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Martínez-Meléndez A, Morfin-Otero R, Villarreal-Treviño L, Baines SD, Camacho-Ortíz A, Garza-González E. Molecular epidemiology of predominant and emerging Clostridioides difficile ribotypes. J Microbiol Methods 2020; 175:105974. [PMID: 32531232 DOI: 10.1016/j.mimet.2020.105974] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 06/05/2020] [Accepted: 06/05/2020] [Indexed: 12/18/2022]
Abstract
There has been an increase in the incidence and severity of Clostridioides difficile infection (CDI) worldwide, and strategies to control, monitor, and diminish the associated morbidity and mortality have been developed. Several typing methods have been used for typing of isolates and studying the epidemiology of CDI; serotyping was the first typing method, but then was replaced by pulsed-field gel electrophoresis (PFGE). PCR ribotyping is now the gold standard method; however, multi locus sequence typing (MLST) schemes have been developed. New sequencing technologies have allowed comparing whole bacterial genomes to address genetic relatedness with a high level of resolution and discriminatory power to distinguish between closely related strains. Here, we review the most frequent C. difficile ribotypes reported worldwide, with a focus on their epidemiology and genetic characteristics.
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Affiliation(s)
- Adrián Martínez-Meléndez
- Universidad Autónoma de Nuevo León, Facultad de Ciencias Químicas, Pedro de Alba S/N, Ciudad Universitaria, CP 66450 San Nicolás de los Garza, Nuevo Leon, Mexico
| | - Rayo Morfin-Otero
- Hospital Civil de Guadalajara "Fray Antonio Alcalde" e Instituto de Patología Infecciosa y Experimental, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara. Sierra Mojada 950, Col. Independencia, CP 44350 Guadalajara, Jalisco, Mexico
| | - Licet Villarreal-Treviño
- Universidad Autónoma de Nuevo León, Facultad de Ciencias Biológicas, Departamento de Microbiología e Inmunología, Pedro de Alba S/N, Ciudad Universitaria, CP 66450 San Nicolás de los Garza, Nuevo Leon, Mexico
| | - Simon D Baines
- University of Hertfordshire, School of Life and Medical Sciences, Department of Biological and Environmental Sciences, Hatfield AL10 9AB, UK
| | - Adrián Camacho-Ortíz
- Universidad Autónoma de Nuevo León, Hospital Universitario "Dr. José Eleuterio González", Servicio de Infectología. Av. Francisco I. Madero Pte. S/N y Av. José E. González. Col. Mitras Centro, CP 64460 Monterrey, Nuevo Leon, Mexico
| | - Elvira Garza-González
- Universidad Autónoma de Nuevo León, Hospital Universitario "Dr. José Eleuterio González", Servicio de Infectología. Av. Francisco I. Madero Pte. S/N y Av. José E. González. Col. Mitras Centro, CP 64460 Monterrey, Nuevo Leon, Mexico.
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52
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Hornung BVH, Kuijper EJ, Smits WK. An in silico survey of Clostridioides difficile extrachromosomal elements . Microb Genom 2020; 5. [PMID: 31526450 PMCID: PMC6807378 DOI: 10.1099/mgen.0.000296] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The Gram-positive enteropathogen Clostridioides difficile (Clostridium difficile) is the major cause of healthcare-associated diarrhoea and is also an important cause of community-acquired infectious diarrhoea. Considering the burden of the disease, many studies have employed whole-genome sequencing of bacterial isolates to identify factors that contribute to virulence and pathogenesis. Though extrachromosomal elements (ECEs) such as plasmids are important for these processes in other bacteria, the few characterized plasmids of C. difficile have no relevant functions assigned and no systematic identification of plasmids has been carried out to date. Here, we perform an in silico analysis of publicly available sequence data to show that ~13 % of all C. difficile strains contain ECEs, with 1–6 elements per strain. Our approach identifies known plasmids (e.g. pCD6, pCD630 and cloning plasmids) and six novel putative plasmid families. Our study shows that plasmids are abundant and may encode functions that are relevant for C. difficile physiology. The newly identified plasmids may also form the basis for the construction of novel cloning plasmids for C. difficile that are compatible with existing tools.
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Affiliation(s)
- Bastian V H Hornung
- Department of Medical Microbiology, Leiden University Medical Center, PO Box 9600, 2300RC, Leiden, The Netherlands
| | - Ed J Kuijper
- Netherlands Centre for One Health, The Netherlands.,Department of Medical Microbiology, Leiden University Medical Center, PO Box 9600, 2300RC, Leiden, The Netherlands
| | - Wiep Klaas Smits
- Netherlands Centre for One Health, The Netherlands.,Department of Medical Microbiology, Leiden University Medical Center, PO Box 9600, 2300RC, Leiden, The Netherlands.,Centre for Microbial Cell Biology, Leiden, The Netherlands
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53
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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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54
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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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55
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Luo Y, Cheong E, Bian Q, Collins DA, Ye J, Shin JH, Yam WC, Takata T, Song X, Wang X, Kamboj M, Gottlieb T, Jiang J, Riley TV, Tang YW, Jin D. Different molecular characteristics and antimicrobial resistance profiles of Clostridium difficile in the Asia-Pacific region. Emerg Microbes Infect 2020; 8:1553-1562. [PMID: 31662120 PMCID: PMC6830245 DOI: 10.1080/22221751.2019.1682472] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Molecular epidemiology of Clostridium difficile infection (CDI) has been extensively studied in North America and Europe; however, limited data on CDI are available in the Asia-Pacific region. A multicentre retrospective study was conducted in this region. C. difficile isolates were subjected to multilocus sequence typing (ST) and antimicrobial susceptibility testing. Totally, 394 isolates were collected from Hangzhou, Hong Kong, China; Busan, South Korea; Fukuoka, Japan; Singapore; Perth, Sydney, Australia; New York, the United States. C. difficile isolates included 337 toxin A-positive/B-positive/binary toxin-negative (A+B+CDT-), 48 A-B+CDT-, and nine A+B+CDT+. Distribution of dominant STs varied geographically with ST17 in Fukuoka (18.6%), Busan (56.0%), ST2 in Sydney (20.4%), Perth (25.8%). The antimicrobial resistance patterns were significantly different among the eight sites (χ2 = 325.64, p < 0.001). Five major clonal complexes correlated with unique antimicrobial resistances. Healthcare-associated (HA) CDI was mainly from older patients with more frequent antimicrobial use and higher A-B+ positive rates. Higher resistance to gatifloxacin, tetracycline, and erythromycin were observed in HA-CDI patients (χ2 = 4.76-7.89, p = 0.005-0.029). In conclusion, multiple C. difficile genotypes with varied antimicrobial resistance patterns have been circulating in the Asia-Pacific region. A-B+ isolates from older patients with prior antimicrobial use were correlated with HA-CDI.
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Affiliation(s)
- Yun Luo
- Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, People's Republic of China.,School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Elaine Cheong
- Department of Infectious Diseases & Microbiology, Concord Repatriation General Hospital, Concord, Australia.,Sydney Medical School, University of Sydney, Sydney, Australia
| | - Qiao Bian
- School of Medicine, Ningbo University, Ningbo, People's Republic of China
| | - Deirdre A Collins
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Australia
| | - Julian Ye
- Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, People's Republic of China
| | - Jeong Hwan Shin
- Department of Laboratory Medicine, Busan Paik Hospital, Inje University College of Medicine, Busan, Republic of Korea.,Paik Institute for Clinical Research, Inje University College of Medicine, Busan, Republic of Korea
| | - Wing Cheong Yam
- Department of Microbiology, Queen Mary Hospital, Faculty of Medicine, The University of Hong Kong, Hong Kong
| | - Tohru Takata
- Department of Infection Control, Fukuoka University Hospital, Fukuoka, Japan.,Division of Infectious Diseases, Fukuoka University School of Medicine, Fukuoka, Japan
| | - Xiaojun Song
- Centre of Laboratory Medicine, Zhejiang Provincial People Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, People's Republic of China
| | - Xianjun Wang
- Department of Laboratory Medicine, Hangzhou First People's Hospital, Hangzhou, People's Republic of China
| | - Mini Kamboj
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Medicine, Weill Medical College of Cornell University, New York, NY, USA
| | - Thomas Gottlieb
- Department of Infectious Diseases & Microbiology, Concord Repatriation General Hospital, Concord, Australia.,Sydney Medical School, University of Sydney, Sydney, Australia
| | - Jianmin Jiang
- Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, People's Republic of China.,Key Laboratory of Vaccine, Prevention and Control of Infectious Disease of Zhejiang Province, Hangzhou, People's Republic of China
| | - Thomas V Riley
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Australia.,School of Veterinary and Life Sciences, Murdoch University, Murdoch, Australia.,Department of Microbiology, PathWest Laboratory Medicine, Nedlands, Australia
| | - Yi-Wei Tang
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA.,Department of Medicine, Weill Medical College of Cornell University, New York, NY, USA
| | - Dazhi Jin
- Department of Microbiology, Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, People's Republic of China.,Centre of Laboratory Medicine, Zhejiang Provincial People Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, People's Republic of China.,Key Laboratory of Vaccine, Prevention and Control of Infectious Disease of Zhejiang Province, Hangzhou, People's Republic of China.,School of Laboratory Medicine, Hangzhou Medical College, Hangzhou, People's Republic of China
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56
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Waker E, Ambrozkiewicz F, Kulecka M, Paziewska A, Skubisz K, Cybula P, Targoński Ł, Mikula M, Walewski J, Ostrowski J. High Prevalence of Genetically Related Clostridium Difficile Strains at a Single Hemato-Oncology Ward Over 10 Years. Front Microbiol 2020; 11:1618. [PMID: 32793147 PMCID: PMC7384382 DOI: 10.3389/fmicb.2020.01618] [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: 03/19/2020] [Accepted: 06/22/2020] [Indexed: 12/19/2022] Open
Abstract
Aims: Clostridium difficile (C. difficile) infection (CDI) is the main cause of healthcare-associated infectious diarrhea. We used whole-genome sequencing (WGS) to measure the prevalence and genetic variability of C. difficile at a single hemato-oncology ward over a 10 year period. Methods: Between 2008 and 2018, 2077 stool samples were obtained from diarrheal patients hospitalized at the Department of Lymphoma; of these, 618 were positive for toxin A/B. 140 isolates were then subjected to WGS on Ion Torrent PGM sequencer. Results: 36 and 104 isolates were recovered from 36 to 46 patients with single and multiple CDIs, respectively. Of these, 131 strains were toxigenic. Toxin gene profiles tcdA(+);tcdB(+);cdtA/cdtB(+) and tcdA(+);tcdB(+);cdtA/cdtB(-) were identified in 122 and nine strains, respectively. No isolates showed reduced susceptibility to metronidazole and vancomycin. All tested strains were resistant to ciprofloxacin, and 72.9, 42.9, and 72.9% of strains were resistant to erythromycin, clindamycin, or moxifloxacin, respectively. Multi-locus sequence typing (MLST) identified 23 distinct sequence types (STs) and two unidentified strains. Strains ST1 and ST42 represented 31 and 30.1% of all strains tested, respectively. However, while ST1 was detected across nearly all years studied, ST42 was detected only from 2009 to 2011. Conclusion: The high proportion of infected patients in 2008-2011 may be explained by the predominance of more transmissible and virulent C. difficile strains. Although this retrospective study was not designed to define outbreaks of C. difficile, the finding that most isolates exhibited high levels of genetic relatedness suggests nosocomial acquisition.
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Affiliation(s)
- Edyta Waker
- Department of Clinical Microbiology, Maria Skłodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Filip Ambrozkiewicz
- Department of Genetics, Maria Skłodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Maria Kulecka
- Department of Genetics, Maria Skłodowska-Curie National Research Institute of Oncology, Warsaw, Poland
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre for Postgraduate Medical Education, Warsaw, Poland
| | - Agnieszka Paziewska
- Department of Genetics, Maria Skłodowska-Curie National Research Institute of Oncology, Warsaw, Poland
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre for Postgraduate Medical Education, Warsaw, Poland
| | - Karolina Skubisz
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre for Postgraduate Medical Education, Warsaw, Poland
| | - Patrycja Cybula
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre for Postgraduate Medical Education, Warsaw, Poland
| | - Łukasz Targoński
- Department of Lymphoproliferative Diseases, Maria Skłodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Michał Mikula
- Department of Genetics, Maria Skłodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Jan Walewski
- Department of Lymphoproliferative Diseases, Maria Skłodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Jerzy Ostrowski
- Department of Genetics, Maria Skłodowska-Curie National Research Institute of Oncology, Warsaw, Poland
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre for Postgraduate Medical Education, Warsaw, Poland
- *Correspondence: Jerzy Ostrowski,
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57
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Collins DA, Sohn KM, Wu Y, Ouchi K, Ishii Y, Elliott B, Riley TV, Tateda K. Clostridioides difficile infection in the Asia-Pacific region. Emerg Microbes Infect 2019; 9:42-52. [PMID: 31873046 PMCID: PMC6968625 DOI: 10.1080/22221751.2019.1702480] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Clostridioides difficile causes healthcare-related diarrhoea in high-income countries. Highly resistant spores persist in healthcare facilities, primarily infecting patients who have recently received antimicrobials. C. difficile infection (CDI) has been studied in detail in North America and Europe; however, the epidemiology of CDI elsewhere, including the Asia-Pacific region, is largely unknown. A survey of CDI was performed in 13 Asia-Pacific countries. Epidemiological data on 600 cases were collected and molecular typing undertaken on 414 C. difficile isolates. Healthcare facility-associated CDI comprised 53.6% of cases, while community-associated CDI was 16.5%. The median age of cases was 63.0 years and 45.3% were female, 77.5% had used antibiotics in the previous 8 weeks, most frequently third-generation cephalosporins (31.7%), and 47.3% had used proton pump inhibitors. Recurrence (9.1%) and mortality (5.2%) rates were low, while complications including colitis or pseudomembranous colitis (13.8%), colectomy (0.4%), and toxic megacolon (0.2%) were uncommon. Common C. difficile strains were ribotypes 017 (16.7%), 014/020 (11.1%) and 018 (9.9%), with wide variation between countries. Binary toxin-positive strains of C. difficile were detected rarely. Overall, disease severity appeared mild, and mortality and recurrence were low. Continued education about, and surveillance of, CDI in Asia are required to reduce the burden of disease.
