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Abad-Fau A, Sevilla E, Martín-Burriel I, Moreno B, Bolea R. Update on Commonly Used Molecular Typing Methods for Clostridioides difficile. Microorganisms 2023; 11:1752. [PMID: 37512924 PMCID: PMC10384772 DOI: 10.3390/microorganisms11071752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 06/26/2023] [Accepted: 07/01/2023] [Indexed: 07/30/2023] Open
Abstract
This review aims to provide a comprehensive overview of the significant Clostridioides difficile molecular typing techniques currently employed in research and medical communities. The main objectives of this review are to describe the key molecular typing methods utilized in C. difficile studies and to highlight the epidemiological characteristics of the most prevalent strains on a global scale. Geographically distinct regions exhibit distinct strain types of C. difficile, with notable concordance observed among various typing methodologies. The advantages that next-generation sequencing (NGS) offers has changed epidemiology research, enabling high-resolution genomic analyses of this pathogen. NGS platforms offer an unprecedented opportunity to explore the genetic intricacies and evolutionary trajectories of C. difficile strains. It is relevant to acknowledge that novel routes of transmission are continually being unveiled and warrant further investigation, particularly in the context of zoonotic implications and environmental contamination.
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Affiliation(s)
- Ana Abad-Fau
- Departamento de Patología Animal, Facultad de Veterinaria, Instituto Agroalimentario de Aragon-IA2-(Universidad de Zaragoza-CITA), 50013 Zaragoza, Spain
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes, Facultad de Veterinaria, Universidad de Zaragoza, 50013 Zaragoza, Spain
| | - Eloísa Sevilla
- Departamento de Patología Animal, Facultad de Veterinaria, Instituto Agroalimentario de Aragon-IA2-(Universidad de Zaragoza-CITA), 50013 Zaragoza, Spain
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes, Facultad de Veterinaria, Universidad de Zaragoza, 50013 Zaragoza, Spain
| | - Inmaculada Martín-Burriel
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes, Facultad de Veterinaria, Universidad de Zaragoza, 50013 Zaragoza, Spain
- Laboratorio de Genética Bioquímica, Facultad de Veterinaria, Instituto Agroalimentario de Aragon-IA2-(Universidad de Zaragoza-CITA), 50013 Zaragoza, Spain
| | - Bernardino Moreno
- Departamento de Patología Animal, Facultad de Veterinaria, Instituto Agroalimentario de Aragon-IA2-(Universidad de Zaragoza-CITA), 50013 Zaragoza, Spain
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes, Facultad de Veterinaria, Universidad de Zaragoza, 50013 Zaragoza, Spain
| | - Rosa Bolea
- Departamento de Patología Animal, Facultad de Veterinaria, Instituto Agroalimentario de Aragon-IA2-(Universidad de Zaragoza-CITA), 50013 Zaragoza, Spain
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes, Facultad de Veterinaria, Universidad de Zaragoza, 50013 Zaragoza, Spain
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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. 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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de Carvalho TP, Dos Santos DO, Oliveira AR, Vasconcelos IMA, Tinoco HP, Coelho CM, Carvalho GM, Xavier RGC, Silva ROS, Paixão TA, Santos RDL. Lethal acute diarrhea associated with Clostridioides difficile toxin A and B in a buffy-tufted-ear marmoset (Callithrix aurita). J Med Primatol 2022; 51:400-403. [PMID: 35989431 DOI: 10.1111/jmp.12609] [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: 05/27/2022] [Revised: 07/29/2022] [Accepted: 08/08/2022] [Indexed: 11/28/2022]
Abstract
This is a case of lethal acute diarrhea associated with a mild neutrophilic enteritis in a buffy-tufted-ear marmoset (Callithrix aurita) with detection of A/B toxins and isolation of a toxigenic clade 3 Clostridioides difficile strain (A+ B+ CDT+ , ST5), which should be considered as a potential cause of enteritis in this species.
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Affiliation(s)
- Thaynara Parente de Carvalho
- Departamento de Clínica e Cirurgia Veterinárias, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Daniel Oliveira Dos Santos
- Departamento de Clínica e Cirurgia Veterinárias, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Ayisa Rodrigues Oliveira
- Departamento de Clínica e Cirurgia Veterinárias, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | | | | | | | - Gabriela Muniz Carvalho
- Departamento de Clínica e Cirurgia Veterinárias, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Rafael Gariglio Clark Xavier
- Departamento de Clínica e Cirurgia Veterinárias, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Rodrigo Otávio Silveira Silva
- Departamento de Clínica e Cirurgia Veterinárias, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Tatiane Alves Paixão
- Departamento de Clínica e Cirurgia Veterinárias, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
| | - Renato de Lima Santos
- Departamento de Clínica e Cirurgia Veterinárias, Escola de Veterinária, Universidade Federal de Minas Gerais, Belo Horizonte, Brazil
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Kordus SL, Thomas AK, Lacy DB. Clostridioides difficile toxins: mechanisms of action and antitoxin therapeutics. Nat Rev Microbiol 2022; 20:285-298. [PMID: 34837014 PMCID: PMC9018519 DOI: 10.1038/s41579-021-00660-2] [Citation(s) in RCA: 71] [Impact Index Per Article: 35.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/21/2021] [Indexed: 01/03/2023]
Abstract
Clostridioides difficile is a Gram-positive anaerobe that can cause a spectrum of disorders that range in severity from mild diarrhoea to fulminant colitis and/or death. The bacterium produces up to three toxins, which are considered the major virulence factors in C. difficile infection. These toxins promote inflammation, tissue damage and diarrhoea. In this Review, we highlight recent biochemical and structural advances in our understanding of the mechanisms that govern host-toxin interactions. Understanding how C. difficile toxins affect the host forms a foundation for developing novel strategies for treatment and prevention of C. difficile infection.
