1
|
Dost I, Abdel-Glil M, Persson S, Conza KL, Oleastro M, Alves F, Maurischat S, Scholtzek A, Mazuet C, Diancourt L, Tenson T, Schmoock G, Neubauer H, Schwarz S, Seyboldt C. Genomic study of European Clostridioides difficile ribotype 002/sequence type 8. Microb Genom 2024; 10:001270. [PMID: 39051872 PMCID: PMC11316560 DOI: 10.1099/mgen.0.001270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 06/21/2024] [Indexed: 07/27/2024] Open
Abstract
Clostridioides difficile has significant clinical importance as a leading cause of healthcare-associated infections, with symptoms ranging from mild diarrhoea to severe colitis, and possible life-threatening complications. C. difficile ribotype (RT) 002, mainly associated with MLST sequence type (ST) 8, is one of the most common RTs found in humans. This study aimed at investigating the genetic characteristics of 537 C. difficile genomes of ST8/RT002. To this end, we sequenced 298 C. difficile strains representing a new European genome collection, with strains from Germany, Denmark, France and Portugal. These sequences were analysed against a global dataset consisting of 1,437 ST8 genomes available through Enterobase. Our results showed close genetic relatedness among the studied ST8 genomes, a diverse array of antimicrobial resistance (AMR) genes and the presence of multiple mobile elements. Notably, the pangenome analysis revealed an open genomic structure. ST8 shows relatively low overall variation. Thus, clonal isolates were found across different One Health sectors (humans, animals, environment and food), time periods, and geographical locations, suggesting the lineage's stability and a universal environmental source. Importantly, this stability did not hinder the acquisition of AMR genes, emphasizing the adaptability of this bacterium to different selective pressures. Although only 2.4 % (41/1,735) of the studied genomes originated from non-human sources, such as animals, food, or the environment, we identified 9 cross-sectoral core genome multilocus sequence typing (cgMLST) clusters. Our study highlights the importance of ST8 as a prominent lineage of C. difficile with critical implications in the context of One Health. In addition, these findings strongly support the need for continued surveillance and investigation of non-human samples to gain a more comprehensive understanding of the epidemiology of C. difficile.
Collapse
Affiliation(s)
- Ines Dost
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Naumburger Straße 96a, 07743 Jena, Germany
| | - Mostafa Abdel-Glil
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Naumburger Straße 96a, 07743 Jena, Germany
| | - Søren Persson
- Statens Serum Institut, Dept. Bacteria, Parasites and Fungi, Unit of Foodborne Infections, Artillerivej 5, 2300 Copenhagen, Denmark
| | - Karen Loaiza Conza
- Statens Serum Institut, Dept. Bacteria, Parasites and Fungi, Unit of Foodborne Infections, Artillerivej 5, 2300 Copenhagen, Denmark
| | - Mónica Oleastro
- National Reference Laboratory of Gastrointestinal Infections, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), 1649-016 Lisbon, Portugal
| | - Frederico Alves
- National Reference Laboratory of Gastrointestinal Infections, Department of Infectious Diseases, National Institute of Health Doutor Ricardo Jorge (INSA), 1649-016 Lisbon, Portugal
- Chief Scientific Office, European Food Safety Authority (EFSA), Parma, Italy
| | - Sven Maurischat
- German Federal Institute for Risk Assessment, Department Biological Safety, Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
| | - Anissa Scholtzek
- German Federal Institute for Risk Assessment, Department Biological Safety, Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
| | - Christelle Mazuet
- Institut Pasteur, Université Paris Cité, Centre National de Référence Bactéries anaérobies et Botulisme, F-75015 Paris, France
| | - Laure Diancourt
- Institut Pasteur, Université Paris Cité, Centre National de Référence Bactéries anaérobies et Botulisme, F-75015 Paris, France
| | - Tanel Tenson
- Institute of Technology, University of Tartu, Nooruse 1, 50411 Tartu, Estonia
| | - Gernot Schmoock
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Naumburger Straße 96a, 07743 Jena, Germany
| | - Heinrich Neubauer
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Naumburger Straße 96a, 07743 Jena, Germany
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, School of Veterinary Medicine, Freie Universität Berlin, 14163 Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, 14163 Berlin, Germany
| | - Christian Seyboldt
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Naumburger Straße 96a, 07743 Jena, Germany
| |
Collapse
|
2
|
Hussain H, Nubgan A, Rodríguez C, Imwattana K, Knight DR, Parthala V, Mullany P, Goh S. Removal of mobile genetic elements from the genome of Clostridioides difficile and the implications for the organism's biology. Front Microbiol 2024; 15:1416665. [PMID: 38966395 PMCID: PMC11222575 DOI: 10.3389/fmicb.2024.1416665] [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: 04/12/2024] [Accepted: 06/04/2024] [Indexed: 07/06/2024] Open
Abstract
Clostridioides difficile is an emerging pathogen of One Health significance. Its highly variable genome contains mobile genetic elements (MGEs) such as transposons and prophages that influence its biology. Systematic deletion of each genetic element is required to determine their precise role in C. difficile biology and contribution to the wider mobilome. Here, Tn5397 (21 kb) and ϕ027 (56 kb) were deleted from C. difficile 630 and R20291, respectively, using allele replacement facilitated by CRISPR-Cas9. The 630 Tn5397 deletant transferred PaLoc at the same frequency (1 × 10-7) as 630 harboring Tn5397, indicating that Tn5397 alone did not mediate conjugative transfer of PaLoc. The R20291 ϕ027 deletant was sensitive to ϕ027 infection, and contained two unexpected features, a 2.7 kb remnant of the mutagenesis plasmid, and a putative catalase gene adjacent to the deleted prophage was also deleted. Growth kinetics of R20291 ϕ027 deletant was similar to wild type (WT) in rich medium but marginally reduced compared with WT in minimal medium. This work indicates the commonly used pMTL8000 plasmid series works well for CRISPR-Cas9-mediated gene deletion, resulting in the largest deleted locus (56.8 kb) described in C. difficile. Removal of MGEs was achieved by targeting conjugative/integrative regions to promote excision and permanent loss. The deletants created will be useful strains for investigating Tn5397 or ϕ027 prophage contribution to host virulence, fitness, and physiology, and a platform for other mutagenesis studies aimed at functional gene analysis without native transposon or phage interference in C. difficile 630 and R20291.
Collapse
Affiliation(s)
- Haitham Hussain
- Department of Microbial Diseases, Eastman Dental Institute, University College London, London, United Kingdom
| | - Amer Nubgan
- Department of Clinical, Pharmaceutical and Biological Sciences, University of Hertfordshire, Hatfield, United Kingdom
| | - César Rodríguez
- Facultad de Microbiología and Centro de Investigación en Enfermedades Tropicales (CIET), Universidad de Costa Rica, San José, Costa Rica
| | - Korakrit Imwattana
- School of Biomedical Sciences, The University of Western Australia, Perth, WA, Australia
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Salaya, Thailand
| | - Daniel R. Knight
- School of Biomedical Sciences, The University of Western Australia, Perth, WA, Australia
- Department of Microbiology, PathWest Laboratory Medicine WA, Queen Elizabeth II Medical Centre, Nedlands, WA, Australia
| | - Valerija Parthala
- Department of Clinical, Pharmaceutical and Biological Sciences, University of Hertfordshire, Hatfield, United Kingdom
| | - Peter Mullany
- Department of Microbial Diseases, Eastman Dental Institute, University College London, London, United Kingdom
| | - Shan Goh
- Department of Clinical, Pharmaceutical and Biological Sciences, University of Hertfordshire, Hatfield, United Kingdom
| |
Collapse
|
3
|
Dabernig-Heinz J, Wagner GE, Prior K, Lipp M, Kienesberger S, Ruppitsch W, Rønning TG, Harmsen D, Steinmetz I, Leitner E. Core genome multilocus sequence typing (cgMLST) applicable to the monophyletic Klebsiella oxytoca species complex. J Clin Microbiol 2024; 62:e0172523. [PMID: 38780286 PMCID: PMC11237601 DOI: 10.1128/jcm.01725-23] [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: 01/08/2024] [Accepted: 04/26/2024] [Indexed: 05/25/2024] Open
Abstract
The environmental bacterium Klebsiella oxytoca displays an alarming increase of antibiotic-resistant strains that frequently cause outbreaks in intensive care units. Due to its prevalence in the environment and opportunistic presence in humans, molecular surveillance (including resistance marker screening) and high-resolution cluster analysis are of high relevance. Furthermore, K. oxytoca previously described in studies is rather a species complex (KoSC) than a single species comprising at least six closely related species that are not easily differentiated by standard typing methods. To reach a discriminatory power high enough to identify and resolve clusters within these species, whole genome sequencing is necessary. The resolution is achievable with core genome multilocus sequence typing (cgMLST) extending typing of a few housekeeping genes to thousands of core genome genes. CgMLST is highly standardized and provides a nomenclature enabling cross laboratory reproducibility and data exchange for routine diagnostics. Here, we established a cgMLST scheme not only capable of resolving the KoSC species but also producing reliable and consistent results for published outbreaks. Our cgMLST scheme consists of 2,536 core genome and 2,693 accessory genome targets, with a percentage of good cgMLST targets of 98.31% in 880 KoSC genomes downloaded from the National Center for Biotechnology Information (NCBI). We also validated resistance markers against known resistance gene patterns and successfully linked genetic results to phenotypically confirmed toxic strains carrying the til gene cluster. In conclusion, our novel cgMLST enables highly reproducible typing of four different clinically relevant species of the KoSC and thus facilitates molecular surveillance and cluster investigations.
Collapse
Affiliation(s)
- Johanna Dabernig-Heinz
- Diagnostic and Research Institute for Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Gabriel E Wagner
- Diagnostic and Research Institute for Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Karola Prior
- Department of Periodontology and Operative Dentistry, University Hospital Münster, Münster, Germany
| | - Michaela Lipp
- Diagnostic and Research Institute for Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Sabine Kienesberger
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
- Field of Excellence BioHealth, University of Graz, Graz, Austria
| | - Werner Ruppitsch
- Institute of Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety, Vienna, Austria
| | - Torunn G Rønning
- Department of Medical Microbiology, St. Olavs Hospital, Trondheim University Hospital, Trondheim, Norway
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Dag Harmsen
- Department of Periodontology and Operative Dentistry, University Hospital Münster, Münster, Germany
| | - Ivo Steinmetz
- Diagnostic and Research Institute for Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Eva Leitner
- Diagnostic and Research Institute for Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| |
Collapse
|
4
|
Cuperus T, Wit B, Castelijn G, Hengeveld P, Opsteegh M, van der Giessen J, Harmanus C, van Prehn J, Kuijper EJ, Smits WK. Clostridioides difficile in calves, cattle and humans from Dutch dairy farms: Predominance of PCR ribotype 695 (clade 5, sequence type 11) in cattle. One Health 2024; 18:100739. [PMID: 38707933 PMCID: PMC11067380 DOI: 10.1016/j.onehlt.2024.100739] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 04/21/2024] [Indexed: 05/07/2024] Open
Abstract
Background Clostridioides difficile is a leading cause of infectious diarrhea in both humans and livestock. In particular, C. difficile strains belonging to sequence type (ST) 11 are common enteropathogens. The aim of this study was to determine the presence and genetic relatedness of C. difficile types in dairy cattle and calves. Method Dutch dairy farms were visited between February and December 2021. Feces was collected from adult dairy cattle and calves of two age categories (<4 weeks and 4 weeks-4 months). Fecal samples were also requested from dairy farmers, family members and employees. Fecal samples were cultured in an enrichment medium for 10-15 days and subcultured on solid media for capillary PCR ribotyping and whole genome sequencing. Results C. difficile was detected on 31 out of 157 (19.8%) dairy farms. The highest prevalence was found in calves <4 weeks (17.5%). None of the 99 human samples collected were positive. Thirty-seven cultured isolates belonged to 11 different PCR ribotypes (RT) of which RT695 (56.8%) and RT078/126 (16.2%) were most abundant. In the database of the Netherlands National Expertise Centre for C. difficile infections (CDI, >10.000 patient isolates), RT695 was found in only two patients with hospital-onset CDI, diagnosed in 2020 and 2021. Sequence analysis of 21C. difficile RT695 from cattle revealed that all isolates belonged to clade 5, ST11 and contained genes encoding toxin A, toxin B and binary toxin. RT695 strains carried antimicrobial resistance genes typically found in clade 5C. difficile. Groups of genetically related RT695 isolates were found between dairy farms, whereas identical strains were only present in individual farms. Conclusions C. difficile was found in ∼20% of dairy farms with a predominance of the relatively unknown RT695. Isolates of RT695 belonged to the same clade and sequence type as RT078/126, which is recognized as an important zoonotic type.
Collapse
Affiliation(s)
- Tryntsje Cuperus
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Ben Wit
- Netherlands Food and Consumer Product Safety Authority (NVWA), Utrecht, the Netherlands
| | - Greetje Castelijn
- Wageningen Food Safety Research (WFSR), Wageningen University & Research, Wageningen, the Netherlands
| | - Paul Hengeveld
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Marieke Opsteegh
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Joke van der Giessen
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Céline Harmanus
- Leiden University Center for Infectious Diseases (LUCID), Leiden University Medical Center (LUMC), Leiden, the Netherlands
| | - Joffrey van Prehn
- Leiden University Center for Infectious Diseases (LUCID), Leiden University Medical Center (LUMC), Leiden, the Netherlands
- National Expertise Centre for Clostridiodes difficile infections at Leiden University Center for Infectious Diseases (LUCID), Leiden University Medical Centre (LUMC), Leiden, the Netherlands and Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Ed J. Kuijper
- Leiden University Center for Infectious Diseases (LUCID), Leiden University Medical Center (LUMC), Leiden, the Netherlands
- National Expertise Centre for Clostridiodes difficile infections at Leiden University Center for Infectious Diseases (LUCID), Leiden University Medical Centre (LUMC), Leiden, the Netherlands and Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Wiep Klaas Smits
- Leiden University Center for Infectious Diseases (LUCID), Leiden University Medical Center (LUMC), Leiden, the Netherlands
- National Expertise Centre for Clostridiodes difficile infections at Leiden University Center for Infectious Diseases (LUCID), Leiden University Medical Centre (LUMC), Leiden, the Netherlands and Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| |
Collapse
|
5
|
Meijers E, Verhees FB, Heemskerk D, Wessels E, Claas ECJ, Boers SA. Automating the Illumina DNA library preparation kit for whole genome sequencing applications on the flowbot ONE liquid handler robot. Sci Rep 2024; 14:8159. [PMID: 38589623 PMCID: PMC11001922 DOI: 10.1038/s41598-024-58963-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 04/05/2024] [Indexed: 04/10/2024] Open
Abstract
Whole-genome sequencing (WGS) is currently making its transition from research tool into routine (clinical) diagnostic practice. The workflow for WGS includes the highly labor-intensive library preparations (LP), one of the most critical steps in the WGS procedure. Here, we describe the automation of the LP on the flowbot ONE robot to minimize the risk of human error and reduce hands-on time (HOT). For this, the robot was equipped, programmed, and optimized to perform the Illumina DNA Prep automatically. Results obtained from 16 LP that were performed both manually and automatically showed comparable library DNA yields (median of 1.5-fold difference), similar assembly quality values, and 100% concordance on the final core genome multilocus sequence typing results. In addition, reproducibility of results was confirmed by re-processing eight of the 16 LPs using the automated workflow. With the automated workflow, the HOT was reduced to 25 min compared to the 125 min needed when performing eight LPs using the manual workflow. The turn-around time was 170 and 200 min for the automated and manual workflow, respectively. In summary, the automated workflow on the flowbot ONE generates consistent results in terms of reliability and reproducibility, while significantly reducing HOT as compared to manual LP.