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Affiliation(s)
- Deirdre A Collins
- School of Biomedical Sciences, The University of Western Australia, Perth, Australia
| | - Kyung Mok Sohn
- Division of Infectious Diseases, Department of Internal Medicine, Chungnam National University School of Medicine, Daejeon, Republic of Korea
| | - Yuan Wu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, People's Republic of China
| | - Kentaro Ouchi
- Medical Affairs, Otsuka Pharmaceutical Co., Ltd, Osaka, Japan
| | - Yoshikazu Ishii
- Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Tokyo, Japan.,Department of Infection Control, Toho University Medical Center, Omori Hospital, Tokyo, Japan
| | - Briony Elliott
- School of Biomedical Sciences, The University of Western Australia, Perth, Australia
| | - Thomas V Riley
- School of Biomedical Sciences, The University of Western Australia, Perth, Australia.,Department of Microbiology, PathWest Laboratory Medicine (WA), Perth, Australia
| | - Kazuhiro Tateda
- Department of Microbiology and Infectious Diseases, Toho University School of Medicine, Tokyo, Japan.,Department of Infection Control, Toho University Medical Center, Omori Hospital, Tokyo, Japan.,Laboratory Microbiological Section, Toho University Medical Center, Omori Hospital, Tokyo, Japan
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58
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Wu Y, Yang L, Li WG, Zhang WZ, Liu ZJ, Lu JX. Microevolution within ST11 group Clostridioides difficile isolates through mobile genetic elements based on complete genome sequencing. BMC Genomics 2019; 20:796. [PMID: 31666016 PMCID: PMC6822371 DOI: 10.1186/s12864-019-6184-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2019] [Accepted: 10/15/2019] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Clade 5 Clostridioides difficile diverges significantly from the other clades and is therefore, attracting increasing attention due its great heterogeneity. In this study, we used third-generation sequencing techniques to sequence the complete whole genomes of three ST11 C. difficile isolates, RT078 and another two new ribotypes (RTs), obtained from three independent hospitalized elderly patients undergoing antibiotics treatment. Mobile genetic elements (MGEs), antibiotic-resistance, drug resistance genes, and virulent-related genes were analyzed and compared within these three isolates. RESULTS Isolates 10,010 and 12,038 carried a distinct deletion in tcdA compared with isolate 21,062. Furthermore, all three isolates had identical deletions and point-mutations in tcdC, which was once thought to be a unique characteristic of RT078. Isolate 21,062 (RT078) had a unique plasmid, different numbers of transposons and genetic organization, and harboring special CRISPR spacers. All three isolates retained high-level sensitivity to 11 drugs and isolate 21,062 (RT078) carried distinct drug-resistance genes and loss of numerous flagellum-related genes. CONCLUSIONS We concluded that capillary electrophoresis based PCR-ribotyping is important for confirming RT078. Furthermore, RT078 isolates displayed specific MGEs, indicating an independent evolutionary process. In the further study, we could testify these findings with more RT078 isolates of divergent origins.
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Affiliation(s)
- Yuan Wu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China. .,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China.
| | - Lin Yang
- BGI-Shen zhen, main building, Beishan industry zone, Yan tian District, Shenzhen, China
| | - Wen-Ge Li
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Wen Zhu Zhang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Zheng Jie Liu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jin-Xing Lu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China. .,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China.
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59
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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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60
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Affiliation(s)
- Deirdre A Collins
- School of Medical & Health Sciences, Edith Cowan University, Joondalup
| | - Thomas V Riley
- School of Medical & Health Sciences, Edith Cowan University, Joondalup.,Department of Microbiology, PathWest Laboratory Medicine, Nedlands.,School of Veterinary & Life Sciences, Murdoch University, Australia
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61
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Connor MC, McGrath JW, McMullan G, Marks N, Guelbenzu M, Fairley DJ. Emergence of a non-sporulating secondary phenotype in Clostridium (Clostridioides) difficile ribotype 078 isolated from humans and animals. Sci Rep 2019; 9:13722. [PMID: 31548637 PMCID: PMC6757067 DOI: 10.1038/s41598-019-50285-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Accepted: 08/27/2019] [Indexed: 11/09/2022] Open
Abstract
Clostridium (Clostridioides) difficile is a Gram positive, spore forming anaerobic bacterium that is a leading cause of antibiotic associated diarrhoea in the developed world. C. difficile is a genetically diverse species that can be divided into 8 phylogenetically distinct clades with clade 5 found to be genetically distant from all others. Isolates with the PCR ribotype 078 belong to clade 5, and are often associated with C. difficile infection in both humans and animals. Colonisation of animals and humans by ribotype 078 raises questions about possible zoonotic transmission, and also the diversity of reservoirs for ribotype 078 strains within the environment. One of the key factors which enables C. difficile to be a successful, highly transmissible pathogen is its ability to produce oxygen resistant spores capable of surviving harsh conditions. Here we describe the existence of a non-sporulating variant of C. difficile ribotype 078 harbouring mutations leading to premature stop codons within the master regulator, Spo0A. As sporulation is imperative to the successful transmission of C. difficile this study was undertaken to investigate phenotypic characteristics of this asporogenous phenotype with regards to growth rate, antibiotic susceptibility, toxin production and biofilm formation.
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Affiliation(s)
- M C Connor
- School of Biological Sciences and the Institute for Global Food Security, Queen's University Belfast, Belfast, UK.
| | - J W McGrath
- School of Biological Sciences and the Institute for Global Food Security, Queen's University Belfast, Belfast, UK
| | - G McMullan
- School of Biological Sciences and the Institute for Global Food Security, Queen's University Belfast, Belfast, UK
| | - N Marks
- School of Biological Sciences and the Institute for Global Food Security, Queen's University Belfast, Belfast, UK
| | - M Guelbenzu
- Veterinary Science Division, Agri-Food Biosciences Institute, Belfast, UK.,Animal Health Ireland, Carrick on Shannon, Republic of Ireland
| | - D J Fairley
- Department of Microbiology, Belfast Health & Social Care Trust, Belfast, UK
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62
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Emele MF, Joppe FM, Riedel T, Overmann J, Rupnik M, Cooper P, Kusumawati RL, Berger FK, Laukien F, Zimmermann O, Bohne W, Groß U, Bader O, Zautner AE. Proteotyping of Clostridioides difficile as Alternate Typing Method to Ribotyping Is Able to Distinguish the Ribotypes RT027 and RT176 From Other Ribotypes. Front Microbiol 2019; 10:2087. [PMID: 31552001 PMCID: PMC6747054 DOI: 10.3389/fmicb.2019.02087] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Accepted: 08/23/2019] [Indexed: 12/17/2022] Open
Abstract
Clostridioides difficile, a Gram-positive spore-forming bacterium, is the leading cause of nosocomial diarrhea worldwide and therefore a substantial burden to the healthcare system. During the past decade, hypervirulent PCR-ribotypes (RT) e.g., RT027 or RT176 emerged rapidly all over the world, associated with both, increased severity and mortality rates. It is thus of great importance to identify epidemic strains such as RT027 and RT176 as fast as possible. While commonly used diagnostic methods, e.g., multilocus sequence typing (MLST) or PCR-ribotyping, are time-consuming, proteotyping offers a fast, inexpensive, and reliable alternative solution. In this study, we established a MALDI-TOF-based typing scheme for C. difficile. A total of 109 ribotyped strains representative for five MLST clades were analyzed by MALDI-TOF. MLST, based on whole genome sequences, and PCR-ribotyping were used as reference methods. Isoforms of MS-detectable biomarkers, typically ribosomal proteins, were related with the deduced amino acid sequences and added to the C. difficile proteotyping scheme. In total, we were able to associate nine biomarkers with their encoding genes and include them in our proteotyping scheme. The discriminatory capacity of the C. difficile proteotyping scheme was mainly based on isoforms of L28-M (2 main isoforms), L35-M (4 main isoforms), and S20-M (2 main isoforms) giving rise to at least 16 proteotyping-derived types. In our test population, five of these 16 proteotyping-derived types were detected. These five proteotyping-derived types did not correspond exactly to the included five MLST-based C. difficile clades, nevertheless the subtyping depth of both methods was equivalent. Most importantly, proteotyping-derived clade B contained only isolates of the hypervirulent RT027 and RT176. Proteotyping is a stable and easy-to-perform intraspecies typing method and a promising alternative to currently used molecular techniques. It is possible to distinguish the group of RT027 and RT176 isolates from non-RT027/non-RT176 isolates using proteotyping, providing a valuable diagnostic tool.
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Affiliation(s)
- Matthias F Emele
- Institut für Medizinische Mikrobiologie, Universitätsmedizin Göttingen, Göttingen, Germany
| | - Felix M Joppe
- Institut für Medizinische Mikrobiologie, Universitätsmedizin Göttingen, Göttingen, Germany
| | - Thomas Riedel
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Braunschweig, Germany.,Deutsches Zentrum für Infektionsforschung (DZIF), Standort Hannover-Braunschweig, Braunschweig, Germany
| | - Jörg Overmann
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, Braunschweig, Germany.,Deutsches Zentrum für Infektionsforschung (DZIF), Standort Hannover-Braunschweig, Braunschweig, Germany
| | - Maja Rupnik
- National Laboratory for Health, Environment and Food (NLZOH), Maribor, Slovenia.,Faculty of Medicine, University of Maribor, Maribor, Slovenia
| | | | - R Lia Kusumawati
- Department of Microbiology, Faculty of Medicine, Universitas Sumatera Utara, Medan, Indonesia
| | - Fabian K Berger
- National Reference Center for Clostridioides (Clostridium) difficile, Institute of Medical Microbiology and Hygiene, Saarland University, Homburg, Germany
| | - Friederike Laukien
- Institut für Medizinische Mikrobiologie, Universitätsmedizin Göttingen, Göttingen, Germany
| | - Ortrud Zimmermann
- Institut für Medizinische Mikrobiologie, Universitätsmedizin Göttingen, Göttingen, Germany
| | - Wolfgang Bohne
- Institut für Medizinische Mikrobiologie, Universitätsmedizin Göttingen, Göttingen, Germany
| | - Uwe Groß
- Institut für Medizinische Mikrobiologie, Universitätsmedizin Göttingen, Göttingen, Germany
| | - Oliver Bader
- Institut für Medizinische Mikrobiologie, Universitätsmedizin Göttingen, Göttingen, Germany
| | - Andreas E Zautner
- Institut für Medizinische Mikrobiologie, Universitätsmedizin Göttingen, Göttingen, Germany
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63
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Imwattana K, Knight DR, Kullin B, Collins DA, Putsathit P, Kiratisin P, Riley TV. Clostridium difficile ribotype 017 - characterization, evolution and epidemiology of the dominant strain in Asia. Emerg Microbes Infect 2019; 8:796-807. [PMID: 31138041 PMCID: PMC6542179 DOI: 10.1080/22221751.2019.1621670] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Clostridium difficile ribotype (RT) 017 is an important toxigenic C. difficile RT which, due to a deletion in the repetitive region of the tcdA gene, only produces functional toxin B. Strains belonging to this RT were initially dismissed as nonpathogenic and circulated largely undetected for almost two decades until they rose to prominence following a series of outbreaks in the early 2000s. Despite lacking a functional toxin A, C. difficile RT 017 strains have been shown subsequently to be capable of causing disease as severe as that caused by strains producing both toxins A and B. While C. difficile RT 017 strains can be found in almost every continent today, epidemiological studies suggest that the RT is endemic in Asia and that the global spread of this MLST clade 4 lineage member is a relatively recent event. C. difficile RT 017 transmission appears to be mostly from human to human with only a handful of reports of isolations from animals. An important feature of C. difficile RT 017 strains is their resistance to several antimicrobials and this has been documented as a possible factor driving multiple outbreaks in different parts of the world. This review summarizes what is currently known regarding the emergence and evolution of strains belonging to C. difficile RT 017 as well as features that have allowed it to become an RT of global importance.
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Affiliation(s)
- Korakrit Imwattana
- a School of Biomedical Sciences , The University of Western Australia , Crawley, Australia.,b Department of Microbiology, Faculty of Medicine Siriraj Hospital , Mahidol University , Bangkok, Thailand
| | - Daniel R Knight
- c School of Veterinary and Life Sciences , Murdoch University , Murdoch, Australia
| | - Brian Kullin
- d Department of Molecular and Cell Biology , University of Cape Town , Cape Town , South Africa
| | - Deirdre A Collins
- e School of Medical and Health Sciences , Edith Cowan University , Joondalup, Australia
| | - Papanin Putsathit
- e School of Medical and Health Sciences , Edith Cowan University , Joondalup, Australia
| | - Pattarachai Kiratisin
- b Department of Microbiology, Faculty of Medicine Siriraj Hospital , Mahidol University , Bangkok, Thailand
| | - Thomas V Riley
- a School of Biomedical Sciences , The University of Western Australia , Crawley, Australia.,c School of Veterinary and Life Sciences , Murdoch University , Murdoch, Australia.,e School of Medical and Health Sciences , Edith Cowan University , Joondalup, Australia.,f PathWest Laboratory Medicine , Queen Elizabeth II Medical Centre , Nedlands , Australia
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64
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Gumkowski JD, Martinie RJ, Corrigan PS, Pan J, Bauerle MR, Almarei M, Booker SJ, Silakov A, Krebs C, Boal AK. Analysis of RNA Methylation by Phylogenetically Diverse Cfr Radical S-Adenosylmethionine Enzymes Reveals an Iron-Binding Accessory Domain in a Clostridial Enzyme. Biochemistry 2019; 58:3169-3184. [PMID: 31246421 DOI: 10.1021/acs.biochem.9b00197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Cfr is a radical S-adenosylmethionine (SAM) RNA methylase linked to multidrug antibiotic resistance in bacterial pathogens. It catalyzes a chemically challenging C-C bond-forming reaction to methylate C8 of A2503 (Escherichia coli numbering) of 23S rRNA during ribosome assembly. The cfr gene has been identified as a mobile genetic element in diverse bacteria and in the genome of select Bacillales and Clostridiales species. Despite the importance of Cfr, few representatives have been purified and characterized in vitro. Here we show that Cfr homologues from Bacillus amyloliquefaciens, Enterococcus faecalis, Paenibacillus lautus, and Clostridioides difficile act as C8 adenine RNA methylases in biochemical assays. C. difficile Cfr contains an additional Cys-rich C-terminal domain that binds a mononuclear Fe2+ ion in a rubredoxin-type Cys4 motif. The C-terminal domain can be truncated with minimal impact on C. difficile Cfr activity, but the rate of turnover is decreased upon disruption of the Fe2+-binding site by Zn2+ substitution or ligand mutation. These findings indicate an important purpose for the observed C-terminal iron in the native fusion protein. Bioinformatic analysis of the C. difficile Cfr Cys-rich domain shows that it is widespread (∼1400 homologues) as a stand-alone gene in pathogenic or commensal Bacilli and Clostridia, with >10% encoded adjacent to a predicted radical SAM RNA methylase. Although the domain is not essential for in vitro C. difficile Cfr activity, the genomic co-occurrence and high abundance in the human microbiome suggest a possible functional role for a specialized rubredoxin in certain radical SAM RNA methylases that are relevant to human health.