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Affiliation(s)
- Shannon L. Kordus
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA,Center for Structural Biology, Vanderbilt University, Nashville, TN, USA,These authors contributed equally: Shannon L. Kordus, Audrey K. Thomas
| | - Audrey K. Thomas
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA,Center for Structural Biology, Vanderbilt University, Nashville, TN, USA,These authors contributed equally: Shannon L. Kordus, Audrey K. Thomas
| | - D. Borden Lacy
- Department of Pathology, Microbiology, and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA,Center for Structural Biology, Vanderbilt University, Nashville, TN, USA,The Veterans Affairs, Tennessee Valley Healthcare, System, Nashville, TN, USA,
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5
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Wu Y, Wang YY, Bai LL, Zhang WZ, Li GW, Lu JX. A narrative review of Clostridioides difficile infection in China. Anaerobe 2022; 74:102540. [DOI: 10.1016/j.anaerobe.2022.102540] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2021] [Revised: 02/07/2022] [Accepted: 02/17/2022] [Indexed: 12/26/2022]
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Ahn SW, Lee SH, Kim UJ, Jang HC, Choi HJ, Choy HE, Kang SJ, Roh SW. Genomic characterization of nine Clostridioides difficile strains isolated from Korean patients with Clostridioides difficile infection. Gut Pathog 2021; 13:55. [PMID: 34530913 PMCID: PMC8447795 DOI: 10.1186/s13099-021-00451-3] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 09/08/2021] [Indexed: 12/14/2022] Open
Abstract
Background Clostridioides difficile infection (CDI) is an infectious nosocomial disease caused by Clostridioides difficile, an opportunistic pathogen that occurs in the intestine after extensive antibiotic regimens. Results Nine C. difficile strains (CBA7201–CBA7209) were isolated from nine patients diagnosed with CDI at the national university hospital in Korea, and the whole genomes of these strains were sequenced to identify their genomic characteristics. Comparative genomic analysis was performed using 51 reference strains and the nine isolated herein. Phylogenetic analysis based on 16S rRNA gene sequences confirmed that all 60 C. difficile strains belong to the genus Clostridioides, while core-genome tree indicated that they were divided into five groups, which was consistent with the results of MLST clade analysis. All strains were confirmed to have a clindamycin antibiotic resistance gene, but the other antibiotic resistance genes differ depending on the MLST clade. Interestingly, the six strains belonging to the sequence type 17 among the nine C. difficile strains isolated here exhibited unique genomic characteristics for PaLoc and CdtLoc, the two toxin gene loci identified in this study, and harbored similar antibiotic resistance genes. Conclusion In this study, we identified the specific genomic characteristics of Korean C. difficile strains, which could serve as basic information for CDI prevention and treatment in Korea. Supplementary Information The online version contains supplementary material available at 10.1186/s13099-021-00451-3.
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Affiliation(s)
- Seung Woo Ahn
- Microbiology and Functionality Research Group, World Institute of Kimchi, 86, Kimchi-ro, Nam-gu, 61755, Gwangju, Republic of Korea
| | - Se Hee Lee
- Microbiology and Functionality Research Group, World Institute of Kimchi, 86, Kimchi-ro, Nam-gu, 61755, Gwangju, Republic of Korea
| | - Uh Jin Kim
- Department of Infectious Diseases, Chonnam National University Hospital, 61469, Gwangju, Republic of Korea
| | - Hee-Chang Jang
- Department of Infectious Diseases, Chonnam National University Hospital, 61469, Gwangju, Republic of Korea
| | - Hak-Jong Choi
- Microbiology and Functionality Research Group, World Institute of Kimchi, 86, Kimchi-ro, Nam-gu, 61755, Gwangju, Republic of Korea
| | - Hyon E Choy
- Department of Microbiology, Chonnam National University Medical School, 61469, Gwangju, Republic of Korea
| | - Seung Ji Kang
- Department of Infectious Diseases, Chonnam National University Hospital, 61469, Gwangju, Republic of Korea.
| | - Seong Woon Roh
- Microbiology and Functionality Research Group, World Institute of Kimchi, 86, Kimchi-ro, Nam-gu, 61755, Gwangju, Republic of Korea.
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Riedel T, Neumann-Schaal M, Wittmann J, Schober I, Hofmann JD, Lu CW, Dannheim A, Zimmermann O, Lochner M, Groß U, Overmann J. Characterization of Clostridioides difficile DSM 101085 with A-B-CDT+ Phenotype from a Late Recurrent Colonization. Genome Biol Evol 2021; 12:566-577. [PMID: 32302381 PMCID: PMC7250501 DOI: 10.1093/gbe/evaa072] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/10/2020] [Indexed: 12/29/2022] Open
Abstract
During the last decades, hypervirulent strains of Clostridioides difficile with frequent disease recurrence and increased mortality appeared. Clostridioides difficile DSM 101085 was isolated from a patient who suffered from several recurrent infections and colonizations, likely contributing to a fatal outcome. Analysis of the toxin repertoire revealed the presence of a complete binary toxin locus and an atypical pathogenicity locus consisting of only a tcdA pseudogene and a disrupted tcdC gene sequence. The pathogenicity locus shows upstream a transposon and has been subject to homologous recombination or lateral gene transfer events. Matching the results of the genome analysis, neither TcdA nor TcdB production but the expression of cdtA and cdtB was detected. This highlights a potential role of the binary toxin C. difficile toxin in this recurrent colonization and possibly further in a host-dependent virulence. Compared with the C. difficile metabolic model strains DSM 28645 (630Δerm) and DSM 27147 (R20291), strain DSM 101085 showed a specific metabolic profile, featuring changes in the threonine degradation pathways and alterations in the central carbon metabolism. Moreover, products originating from Stickland pathways processing leucine, aromatic amino acids, and methionine were more abundant in strain DSM 101085, indicating a more efficient use of these substrates. The particular characteristics of strain C. difficile DSM 101085 may represent an adaptation to a low-protein diet in a patient with recurrent infections.