Collapse
Affiliation(s)
- Erin Meijers
- Department of Medical Microbiology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Fabienne B Verhees
- Department of Medical Microbiology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Dennis Heemskerk
- Department of Medical Microbiology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Els Wessels
- Department of Medical Microbiology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Eric C J Claas
- Department of Medical Microbiology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands
| | - Stefan A Boers
- Department of Medical Microbiology, Leiden University Medical Center, Albinusdreef 2, 2333 ZA, Leiden, The Netherlands.
| |
Collapse
|
6
|
Zeng J, Fang S, Guo J, Dong M, Tian G, Tao L. Fight or flee, a vital choice for Clostridioides difficile. MLIFE 2024; 3:14-20. [PMID: 38827507 PMCID: PMC11139204 DOI: 10.1002/mlf2.12102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 09/17/2023] [Accepted: 10/08/2023] [Indexed: 06/04/2024]
Abstract
Clostridioides difficile is a leading cause of healthcare-associated infections, causing billions of economic losses every year. Its symptoms range from mild diarrhea to life-threatening damage to the colon. Transmission and recurrence of C. difficile infection (CDI) are mediated by the metabolically dormant spores, while the virulence of C. difficile is mainly due to the two large clostridial toxins, TcdA and TcdB. Producing toxins or forming spores are two different strategies for C. difficile to cope with harsh environmental conditions. It is of great significance to understand the molecular mechanisms for C. difficile to skew to either of the cellular processes. Here, we summarize the current understanding of the regulation and connections between toxin production and sporulation in C. difficile and further discuss the potential solutions for yet-to-be-answered questions.
Collapse
Affiliation(s)
- Ji Zeng
- School of Biomedical and Pharmaceutical SciencesGuangdong University of TechnologyGuangzhouChina
| | - Shuying Fang
- School of Biomedical and Pharmaceutical SciencesGuangdong University of TechnologyGuangzhouChina
| | - Jinquan Guo
- Department of Brest SurgeryPanyu Central HospitalGuangzhouChina
| | - Min Dong
- Department of MicrobiologyHarvard Medical SchoolBostonMassachusettsUSA
- Department of Urology, Boston Children's HospitalHarvard Medical SchoolBostonMassachusettsUSA
| | - Guo‐Bao Tian
- Department of MicrobiologyZhongshan School of Medicine, Sun Yat‐sen UniversityGuangzhouChina
- Advanced Medical Technology Center, The First Affiliated Hospital, Zhongshan School of MedicineSun Yat‐sen UniversityGuangzhouChina
- Key Laboratory of Tropical Diseases Control (Sun Yat‐sen University), Ministry of EducationGuangzhouChina
- School of MedicineXizang Minzu UniversityXianyangChina
| | - Liang Tao
- Center for Infectious Disease Research, Westlake Laboratory of Life Sciences and BiomedicineWestlake UniversityHangzhouChina
- Research Center for Industries of the Future, School of Life SciencesWestlake UniversityHangzhouChina
| |
Collapse
|
7
|
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.
Collapse
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
| |
Collapse
|
8
|
Couturier J, Davies K, Barbut F. Ribotypes and New Virulent Strains Across Europe. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1435:151-168. [PMID: 38175475 DOI: 10.1007/978-3-031-42108-2_8] [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 (formerly Clostridium) difficile is a major bacterial cause of post-antibiotic diarrhoea. The epidemiology of C. difficile infections (CDIs) has dramatically changed since the early 2000s, with an increasing incidence and severity across Europe. This trend is partly due to the emergence and rapid worldwide spread of the hypervirulent and epidemic PCR ribotype 027. Profiles of patients with CDI have also evolved, with description of community-acquired (CA) infections in patients with no traditional risk factors for CDI. However, epidemiological studies indicated that some European countries have successfully controlled the dissemination of the 027 clone whereas other countries reported the emergence of other virulent or unusual strains. The aims of this review are to summarize the current European CDI epidemiology and to describe the new virulent C. difficile strains circulating in Europe, as well as other potential emerging strains described elsewhere. Standardized typing methods and surveillance programmes are mandatory for a better understanding and monitoring of CDI in Europe.
Collapse
Affiliation(s)
- Jeanne Couturier
- National Reference Laboratory for C. difficile, Hôpital Saint-Antoine, Paris, France.
- Université Paris Cité, UMR INSERM 1139, Paris, France.
| | - Kerrie Davies
- Healthcare Associated Infections Research Group, Leeds Teaching Hospitals NHS Trust and University of Leeds, Leeds, UK
- European Society of Clinical Microbiology and Infectious Diseases (ESCMID) study group for Clostridioides difficile (ESGCD), Basel, Switzerland
| | - Frédéric Barbut
- National Reference Laboratory for C. difficile, Hôpital Saint-Antoine, Paris, France
- Université Paris Cité, UMR INSERM 1139, Paris, France
- European Society of Clinical Microbiology and Infectious Diseases (ESCMID) study group for Clostridioides difficile (ESGCD), Basel, Switzerland
| |
Collapse
|
9
|
Filippidis P, Senn L, Poncet F, Grandbastien B, Prod'hom G, Greub G, Guery B, Blanc DS. Core genome multilocus sequence typing of Clostridioides difficile to investigate transmission in the hospital setting. Eur J Clin Microbiol Infect Dis 2023; 42:1469-1476. [PMID: 37870711 PMCID: PMC10651541 DOI: 10.1007/s10096-023-04676-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 10/02/2023] [Indexed: 10/24/2023]
Abstract
PURPOSE Traditional epidemiological investigations of healthcare-associated Clostridioides difficile infection (HA-CDI) are often insufficient. This study aimed to evaluate a procedure that includes secondary isolation and genomic typing of single toxigenic colonies using core genome multilocus sequence typing (cgMLST) for the investigation of C. difficile transmission. METHODS We analyzed retrospectively all toxigenic C. difficile-positive stool samples stored at the Lausanne University Hospital over 6 consecutive months. All isolates were initially typed and classified using a modified double-locus sequence typing (DLST) method. Genome comparison of isolates with the same DLST and clustering were subsequently performed using cgMLST. The electronic administrative records of patients with CDI were investigated for spatiotemporal epidemiological links supporting hospital transmission. A comparative descriptive analysis between genomic and epidemiological data was then performed. RESULTS From January to June 2021, 86 C. difficile isolates were recovered from thawed samples of 71 patients. Thirteen different DLST types were shared by > 1 patient, and 13 were observed in single patients. A genomic cluster was defined as a set of isolates from different patients with ≤ 3 locus differences, determined by cgMLST. Seven genomic clusters were identified, among which plausible epidemiological links were identified in only 4/7 clusters. CONCLUSION Among clusters determined by cgMLST analysis, roughly 40% included unexplained HA-CDI acquisitions, which may be explained by unidentified epidemiological links, asymptomatic colonization, and/or shared common community reservoirs. The use of DLST, followed by whole genome sequencing analysis, is a promising and cost-effective stepwise approach for the investigation of CDI transmission in the hospital setting.
Collapse
Affiliation(s)
- Paraskevas Filippidis
- Infection Prevention and Control Unit, Infectious Diseases Service, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
- Infectious Diseases Service, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Laurence Senn
- Infection Prevention and Control Unit, Infectious Diseases Service, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Fabrice Poncet
- Infection Prevention and Control Unit, Infectious Diseases Service, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
- Swiss National Reference Center for Emerging Antibiotic Resistance (NARA), University of Fribourg, Fribourg, Switzerland
| | - Bruno Grandbastien
- Infection Prevention and Control Unit, Infectious Diseases Service, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Guy Prod'hom
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Gilbert Greub
- Institute of Microbiology, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Benoit Guery
- Infection Prevention and Control Unit, Infectious Diseases Service, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland
| | - Dominique S Blanc
- Infection Prevention and Control Unit, Infectious Diseases Service, Lausanne University Hospital and University of Lausanne, Lausanne, Switzerland.
- Swiss National Reference Center for Emerging Antibiotic Resistance (NARA), University of Fribourg, Fribourg, Switzerland.
| |
Collapse
|
10
|
Toorop MMA, Kraakman MEM, Hoogendijk IV, van Prehn J, Claas ECJ, Wessels E, Boers SA. A core-genome multilocus sequence typing scheme for the detection of genetically related Streptococcus pyogenes clusters. J Clin Microbiol 2023; 61:e0055823. [PMID: 37815371 PMCID: PMC10662357 DOI: 10.1128/jcm.00558-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2023] [Accepted: 08/07/2023] [Indexed: 10/11/2023] Open
Abstract
The recently observed increase in invasive Streptococcus pyogenes infections causes concern in Europe. However, conventional molecular typing methods lack discriminatory power to aid investigations of outbreaks caused by S. pyogenes. Therefore, there is an urgent need for high-resolution molecular typing methods to assess genetic relatedness between S. pyogenes isolates. In the current study, we aimed to develop a novel high-resolution core-genome multilocus sequence typing (cgMLST) scheme for S. pyogenes and compared its discriminatory power to conventional molecular typing methods. The cgMLST scheme was designed with the commercial Ridom SeqSphere+ software package. To define a cluster threshold, the scheme was evaluated using publicly available data from nine defined S. pyogenes outbreaks in the United Kingdom. The cgMLST scheme was then applied to 23 isolates from a suspected S. pyogenes outbreak and 117 S. pyogenes surveillance isolates both from the Netherlands. MLST and emm-typing results were used for comparison to cgMLST results. The allelic differences between isolates from defined outbreaks ranged between 6 and 31 for isolates with the same emm-type, resulting in a proposed cluster threshold of <5 allelic differences out of 1,095 target loci. Seven out of twenty-three (30%) isolates from the suspected outbreak had an allelic difference of <2, thereby identifying a potential cluster that could not be linked to other isolates. The proposed cgMLST scheme shows a higher discriminatory ability when compared to conventional typing methods. The rapid and simple analysis workflow allows for extended detection of clusters of potential outbreak isolates and surveillance and may facilitate the sharing of sequencing results between (inter)national laboratories.
Collapse
Affiliation(s)
- Myrthe M. A. Toorop
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Margriet E. M. Kraakman
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Irene V. Hoogendijk
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Joffrey van Prehn
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Eric C. J. Claas
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Els Wessels
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| | - Stefan A. Boers
- Department of Medical Microbiology, Leiden University Medical Center, Leiden, the Netherlands
| |
Collapse
|
11
|
Abdrabou AMM, Sy I, Bischoff M, Arroyo MJ, Becker SL, Mellmann A, von Müller L, Gärtner B, Berger FK. Discrimination between hypervirulent and non-hypervirulent ribotypes of Clostridioides difficile by MALDI-TOF mass spectrometry and machine learning. Eur J Clin Microbiol Infect Dis 2023; 42:1373-1381. [PMID: 37721704 PMCID: PMC10587247 DOI: 10.1007/s10096-023-04665-y] [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: 02/20/2023] [Accepted: 09/03/2023] [Indexed: 09/19/2023]
Abstract
Hypervirulent ribotypes (HVRTs) of Clostridioides difficile such as ribotype (RT) 027 are epidemiologically important. This study evaluated whether MALDI-TOF can distinguish between strains of HVRTs and non-HVRTs commonly found in Europe. Obtained spectra of clinical C. difficile isolates (training set, 157 isolates) covering epidemiologically relevant HVRTs and non-HVRTs found in Europe were used as an input for different machine learning (ML) models. Another 83 isolates were used as a validation set. Direct comparison of MALDI-TOF spectra obtained from HVRTs and non-HVRTs did not allow to discriminate between these two groups, while using these spectra with certain ML models could differentiate HVRTs from non-HVRTs with an accuracy >95% and allowed for a sub-clustering of three HVRT subgroups (RT027/RT176, RT023, RT045/078/126/127). MALDI-TOF combined with ML represents a reliable tool for rapid identification of major European HVRTs.
Collapse
Affiliation(s)
- Ahmed Mohamed Mostafa Abdrabou
- Institute of Medical Microbiology and Hygiene, Saarland University, Kirrberger Straße 100, Building 43, D-66421, Homburg, Saar, Germany.
- Medical Microbiology and Immunology Department, Faculty of Medicine, Mansoura University, El Gomhouria Street, Mansoura, 35516, Egypt.