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Affiliation(s)
- James D Gumkowski
- Department of Chemistry , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Ryan J Martinie
- Department of Chemistry , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Patrick S Corrigan
- Department of Chemistry , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Juan Pan
- Department of Chemistry , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Matthew R Bauerle
- Department of Chemistry , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Mohamed Almarei
- Department of Biochemistry and Molecular Biology , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Squire J Booker
- Department of Chemistry , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States.,Department of Biochemistry and Molecular Biology , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States.,Howard Hughes Medical Institute , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Alexey Silakov
- Department of Chemistry , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Carsten Krebs
- Department of Chemistry , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States.,Department of Biochemistry and Molecular Biology , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
| | - Amie K Boal
- Department of Chemistry , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States.,Department of Biochemistry and Molecular Biology , The Pennsylvania State University , University Park , Pennsylvania 16802 , United States
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65
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Cao H, Wong SCY, Yam WC, Liu MCJ, Chow KH, Wu AKL, Ho PL. Genomic investigation of a sequence type 67 Clostridium difficile causing community-acquired fulminant colitis in Hong Kong. Int J Med Microbiol 2019; 309:270-273. [DOI: 10.1016/j.ijmm.2019.05.003] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 04/24/2019] [Accepted: 05/10/2019] [Indexed: 12/20/2022] Open
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66
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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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67
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Moore RJ, Lacey JA. Genomics of the Pathogenic Clostridia. Microbiol Spectr 2019; 7:10.1128/microbiolspec.gpp3-0033-2018. [PMID: 31215504 PMCID: PMC11257213 DOI: 10.1128/microbiolspec.gpp3-0033-2018] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Indexed: 12/12/2022] Open
Abstract
Whole-genome sequences are now available for all the clinically important clostridia and many of the lesser or opportunistically pathogenic clostridia. The complex clade structures of C. difficile, C. perfringens, and the species that produce botulinum toxins have been delineated by whole-genome sequence analysis. The true clostridia of cluster I show relatively low levels of gross genomic rearrangements within species, in contrast to the species of cluster XI, notably C. difficile, which have been found to have very plastic genomes with significant levels of chromosomal rearrangement. Throughout the clostridial phylotypes, a large proportion of the strain diversity is driven by the acquisition and loss of mobile elements, including phages, plasmids, insertion sequences, and transposons. Genomic analysis has been used to investigate the diversity and spread of C. difficile within hospital settings, the zoonotic transfer of isolates, and the emergence, origins, and geographic spread of epidemic ribotypes. In C. perfringens the clades defined by chromosomal sequence analysis show no indications of clustering based on host species or geographical location. Whole-genome sequence analysis helps to define the different survival and pathogenesis strategies that the clostridia use. Some, such as C. botulinum, produce toxins which rapidly act to kill the host, whereas others, such as C. perfringens and C. difficile, produce less lethal toxins which can damage tissue but do not rapidly kill the host. The genomes provide a resource that can be mined to identify potential vaccine antigens and targets for other forms of therapeutic intervention.
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Affiliation(s)
- Robert J Moore
- Host-Microbe Interactions Laboratory, School of Science, RMIT University, Bundoora, Victoria 3083, Australia
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
| | - Jake A Lacey
- Doherty Department, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia
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68
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Revitt-Mills SA, Vidor CJ, Watts TD, Lyras D, Rood JI, Adams V. Virulence Plasmids of the Pathogenic Clostridia. Microbiol Spectr 2019; 7:10.1128/microbiolspec.gpp3-0034-2018. [PMID: 31111816 PMCID: PMC11257192 DOI: 10.1128/microbiolspec.gpp3-0034-2018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Indexed: 12/12/2022] Open
Abstract
The clostridia cause a spectrum of diseases in humans and animals ranging from life-threatening tetanus and botulism, uterine infections, histotoxic infections and enteric diseases, including antibiotic-associated diarrhea, and food poisoning. The symptoms of all these diseases are the result of potent protein toxins produced by these organisms. These toxins are diverse, ranging from a multitude of pore-forming toxins to phospholipases, metalloproteases, ADP-ribosyltransferases and large glycosyltransferases. The location of the toxin genes is the unifying theme of this review because with one or two exceptions they are all located on plasmids or on bacteriophage that replicate using a plasmid-like intermediate. Some of these plasmids are distantly related whilst others share little or no similarity. Many of these toxin plasmids have been shown to be conjugative. The mobile nature of these toxin genes gives a ready explanation of how clostridial toxin genes have been so widely disseminated both within the clostridial genera as well as in the wider bacterial community.
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Affiliation(s)
- Sarah A Revitt-Mills
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
| | - Callum J Vidor
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
| | - Thomas D Watts
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
| | - Dena Lyras
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
| | - Julian I Rood
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
| | - Vicki Adams
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
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69
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Eyre DW, Shaw R, Adams H, Cooper T, Crook DW, Griffin RM, Mannion P, Morgan M, Morris T, Perry M, Jones S, Peto TEA, Sutton J, Walker AS, Williams D, Craine N. WGS to determine the extent of Clostridioides difficile transmission in a high incidence setting in North Wales in 2015. J Antimicrob Chemother 2019; 74:1092-1100. [PMID: 30561656 DOI: 10.1093/jac/dky523] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2018] [Revised: 11/06/2018] [Accepted: 11/16/2018] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES Rates of Clostridioides (Clostridium) difficile infection (CDI) are higher in North Wales than elsewhere in the UK. We used WGS to investigate if this is due to increased healthcare-associated transmission from other cases. METHODS Healthcare and community C. difficile isolates from patients across North Wales (February-July 2015) from glutamate dehydrogenase (GDH)-positive faecal samples underwent WGS. Data from patient records, hospital management systems and national antimicrobial use surveillance were used. RESULTS Of the 499 GDH-positive samples, 338 (68%) were sequenced and 299 distinct infections/colonizations were identified, 229/299 (77%) with toxin genes. Only 39/229 (17%) toxigenic isolates were related within ≤2 SNPs to ≥1 infections/colonizations from a previously sampled patient, i.e. demonstrated evidence of possible transmission. Independent predictors of possible transmission included healthcare exposure in the last 12 weeks (P = 0.002, with rates varying by hospital), infection with MLST types ST-1 (ribotype 027) and ST-11 (predominantly ribotype 078) compared with all other toxigenic STs (P < 0.001), and cephalosporin exposure in the potential transmission recipient (P = 0.02). Adjusting for all these factors, there was no additional effect of ward workload (P = 0.54) or failure to meet cleaning targets (P = 0.25). Use of antimicrobials is higher in North Wales compared with England and the rest of Wales. CONCLUSIONS Levels of transmission detected by WGS were comparable to previously described rates in endemic settings; other explanations, such as variations in antimicrobial use, are required to explain the high levels of CDI. Cephalosporins are a risk factor for infection with C. difficile from another infected or colonized case.
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Affiliation(s)
- David W Eyre
- Big Data Institute, University of Oxford, England, UK.,Nuffield Department of Medicine, University of Oxford, England, UK
| | - Robert Shaw
- Nuffield Department of Medicine, University of Oxford, England, UK
| | - Helen Adams
- Betsi Cadwaladr University Health Board, Ysbyty Gwynedd, Bangor, Wales, UK
| | - Tracey Cooper
- Betsi Cadwaladr University Health Board, Ysbyty Glan Clwyd, Bangor, Wales, UK
| | - Derrick W Crook
- Nuffield Department of Medicine, University of Oxford, England, UK
| | | | - Phil Mannion
- Public Health Wales, Microbiology, Ysbyty Glan Clwyd, Rhyl, Wales, UK
| | - Mari Morgan
- Public Health Wales, Health Protection, Capital Quarter, Cardiff, Wales, UK
| | - Trefor Morris
- Public Health Wales, Microbiology, Heath Hospital, Cardiff, Wales, UK
| | - Michael Perry
- Public Health Wales, Microbiology, Heath Hospital, Cardiff, Wales, UK
| | - Sophie Jones
- Public Health Wales, Microbiology, Heath Hospital, Cardiff, Wales, UK
| | - Tim E A Peto
- Nuffield Department of Medicine, University of Oxford, England, UK
| | - Jonathan Sutton
- Betsi Cadwaladr University Health Board, Ysbyty Gwynedd, Bangor, Wales, UK
| | - A Sarah Walker
- Nuffield Department of Medicine, University of Oxford, England, UK
| | - Dafydd Williams
- Betsi Cadwaladr University Health Board, Ysbyty Gwynedd, Bangor, Wales, UK
| | - Noel Craine
- Public Health Wales, Health Protection, Ysbyty Gwynedd, Bangor, Wales, UK
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70
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Imwattana K, Wangroongsarb P, Riley TV. High prevalence and diversity of tcdA-negative and tcdB-positive, and non-toxigenic, Clostridium difficile in Thailand. Anaerobe 2019; 57:4-10. [PMID: 30862468 DOI: 10.1016/j.anaerobe.2019.03.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2018] [Revised: 03/04/2019] [Accepted: 03/06/2019] [Indexed: 02/05/2023]
Abstract
Studies on the prevalence and diversity of Clostridium difficile in Thailand have been limited to those derived from a few tertiary hospitals in Central Thailand. In this study, 145 C. difficile isolates collected in 13 provinces in Thailand during 2006-2018 were characterized by ribotyping and detection of toxin genes. Minimum inhibitory concentrations of eight antimicrobial agents were determined also for all 100 C. difficile strains collected from 2006 until 2015. Of the 145 strains of C. difficile, 71 (49%) were non-toxigenic, 46 (32%) were toxin A-negative, toxin B-positive (A-B+) and 28 (19%) were A+B+. No binary toxin-positive strain was found. The most common ribotype (RT) was RT 017 (A-B+CDT-, 19%, 28/145). Besides RT 017, 20 novel non-toxigenic and A-B+ ribotyping profiles, which may be related to RT 017 by the similarity of ribotyping profile, were identified. All C. difficile strains remained susceptible to metronidazole and vancomycin, however, a slight increase in MIC for metronidazole was seen in both toxigenic and non-toxigenic strains (overall MIC50/90 0.25/0.25 mg/L during 2006-2010 compared to overall MIC50/90 1.0/2.0 mg/L during 2011-2015). There was a high rate of fluoroquinolone resistance among RT 017 strains (77%), but there was little resistance among non-toxigenic strains. These results suggest that RT 017 is endemic in Thailand, and that the misuse of fluoroquinolones may lead to outbreaks of RT 017 infection in this country. Further studies on non-toxigenic C. difficile are needed to understand whether they have a role in the pathogenesis of C. difficile infection in Asia.
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Affiliation(s)
- Korakrit Imwattana
- School of Biomedical Sciences, The University of Western Australia, Western Australia, 6009, Australia
| | - Piyada Wangroongsarb
- The National Institute of Health, Department of Medical Sciences, Ministry of Public Health, Nonthaburi, 11000, Thailand
| | - Thomas V Riley
- School of Biomedical Sciences, The University of Western Australia, Western Australia, 6009, Australia; School of Veterinary and Life Sciences, Murdoch University, Western Australia, 6150, Australia; School of Medical and Health Sciences, Edith Cowan University, Western Australia, 6027, Australia; Department of Microbiology, PathWest Laboratory Medicine, Queen Elizabeth II Medical Centre, Western Australia, 6009, Australia.
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71
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Camorlinga M, Sanchez-Rojas M, Torres J, Romo-Castillo M. Phenotypic Characterization of Non-toxigenic Clostridioides difficile Strains Isolated From Patients in Mexico. Front Microbiol 2019; 10:84. [PMID: 30774626 PMCID: PMC6367242 DOI: 10.3389/fmicb.2019.00084] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2018] [Accepted: 01/16/2019] [Indexed: 02/04/2023] Open
Abstract
Clostridioides difficile is a Gram positive, sporulated, rod-shape, anaerobic pathogen responsible for nosocomial diarrhea and colitis, mainly in antibiotic treated patients. C. difficile produce two toxins responsible for disease, toxin A (TcdA) and toxin B (TcdB), although not all strains produce them. Non-toxigenic C. difficile (NTCD) strains are able to colonize the intestinal mucosa and are often isolated from asymptomatic individuals. NTCD are poorly studied, their evolutionary history has not been elucidated, and their relationship with illness remains controversial. The aim of this work was to analyze the phenotype of NTCD strains isolated from clinical cases in hospitals of México, and whether NTCD strains present characteristics that differentiate them from the toxigenic strains. Seventy-four C. difficile strains isolated from patients were tested for cytotoxicity and 14 were identified as NTCD strains. We analyzed phenotypical characteristics that are important for the biology of C. difficile like colony morphology, antibiotic resistance, motility, sporulation, and adherence. Strains were also genotyped to determine the presence of genes coding for TcdA, TcdB and binary toxin and ribotyped for 027 type. When compared with toxigenic strains, NTCD strains presented an enlarged branched colony morphology, higher resistance to metronidazole, and increased sporulation efficiency. This phenotype has been reported associated with mutations that regulates phenotypic characteristics like swimming, sporulation or adhesion. Our results show that phenotype of NTCD strains is heterogeneous but still present characteristics that differentiate them from toxigenic strains.