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Affiliation(s)
- Thomas Riedel
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.,German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, Germany
| | - Meina Neumann-Schaal
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.,Department of Bioinformatics and Biochemistry and Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Germany
| | - Johannes Wittmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Isabel Schober
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Julia Danielle Hofmann
- Department of Bioinformatics and Biochemistry and Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Germany
| | - Chia-Wen Lu
- Institute of Infection Immunology, TWINCORE, Centre for Experimental and Clinical Infection Research, a Joint Venture between the Medical School Hannover (MHH) and the Helmholtz Centre for Infection Research (HZI), Hannover, Germany
| | - Antonia Dannheim
- Department of Bioinformatics and Biochemistry and Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Germany
| | - Ortrud Zimmermann
- Institute of Medical Microbiology, University Medical Center Göttingen, Germany
| | - Matthias Lochner
- Institute of Infection Immunology, TWINCORE, Centre for Experimental and Clinical Infection Research, a Joint Venture between the Medical School Hannover (MHH) and the Helmholtz Centre for Infection Research (HZI), Hannover, Germany
| | - Uwe Groß
- Institute of Medical Microbiology, University Medical Center Göttingen, Germany.,Göttingen International Health Network, Göttingen, Germany
| | - Jörg Overmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.,German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, Germany.,Institute of Microbiology, Technical University of Braunschweig, Germany
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Okada Y, Okugawa S, Ikeda M, Kobayashi T, Saito R, Higurashi Y, Moriya K. Genetic diversity and epidemiology of accessory gene regulator loci in Clostridioides difficile. Access Microbiol 2020; 2:acmi000134. [PMID: 32974597 PMCID: PMC7497831 DOI: 10.1099/acmi.0.000134] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Accepted: 04/25/2020] [Indexed: 02/04/2023] Open
Abstract
Quorum sensing is known to regulate bacterial virulence, and the accessory gene regulator (agr) loci is one of the genetic loci responsible for its regulation. Recent reports examining Clostridioides difficile show that two agr loci, agr1 and agr2, regulate toxin production, but the diversity of agr loci and their epidemiology is unknown. In our study, in silico analysis was performed to research genetic diversity of agr, and C. difficile isolates from clinical samples underwent multilocus sequence typing (MLST) and PCR analysis of agr loci. To reveal the distribution of agr among different strains, phylogenetic analysis was also performed. In our in silico analysis, two different subtypes, named agr2R and agr2M, were found in agr2, which were previously reported. PCR analysis of 133 C . difficile isolates showed that 131 strains had agr1, 61 strains had agr2R, and 26 strains had agr2M; agr2R was mainly found in clade 1 or clade 2 organisms, whereas agr2M was only found in clade 4. With rare exception, agr1-negative sequence types (STs) belonged to clade C-Ⅰ and C-Ⅲ, and one clade 4 strain had agr2R. Our study revealed subtypes of agr2 not previously recognized, and the distribution of several agr loci in C. difficile . These findings provide a foundation for further functional and clinical research of the agr loci.
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Affiliation(s)
- Yuta Okada
- Department of Infectious Diseases, The University of Tokyo Hospital, Bunkyo-ku, Tokyo, Japan
| | - Shu Okugawa
- Department of Infectious Diseases, The University of Tokyo Hospital, Bunkyo-ku, Tokyo, Japan
| | - Mahoko Ikeda
- Department of Infectious Diseases, The University of Tokyo Hospital, Bunkyo-ku, Tokyo, Japan
- Department of Infection Control and Prevention, The University of Tokyo Hospital, Bunkyo-ku, Tokyo, Japan
| | - Tatsuya Kobayashi
- Department of Infectious Diseases, The University of Tokyo Hospital, Bunkyo-ku, Tokyo, Japan
| | - Ryoichi Saito
- Department of Molecular Microbiology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Bunkyo-ku, Tokyo, Japan
| | - Yoshimi Higurashi
- Department of Infection Control and Prevention, The University of Tokyo Hospital, Bunkyo-ku, Tokyo, Japan
| | - Kyoji Moriya
- Department of Infectious Diseases, The University of Tokyo Hospital, Bunkyo-ku, Tokyo, Japan
- Department of Infection Control and Prevention, The University of Tokyo Hospital, Bunkyo-ku, Tokyo, Japan
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Dai W, Yang T, Yan L, Niu S, Zhang C, Sun J, Wang Z, Xia Y. Characteristics of Clostridium difficile isolates and the burden of hospital-acquired Clostridium difficile infection in a tertiary teaching hospital in Chongqing, Southwest China. BMC Infect Dis 2020; 20:277. [PMID: 32293302 PMCID: PMC7157987 DOI: 10.1186/s12879-020-05014-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2019] [Accepted: 04/06/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Clostridium difficile infection (CDI), especially hospital-acquired Clostridium difficile infection (HA-CDI), continues to be a public health problem and has aroused great concern worldwide for years. This study aimed to elucidate the clinical and epidemiological features of HA-CDI and the characteristics of C.difficile isolates in Chongqing, Southwest China. METHODS A case-control study was performed to identify the clinical incidence and risk factors of HA-CDI. C. difficile isolates were characterised by polymerase chain reaction (PCR) ribotyping, multilocus sequence typing (MLST), toxin gene detection and antimicrobial susceptibility testing. RESULTS Of the 175 suspicious patients, a total of 122 patients with antibiotic-associated diarrhea (AAD) were included in the study; among them, 38 had HA-CDI. The incidence of AAD and HA-CDI was 0.58 and 0.18 per 1000 patient admissions, respectively. Chronic renal disease and cephalosporin use were independent risk factors for HA-CDI. Fifty-five strains were assigned into 16 sequence types (STs) and 15 ribotypes (RTs). ST2/RT449 (8, 14.5%) was the predominant genotype. Of the 38 toxigenic isolates, A + B + CDT- isolates accounted for most (34, 89.5%) and 1 A + B + CDT+ isolate emerged. No isolate was resistant to vancomycin, metronidazole or tigecycline, with A-B-CDT- being more resistant than A + B + CDT-. CONCLUSIONS Different genotypes of C. difficile strains were witnessed in Chongqing, which hinted at the necessary surveillance of HA-CDI. Adequate awareness of patients at high risk of HA-CDI acquisition is advocated and cautious adoption of cephalosporins should be highlighted.