- National Reference Center for Clostridioides (Clostridium) difficile, Homburg-Münster-Coesfeld, Germany.
| | - Issa Sy
- Institute of Medical Microbiology and Hygiene, Saarland University, Kirrberger Straße 100, Building 43, D-66421, Homburg, Saar, Germany
| | - Markus Bischoff
- Institute of Medical Microbiology and Hygiene, Saarland University, Kirrberger Straße 100, Building 43, D-66421, Homburg, Saar, Germany
- National Reference Center for Clostridioides (Clostridium) difficile, Homburg-Münster-Coesfeld, Germany
| | - Manuel J Arroyo
- Clover Bioanalytical Software, Av. del Conocimiento, 41, 18016, Granada, Spain
| | - Sören L Becker
- Institute of Medical Microbiology and Hygiene, Saarland University, Kirrberger Straße 100, Building 43, D-66421, Homburg, Saar, Germany
| | - Alexander Mellmann
- National Reference Center for Clostridioides (Clostridium) difficile, Homburg-Münster-Coesfeld, Germany
- Institute of Hygiene, University of Münster, Robert-Koch-Straße 41, 48149, Münster, Germany
| | - Lutz von Müller
- National Reference Center for Clostridioides (Clostridium) difficile, Homburg-Münster-Coesfeld, Germany
- Christophorus Kliniken Coesfeld, Coesfeld, Germany
| | - Barbara Gärtner
- Institute of Medical Microbiology and Hygiene, Saarland University, Kirrberger Straße 100, Building 43, D-66421, Homburg, Saar, Germany
- National Reference Center for Clostridioides (Clostridium) difficile, Homburg-Münster-Coesfeld, Germany
| | - Fabian K Berger
- Institute of Medical Microbiology and Hygiene, Saarland University, Kirrberger Straße 100, Building 43, D-66421, Homburg, Saar, Germany
- National Reference Center for Clostridioides (Clostridium) difficile, Homburg-Münster-Coesfeld, Germany
| |
Collapse
|
12
|
Blau K, Berger FK, Mellmann A, Gallert C. Clostridioides difficile from Fecally Contaminated Environmental Sources: Resistance and Genetic Relatedness from a Molecular Epidemiological Perspective. Microorganisms 2023; 11:2497. [PMID: 37894155 PMCID: PMC10608975 DOI: 10.3390/microorganisms11102497] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 09/28/2023] [Accepted: 09/28/2023] [Indexed: 10/29/2023] Open
Abstract
Clostridioides difficile is the most important pathogen causing antimicrobial-associated diarrhea and has recently been recognized as a cause of community-associated C. difficile infection (CA-CDI). This study aimed to characterize virulence factors, antimicrobial resistance (AMR), ribotype (RT) distribution and genetic relationship of C. difficile isolates from diverse fecally contaminated environmental sources. C. difficile isolates were recovered from different environmental samples in Northern Germany. Antimicrobial susceptibility testing was determined by E-test or disk diffusion method. Toxin genes (tcdA and tcdB), genes coding for binary toxins (cdtAB) and ribotyping were determined by PCR. Furthermore, 166 isolates were subjected to whole genome sequencing (WGS) for core genome multi-locus sequence typing (cgMLST) and extraction of AMR and virulence-encoding genes. Eighty-nine percent (148/166) of isolates were toxigenic, and 51% (76/148) were positive for cdtAB. Eighteen isolates (11%) were non-toxigenic. Thirty distinct RTs were identified. The most common RTs were RT127, RT126, RT001, RT078, and RT014. MLST identified 32 different sequence types (ST). The dominant STs were ST11, followed by ST2, ST3, and ST109. All isolates were susceptible to vancomycin and metronidazole and displayed a variable rate of resistance to moxifloxacin (14%), clarithromycin (26%) and rifampicin (2%). AMR genes, such as gyrA/B, blaCDD-1/2, aph(3')-llla-sat-4-ant(6)-la cassette, ermB, tet(M), tet(40), and tetA/B(P), conferring resistance toward fluoroquinolone, beta-lactam, aminoglycoside, macrolide and tetracycline antimicrobials, were found in 166, 137, 29, 32, 21, 72, 17, and 9 isolates, respectively. Eleven "hypervirulent" RT078 strains were detected, and several isolates belonged to RTs (i.e., RT127, RT126, RT023, RT017, RT001, RT014, RT020, and RT106) associated with CA-CDI, indicating possible transmission between humans and environmental sources pointing out to a zoonotic potential.
Collapse
Affiliation(s)
- Khald Blau
- Department of Microbiology–Biotechnology, Faculty of Technology, University of Applied Sciences Emden/Leer, 26723 Emden, Germany;
| | - Fabian K. Berger
- Institute of Medical Microbiology and Hygiene, Saarland University Medical Center, 66421 Homburg, Germany;
- German National Reference Center for Clostridioides Difficile, 66421 Homburg, Germany;
| | - Alexander Mellmann
- German National Reference Center for Clostridioides Difficile, 66421 Homburg, Germany;
- Institute of Hygiene, University of Münster, 48149 Münster, Germany
| | - Claudia Gallert
- Department of Microbiology–Biotechnology, Faculty of Technology, University of Applied Sciences Emden/Leer, 26723 Emden, Germany;
| |
Collapse
|
13
|
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.
Collapse
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
| |
Collapse
|
14
|
Williamson CHD, Roe CC, Terriquez J, Hornstra H, Lucero S, Nunnally AE, Vazquez AJ, Vinocur J, Plude C, Nienstadt L, Stone NE, Celona KR, Wagner DM, Keim P, Sahl JW. A local-scale One Health genomic surveillance of Clostridioides difficile demonstrates highly related strains from humans, canines, and the environment. Microb Genom 2023; 9. [PMID: 37347682 DOI: 10.1099/mgen.0.001046] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/24/2023] Open
Abstract
Although infections caused by Clostridioides difficile have historically been attributed to hospital acquisition, growing evidence supports the role of community acquisition in C. difficile infection (CDI). Symptoms of CDI can range from mild, self-resolving diarrhoea to toxic megacolon, pseudomembranous colitis, and death. In this study, we sampled C. difficile from clinical, environmental, and canine reservoirs in Flagstaff, Arizona, USA, to understand the distribution and transmission of the pathogen in a One Health framework; Flagstaff is a medium-sized, geographically isolated city with a single hospital system, making it an ideal site to characterize genomic overlap between sequenced C. difficile isolates across reservoirs. An analysis of 562 genomes from Flagstaff isolates identified 65 sequence types (STs), with eight STs being found across all three reservoirs and another nine found across two reservoirs. A screen of toxin genes in the pathogenicity locus identified nine STs where all isolates lost the toxin genes needed for CDI manifestation (tcdB, tcdA), demonstrating the widespread distribution of non-toxigenic C. difficile (NTCD) isolates in all three reservoirs; 15 NTCD genomes were sequenced from symptomatic, clinical samples, including two from mixed infections that contained both tcdB+ and tcdB- isolates. A comparative single nucleotide polymorphism (SNP) analysis of clinically derived isolates identified 78 genomes falling within clusters separated by ≤2 SNPs, indicating that ~19 % of clinical isolates are associated with potential healthcare-associated transmission clusters; only symptomatic cases were sampled in this study, and we did not sample asymptomatic transmission. Using this same SNP threshold, we identified genomic overlap between canine and soil isolates, as well as putative transmission between environmental and human reservoirs. The core genome of isolates sequenced in this study plus a representative set of public C. difficile genomes (n=136), was 2690 coding region sequences, which constitutes ~70 % of an individual C. difficile genome; this number is significantly higher than has been published in some other studies, suggesting that genome data quality is important in understanding the minimal number of genes needed by C. difficile. This study demonstrates the close genomic overlap among isolates sampled across reservoirs, which was facilitated by maximizing the genomic search space used for comprehensive identification of potential transmission events. Understanding the distribution of toxigenic and non-toxigenic C. difficile across reservoirs has implications for surveillance sampling strategies, characterizing routes of infections, and implementing mitigation measures to limit human infection.
Collapse
Affiliation(s)
| | - Chandler C Roe
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | | | - Heidie Hornstra
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Samantha Lucero
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Amalee E Nunnally
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Adam J Vazquez
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | | | | | | | - Nathan E Stone
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Kimberly R Celona
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - David M Wagner
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Paul Keim
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| | - Jason W Sahl
- The Pathogen and Microbiome Institute, Northern Arizona University, Flagstaff, AZ, USA
| |
Collapse
|
15
|
Wang YY, Xie L, Zhang WZ, Du XL, Li WG, Bia LL, Cui ZG, Wu Y, Lu JX. Application of a core genome sequence typing (cgMLST) pipeline for surveillance of Clostridioides difficile in China. Front Cell Infect Microbiol 2023; 13:1109153. [PMID: 36992688 PMCID: PMC10040748 DOI: 10.3389/fcimb.2023.1109153] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Accepted: 02/28/2023] [Indexed: 03/14/2023] Open
Abstract
IntroductionClostridioides difficile (C. difficile) is a nosocomial bacterial pathogen that causes antibiotic-associated diarrhea mediated by cellular exotoxins secreted into the intestine during bacterial growth. Multilocus sequence typing (MLST) and PCR ribotyping are the main molecular typing for C. difficile. Whole genome sequencing (WGS) core genome multilocus sequence typing (cgMLST) was developed for genetic evolution and outbreak investigation of C. difficile with higher precision and accuracy.MethodsA total of 699 whole (complete and draft) genome sequences of distinct C. difficile strains were used in this study to identify core gene set (2469 core genes) and the cgMLST scheme for the phylogeny analysis of C. difficile. This cgMLST pipeline was then carried the Chinese Pathogen Identification Net (China PIN) for surveillance of C. difficile in China. Within the China PIN, 195 WGS of C. difficile and an outbreak of CDI with 12 WGS of C. difficile were used to evaluate the cgMLST pipeline.ResultsThe result displayed that mostly tested C. difficile isolates could be successfully divided into 5 classic clades and the outbreak event was also successfully identified.DiscussionThe results are meaningful and offer a practicable pipeline for a national-wide surveillance of C. difficile in China.
Collapse
Affiliation(s)
- Yuan Yuan Wang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Lu Xie
- Research Center for Micro-Ecological Agent Engineering and Technology of Guangdong Province, Guangzhou, China
| | - Wen Zhu Zhang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xiao li Du
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Wen Ge Li
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Lu Lu Bia
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Zhi Gang Cui
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yuan Wu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
- *Correspondence: Yuan Wu,
| | - Jin Xing Lu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, China
| |
Collapse
|
16
|
Barbar R, Brazelton JN, Carroll KC, Lewis S, Bourdas D, Tembo A, Gluck L, Hakim H, Hayden RT. Molecular Epidemiology and Genetic Relatedness of Clostridioides difficile Isolates in Pediatric Oncology and Transplant Patients Using Whole Genome Sequencing. Clin Infect Dis 2023; 76:e1071-e1078. [PMID: 35675378 DOI: 10.1093/cid/ciac459] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 05/21/2022] [Accepted: 06/02/2022] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND The incidence of Clostridioides difficile infection (CDI) has been rising among hospitalized children, with poor understanding of genomic variability of C. difficile isolates in this population. METHODS This was a retrospective cohort study of CDI in inpatient and outpatient pediatric oncology and cell transplant patients (POTPs) in 2016 and 2017. CDI cases were identified by positive C. difficile toxin polymerase chain reaction tests. Retrieved residual stool specimens were cultured anaerobically and toxin-producing C. difficile isolates underwent whole genome sequencing (WGS) followed by core genome multilocus sequence typing. Plausible time and location epidemiologic links among the closely related strains were evaluated to identify potential transmission events. RESULTS Among 226 CDI episodes in 157 patients, 202 stool samples were cultured and had positive cytotoxicity tests. Sequencing identified 33 different strain types in 162 (80%) isolates. Thirty-nine (28%) patients had multiple episodes of CDI, and 31 clusters of related isolates were identified, 15 (47%) of which involved exclusively multiple specimens from the same patient. For the 16 clusters involving multiple patients, epidemiologic investigation revealed only 2 (12.5%) clusters with potential transmission events. CONCLUSIONS WGS identified a highly diverse group of C. difficile isolates among POTPs with CDI. Although WGS identified clusters of closely related isolates in multiple patients, epidemiologic investigation of shared inpatient exposures identified potential transmission in only 2 clusters. Clostridioides difficile transmission was uncommon in this population. More than 70% of new CDI reinfections in POTPs are actually recurrences caused by a previous CDI strain.
Collapse
Affiliation(s)
- Ruba Barbar
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Jessica N Brazelton
- Department of Pathology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Karen C Carroll
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
| | - Shawna Lewis
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
| | - Dimitrios Bourdas
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
| | - Anita Tembo
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
| | - Linda Gluck
- Department of Pathology, Johns Hopkins Medical Institutions, Baltimore, Maryland, USA
| | - Hana Hakim
- Department of Infectious Diseases, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Randall T Hayden
- Department of Pathology, St Jude Children's Research Hospital, Memphis, Tennessee, USA
| |
Collapse
|
17
|
Dost I, Abdel-Glil M, Schmoock G, Menge C, Berens C, González-Santamarina B, Wiegand E, Neubauer H, Schwarz S, Seyboldt C. Clostridioides difficile in South American Camelids in Germany: First Insights into Molecular and Genetic Characteristics and Antimicrobial Resistance. Antibiotics (Basel) 2023; 12:antibiotics12010086. [PMID: 36671289 PMCID: PMC9854998 DOI: 10.3390/antibiotics12010086] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2022] [Revised: 12/22/2022] [Accepted: 12/23/2022] [Indexed: 01/06/2023] Open
Abstract
Little is known about zoonotic pathogens and their antimicrobial resistance in South American camelids (SAC) in Germany including Clostridioides (C.) difficile. The aim of this study was to investigate prevalence, molecular characteristics and antimicrobial resistance of C. difficile in SAC. Composite SAC faecal samples were collected in 43 husbandries in Central Germany and cultured for C. difficile. Toxinotyping and ribotyping was done by PCR. Whole genome sequencing was performed with Illumina® Miseq™. The genomes were screened for antimicrobial resistance determinants. Genetic relatedness of the isolates was investigated using core genome multi locus sequence typing (cgMLST) and single nucleotide polymorphism analysis. Antimicrobial susceptibility testing was done using the Etest® method. Eight C. difficile isolates were recovered from seven farms. The isolates belonged to different PCR ribotypes. All isolates were toxinogenic. cgMLST revealed a cluster containing isolates recovered from different farms. Seven isolates showed similar resistance gene patterns. Different phenotypic resistance patterns were found. Agreement between phenotypic and genotypic resistance was identified only in some cases. Consequently, SAC may act as a reservoir for C. difficile. Thus, SAC may pose a risk regarding zoonotic transmission of toxinogenic, potentially human-pathogenic and resistant C. difficile isolates.
