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Janezic S, Garneau JR, Monot M. Comparative Genomics of Clostridioides difficile. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1435:199-218. [PMID: 38175477 DOI: 10.1007/978-3-031-42108-2_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Clostridioides difficile, a Gram-positive spore-forming anaerobic bacterium, has rapidly emerged as the leading cause of nosocomial diarrhoea in hospitals. The availability of large numbers of genome sequences, mainly due to the use of next-generation sequencing methods, has undoubtedly shown their immense advantages in the determination of C. difficile population structure. The implementation of fine-scale comparative genomic approaches has paved the way for global transmission and recurrence studies, as well as more targeted studies, such as the PaLoc or CRISPR/Cas systems. In this chapter, we provide an overview of recent and significant findings on C. difficile using comparative genomic studies with implications for epidemiology, infection control and understanding of the evolution of C. difficile.
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Affiliation(s)
- Sandra Janezic
- National Laboratory for Health, Environment and Food (NLZOH), Maribor, Slovenia.
- Faculty of Medicine, University of Maribor, Maribor, Slovenia.
| | - Julian R Garneau
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Marc Monot
- Institut Pasteur, Université Paris Cité, Plate-forme Technologique Biomics, Paris, France
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2
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Abad-Fau A, Sevilla E, Martín-Burriel I, Moreno B, Bolea R. Update on Commonly Used Molecular Typing Methods for Clostridioides difficile. Microorganisms 2023; 11:1752. [PMID: 37512924 PMCID: PMC10384772 DOI: 10.3390/microorganisms11071752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 06/26/2023] [Accepted: 07/01/2023] [Indexed: 07/30/2023] Open
Abstract
This review aims to provide a comprehensive overview of the significant Clostridioides difficile molecular typing techniques currently employed in research and medical communities. The main objectives of this review are to describe the key molecular typing methods utilized in C. difficile studies and to highlight the epidemiological characteristics of the most prevalent strains on a global scale. Geographically distinct regions exhibit distinct strain types of C. difficile, with notable concordance observed among various typing methodologies. The advantages that next-generation sequencing (NGS) offers has changed epidemiology research, enabling high-resolution genomic analyses of this pathogen. NGS platforms offer an unprecedented opportunity to explore the genetic intricacies and evolutionary trajectories of C. difficile strains. It is relevant to acknowledge that novel routes of transmission are continually being unveiled and warrant further investigation, particularly in the context of zoonotic implications and environmental contamination.
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Affiliation(s)
- Ana Abad-Fau
- Departamento de Patología Animal, Facultad de Veterinaria, Instituto Agroalimentario de Aragon-IA2-(Universidad de Zaragoza-CITA), 50013 Zaragoza, Spain
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes, Facultad de Veterinaria, Universidad de Zaragoza, 50013 Zaragoza, Spain
| | - Eloísa Sevilla
- Departamento de Patología Animal, Facultad de Veterinaria, Instituto Agroalimentario de Aragon-IA2-(Universidad de Zaragoza-CITA), 50013 Zaragoza, Spain
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes, Facultad de Veterinaria, Universidad de Zaragoza, 50013 Zaragoza, Spain
| | - Inmaculada Martín-Burriel
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes, Facultad de Veterinaria, Universidad de Zaragoza, 50013 Zaragoza, Spain
- Laboratorio de Genética Bioquímica, Facultad de Veterinaria, Instituto Agroalimentario de Aragon-IA2-(Universidad de Zaragoza-CITA), 50013 Zaragoza, Spain
| | - Bernardino Moreno
- Departamento de Patología Animal, Facultad de Veterinaria, Instituto Agroalimentario de Aragon-IA2-(Universidad de Zaragoza-CITA), 50013 Zaragoza, Spain
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes, Facultad de Veterinaria, Universidad de Zaragoza, 50013 Zaragoza, Spain
| | - Rosa Bolea
- Departamento de Patología Animal, Facultad de Veterinaria, Instituto Agroalimentario de Aragon-IA2-(Universidad de Zaragoza-CITA), 50013 Zaragoza, Spain
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes, Facultad de Veterinaria, Universidad de Zaragoza, 50013 Zaragoza, Spain
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Kim J, Kim B, Pai H. Diversity of binary toxin positive Clostridioides difficile in Korea. Sci Rep 2023; 13:576. [PMID: 36631661 PMCID: PMC9834304 DOI: 10.1038/s41598-023-27768-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 01/06/2023] [Indexed: 01/13/2023] Open
Abstract
The objective of this study is to determine the trend and diversity of binary toxin-positive Clostridioides difficile over 10 years in Korea. Binary toxin-positive strains were selected from a tertiary hospital in Korea in 2009-2018. The multi-locus sequence typing and antibiotic susceptibility test were performed. Among the 3278 isolates in 2009-2018, 58 possessed binary toxin genes (1.7%). The proportion of CDT- positive isolates was 0.51-4.82% in 2009-2018, which increased over the 10-year period (P = 0.023). Thirteen sequence types (STs) were identified; ST5 (14 [24%]), ST11 (11 [19%]), ST221 (10 [17%]), ST201 (7 [12%]) and ST1 (5 [9%]) were popular. All 58 isolates were susceptible to vancomycin and piperacillin/tazobactam, and clindamycin and moxifloxacin were active in 69.0% and 62% of isolates, respectively. ST1 strains were resistant to several antibiotics, including moxifloxacin (80%), clindamycin (60%) and rifaximin (60%). Moreover, four of five ST1 presented a metronidazole minimum inhibitory concentration of 4 µg/mL. Moxifloxacin resistance was highest (72.3%) for ST11. In conclusion, binary toxin-positive strains are non-prevalent in Korea and involve diverse STs. ST1 strains were resistant to several antibiotics.
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Affiliation(s)
- Jieun Kim
- grid.49606.3d0000 0001 1364 9317Division of Infectious Diseases, Department of Internal Medicine, Hanyang University College of Medicine, 222-1 Wangsimni-Ro, Seongdong-Gu, Seoul, 04763 Korea
| | - Bongyoung Kim
- grid.49606.3d0000 0001 1364 9317Division of Infectious Diseases, Department of Internal Medicine, Hanyang University College of Medicine, 222-1 Wangsimni-Ro, Seongdong-Gu, Seoul, 04763 Korea
| | - Hyunjoo Pai
- Division of Infectious Diseases, Department of Internal Medicine, Hanyang University College of Medicine, 222-1 Wangsimni-Ro, Seongdong-Gu, Seoul, 04763, Korea.
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Roseboom AM, Ducarmon QR, Hornung BVH, Harmanus C, Crobach MJT, Kuijper EJ, Vossen RHAM, Kloet SL, Smits WK. Carriage of three plasmids in a single human clinical isolate of Clostridioides difficile. Plasmid 2023; 125:102669. [PMID: 36572199 DOI: 10.1016/j.plasmid.2022.102669] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2022] [Revised: 11/17/2022] [Accepted: 12/20/2022] [Indexed: 12/24/2022]
Abstract
A subset of clinical isolates of Clostridioides difficile contains one or more plasmids and these plasmids can harbor virulence and antimicrobial resistance determinants. Despite their potential importance, C. difficile plasmids remain poorly characterized. Here, we provide the complete genome sequence of a human clinical isolate that carries three high-copy number plasmids from three different plasmid families that are therefore compatible. For two of these, we identify a region capable of sustaining plasmid replication in C. difficile that is also compatible with the plasmid pCD630 that is found in many laboratory strains. Together, our data advance our understanding of C. difficile plasmid biology.
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Affiliation(s)
- Anna M Roseboom
- Department of Medical Microbiology and Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, the Netherlands.
| | - Quinten R Ducarmon
- Department of Medical Microbiology and Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, the Netherlands.
| | - Bastian V H Hornung
- Department of Medical Microbiology and Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, the Netherlands
| | - Céline Harmanus
- Department of Medical Microbiology and Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, the Netherlands.
| | - Monique J T Crobach
- Department of Medical Microbiology and Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, the Netherlands.
| | - Ed J Kuijper
- Department of Medical Microbiology and Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, the Netherlands.
| | - Rolf H A M Vossen
- Department of Human Genetics, Leiden Genome Technology Center, Leiden University Medical Center, Leiden, the Netherlands.
| | - Susan L Kloet
- Department of Human Genetics, Leiden Genome Technology Center, Leiden University Medical Center, Leiden, the Netherlands.
| | - Wiep Klaas Smits
- Department of Medical Microbiology and Leiden University Center of Infectious Diseases (LU-CID), Leiden University Medical Center, Leiden, the Netherlands; Centre for Microbial Cell Biology, Leiden, the Netherlands.
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5
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Brajerova M, Zikova J, Krutova M. Clostridioides difficile epidemiology in the Middle and the Far East. Anaerobe 2022; 74:102542. [PMID: 35240336 DOI: 10.1016/j.anaerobe.2022.102542] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Revised: 02/14/2022] [Accepted: 02/20/2022] [Indexed: 12/18/2022]
Abstract
OBJECTIVES Clostridioides difficile is an important pathogen of healthcare-associated gastrointestinal infections. Recently, an increased number of C. difficile infection (CDI) surveillance data has been reported from Asia. The aim of this review is to summarize the data on the prevalence, distribution and molecular epidemiology of CDI in the Middle and the Far East. METHODS Literature was drawn from a search of PubMed up to September 30, 2021. RESULTS The meta-analysis of data from 111 studies revealed the pooled CDI prevalence rate in the Middle and the Far East of 12.4% (95% CI 11.4-13.3); 48 studies used PCR for CDI laboratory diagnoses. The predominant types (RT)/sequence type (ST) differ between individual countries (24 studies, 14 countries). Frequently found RTs were 001, 002, 012, 017, 018 and 126; RT017 was predominant in the Far East. The epidemic RT027 was detected in 8 countries (22 studies), but its predominance was reported only in three studies (Israel and Iran). The contamination of vegetable and meat or meat products and/or intestinal carriage of C. difficile in food and companion animals have been reported; the C. difficile RTs/STs identified overlapped with those identified in humans. CONCLUSIONS A large number of studies on CDI prevalence in humans from the Middle and the Far East have been published; countries with no available data were identified. The number of studies on C. difficile from non-human sources is limited. Comparative genomic studies of isolates from different sources are needed.
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Affiliation(s)
- Marie Brajerova
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Czech Republic
| | - Jaroslava Zikova
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Czech Republic; Department of Genetics and Microbiology, Faculty of Science, Charles University, Czech Republic
| | - Marcela Krutova
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Czech Republic.
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Karpiński P, Wultańska D, Piotrowski M, Brajerova M, Mikucka A, Pituch H, Krutova M. Motility and the genotype diversity of the flagellin genes fliC and fliD among Clostridioides difficile ribotypes. Anaerobe 2022; 73:102476. [PMID: 34780914 DOI: 10.1016/j.anaerobe.2021.102476] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2021] [Revised: 10/29/2021] [Accepted: 11/10/2021] [Indexed: 01/05/2023]
Abstract
OBJECTIVE The motility and genotype of the flagellin fliC and fliD genes were investigated in 82 Clostridioides difficile isolates belonging to the ribotypes (RTs): 027 (n = 41), 176 (n = 17), 023 (n = 8), 017 (n = 6) and 046 (n = 10). The reference C. difficile strains 630 and M120 were included as controls for the motility assay. METHODS A Multiple Locus Variable-number Tandem Repeat Analysis (MLVA) was used to exclude the genetic relatedness of C. difficile isolates belonging to the same RT. The variability of the fliC and fliD genes was determined by PCR-restriction fragment length polymorphism (RFLP) analysis and Sanger sequencing. The motility assay was carried out with 0.175% BHI agar tubes and BHI solid media plates with 0.4% agar. RESULTS The highest motility was observed in C. difficile RT023 isolates (p < 0.01), followed by RTs 027 and 176. C. difficile isolates of RTs 017 and 046 were less motile than RTs 027, 176 and 023 (p < 0.01). The fliC and fliD genes were present in all clinical isolates irrespective of the motility results. In the fliC gene analysis, four different RFLP groups were identified (I, II, VII, X). The fliC group VII was identified in two RTs (027 and 176), whereas the remaining three groups (I, II and X) belonged to a single RT 046, 017 and 023, respectively. The fliD gene analysis identified four new RFLP groups (a, b, c and d). CONCLUSIONS C. difficile RT023 is highly motile and its motility is comparable to the hypervirulent RT027 and its genetic relative RT176.