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Affiliation(s)
- Wei Dai
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, No.1 Youyi Road, Yuzhong District, Chongqing, 400016, People's Republic of China
| | - Tianxiang Yang
- Department of Laboratory Medicine, Dianjiang People's Hospital of Chongqing, No.116 North Street, Guixi Street, Dianjiang County, Chongqing, 408300, People's Republic of China
| | - Li Yan
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, No.1 Youyi Road, Yuzhong District, Chongqing, 400016, People's Republic of China
| | - Siqiang Niu
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, No.1 Youyi Road, Yuzhong District, Chongqing, 400016, People's Republic of China
| | - Chuanming Zhang
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, No.1 Youyi Road, Yuzhong District, Chongqing, 400016, People's Republic of China
| | - Jide Sun
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, No.1 Youyi Road, Yuzhong District, Chongqing, 400016, People's Republic of China
| | - Zhu Wang
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, No.1 Youyi Road, Yuzhong District, Chongqing, 400016, People's Republic of China
| | - Yun Xia
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, No.1 Youyi Road, Yuzhong District, Chongqing, 400016, People's Republic of China.
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10
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Shaw HA, Preston MD, Vendrik KEW, Cairns MD, Browne HP, Stabler RA, Crobach MJT, Corver J, Pituch H, Ingebretsen A, Pirmohamed M, Faulds-Pain A, Valiente E, Lawley TD, Fairweather NF, Kuijper EJ, Wren BW. The recent emergence of a highly related virulent Clostridium difficile clade with unique characteristics. Clin Microbiol Infect 2020; 26:492-498. [PMID: 31525517 PMCID: PMC7167513 DOI: 10.1016/j.cmi.2019.09.004] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2019] [Revised: 09/06/2019] [Accepted: 09/07/2019] [Indexed: 01/06/2023]
Abstract
OBJECTIVES Clostridium difficile is a major global human pathogen divided into five clades, of which clade 3 is the least characterized and consists predominantly of PCR ribotype (RT) 023 strains. Our aim was to analyse and characterize this clade. METHODS In this cohort study the clinical presentation of C. difficile RT023 infections was analysed in comparison with known 'hypervirulent' and non-hypervirulent strains, using data from the Netherlands national C. difficile surveillance programme. European RT023 strains of diverse origin were collected and whole-genome sequenced to determine the genetic similarity between isolates. Distinctive features were investigated and characterized. RESULTS Clinical presentation of C. difficile RT023 infections show severe infections akin to those seen with 'hypervirulent' strains from clades 2 (RT027) and 5 (RT078) (35%, 29% and 27% severe CDI, respectively), particularly with significantly more bloody diarrhoea than RT078 and non-hypervirulent strains (RT023 8%, other RTs 4%, p 0.036). The full genome sequence of strain CD305 is presented as a robust reference. Phylogenetic comparison of CD305 and a further 79 previously uncharacterized European RT023 strains of diverse origin revealed minor genetic divergence with >99.8% pairwise identity between strains. Analyses revealed distinctive features among clade 3 strains, including conserved pathogenicity locus, binary toxin and phage insertion toxin genotypes, glycosylation of S-layer proteins, presence of the RT078 four-gene trehalose cluster and an esculinase-negative genotype. CONCLUSIONS Given their recent emergence, virulence and genomic characteristics, the surveillance of clade 3 strains should be more highly prioritized.
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Affiliation(s)
- H A Shaw
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London, UK; Division of Bacteriology, National Institute for Biological Standards and Controls, South Mimms, Potters Bar, UK
| | - M D Preston
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London, UK; Analytical Biological Service Division, National Institute for Biological Standards and Controls, Potters Bar, UK
| | - K E W Vendrik
- National Reference Laboratory for CDI Surveillance, Department of Medical Microbiology and RIVM, Leiden University Medical Centre, Leiden, the Netherlands
| | - M D Cairns
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London, UK; Public Health Laboratory London, Division of Infection, The Royal London Hospital, London, UK
| | - H P Browne
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | - R A Stabler
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London, UK
| | - M J T Crobach
- National Reference Laboratory for CDI Surveillance, Department of Medical Microbiology and RIVM, Leiden University Medical Centre, Leiden, the Netherlands
| | - J Corver
- National Reference Laboratory for CDI Surveillance, Department of Medical Microbiology and RIVM, Leiden University Medical Centre, Leiden, the Netherlands
| | - H Pituch
- Department of Medical Microbiology, Medical University of Warsaw, Warsaw, Poland
| | - A Ingebretsen
- Department of Microbiology, Oslo University Hospital, Oslo, Norway; Department of Infection Prevention, Oslo University Hospital, Oslo, Norway
| | - M Pirmohamed
- Department of Molecular and Clinical Pharmacology, The University of Liverpool, Liverpool, UK
| | - A Faulds-Pain
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London, UK
| | - E Valiente
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London, UK
| | - T D Lawley
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK
| | | | - E J Kuijper
- National Reference Laboratory for CDI Surveillance, Department of Medical Microbiology and RIVM, Leiden University Medical Centre, Leiden, the Netherlands
| | - B W Wren
- Department of Pathogen Molecular Biology, London School of Hygiene and Tropical Medicine, London, UK.
