms and shortens the time to reporting. These methods can be used to detect antibiotic resistance genes directly from the specimen and help direct targeted therapy. Since these methods will not fulfill all the diagnostic needs, a second approach is being used to shorten the time to identification after the organism has already grown. Mass spectrometry and bioinformatics are the tools making this possible. This review gives a historical perspective on diagnostic microbiology, discusses the pitfalls of current methodology and provides an overview of newer and future methods.
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Affiliation(s)
- N Khardori
- Department of Internal Medicine, Division of Infectious Disease, Department of Microbiology and Molecular Cell Biology, Eastern Virginia Medical School, Norfolk, Virginia, USA
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