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Affiliation(s)
- Paweł Karpiński
- Department of Medical Microbiology, Medical University of Warsaw, Warsaw, Poland
| | - Dorota Wultańska
- Department of Medical Microbiology, Medical University of Warsaw, Warsaw, Poland
| | - Michał Piotrowski
- Department of Medical Microbiology, Medical University of Warsaw, Warsaw, Poland; The member of European Society of Clinical Microbiology and Infectious Disease (ESCMID) Study group for Clostridioides difficile (ESGCD), Poland
| | - Marie Brajerova
- Department of Medical Microbiology, Charles University 2nd Faculty of Medicine and Motol University Hospital, Prague, Czech Republic; The member of European Society of Clinical Microbiology and Infectious Disease (ESCMID) Study group for Clostridioides difficile (ESGCD), Poland
| | - Agnieszka Mikucka
- Dr Antoni Jurasz University Hospital No. 1 Bydgoszcz, Ludwik Rydygier Collegium Medicum in Bydgoszcz, Nicolaus Copernicus University in Toruń, Poland
| | - Hanna Pituch
- Department of Medical Microbiology, Medical University of Warsaw, Warsaw, Poland; The member of European Society of Clinical Microbiology and Infectious Disease (ESCMID) Study group for Clostridioides difficile (ESGCD), Poland.
| | - Marcela Krutova
- Department of Medical Microbiology, Charles University 2nd Faculty of Medicine and Motol University Hospital, Prague, Czech Republic; The member of European Society of Clinical Microbiology and Infectious Disease (ESCMID) Study group for Clostridioides difficile (ESGCD), Poland
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Perumalsamy S, Riley TV. Molecular Epidemiology of Clostridioides difficile Infections in Children. J Pediatric Infect Dis Soc 2021; 10:S34-S40. [PMID: 34791401 DOI: 10.1093/jpids/piab057] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Clostridioides difficile is a prominent cause of health care-related gastrointestinal illness in adults. C. difficile infection (CDI) has been researched for over 40 years; however, research on pediatric CDI specifically has lagged behind for various reasons. Over the past decade, C. difficile has been increasingly reported as a cause of a broad spectrum of gastrointestinal diseases in children, ranging from mild self-limiting diarrhea to severe conditions such as pseudomembranous colitis and toxic megacolon. Recent publications have shown a rise in CDI incidence in children in different parts of the world, especially in patients with particular comorbidities such as hematological malignancies and inflammatory bowel disease. In addition, rising CDI rates have been reported in children in the community without traditional risk factors for CDI. Due to the extensive use of sensitive molecular detection methods to diagnose CDI in many countries, differentiating children who require treatment from those colonized with toxigenic strains remains a problem. Consequently, the molecular epidemiology of pediatric CDI is poorly understood. Even though well-known C. difficile strains causing CDI in children have been described (including hypervirulent strains such as ribotypes 027 and 078), there is a paucity of information about specific C. difficile strains. This mini-review summarizes the information that is currently available on the molecular epidemiology of CDI in children.
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Affiliation(s)
- Sicilia Perumalsamy
- The University of Western Australia, School of Biomedical Sciences, Queen Elizabeth II Medical Centre, Nedlands, Western Australia, Australia
| | - Thomas V Riley
- The University of Western Australia, School of Biomedical Sciences, Queen Elizabeth II Medical Centre, Nedlands, Western Australia, Australia.,School of Veterinary and Life Sciences, Murdoch University, Murdoch, Western Australia, Australia.,PathWest Laboratory Medicine, Department of Microbiology, Queen Elizabeth II Medical Centre, Nedlands, Western Australia, Australia.,School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia
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8
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Noori M, Ghalavand Z, Azimirad M, Yadegar A, Eslami G, Krutova M, Brajerova M, Goudarzi M, Zali MR. Genetic diversity and phylogenetic analysis of the surface layer protein A gene (slpA) among Clostridioides difficile clinical isolates from Tehran, Iran. Anaerobe 2021; 70:102403. [PMID: 34111549 DOI: 10.1016/j.anaerobe.2021.102403] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 05/24/2021] [Accepted: 06/04/2021] [Indexed: 12/15/2022]
Abstract
Clostridioides difficile is the most common causative agent of healthcare-associated diarrhea. C. difficile strains produce a crystalline surface layer protein (SlpA), encoded by the slpA gene. Previous studies have shown that SlpA varies among C. difficile strains. In this study, we used the SlpA sequence-based typing system (SlpAST) for the molecular genotyping of C. difficile clinical isolates identified in Iran; the PCR ribotypes (RTs) and toxin profiles of the isolates were also characterized. Forty-eight C. difficile isolates were obtained from diarrheal patients, and characterized by capillary electrophoresis (CE) PCR ribotyping and the detection of toxin genes. In addition, the genetic diversity of the slpA gene was investigated by Sanger sequencing. The most common RTs were RT126 (20.8%), followed by RT001 (12.5%) and RT084 (10.4%). The intact PaLoc arrangement representing cdu2+/tcdR+/tcdB+/tcdE+/tcdA+/tcdC+/cdd3+ profile was the predominant pattern and cdtA and cdtB genes were found in one-third of the isolates. Using the SlpA genotyping, 12 main genotypes and 16 subtypes were identified. The SlpA type 078-1 was the most prevalent genotype (20.8%), and identified within the isolates of RT126. The yok-1, gr-1, cr-1 and kr-3 genotypes were detected in 14.5%, 12.5%, 12.5% and 8.3% of isolates, respectively. Almost all the isolates with the same RT were clustered in similar SlpA sequence types. In comparison to PCR ribotyping, SlpAST, as a simple and highly reproducible sequenced-based technique, can discriminate well between C. difficile isolates. This typing method appears to be a valuable tool for the epidemiological study of C. difficile isolates worldwide.
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Affiliation(s)
- Maryam Noori
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Zohreh Ghalavand
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Masoumeh Azimirad
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Abbas Yadegar
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Gita Eslami
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Marcela Krutova
- Department of Medical Microbiology, Charles University, 2nd Faculty of Medicine and Motol University Hospital, Prague, Czech Republic
| | - Marie Brajerova
- Department of Medical Microbiology, Charles University, 2nd Faculty of Medicine and Motol University Hospital, Prague, Czech Republic
| | - Mehdi Goudarzi
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Zali
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Knight DR, Imwattana K, Kullin B, Guerrero-Araya E, Paredes-Sabja D, Didelot X, Dingle KE, Eyre DW, Rodríguez C, Riley TV. Major genetic discontinuity and novel toxigenic species in Clostridioides difficile taxonomy. eLife 2021; 10:64325. [PMID: 34114561 PMCID: PMC8241443 DOI: 10.7554/elife.64325] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 06/08/2021] [Indexed: 12/17/2022] Open
Abstract
Clostridioides difficile infection (CDI) remains an urgent global One Health threat. The genetic heterogeneity seen across C. difficile underscores its wide ecological versatility and has driven the significant changes in CDI epidemiology seen in the last 20 years. We analysed an international collection of over 12,000 C. difficile genomes spanning the eight currently defined phylogenetic clades. Through whole-genome average nucleotide identity, and pangenomic and Bayesian analyses, we identified major taxonomic incoherence with clear species boundaries for each of the recently described cryptic clades CI–III. The emergence of these three novel genomospecies predates clades C1–5 by millions of years, rewriting the global population structure of C. difficile specifically and taxonomy of the Peptostreptococcaceae in general. These genomospecies all show unique and highly divergent toxin gene architecture, advancing our understanding of the evolution of C. difficile and close relatives. Beyond the taxonomic ramifications, this work may impact the diagnosis of CDI.
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Affiliation(s)
- Daniel R Knight
- Medical, Molecular and Forensic Sciences, Murdoch University, Murdoch, Australia.,School of Biomedical Sciences, the University of Western Australia, Nedlands, Australia
| | - Korakrit Imwattana
- School of Biomedical Sciences, the University of Western Australia, Nedlands, Australia.,Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Brian Kullin
- Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Enzo Guerrero-Araya
- Microbiota-Host Interactions and Clostridia Research Group, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile.,Millenium Nucleus in the Biology of Intestinal Microbiota, Santiago, Chile
| | - Daniel Paredes-Sabja
- Microbiota-Host Interactions and Clostridia Research Group, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile.,Millenium Nucleus in the Biology of Intestinal Microbiota, Santiago, Chile.,Department of Biology, Texas A&M University, College Station, United States
| | - Xavier Didelot
- School of Life Sciences and Department of Statistics, University of Warwick, Coventry, United Kingdom
| | - Kate E Dingle
- Nuffield Department of Clinical Medicine, University of Oxford, National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
| | - David W Eyre
- Big Data Institute, Nuffield Department of Population Health, University of Oxford, National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
| | - César Rodríguez
- Facultad de Microbiología & Centro de Investigación en Enfermedades Tropicales (CIET), Universidad de Costa Rica, San José, Costa Rica
| | - Thomas V Riley
- Medical, Molecular and Forensic Sciences, Murdoch University, Murdoch, Australia.,School of Biomedical Sciences, the University of Western Australia, Nedlands, Australia.,Department of Microbiology, PathWest Laboratory Medicine, Queen Elizabeth II Medical Centre, Nedlands, Australia.,School of Medical and Health Sciences, Edith Cowan University, Joondalup, Australia
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10
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An outbreak of Clostridioides difficile infections due to a 027-like PCR ribotype 181 in a rehabilitation centre: Epidemiological and microbiological characteristics. Anaerobe 2020; 65:102252. [PMID: 32781108 DOI: 10.1016/j.anaerobe.2020.102252] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 07/22/2020] [Accepted: 08/03/2020] [Indexed: 12/17/2022]
Abstract
Clostridioides difficile is one of the most important healthcare-associated pathogens. Recently, several new 027-like types have been found that all belong to the multilocus sequence typing (MLST) Clade 2. We report a rapidly spreading outbreak of C. difficile infections (CDI) due to a newly identified PCR ribotype (RT) 181 in a Rehabilitation Centre (RC). Genomic analysis revealed the outbreak strain, not previously identified in Greece, belonged to clade 2, sequence type (ST) 1 and had a 18bp deletion in tcdC at position 311 together with a single nucleotide deletion at position 117, similarly to RT 027. The presence of a clonal outbreak was confirmed by whole genome sequencing, yet the source of this ribotype remained unclear. The emergence and rapid spread of new C. difficile ribotypes highlights the need for ongoing C. difficile surveillance and better understanding of overall Clade 2 phylogeny.