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Clostridium difficile clade 3 (RT023) have a modified cell surface and contain a large transposable island with novel cargo. Sci Rep 2019; 9:15330. [PMID: 31653906 PMCID: PMC6814731 DOI: 10.1038/s41598-019-51628-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 10/02/2019] [Indexed: 12/16/2022] Open
Abstract
The major global pathogen Clostridium difficile (recently renamed Clostridioides difficile) has large genetic diversity including multiple mobile genetic elements. In this study, whole genome sequencing of 86 strains from the poorly characterised clade 3, predominantly PCR ribotype (RT)023, of C. difficile revealed distinctive surface architecture characteristics and a large mobile genetic island. These strains have a unique sortase substrate phenotype compared with well-characterised strains of C. difficile, and loss of the phage protection protein CwpV. A large genetic insertion (023_CTnT) comprised of three smaller elements (023_CTn1-3) is present in 80/86 strains analysed in this study, with genes common among other bacterial strains in the gut microbiome. Novel cargo regions of 023_CTnT include genes encoding a sortase, putative sortase substrates, lantibiotic ABC transporters and a putative siderophore biosynthetic cluster. We demonstrate the excision of 023_CTnT and sub-elements 023_CTn2 and 023_CTn3 from the genome of RT023 reference strain CD305 and the transfer of 023_CTn3 to a non-toxigenic C. difficile strain, which may have implications for the use of non-toxigenic C. difficile strains as live attenuated vaccines. Finally, we show that the genes within the island are expressed in a regulated manner in C. difficile RT023 strains conferring a distinct "niche adaptation".
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Mileto S, Das A, Lyras D. Enterotoxic Clostridia: Clostridioides difficile Infections. Microbiol Spectr 2019; 7:10.1128/microbiolspec.gpp3-0015-2018. [PMID: 31124432 PMCID: PMC11026080 DOI: 10.1128/microbiolspec.gpp3-0015-2018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2018] [Indexed: 12/17/2022] Open
Abstract
Clostridioides difficile is a Gram-positive, anaerobic, spore forming pathogen of both humans and animals and is the most common identifiable infectious agent of nosocomial antibiotic-associated diarrhea. Infection can occur following the ingestion and germination of spores, often concurrently with a disruption to the gastrointestinal microbiota, with the resulting disease presenting as a spectrum, ranging from mild and self-limiting diarrhea to severe diarrhea that may progress to life-threating syndromes that include toxic megacolon and pseudomembranous colitis. Disease is induced through the activity of the C. difficile toxins TcdA and TcdB, both of which disrupt the Rho family of GTPases in host cells, causing cell rounding and death and leading to fluid loss and diarrhea. These toxins, despite their functional and structural similarity, do not contribute to disease equally. C. difficile infection (CDI) is made more complex by a high level of strain diversity and the emergence of epidemic strains, including ribotype 027-strains which induce more severe disease in patients. With the changing epidemiology of CDI, our understanding of C. difficile disease, diagnosis, and pathogenesis continues to evolve. This article provides an overview of the current diagnostic tests available for CDI, strain typing, the major toxins C. difficile produces and their mode of action, the host immune response to each toxin and during infection, animal models of disease, and the current treatment and prevention strategies for CDI.
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Affiliation(s)
- S Mileto
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia, 3800
| | - A Das
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia, 3800
| | - D Lyras
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia, 3800
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Independent Microevolution Mediated by Mobile Genetic Elements of Individual Clostridium difficile Isolates from Clade 4 Revealed by Whole-Genome Sequencing. mSystems 2019; 4:mSystems00252-18. [PMID: 30944881 PMCID: PMC6435816 DOI: 10.1128/msystems.00252-18] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 01/18/2019] [Indexed: 12/15/2022] Open
Abstract
Mobile genetic elements play a key role in the continuing evolution of Clostridium difficile, resulting in the emergence of new phenotypes for individual isolates. On the basis of whole-genome sequencing analysis, we comprehensively explored transposons, CRISPR, prophage, and genetic sites for drug resistance within clade 4 C. difficile isolates with different sequence types. Great diversity in MGEs and a high rate of multidrug resistance were found within this clade, including new transposons, Tn4453a/b with aac(6′) aph(2′′) instead of catD, and a relatively high rate of prophage-carried CRISPR arrays. These findings provide important new insights into the mechanism of genome remodeling within clade 4 and offer a new method for typing and tracing the origins of closely related isolates. Horizontal gene transfer of mobile genetic elements (MGEs) accounts for the mosaic genome of Clostridium difficile, leading to acquisition of new phenotypes, including drug resistance and reconstruction of the genomes. MGEs were analyzed according to the whole-genome sequences of 37 C. difficile isolates with a variety of sequence types (STs) within clade 4 from China. Great diversity was found in each transposon even within isolates with the same ST. Two novel transposons were identified in isolates ZR9 and ZR18, of which approximately one third to half of the genes showed heterogenous origins compared with the usual intestinal bacterial genes. Most importantly, catD, known to be harbored by Tn4453a/b, was replaced by aac(6′) aph(2′′) in isolates 2, 7, and 28. This phenomenon illustrated the frequent occurrence of gene exchanges between C. difficile and other enterobacteria with individual heterogeneity. Numerous prophages and CRISPR arrays were identified in C. difficile isolates of clade 4. Approximately 20% of spacers were located in prophage-carried CRISPR arrays, providing a new method for typing and tracing the origins of closely related isolates, as well as in-depth studies of the mechanism underlying genome remodeling. The rates of drug resistance were obviously higher than those reported previously around the world, although all isolates retained high sensitivity to vancomycin and metronidazole. The increasing number of C. difficile isolates resistant to all antibiotics tested here suggests the ease with which resistance is acquired in vivo. This study gives insights into the genetic mechanism of microevolution within clade 4. IMPORTANCE Mobile genetic elements play a key role in the continuing evolution of Clostridium difficile, resulting in the emergence of new phenotypes for individual isolates. On the basis of whole-genome sequencing analysis, we comprehensively explored transposons, CRISPR, prophage, and genetic sites for drug resistance within clade 4 C. difficile isolates with different sequence types. Great diversity in MGEs and a high rate of multidrug resistance were found within this clade, including new transposons, Tn4453a/b with aac(6′) aph(2′′) instead of catD, and a relatively high rate of prophage-carried CRISPR arrays. These findings provide important new insights into the mechanism of genome remodeling within clade 4 and offer a new method for typing and tracing the origins of closely related isolates.