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Affiliation(s)
- Margarita Camorlinga
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | | | - Javier Torres
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Mariana Romo-Castillo
- CONACYT-IMSS, Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, IMSS, Mexico City, Mexico
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72
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Clostridium difficile in Asia: Opportunities for One Health Management. Trop Med Infect Dis 2018; 4:tropicalmed4010007. [PMID: 30597880 PMCID: PMC6473466 DOI: 10.3390/tropicalmed4010007] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 12/22/2018] [Accepted: 12/23/2018] [Indexed: 01/05/2023] Open
Abstract
Clostridium difficile is a ubiquitous spore-forming bacterium which causes toxin-mediated diarrhoea and colitis in people whose gut microflora has been depleted by antimicrobial use, so it is a predominantly healthcare-associated disease. However, there are many One Health implications to C. difficile, given high colonisation rates in food production animals, contamination of outdoor environments by use of contaminated animal manure, increasing incidence of community-associated C. difficile infection (CDI), and demonstration of clonal groups of C. difficile shared between human clinical cases and food animals. In Asia, the epidemiology of CDI is not well understood given poor testing practices in many countries. The growing middle-class populations of Asia are presenting increasing demands for meat, thus production farming, particularly of pigs, chicken and cattle, is rapidly expanding in Asian countries. Few reports on C. difficile colonisation among production animals in Asia exist, but those that do show high prevalence rates, and possible importation of European strains of C. difficile like ribotype 078. This review summarises our current understanding of the One Health aspects of the epidemiology of CDI in Asia.
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Andrés Lasheras S, Martín Burriel I, Aspiroz C, Mainar Jaime RC, Robres P, Sevilla E, Kuijper E, Chirino Trejo M, Bolea R. Incidence and characterization of Clostridium difficile in a secondary care hospital in Spain. REVISTA ESPANOLA DE ENFERMEDADES DIGESTIVAS 2018; 111:338-344. [PMID: 30569726 DOI: 10.17235/reed.2018.5288/2017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
INTRODUCTION Clostridium difficile (C. difficile) is a major nosocomial infectious agent in hospitals. Previous studies have addressed the high proportion of infection episodes that are overlooked in health care facilities. OBJECTIVE the main aim of this study was to characterize C. difficile clinical cases that occurred in a secondary care hospital during a five-month period. MATERIAL AND METHODS for this purpose, a total of 137 stool samples from the same number of patients with diarrhea were analyzed for the presence of C. difficile by culture techniques. An enzyme immunoassay (EIA) test for the detection of C. difficile and its toxins was also used in 50 cases (36.5%) for diagnostic purposes. RESULTS a total of 14 (10.2%) C. difficile isolates were obtained, of which nine (64.3%) were toxigenic. A mean incidence of 3.2 episodes of C. difficile infections (CDI) per 10,000 patients-days was estimated for the study period. Around 56% of the CDI cases were determined as hospital-acquired, whereas 44% originated in the community. Among these, only two episodes (22.2%) were detected in the hospital by the EIA test, which indicated that the hospital CDI detection protocol needed to be revised. One unusual C. difficile isolate was negative for all toxin genes examined and also for the non-toxigenic strain assay, which highlights the need to perform genome sequencing to study its pathogenicity locus insertion site organization. A stable metronidazole-resistant C. difficile strain and three strains showing multidrug resistance were detected in this study, suggesting that C. difficile antimicrobial susceptibility surveillance programs should be established in this health-care facility.
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Affiliation(s)
- Sara Andrés Lasheras
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Canadá
| | - Inma Martín Burriel
- Laboratorio de Genética Bioquímica (LAGENBIO), Facultad de Veterinaria. Universidad de Zaragoza, España
| | - Carmen Aspiroz
- Sección de Microbiología y Parasitología, Hospital Royo Villanova, España
| | | | - Pilar Robres
- Sección de Microbiología y Parasitología, Hospital Royo Villanova, España
| | - Eloísa Sevilla
- Microbiología e Inmunología, Facultad de Veterinaria. Universidad de Zaragoza, España
| | - Ed Kuijper
- Department of Medical Microbiology, Centre of Infe, Leiden University Medical Centre, The Netherlands
| | - Manuel Chirino Trejo
- Department of Veterinary Microbiology, Western College of Veterinary Medicine. University of Saskatchewan, Canadá
| | - Rosa Bolea
- Microbiología e Inmunología, Facultad de Veterinaria. Universidad de Zaragoza, España
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74
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Kuroda M, Sekizuka T, Matsui H, Suzuki K, Seki H, Saito M, Hanaki H. Complete Genome Sequence and Characterization of Linezolid-Resistant Enterococcus faecalis Clinical Isolate KUB3006 Carrying a cfr(B)-Transposon on Its Chromosome and optrA-Plasmid. Front Microbiol 2018; 9:2576. [PMID: 30410481 PMCID: PMC6209644 DOI: 10.3389/fmicb.2018.02576] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Accepted: 10/09/2018] [Indexed: 01/01/2023] Open
Abstract
Linezolid (LZD) has become one of the most important antimicrobial agents for infections caused by gram-positive bacteria, including those caused by Enterococcus species. LZD-resistant (LR) genetic features include mutations in 23S rRNA/ribosomal proteins, a plasmid-borne 23S rRNA methyltransferase gene cfr, and ribosomal protection genes (optrA and poxtA). Recently, a cfr gene variant, cfr(B), was identified in a Tn6218-like transposon (Tn) in a Clostridioides difficile isolate. Here, we isolated an LR Enterococcus faecalis clinical isolate, KUB3006, from a urine specimen of a patient with urinary tract infection during hospitalization in 2017. Comparative and whole-genome analyses were performed to characterize the genetic features and overall antimicrobial resistance genes in E. faecalis isolate KUB3006. Complete genome sequencing of KUB3006 revealed that it carried cfr(B) on a chromosomal Tn6218-like element. Surprisingly, this Tn6218-like element was almost (99%) identical to that of C. difficile Ox3196, which was isolated from a human in the UK in 2012, and to that of Enterococcus faecium 5_Efcm_HA-NL, which was isolated from a human in the Netherlands in 2012. An additional oxazolidinone and phenicol resistance gene, optrA, was also identified on a plasmid. KUB3006 is sequence type (ST) 729, suggesting that it is a minor ST that has not been reported previously and is unlikely to be a high-risk E. faecalis lineage. In summary, LR E. faecalis KUB3006 possesses a notable Tn6218-like-borne cfr(B) and a plasmid-borne optrA. This finding raises further concerns regarding the potential declining effectiveness of LZD treatment in the future.
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Affiliation(s)
- Makoto Kuroda
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Tsuyoshi Sekizuka
- Pathogen Genomics Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Hidehito Matsui
- Infection Control Research Center, Kitasato University, Tokyo, Japan
| | - Katsunori Suzuki
- Division of Infection Control and Prevention, University of Occupational and Environmental Health, Kitakyusyu, Japan
| | - Hiroyuki Seki
- Division of Infection Control and Prevention, University of Occupational and Environmental Health, Kitakyusyu, Japan
| | - Mitsumasa Saito
- Division of Infection Control and Prevention, University of Occupational and Environmental Health, Kitakyusyu, Japan.,Department of Microbiology, School of Medicine, University of Occupational and Environmental Health, Kitakyusyu, Japan
| | - Hideaki Hanaki
- Infection Control Research Center, Kitasato University, Tokyo, Japan
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75
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Cabal A, Jun SR, Jenjaroenpun P, Wanchai V, Nookaew I, Wongsurawat T, Burgess MJ, Kothari A, Wassenaar TM, Ussery DW. Genome-Based Comparison of Clostridioides difficile: Average Amino Acid Identity Analysis of Core Genomes. MICROBIAL ECOLOGY 2018; 76:801-813. [PMID: 29445826 PMCID: PMC6132499 DOI: 10.1007/s00248-018-1155-7] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 02/02/2018] [Indexed: 06/08/2023]
Abstract
Infections due to Clostridioides difficile (previously known as Clostridium difficile) are a major problem in hospitals, where cases can be caused by community-acquired strains as well as by nosocomial spread. Whole genome sequences from clinical samples contain a lot of information but that needs to be analyzed and compared in such a way that the outcome is useful for clinicians or epidemiologists. Here, we compare 663 public available complete genome sequences of C. difficile using average amino acid identity (AAI) scores. This analysis revealed that most of these genomes (640, 96.5%) clearly belong to the same species, while the remaining 23 genomes produce four distinct clusters within the Clostridioides genus. The main C. difficile cluster can be further divided into sub-clusters, depending on the chosen cutoff. We demonstrate that MLST, either based on partial or full gene-length, results in biased estimates of genetic differences and does not capture the true degree of similarity or differences of complete genomes. Presence of genes coding for C. difficile toxins A and B (ToxA/B), as well as the binary C. difficile toxin (CDT), was deduced from their unique PfamA domain architectures. Out of the 663 C. difficile genomes, 535 (80.7%) contained at least one copy of ToxA or ToxB, while these genes were missing from 128 genomes. Although some clusters were enriched for toxin presence, these genes are variably present in a given genetic background. The CDT genes were found in 191 genomes, which were restricted to a few clusters only, and only one cluster lacked the toxin A/B genes consistently. A total of 310 genomes contained ToxA/B without CDT (47%). Further, published metagenomic data from stools were used to assess the presence of C. difficile sequences in blinded cases of C. difficile infection (CDI) and controls, to test if metagenomic analysis is sensitive enough to detect the pathogen, and to establish strain relationships between cases from the same hospital. We conclude that metagenomics can contribute to the identification of CDI and can assist in characterization of the most probable causative strain in CDI patients.
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Affiliation(s)
- Adriana Cabal
- Molecular Microbiology and Genomics Consultants, Tannenstrasse 7, 55576, Zotzenheim, Germany
| | - Se-Ran Jun
- Arkansas Center for Genomic Epidemiology and Medicine, Department of Biomedical Informatics, University of Arkansas for Medical Sciences, 4301 W. Markham Str., Slot 782, Little Rock, AR, 72205, USA
| | - Piroon Jenjaroenpun
- Arkansas Center for Genomic Epidemiology and Medicine, Department of Biomedical Informatics, University of Arkansas for Medical Sciences, 4301 W. Markham Str., Slot 782, Little Rock, AR, 72205, USA
| | - Visanu Wanchai
- Arkansas Center for Genomic Epidemiology and Medicine, Department of Biomedical Informatics, University of Arkansas for Medical Sciences, 4301 W. Markham Str., Slot 782, Little Rock, AR, 72205, USA
| | - Intawat Nookaew
- Arkansas Center for Genomic Epidemiology and Medicine, Department of Biomedical Informatics, University of Arkansas for Medical Sciences, 4301 W. Markham Str., Slot 782, Little Rock, AR, 72205, USA
| | - Thidathip Wongsurawat
- Arkansas Center for Genomic Epidemiology and Medicine, Department of Biomedical Informatics, University of Arkansas for Medical Sciences, 4301 W. Markham Str., Slot 782, Little Rock, AR, 72205, USA
| | - Mary J Burgess
- Division of Infectious Diseases, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Atul Kothari
- Division of Infectious Diseases, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Trudy M Wassenaar
- Molecular Microbiology and Genomics Consultants, Tannenstrasse 7, 55576, Zotzenheim, Germany
- Arkansas Center for Genomic Epidemiology and Medicine, Department of Biomedical Informatics, University of Arkansas for Medical Sciences, 4301 W. Markham Str., Slot 782, Little Rock, AR, 72205, USA
| | - David W Ussery
- Arkansas Center for Genomic Epidemiology and Medicine, Department of Biomedical Informatics, University of Arkansas for Medical Sciences, 4301 W. Markham Str., Slot 782, Little Rock, AR, 72205, USA.
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Ramírez-Vargas G, López-Ureña D, Badilla A, Orozco-Aguilar J, Murillo T, Rojas P, Riedel T, Overmann J, González G, Chaves-Olarte E, Quesada-Gómez C, Rodríguez C. Novel Clade C-I Clostridium difficile strains escape diagnostic tests, differ in pathogenicity potential and carry toxins on extrachromosomal elements. Sci Rep 2018; 8:13951. [PMID: 30224751 PMCID: PMC6141592 DOI: 10.1038/s41598-018-32390-6] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 06/04/2018] [Indexed: 01/05/2023] Open
Abstract
The population structure of Clostridium difficile currently comprises eight major genomic clades. For the highly divergent C-I clade, only two toxigenic strains have been reported, which lack the tcdA and tcdC genes and carry a complete locus for the binary toxin (CDT) next to an atypical TcdB monotoxin pathogenicity locus (PaLoc). As part of a routine surveillance of C. difficile in stool samples from diarrheic human patients, we discovered three isolates that consistently gave negative results in a PCR-based screening for tcdC. Through phenotypic assays, whole-genome sequencing, experiments in cell cultures, and infection biomodels we show that these three isolates (i) escape common laboratory diagnostic procedures, (ii) represent new ribotypes, PFGE-types, and sequence types within the Clade C-I, (iii) carry chromosomal or plasmidal TcdBs that induce classical or variant cytopathic effects (CPE), and (iv) cause different levels of cytotoxicity and hamster mortality rates. These results show that new strains of C. difficile can be detected by more refined techniques and raise questions on the origin, evolution, and distribution of the toxin loci of C. difficile and the mechanisms by which this emerging pathogen causes disease.
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Affiliation(s)
- Gabriel Ramírez-Vargas
- Research Center for Tropical Diseases (CIET) and Faculty of Microbiology, University of Costa Rica, San José, Costa Rica
| | - Diana López-Ureña
- Research Center for Tropical Diseases (CIET) and Faculty of Microbiology, University of Costa Rica, San José, Costa Rica
| | - Adriana Badilla
- Research Center for Tropical Diseases (CIET) and Faculty of Microbiology, University of Costa Rica, San José, Costa Rica
| | - Josué Orozco-Aguilar
- Laboratory for Biological Assays (LEBi), University of Costa Rica, San José, Costa Rica
| | - Tatiana Murillo
- Research Center for Tropical Diseases (CIET) and Faculty of Microbiology, University of Costa Rica, San José, Costa Rica
| | - Priscilla Rojas
- Research Center for Tropical Diseases (CIET) and Faculty of Microbiology, University of Costa Rica, San José, Costa Rica
| | - 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
| | - 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
| | - Gabriel González
- Research Center for Zoonosis Control, Hokkaido University, Hokkaido, Japan
| | - Esteban Chaves-Olarte
- Research Center for Tropical Diseases (CIET) and Faculty of Microbiology, University of Costa Rica, San José, Costa Rica
| | - Carlos Quesada-Gómez
- Research Center for Tropical Diseases (CIET) and Faculty of Microbiology, University of Costa Rica, San José, Costa Rica
| | - César Rodríguez
- Research Center for Tropical Diseases (CIET) and Faculty of Microbiology, University of Costa Rica, San José, Costa Rica.