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11
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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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12
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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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13
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Novakova E, Stefkovicova M, Kopilec MG, Novak M, Kotlebova N, Kuijper E, Krutova M. The emergence of Clostridium difficile ribotypes 027 and 176 with a predominance of the Clostridium difficile ribotype 001 recognized in Slovakia following the European standardized Clostridium difficile infection surveillance of 2016. Int J Infect Dis 2020; 90:111-115. [PMID: 31707136 PMCID: PMC6912155 DOI: 10.1016/j.ijid.2019.10.038] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2019] [Revised: 10/25/2019] [Accepted: 10/29/2019] [Indexed: 12/26/2022] Open
Abstract
AIM To obtain standardized epidemiological data for Clostridium difficile infection (CDI) in Slovakia. METHODS Between October and December 2016, 36 hospitals in Slovakia used the European Centre for Disease Prevention and Control (ECDC) Clostridium difficile infection (CDI) surveillance protocol. RESULTS The overall mean CDI incidence density was 2.8 (95% confidence interval 1.9-3.9) cases per 10 000 patient-days. Of 332 CDI cases, 273 (84.9%) were healthcare-associated, 45 (15.1%) were community-associated, and 14 (4.2%) were cases of recurrent CDI. A complicated course of CDI was reported in 14.8% of cases (n=51). CDI outcome data were available for 95.5% of cases (n=317). Of the 35 patients (11.1%) who died, 34 did so within 30 days after their CDI diagnosis. Of the 78 isolates obtained from 12 hospitals, 46 belonged to PCR ribotype 001 (59.0%; 11 hospitals) and 23 belonged to ribotype 176 (29.5%; six hospitals). A total of 73 isolates (93.6%) showed reduced susceptibility to moxifloxacin (ribotypes 001 and 176; p< 0.01). A reduced susceptibility to metronidazole was observed in 13 isolates that subsequently proved to be metronidazole-susceptible when, after thawing, they were retested using the agar dilution method. No reduced susceptibility to vancomycin was found. CONCLUSIONS These results show the emergence of C. difficile ribotypes 027 and 176 with a predominance of ribotype 001 in Slovakia in 2016. Given that an almost homogeneous reduced susceptibility to moxifloxacin was detected in C. difficile isolates, this stresses the importance of reducing fluoroquinolone prescriptions in Slovak healthcare settings.
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Affiliation(s)
- Elena Novakova
- Department of Microbiology and Immunology, Comenius University, Jessenius Faculty of Medicine in Martin, Slovakia
| | - Maria Stefkovicova
- Department of Epidemiology, Regional Public Health Authority, Trenčín, Slovakia; Department of Laboratory Medicine and Public Health, Faculty of Health Care, Alexander Dubcek University, Trenčín, Slovakia
| | | | - Martin Novak
- Department of Public Health, Comenius University, Jessenius Faculty of Medicine in Martin, Slovakia
| | - Nina Kotlebova
- Department of Microbiology and Immunology, Comenius University, Jessenius Faculty of Medicine in Martin, Slovakia
| | - Ed Kuijper
- Department of Medical Microbiology, Leiden University Medical Centre, Leiden, The Netherlands
| | - Marcela Krutova
- Department of Medical Microbiology, Charles University in Prague, 2nd Faculty of Medicine and Motol University Hospital, Prague, Czech Republic.
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14
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Rivas L, Dupont PY, Gilpin BJ, Cornelius AJ. Isolation and characterization of Clostridium difficile from a small survey of wastewater, food and animals in New Zealand. Lett Appl Microbiol 2019; 70:29-35. [PMID: 31631350 DOI: 10.1111/lam.13238] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 10/17/2019] [Accepted: 10/17/2019] [Indexed: 11/29/2022]
Abstract
The objective of this study was to undertake a microbiological survey of foods, animal faeces and wastewater samples for Clostridium difficile, and determine the genotypes and antimicrobial susceptibilities of isolates. A total of 211 samples were tested for C. difficile using culture methods. Thirteen toxigenic C. difficile isolates were obtained; ten from wastewater samples, one each from pig and duck faeces and another from a raw meat product. Eight PCR-ribotypes (RTs) were identified, including two novel RTs (878 and 879). Single-nucleotide polymorphism analysis using WGS data for all isolates provided greater discrimination between C. difficile isolates within the same RT and multilocus sequence typing (MLST) profiles. All C. difficile isolates were found to be susceptible to the first-line human antimicrobials used to treat C. difficile infection. SIGNIFICANCE AND IMPACT OF THE STUDY: This is the first study to report the isolation of Clostridium difficile from animals, food and wastewater in New Zealand (NZ) and provides important data with respect to ribotypes and multilocus sequence typing profiles, whole genome sequence and antimicrobial susceptibilities. The results highlight the need for further investigations into the epidemiology of C. difficile in NZ and to elucidate the role of the environmental and food sources as transmission routes of human infection.
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Affiliation(s)
- L Rivas
- Health and Environment, Institute of Environmental Science and Research, Christchurch Science Centre, Christchurch, New Zealand
| | - P-Y Dupont
- Health and Environment, Institute of Environmental Science and Research, Christchurch Science Centre, Christchurch, New Zealand
| | - B J Gilpin
- Health and Environment, Institute of Environmental Science and Research, Christchurch Science Centre, Christchurch, New Zealand
| | - A J Cornelius
- Health and Environment, Institute of Environmental Science and Research, Christchurch Science Centre, Christchurch, New Zealand
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15
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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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16
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Williamson CHD, Stone NE, Nunnally AE, Hornstra HM, Wagner DM, Roe CC, Vazquez AJ, Nandurkar N, Vinocur J, Terriquez J, Gillece J, Travis J, Lemmer D, Keim P, Sahl JW. A global to local genomics analysis of Clostridioides difficile ST1/RT027 identifies cryptic transmission events in a northern Arizona healthcare network. Microb Genom 2019; 5:e000271. [PMID: 31107202 PMCID: PMC6700662 DOI: 10.1099/mgen.0.000271] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2019] [Accepted: 04/04/2019] [Indexed: 12/15/2022] Open
Abstract
Clostridioides difficile is a ubiquitous, diarrhoeagenic pathogen often associated with healthcare-acquired infections that can cause a range of symptoms from mild, self-limiting disease to toxic megacolon and death. Since the early 2000s, a large proportion of C. difficile cases have been attributed to the ribotype 027 (RT027) lineage, which is associated with sequence type 1 (ST1) in the C. difficile multilocus sequence typing scheme. The spread of ST1 has been attributed, in part, to resistance to fluoroquinolones used to treat unrelated infections, which creates conditions ideal for C. difficile colonization and proliferation. In this study, we analysed 27 isolates from a healthcare network in northern Arizona, USA, and 1352 publicly available ST1 genomes to place locally sampled isolates into a global context. Whole genome, single nucleotide polymorphism analysis demonstrated that at least six separate introductions of ST1 were observed in healthcare facilities in northern Arizona over an 18-month sampling period. A reconstruction of transmission networks identified potential nosocomial transmission of isolates, which were only identified via whole genome sequence analysis. Antibiotic resistance heterogeneity was observed among ST1 genomes, including variability in resistance profiles among locally sampled ST1 isolates. To investigate why ST1 genomes are so common globally and in northern Arizona, we compared all high-quality C. difficile genomes and identified that ST1 genomes have gained and lost a number of genomic regions compared to all other C. difficile genomes; analyses of other toxigenic C. difficile sequence types demonstrate that this loss may be anomalous and could be related to niche specialization. These results suggest that a combination of antimicrobial resistance and gain and loss of specific genes may explain the prominent association of this sequence type with C. difficile infection cases worldwide. The degree of genetic variability in ST1 suggests that classifying all ST1 genomes into a quinolone-resistant hypervirulent clone category may not be appropriate. Whole genome sequencing of clinical C. difficile isolates provides a high-resolution surveillance strategy for monitoring persistence and transmission of C. difficile and for assessing the performance of infection prevention and control strategies.
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Affiliation(s)
| | - Nathan E. Stone
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Amalee E. Nunnally
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Heidie M. Hornstra
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - David M. Wagner
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Chandler C. Roe
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Adam J. Vazquez
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Nivedita Nandurkar
- Northern Arizona Healthcare, Flagstaff Medical Center, Flagstaff, AZ 86001, USA
| | - Jacob Vinocur
- Northern Arizona Healthcare, Flagstaff Medical Center, Flagstaff, AZ 86001, USA
| | - Joel Terriquez
- Northern Arizona Healthcare, Flagstaff Medical Center, Flagstaff, AZ 86001, USA
| | - John Gillece
- Translational Genomics Research Institute, Flagstaff, AZ 86001, USA
| | - Jason Travis
- Translational Genomics Research Institute, Flagstaff, AZ 86001, USA
| | - Darrin Lemmer
- Translational Genomics Research Institute, Flagstaff, AZ 86001, USA
| | - Paul Keim
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
| | - Jason W. Sahl
- Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ 86011, USA
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17
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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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18
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Dingle KE, Didelot X, Quan TP, Eyre DW, Stoesser N, Marwick CA, Coia J, Brown D, Buchanan S, Ijaz UZ, Goswami C, Douce G, Fawley WN, Wilcox MH, Peto TEA, Walker AS, Crook DW. A Role for Tetracycline Selection in Recent Evolution of Agriculture-Associated Clostridium difficile PCR Ribotype 078. mBio 2019; 10:e02790-18. [PMID: 30862754 PMCID: PMC6414706 DOI: 10.1128/mbio.02790-18] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 01/31/2019] [Indexed: 02/04/2023] Open
Abstract
The increasing clinical importance of human infections (frequently severe) caused by Clostridium difficile PCR ribotype 078 (RT078) was first reported in 2008. The severity of symptoms (mortality of ≤30%) and the higher proportion of infections among community and younger patients raised concerns. Farm animals, especially pigs, have been identified as RT078 reservoirs. We aimed to understand the recent changes in RT078 epidemiology by investigating a possible role for antimicrobial selection in its recent evolutionary history. Phylogenetic analysis of international RT078 genomes (isolates from 2006 to 2014, n = 400), using time-scaled, recombination-corrected, maximum likelihood phylogenies, revealed several recent clonal expansions. A common ancestor of each expansion had independently acquired a different allele of the tetracycline resistance gene tetM Consequently, an unusually high proportion (76.5%) of RT078 genomes were tetM positive. Multiple additional tetracycline resistance determinants were also identified (including efflux pump tet40), frequently sharing a high level of nucleotide sequence identity (up to 100%) with sequences found in the pig pathogen Streptococcus suis and in other zoonotic pathogens such as Campylobacter jejuni and Campylobacter coli Each RT078 tetM clonal expansion lacked geographic structure, indicating rapid, recent international spread. Resistance determinants for C. difficile infection-triggering antimicrobials, including fluoroquinolones and clindamycin, were comparatively rare in RT078. Tetracyclines are used intensively in agriculture; this selective pressure, plus rapid, international spread via the food chain, may explain the increased RT078 prevalence in humans. Our work indicates that the use of antimicrobials outside the health care environment has selected for resistant organisms, and in the case of RT078, has contributed to the emergence of a human pathogen.IMPORTANCEClostridium difficile PCR ribotype 078 (RT078) has multiple reservoirs; many are agricultural. Since 2005, this genotype has been increasingly associated with human infections in both clinical settings and the community. Investigations of RT078 whole-genome sequences revealed that tetracycline resistance had been acquired on multiple independent occasions. Phylogenetic analysis revealed a rapid, recent increase in numbers of closely related tetracycline-resistant RT078 (clonal expansions), suggesting that tetracycline selection has strongly influenced its recent evolutionary history. We demonstrate recent international spread of emergent, tetracycline-resistant RT078. A similar tetracycline-positive clonal expansion was also identified in unrelated nontoxigenic C. difficile, suggesting that this process may be widespread and may be independent of disease-causing ability. Resistance to typical C. difficile infection-associated antimicrobials (e.g., fluoroquinolones, clindamycin) occurred only sporadically within RT078. Selective pressure from tetracycline appears to be a key factor in the emergence of this human pathogen and the rapid international dissemination that followed, plausibly via the food chain.