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14
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Zhou Y, Mao L, Yu J, Lin Q, Luo Y, Zhu X, Sun Z. Epidemiology of Clostridium difficile infection in hospitalized adults and the first isolation of C. difficile PCR ribotype 027 in central China. BMC Infect Dis 2019; 19:232. [PMID: 30845918 PMCID: PMC6407249 DOI: 10.1186/s12879-019-3841-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2018] [Accepted: 02/21/2019] [Indexed: 02/08/2023] Open
Abstract
Background Clostridium difficile infection (CDI) is an emerging healthcare problem in the world. The purpose of this study was to perform a systematic epidemiological research of CDI in Tongji hospital, the central of China. Methods Stool samples from hospitalized adults suspected of CDI were enrolled. The diagnosis of CDI were based on the combination of clinical symptoms and laboratory results. Clinical features of CDI and non-CDI patients were compared by appropriate statistical tests to determine the risk factors of CDI. Multilocus sequence typing (MLST) was employed for molecular epidemiological analysis. Susceptibility testing and relevant antimicrobial agent resistance genes were performed as well. Results From June 2016 to September 2017, 839 hospitalized adults were enrolled. Among them, 107 (12.8%, 107/839) patients were C. difficile culture positive, and 73 (8.7%, 73/839) were infected with toxigenic C. difficile (TCD), with tcdA + tcdB+ strains accounting for 90.4% (66/73) and tcdA-tcdB+ for 9.6% (7/73). Meanwhile, two TCD strains were binary toxin positive and one of them was finally identified as CD027. Severe symptoms were observed in these two cases. Multivariate analysis indicated antibiotic exposure (p = 0.001, OR = 5.035) and kidney disease (p = 0.015, OR = 8.329) significantly increased the risk of CDI. Phylogenetic tree analysis demonstrated 21 different STs, including one new ST (ST467); and the most dominant type was ST54 (35.6%, 26/73). Multidrug-resistant (MDR) TCD were 53.4% (39/73); resistance to ciprofloxacin, erythromycin, and clindamycin were > 50%. Other antibiotics showed relative efficiency and all strains were susceptible to metronidazole and vancomycin. All moxifloxacin-resistant isolates carried a mutation in GyrA (Thr82 → Ile), with one both having mutation in GyrB (Ser366 → Ala). Conclusions Knowledge of epidemiological information for CDI is limited in China. Our finding indicated tcdA + tcdB+ C. difficile strains were the dominant for CDI in our hospital. Significant risk factors for CDI in our setting appeared to be antibiotic exposure and kidney disease. Metronidazole and vancomycin were still effective for CDI. Although no outbreak was observed, the first isolation of CD027 in center China implied the potential spread of this hypervirulent clone. Further studies are needed to enhance our understanding of the epidemiology of CDI in China. Electronic supplementary material The online version of this article (10.1186/s12879-019-3841-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yu Zhou
- Department of Laboratory Medicine, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Zhejiang, 310014, Hangzhou, China
| | - Liyan Mao
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1095 Jiefang Road, Wuhan, 430030, China
| | - Jing Yu
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1095 Jiefang Road, Wuhan, 430030, China
| | - Qun Lin
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1095 Jiefang Road, Wuhan, 430030, China
| | - Ying Luo
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1095 Jiefang Road, Wuhan, 430030, China
| | - Xuhui Zhu
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1095 Jiefang Road, Wuhan, 430030, China.
| | - Ziyong Sun
- Department of Laboratory Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1095 Jiefang Road, Wuhan, 430030, China.