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Comparative inhibitory profile and distribution of bacterial PARPs, using Clostridioides difficile CD160 PARP as a model. Sci Rep 2018; 8:8056. [PMID: 29795234 PMCID: PMC5966428 DOI: 10.1038/s41598-018-26450-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2018] [Accepted: 05/14/2018] [Indexed: 01/23/2023] Open
Abstract
Poly-ADP-ribose polymerases (PARPs) are involved in the regulation of important cellular processes, such as DNA repair, aging and apoptosis, among others. They have been considered as promising therapeutic targets, since human cancer cells carrying BRCA1 and BRCA2 mutations are highly sensitive to human PARP-1 inhibitors. Although extensive work has been carried out with the latter enzyme, little is known on bacterial PARPs, of which only one has been demonstrated to be active. To extend this limited knowledge, we demonstrate that the Gram-positive bacterium Clostridioides difficile CD160 PARP is a highly active enzyme with a high production yield. Its phylogenetic analysis also pointed to a singular domain organization in contrast to other clostridiales, which could be due to the long-term divergence of C. difficile CD160. Surprisingly, its PARP becomes the first enzyme to be characterized from this strain, which has a genotype never before described based on its sequenced genome. Finally, the inhibition study carried out after a high-throughput in silico screening and an in vitro testing with hPARP1 and bacterial PARPs identified a different inhibitory profile, a new highly inhibitory compound never before described for hPARP1, and a specificity of bacterial PARPs for a compound that mimics NAD+ (EB-47).
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78
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Liu XS, Li WG, Zhang WZ, Wu Y, Lu JX. Molecular Characterization of Clostridium difficile Isolates in China From 2010 to 2015. Front Microbiol 2018; 9:845. [PMID: 29760687 PMCID: PMC5936795 DOI: 10.3389/fmicb.2018.00845] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2018] [Accepted: 04/12/2018] [Indexed: 12/19/2022] Open
Abstract
Clostridium difficile infection (CDI) has become a worldwide public health problem causing high mortality and a large disease burden. Molecular typing and analysis is important for surveillance and infection control of CDI. However, molecular characterization of C. difficile across China is extremely rare. Here, we report on the toxin profiles, molecular subtyping with multilocus sequence typing (MLST) and PCR ribotyping, and epidemiological characteristics of 199 C. difficile isolates collected between 2010 through 2015 from 13 participating centers across China. We identified 35 STs and 27 ribotypes (RTs) among the 199 C. difficile isolates: ST35 (15.58%), ST3 (15.08%), ST37 (12.06%), and RT017 (14.07%), RT001 (12.06%), RT012 (11.56%) are the most prevalent. One isolate with ST1 and 8 isolates with ST 11 were identified. We identified a new ST in this study, denoted ST332. The toxin profile tcdA+tcdB+tcdC+tcdR+tcdE+CDT- (65.83%) was the predominant profile. Furthermore, 11 isolates with positive binary toxin genes were discovered. According to the PCR ribotyping, one isolate with RT 027, and 6 isolates with RT 078 were confirmed. The epidemiological characteristics of C. difficile in China shows geographical differences, and both the toxin profile and molecular types exhibit great diversity across the different areas.
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Affiliation(s)
- Xiao-Shu Liu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Wen-Ge Li
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Wen-Zhu Zhang
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yuan Wu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jin-Xing Lu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
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79
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Andrés-Lasheras S, Martín-Burriel I, Mainar-Jaime RC, Morales M, Kuijper E, Blanco JL, Chirino-Trejo M, Bolea R. Preliminary studies on isolates of Clostridium difficile from dogs and exotic pets. BMC Vet Res 2018. [PMID: 29523201 PMCID: PMC5845233 DOI: 10.1186/s12917-018-1402-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Background Clostridium difficile infection (CDI) is recognised as an emerging disease in both humans and some animal species. During the past few years, insights into human CDI epidemiology changed and C. difficile is also considered as an emerging community-acquired pathogen. Certain ribotypes (RT) are possibly associated with zoonotic transmission. The objective of this study was to assess the presence of C. difficile in a population of pets and to characterise the isolates. Results Faecal samples from a total of 90 diarrhoeic dogs and 24 from exotic animal species (both diarrhoeic and non-diarrhoeic) were analysed. Clostridium difficile was isolated from 6 (6.7%) dogs and one reptile sample (4.2%). Four (66.7%) of the six dog strains were capable of producing toxins. Four known different RTs were detected in dogs (010, 014, 123 and 358) and a new one was found in a faecal sample of an exotic animal. This new RT isolate was negative for all toxin genes tested and belonged to sequence type 347 which has been proposed as a Clade-III member. Importantly, two dog strains showed a stable resistance to metronidazole (initial MIC values: 128 and 48 μg/ml). Conclusions The results obtained in this study suggest the implementation of antimicrobial susceptibility surveillance programs to assess the prevalence of metronidazole resistance in dogs; molecular studies to elucidate C. difficile metronidazole resistance mechanisms are warranted. Based on the similarity between the ribotypes observed in dogs and those described in humans, the zoonotic transmission should be further explored. Furthermore, exotic animals have shown to harbor uncommon C. difficile strains which require further genomic studies. Electronic supplementary material The online version of this article (10.1186/s12917-018-1402-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Sara Andrés-Lasheras
- Departamento de Patología Animal, Facultad de Veterinaria, Instituto Agroalimentario de Aragón - IA2 - (Universidad de Zaragoza-CITA), 50013, Zaragoza, Spain
| | - Inma Martín-Burriel
- Laboratorio de Genética Bioquímica (LAGENBIO), Facultad de Veterinaria, Instituto Agroalimentario de Aragón - IA2 - (Universidad de Zaragoza-CITA), Zaragoza, Spain
| | - Raúl Carlos Mainar-Jaime
- Departamento de Patología Animal, Facultad de Veterinaria, Instituto Agroalimentario de Aragón - IA2 - (Universidad de Zaragoza-CITA), 50013, Zaragoza, Spain
| | - Mariano Morales
- Departamento de Patología Animal, Facultad de Veterinaria, Instituto Agroalimentario de Aragón - IA2 - (Universidad de Zaragoza-CITA), 50013, Zaragoza, Spain.,Laboratorios Albéitar, Zaragoza, Spain
| | - Ed Kuijper
- Department of Medical Microbiology, Centre of Infectious Diseases, Leiden University Medical Centre, Leiden, The Netherlands
| | - José L Blanco
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense, Madrid, Spain
| | - Manuel Chirino-Trejo
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Canada
| | - Rosa Bolea
- Departamento de Patología Animal, Facultad de Veterinaria, Instituto Agroalimentario de Aragón - IA2 - (Universidad de Zaragoza-CITA), 50013, Zaragoza, Spain.
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80
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Liao F, Li W, Gu W, Zhang W, Liu X, Fu X, Xu W, Wu Y, Lu J. A retrospective study of community-acquired Clostridium difficile infection in southwest China. Sci Rep 2018; 8:3992. [PMID: 29507300 PMCID: PMC5838233 DOI: 10.1038/s41598-018-21762-7] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2017] [Accepted: 02/09/2018] [Indexed: 12/22/2022] Open
Abstract
To identify the prevalence and characteristics of community-acquired Clostridium difficile infection (CA-CDI) in southwest China, we conducted a cross-sectional study. 978 diarrhea patients were enrolled and stool specimens’ DNA was screened for virulence genes. Bacterial culture was performed and isolates were characterized by PCR ribotyping and multilocus sequence typing. Toxin genes tcdA and/or tcdB were found in 138/978 (14.11%) cases for fecal samples. A total of 55 C. difficile strains were isolated (5.62%). The positive rate of toxin genes and isolation results had no statistical significance between children and adults groups. However, some clinical features, such as fecal property, diarrhea times before hospital treatment shown difference between two groups. The watery stool was more likely found in children, while the blood stool for adults; most of children cases diarrhea ≤3 times before hospital treatment, and adults diarrhea >3 times. Independent risk factor associated with CA-CDI was patients with fever. ST35/RT046 (18.18%), ST54/RT012 (14.55%), ST3/RT001 (14.55%) and ST3/RT009 (12.73%) were the most distributed genotype profiles. ST35/RT046, ST3/RT001 and ST3/RT009 were the commonly found in children patients but ST54/RT012 for adults. The prevalence of CA-CDI in Yunnan province was relatively high, and isolates displayed heterogeneity between children and adults groups.
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Affiliation(s)
- Feng Liao
- Department of Respiratory Medicine, the First People's Hospital of Yunnan province, 650022, Kunming, China
| | - Wenge Li
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 102206, Beijing, China
| | - Wenpeng Gu
- Department of Acute Infectious Diseases Control and Prevention, Yunnan Provincial Centre for Disease Control and Prevention, 650022, Kunming, China
| | - Wenzhu Zhang
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 102206, Beijing, China
| | - Xiaoshu Liu
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 102206, Beijing, China
| | - Xiaoqing Fu
- Department of Acute Infectious Diseases Control and Prevention, Yunnan Provincial Centre for Disease Control and Prevention, 650022, Kunming, China
| | - Wen Xu
- Department of Acute Infectious Diseases Control and Prevention, Yunnan Provincial Centre for Disease Control and Prevention, 650022, Kunming, China
| | - Yuan Wu
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 102206, Beijing, China.
| | - Jinxing Lu
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, 102206, Beijing, China.
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81
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Moradigaravand D, Gouliouris T, Ludden C, Reuter S, Jamrozy D, Blane B, Naydenova P, Judge K, H. Aliyu S, F. Hadjirin N, A. Holmes M, Török E, M. Brown N, Parkhill J, Peacock S. Genomic survey of Clostridium difficile reservoirs in the East of England implicates environmental contamination of wastewater treatment plants by clinical lineages. Microb Genom 2018; 4:e000162. [PMID: 29498619 PMCID: PMC5885014 DOI: 10.1099/mgen.0.000162] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Accepted: 02/09/2018] [Indexed: 01/03/2023] Open
Abstract
There is growing evidence that patients with Clostridiumdifficile-associated diarrhoea often acquire their infecting strain before hospital admission. Wastewater is known to be a potential source of surface water that is contaminated with C. difficile spores. Here, we describe a study that used genome sequencing to compare C. difficile isolated from multiple wastewater treatment plants across the East of England and from patients with clinical disease at a major hospital in the same region. We confirmed that C. difficile from 65 patients were highly diverse and that most cases were not linked to other active cases in the hospital. In total, 186 C. difficile isolates were isolated from effluent water obtained from 18 municipal treatment plants at the point of release into the environment. Whole genome comparisons of clinical and environmental isolates demonstrated highly related populations, and confirmed extensive release of toxigenic C. difficile into surface waters. An analysis based on multilocus sequence types (STs) identified 19 distinct STs in the clinical collection and 38 STs in the wastewater collection, with 13 of 44 STs common to both clinical and wastewater collections. Furthermore, we identified five pairs of highly similar isolates (≤2 SNPs different in the core genome) in clinical and wastewater collections. Strategies to control community acquisition should consider the need for bacterial control of treated wastewater.
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Affiliation(s)
| | | | | | - Sandra Reuter
- University of Freiburg, Freiburg im Breisgau, Germany
| | | | | | | | - Kim Judge
- Wellcome Trust Sanger Institute, Hinxton, UK
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82
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Muñoz M, Ríos-Chaparro DI, Herrera G, Soto-De Leon SC, Birchenall C, Pinilla D, Pardo-Oviedo JM, Josa DF, Patarroyo MA, Ramírez JD. New Insights into Clostridium difficile (CD) Infection in Latin America: Novel Description of Toxigenic Profiles of Diarrhea-Associated to CD in Bogotá, Colombia. Front Microbiol 2018; 9:74. [PMID: 29441053 PMCID: PMC5797639 DOI: 10.3389/fmicb.2018.00074] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 01/11/2018] [Indexed: 12/18/2022] Open
Abstract
Clostridium difficile (CD) produces antibiotic associated diarrhea and leads to a broad range of diseases. The source of CD infection (CDI) acquisition and toxigenic profile are factors determining the impact of CD. This study aimed at detecting healthcare facility onset- (HCFO) and community-onset (CO) CDI and describing their toxigenic profiles in Bogotá, Colombia. A total of 217 fecal samples from patients suffering diarrhea were simultaneously submitted to two CDI detection strategies: (i) in vitro culture using selective chromogenic medium (SCM; chromID, bioMérieux), followed verification by colony screening (VCS), and (ii) molecular detection targeting constitutive genes, using two conventional PCR tests (conv.PCR) (conv.16S y conv.gdh) and a quantitative test (qPCR.16s). The CD toxigenic profile identified by any molecular test was described using 6 tests independently for describing PaLoc and CdtLoc organization. High overall CDI frequencies were found by both SCM (52.1%) and conv.PCR (45.6% for conv.16S and 42.4% for conv.gdh), compared to reductions of up to half the frequency by VCS (27.2%) or qPCR.16S (22.6%). Infection frequencies were higher for SCM and conv.16S regarding HCFO but greater for CO concerning conv.gdh, such differences being statistically significant. Heterogeneous toxigenic profiles were found, including amplification with lok1/3 primers simultaneously with other PaLoc markers (tcdA, tcdB or tcdC). These findings correspond the first report regarding the differential detection of CDI using in vitro culture and molecular detection tests in Colombia, the circulation of CD having heterogeneous toxigenic profiles and molecular arrays which could affect the impact of CDI epidemiology.