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Affiliation(s)
- Kate E Dingle
- Nuffield Department of Clinical Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
- National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
- NIHR Oxford Health Protection Research Unit on Healthcare Associated Infection and Antimicrobial Resistance, John Radcliffe Hospital, Oxford University, Oxford, United Kingdom
| | - Xavier Didelot
- School of Life Sciences and Department of Statistics, University of Warwick, Coventry, United Kingdom
| | - T Phuong Quan
- Nuffield Department of Clinical Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
- National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
- NIHR Oxford Health Protection Research Unit on Healthcare Associated Infection and Antimicrobial Resistance, John Radcliffe Hospital, Oxford University, Oxford, United Kingdom
| | - David W Eyre
- Nuffield Department of Clinical Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
- National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
| | - Nicole Stoesser
- Nuffield Department of Clinical Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
- National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
| | - Charis A Marwick
- Population Health Sciences, School of Medicine, University of Dundee, Scotland, United Kingdom
| | - John Coia
- Scottish Microbiology Reference Laboratories, Glasgow, United Kingdom
| | - Derek Brown
- Scottish Microbiology Reference Laboratories, Glasgow, United Kingdom
| | | | - Umer Z Ijaz
- University of Glasgow, Scotland, United Kingdom
| | | | - Gill Douce
- University of Glasgow, Scotland, United Kingdom
| | - Warren N Fawley
- Department of Microbiology, Leeds General Infirmary, Leeds Teaching Hospitals, University of Leeds, Leeds, United Kingdom
| | - Mark H Wilcox
- Department of Microbiology, Leeds General Infirmary, Leeds Teaching Hospitals, University of Leeds, Leeds, United Kingdom
| | - Timothy E A Peto
- Nuffield Department of Clinical Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
- National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
- NIHR Oxford Health Protection Research Unit on Healthcare Associated Infection and Antimicrobial Resistance, John Radcliffe Hospital, Oxford University, Oxford, United Kingdom
| | - A Sarah Walker
- Nuffield Department of Clinical Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
- National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
- NIHR Oxford Health Protection Research Unit on Healthcare Associated Infection and Antimicrobial Resistance, John Radcliffe Hospital, Oxford University, Oxford, United Kingdom
| | - Derrick W Crook
- Nuffield Department of Clinical Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
- National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
- NIHR Oxford Health Protection Research Unit on Healthcare Associated Infection and Antimicrobial Resistance, John Radcliffe Hospital, Oxford University, Oxford, United Kingdom
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19
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Genome Location Dictates the Transcriptional Response to PolC Inhibition in Clostridium difficile. Antimicrob Agents Chemother 2019; 63:AAC.01363-18. [PMID: 30455241 DOI: 10.1128/aac.01363-18] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2018] [Accepted: 11/04/2018] [Indexed: 01/08/2023] Open
Abstract
Clostridium difficile is a potentially lethal gut pathogen that causes nosocomial and community-acquired infections. Limited treatment options and reports of reduced susceptibility to current treatment emphasize the necessity for novel antimicrobials. The DNA polymerase of Gram-positive organisms is an attractive target for the development of antimicrobials. ACX-362E [N 2-(3,4-dichlorobenzyl)-7-(2-[1-morpholinyl]ethyl)guanine; MorE-DCBG] is a DNA polymerase inhibitor in preclinical development as a novel therapeutic against C. difficile infection. This synthetic purine shows preferential activity against C. difficile PolC over those of other organisms in vitro and is effective in an animal model of C. difficile infection. In this study, we have determined its efficacy against a large collection of clinical isolates. At concentrations below the MIC, the presumed slowing (or stalling) of replication forks due to ACX-362E leads to a growth defect. We have determined the transcriptional response of C. difficile to replication inhibition and observed an overrepresentation of upregulated genes near the origin of replication in the presence of PolC inhibitors, but not when cells were subjected to subinhibitory concentrations of other antibiotics. This phenomenon can be explained by a gene dosage shift, as we observed a concomitant increase in the ratio between origin-proximal and terminus-proximal gene copy number upon exposure to PolC inhibitors. Moreover, we show that certain genes differentially regulated under PolC inhibition are controlled by the origin-proximal general stress response regulator sigma factor B. Together, these data suggest that genome location both directly and indirectly determines the transcriptional response to replication inhibition in C. difficile.
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20
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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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21
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Characterization of the virulence of a non-RT027, non-RT078 and binary toxin-positive Clostridium difficile strain associated with severe diarrhea. Emerg Microbes Infect 2018; 7:211. [PMID: 30542069 PMCID: PMC6291415 DOI: 10.1038/s41426-018-0211-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 11/01/2018] [Accepted: 11/11/2018] [Indexed: 02/06/2023]
Abstract
The expression of the Clostridium difficile binary toxin CDT is generally observed in the RT027 (ST1) and RT078 (ST11) C. difficile isolates, which are associated with severe C. difficile infection (CDI). However, we recently reported that the non-RT027 and non-RT078 C. difficile strain LC693 (TcdA+TcdB+ CDT+, ST201) caused severe diarrhea in a patient in Xiangya Hospital in China. C.difficile LC693 is a member of Clade 3, and in this study, we identified LC693 as RT871 and compared its virulence and pathogenicity to those of C.difficile R20291 (TcdA+TcdB+CDT+, ST1/RT027), UK6 (TcdA+TcdB+CDT+, ST35/RT027), CD630 (TcdA+TcdB+CDT−, ST54, RT012), and 1379 (TcdA+TcdB+CDT−, ST54/RT012), with strain 1379 being an epidemic C.difficile isolate from the same hospital. LC693 displayed a higher sporulation rate than R20291, CD630 or strain 1379. LC693 was comparable to R20291 with respect to spore germination, motility, and biofilm formation, but showed a faster germination rate, higher motility and a higher biofilm formation capability compared to CD630 and strain 1379. The adherence of spores to human gut epithelial cells was similar for all strains.The total toxin release of LC693 was lower than that of R20291, but higher than that of CD630 and strain 1379. Finally, in a mouse model of CDI, LC693 was capable of causing moderate to severe disease. Our findings demonstrate the pathogenicity of non-RT027 and non-RT078 binary toxin-positive C. difficile strains. Furthermore, our data indicate that LC693 may be more virulent than strain 1379, an epidemic strain from the same hospital, and provide the first phenotypic characterization of a non-RT027 and non-RT078 binary toxin-positive ST201 isolate.
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22
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Kociolek LK, Perdue ER, Fawley WN, Wilcox MH, Gerding DN, Johnson S. Correlation between restriction endonuclease analysis and PCR ribotyping for the identification of Clostridioides (Clostridium) difficile clinical strains. Anaerobe 2018; 54:1-7. [PMID: 30009944 PMCID: PMC6924008 DOI: 10.1016/j.anaerobe.2018.07.004] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2018] [Revised: 07/03/2018] [Accepted: 07/12/2018] [Indexed: 01/05/2023]
Abstract
Restriction endonuclease analysis (REA) and PCR ribotyping are two typing systems that have been frequently utilized for molecular epidemiologic characterization of Clostridioides (Clostridium) difficile. To correlate typing data obtained from each method, we performed both REA and PCR ribotyping on a large and diverse set of historical and contemporary C. difficile infection clinical isolates. Eighty isolates were selected from each reference laboratory in the United States (Microbiology Reference Laboratory, Hines VA Medical Center) and United Kingdom (Clostridium difficile Network for England and Northern Ireland laboratory, University of Leeds). The 160 isolates were assigned to 82 unique ribotypes and 51 unique REA groups (116 unique REA types). In general, concordance between typing methods was good. Dendrogram analysis of PCR ribotype band patterns demonstrated close genetic relationships among strain types with discordant REA and ribotype assignments. While REA typing was more discriminatory, several REA types in this study were further discriminated by PCR ribotyping, indicating that discriminatory value of these typing methods may be strain dependent. These data will assist with molecular epidemiologic surveillance of strains identified by these two commonly used C. difficile typing systems.
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Affiliation(s)
- Larry K Kociolek
- Northwestern University Feinberg School of Medicine, 420 E. Superior St, Chicago, IL, 60611, USA; Ann & Robert H. Lurie Children's Hospital of Chicago, 225 E. Chicago Ave., Chicago, IL, 60611, USA.
| | - Eric R Perdue
- Edward Hines, Jr. Veterans Administration Hospital, 5000 5th Ave., Hines, IL, 60141, USA.
| | - Warren N Fawley
- Leeds Teaching Hospitals and University of Leeds, Leeds, LS2 9JT, UK.
| | - Mark H Wilcox
- Leeds Teaching Hospitals and University of Leeds, Leeds, LS2 9JT, UK.
| | - Dale N Gerding
- Edward Hines, Jr. Veterans Administration Hospital, 5000 5th Ave., Hines, IL, 60141, USA; Loyola University Chicago Stritch School of Medicine, 2160 S 1st Ave., Maywood, IL, 60153, USA.
| | - Stuart Johnson
- Edward Hines, Jr. Veterans Administration Hospital, 5000 5th Ave., Hines, IL, 60141, USA; Loyola University Chicago Stritch School of Medicine, 2160 S 1st Ave., Maywood, IL, 60153, USA.
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23
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Corver J, Sen J, Hornung BVH, Mertens BJ, Berssenbrugge EKL, Harmanus C, Sanders IMJG, Kumar N, Lawley TD, Kuijper EJ, Hensbergen PJ, Nicolardi S. Identification and validation of two peptide markers for the recognition of Clostridioides difficile MLST-1 and MLST-11 by MALDI-MS. Clin Microbiol Infect 2018; 25:904.e1-904.e7. [PMID: 31130255 DOI: 10.1016/j.cmi.2018.10.008] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 10/08/2018] [Accepted: 10/13/2018] [Indexed: 12/15/2022]
Abstract
OBJECTIVES Clostridioides difficile infection (CDI) has become the main cause of nosocomial infective diarrhoea. To survey and control the spread of different C. difficile strains, there is a need for suitable rapid tests. The aim of this study was to identify peptide/protein markers for the rapid recognition of C. difficile strains by matrix-assisted laser desorption/ionization mass spectrometry (MALDI-MS). METHODS We analysed 44 well-characterized strains, belonging to eight different multi-locus sequence types (MLST), using ultrahigh-resolution Fourier transform ion cyclotron resonance (FTICR) MS. The amino acid sequence of two peptide markers specific for MLST-1 and MLST-11 strains was elucidated by MALDI-TOF-MS/MS. The investigation of 2689 C. difficile genomes allowed the determination of the sensitivity and specificity of these markers. C18-solid-phased extraction was used to enrich the MLST-1 marker. RESULTS Two peptide markers (m/z 4927.81 and m/z 5001.84) were identified and characterized for MLST-1 and MLST-11 strains, respectively. The MLST-1 marker was found in 786 genomes of which three did not belong to MLST-1. The MLST-11 marker was found in 319 genomes, of which 14 did not belong to MLST-11. Importantly, all MLST-1 and MLST-11 genomes were positive for their respective marker. Furthermore, a peptide marker (m/z 5015.86) specific for MLST-15 was found in 59 genomes. We translated our findings into a fast and simple method that allowed the unambiguous identification of the MLST-1 marker on a MALDI-TOF-MS platform. CONCLUSIONS MALDI-FTICR MS-based peptide profiling resulted in the identification of peptide markers for C. difficile MLST-1 and MLST-11.