Collapse
Affiliation(s)
- Ines Dost
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Naumburger Straße 96a, 07743 Jena, Germany
- Correspondence: ; Tel.: +49-3641-804-2488
| | - Mostafa Abdel-Glil
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Naumburger Straße 96a, 07743 Jena, Germany
| | - Gernot Schmoock
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Naumburger Straße 96a, 07743 Jena, Germany
| | - Christian Menge
- Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Naumburger Straße 96a, 07743 Jena, Germany
| | - Christian Berens
- Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Naumburger Straße 96a, 07743 Jena, Germany
| | - Belén González-Santamarina
- Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Naumburger Straße 96a, 07743 Jena, Germany
| | - Elisabeth Wiegand
- Institute of Molecular Pathogenesis, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Naumburger Straße 96a, 07743 Jena, Germany
| | - Heinrich Neubauer
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Naumburger Straße 96a, 07743 Jena, Germany
| | - Stefan Schwarz
- Institute of Microbiology and Epizootics, Centre for Infection Medicine, Department of Veterinary Medicine, Freie Universität Berlin, 14163 Berlin, Germany
- Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, 14163 Berlin, Germany
| | - Christian Seyboldt
- Institute of Bacterial Infections and Zoonoses, Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Naumburger Straße 96a, 07743 Jena, Germany
| |
Collapse
|
18
|
Dirks EE, Luković JA, Peltroche-Llacsahuanga H, Herrmann A, Mellmann A, Arvand M. Molecular Epidemiology, Clinical Course, and Implementation of Specific Hygiene Measures in Hospitalised Patients with Clostridioides difficile Infection in Brandenburg, Germany. Microorganisms 2022; 11:44. [PMID: 36677336 PMCID: PMC9862616 DOI: 10.3390/microorganisms11010044] [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: 11/25/2022] [Revised: 12/14/2022] [Accepted: 12/19/2022] [Indexed: 12/25/2022] Open
Abstract
(1) Background: Clostridioides difficile infections (CDI) have increased worldwide, and the disease is one of the most common healthcare-associated infections (HAI). This study aimed to evaluate the molecular epidemiology of C. difficile, the clinical outcome, and the time of initiation of specific hygiene measures in patients with CDI in a large tertiary-care hospital in Brandenburg. (2) Methods: Faecal samples and data from hospitalised patients diagnosed with CDI were analysed from October 2016 to October 2017. The pathogens were isolated, identified as toxigenic C. difficile, and subsequently subtyped using PCR ribotyping and whole genome sequencing (WGS). Data regarding specific hygiene measures for handling CDI patients were collected. (3) Results: 92.1% of cases could be classified as healthcare-associated (HA)-CDI. The recurrence rate within 30 and 90 days after CDI diagnosis was 15.7% and 18.6%, and the mortality rate was 21.4% and 41.4%, respectively. The most frequent ribotypes (RT) were RT027 (31.3%), RT014 (18.2%), and RT005 (14.1%). Analysis of WGS data using cgMLST showed that all RT027 isolates were closely related; they were assigned to two subclusters. Single-room isolation or barrier measures were implemented in 95.7% patients. (4) Conclusions: These data show that RT027 is regionally predominant, thus highlighting the importance of specific hygiene measures to prevent and control CDI and the need to improve molecular surveillance of C. difficile at the local and national level.
Collapse
Affiliation(s)
- Esther E. Dirks
- Unit for Hospital Hygiene, Infection Prevention and Control, Department of Infectious Diseases, Robert Koch Institute, 13353 Berlin, Germany
| | - Jasminka A. Luković
- Institute for Microbiology and Hospital Hygiene, Carl-Thiem-Hospital, 03048 Cottbus, Germany
| | | | - Anke Herrmann
- Unit for Hospital Hygiene, Infection Prevention and Control, Department of Infectious Diseases, Robert Koch Institute, 13353 Berlin, Germany
| | - Alexander Mellmann
- Institute of Hygiene, University Hospital Muenster and National Reference Center for Clostridioides Difficile, Münster Branch, 48149 Münster, Germany
| | - Mardjan Arvand
- Unit for Hospital Hygiene, Infection Prevention and Control, Department of Infectious Diseases, Robert Koch Institute, 13353 Berlin, Germany
| |
Collapse
|
19
|
Magnusson C, Mernelius S, Bengnér M, Norén T, Serrander L, Forshell S, Matussek A. Characterization of a Clostridioides difficile outbreak caused by PCR ribotype 046, associated with increased mortality. Emerg Microbes Infect 2022; 11:850-859. [PMID: 35240942 PMCID: PMC8942542 DOI: 10.1080/22221751.2022.2049981] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
This study describes a large nosocomial outbreak of Clostridioides difficile infections (CDI) dominated by ribotype (RT) 046 in a Swedish hospital. The present study aimed to examine the pathogenicity of this RT, explore epidemiological links by whole genome sequencing (WGS), and evaluate different interventions implemented to stop the outbreak. Clinical isolates (n = 366) collected during and after the outbreak were ribotyped and 246 isolates were subjected to WGS. Medical records of patients infected with the seven most common RTs were evaluated. RT046 was spread effectively throughout the hospital and was the most common among the 44 different RTs found (114/366 isolates). Infection with RT046 was associated with higher mortality compared to other strains (20.2% to 7.8%), although there were no differences in concomitant disease, age or antibiotic treatment. To control the outbreak, several measures were successfully implemented.
Collapse
Affiliation(s)
- Cecilia Magnusson
- Department of Infectious Diseases, Region Jönköping County, Jönköping and Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Sara Mernelius
- Laboratory Medicine, Region Jönköping County, Jönköping and Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Malin Bengnér
- Office for control of Communicable Diseases, Region Jönköping County, Jönköping, Sweden
| | - Torbjörn Norén
- Faculty of Medicine and Health, Department of Laboratory Medicine, National Reference Laboratory for Clostridioides difficile, Clinical Microbiology, Örebro University, Örebro, Sweden
| | - Lena Serrander
- Division of Clinical Microbiology, Department of Clinical and Experimental Medicine, Faculty of Health Sciences, Linköping University, Linköping, Sweden
| | - Sophie Forshell
- Department of Infectious Diseases, Region Jönköping County, Jönköping and Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden
| | - Andreas Matussek
- Laboratory Medicine, Region Jönköping County, Jönköping and Department of Biomedical and Clinical Sciences, Linköping University, Linköping, Sweden.,Division of Laboratory Medicine, Institute of Clinical Medicine, University of Oslo, Oslo, Norway.,Division of Laboratory Medicine, Oslo University Hospital, Oslo, Norway
| |
Collapse
|
20
|
Development and Evaluation of a Core Genome Multilocus Sequencing Typing (cgMLST) Scheme for Serratia marcescens Molecular Surveillance and Outbreak Investigations. J Clin Microbiol 2022; 60:e0119622. [PMID: 36214584 PMCID: PMC9667775 DOI: 10.1128/jcm.01196-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Serratia marcescens can cause a range of severe infections and contributes to nosocomial outbreaks. Although whole-genome sequencing (WGS)-based typing is the standard method for molecular surveillance and outbreak investigation, there is no standardized analytic scheme for S. marcescens core genome multilocus sequence typing (cgMLST). Here, the development and evaluation of a S. marcescens cgMLST scheme is reported with the goal of enabling a standardized methodology and typing nomenclature. Four hundred ninety-one high-quality S. marcescens WGS data sets were extracted from public databases and-using the genomic sequence of NCBI reference strain S. marcescens Db11 (NZ_HG326223.1) as a starting point-all Db11 genes present in ≥97% data sets used to create a cgMLST scheme. The novel scheme was evaluated using WGS data from 24 outbreak investigations (n = 175 isolates) distributed over three continents. Analysis of Db11 genes within the 491 data sets identified 2,692 target genes present in ≥97% of genomes (mean, 99.1%; median, 99.9%). These genes formed the novel cgMLST scheme, covering 47.8% of nucleotides in the Db11 genome. Analyzing 175 isolates from 24 outbreaks using the novel scheme gave comparable results to previous typing efforts for both general groupings and allelic distances within clusters. In summary, a novel cgMLST scheme for S. marcescens was developed and evaluated. The scheme and its associated nomenclature will improve standardization of typing efforts for molecular surveillance and outbreak investigation, allowing better understanding of S. marcescens genomic epidemiology and facilitating interlaboratory comparisons.
Collapse
|
21
|
Finsterwalder SK, Loncaric I, Cabal A, Szostak MP, Barf LM, Marz M, Allerberger F, Burgener IA, Tichy A, Feßler AT, Schwarz S, Monecke S, Ehricht R, Ruppitsch W, Spergser J, Künzel F. Dogs as carriers of virulent and resistant genotypes of Clostridioides difficile. Zoonoses Public Health 2022; 69:673-681. [PMID: 35546073 PMCID: PMC9544694 DOI: 10.1111/zph.12956] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 04/19/2022] [Accepted: 04/25/2022] [Indexed: 11/29/2022]
Abstract
While previous research on zoonotic transmission of community-acquired Clostridioides difficile infection (CA-CDI) focused on food-producing animals, the present study aimed to investigate whether dogs are carriers of resistant and/or virulent C. difficile strains. Rectal swabs were collected from 323 dogs and 38 C. difficile isolates (11.8%) were obtained. Isolates were characterized by antimicrobial susceptibility testing, whole-genome sequencing (WGS) and a DNA hybridization assay. Multilocus sequence typing (MLST), core genome MLST (cgMLST) and screening for virulence and antimicrobial resistance genes were performed based on WGS. Minimum inhibitory concentrations for erythromycin, clindamycin, tetracycline, vancomycin and metronidazole were determined by E-test. Out of 38 C. difficile isolates, 28 (73.7%) carried genes for toxins. The majority of isolates belonged to MLST sequence types (STs) of clade I and one to clade V. Several isolates belonged to STs previously associated with human CA-CDI. However, cgMLST showed low genetic relatedness between the isolates of this study and C. difficile strains isolated from humans in Austria for which genome sequences were publicly available. Four isolates (10.5%) displayed resistance to three of the tested antimicrobial agents. Isolates exhibited resistance to erythromycin, clindamycin, tetracycline and metronidazole. These phenotypic resistances were supported by the presence of the resistance genes erm(B), cfr(C) and tet(M). All isolates were susceptible to vancomycin. Our results indicate that dogs may carry virulent and antimicrobial-resistant C. difficile strains.
Collapse
Affiliation(s)
- S K Finsterwalder
- Institute of Microbiology, University of Veterinary Medicine Vienna, Vienna, Austria.,Clinical Unit of Internal Medicine Small Animals, University of Veterinary Medicine Vienna, Vienna, Austria
| | - I Loncaric
- Institute of Microbiology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - A Cabal
- AGES - Austrian Agency for Health and Food Safety, Vienna, Austria
| | - M P Szostak
- Institute of Microbiology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - L M Barf
- Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, Jena, Germany.,Max Planck Institute for Science of Human History, Jena, Germany
| | - M Marz
- Faculty of Mathematics and Computer Science, Friedrich Schiller University Jena, Jena, Germany.,FLI Leibniz Institute for Age Research, Jena, Germany.,InfectoGnostics Research Campus Jena, Jena, Germany
| | - F Allerberger
- AGES - Austrian Agency for Health and Food Safety, Vienna, Austria
| | - I A Burgener
- Clinical Unit of Internal Medicine Small Animals, University of Veterinary Medicine Vienna, Vienna, Austria
| | - A Tichy
- Department of Biomedical Science, University of Veterinary Medicine Vienna, Vienna, Austria
| | - A T Feßler
- Department of Veterinary Medicine, Centre of Infection Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany.,Department of Veterinary Medicine, Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, Berlin, Germany
| | - S Schwarz
- Department of Veterinary Medicine, Centre of Infection Medicine, Institute of Microbiology and Epizootics, Freie Universität Berlin, Berlin, Germany.,Department of Veterinary Medicine, Veterinary Centre for Resistance Research (TZR), Freie Universität Berlin, Berlin, Germany
| | - S Monecke
- InfectoGnostics Research Campus Jena, Jena, Germany.,Leibniz Institute of Photonic Technology (IPHT), Jena, Germany.,Institut für Medizinische Mikrobiologie und Hygiene, Universitätsklinik Dresden, Dresden, Germany
| | - R Ehricht
- InfectoGnostics Research Campus Jena, Jena, Germany.,Leibniz Institute of Photonic Technology (IPHT), Jena, Germany.,Institute of Physical Chemistry, Friedrich Schiller University Jena, Jena, Germany
| | - W Ruppitsch
- AGES - Austrian Agency for Health and Food Safety, Vienna, Austria
| | - J Spergser
- Institute of Microbiology, University of Veterinary Medicine Vienna, Vienna, Austria
| | - F Künzel
- Clinical Unit of Internal Medicine Small Animals, University of Veterinary Medicine Vienna, Vienna, Austria
| |
Collapse
|
22
|
Büchler AC, Wicki M, Frei R, Hinic V, Seth-Smith HMB, Egli A, Widmer AF. Matching Clostridioides difficile strains obtained from shoe soles of healthcare workers epidemiologically linked to patients and confirmed by whole genome sequencing. J Hosp Infect 2022; 126:10-15. [PMID: 35562075 DOI: 10.1016/j.jhin.2022.04.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 04/27/2022] [Indexed: 11/17/2022]
Abstract
BACKGROUND The source of transmission of Clostridioides difficile in healthcare institutions is frequently unknown. The aim of this prospective cohort study was to assess the association between strains cultured from patients and shoe soles of healthcare workers (HCW), as already shown in the operation theatre, but not on general hospital wards in an acute care institution. METHODS We conducted a study at a university tertiary care center in Switzerland. From October 2019 to July 2020, shoe soles of HCW were cultured for C. difficile twice per shift while taking care of a patient infected with toxigenic C. difficile. Additional risk factors were assessed by interviewing involved HCW. Patients' fecal samples were processed by routine microbiological methods. Similarity of the HCWs' and patients' strains was determined by whole genome sequencing (WGS). RESULTS 103 HCW exposed to 42 hospitalized patients participated in the study, providing 206 samples. Contamination of shoe soles with C. difficile was detected in 37 samples (17.8%) of HCW taking care of patients infected with C. difficile. Overall, transmission was suspected by epidemiological link and matching strains demonstrated by WGS in 74%. CONCLUSIONS HCW' shoe soles were positive in 17.8% with C. difficile strains linked epidemiologically and confirmed by WGS to infected patients suggesting potential transmission by HCWs' shoe soles. This pilot study provides sufficient evidence to further evaluate this potential mode of healthcare-associated transmission of C. difficile by a larger clinical trial.