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Affiliation(s)
- Marina Muñoz
- Universidad del Rosario, Facultad de Ciencias Naturales y Matemáticas, Programa de Biología, Grupo de Investigaciones Microbiológicas-UR (GIMUR), Bogotá, Colombia.,Posgrado Interfacultades Doctorado en Biotecnología, Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Dora I Ríos-Chaparro
- Universidad del Rosario, Facultad de Ciencias Naturales y Matemáticas, Programa de Biología, Grupo de Investigaciones Microbiológicas-UR (GIMUR), Bogotá, Colombia
| | - Giovanny Herrera
- Universidad del Rosario, Facultad de Ciencias Naturales y Matemáticas, Programa de Biología, Grupo de Investigaciones Microbiológicas-UR (GIMUR), Bogotá, Colombia
| | - Sara C Soto-De Leon
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia, Bogotá, Colombia
| | | | - Darío Pinilla
- Hospital Universitario Mayor-Méderi, Bogotá, Colombia
| | | | | | - Manuel A Patarroyo
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia, Bogotá, Colombia.,Universidad del Rosario, School of Medicine and Health Sciences, Bogotá, Colombia
| | - Juan D Ramírez
- Universidad del Rosario, Facultad de Ciencias Naturales y Matemáticas, Programa de Biología, Grupo de Investigaciones Microbiológicas-UR (GIMUR), Bogotá, Colombia
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83
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Ramírez-Vargas G, Goh S, Rodríguez C. The Novel Phages phiCD5763 and phiCD2955 Represent Two Groups of Big Plasmidial Siphoviridae Phages of Clostridium difficile. Front Microbiol 2018; 9:26. [PMID: 29403466 PMCID: PMC5786514 DOI: 10.3389/fmicb.2018.00026] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2017] [Accepted: 01/08/2018] [Indexed: 12/27/2022] Open
Abstract
Until recently, Clostridium difficile phages were limited to Myoviruses and Siphoviruses of medium genome length (32–57 kb). Here we report the finding of phiCD5763, a Siphovirus with a large extrachromosomal circular genome (132.5 kb, 172 ORFs) and a large capsid (205.6 ± 25.6 nm in diameter) infecting MLST Clade 1 strains of C. difficile. Two subgroups of big phage genomes similar to phiCD5763 were identified in 32 NAPCR1/RT012/ST-54 C. difficile isolates from Costa Rica and in whole genome sequences (WGS) of 41 C. difficile isolates of Clades 1, 2, 3, and 4 from Canada, USA, UK, Belgium, Iraq, and China. Through comparative genomics we discovered another putative big phage genome in a non-NAPCR1 isolate from Costa Rica, phiCD2955, which represents other big phage genomes found in 130 WGS of MLST Clade 1 and 2 isolates from Canada, USA, Hungary, France, Austria, and UK. phiCD2955 (131.6 kb, 172 ORFs) is related to a previously reported C. difficile phage genome, phiCD211/phiCDIF1296T. Detailed genome analyses of phiCD5763, phiCD2955, phiCD211/phiCDIF1296T, and seven other putative C. difficile big phage genome sequences of 131–136 kb reconstructed from publicly available WGS revealed a modular gene organization and high levels of sequence heterogeneity at several hotspots, suggesting that these genomes correspond to biological entities undergoing recombination. Compared to other C. difficile phages, these big phages have unique predicted terminase, capsid, portal, neck and tail proteins, receptor binding proteins (RBPs), recombinases, resolvases, primases, helicases, ligases, and hypothetical proteins. Moreover, their predicted gene load suggests a complex regulation of both phage and host functions. Overall, our results indicate that the prevalence of C. difficile big bacteriophages is more widespread than realized and open new avenues of research aiming to decipher how these viral elements influence the biology of this emerging pathogen.
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Affiliation(s)
- Gabriel Ramírez-Vargas
- Facultad de Microbiología and Centro de Investigación en Enfermedades Tropicales, Universidad de Costa Rica, San José, Costa Rica
| | - Shan Goh
- Pathobiology and Population Studies, Royal Veterinary College, Hatfield, United Kingdom
| | - César Rodríguez
- Facultad de Microbiología and Centro de Investigación en Enfermedades Tropicales, Universidad de Costa Rica, San José, Costa Rica
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84
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High Prevalence and Genetic Diversity of Large phiCD211 (phiCDIF1296T)-Like Prophages in Clostridioides difficile. Appl Environ Microbiol 2018; 84:AEM.02164-17. [PMID: 29150513 DOI: 10.1128/aem.02164-17] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2017] [Accepted: 11/10/2017] [Indexed: 02/08/2023] Open
Abstract
Clostridioides difficile (formerly Clostridium difficile) is a pathogenic bacterium displaying great genetic diversity. A significant proportion of this diversity is due to the presence of integrated prophages. Here, we provide an in-depth analysis of phiCD211, also known as phiCDIF1296T, the largest phage identified in C. difficile so far, with a genome of 131 kbp. It shares morphological and genomic similarity with other large siphophages, like phage 949, infecting Lactococcus lactis, and phage c-st, infecting Clostridium botulinum A PhageTerm analysis indicated the presence of 378-bp direct terminal repeats at the phiCD211 genome termini. Among striking features of phiCD211, the presence of several transposase and integrase genes suggests past recombination events with other mobile genetic elements. Several gene products potentially influence the bacterial lifestyle and fitness, including a putative AcrB/AcrD/AcrF multidrug resistance protein, an EzrA septation ring formation regulator, and a spore protease. We also identified a CRISPR locus and a cas3 gene. We screened 2,584 C. difficile genomes available and detected 149 prophages sharing ≥80% nucleotide identity with phiCD211 (5% prevalence). Overall, phiCD211-like phages were detected in C. difficile strains corresponding to 21 different multilocus sequence type groups, showing their high prevalence. Comparative genomic analyses revealed the existence of several clusters of highly similar phiCD211-like phages. Of note, large chromosome inversions were observed in some members, as well as multiple gene insertions and module exchanges. This highlights the great plasticity and gene coding potential of the phiCD211/phiCDIF1296T genome. Our analyses also suggest active evolution involving recombination with other mobile genetic elements.IMPORTANCEClostridioides difficile is a clinically important pathogen representing a serious threat to human health. Our hypothesis is that genetic differences between strains caused by the presence of integrated prophages could explain the apparent differences observed in the virulence of different C. difficile strains. In this study, we provide a full characterization of phiCD211, also known as phiCDIF1296T, the largest phage known to infect C. difficile so far. Screening 2,584 C. difficile genomes revealed the presence of highly similar phiCD211-like phages in 5% of the strains analyzed, showing their high prevalence. Multiple-genome comparisons suggest that evolution of the phiCD211-like phage community is dynamic, and some members have acquired genes that could influence bacterial biology and fitness. Our study further supports the relevance of studying phages in C. difficile to better understand the epidemiology of this clinically important human pathogen.
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85
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Clostridium sordellii Pathogenicity Locus Plasmid pCS1-1 Encodes a Novel Clostridial Conjugation Locus. mBio 2018; 9:mBio.01761-17. [PMID: 29339424 PMCID: PMC5770547 DOI: 10.1128/mbio.01761-17] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
A major virulence factor in Clostridium sordellii-mediated infection is the toxin TcsL, which is encoded within a region of the genome called the pathogenicity locus (PaLoc). C. sordellii isolates carry the PaLoc on the pCS1 family of plasmids, of which there are four characterized members. Here, we determined the potential mobility of pCS1 plasmids and characterized a fifth unique pCS1 member. Using a derivative of the pCS1-1 plasmid from strain ATCC 9714 which had been marked with the ermB erythromycin resistance gene, conjugative transfer into a recipient C. sordellii isolate, R28058, was demonstrated. Bioinformatic analysis of pCS1-1 identified a novel conjugation gene cluster defined as the C. sordellii transfer (cst) locus. Interruption of genes within the cst locus resulted in loss of pCS1-1 transfer, which was restored upon complementation in trans. These studies provided clear evidence that genes within the cst locus are essential for the conjugative transfer of pCS1-1. The cst locus is present on all pCS1 subtypes, and homologous loci were identified on toxin-encoding plasmids from Clostridium perfringens and Clostridium botulinum and also carried within genomes of Clostridium difficile isolates, indicating that it is a widespread clostridial conjugation locus. The results of this study have broad implications for the dissemination of toxin genes and, potentially, antibiotic resistance genes among members of a diverse range of clostridial pathogens, providing these microorganisms with a survival advantage within the infected host. C. sordellii is a bacterial pathogen that causes severe infections in humans and animals, with high mortality rates. While the pathogenesis of C. sordellii infections is not well understood, it is known that the toxin TcsL is an important virulence factor. Here, we have shown the ability of a plasmid carrying the tcsL gene to undergo conjugative transfer between distantly related strains of C. sordellii, which has far-reaching implications for the ability of C. sordellii to acquire the capacity to cause disease. Plasmids that carry tcsL encode a previously uncharacterized conjugation locus, and individual genes within this locus were shown to be required for conjugative transfer. Furthermore, homologues on toxin plasmids from other clostridial species were identified, indicating that this region represents a novel clostridial conjugation locus. The results of this study have broad implications for the dissemination of virulence genes among members of a diverse range of clostridial pathogens.
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86
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Antibiotic Resistances of Clostridium difficile. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1050:137-159. [PMID: 29383668 DOI: 10.1007/978-3-319-72799-8_9] [Citation(s) in RCA: 36] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The rapid evolution of antibiotic resistance in Clostridium difficile and the consequent effects on prevention and treatment of C. difficile infections (CDIs) are matter of concern for public health. Antibiotic resistance plays an important role in driving C. difficile epidemiology. Emergence of new types is often associated with the emergence of new resistances and most of epidemic C. difficile clinical isolates is currently resistant to multiple antibiotics. In particular, it is to worth to note the recent identification of strains with reduced susceptibility to the first-line antibiotics for CDI treatment and/or for relapsing infections. Antibiotic resistance in C. difficile has a multifactorial nature. Acquisition of genetic elements and alterations of the antibiotic target sites, as well as other factors, such as variations in the metabolic pathways and biofilm production, contribute to the survival of this pathogen in the presence of antibiotics. Different transfer mechanisms facilitate the spread of mobile elements among C. difficile strains and between C. difficile and other species. Furthermore, recent data indicate that both genetic elements and alterations in the antibiotic targets can be maintained in C. difficile regardless of the burden imposed on fitness, and therefore resistances may persist in C. difficile population in absence of antibiotic selective pressure.
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87
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Comparative Genomics of Clostridium difficile. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1050:59-75. [PMID: 29383664 DOI: 10.1007/978-3-319-72799-8_5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Clostridium difficile, a gram-positive spore-forming anaerobic bacterium, has rapidly emerged as the leading cause of nosocomial diarrhoea in hospitals. The availability of genome sequences in large numbers, mainly due to the use of next-generation sequencing methods, have undoubtedly shown their immense advantages in the determination of the C. difficile population structure. The implementation of fine-scale comparative genomic approaches have paved the way to global transmission and recurrence studies, but also more targeted studies such as the PaLoc or the CRISPR/Cas systems. In this chapter, we provide an overview of the recent and significant findings on C. difficile using comparative genomics studies with implication for the epidemiology, infection control and understanding of the evolution of C. difficile.
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88
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Peng Z, Addisu A, Alrabaa S, Sun X. Antibiotic Resistance and Toxin Production of Clostridium difficile Isolates from the Hospitalized Patients in a Large Hospital in Florida. Front Microbiol 2017; 8:2584. [PMID: 29312258 PMCID: PMC5744170 DOI: 10.3389/fmicb.2017.02584] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2017] [Accepted: 12/12/2017] [Indexed: 12/15/2022] Open
Abstract
Clostridium difficile is an important cause of nosocomial acquired antibiotic-associated diarrhea causing an estimated 453,000 cases with 29,000 deaths yearly in the U.S. Both antibiotic resistance and toxin expression of C. difficile correlate with the severity of C. difficile infection (CDI). In this report, a total of 139 C. difficile isolates from patients diagnosed with CDI in Tampa General Hospital (Florida) in 2016 were studied for antibiotic resistance profiles of 12 types of antibiotics and toxin production. Antibiotic resistance determined by broth microdilution method showed that strains resistant to multi-antibiotics are common. Six strains (4.32%) showed resistance to six types of antibiotics. Twenty strains (14.39%) showed resistance to five types of antibiotics. Seventeen strains (12.24%) showed resistance to four types of antibiotics. Thirty-nine strains (28.06%) showed resistance to three types of antibiotic. Thirty-four strains (24.46%) showed resistance to two types of antibiotics. While, all isolates were susceptible to metronidazole, and rifaximin, we found that one isolate (0.72%) displayed resistance to vancomycin (MIC ≥ 8 μg/ml), and another one was resistant to fidaxomicin (MIC >1 μg/ml). The percentage of isolates resistant to cefoxitin, ceftriaxone, chloramphenicol, ampicillin, clindamycin, erythromycin, gatifloxacin, and moxifloxacin was 75.54, 10.79, 5.76, 67.63, 82.70, 45.32, 28.06, and 28.78%, respectively. Toxin profiling by PCR showed the isolates include 101 (72.66%) A+B+CDT-strains, 23 (16.55%) A+B+CDT+ strains, 3 (2.16%) A-B+CDT+ strains, 1 (0.72%) A-B+CDT-strains, and 11 (7.91%) A-B-CDT-strains. Toxin production determined by ELISA using supernatants of bacterial culture harvested at 12, 24, 48, and 72 h of post inoculation (hpi) showed that the toxins were mainly produced between 48 and 72 hpi, and toxin B (TcdB) was produced faster than toxin A (TcdA) during the experimental time (72 hpi). In addition, the binary-positive strains were likely to yield more toxins compared to the binary-negative strains. This work contributes to the current understanding of the antibiotic resistance and virulence of C. difficile clinical strains.
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Affiliation(s)
- Zhong Peng
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, United States.,State Key Laboratory of Agricultural Microbiology, College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Anteneh Addisu
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, United States
| | - Sally Alrabaa
- Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, United States
| | - Xingmin Sun
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, United States.,Department of Internal Medicine, Morsani College of Medicine, University of South Florida, Tampa, FL, United States
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89
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The Obscure World of Integrative and Mobilizable Elements, Highly Widespread Elements that Pirate Bacterial Conjugative Systems. Genes (Basel) 2017; 8:genes8110337. [PMID: 29165361 PMCID: PMC5704250 DOI: 10.3390/genes8110337] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2017] [Revised: 11/15/2017] [Accepted: 11/15/2017] [Indexed: 12/22/2022] Open
Abstract
Conjugation is a key mechanism of bacterial evolution that involves mobile genetic elements. Recent findings indicated that the main actors of conjugative transfer are not the well-known conjugative or mobilizable plasmids but are the integrated elements. This paper reviews current knowledge on “integrative and mobilizable elements” (IMEs) that have recently been shown to be highly diverse and highly widespread but are still rarely described. IMEs encode their own excision and integration and use the conjugation machinery of unrelated co-resident conjugative element for their own transfer. Recent studies revealed a much more complex and much more diverse lifecycle than initially thought. Besides their main transmission as integrated elements, IMEs probably use plasmid-like strategies to ensure their maintenance after excision. Their interaction with conjugative elements reveals not only harmless hitchhikers but also hunters that use conjugative elements as target for their integration or harmful parasites that subvert the conjugative apparatus of incoming elements to invade cells that harbor them. IMEs carry genes conferring various functions, such as resistance to antibiotics, that can enhance the fitness of their hosts and that contribute to their maintenance in bacterial populations. Taken as a whole, IMEs are probably major contributors to bacterial evolution.