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Affiliation(s)
- J Corver
- Leiden University Medical Centre, Centre of Infectious Diseases, Department Medical Microbiology, Section Experimental Bacteriology, Leiden, the Netherlands; Centre for Microbiota Analysis and Therapeutics, Department Medical Microbiology, Leiden University, Leiden, the Netherlands
| | - J Sen
- Leiden University Medical Centre, Centre for Proteomics and Metabolomics, Leiden, the Netherlands
| | - B V H Hornung
- Leiden University Medical Centre, Centre of Infectious Diseases, Department Medical Microbiology, Section Experimental Bacteriology, Leiden, the Netherlands; Centre for Microbiota Analysis and Therapeutics, Department Medical Microbiology, Leiden University, Leiden, the Netherlands
| | - B J Mertens
- Leiden University Medical Centre, Department of Medical Statistics and Bioinformatics, Leiden, the Netherlands
| | - E K L Berssenbrugge
- Leiden University Medical Centre, Centre of Infectious Diseases, Department Medical Microbiology, Section Experimental Bacteriology, Leiden, the Netherlands
| | - C Harmanus
- Leiden University Medical Centre, Centre of Infectious Diseases, Department Medical Microbiology, Section Experimental Bacteriology, Leiden, the Netherlands
| | - I M J G Sanders
- Leiden University Medical Centre, Centre of Infectious Diseases, Department Medical Microbiology, Section Experimental Bacteriology, Leiden, the Netherlands
| | - N Kumar
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | - T D Lawley
- Host-Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, UK
| | - E J Kuijper
- Leiden University Medical Centre, Centre of Infectious Diseases, Department Medical Microbiology, Section Experimental Bacteriology, Leiden, the Netherlands; Centre for Microbiota Analysis and Therapeutics, Department Medical Microbiology, Leiden University, Leiden, the Netherlands
| | - P J Hensbergen
- Leiden University Medical Centre, Centre for Proteomics and Metabolomics, Leiden, the Netherlands.
| | - S Nicolardi
- Leiden University Medical Centre, Centre for Proteomics and Metabolomics, Leiden, the Netherlands.
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24
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Krehelova M, Nyč O, Sinajová E, Krutova M. The predominance and clustering of Clostridioides (Clostridium) difficile PCR ribotype 001 isolates in three hospitals in Eastern Slovakia, 2017. Folia Microbiol (Praha) 2018; 64:49-54. [PMID: 29971567 DOI: 10.1007/s12223-018-0629-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2018] [Accepted: 06/27/2018] [Indexed: 12/20/2022]
Abstract
This study aimed to implement a toxigenic culture as an optional third diagnostic step for glutamate dehydrogenase (GDH)-positive and toxin A/B-negative diarrheal stool samples into a diagnostic algorithm for Clostridioides (Clostridium) difficile infection (CDI), and to characterise C. difficile isolates for epidemiological purposes. During the 5-month study, 481 diarrhoeal stool samples from three Slovak hospitals were investigated and 66 non-duplicated GDH-positive stool samples were found. Of them, 36 were also toxin A/B-positive. Twenty-three GDH-positive and toxin A/B-negative stool samples were shown subsequently to be positive following toxigenic culture (TC). Molecular characterisation of C. difficile isolates showed the predominance of PCR ribotype (RT) 001 (n = 37, 56.1%) and the occurrence of RT 176 (n = 3, 4.5%). C. difficile RT 001 isolates clustered to eight clonal complexes (CCs) using multiple-locus variable-number tandem repeats analysis (MLVA). Interestingly, one third of RT 001 isolates clustering in these CCs were cultured from toxin A/B-negative stool samples. Our observations highlight the need of use multiple step diagnostic algorithm in CDI diagnosis in order to detect all CDI cases and to avoid the spread of C. difficile in healthcare settings.
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Affiliation(s)
| | - Otakar Nyč
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University and Motol University Hospital, V Uvalu 84, 150 06, Prague 5, Czech Republic
| | - Eva Sinajová
- Department of Microbiology, Medirex Group, Kosice, Slovakia
| | - Marcela Krutova
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University and Motol University Hospital, V Uvalu 84, 150 06, Prague 5, Czech Republic.
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25
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Defining and Evaluating a Core Genome Multilocus Sequence Typing Scheme for Genome-Wide Typing of Clostridium difficile. J Clin Microbiol 2018; 56:JCM.01987-17. [PMID: 29618503 DOI: 10.1128/jcm.01987-17] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2017] [Accepted: 03/28/2018] [Indexed: 01/18/2023] Open
Abstract
Clostridium difficile, recently renamed Clostridioides difficile, is the most common cause of antibiotic-associated nosocomial gastrointestinal infections worldwide. To differentiate endogenous infections and transmission events, highly discriminatory subtyping is necessary. Today, methods based on whole-genome sequencing data are increasingly used to subtype bacterial pathogens; however, frequently a standardized methodology and typing nomenclature are missing. Here we report a core genome multilocus sequence typing (cgMLST) approach developed for C. difficile Initially, we determined the breadth of the C. difficile population based on all available MLST sequence types with Bayesian inference (BAPS). The resulting BAPS partitions were used in combination with C. difficile clade information to select representative isolates that were subsequently used to define cgMLST target genes. Finally, we evaluated the novel cgMLST scheme with genomes from 3,025 isolates. BAPS grouping (n = 6 groups) together with the clade information led to a total of 11 representative isolates that were included for cgMLST definition and resulted in 2,270 cgMLST genes that were present in all isolates. Overall, 2,184 to 2,268 cgMLST targets were detected in the genome sequences of 70 outbreak-associated and reference strains, and on average 99.3% cgMLST targets (1,116 to 2,270 targets) were present in 2,954 genomes downloaded from the NCBI database, underlining the representativeness of the cgMLST scheme. Moreover, reanalyzing different cluster scenarios with cgMLST were concordant to published single nucleotide variant analyses. In conclusion, the novel cgMLST is representative for the whole C. difficile population, is highly discriminatory in outbreak situations, and provides a unique nomenclature facilitating interlaboratory exchange.
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26
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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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27
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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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28
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Krutova M, Wilcox MH, Kuijper EJ. The pitfalls of laboratory diagnostics of Clostridium difficile infection. Clin Microbiol Infect 2018; 24:682-683. [PMID: 29505883 DOI: 10.1016/j.cmi.2018.02.026] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2018] [Revised: 02/21/2018] [Accepted: 02/22/2018] [Indexed: 02/04/2023]
Affiliation(s)
- M Krutova
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University in Prague and Motol University Hospital, Prague, Czech Republic; European Society of Clinical Microbiology and Infectious Diseases (ESCMID) Study Group for Clostridium difficile (ESGCD).
| | - M H Wilcox
- Leeds Teaching Hospitals NHS Trust & University of Leeds, Leeds, United Kingdom; European Society of Clinical Microbiology and Infectious Diseases (ESCMID) Study Group for Clostridium difficile (ESGCD)
| | - E J Kuijper
- Department of Medical Microbiology, Leiden University Medical Centre, Leiden, The Netherlands; European Society of Clinical Microbiology and Infectious Diseases (ESCMID) Study Group for Clostridium difficile (ESGCD)
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29
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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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30
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Chen YB, Gu SL, Shen P, Lv T, Fang YH, Tang LL, Li LJ. Molecular epidemiology and antimicrobial susceptibility of Clostridium difficile isolated from hospitals during a 4-year period in China. J Med Microbiol 2017; 67:52-59. [PMID: 29160203 DOI: 10.1099/jmm.0.000646] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
OBJECTIVE The aim of this study was to perform molecular characterization for and determine the antimicrobial susceptibility profiles of Clostridium difficile collected from hospitals during a 4-year period (2009-2013) in China. METHODS Strains of toxigenic C. difficile were isolated from patients with diarrhoea, and this was followed by typing using multilocus sequence typing (MLST) and testing for susceptibility to 10 antimicrobials by using the E-test. The mechanisms of resistance to moxifloxacin, erythromycin, clindamycin and tetracycline were investigated by PCR. RESULTS A total of 405 non-duplicate toxigenic C. difficile isolates were identified, while 31 sequence types (STs) were identified. A predominant type, ST-54, accounted for 20.2 % of the STs, followed by ST-35 (16.3 %) and ST-37 (13.6 %). We found that 6.2 % of the isolates were binary toxin genes-positive, and 83.7 % of these belonged to ST-5. All of the isolates demonstrated 100 % susceptibility to first-line Clostridium difficile infection (CDI) therapies (i.e. metronidazole and vancomycin), while the resistance rates varied for the other antibiotics tested. Two hundred and ninety three (72.3 %) isolates were susceptible to moxifloxacin. All 112 moxifloxacin-resistant isolates had mutations resulting in an amino acid substitution in gryA and/or gyrB. The ermB gene was detected in 86.7 % (241/278) of the erythromycin- and clindamycin-resistant isolates, while the tetM gene was present in 97.1 % (85/87) of the tetracycline-resistant isolates. CONCLUSION MLST typing revealed a wide variety of STs causing CDI, while ST-54 was the most common ST. All of the isolates were susceptible to metronidazole and vancomycin, while the resistance rates varied for the other antibiotics tested. There were no changes in the trends for the STs and antibiotic susceptibility profiles over 4 years.
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Affiliation(s)
- Yun-Bo Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, PR China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, PR China
| | - Si-Lan Gu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, PR China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, PR China
| | - Ping Shen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, PR China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, PR China
| | - Tao Lv
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, PR China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, PR China
| | - Yun-Hui Fang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, PR China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, PR China
| | - Ling-Ling Tang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, PR China.,Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, PR China.,Hospital Infection-Control Department, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, PR China
| | - Lan-Juan Li
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, PR China.,State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, School of Medicine, Zhejiang University, Hangzhou, Zhejiang, PR China
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Clostridium difficile RT 078/ST11: A Threat to Community Population and Pigs Identified in Elder Hospitalized Patients in Beijing, China. Infect Control Hosp Epidemiol 2017; 38:1383-1385. [PMID: 28950917 DOI: 10.1017/ice.2017.206] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Is there a relationship between the presence of the binary toxin genes in Clostridium difficile strains and the severity of C. difficile infection (CDI)? Eur J Clin Microbiol Infect Dis 2017; 36:2405-2415. [PMID: 28780742 DOI: 10.1007/s10096-017-3075-8] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 07/20/2017] [Indexed: 12/18/2022]
Abstract
Some strains of Clostridium difficile produce a binary toxin, in addition to the main C. difficile virulence factors (toxins A and B). There have been conflicting reports regarding the role of binary toxin and its relationship to the severity of C. difficile infection (CDI). Samples, isolates and clinical data were collected as part of a prospective multicentre diagnostic study. Clostridium difficile isolates (n = 1259) were tested by polymerase chain reaction (PCR) assay to detect binary toxin genes cdtA and cdtB. The PCR binary toxin gene results were compared with clinical severity and outcome data, including 30-day all-cause mortality. The 1259 isolates corresponded to 1083 different patients (October 2010 to September 2011). The prevalence of binary toxin positive strains was significantly higher in faecal samples with detectable toxin A/B than in those without toxin but that were positive by cytotoxigenic culture (26.3% vs. 10.3%, p < 0.001). The presence of binary toxin correlated moderately with markers of CDI severity (white cell count, serum albumin concentration and serum creatinine concentration). However, the risk ratio for all-cause mortality was 1.68 for binary toxin positive patients and patients were significantly less likely to survive if they had CDI caused by a binary toxin gene positive strain, even after adjusting for age (p < 0.001). The presence of binary toxin genes does not predict the clinical severity of CDI, but it is significantly associated with the risk of all-cause mortality.