Collapse
Affiliation(s)
- A C Büchler
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - M Wicki
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - R Frei
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - V Hinic
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland; Clinical Bacteriology and Mycology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - H M B Seth-Smith
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland; Clinical Bacteriology and Mycology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - A Egli
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Basel, Switzerland; Clinical Bacteriology and Mycology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - A F Widmer
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, University of Basel, Basel, Switzerland.
| |
Collapse
|
23
|
Annotated Whole-Genome Multilocus Sequence Typing Schema for Scalable High-Resolution Typing of Streptococcus pyogenes. J Clin Microbiol 2022; 60:e0031522. [DOI: 10.1128/jcm.00315-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Streptococcus pyogenes
is a major human pathogen with high genetic diversity, largely created by recombination and horizontal gene transfer, making it difficult to use single nucleotide polymorphism (SNP)-based genome-wide analyses for surveillance. Using a gene-by-gene approach on 208 complete genomes of
S. pyogenes
, a novel whole-genome multilocus sequence typing (wgMLST) schema was developed, comprising 3,044 target loci.
Collapse
|
24
|
Systems biology approach to functionally assess the Clostridioides difficile pangenome reveals genetic diversity with discriminatory power. Proc Natl Acad Sci U S A 2022; 119:e2119396119. [PMID: 35476524 PMCID: PMC9170149 DOI: 10.1073/pnas.2119396119] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
SignificanceClostridioides difficile infections are the most common source of hospital-acquired infections and are responsible for an extensive burden on the health care system. Strains of the C. difficile species comprise diverse lineages and demonstrate genome variability, with advantageous trait acquisition driving the emergence of endemic lineages. Here, we present a systems biology analysis of C. difficile that evaluates strain-specific genotypes and phenotypes to investigate the overall diversity of the species. We develop a strain typing method based on similarity of accessory genomes to identify and contextualize genetic loci capable of discriminating between strain groups.
Collapse
|
25
|
Alves F, Nunes A, Castro R, Sequeira A, Moreira O, Matias R, Rodrigues JC, Silveira L, Gomes JP, Oleastro M. Assessment of the Transmission Dynamics of Clostridioides difficile in a Farm Environment Reveals the Presence of a New Toxigenic Strain Connected to Swine Production. Front Microbiol 2022; 13:858310. [PMID: 35495679 PMCID: PMC9050547 DOI: 10.3389/fmicb.2022.858310] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Accepted: 03/21/2022] [Indexed: 01/05/2023] Open
Abstract
The recent increase in community-acquired Clostridioides difficile infections discloses the shift in this bacterium epidemiology. This study aimed at establishing a transmission network involving One Health components, as well as assessing the zoonotic potential and genomic features of dominant clones. Samples were collected from different compartments of animal, human and environmental origin, from an animal production unit. C. difficile isolates were characterized for toxigenic profile by multiplex-PCR, while genetic diversity was evaluated by PCR-ribotyping and whole genome-based analysis. The overall C. difficile prevalence was 37.2% (70/188), and included samples from environmental (58.3%, 35/60) and animal (31.5%, 35/111) compartments; human samples (n = 17) taken from healthy workers were negative. A predominant clone from RT033 was found in almost 90% of the positive samples, including samples from all compartments connected to the pig production unit, with core-genome single nucleotide variant (SNV)-based Analysis supporting a clonal transmission between them (mean distance of 0.1 ± 0.1 core-SNVs). The isolates from this clone (herein designated PT RT033) were positive for all C. difficile toxin genes (tcdA, tcdB, cdtA/cdtB). The phyloGenetic positioning of this clone was clearly distinct from the classical RT033 cluster, suggesting a different evolutionary route. This new clone shares genomic features with several RTs from the clade 5 Sequence Type (ST) 11, including a complete pathogenicity locus (PaLoc) that is more similar to the one found in toxigenic strains and contrasting to the less virulent classical RT033 (tcdA-, tcdB-, cdtA + /cdtB +). The presence of a tcdA gene truncated into two ORFs, not previously described, requires further evaluation concerning toxin functionality. We hypothesize that the unique combination of genetic elements found in the PT RT033 clone may contribute to host tropism and environmental dissemination and maintenance. This study constitutes the first report of a toxigenic RT033 clone and adds to the overall knowledge on Clade 5 sequence type 11, considered the C. difficile evolutionary lineage with the highest zoonotic potential. The presence of this clone in all compartments associated with the pig production unit suggests a transmission chain involving these animals and contributes to unveil the role played by animal and environmental reservoirs in this pathogen epidemiology.
Collapse
Affiliation(s)
- Frederico Alves
- Infectious Diseases Department, National Institute of Health Dr. Ricardo Jorge (INSA), Lisbon, Portugal
| | - Alexandra Nunes
- Infectious Diseases Department, National Institute of Health Dr. Ricardo Jorge (INSA), Lisbon, Portugal
- Faculty of Veterinary Medicine, Lusófona University, Lisbon, Portugal
- CBIOS – Lusófona University Research Centre for Biosciences & Health Technologies, Lisbon, Portugal
| | - Rita Castro
- Infectious Diseases Department, National Institute of Health Dr. Ricardo Jorge (INSA), Lisbon, Portugal
| | - António Sequeira
- National Zootechnical Station, National Institute for Agrarian and Veterinarian Research, Santarém, Portugal
| | - Olga Moreira
- National Zootechnical Station, National Institute for Agrarian and Veterinarian Research, Santarém, Portugal
| | - Rui Matias
- Infectious Diseases Department, National Institute of Health Dr. Ricardo Jorge (INSA), Lisbon, Portugal
| | - João Carlos Rodrigues
- Infectious Diseases Department, National Institute of Health Dr. Ricardo Jorge (INSA), Lisbon, Portugal
| | - Leonor Silveira
- Infectious Diseases Department, National Institute of Health Dr. Ricardo Jorge (INSA), Lisbon, Portugal
| | - João Paulo Gomes
- Infectious Diseases Department, National Institute of Health Dr. Ricardo Jorge (INSA), Lisbon, Portugal
- Faculty of Veterinary Medicine, Lusófona University, Lisbon, Portugal
| | - Mónica Oleastro
- Infectious Diseases Department, National Institute of Health Dr. Ricardo Jorge (INSA), Lisbon, Portugal
| |
Collapse
|
26
|
Moore MP, Wilcox MH, Walker AS, Eyre DW. K-mer based prediction of Clostridioides difficile relatedness and ribotypes. Microb Genom 2022; 8. [PMID: 35384833 PMCID: PMC9453075 DOI: 10.1099/mgen.0.000804] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Comparative analysis of Clostridioides difficile whole-genome sequencing (WGS) data enables fine scaled investigation of transmission and is increasingly becoming part of routine surveillance. However, these analyses are constrained by the computational requirements of the large volumes of data involved. By decomposing WGS reads or assemblies into k-mers and using the dimensionality reduction technique MinHash, it is possible to rapidly approximate genomic distances without alignment. Here we assessed the performance of MinHash, as implemented by sourmash, in predicting single nucleotide differences between genomes (SNPs) and C. difficile ribotypes (RTs). For a set of 1905 diverse C. difficile genomes (differing by 0–168 519 SNPs), using sourmash to screen for closely related genomes, at a sensitivity of 100 % for pairs ≤10 SNPs, sourmash reduced the number of pairs from 1 813 560 overall to 161 934, i.e. by 91 %, with a positive predictive value of 32 % to correctly identify pairs ≤10 SNPs (maximum SNP distance 4144). At a sensitivity of 95 %, pairs were reduced by 94 % to 108 266 and PPV increased to 45 % (maximum SNP distance 1009). Increasing the MinHash sketch size above 2000 produced minimal performance improvement. We also explored a MinHash similarity-based ribotype prediction method. Genomes with known ribotypes (n=3937) were split into a training set (2937) and test set (1000) randomly. The training set was used to construct a sourmash index against which genomes from the test set were compared. If the closest five genomes in the index had the same ribotype this was taken to predict the searched genome’s ribotype. Using our MinHash ribotype index, predicted ribotypes were correct in 780/1000 (78 %) genomes, incorrect in 20 (2 %), and indeterminant in 200 (20 %). Relaxing the classifier to 4/5 closest matches with the same RT improved the correct predictions to 87 %. Using MinHash it is possible to subsample C. difficile genome k-mer hashes and use them to approximate small genomic differences within minutes, significantly reducing the search space for further analysis.
Collapse
Affiliation(s)
- Matthew Phillip Moore
- Big Data Institute, Nuffield Department of Population Health, University of Oxford, Oxford, UK.,Nuffield Department of Medicine, University of Oxford, Oxford, UK.,NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK
| | - Mark H Wilcox
- Healthcare Associated Infection Research Group, Leeds Teaching Hospitals NHS Trust and University of Leeds, Leeds, UK
| | - A Sarah Walker
- Nuffield Department of Medicine, University of Oxford, Oxford, UK.,NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK.,NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford, UK
| | - David W Eyre
- Big Data Institute, Nuffield Department of Population Health, University of Oxford, Oxford, UK.,NIHR Oxford Biomedical Research Centre, University of Oxford, Oxford, UK.,NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford, UK
| |
Collapse
|
27
|
Williamson CHD, Stone NE, Nunnally AE, Roe CC, Vazquez AJ, Lucero SA, Hornstra H, Wagner DM, Keim P, Rupnik M, Janezic S, Sahl JW. Identification of novel, cryptic Clostridioides species isolates from environmental samples collected from diverse geographical locations. Microb Genom 2022; 8. [PMID: 35166655 PMCID: PMC8942030 DOI: 10.1099/mgen.0.000742] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Clostridioides difficile is a pathogen often associated with hospital-acquired infection or antimicrobial-induced disease; however, increasing evidence indicates infections can result from community or environmental sources. Most genomic sequencing of C. difficile has focused on clinical strains, although evidence is growing that C. difficile spores are widespread in soil and water in the environment. In this study, we sequenced 38 genomes collected from soil and water isolates in Flagstaff (AZ, USA) and Slovenia in an effort targeted towards environmental surveillance of C. difficile. At the average nucleotide identity (ANI) level, the genomes were divergent to C. difficile at a threshold consistent with different species. A phylogenetic analysis of these divergent genomes together with Clostridioides genomes available in public repositories confirmed the presence of three previously described, cryptic Clostridioides species and added two additional clades. One of the cryptic species (C-III) was almost entirely composed of Arizona and Slovenia genomes, and contained distinct sub-groups from each region (evidenced by SNP and gene-content differences). A comparative genomics analysis identified multiple unique coding sequences per clade, which can serve as markers for subsequent environmental surveys of these cryptic species. Homologues to the C. difficile toxin genes, tcdA and tcdB, were found in cryptic species genomes, although they were not part of the typical pathogenicity locus observed in C. difficile, and in silico PCR suggested that some would not amplify with widely used PCR diagnostic tests. We also identified gene homologues in the binary toxin cluster, including some present on phage and, for what is believed to be the first time, on a plasmid. All isolates were obtained from environmental samples, so the function and disease potential of these toxin homologues is currently unknown. Enzymatic profiles of a subset of cryptic isolates (n=5) demonstrated differences, suggesting that these isolates contain substantial metabolic diversity. Antimicrobial resistance (AMR) was observed across a subset of isolates (n=4), suggesting that AMR mechanisms are intrinsic to the genus, perhaps originating from a shared environmental origin. This study greatly expands our understanding of the genomic diversity of Clostridioides. These results have implications for C. difficile One Health research, for more sensitive C. difficile diagnostics, as well as for understanding the evolutionary history of C. difficile and the development of pathogenesis.
Collapse
Affiliation(s)
| | - Nathan E Stone
- Pathogen and Microbiome Institute, Northern Arizona University, PO Box 4073, Flagstaff, AZ 86011, USA
| | - Amalee E Nunnally
- Pathogen and Microbiome Institute, Northern Arizona University, PO Box 4073, Flagstaff, AZ 86011, USA
| | - Chandler C Roe
- Pathogen and Microbiome Institute, Northern Arizona University, PO Box 4073, Flagstaff, AZ 86011, USA
| | - Adam J Vazquez
- Pathogen and Microbiome Institute, Northern Arizona University, PO Box 4073, Flagstaff, AZ 86011, USA
| | - Samantha A Lucero
- Pathogen and Microbiome Institute, Northern Arizona University, PO Box 4073, Flagstaff, AZ 86011, USA
| | - Heidie Hornstra
- Pathogen and Microbiome Institute, Northern Arizona University, PO Box 4073, Flagstaff, AZ 86011, USA
| | - David M Wagner
- Pathogen and Microbiome Institute, Northern Arizona University, PO Box 4073, Flagstaff, AZ 86011, USA
| | - Paul Keim
- Pathogen and Microbiome Institute, Northern Arizona University, PO Box 4073, Flagstaff, AZ 86011, USA
| | - Maja Rupnik
- National Laboratory for Health, Environment and Food, Prvomajska Ulica 1, 2000 Maribor, Slovenia
| | - Sandra Janezic
- Faculty of Medicine, University of Maribor, Taborska 8, 2000 Maribor, Slovenia
| | - Jason William Sahl
- Pathogen and Microbiome Institute, Northern Arizona University, PO Box 4073, Flagstaff, AZ 86011, USA
| |
Collapse
|
28
|
Baktash A, Corver J, Harmanus C, Smits WK, Fawley W, Wilcox MH, Kumar N, Eyre DW, Indra A, Mellmann A, Kuijper EJ. Comparison of Whole-Genome Sequence-Based Methods and PCR Ribotyping for Subtyping of Clostridioides difficile. J Clin Microbiol 2022; 60:e0173721. [PMID: 34911367 PMCID: PMC8849210 DOI: 10.1128/jcm.01737-21] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 11/22/2021] [Indexed: 11/20/2022] Open
Abstract
Clostridioides difficile is the most common cause of antibiotic-associated gastrointestinal infections. Capillary electrophoresis (CE)-PCR ribotyping is currently the gold standard for C. difficile typing but lacks the discriminatory power to study transmission and outbreaks in detail. New molecular methods have the capacity to differentiate better and provide standardized and interlaboratory exchangeable data. Using a well-characterized collection of diverse strains (N = 630; 100 unique ribotypes [RTs]), we compared the discriminatory power of core genome multilocus sequence typing (cgMLST) (SeqSphere and EnteroBase), whole-genome MLST (wgMLST) (EnteroBase), and single-nucleotide polymorphism (SNP) analysis. A unique cgMLST profile (more than six allele differences) was observed in 82 of 100 RTs, indicating that cgMLST could distinguish most, but not all, RTs. Application of cgMLST in two outbreak settings with RT078 and RT181 (known to have low intra-RT allele differences) showed no distinction between outbreak and nonoutbreak strains in contrast to wgMLST and SNP analysis. We conclude that cgMLST has the potential to be an alternative to CE-PCR ribotyping. The method is reproducible, easy to standardize, and offers higher discrimination. However, adjusted cutoff thresholds and epidemiological data are necessary to recognize outbreaks of some specific RTs. We propose to use an allelic threshold of three alleles to identify outbreaks.