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90
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Martín-Burriel I, Andrés-Lasheras S, Harders F, Mainar-Jaime RC, Ranera B, Zaragoza P, Falceto V, Bolea Y, Kuijper E, Bolea R, Bossers A, Chirino-Trejo M. Molecular analysis of three Clostridium difficile strain genomes isolated from pig farm-related samples. Anaerobe 2017; 48:224-231. [PMID: 28928035 DOI: 10.1016/j.anaerobe.2017.09.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2017] [Revised: 08/08/2017] [Accepted: 09/14/2017] [Indexed: 02/08/2023]
Abstract
Clostridium difficile is an anaerobic spore-forming bacillus that usually causes gastrointestinal disorders in man and other animal species. Most of the strains isolated from animals are toxigenic being the virulent ribotype (RT) 078 predominant in several animal species. Although C. difficile is pathogenic to both humans and animals, there is no direct evidence of zoonosis. Deep genome sequencing provides sufficient resolution to analyse which strains found in animals might be related to human pathogens. So far, there are only a few fully sequenced genomes of C. difficile strains isolated from domestic and wild animals. Using Illumina technology, we have sequenced the genome of three isolates; a strain isolated from the vagina of a sow (5754), one from rat (Rattus spp) intestinal content (RC10) and a third one isolated from environmental rat faeces (RF17). Both, rat and rat faeces were sampled in fattening pig farms. Our study reveals a close genetic relationship of two of these isolates with the virulent strain M120 (RT078) isolated from a human patient. The analysis of the sequences has revealed the presence of antibiotic resistance genes, mobile elements, including the transposon linked with virulence Tn6164, and the similarity of virulence factors between these isolates and human strains. This is the first study focused on the sequencing of C. difficile genomes obtained from wild animals like rats, which can be considered as potential reservoirs for humans and other animal species. This study can help to understand the genome composition and epidemiology of this bacterium species.
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Affiliation(s)
- I Martín-Burriel
- Laboratorio de Genética Bioquímica (LAGENBIO), Facultad de Veterinaria, Instituto Agroalimentario de Aragón - IA2 - (Universidad de Zaragoza-CITA), Zaragoza, Spain.
| | - S Andrés-Lasheras
- Departamento de Patología Animal, Facultad de Veterinaria, Instituto Agroalimentario de Aragón - IA2 - (Universidad de Zaragoza-CITA), Zaragoza, Spain
| | - F Harders
- Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - R C Mainar-Jaime
- Departamento de Patología Animal, Facultad de Veterinaria, Instituto Agroalimentario de Aragón - IA2 - (Universidad de Zaragoza-CITA), Zaragoza, Spain
| | - B Ranera
- Laboratorio de Genética Bioquímica (LAGENBIO), Facultad de Veterinaria, Instituto Agroalimentario de Aragón - IA2 - (Universidad de Zaragoza-CITA), Zaragoza, Spain
| | - P Zaragoza
- Laboratorio de Genética Bioquímica (LAGENBIO), Facultad de Veterinaria, Instituto Agroalimentario de Aragón - IA2 - (Universidad de Zaragoza-CITA), Zaragoza, Spain
| | - V Falceto
- Departamento de Patología Animal, Facultad de Veterinaria, Instituto Agroalimentario de Aragón - IA2 - (Universidad de Zaragoza-CITA), Zaragoza, Spain
| | - Y Bolea
- Departamento de Patología Animal, Facultad de Veterinaria, Instituto Agroalimentario de Aragón - IA2 - (Universidad de Zaragoza-CITA), Zaragoza, Spain
| | - E Kuijper
- Department of Medical Microbiology, Centre of Infectious Diseases, Leiden University Medical Centre, Leiden, The Netherlands
| | - R Bolea
- Departamento de Patología Animal, Facultad de Veterinaria, Instituto Agroalimentario de Aragón - IA2 - (Universidad de Zaragoza-CITA), Zaragoza, Spain
| | - A Bossers
- Wageningen Bioveterinary Research, Lelystad, The Netherlands
| | - M Chirino-Trejo
- Department of Veterinary Microbiology, Western College of Veterinary Medicine, University of Saskatchewan, Saskatoon, Canada
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91
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Pathogenicity Locus, Core Genome, and Accessory Gene Contributions to Clostridium difficile Virulence. mBio 2017; 8:mBio.00885-17. [PMID: 28790208 PMCID: PMC5550754 DOI: 10.1128/mbio.00885-17] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Clostridium difficile is a spore-forming anaerobic bacterium that causes colitis in patients with disrupted colonic microbiota. While some individuals are asymptomatic C. difficile carriers, symptomatic disease ranges from mild diarrhea to potentially lethal toxic megacolon. The wide disease spectrum has been attributed to the infected host’s age, underlying diseases, immune status, and microbiome composition. However, strain-specific differences in C. difficile virulence have also been implicated in determining colitis severity. Because patients infected with C. difficile are unique in terms of medical history, microbiome composition, and immune competence, determining the relative contribution of C. difficile virulence to disease severity has been challenging, and conclusions regarding the virulence of specific strains have been inconsistent. To address this, we used a mouse model to test 33 clinical C. difficile strains isolated from patients with disease severities ranging from asymptomatic carriage to severe colitis, and we determined their relative in vivo virulence in genetically identical, antibiotic-pretreated mice. We found that murine infections with C. difficile clade 2 strains (including multilocus sequence type 1/ribotype 027) were associated with higher lethality and that C. difficile strains associated with greater human disease severity caused more severe disease in mice. While toxin production was not strongly correlated with in vivo colonic pathology, the ability of C. difficile strains to grow in the presence of secondary bile acids was associated with greater disease severity. Whole-genome sequencing and identification of core and accessory genes identified a subset of accessory genes that distinguish high-virulence from lower-virulence C. difficile strains. Clostridium difficile is an important cause of hospital-associated intestinal infections, and recent years have seen an increase in the number and severity of cases in the United States. A patient’s antibiotic history, immune status, and medical comorbidities determine, in part, the severity of C. difficile infection. The relative virulence of different clinical C. difficile strains, although postulated to determine disease severity in patients, has been more difficult to consistently associate with mild versus severe colitis. We tested 33 distinct clinical C. difficile isolates for their ability to cause disease in genetically identical mice and found that C. difficile strains belonging to clade 2 were associated with higher mortality. Differences in survival were not attributed to differences in toxin production but likely resulted from the distinct gene content in the various clinical isolates.
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92
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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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93
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Riedel T, Wetzel D, Hofmann JD, Plorin SPEO, Dannheim H, Berges M, Zimmermann O, Bunk B, Schober I, Spröer C, Liesegang H, Jahn D, Overmann J, Groß U, Neumann-Schaal M. High metabolic versatility of different toxigenic and non-toxigenic Clostridioides difficile isolates. Int J Med Microbiol 2017; 307:311-320. [PMID: 28619474 DOI: 10.1016/j.ijmm.2017.05.007] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 05/22/2017] [Accepted: 05/28/2017] [Indexed: 12/14/2022] Open
Abstract
Clostridioides difficile (formerly Clostridium difficile) is a major nosocomial pathogen with an increasing number of community-acquired infections causing symptoms from mild diarrhea to life-threatening colitis. The pathogenicity of C. difficile is considered to be mainly associated with the production of genome-encoded toxins A and B. In addition, some strains also encode and express the binary toxin CDT. However; a large number of non-toxigenic C. difficile strains have been isolated from the human gut and the environment. In this study, we characterized the growth behavior, motility and fermentation product formation of 17 different C. difficile isolates comprising five different major genomic clades and five different toxin inventories in relation to the C. difficile model strains 630Δerm and R20291. Within 33 determined fermentation products, we identified two yet undescribed products (5-methylhexanoate and 4-(methylthio)-butanoate) of C. difficile. Our data revealed major differences in the fermentation products obtained after growth in a medium containing casamino acids and glucose as carbon and energy source. While the metabolism of branched chain amino acids remained comparable in all isolates, the aromatic amino acid uptake and metabolism and the central carbon metabolism-associated fermentation pathways varied strongly between the isolates. The patterns obtained followed neither the classification of the clades nor the ribotyping patterns nor the toxin distribution. As the toxin formation is strongly connected to the metabolism, our data allow an improved differentiation of C. difficile strains. The observed metabolic flexibility provides the optimal basis for the adaption in the course of infection and to changing conditions in different environments including the human gut.
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Affiliation(s)
- Thomas Riedel
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Daniela Wetzel
- University Medical Center Göttingen, Institute of Medical Microbiology, Kreuzbergring 57, 37075 Göttingen, Germany
| | - Julia Danielle Hofmann
- Technische Universität Braunschweig, Department of Bioinformatics and Biochemistry, Rebenring 56, 38106 Braunschweig, Germany; Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany
| | - Simon Paul Erich Otto Plorin
- University Medical Center Göttingen, Institute of Medical Microbiology, Kreuzbergring 57, 37075 Göttingen, Germany
| | - Henning Dannheim
- Technische Universität Braunschweig, Department of Bioinformatics and Biochemistry, Rebenring 56, 38106 Braunschweig, Germany; Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany
| | - Mareike Berges
- Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany; Technische Universität Braunschweig, Department of Microbiology, Rebenring 56, 38106 Braunschweig, Germany
| | - Ortrud Zimmermann
- University Medical Center Göttingen, Institute of Medical Microbiology, Kreuzbergring 57, 37075 Göttingen, Germany
| | - Boyke Bunk
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany; German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Isabel Schober
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Cathrin Spröer
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany; German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Heiko Liesegang
- Department of Genomic and Applied Microbiology and Göttingen Genomics Laboratory, Georg-August-University Göttingen, Grisebachstraße 8, 37077 Göttingen, Germany
| | - Dieter Jahn
- Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany; Technische Universität Braunschweig, Department of Microbiology, Rebenring 56, 38106 Braunschweig, Germany
| | - Jörg Overmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Inhoffenstraße 7B, 38124 Braunschweig, Germany; Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany; German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Inhoffenstraße 7B, 38124 Braunschweig, Germany
| | - Uwe Groß
- University Medical Center Göttingen, Institute of Medical Microbiology, Kreuzbergring 57, 37075 Göttingen, Germany; Göttingen International Health Network, Göttingen, Germany
| | - Meina Neumann-Schaal
- Technische Universität Braunschweig, Department of Bioinformatics and Biochemistry, Rebenring 56, 38106 Braunschweig, Germany; Braunschweig Integrated Centre of Systems Biology (BRICS), Braunschweig, Germany.
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94
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Update on Antimicrobial Resistance in Clostridium difficile: Resistance Mechanisms and Antimicrobial Susceptibility Testing. J Clin Microbiol 2017; 55:1998-2008. [PMID: 28404671 DOI: 10.1128/jcm.02250-16] [Citation(s) in RCA: 164] [Impact Index Per Article: 23.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Oral antibiotics such as metronidazole, vancomycin and fidaxomicin are therapies of choice for Clostridium difficile infection. Several important mechanisms for C. difficile antibiotic resistance have been described, including the acquisition of antibiotic resistance genes via the transfer of mobile genetic elements, selective pressure in vivo resulting in gene mutations, altered expression of redox-active proteins, iron metabolism, and DNA repair, as well as via biofilm formation. This update summarizes new information published since 2010 on phenotypic and genotypic resistance mechanisms in C. difficile and addresses susceptibility test methods and other strategies to counter antibiotic resistance of C. difficile.
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95
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Elliott B, Androga GO, Knight DR, Riley TV. Clostridium difficile infection: Evolution, phylogeny and molecular epidemiology. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2017; 49:1-11. [PMID: 28012982 DOI: 10.1016/j.meegid.2016.12.018] [Citation(s) in RCA: 63] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2016] [Revised: 12/19/2016] [Accepted: 12/19/2016] [Indexed: 02/07/2023]
Abstract
Over the recent decades, Clostridium difficile infection (CDI) has emerged as a global public health threat. Despite growing attention, C. difficile remains a poorly understood pathogen, however, the exquisite sensitivity offered by next generation sequencing (NGS) technology has enabled analysis of the genome of C. difficile, giving us access to massive genomic data on factors such as virulence, evolution, and genetic relatedness within C. difficile groups. NGS has also demonstrated excellence in investigations of outbreaks and disease transmission, in both small and large-scale applications. This review summarizes the molecular epidemiology, evolution, and phylogeny of C. difficile, one of the most important pathogens worldwide in the current antibiotic resistance era.
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Affiliation(s)
- Briony Elliott
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Australia
| | - Grace O Androga
- School of Pathology and Laboratory Medicine, The University of Western Australia, Crawley, Australia
| | - Daniel R Knight
- School of Pathology and Laboratory Medicine, The University of Western Australia, Crawley, Australia
| | - Thomas V Riley
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Australia; School of Pathology and Laboratory Medicine, The University of Western Australia, Crawley, Australia; School of Veterinary and Life Sciences, Murdoch University, Murdoch, Australia; Department of Microbiology, PathWest Laboratory Medicine, Perth, Australia.