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15
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Antimicrobial susceptibility and mechanisms of resistance of Greek Clostridium difficile clinical isolates. J Glob Antimicrob Resist 2019; 16:53-58. [DOI: 10.1016/j.jgar.2018.09.009] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Revised: 09/07/2018] [Accepted: 09/17/2018] [Indexed: 12/17/2022] Open
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16
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Characterization of the virulence of a non-RT027, non-RT078 and binary toxin-positive Clostridium difficile strain associated with severe diarrhea. Emerg Microbes Infect 2018; 7:211. [PMID: 30542069 PMCID: PMC6291415 DOI: 10.1038/s41426-018-0211-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 11/01/2018] [Accepted: 11/11/2018] [Indexed: 02/06/2023]
Abstract
The expression of the Clostridium difficile binary toxin CDT is generally observed in the RT027 (ST1) and RT078 (ST11) C. difficile isolates, which are associated with severe C. difficile infection (CDI). However, we recently reported that the non-RT027 and non-RT078 C. difficile strain LC693 (TcdA+TcdB+ CDT+, ST201) caused severe diarrhea in a patient in Xiangya Hospital in China. C.difficile LC693 is a member of Clade 3, and in this study, we identified LC693 as RT871 and compared its virulence and pathogenicity to those of C.difficile R20291 (TcdA+TcdB+CDT+, ST1/RT027), UK6 (TcdA+TcdB+CDT+, ST35/RT027), CD630 (TcdA+TcdB+CDT−, ST54, RT012), and 1379 (TcdA+TcdB+CDT−, ST54/RT012), with strain 1379 being an epidemic C.difficile isolate from the same hospital. LC693 displayed a higher sporulation rate than R20291, CD630 or strain 1379. LC693 was comparable to R20291 with respect to spore germination, motility, and biofilm formation, but showed a faster germination rate, higher motility and a higher biofilm formation capability compared to CD630 and strain 1379. The adherence of spores to human gut epithelial cells was similar for all strains.The total toxin release of LC693 was lower than that of R20291, but higher than that of CD630 and strain 1379. Finally, in a mouse model of CDI, LC693 was capable of causing moderate to severe disease. Our findings demonstrate the pathogenicity of non-RT027 and non-RT078 binary toxin-positive C. difficile strains. Furthermore, our data indicate that LC693 may be more virulent than strain 1379, an epidemic strain from the same hospital, and provide the first phenotypic characterization of a non-RT027 and non-RT078 binary toxin-positive ST201 isolate.
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Hong W, Cheng Y, Rao F, Yang J, Cui G, Chen Z, Liao J, Huang X, Zhang J, Wang P, Wang S, Wang Y, Guan Z, Qi X. Co-infection of Clostridioides (Clostridium) difficile GMU1 and Bacillus cereus GMU2 in one patient in Guizhou, China. Anaerobe 2018; 54:159-163. [PMID: 30273671 DOI: 10.1016/j.anaerobe.2018.08.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2018] [Revised: 08/02/2018] [Accepted: 08/12/2018] [Indexed: 01/05/2023]
Abstract
Clostridioides (Clostridium) difficile and Bacillus cereus infections are frequently reported in human individually. However, co-infection of both pathogens in human is extremely rare. In the present study, we reported a case of human enteric disease caused by co-infection of C. difficile and B. cereus in Guizhou, China. The 16S rDNA sequencing result showed that C. difficile GMU1 and B. cereus GMU2 were most related to C. difficile ATCC 9689 and B. cereus ATCC 14579. The toxin genotype of C. difficile GMU1 and B. cereus GMU2 were tcdA+tcdB+tcdC+ and bceT+nheA+nheB+nheC+, respectively. Cytotoxicity assay demonstrated that C. difficile GMU1 produced significantly higher toxin B compare to C. difficile 630 stain. In contrast, B. cereus GMU2 has comparable NheA toxin productivity compare to previous report. The antimicrobial susceptibility test showed that the combination of ampicillin and vancomycin was most efficient to inhibit both C. difficile GMU1 and B. cereus GMU2.
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Affiliation(s)
- Wei Hong
- Key Laboratory of Endemic and Ethnic Diseases, Guizhou Medical University, Ministry of Education, Guiyang, 550004, China; Key Laboratory of Medical Molecular Biology, Guizhou Medical University, Guiyang, 550004, China.
| | - Yumei Cheng
- Department of Critical Care Medicine, The Affiliate Hospital of Guizhou Medical University, Guiyang, 550004, China
| | - Fengqin Rao
- Key Laboratory of Endemic and Ethnic Diseases, Guizhou Medical University, Ministry of Education, Guiyang, 550004, China; Key Laboratory of Medical Molecular Biology, Guizhou Medical University, Guiyang, 550004, China
| | - Jing Yang
- Guiyang Maternal and Child Health Hospital, Guiyang, 550004, China
| | - Guzhen Cui
- School of Basic Medical Science, Guizhou Medical University, Guiyang, 550025, China
| | - Zhenghong Chen
- School of Basic Medical Science, Guizhou Medical University, Guiyang, 550025, China
| | - Jian Liao
- Key Laboratory of Endemic and Ethnic Diseases, Guizhou Medical University, Ministry of Education, Guiyang, 550004, China; Key Laboratory of Medical Molecular Biology, Guizhou Medical University, Guiyang, 550004, China
| | - Xiaolin Huang
- Key Laboratory of Endemic and Ethnic Diseases, Guizhou Medical University, Ministry of Education, Guiyang, 550004, China; Key Laboratory of Medical Molecular Biology, Guizhou Medical University, Guiyang, 550004, China
| | - Jie Zhang
- Department of Biosystems Engineering, Auburn University, Auburn, AL, 36849, USA
| | - Pixiang Wang
- Department of Biosystems Engineering, Auburn University, Auburn, AL, 36849, USA
| | - Shaohua Wang
- Department of Biosystems Engineering, Auburn University, Auburn, AL, 36849, USA
| | - Yi Wang
- Department of Biosystems Engineering, Auburn University, Auburn, AL, 36849, USA
| | - Zhizhong Guan
- Key Laboratory of Endemic and Ethnic Diseases, Guizhou Medical University, Ministry of Education, Guiyang, 550004, China; Key Laboratory of Medical Molecular Biology, Guizhou Medical University, Guiyang, 550004, China
| | - Xiaolan Qi
- Key Laboratory of Endemic and Ethnic Diseases, Guizhou Medical University, Ministry of Education, Guiyang, 550004, China; Key Laboratory of Medical Molecular Biology, Guizhou Medical University, Guiyang, 550004, China.