Collapse
Affiliation(s)
- A. Baktash
- Department of Medical Microbiology, Section Experimental Bacteriology, Leiden University Medical Center, Leiden, The Netherlands
| | - J. Corver
- Department of Medical Microbiology, Section Experimental Bacteriology, Leiden University Medical Center, Leiden, The Netherlands
| | - C. Harmanus
- Department of Medical Microbiology, Section Experimental Bacteriology, Leiden University Medical Center, Leiden, The Netherlands
- National Reference Laboratory for Clostridioides difficile, National Institute of Public Health and the Environment, Leiden University Medical Center, Leiden, The Netherlands
| | - W. K. Smits
- Department of Medical Microbiology, Section Experimental Bacteriology, Leiden University Medical Center, Leiden, The Netherlands
| | - W. Fawley
- National Infection Service, Public Health England, and University of Leeds, Leeds, United Kingdom
| | - M. H. Wilcox
- Department of Microbiology, Leeds Teaching Hospitals and University of Leeds, Leeds, United Kingdom
| | - N. Kumar
- Microbiota Interactions Laboratory, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - D. W. Eyre
- Big Data Institute, Nuffield Department of Population Health, University of Oxford, Oxford, United Kingdom
| | - A. Indra
- Paracelsus Medical University of Salzburg, Salzburg, Austria
| | - A. Mellmann
- Institute of Hygiene, University Hospital Münster, and National Reference Center for C. difficile, Münster Branch, Münster, Germany
| | - E. J. Kuijper
- Department of Medical Microbiology, Section Experimental Bacteriology, Leiden University Medical Center, Leiden, The Netherlands
- National Reference Laboratory for Clostridioides difficile, National Institute of Public Health and the Environment, Leiden University Medical Center, Leiden, The Netherlands
| |
Collapse
|
29
|
Ressler A, Wang J, Rao K. Defining the black box: a narrative review of factors associated with adverse outcomes from severe Clostridioides difficile infection. Therap Adv Gastroenterol 2021; 14:17562848211048127. [PMID: 34646358 PMCID: PMC8504270 DOI: 10.1177/17562848211048127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Accepted: 08/31/2021] [Indexed: 02/04/2023] Open
Abstract
In the United States, Clostridioides difficile infection (CDI) is the leading cause of healthcare-associated infection, affecting nearly half a million people and resulting in more than 20,000 in-hospital deaths every year. It is therefore imperative to better characterize the intricate interplay between C. difficile microbial factors, host immunologic signatures, and clinical features that are associated with adverse outcomes of severe CDI. In this narrative review, we discuss the implications of C. difficile genetics and virulence factors in the molecular epidemiology of CDI, and the utility of early biomarkers in predicting the clinical trajectory of patients at risk of developing severe CDI. Furthermore, we identify associations between host immune factors and CDI outcomes in both animal models and human studies. Next, we highlight clinical factors including renal dysfunction, aging, blood biomarkers, level of care, and chronic illnesses that can affect severe CDI diagnosis and outcome. Finally, we present our perspectives on two specific treatments pertinent to patient outcomes: metronidazole administration and surgery. Together, this review explores the various venues of CDI research and highlights the importance of integrating microbial, host, and clinical data to help clinicians make optimal treatment decisions based on accurate prediction of disease progression.
Collapse
Affiliation(s)
- Adam Ressler
- Division of Infectious Diseases, Department of Internal Medicine, University of Michigan Medical School, Ann Arbor, MI, USA
| | - Joyce Wang
- Department of Microbiology and Immunology, University of Michigan Medical School, Ann Arbor, MI, USA
| | | |
Collapse
|
30
|
Development and Validation of a Burkholderia pseudomallei Core Genome Multilocus Sequence Typing Scheme To Facilitate Molecular Surveillance. J Clin Microbiol 2021; 59:e0009321. [PMID: 33980649 PMCID: PMC8373231 DOI: 10.1128/jcm.00093-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Burkholderia pseudomallei causes the severe disease melioidosis. Whole-genome sequencing (WGS)-based typing methods currently offer the highest resolution for molecular investigations of this genetically diverse pathogen. Still, its routine application in diagnostic laboratories is limited by the need for high computing power, bioinformatic skills, and variable bioinformatic approaches, with the latter affecting the results. We therefore aimed to establish and validate a WGS-based core genome multilocus sequence typing (cgMLST) scheme, applicable in routine diagnostic settings. A soft defined core genome was obtained by challenging the B. pseudomallei reference genome K96243 with 469 environmental and clinical genomes, resulting in 4,221 core and 1,351 accessory targets. The scheme was validated with 320 WGS data sets. We compared our novel typing scheme with single nucleotide polymorphism-based approaches investigating closely and distantly related strains. Finally, we applied our scheme for tracking the environmental source of a recent infection. The validation of the scheme detected >95% good cgMLST target genes in 98.4% of the genomes. Comparison with existing typing methods revealed very good concordance. Our scheme proved to be applicable to investigating not only closely related strains but also the global B. pseudomallei population structure. We successfully utilized our scheme to identify a sugarcane field as the presumable source of a recent melioidosis case. In summary, we developed a robust cgMLST scheme that integrates high resolution, maximized standardization, and fast analysis for the nonbioinformatician. Our typing scheme has the potential to serve as a routinely applicable classification system in B. pseudomallei molecular epidemiology.
Collapse
|
31
|
Seth-Smith HMB, Biggel M, Roloff T, Hinic V, Bodmer T, Risch M, Casanova C, Widmer A, Sommerstein R, Marschall J, Tschudin-Sutter S, Egli A. Transition From PCR-Ribotyping to Whole Genome Sequencing Based Typing of Clostridioides difficile. Front Cell Infect Microbiol 2021; 11:681518. [PMID: 34141631 PMCID: PMC8204696 DOI: 10.3389/fcimb.2021.681518] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Accepted: 05/04/2021] [Indexed: 11/13/2022] Open
Abstract
Clostridioides difficile causes nosocomial outbreaks which can lead to severe and even life-threatening colitis. Rapid molecular diagnostic tests allow the identification of toxin-producing, potentially hypervirulent strains, which is critical for patient management and infection control. PCR-ribotyping has been used for decades as the reference standard to investigate transmission in suspected outbreaks. However, the introduction of whole genome sequencing (WGS) for molecular epidemiology provides a realistic alternative to PCR-ribotyping. In this transition phase it is crucial to understand the strengths and weaknesses of the two technologies, and to assess their correlation. We aimed to investigate ribotype prediction from WGS data, and options for analysis at different levels of analytical granularity. Ribotypes cannot be directly determined from short read Illumina sequence data as the rRNA operons including the ribotype-defining ISR fragments collapse in genome assemblies, and comparison with traditional PCR-ribotyping results becomes impossible. Ribotype extraction from long read Oxford nanopore data also requires optimization. We have compared WGS-based typing with PCR-ribotyping in nearly 300 clinical and environmental isolates from Switzerland, and in addition from the Enterobase database (n=1778). Our results show that while multi-locus sequence type (MLST) often correlates with a specific ribotype, the agreement is not complete, and for some ribotypes the resolution is insufficient. Using core genome MLST (cgMLST) analysis, there is an improved resolution and ribotypes can often be predicted within clusters, using cutoffs of 30-50 allele differences. The exceptions are ribotypes within known ribotype complexes such as RT078/RT106, where the genome differences in cgMLST do not reflect the ribotype segregation. We show that different ribotype clusters display different degrees of diversity, which could be important for the definition of ribotype cluster specific cutoffs. WGS-based analysis offers the ultimate resolution to the SNP level, enabling exploration of patient-to-patient transmission. PCR-ribotyping does not sufficiently discriminate to prove nosocomial transmission with certainty. We discuss the associated challenges and opportunities in a switch to WGS from conventional ribotyping for C. difficile.
Collapse
Affiliation(s)
- Helena M B Seth-Smith
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland.,Applied Microbiology Research, Department Biomedicine, University of Basel, Basel, Switzerland.,Swiss Institute for Bioinformatics, Basel, Switzerland
| | - Michael Biggel
- Institute for Food Safety and Hygiene, Vetsuisse Faculty, University of Zurich, Zurich, Switzerland
| | - Tim Roloff
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland.,Applied Microbiology Research, Department Biomedicine, University of Basel, Basel, Switzerland.,Swiss Institute for Bioinformatics, Basel, Switzerland
| | - Vladimira Hinic
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland
| | - Thomas Bodmer
- Clinical Microbiology, Labormedizinisches Zentrum Dr Risch, Liebefeld, Switzerland
| | - Martin Risch
- Clinical Microbiology, Labormedizinisches Zentrum Dr Risch, Liebefeld, Switzerland
| | - Carlo Casanova
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Andreas Widmer
- Division of Infectious Diseases & Hospital Epidemiology, University Hospital Basel, University Basel, Basel, Switzerland
| | - Rami Sommerstein
- Department of Infectious Diseases, Bern University Hospital and University of Bern, Bern, Switzerland.,Infectious Diseases, Hirslanden Central Switzerland, Lucerne, Switzerland
| | - Jonas Marschall
- Department of Infectious Diseases, Bern University Hospital and University of Bern, Bern, Switzerland
| | - Sarah Tschudin-Sutter
- Division of Infectious Diseases & Hospital Epidemiology, University Hospital Basel, University Basel, Basel, Switzerland
| | - Adrian Egli
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Basel, Switzerland.,Applied Microbiology Research, Department Biomedicine, University of Basel, Basel, Switzerland
| |
Collapse
|
32
|
Cho J, Cunningham S, Pu M, Lennon RJ, Dens Higano J, Jeraldo P, Sampathkumar P, Shannon S, Kashyap PC, Patel R. Clostridioides difficile Whole-genome Sequencing Differentiates Relapse With the Same Strain From Reinfection With a New Strain. Clin Infect Dis 2021; 72:806-813. [PMID: 32064535 DOI: 10.1093/cid/ciaa159] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Accepted: 02/14/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Current approaches in tracking Clostridioides difficile infection (CDI) and individualizing patient management are incompletely defined. METHODS We recruited 468 subjects with CDI at Mayo Clinic Rochester between May and December 2016 and performed whole-genome sequencing (WGS) on C. difficile isolates from 397. WGS was also performed on isolates from a subset of the subjects at the time of a recurrence of infection. The sequence data were analyzed by determining core genome multilocus sequence type (cgMLST), with isolates grouped by allelic differences and the predicted ribotype. RESULTS There were no correlations between C. difficile isolates based either on cgMLST or ribotype groupings and CDI outcome. An epidemiologic assessment of hospitalized subjects harboring C. difficile isolates with ≤2 allelic differences, based on standard infection prevention and control assessment, revealed no evidence of person-to-person transmission. Interestingly, community-acquired CDI subjects in 40% of groups with ≤2 allelic differences resided within the same zip code. Among 18 subjects clinically classified as having recurrent CDI, WGS revealed 14 with initial and subsequent isolates differing by ≤2 allelic differences, suggesting a relapse of infection with the same initial strain, and 4 with isolates differing by >50 allelic differences, suggesting reinfection. Among the 5 subjects classified as having a reinfection based on the timing of recurrence, 3 had isolates with ≤2 allelic differences between them, suggesting a relapse, and 2 had isolates differing by >50 allelic differences, suggesting reinfection. CONCLUSIONS Our findings point to potential transmission of C. difficile in the community. WGS better differentiates relapse from reinfection than do definitions based on the timing of recurrence.
Collapse
Affiliation(s)
- Janice Cho
- Division of Gastroenterology, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Scott Cunningham
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Meng Pu
- Division of Gastroenterology, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Ryan J Lennon
- Division of Biomedical Statistics and Informatics, Department of Health Sciences Research, Mayo Clinic, Rochester, Minnesota, USA
| | | | - Patricio Jeraldo
- Division of Surgical Research, Department of Surgery, Mayo Clinic, Rochester, Minnesota, USA
| | - Priya Sampathkumar
- Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Samantha Shannon
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA
| | - Purna C Kashyap
- Division of Gastroenterology, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| | - Robin Patel
- Division of Clinical Microbiology, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, Minnesota, USA.,Division of Infectious Diseases, Department of Medicine, Mayo Clinic, Rochester, Minnesota, USA
| |
Collapse
|
33
|
Badilla-Lobo A, Rodríguez C. Microbiological features, epidemiology, and clinical presentation of Clostridioidesdifficile strains from MLST Clade 2: A narrative review. Anaerobe 2021; 69:102355. [PMID: 33711422 DOI: 10.1016/j.anaerobe.2021.102355] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Revised: 02/25/2021] [Accepted: 02/26/2021] [Indexed: 02/06/2023]
Abstract
Clostridioides difficile is an emerging One Health pathogen and a common etiologic agent of diarrhea, both in healthcare settings and the community. This bacterial species is highly diverse, and its global population has been classified in eight clades by multilocus sequence typing (MLST). The C. difficile MLST Clade 2 includes the NAP1/RT027/ST01 strain, which is highly recognized due to its epidemicity and association with severe disease presentation and mortality. By contrast, the remaining 83 sequence types (STs) that compose this clade have received much less attention. In response to this shortcoming, we reviewed articles published in English between 1999 and 2020 and collected information for 27 Clade 2 STs, with an emphasis on STs 01, 67, 41 and 188/231/365. Our analysis provides evidence of large phenotypic differences that preclude support of the rather widespread notion that ST01 and Clade 2 strains are "hypervirulent". Moreover, it revealed a profound lack of (meta)data for nearly 70% of the Clade 2 STs that have been identified in surveillance efforts. Targeted studies aiming to relate wet-lab and bioinformatics results to patient and clinical parameters should be performed to gain a more in-depth insight into the biology of this intriguing group of C. difficile isolates.