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96
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A Clostridium difficile Lineage Endemic to Costa Rican Hospitals Is Multidrug Resistant by Acquisition of Chromosomal Mutations and Novel Mobile Genetic Elements. Antimicrob Agents Chemother 2017; 61:AAC.02054-16. [PMID: 28137804 DOI: 10.1128/aac.02054-16] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2016] [Accepted: 01/17/2017] [Indexed: 12/28/2022] Open
Abstract
The antimicrobial resistance (AMR) rates and levels recorded for Clostridium difficile are on the rise. This study reports the nature, levels, diversity, and genomic context of the antimicrobial resistance of human C. difficile isolates of the NAPCR1/RT012/ST54 genotype, which caused an outbreak in 2009 and is endemic in Costa Rican hospitals. To this end, we determined the susceptibilities of 38 NAPCR1 isolates to 10 antibiotics from seven classes using Etests or macrodilution tests and examined 31 NAPCR1 whole-genome sequences to identify single nucleotide polymorphisms (SNPs) and genes that could explain the resistance phenotypes observed. The NAPCR1 isolates were multidrug resistant (MDR) and commonly exhibited very high resistance levels. By sequencing their genomes, we showed that they possessed resistance-associated SNPs in gyrA and rpoB and carried eight to nine acquired antimicrobial resistance (AMR) genes. Most of these genes were located on known or novel mobile genetic elements shared by isolates recovered at different hospitals and at different time points. Metronidazole and vancomycin remain the first-line treatment options for these isolates. Overall, the NAPCR1 lineage showed an enhanced ability to acquire AMR genes through lateral gene transfer. On the basis of this finding, we recommend further vigilance and the adoption of improved control measures to limit the dissemination of this lineage and the emergence of more C. difficile MDR strains.
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97
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Muñoz M, Ríos-Chaparro DI, Patarroyo MA, Ramírez JD. Determining Clostridium difficile intra-taxa diversity by mining multilocus sequence typing databases. BMC Microbiol 2017; 17:62. [PMID: 28288567 PMCID: PMC5348806 DOI: 10.1186/s12866-017-0969-7] [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] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Accepted: 03/03/2017] [Indexed: 12/18/2022] Open
Abstract
Background Multilocus sequence typing (MLST) is a highly discriminatory typing strategy; it is reproducible and scalable. There is a MLST scheme for Clostridium difficile (CD), a gram positive bacillus causing different pathologies of the gastrointestinal tract. This work was aimed at describing the frequency of sequence types (STs) and Clades (C) reported and evalute the intra-taxa diversity in the CD MLST database (CD-MLST-db) using an MLSA approach. Results Analysis of 1778 available isolates showed that clade 1 (C1) was the most frequent worldwide (57.7%), followed by C2 (29.1%). Regarding sequence types (STs), it was found that ST-1, belonging to C2, was the most frequent. The isolates analysed came from 17 countries, mostly from the United Kingdom (UK) (1541 STs, 87.0%). The diversity of the seven housekeeping genes in the MLST scheme was evaluated, and alleles from the profiles (STs), for identifying CD population structure. It was found that adk and atpA are conserved genes allowing a limited amount of clusters to be discriminated; however, different genes such as drx, glyA and particularly sodA showed high diversity indexes and grouped CD populations in many clusters, suggesting that these genes’ contribution to CD typing should be revised. It was identified that CD STs reported to date have a mostly clonal population structure with foreseen events of recombination; however, one group of STs was not assigned to a clade being highly different containing at least nine well-supported clusters, suggesting a greater amount of clades for CD. Conclusions This study shows the usefulness of CD-MLST-db as a tool for studying CD distribution and population structure, identifying the need for reviewing the usefulness of sodA as housekeeping gene within the MLST scheme and suggesting the existence of a greater amount of CD clades. The study also shows the plausible exchange of genetic material between STs, contributing towards intra-taxa genetic diversity. Electronic supplementary material The online version of this article (doi:10.1186/s12866-017-0969-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Marina Muñoz
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Programa de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Carrera 24 # 63C - 69, Bogotá, Colombia.,Posgrado Interfacultades Doctorado en Biotecnología, Facultad de Ciencias, Universidad Nacional de Colombia, Bogotá, Colombia
| | - Dora Inés Ríos-Chaparro
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Programa de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Carrera 24 # 63C - 69, Bogotá, Colombia
| | - Manuel Alfonso Patarroyo
- Molecular Biology and Immunology Department, Fundación Instituto de Inmunología de Colombia (FIDIC), Bogotá, Colombia.,School of Medicine and Health Sciences, Universidad del Rosario, Bogotá, Colombia
| | - Juan David Ramírez
- Grupo de Investigaciones Microbiológicas-UR (GIMUR), Programa de Biología, Facultad de Ciencias Naturales y Matemáticas, Universidad del Rosario, Carrera 24 # 63C - 69, Bogotá, Colombia.
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98
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Whole genome sequences of three Clade 3 Clostridium difficile strains carrying binary toxin genes in China. Sci Rep 2017; 7:43555. [PMID: 28262711 PMCID: PMC5337907 DOI: 10.1038/srep43555] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Accepted: 01/25/2017] [Indexed: 02/05/2023] Open
Abstract
Clostridium difficile consists of six clades but studies on Clade 3 are limited. Here, we report genome sequences of three Clade 3 C. difficile strains carrying genes encoding toxin A and B and the binary toxin. Isolates 103 and 133 (both of ST5) and isolate 106 (ST285) were recovered from three ICU patients. Whole genome sequencing using HiSeq 2500 revealed 4.1-Mb genomes with 28–29% GC content. There were ≥1,104 SNP between the isolates, suggesting they were not of a single clone. The toxin A and B gene-carrying pathogenicity locus (PaLoc) of the three isolates were identical and had the insertion of the transposon Tn6218. The genetic components of PaLoc among Clade 3 strains were the same with only a few nucleotide mutations and deletions/insertions, suggesting that the Tn6218 insertion might have occurred before the divergence within Clade 3. The binary toxin-genes carrying CDT locus (CdtLoc) of the three isolates were identical and were highly similar to those of other Clade 3 strains, but were more divergent from those of other clades. In conclusion, Clade 3 has an unusual clade-specific PaLoc characteristic of a Tn6218 insertion which appears to be the main feature to distinguish Clade 3 from other C. difficile.
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99
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Evolutionary clade affects resistance of Clostridium difficile spores to Cold Atmospheric Plasma. Sci Rep 2017; 7:41814. [PMID: 28155914 PMCID: PMC5290531 DOI: 10.1038/srep41814] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Accepted: 12/30/2016] [Indexed: 12/18/2022] Open
Abstract
Clostridium difficile is a spore forming bacterium and the leading cause of colitis and antibiotic associated diarrhoea in the developed world. Spores produced by C. difficile are robust and can remain viable for months, leading to prolonged healthcare-associated outbreaks with high mortality. Exposure of C. difficile spores to a novel, non-thermal atmospheric pressure gas plasma was assessed. Factors affecting sporicidal efficacy, including percentage of oxygen in the helium carrier gas admixture, and the effect on spores from different strains representing the five evolutionary C. difficile clades was investigated. Strains from different clades displayed varying resistance to cold plasma. Strain R20291, representing the globally epidemic ribotype 027 type, was the most resistant. However all tested strains displayed a ~3 log reduction in viable spore counts after plasma treatment for 5 minutes. Inactivation of a ribotype 078 strain, the most prevalent clinical type seen in Northern Ireland, was further assessed with respect to surface decontamination, pH, and hydrogen peroxide concentration. Environmental factors affected plasma activity, with dry spores without the presence of organic matter being most susceptible. This study demonstrates that cold atmospheric plasma can effectively inactivate C. difficile spores, and highlights factors that can affect sporicidal activity.
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100
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Dingle KE, Didelot X, Quan TP, Eyre DW, Stoesser N, Golubchik T, Harding RM, Wilson DJ, Griffiths D, Vaughan A, Finney JM, Wyllie DH, Oakley SJ, Fawley WN, Freeman J, Morris K, Martin J, Howard P, Gorbach S, Goldstein EJC, Citron DM, Hopkins S, Hope R, Johnson AP, Wilcox MH, Peto TEA, Walker AS, Crook DW. Effects of control interventions on Clostridium difficile infection in England: an observational study. THE LANCET. INFECTIOUS DISEASES 2017; 17:411-421. [PMID: 28130063 PMCID: PMC5368411 DOI: 10.1016/s1473-3099(16)30514-x] [Citation(s) in RCA: 218] [Impact Index Per Article: 31.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Revised: 11/09/2016] [Accepted: 11/11/2016] [Indexed: 01/02/2023]
Abstract
BACKGROUND The control of Clostridium difficile infections is an international clinical challenge. The incidence of C difficile in England declined by roughly 80% after 2006, following the implementation of national control policies; we tested two hypotheses to investigate their role in this decline. First, if C difficile infection declines in England were driven by reductions in use of particular antibiotics, then incidence of C difficile infections caused by resistant isolates should decline faster than that caused by susceptible isolates across multiple genotypes. Second, if C difficile infection declines were driven by improvements in hospital infection control, then transmitted (secondary) cases should decline regardless of susceptibility. METHODS Regional (Oxfordshire and Leeds, UK) and national data for the incidence of C difficile infections and antimicrobial prescribing data (1998-2014) were combined with whole genome sequences from 4045 national and international C difficile isolates. Genotype (multilocus sequence type) and fluoroquinolone susceptibility were determined from whole genome sequences. The incidence of C difficile infections caused by fluoroquinolone-resistant and fluoroquinolone-susceptible isolates was estimated with negative-binomial regression, overall and per genotype. Selection and transmission were investigated with phylogenetic analyses. FINDINGS National fluoroquinolone and cephalosporin prescribing correlated highly with incidence of C difficile infections (cross-correlations >0·88), by contrast with total antibiotic prescribing (cross-correlations <0·59). Regionally, C difficile decline was driven by elimination of fluoroquinolone-resistant isolates (approximately 67% of Oxfordshire infections in September, 2006, falling to approximately 3% in February, 2013; annual incidence rate ratio 0·52, 95% CI 0·48-0·56 vs fluoroquinolone-susceptible isolates: 1·02, 0·97-1·08). C difficile infections caused by fluoroquinolone-resistant isolates declined in four distinct genotypes (p<0·01). The regions of phylogenies containing fluoroquinolone-resistant isolates were short-branched and geographically structured, consistent with selection and rapid transmission. The importance of fluoroquinolone restriction over infection control was shown by significant declines in inferred secondary (transmitted) cases caused by fluoroquinolone-resistant isolates with or without hospital contact (p<0·0001) versus no change in either group of cases caused by fluoroquinolone-susceptible isolates (p>0·2). INTERPRETATION Restricting fluoroquinolone prescribing appears to explain the decline in incidence of C difficile infections, above other measures, in Oxfordshire and Leeds, England. Antimicrobial stewardship should be a central component of C difficile infection control programmes. FUNDING UK Clinical Research Collaboration (Medical Research Council, Wellcome Trust, National Institute for Health Research); NIHR Oxford Biomedical Research Centre; NIHR Health Protection Research Unit on Healthcare Associated Infection and Antimicrobial Resistance (Oxford University in partnership with Public Health England [PHE]), and on Modelling Methodology (Imperial College, London in partnership with PHE); and the Health Innovation Challenge Fund.
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Affiliation(s)
- Kate E Dingle
- Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK; National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK; NIHR Health Protection Research Unit in Healthcare Associated Infection and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford, UK.
| | - Xavier Didelot
- Department of Infectious Disease Epidemiology, and NIHR Health Protection Research Unit in Healthcare Associated Infection and Antimicrobial Resistance at Imperial College London in partnership with Public Health England, Imperial College, London, London, UK
| | - T Phuong Quan
- Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK; National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK; NIHR Health Protection Research Unit in Healthcare Associated Infection and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford, UK
| | - David W Eyre
- Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK; National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
| | - Nicole Stoesser
- Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK; National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
| | - Tanya Golubchik
- Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK; National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
| | - Rosalind M Harding
- National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK; Department of Zoology, Oxford University, Oxford, UK
| | - Daniel J Wilson
- Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK; National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK; Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK
| | - David Griffiths
- Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK; National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
| | - Alison Vaughan
- Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK; National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
| | - John M Finney
- Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK; National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK
| | - David H Wyllie
- Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK; National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK; Public Health England Academic Collaborating Centre, Oxford, UK
| | - Sarah J Oakley
- Microbiology Department, Oxford University Hospitals NHS Trust, Oxford, UK
| | - Warren N Fawley
- Leeds Teaching Hospitals and University of Leeds, Department of Microbiology, Leeds General Infirmary, Leeds, UK
| | - Jane Freeman
- Leeds Teaching Hospitals and University of Leeds, Department of Microbiology, Leeds General Infirmary, Leeds, UK
| | - Kirsti Morris
- Leeds Teaching Hospitals and University of Leeds, Department of Microbiology, Leeds General Infirmary, Leeds, UK
| | - Jessica Martin
- Leeds Teaching Hospitals and University of Leeds, Department of Microbiology, Leeds General Infirmary, Leeds, UK
| | | | - Sherwood Gorbach
- Cubist Pharmaceuticals, Lexington, MA, USA; Tufts University School of Medicine, Boston, MA, USA
| | | | | | - Susan Hopkins
- NIHR Health Protection Research Unit in Healthcare Associated Infection and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford, UK; Healthcare-Associated Infection, Antimicrobial Resistance and Stewardship and Healthcare-Associated Infections Programme, Public Health England, London, UK; Royal Free London NHS Foundation Trust and Public Health England, London, UK
| | - Russell Hope
- Department of Healthcare-Associated Infections and Antimicrobial Resistance, Centre for Infectious Disease Surveillance and Control, National Infection Service, Public Health England, London, UK
| | - Alan P Johnson
- NIHR Health Protection Research Unit in Healthcare Associated Infection and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford, UK; Department of Infectious Disease Epidemiology, and NIHR Health Protection Research Unit in Healthcare Associated Infection and Antimicrobial Resistance at Imperial College London in partnership with Public Health England, Imperial College, London, London, UK; Department of Healthcare-Associated Infections and Antimicrobial Resistance, Centre for Infectious Disease Surveillance and Control, National Infection Service, Public Health England, London, UK
| | - Mark H Wilcox
- Leeds Teaching Hospitals and University of Leeds, Department of Microbiology, Leeds General Infirmary, Leeds, UK
| | - Timothy E A Peto
- Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK; National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK; NIHR Health Protection Research Unit in Healthcare Associated Infection and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford, UK
| | - A Sarah Walker
- Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK; National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK; NIHR Health Protection Research Unit in Healthcare Associated Infection and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford, UK
| | - Derrick W Crook
- Nuffield Department of Clinical Medicine, Oxford University, Oxford, UK; National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, UK; NIHR Health Protection Research Unit in Healthcare Associated Infection and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford, UK
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