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Complete Genome Sequences of Four Toxigenic Clostridium difficile Clinical Isolates from Patients of the Lower Hudson Valley, New York, USA. GENOME ANNOUNCEMENTS 2018; 6:6/4/e01537-17. [PMID: 29371361 PMCID: PMC5786687 DOI: 10.1128/genomea.01537-17] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Complete genome sequences of four toxigenic Clostridium difficile isolates from patients in the lower Hudson Valley, New York, USA, were achieved. These isolates represent four common sequence types (ST1, ST2, ST8, and ST42) belonging to two distinct phylogenetic clades. All isolates have a 4.0- to 4.2-Mb circular chromosome, and one carries a phage.
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Yan D, Chen Y, Lv T, Huang Y, Yang J, Li Y, Huang J, Li L. Clostridium difficile colonization and infection in patients with hepatic cirrhosis. J Med Microbiol 2017; 66:1483-1488. [PMID: 28945189 DOI: 10.1099/jmm.0.000596] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Affiliation(s)
- Dong Yan
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, PR China
| | - Yunbo Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, PR China
| | - Tao Lv
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, PR China
| | - Yandi Huang
- Department of Laboratory Medicine, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, PR China
| | - Jiezuan Yang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, PR China
| | - Yongtao Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, PR China
| | - Jianrong Huang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, PR China
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, PR China
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Peng Z, Liu S, Meng X, Liang W, Xu Z, Tang B, Wang Y, Duan J, Fu C, Wu B, Wu A, Li C. Genome characterization of a novel binary toxin-positive strain of Clostridium difficile and comparison with the epidemic 027 and 078 strains. Gut Pathog 2017; 9:42. [PMID: 28794800 PMCID: PMC5547579 DOI: 10.1186/s13099-017-0191-z] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 07/25/2017] [Indexed: 12/13/2022] Open
Abstract
Background Clostridium difficile is an anaerobic Gram-positive spore-forming gut pathogen that causes antibiotic-associated diarrhea worldwide. A small number of C. difficile strains express the binary toxin (CDT), which is generally found in C. difficile 027 (ST1) and/or 078 (ST11) in clinic. However, we isolated a binary toxin-positive non-027, non-078 C. difficile LC693 that is associated with severe diarrhea in China. The genotype of this strain was determined as ST201. To understand the pathogenesis-basis of C. difficile ST201, the strain LC693 was chosen for whole genome sequencing, and its genome sequence was analyzed together with the other two ST201 strains VL-0104 and VL-0391 and compared to the epidemic 027/ST1 and 078/ST11 strains. Results The project finally generated an estimated genome size of approximately 4.07 Mbp for strain LC693. Genome size of the three ST201 strains ranged from 4.07 to 4.16 Mb, with an average GC content between 28.5 and 28.9%. Phylogenetic analysis demonstrated that the ST201 strains belonged to clade 3. The ST201 genomes contained more than 40 antibiotic resistance genes and 15 of them were predicted to be associated with vancomycin-resistance. The ST201 strains contained a larger PaLoc with a Tn6218 element inserted than the 027/ST1 and 078/ST11 strains, and encoded a truncated TcdC. In addition, the ST201 strains contained intact binary toxin coding and regulation genes which are highly homologous to the 027/ST1 strain. Genome comparison of the ST201 strains with the epidemic 027 and 078 strain identified 641 genes specific for C. difficile ST201, and a number of them were predicted as fitness and virulence associated genes. The presence of those genes also contributes to the pathogenesis of the ST201 strains. Conclusions In this study, the genomic characterization of three binary toxin-positive C. difficile ST201 strains in clade 3 was discussed and compared to the genomes of the epidemic 027 and the 078 strains. Our analysis identified a number fitness and virulence associated genes/loci in the ST201 genomes that contribute to the pathogenesis of C. difficile ST201. Electronic supplementary material The online version of this article (doi:10.1186/s13099-017-0191-z) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Zhong Peng
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Sidi Liu
- Infection Control Center, Xiangya Hospital of Central South University, Changsha, 410008 Hunan China
| | - Xiujuan Meng
- Infection Control Center, Xiangya Hospital of Central South University, Changsha, 410008 Hunan China
| | - Wan Liang
- MOE Key Laboratory of Animal Genetics, Breeding, and Reproduction, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Zhuofei Xu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Biao Tang
- Institute of Quality and Standard for Agro-products, Zhejiang Academy of Agricultural Sciences, Hangzhou, Zhejiang China
| | - Yuanguo Wang
- The Hormel Institute, University of Minnesota, Austin, MN 55912 USA
| | - Juping Duan
- Infection Control Center, Xiangya Hospital of Central South University, Changsha, 410008 Hunan China.,Department of Pharmacy, Changsha Hospital of Traditional Chinese Medicine, Changsha, 410000 Hunan China
| | - Chenchao Fu
- Infection Control Center, Xiangya Hospital of Central South University, Changsha, 410008 Hunan China
| | - Bin Wu
- State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, 430070 Hubei China
| | - Anhua Wu
- Infection Control Center, Xiangya Hospital of Central South University, Changsha, 410008 Hunan China
| | - Chunhui Li
- Infection Control Center, Xiangya Hospital of Central South University, Changsha, 410008 Hunan China
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