Collapse
Affiliation(s)
- Adriana Badilla-Lobo
- Centro de Investigación en Enfermedades Tropicales, Facultad de Microbiología, and Master's Program in Microbiology, Parasitology, Clinical Chemistry and Immunology, Universidad de Costa Rica, Costa Rica
| | - César Rodríguez
- Centro de Investigación en Enfermedades Tropicales, Facultad de Microbiología, and Master's Program in Microbiology, Parasitology, Clinical Chemistry and Immunology, Universidad de Costa Rica, Costa Rica.
| |
Collapse
|
34
|
Establishment and Evaluation of a Core Genome Multilocus Sequence Typing Scheme for Whole-Genome Sequence-Based Typing of Pseudomonas aeruginosa. J Clin Microbiol 2021; 59:JCM.01987-20. [PMID: 33328175 DOI: 10.1128/jcm.01987-20] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2020] [Accepted: 12/07/2020] [Indexed: 01/04/2023] Open
Abstract
The environmental bacterium Pseudomonas aeruginosa, particularly multidrug-resistant clones, is often associated with nosocomial infections and outbreaks. Today, core genome multilocus sequence typing (cgMLST) is frequently applied to delineate sporadic cases from nosocomial transmissions. However, until recently, no cgMLST scheme for a standardized typing of P. aeruginosa was available. To establish a novel cgMLST scheme for P. aeruginosa, we initially determined the breadth of the P. aeruginosa population based on MLST data with a Bayesian approach (BAPS). Using genomic data of representative isolates for the whole population and all 12 serogroups, we extracted target genes and further refined them using a random data set of 1,000 P. aeruginosa genomes. Subsequently, we investigated reproducibility and discriminatory ability with repeatedly sequenced isolates and isolates from well-defined outbreak scenarios, respectively, and compared clustering applying two recently published cgMLST schemes. BAPS generated seven P. aeruginosa groups. To cover these and all serogroups, 15 reference strains were used to determine genes common in all strains. After refinement with the data set of 1,000 genomes, the cgMLST scheme consisted of 3,867 target genes, which are representative of the P. aeruginosa population and highly reproducible using biological replicates. We finally evaluated the scheme by reanalyzing two published outbreaks where the authors used single-nucleotide polymorphism (SNP) typing. In both cases, cgMLST was concordant with the previous SNP results and the results of the two other cgMLST schemes. In conclusion, the highly reproducible novel P. aeruginosa cgMLST scheme facilitates outbreak investigations due to the publicly available cgMLST nomenclature.
Collapse
|
35
|
Pu M, Cho JM, Cunningham SA, Behera G, Becker S, Amjad T, Greenwood-Quaintance KE, Mendes-Soares H, Jones-Hall Y, Jeraldo PR, Chen J, Dunny G, Patel R, Kashyap PC. Plasmid Acquisition Alters Vancomycin Susceptibility in Clostridioides difficile. Gastroenterology 2021; 160:941-945.e8. [PMID: 33197449 PMCID: PMC7878333 DOI: 10.1053/j.gastro.2020.10.046] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/31/2020] [Revised: 10/21/2020] [Accepted: 10/22/2020] [Indexed: 12/20/2022]
Abstract
The increasing incidence of primary and recurring Clostridioides difficile infections (CDI), which evade current treatment strategies, reflects the changing biology of C difficile. Here, we describe a putative plasmid-mediated mechanism potentially driving decreased sensitivity of C difficile to vancomycin treatment. We identified a broad host range transferable plasmid in a C difficile strain associated with lack of adequate response to vancomycin treatment. The transfer of this plasmid to a vancomycin-susceptible C difficile isolate decreased its susceptibility to vancomycin in vitro and resulted in more severe disease in a humanized mouse model. Our findings suggest plasmid acquisition in the gastrointestinal tract to be a possible mechanism underlying vancomycin treatment failure in patients with CDI, but further work is needed to characterize the mechanism by which plasmid genes determine vancomycin susceptibility in C difficile.
Collapse
Affiliation(s)
- Meng Pu
- Department of Medicine, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Janice M. Cho
- Department of Medicine, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Scott A. Cunningham
- Department of Laboratory Medicine and Pathology, Division of Clinical Microbiology, Mayo Clinic, Rochester, MN, USA
| | - Gaurav Behera
- Department of Medicine, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Sarah Becker
- Department of Medicine, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | - Talal Amjad
- Department of Medicine, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA
| | | | | | - Yava Jones-Hall
- Department of Veterinary Pathobiology, Texas A&M College of Veterinary Medicine & Biomedical Sciences, College Station, TX, USA
| | | | - Jun Chen
- Department of Health Sciences Research, Mayo Clinic, Rochester, MN, USA
| | - Gary Dunny
- Department of Microbiology, University of Minnesota Medical School, Minneapolis, MN, USA
| | - Robin Patel
- Department of Laboratory Medicine and Pathology, Division of Clinical Microbiology, Mayo Clinic, Rochester, MN, USA,Department of Medicine, Division of Infectious Diseases, Mayo Clinic, Rochester, MN, USA
| | - Purna C. Kashyap
- Department of Medicine, Division of Gastroenterology and Hepatology, Mayo Clinic, Rochester, MN, USA,Department of Physiology & Biomedical Engineering, Mayo Clinic, Rochester, MN, USA
| |
Collapse
|
36
|
Bjöersdorff OG, Lindberg S, Kiil K, Persson S, Guardabassi L, Damborg P. Dogs are carriers of Clostridioides difficile lineages associated with human community-acquired infections. Anaerobe 2021; 67:102317. [PMID: 33418077 DOI: 10.1016/j.anaerobe.2020.102317] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 12/26/2020] [Indexed: 12/19/2022]
Abstract
There is an increasing concern about the role of animals as reservoirs of Clostridioides difficile. In this study, we investigated prevalence, antimicrobial resistance and zoonotic potential of C. difficile in dogs. Two-hundred and twenty-five dog faecal deposits were collected from trashcans in nine public gardens. C. difficile was isolated using selective plating and enrichment culture, identified by MALDI-TOF, tested for susceptibility to seven antibiotics by E-test, and sequenced on an Illumina NextSeq platform. Genome sequences were analysed to determine multilocus sequence types and resistance and toxin gene profiles. Zoonotic potential was assessed by measuring genetic variations of core genome (cg)MLST types between canine isolates and 216 temporally and spatially related human clinical isolates from a national database. C. difficile was isolated from 11 samples (4.9%). Seven isolates were toxigenic (tcdA+, tcdB+, cdtA/B-) and belonged to the sequence types ST2, ST6, ST10 and ST42. The four non-toxigenic isolates were assigned to ST15, ST26 and one novel ST. ST2, corresponding to PCR ribotype RT014/020, was the dominating lineage (n = 4) and, together with ST26 and ST42 isolates, showed close resemblance to human isolates, i.e. 2-5 allelic differences among the 1999 genes analysed by cgMLST. Three non-toxigenic isolates displayed resistance to clindamycin, erythromycin and tetracycline mediated by erm(B) and tet(M). Resistance to metronidazole, moxifloxacine, rifampicin or vancomycin was not detected. In conclusion, a small proportion of faecal deposits contained toxigenic C. difficile such as ST2 (RT014/020), which is a major cause of community-acquired infections. Our finding suggests that pathogenic strains can be exchanged between dogs and humans.
Collapse
Affiliation(s)
- Olivia Graaf Bjöersdorff
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Sanna Lindberg
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Kristoffer Kiil
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Artillerivej 5, 2300, Copenhagen, Denmark
| | - Søren Persson
- Department of Bacteria, Parasites and Fungi, Statens Serum Institut, Artillerivej 5, 2300, Copenhagen, Denmark
| | - Luca Guardabassi
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Peter Damborg
- Department of Veterinary and Animal Sciences, University of Copenhagen, Frederiksberg C, Denmark.
| |
Collapse
|
37
|
Aguilar-Zamora E, Weimer BC, Torres RC, Gómez-Delgado A, Ortiz-Olvera N, Aparicio-Ozores G, Barbero-Becerra VJ, Torres J, Camorlinga-Ponce M. Molecular Epidemiology and Antimicrobial Resistance of Clostridioides difficile in Hospitalized Patients From Mexico. Front Microbiol 2021; 12:787451. [PMID: 35360652 PMCID: PMC8960119 DOI: 10.3389/fmicb.2021.787451] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 12/29/2021] [Indexed: 01/05/2023] Open
Abstract
Clostridioides difficile is a global public health problem, which is a primary cause of antibiotic-associated diarrhea in humans. The emergence of hypervirulent and antibiotic-resistant strains is associated with the increased incidence and severity of the disease. There are limited studies on genomic characterization of C. difficile in Latin America. We aimed to learn about the molecular epidemiology and antimicrobial resistance in C. difficile strains from adults and children in hospitals of México. We studied 94 C. difficile isolates from seven hospitals in Mexico City from 2014 to 2018. Whole-genome sequencing (WGS) was used to determine the genotype and examine the toxigenic profiles. Susceptibility to antibiotics was determined by E-test. Multilocus sequence typing (MLST) was used to determine allelic profiles. Results identified 20 different sequence types (ST) in the 94 isolates, mostly clade 2 and clade 1. ST1 was predominant in isolates from adult and children. Toxigenic strains comprised 87.2% of the isolates that were combinations of tcdAB and cdtAB (tcdA+/tcdB+/cdtA+/cdtB+, followed by tcdA+/tcdB+/cdtA-/cdtB-, tcdA-/tcdB+/cdtA-/ cdtB-, and tcdA-/tcdB-/cdtA+/cdtB+). Toxin profiles were more diverse in isolates from children. All 94 isolates were susceptible to metronidazole and vancomycin, whereas a considerable number of isolates were resistant to clindamycin, fluroquinolones, rifampicin, meropenem, and linezolid. Multidrug-resistant isolates (≥3 antibiotics) comprised 65% of the isolates. The correlation between resistant genotypes and phenotypes was evaluated by the kappa test. Mutations in rpoB and rpoC showed moderate concordance with resistance to rifampicin and mutations in fusA substantial concordance with fusidic acid resistance. cfrE, a gene recently described in one Mexican isolate, was present in 65% of strains linezolid resistant, all ST1 organisms. WGS is a powerful tool to genotype and characterize virulence and antibiotic susceptibility patterns.
Collapse
Affiliation(s)
- Emmanuel Aguilar-Zamora
- Unidad de Investigación Medica en Enfermedades Infecciosas y Parasitarias, UMAE Pediatría, CMN Siglo XXI, IMSS, México City, Mexico
- Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, México City, Mexico
| | - Bart C. Weimer
- Department of Population Health and Reproduction, School of Veterinary Medicine, 100K Pathogen Genome Project, University of California, Davis, Davis, CA, United States
| | - Roberto C. Torres
- Unidad de Investigación Medica en Enfermedades Infecciosas y Parasitarias, UMAE Pediatría, CMN Siglo XXI, IMSS, México City, Mexico
| | - Alejandro Gómez-Delgado
- Unidad de Investigación Medica en Enfermedades Infecciosas y Parasitarias, UMAE Pediatría, CMN Siglo XXI, IMSS, México City, Mexico
| | - Nayeli Ortiz-Olvera
- Departamento de Gastroenterología, UMAE Hospital de Especialidades, Instituto Mexicano del Seguro Social, México City, Mexico
| | - Gerardo Aparicio-Ozores
- Departamento de Microbiología, Escuela Nacional de Ciencias Biológicas, Instituto Politécnico Nacional, México City, Mexico
| | | | - Javier Torres
- Unidad de Investigación Medica en Enfermedades Infecciosas y Parasitarias, UMAE Pediatría, CMN Siglo XXI, IMSS, México City, Mexico
- *Correspondence: Javier Torres,
| | - Margarita Camorlinga-Ponce
- Unidad de Investigación Medica en Enfermedades Infecciosas y Parasitarias, UMAE Pediatría, CMN Siglo XXI, IMSS, México City, Mexico
- Margarita Camorlinga-Ponce,
| |
Collapse
|
38
|
Phylogenomics of 8,839 Clostridioides difficile genomes reveals recombination-driven evolution and diversification of toxin A and B. PLoS Pathog 2020; 16:e1009181. [PMID: 33370413 PMCID: PMC7853461 DOI: 10.1371/journal.ppat.1009181] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2020] [Revised: 02/02/2021] [Accepted: 11/23/2020] [Indexed: 12/15/2022] Open
Abstract
Clostridioides difficile is the major worldwide cause of antibiotic-associated gastrointestinal infection. A pathogenicity locus (PaLoc) encoding one or two homologous toxins, toxin A (TcdA) and toxin B (TcdB), is essential for C. difficile pathogenicity. However, toxin sequence variation poses major challenges for the development of diagnostic assays, therapeutics, and vaccines. Here, we present a comprehensive phylogenomic analysis of 8,839 C. difficile strains and their toxins including 6,492 genomes that we assembled from the NCBI short read archive. A total of 5,175 tcdA and 8,022 tcdB genes clustered into 7 (A1-A7) and 12 (B1-B12) distinct subtypes, which form the basis of a new method for toxin-based subtyping of C. difficile. We developed a haplotype coloring algorithm to visualize amino acid variation across all toxin sequences, which revealed that TcdB has diversified through extensive homologous recombination throughout its entire sequence, and formed new subtypes through distinct recombination events. In contrast, TcdA varies mainly in the number of repeats in its C-terminal repetitive region, suggesting that recombination-mediated diversification of TcdB provides a selective advantage in C. difficile evolution. The application of toxin subtyping is then validated by classifying 351 C. difficile clinical isolates from Brigham and Women's Hospital in Boston, demonstrating its clinical utility. Subtyping partitions TcdB into binary functional and antigenic groups generated by intragenic recombinations, including two distinct cell-rounding phenotypes, whether recognizing frizzled proteins as receptors, and whether it can be efficiently neutralized by monoclonal antibody bezlotoxumab, the only FDA-approved therapeutic antibody. Our analysis also identifies eight universally conserved surface patches across the TcdB structure, representing ideal targets for developing broad-spectrum therapeutics. Finally, we established an open online database (DiffBase) as a central hub for collection and classification of C. difficile toxins, which will help clinicians decide on therapeutic strategies targeting specific toxin variants, and allow researchers to monitor the ongoing evolution and diversification of C. difficile.