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Increasing incidence of Clostridium difficile ribotype 001 associated with severe course of the infection and previous fluoroquinolone use in the Czech Republic, 2015. Eur J Clin Microbiol Infect Dis 2017; 36:2251-2258. [DOI: 10.1007/s10096-017-3055-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2017] [Accepted: 06/22/2017] [Indexed: 02/04/2023]
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Krutova M, Nyc O, Matejkova J, Kuijper EJ, Jalava J, Mentula S. The recognition and characterisation of Finnish Clostridium difficile isolates resembling PCR-ribotype 027. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2017; 51:344-351. [PMID: 28583353 DOI: 10.1016/j.jmii.2017.02.002] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Revised: 01/03/2017] [Accepted: 02/06/2017] [Indexed: 02/08/2023]
Abstract
PURPOSE To characterise and compare twenty-eight Finnish Clostridium difficile RT027-like isolates, selected based on the presence of 18 bp deletion in the tcdC gene and toxin gene profile (A, B, binary), with eleven RT027 isolates from different Finnish geographical areas and time periods. METHODS Twenty-eight C. difficile RT027-like isolates and 11 RT027 comparative strains were characterised by capillary-electrophoresis (CE) ribotyping, multi-locus variable tandem-repeats analysis (MLVA), multi-locus sequence typing (MLST), and sequencing of tcdC and gyrA gene fragments. Susceptibility to moxifloxacin was determined by E-test. RESULTS Of 28 RT027-like isolates, seven RTs (016, 034, 075, 080, 153, 176 and 328), three WEBRIBO types (411, 475, AI-78) and three new profiles (F1-F3) were identified. MLVA revealed six clonal complexes (RTs 016, 027, 176 and F3). MLST showed eleven sequence types (1, 41, 47, 67, 95, 191,192, 223, 229, 264 and new ST). Twenty-two isolates (RTs 016, 080, 176, 328, F1, F2, F3 and WRTAI-78) carried Δ117 in the tcdC gene. Isolates of RTs 016, 027 and 176 were moxifloxacin resistant and harboured Thr82Ile in the GyrA. CONCLUSION Our results show a high diversity within 28 Finnish RT027-like C. difficile isolates, with twelve CE-ribotyping profiles and eleven STs. MLVA revealed the regional spread of RTs 016, 027, 176 and F3. The presence of Δ117 in the tcdC gene in eight non-027 RTs highlights the importance of careful interpretation of the results from molecular systems targeting this site in the genome of C. difficile and the need of strain typing for epidemiological purposes.
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Affiliation(s)
- Marcela Krutova
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University in Prague and Motol University Hospital, Czech Republic; DNA Laboratory, Department of Paediatric Neurology, 2nd Faculty of Medicine, Charles University in Prague and Motol University Hospital, Czech Republic.
| | - Otakar Nyc
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University in Prague and Motol University Hospital, Czech Republic
| | - Jana Matejkova
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University in Prague and Motol University Hospital, Czech Republic
| | - Ed J Kuijper
- Leiden University Medical Centre, Leiden, The Netherlands
| | - Jari Jalava
- Bacterial Infections Unit, Department of Infectious Diseases, National Institute for Health and Welfare, Helsinki, Finland
| | - Silja Mentula
- Bacterial Infections Unit, Department of Infectious Diseases, National Institute for Health and Welfare, Helsinki, Finland
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35
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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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36
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Anjuwon-Foster BR, Tamayo R. A genetic switch controls the production of flagella and toxins in Clostridium difficile. PLoS Genet 2017; 13:e1006701. [PMID: 28346491 PMCID: PMC5386303 DOI: 10.1371/journal.pgen.1006701] [Citation(s) in RCA: 65] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Revised: 04/10/2017] [Accepted: 03/16/2017] [Indexed: 12/15/2022] Open
Abstract
In the human intestinal pathogen Clostridium difficile, flagella promote adherence to intestinal epithelial cells. Flagellar gene expression also indirectly impacts production of the glucosylating toxins, which are essential to diarrheal disease development. Thus, factors that regulate the expression of the flgB operon will likely impact toxin production in addition to flagellar motility. Here, we report the identification a "flagellar switch" that controls the phase variable production of flagella and glucosylating toxins. The flagellar switch, located upstream of the flgB operon containing the early stage flagellar genes, is a 154 bp invertible sequence flanked by 21 bp inverted repeats. Bacteria with the sequence in one orientation expressed flagellum and toxin genes, produced flagella, and secreted the toxins ("flg phase ON"). Bacteria with the sequence in the inverse orientation were attenuated for flagellar and toxin gene expression, were aflagellate, and showed decreased toxin secretion ("flg phase OFF"). The orientation of the flagellar switch is reversible during growth in vitro. We provide evidence that gene regulation via the flagellar switch occurs post-transcription initiation and requires a C. difficile-specific regulatory factor to destabilize or degrade the early flagellar gene mRNA when the flagellar switch is in the OFF orientation. Lastly, through mutagenesis and characterization of flagellar phase locked isolates, we determined that the tyrosine recombinase RecV, which catalyzes inversion at the cwpV switch, is also responsible for inversion at the flagellar switch in both directions. Phase variable flagellar motility and toxin production suggests that these important virulence factors have both advantageous and detrimental effects during the course of infection.
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Affiliation(s)
- Brandon R. Anjuwon-Foster
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, United States of America
| | - Rita Tamayo
- Department of Microbiology and Immunology, University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, North Carolina, United States of America
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37
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Färber J, Illiger S, Berger F, Gärtner B, von Müller L, Lohmann CH, Bauer K, Grabau C, Zibolka S, Schlüter D, Geginat G. Management of a cluster of Clostridium difficile infections among patients with osteoarticular infections. Antimicrob Resist Infect Control 2017; 6:22. [PMID: 28239451 PMCID: PMC5312516 DOI: 10.1186/s13756-017-0181-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2016] [Accepted: 02/08/2017] [Indexed: 01/25/2023] Open
Abstract
Background Here we describe a cluster of hospital-acquired Clostridium difficile infections (CDI) among 26 patients with osteoarticular infections. The aim of the study was to define the source of C. difficile and to evaluate the impact of general infection control measures and antibiotic stewardship on the incidence of CDI. Methods Epidemiological analysis included typing of C. difficile strains and analysis of possible patient to patient transmission. Infection control measures comprised strict isolation of CDI patients, additional hand washings, and intensified environmental cleaning with sporicidal disinfection. In addition an antibiotic stewardship program was implemented in order to prevent the use of CDI high risk antimicrobials such as fluoroquinolones, clindamycin, and cephalosporins. Results The majority of CDI (n = 15) were caused by C. difficile ribotype 027 (RT027). Most RT027 isolates (n = 9) showed high minimal inhibitory concentrations (MIC) for levofloxacin, clindamycin, and remarkably to rifampicin, which were all used for the treatment of osteoarticular infections. Epidemiological analysis, however, revealed no closer genetic relationship among the majority of RT027 isolates. The incidence of CDI was reduced only when a significant reduction in the use of fluoroquinolones (p = 0.006), third generation cephalosporins (p = 0.015), and clindamycin (p = 0.001) was achieved after implementation of an intensified antibiotic stewardship program which included a systematic review of all antibiotic prescriptions. Conclusion The successful reduction of the CDI incidence demonstrates the importance of antibiotic stewardship programs focused on patients treated for osteoarticular infections.
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Affiliation(s)
- Jacqueline Färber
- Institute of Medical Microbiology, Infection Control and Prevention, Otto-von-Guericke University of Magdeburg, Leipziger Straße 44, 39120 Magdeburg, Germany
| | - Sebastian Illiger
- Department of Orthopedic Surgery, Otto-von-Guericke University of Magdeburg, Magdeburg, Germany
| | - Fabian Berger
- Institute of Medical Microbiology and Hygiene, Consultant Laboratory for Clostridium difficile, University of Saarland, Saarland, Germany
| | - Barbara Gärtner
- Institute of Medical Microbiology and Hygiene, Consultant Laboratory for Clostridium difficile, University of Saarland, Saarland, Germany
| | - Lutz von Müller
- Institute for Laboratory Medicine, Microbiology and Hygiene, Christophorus Kliniken, Coesfeld, Germany
| | - Christoph H Lohmann
- Department of Orthopedic Surgery, Otto-von-Guericke University of Magdeburg, Magdeburg, Germany
| | - Katja Bauer
- Institute of Medical Microbiology, Infection Control and Prevention, Otto-von-Guericke University of Magdeburg, Leipziger Straße 44, 39120 Magdeburg, Germany
| | - Christina Grabau
- Central pharmacy, Otto-von-Guericke University of Magdeburg, Magdeburg, Germany
| | - Stefanie Zibolka
- Central pharmacy, Otto-von-Guericke University of Magdeburg, Magdeburg, Germany
| | - Dirk Schlüter
- Institute of Medical Microbiology, Infection Control and Prevention, Otto-von-Guericke University of Magdeburg, Leipziger Straße 44, 39120 Magdeburg, Germany.,Organ-specific Immune Regulation, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Gernot Geginat
- Institute of Medical Microbiology, Infection Control and Prevention, Otto-von-Guericke University of Magdeburg, Leipziger Straße 44, 39120 Magdeburg, Germany
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Knight DR, Squire MM, Collins DA, Riley TV. Genome Analysis of Clostridium difficile PCR Ribotype 014 Lineage in Australian Pigs and Humans Reveals a Diverse Genetic Repertoire and Signatures of Long-Range Interspecies Transmission. Front Microbiol 2017; 7:2138. [PMID: 28123380 PMCID: PMC5225093 DOI: 10.3389/fmicb.2016.02138] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 12/19/2016] [Indexed: 12/19/2022] Open
Abstract
Clostridium difficile PCR ribotype (RT) 014 is well-established in both human and porcine populations in Australia, raising the possibility that C. difficile infection (CDI) may have a zoonotic or foodborne etiology. Here, whole genome sequencing and high-resolution core genome phylogenetics were performed on a contemporaneous collection of 40 Australian RT014 isolates of human and porcine origin. Phylogenies based on MLST (7 loci, STs 2, 13, and 49) and core orthologous genes (1260 loci) showed clustering of human and porcine strains indicative of very recent shared ancestry. Core genome single nucleotide variant (SNV) analysis found 42% of human strains showed a clonal relationship (separated by ≤2 SNVs in their core genome) with one or more porcine strains, consistent with recent inter-host transmission. Clones were spread over a vast geographic area with 50% of the human cases occurring without recent healthcare exposure. These findings suggest a persistent community reservoir with long-range dissemination, potentially due to agricultural recycling of piggery effluent. We also provide the first pan-genome analysis for this lineage, characterizing its resistome, prophage content, and in silico virulence potential. The RT014 is defined by a large "open" pan-genome (7587 genes) comprising a core genome of 2296 genes (30.3% of the total gene repertoire) and an accessory genome of 5291 genes. Antimicrobial resistance genotypes and phenotypes varied across host populations and ST lineages and were characterized by resistance to tetracycline [tetM, tetA(P), tetB(P) and tetW], clindamycin/erythromycin (ermB), and aminoglycosides (aph3-III-Sat4A-ant6-Ia). Resistance was mediated by clinically important mobile genetic elements, most notably Tn6194 (harboring ermB) and a novel variant of Tn5397 (harboring tetM). Numerous clinically important prophages (Siphoviridae and Myoviridae) were identified as well as an uncommon accessory gene regulator locus (agr3). Conservation in the pathogenicity locus and S-layer correlated with ST affiliation, further extending the concept of clonal C. difficile lineages. This study provides novel insights on the genetic variability and strain relatedness of C. difficile RT014, a lineage of emerging One Health importance. Ongoing molecular and genomic surveillance of strains in humans, animals, food, and the environment is imperative to identify opportunities to reduce the overall CDI burden.
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Affiliation(s)
- Daniel R. Knight
- Microbiology and Immunology, School of Pathology and Laboratory Medicine, The University of Western AustraliaNedlands, WA, Australia
| | - Michele M. Squire
- Microbiology and Immunology, School of Pathology and Laboratory Medicine, The University of Western AustraliaNedlands, WA, Australia
| | - Deirdre A. Collins
- Microbiology and Immunology, School of Pathology and Laboratory Medicine, The University of Western AustraliaNedlands, WA, Australia
- Department of Population Health, School of Medical and Health Sciences, Edith Cowan UniversityJoondalup, WA, Australia
| | - Thomas V. Riley
- Department of Population Health, School of Medical and Health Sciences, Edith Cowan UniversityJoondalup, WA, Australia
- PathWest Laboratory Medicine, Department of Microbiology, Queen Elizabeth II Medical CentreNedlands, WA, Australia
- Department of Medical and Molecular Sciences, School of Veterinary and Life Sciences, Murdoch UniversityMurdoch, WA, Australia
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Comparative Genome Analysis and Global Phylogeny of the Toxin Variant Clostridium difficile PCR Ribotype 017 Reveals the Evolution of Two Independent Sublineages. J Clin Microbiol 2016; 55:865-876. [PMID: 28031436 PMCID: PMC5328454 DOI: 10.1128/jcm.01296-16] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2016] [Accepted: 11/09/2016] [Indexed: 12/21/2022] Open
Abstract
The diarrheal pathogen Clostridium difficile consists of at least six distinct evolutionary lineages. The RT017 lineage is anomalous, as strains only express toxin B, compared to strains from other lineages that produce toxins A and B and, occasionally, binary toxin. Historically, RT017 initially was reported in Asia but now has been reported worldwide. We used whole-genome sequencing and phylogenetic analysis to investigate the patterns of global spread and population structure of 277 RT017 isolates from animal and human origins from six continents, isolated between 1990 and 2013. We reveal two distinct evenly split sublineages (SL1 and SL2) of C. difficile RT017 that contain multiple independent clonal expansions. All 24 animal isolates were contained within SL1 along with human isolates, suggesting potential transmission between animals and humans. Genetic analyses revealed an overrepresentation of antibiotic resistance genes. Phylogeographic analyses show a North American origin for RT017, as has been found for the recently emerged epidemic RT027 lineage. Despite having only one toxin, RT017 strains have evolved in parallel from at least two independent sources and can readily transmit between continents.
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40
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Janezic S, Potocnik M, Zidaric V, Rupnik M. Highly Divergent Clostridium difficile Strains Isolated from the Environment. PLoS One 2016; 11:e0167101. [PMID: 27880843 PMCID: PMC5120845 DOI: 10.1371/journal.pone.0167101] [Citation(s) in RCA: 70] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2016] [Accepted: 11/07/2016] [Indexed: 01/05/2023] Open
Abstract
Clostridium difficile is one of the most important human and animal pathogens. However, the bacterium is ubiquitous and can be isolated from various sources. Here we report the prevalence and characterization of C. difficile in less studied environmental samples, puddle water (n = 104) and soil (n = 79). C. difficile was detected in 14.4% of puddle water and in 36.7% of soil samples. Environmental strains displayed antimicrobial resistance patterns comparable to already published data of human and animal isolates. A total of 480 isolates were grouped into 34 different PCR ribotypes. More than half of these (52.9%; 18 of 34) were already described in humans or animals. However, 14 PCR ribotypes were new in our PCR ribotype library and all but one were non-toxigenic. The multilocus sequence analysis of these new PCR ribotypes revealed that non-toxigenic environmental isolates are phylogenetically distinct and belong to three highly divergent clades, two of which have not been described before. Our data suggest that environment is a potential reservoir of genetically diverse population of C. difficile.
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Affiliation(s)
- Sandra Janezic
- National Laboratory for Health, Environment and Food (NLZOH), Maribor, Slovenia
- University of Maribor, Faculty of Medicine, Maribor, Slovenia
- * E-mail:
| | - Mojca Potocnik
- National Laboratory for Health, Environment and Food (NLZOH), Maribor, Slovenia
| | - Valerija Zidaric
- National Laboratory for Health, Environment and Food (NLZOH), Maribor, Slovenia
| | - Maja Rupnik
- National Laboratory for Health, Environment and Food (NLZOH), Maribor, Slovenia
- University of Maribor, Faculty of Medicine, Maribor, Slovenia
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41
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van Dorp SM, Smajlović E, Knetsch CW, Notermans DW, de Greeff SC, Kuijper EJ. Clinical and Microbiological Characteristics of Clostridium difficile Infection Among Hospitalized Children in the Netherlands. Clin Infect Dis 2016; 64:192-198. [PMID: 27986664 DOI: 10.1093/cid/ciw699] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2016] [Accepted: 10/18/2016] [Indexed: 01/25/2023] Open
Abstract
BACKGROUND Little is known about pediatric Clostridium difficile infection (CDI) epidemiology. We describe the clinical and microbiological characteristics of CDI among hospitalized children in the Netherlands. METHODS Between May 2009 and May 2015, 26 hospitals registered characteristics of pediatric (aged 2-18 years) and adult (aged 18 years) CDI in a national sentinel surveillance study. Routine polymerase chain reaction (PCR) ribotyping and multiple-locus variable-number tandem-repeat analysis (MLVA) of selected strains was performed. Pediatric and adult results were compared using proportion and 95% confidence interval (CI). Time trend of pediatric CDI was evaluated using a mixed-effect Poisson model. RESULTS Pediatric CDIs were reported in 17 of the 26 participating hospitals (n = 135; 3% of all CDIs); the monthly number was constant over time. The median age of pediatric cases was 10 years (interquartile range, 4.7-14.5 years). Fifty-five percent of the children had community onset and 31% had severe CDI. Compared with adults (n = 4,556), complication and mortality rates were lower. Clostridium difficile PCR ribotype 265 (toxin A negative, B positive) was most prevalent in children (15%; 95% CI, 8.8%-24.0%) but rarely found in adults (1%; 95% CI, 0.9%-1.6%). This strain was rarely found in other countries, except for Belgium. MLVA showed genetic relatedness between three-fourths of pediatric and adult ribotype 265 strains, without a clear epidemiological link. CONCLUSIONS Pediatric CDI in hospitals has remained stable over the last 6 years and resulted in fewer complications than for adult CDI. Further studies are needed to elucidate the source and epidemiology of PCR ribotype 265, primarily found in children.
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Affiliation(s)
- Sofie M van Dorp
- Department of Medical Microbiology, Leiden University Medical Center, The Netherlands; and
| | - Edela Smajlović
- Department of Medical Microbiology, Leiden University Medical Center, The Netherlands; and
| | - Cornelis W Knetsch
- Department of Medical Microbiology, Leiden University Medical Center, The Netherlands; and
| | - Daan W Notermans
- Centre for Infectious Disease Control, the National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Sabine C de Greeff
- Centre for Infectious Disease Control, the National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Ed J Kuijper
- Department of Medical Microbiology, Leiden University Medical Center, The Netherlands; and
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42
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Thabit AK, Alam MJ, Burnham CAD, Nicolau DP. Clinical use comparison of a semiautomated PCR with fluorescent ribotyping for typing of Clostridium difficile. Arch Microbiol 2016; 199:317-323. [PMID: 27730251 DOI: 10.1007/s00203-016-1305-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2015] [Revised: 02/11/2016] [Accepted: 10/05/2016] [Indexed: 11/25/2022]
Abstract
Molecular typing of Clostridium difficile is performed to assess strain relatedness or place strains within an epidemiological context. Different C. difficile ribotyping systems are available. However, a common strain library does not exist. We aimed to compare ribotyping results of 29 clinical C. difficile isolates by two methods: semiautomated PCR-ribotyping and fluorescent PCR-ribotyping. For certain ribotypes (n = 16/29; 55.2 %), the inter-laboratory reproducibility was consistent among multiple samples from individual subjects, while 54.8 % (n = 14/29) were discordant. Additionally, 11/29 ribotypes (38 %) and 12/29 ribotypes (41 %) did not match with known reference strains in the semiautomated PCR-fluorescent ribotyping systems' libraries, respectively. The identification of 027 ribotype by both systems was consistent for 75 % of the isolates. Discriminatory indices for the semiautomated PCR-ribotyping and fluorescent PCR-ribotyping systems are 0.906 and 0.886, respectively. Although ribotyping provides important epidemiologic insights, the lack of a common strain library makes interpretation of results using different ribotyping protocols difficult.
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Affiliation(s)
- Abrar K Thabit
- Center for Anti-infective Research and Development, Hartford Hospital, 80 Seymour Street, Hartford, CT, 06102, USA
- Faculty of Pharmacy, King Abdulaziz University, Jeddah, Saudi Arabia
| | | | - Carey-Ann D Burnham
- Department of Pathology and Immunology, Washington University School of Medicine in St. Louis, St. Louis, MO, USA
| | - David P Nicolau
- Center for Anti-infective Research and Development, Hartford Hospital, 80 Seymour Street, Hartford, CT, 06102, USA.
- Division of Infectious Diseases, Hartford Hospital, Hartford, CT, USA.
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43
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Barbanti F, Spigaglia P. Characterization of Clostridium difficile PCR-ribotype 018: A problematic emerging type. Anaerobe 2016; 42:123-129. [PMID: 27725230 DOI: 10.1016/j.anaerobe.2016.10.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 09/20/2016] [Accepted: 10/06/2016] [Indexed: 10/20/2022]
Abstract
Recent surveys indicate that the majority of toxigenic Clostridium difficile strains isolated in European hospitals belonged to PCR-ribotypes (RTs) different from RT 027 or RT 078. Among these types, RT 018 has been reported in Italy and, more recently, in Korea and Japan. In Italy, strains RT 018 have become predominant in the early 2000s, whereas the majority of strains isolated before were RT 126, a type belonging to the same lineage as the RT 078. In this study, we have found that Italian strains RT 018 are resistant to erythromycin, clindamycin, moxifloxacin and rifampicin. Rifampicin resistance is rarely observed in strains RT 018 from other countries and in Italian strains RT 078 and RT 126, therefore the decennial use of rifamycin antibiotics in Italy may be one of the driving factors for the spread of RT 018 in our country. The strains RT 018 examined showed a significant higher adhesion to Caco-2 cells compared to strains RT 078 and RT 126. Furthermore, strains RT 018 became predominant in in vitro competition assays with strains RT 078 or RT 126. If maintained in vivo, these characteristics could lead to a rapid colonization of the intestine by strains RT 018. Under the conditions used, isolates RT 018 produced significantly higher toxins levels compared to strains RT 078 and RT 126, while heat-resistant CFUs production seems to be strain-dependent. Robust toxin production and enhanced sporulation could in part explain the high diffusion and interpatient transmissibility observed for strains RT 018 in the hospital environment. In conclusion, the characteristics observed in the Italian isolates RT 018 seem to contribute in conferring an adaptive advantage to these strains, allowing their successful spread in our country.
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Affiliation(s)
- Fabrizio Barbanti
- Department of Infectious, Parasitic and Immune-mediated Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Patrizia Spigaglia
- Department of Infectious, Parasitic and Immune-mediated Diseases, Istituto Superiore di Sanità, Rome, Italy.
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44
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Andersen JM, Shoup M, Robinson C, Britton R, Olsen KEP, Barrangou R. CRISPR Diversity and Microevolution in Clostridium difficile. Genome Biol Evol 2016; 8:2841-55. [PMID: 27576538 PMCID: PMC5630864 DOI: 10.1093/gbe/evw203] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/12/2016] [Indexed: 12/20/2022] Open
Abstract
Virulent strains of Clostridium difficile have become a global health problem associated with morbidity and mortality. Traditional typing methods do not provide ideal resolution to track outbreak strains, ascertain genetic diversity between isolates, or monitor the phylogeny of this species on a global basis. Here, we investigate the occurrence and diversity of clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated genes (cas) in C. difficile to assess the potential of CRISPR-based phylogeny and high-resolution genotyping. A single Type-IB CRISPR-Cas system was identified in 217 analyzed genomes with cas gene clusters present at conserved chromosomal locations, suggesting vertical evolution of the system, assessing a total of 1,865 CRISPR arrays. The CRISPR arrays, markedly enriched (8.5 arrays/genome) compared with other species, occur both at conserved and variable locations across strains, and thus provide a basis for typing based on locus occurrence and spacer polymorphism. Clustering of strains by array composition correlated with sequence type (ST) analysis. Spacer content and polymorphism within conserved CRISPR arrays revealed phylogenetic relationship across clades and within ST. Spacer polymorphisms of conserved arrays were instrumental for differentiating closely related strains, e.g., ST1/RT027/B1 strains and pathogenicity locus encoding ST3/RT001 strains. CRISPR spacers showed sequence similarity to phage sequences, which is consistent with the native role of CRISPR-Cas as adaptive immune systems in bacteria. Overall, CRISPR-Cas sequences constitute a valuable basis for genotyping of C. difficile isolates, provide insights into the micro-evolutionary events that occur between closely related strains, and reflect the evolutionary trajectory of these genomes.
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Affiliation(s)
- Joakim M Andersen
- Department of Food, Processing and Nutritional Sciences, North Carolina State University, NC
| | - Madelyn Shoup
- Department of Microbiology and Molecular Genetics, Michigan State University, MI
| | - Cathy Robinson
- Department of Microbiology and Molecular Genetics, Michigan State University, MI
| | - Robert Britton
- Department of Molecular Virology and Microbiology, Center for Metagenomics and Microbiome Research, Baylor College of Medicine, TX
| | - Katharina E P Olsen
- Microbial Competence Centre, Novo Nordisk, Bagsværd, Denmark (Former Employment: Department of Microbiology & Infection Control, Statens Serum Institut, Copenhagen, Denmark)
| | - Rodolphe Barrangou
- Department of Food, Processing and Nutritional Sciences, North Carolina State University, NC
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Draft Genome Sequence of Clostridium difficile Belonging to Ribotype 018 and Sequence Type 17. GENOME ANNOUNCEMENTS 2016; 4:4/5/e00907-16. [PMID: 27587821 PMCID: PMC5009978 DOI: 10.1128/genomea.00907-16] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Clostridium difficile, belonging to ribotype 018 (RT018), is one of the most prevalent genotypes circulating in hospital settings in Italy. Here, we report the draft genome of C. difficile CD8-15 belonging to RT018, isolated from a patient with fatal C. difficile-associated infection.
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46
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Krutova M, Nyc O, Matejkova J, Allerberger F, Wilcox MH, Kuijper EJ. Molecular characterisation of Czech Clostridium difficile isolates collected in 2013-2015. Int J Med Microbiol 2016; 306:479-485. [PMID: 27519407 DOI: 10.1016/j.ijmm.2016.07.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Revised: 07/27/2016] [Accepted: 07/31/2016] [Indexed: 12/16/2022] Open
Abstract
Clostridium difficile is a leading nosocomial pathogen and molecular typing is a crucial part of monitoring its occurrence and spread. Over a three-year period (2013-2015), clinical C. difficile isolates from 32 Czech hospitals were collected for molecular characterisation. Of 2201 C. difficile isolates, 177 (8%) were non-toxigenic, 2024 (92%) were toxigenic (tcdA and tcdB) and of these, 677 (33.5%) carried genes for binary toxin production (cdtA, cdtB). Capillary-electrophoresis (CE) ribotyping of the 2201 isolates yielded 166 different CE-ribotyping profiles, of which 53 were represented by at least two isolates for each profile. Of these, 29 CE-ribotyping patterns were common to the Leeds-Leiden C. difficile reference strain library and the WEBRIBO database (83.7% isolates), and 24 patterns were recognized only by the WEBRIBO database (11.2% isolates). Isolates belonging to these 53 CE-ribotyping profiles comprised 94.9% of all isolates. The ten most frequent CE-ribotyping profiles were 176 (n=588, 26.7%), 001 (n=456, 20.7%), 014 (n=176, 8%), 012 (n=127, 5.8%), 017 (n=85, 3.9%), 020 (n=68, 3.1%), 596 (n=55, 2.5%), 002-like (n=45, 2.1%), 010 (n=35, 1.6%) and 078 (n=34, 1.6%). Multi-locus sequence typing (MLST) of seven housekeeping genes performed in one isolate of each of 53 different CE-ribotyping profiles revealed 40 different sequence types (STs). We conclude that molecular characterisation of Czech C. difficile isolates revealed a high diversity of CE-ribotyping profiles; the prevailing RTs were 001 (20.7%) and 176 (027-like, 26.7%).
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Affiliation(s)
- M Krutova
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University in Prague and Motol University Hospital, Czech Republic; DNA Laboratory, Department of Paediatric Neurology, 2nd Faculty of Medicine, Charles University in Prague and Motol University Hospital, Czech Republic.
| | - O Nyc
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University in Prague and Motol University Hospital, Czech Republic
| | - J Matejkova
- Department of Medical Microbiology, 2nd Faculty of Medicine, Charles University in Prague and Motol University Hospital, Czech Republic
| | - F Allerberger
- Austrian Agency for Health and Food Safety (AGES), Wien, Austria
| | - M H Wilcox
- Leeds Teaching Hospitals NHS Trust, Leeds, United Kingdom
| | - E J Kuijper
- Leiden University Medical Centre, Leiden, The Netherlands
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47
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Abstract
Infection of the colon with the Gram-positive bacterium Clostridium difficile is potentially life threatening, especially in elderly people and in patients who have dysbiosis of the gut microbiota following antimicrobial drug exposure. C. difficile is the leading cause of health-care-associated infective diarrhoea. The life cycle of C. difficile is influenced by antimicrobial agents, the host immune system, and the host microbiota and its associated metabolites. The primary mediators of inflammation in C. difficile infection (CDI) are large clostridial toxins, toxin A (TcdA) and toxin B (TcdB), and, in some bacterial strains, the binary toxin CDT. The toxins trigger a complex cascade of host cellular responses to cause diarrhoea, inflammation and tissue necrosis - the major symptoms of CDI. The factors responsible for the epidemic of some C. difficile strains are poorly understood. Recurrent infections are common and can be debilitating. Toxin detection for diagnosis is important for accurate epidemiological study, and for optimal management and prevention strategies. Infections are commonly treated with specific antimicrobial agents, but faecal microbiota transplants have shown promise for recurrent infections. Future biotherapies for C. difficile infections are likely to involve defined combinations of key gut microbiota.
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Affiliation(s)
- Wiep Klaas Smits
- Section Experimental Bacteriology, Department of Medical Microbiology, Leiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands
| | - Dena Lyras
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, and Department of Microbiology, Monash University, Victoria, Australia
| | - D. Borden Lacy
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, and The Veterans Affairs Tennessee Valley Healthcare System, Nashville Tennessee, USA
| | - Mark H. Wilcox
- Institute of Biomedical and Clinical Sciences, University of Leeds, Leeds, UK
| | - Ed J. Kuijper
- Section Experimental Bacteriology, Department of Medical Microbiology, Leiden University Medical Center, PO Box 9600, 2300 RC Leiden, The Netherlands
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48
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van der Plas-Duivesteijn SJ, Wulff T, Klychnikov O, Ohana D, Dalebout H, van Veelen PA, de Keijzer J, Nessen MA, van der Burgt YEM, Deelder AM, Palmblad M. Differentiating samples and experimental protocols by direct comparison of tandem mass spectra. RAPID COMMUNICATIONS IN MASS SPECTROMETRY : RCM 2016; 30:731-738. [PMID: 26864526 DOI: 10.1002/rcm.7494] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Revised: 12/16/2015] [Accepted: 12/20/2015] [Indexed: 06/05/2023]
Abstract
RATIONALE Peptide tandem mass spectra can be analyzed by a number of means. They can be compared against predicted spectra of peptides derived from genome sequences, compared against previously acquired and identified spectra, or - sometimes - sequenced de novo. We recently introduced another method which compares spectra between liquid chromatography/tandem mass spectrometry (LC/MS/MS) datasets to determine the shared spectral content, and demonstrated how this can be applied in a molecular phylogenetic study using sera from human and non-human primates. We will here explore if such a method have other, serendipitous uses. METHODS We used the existing compareMS2 algorithm without modification on a diverse set of experiments. RESULTS First we conducted a small phylogenetic study, using (mammalian) bone samples to study old material, and human pathogens aiming to distinguish clinically important strains. Although not as straightforward as primate sera analysis, the method shows significant promise for all these applications. We also used the algorithm to compare 24 different protocols for extraction of proteins from muscle tissue. The results provided useful information in comparing protocols. Finally, we applied compareMS2 aiming for quality control of two traceable protein reference standards (troponin) used in clinical chemistry assays, by analysing the effect of storage conditions. CONCLUSIONS The results illustrate a broad applicability of the metric based on shared tandem mass spectra between LC/MS/MS datasets for analysing protein digests in different types of experiments. There is no reason to assume that our instance of this method is optimal in any of these situations, as it makes limited or no use of accurate mass and chromatographic retention time. We propose that with further improvement and refinement, this type of analysis can be applied as a simple but informative first step in many pipelines for bottom-up tandem mass spectrometry data analysis in proteomics and other fields, comparing or analysing large numbers of samples or datasets.
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Affiliation(s)
| | - Tune Wulff
- Novo Nordisk Foundation Center for Biosustainability, Technical University of Denmark, Hørsholm, Denmark
| | - Oleg Klychnikov
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Dana Ohana
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Hans Dalebout
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Peter A van Veelen
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Jeroen de Keijzer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Yuri E M van der Burgt
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
- Department of Clinical Chemistry, Leiden University Medical Center, Leiden, The Netherlands
| | - André M Deelder
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Magnus Palmblad
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
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49
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Abstract
Clostridium difficile infection (CDI) is the leading cause of antimicrobial and health care-associated diarrhea in humans, presenting a significant burden to global health care systems. In the last 2 decades, PCR- and sequence-based techniques, particularly whole-genome sequencing (WGS), have significantly furthered our knowledge of the genetic diversity, evolution, epidemiology, and pathogenicity of this once enigmatic pathogen. C. difficile is taxonomically distinct from many other well-known clostridia, with a diverse population structure comprising hundreds of strain types spread across at least 6 phylogenetic clades. The C. difficile species is defined by a large diverse pangenome with extreme levels of evolutionary plasticity that has been shaped over long time periods by gene flux and recombination, often between divergent lineages. These evolutionary events are in response to environmental and anthropogenic activities and have led to the rapid emergence and worldwide dissemination of virulent clonal lineages. Moreover, genome analysis of large clinically relevant data sets has improved our understanding of CDI outbreaks, transmission, and recurrence. The epidemiology of CDI has changed dramatically over the last 15 years, and CDI may have a foodborne or zoonotic etiology. The WGS era promises to continue to redefine our view of this significant pathogen.
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50
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Mentula S, Laakso S, Lyytikäinen O, Kirveskari J. Differentiating virulent 027 and non-027 Clostridium difficile strains by molecular methods. Expert Rev Mol Diagn 2015; 15:1225-9. [PMID: 26289601 DOI: 10.1586/14737159.2015.1069710] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
OBJECTIVE Hypervirulent Clostridium difficile clade has been shown to include several lineages of ribotype 027 and also other ribotypes. We present data on additional non-027 strains, identified as presumptive 027 by two commercial molecular C. difficile assays. METHODS The tested clinical isolates were selected from the national reference laboratory collection on the basis of toxin gene profile similarities with ribotype 027 and tested with XpertC. difficile/Epi and Amplidiag C. difficile+027 assay. RESULT Xpert misclassified five ribotypes (016, 019, 080, 176 and variant of type 046) as presumptive 027 and Amplidiag two ribotypes (016, 176). The misclassified strains were rare, covering 1.6% of reference laboratory strain collection. CONCLUSION Our findings confirm the concept that there are closely related outliers to hypervirulent 027 clones that can be misclassified as 027, and that these comprise numerous ribotypes, including previously reported four ribotypes (198, 176, 244, 019), and additional three (016, v046, 080) identified in the present study.
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Affiliation(s)
- Silja Mentula
- a 1 National Institute for Health and Welfare - Infectious Diseases, P.O. Box 30, Helsinki 00271, Finland
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