Collapse
|
39
|
Werner A, Mölling P, Fagerström A, Dyrkell F, Arnellos D, Johansson K, Sundqvist M, Norén T. Whole genome sequencing of Clostridioides difficile PCR ribotype 046 suggests transmission between pigs and humans. PLoS One 2020; 15:e0244227. [PMID: 33347506 PMCID: PMC7751860 DOI: 10.1371/journal.pone.0244227] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 12/04/2020] [Indexed: 01/16/2023] Open
Abstract
Background A zoonotic association has been suggested for several PCR ribotypes (RTs) of Clostridioides difficile. In central parts of Sweden, RT046 was found dominant in neonatal pigs at the same time as a RT046 hospital C. difficile infection (CDI) outbreak occurred in the southern parts of the country. Objective To detect possible transmission of RT046 between pig farms and human CDI cases in Sweden and investigate the diversity of RT046 in the pig population using whole genome sequencing (WGS). Methods WGS was performed on 47 C. difficile isolates from pigs (n = 22), the farm environment (n = 7) and human cases of CDI (n = 18). Two different core genome multilocus sequencing typing (cgMLST) schemes were used together with a single nucleotide polymorphisms (SNP) analysis and the results were related to time and location of isolation of the isolates. Results The pig isolates were closely related (≤6 cgMLST alleles differing in both cgMLST schemes) and conserved over time and were clearly separated from isolates from the human hospital outbreak (≥76 and ≥90 cgMLST alleles differing in the two cgMLST schemes). However, two human isolates were closely related to the pig isolates, suggesting possible transmission. The SNP analysis was not more discriminate than cgMLST. Conclusion No general pattern suggesting zoonotic transmission was apparent between pigs and humans, although contrasting results from two isolates still make transmission possible. Our results support the need for high resolution WGS typing when investigating hospital and environmental transmission of C. difficile.
Collapse
Affiliation(s)
- Anders Werner
- Department of Clinical Microbiology, Sahlgrenska University Hospital, Göteborg, Region Västra Götaland, Sweden
- * E-mail:
| | - Paula Mölling
- Faculty of Medicine and Health, Department of Laboratory Medicine, National Reference Laboratory for Clostridioides difficile, Clinical Microbiology, Örebro University, Örebro, Sweden
| | - Anna Fagerström
- Faculty of Medicine and Health, Department of Laboratory Medicine, National Reference Laboratory for Clostridioides difficile, Clinical Microbiology, Örebro University, Örebro, Sweden
| | | | | | - Karin Johansson
- Faculty of Medicine and Health, Department of Laboratory Medicine, National Reference Laboratory for Clostridioides difficile, Clinical Microbiology, Örebro University, Örebro, Sweden
| | - Martin Sundqvist
- Faculty of Medicine and Health, Department of Laboratory Medicine, National Reference Laboratory for Clostridioides difficile, Clinical Microbiology, Örebro University, Örebro, Sweden
| | - Torbjörn Norén
- Faculty of Medicine and Health, Department of Laboratory Medicine, National Reference Laboratory for Clostridioides difficile, Clinical Microbiology, Örebro University, Örebro, Sweden
| |
Collapse
|
40
|
Heise J, Witt P, Maneck C, Wichmann-Schauer H, Maurischat S. Prevalence and phylogenetic relationship of Clostridioides difficile strains in fresh poultry meat samples processed in different cutting plants. Int J Food Microbiol 2020; 339:109032. [PMID: 33388709 DOI: 10.1016/j.ijfoodmicro.2020.109032] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 12/11/2020] [Accepted: 12/15/2020] [Indexed: 01/07/2023]
Abstract
Clostridioides difficile is one of the most frequent causes of nosocomial infections in humans leading to (antibiotic-associated) diarrhea and severe pseudomembranous colitis. With an increasing frequency, C. difficile infections (CDI) are also observed independently of hospitalization and the age of the patients in an ambulant setting. One potential source of so-called community-acquired CDI is a zoonotic transmission to humans based on direct contact with animals or the consumption of food. To estimate the exposure of humans with C. difficile via food, we screened 364 different retail fresh poultry meat products purchased in Berlin and Brandenburg, Germany and further characterized the isolates. None of the 42 turkey or chicken meat samples without skin was contaminated. However, 51 (15.8%) of 322 tested fresh chicken meat samples with skin were C. difficile-positive. The vast majority (84.3%) of all isolates exhibited toxin genes tcdA and tcdB, whereas the binary toxin cdtA/B was absent. Most of the isolates (50/51) were susceptible to all six investigated antimicrobials. However, one non-toxigenic strain was multidrug resistant to the antimicrobials clindamycin and erythromycin. The isolates were mainly represented by PCR-ribotypes (RT) 001, RT002, RT005, and RT014, which were already associated with human CDI cases in Germany and were partially detected in poultry. The relatively high contamination rate of fresh retail chicken meat with skin purchased in Germany indicates chicken meat as a potential source of human infections. Moreover, we identified cutting plants with a higher rate of a C. difficile-contamination (21.4-32.8%). To compare the phylogenetic relationship of the isolated strains from certain cutting plants over several months in 2018 and 2019, we analyzed them using NGS followed by core genome MLST. Interestingly, highly related strains (0-3 alleles distance) of common clinical RT001 and RT002 isolates, as well as of the non-toxigenic RT205 isolates were detectable in same cutting plants over a period of three and 16 months, respectively.The continuous contamination with the same strain could be explained by the longterm persistence of this strain within the cutting plant (e.g., within the scalder), or with a recurring entry e.g. from the same fattening farm.
Collapse
Affiliation(s)
- Janine Heise
- German Federal Institute for Risk Assessment, Department Biological Safety, Unit Bacterial Toxins, Food Service, Max-Dohrn-Str. 8-10, 10589 Berlin, Germany.
| | - Pascal Witt
- German Federal Institute for Risk Assessment, Department Biological Safety, Unit Bacterial Toxins, Food Service, Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
| | - Corinna Maneck
- German Federal Institute for Risk Assessment, Department Biological Safety, Unit Bacterial Toxins, Food Service, Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
| | - Heidi Wichmann-Schauer
- German Federal Institute for Risk Assessment, Department Biological Safety, Unit Bacterial Toxins, Food Service, Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
| | - Sven Maurischat
- German Federal Institute for Risk Assessment, Department Biological Safety, Unit Bacterial Toxins, Food Service, Max-Dohrn-Str. 8-10, 10589 Berlin, Germany
| |
Collapse
|
41
|
McLean K, Balada-Llasat JM, Waalkes A, Pancholi P, Salipante SJ. Whole-genome sequencing of clinical Clostridioides difficile isolates reveals molecular epidemiology and discrepancies with conventional laboratory diagnostic testing. J Hosp Infect 2020; 108:64-71. [PMID: 33227298 DOI: 10.1016/j.jhin.2020.11.014] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 10/06/2020] [Accepted: 11/16/2020] [Indexed: 12/29/2022]
Abstract
BACKGROUND The high clinical burden of Clostridioides difficile infections merits rapid and sensitive identification of affected individuals. However, effective diagnosis remains challenging. Current best practice guidelines recommend molecular and/or direct toxin detection-based screening for symptomatic individuals, but previous work has called into question the concordance and performance of extant clinical assays. AIM To better correlate the genomic and phenotypic properties of clinical C. difficile isolates with laboratory testing outcomes in both C. difficile-infected patients and asymptomatic carriers. METHODS Whole-genome sequencing of clinical C. difficile isolates collected from an inpatient population at a single healthcare institution was performed, enabling examination of their molecular epidemiology and toxigenic gene content. Genomic findings were compared with clinical testing outcomes, identifying multiple diagnostic discrepancies. FINDINGS Toxigenic culture, considered a 'reference standard', provided perfect sensitivity and specificity in predicting toxigenic gene content, whereas reduced performance was observed for Simplexa C. difficile Direct Assay (100% specificity, 88% sensitivity), Gene Xpert CD/Epi Assay (86% specificity, 83% sensitivity), and Quick Check Complete Tox A/B (100% specificity, 30% sensitivity). Genomic analysis additionally revealed variability in toxin gene sequences among C. difficile strains, phylogenomic equivalency between isolates from affected patients and carriers, and patient carriage with uncommon environmentally derived C. difficile lineages, as well as presenting opportunities for tracing pathogen transmission events. CONCLUSION These results highlight the variable performance of clinical stool-based testing approaches as well as the potential diagnostic utility of whole-genome sequencing as an alternative to conventional testing algorithms.
Collapse
Affiliation(s)
- K McLean
- University of Washington Department of Laboratory Medicine, Seattle, WA, USA
| | - J-M Balada-Llasat
- Ohio State University Wexner Medical Center, Department of Pathology, Columbus, OH, USA
| | - A Waalkes
- University of Washington Department of Laboratory Medicine, Seattle, WA, USA
| | - P Pancholi
- Ohio State University Wexner Medical Center, Department of Pathology, Columbus, OH, USA.
| | - S J Salipante
- University of Washington Department of Laboratory Medicine, Seattle, WA, USA.
| |
Collapse
|
42
|
Liang KYH, Orata FD, Islam MT, Nasreen T, Alam M, Tarr CL, Boucher YF. A Vibrio cholerae Core Genome Multilocus Sequence Typing Scheme To Facilitate the Epidemiological Study of Cholera. J Bacteriol 2020; 202:e00086-20. [PMID: 32540931 PMCID: PMC7685551 DOI: 10.1128/jb.00086-20] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 06/07/2020] [Indexed: 12/11/2022] Open
Abstract
Core genome multilocus sequence typing (cgMLST) has gained popularity in recent years in epidemiological research and subspecies-level classification. cgMLST retains the intuitive nature of traditional MLST but offers much greater resolution by utilizing significantly larger portions of the genome. Here, we introduce a cgMLST scheme for Vibrio cholerae, a bacterium abundant in marine and freshwater environments and the etiologic agent of cholera. A set of 2,443 core genes ubiquitous in V. cholerae were used to analyze a comprehensive data set of 1,262 clinical and environmental strains collected from 52 countries, including 65 newly sequenced genomes in this study. We established a sublineage threshold based on 133 allelic differences that creates clusters nearly identical to traditional MLST types, providing backwards compatibility to new cgMLST classifications. We also defined an outbreak threshold based on seven allelic differences that is capable of identifying strains from the same outbreak and closely related isolates that could give clues on outbreak origin. Using cgMLST, we confirmed the South Asian origin of modern epidemics and identified clustering affinity among sublineages of environmental isolates from the same geographic origin. Advantages of this method are highlighted by direct comparison with existing classification methods, such as MLST and single-nucleotide polymorphism-based methods. cgMLST outperforms all existing methods in terms of resolution, standardization, and ease of use. We anticipate this scheme will serve as a basis for a universally applicable and standardized classification system for V. cholerae research and epidemiological surveillance in the future. This cgMLST scheme is publicly available on PubMLST (https://pubmlst.org/vcholerae/).IMPORTANCE Toxigenic Vibrio cholerae isolates of the O1 and O139 serogroups are the causative agents of cholera, an acute diarrheal disease that plagued the world for centuries, if not millennia. Here, we introduce a core genome multilocus sequence typing scheme for V. cholerae Using this scheme, we have standardized the definition for subspecies-level classification, facilitating global collaboration in the surveillance of V. cholerae In addition, this typing scheme allows for quick identification of outbreak-related isolates that can guide subsequent analyses, serving as an important first step in epidemiological research. This scheme is also easily scalable to analyze thousands of isolates at various levels of resolution, making it an invaluable tool for large-scale ecological and evolutionary analyses.
Collapse
Affiliation(s)
- Kevin Y H Liang
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Fabini D Orata
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | | | - Tania Nasreen
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
| | - Munirul Alam
- Infectious Diseases Division, International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh
| | - Cheryl L Tarr
- Enteric Diseases Laboratory Branch, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Yann F Boucher
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta, Canada
- Saw Swee Hock School of Public Health, National University of Singapore, Singapore, Singapore
- Singapore Center for Environmental Life Sciences Engineering, National University of Singapore, Singapore, Singapore
| |
Collapse
|
43
|
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.
Collapse
|
44
|
Frentrup M, Zhou Z, Steglich M, Meier-Kolthoff JP, Göker M, Riedel T, Bunk B, Spröer C, Overmann J, Blaschitz M, Indra A, von Müller L, Kohl TA, Niemann S, Seyboldt C, Klawonn F, Kumar N, Lawley TD, García-Fernández S, Cantón R, del Campo R, Zimmermann O, Groß U, Achtman M, Nübel U. A publicly accessible database for Clostridioides difficile genome sequences supports tracing of transmission chains and epidemics. Microb Genom 2020; 6:mgen000410. [PMID: 32726198 PMCID: PMC7641423 DOI: 10.1099/mgen.0.000410] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Accepted: 06/30/2020] [Indexed: 01/02/2023] Open
Abstract
Clostridioides difficile is the primary infectious cause of antibiotic-associated diarrhea. Local transmissions and international outbreaks of this pathogen have been previously elucidated by bacterial whole-genome sequencing, but comparative genomic analyses at the global scale were hampered by the lack of specific bioinformatic tools. Here we introduce a publicly accessible database within EnteroBase (http://enterobase.warwick.ac.uk) that automatically retrieves and assembles C. difficile short-reads from the public domain, and calls alleles for core-genome multilocus sequence typing (cgMLST). We demonstrate that comparable levels of resolution and precision are attained by EnteroBase cgMLST and single-nucleotide polymorphism analysis. EnteroBase currently contains 18 254 quality-controlled C. difficile genomes, which have been assigned to hierarchical sets of single-linkage clusters by cgMLST distances. This hierarchical clustering is used to identify and name populations of C. difficile at all epidemiological levels, from recent transmission chains through to epidemic and endemic strains. Moreover, it puts newly collected isolates into phylogenetic and epidemiological context by identifying related strains among all previously published genome data. For example, HC2 clusters (i.e. chains of genomes with pairwise distances of up to two cgMLST alleles) were statistically associated with specific hospitals (P<10-4) or single wards (P=0.01) within hospitals, indicating they represented local transmission clusters. We also detected several HC2 clusters spanning more than one hospital that by retrospective epidemiological analysis were confirmed to be associated with inter-hospital patient transfers. In contrast, clustering at level HC150 correlated with k-mer-based classification and was largely compatible with PCR ribotyping, thus enabling comparisons to earlier surveillance data. EnteroBase enables contextual interpretation of a growing collection of assembled, quality-controlled C. difficile genome sequences and their associated metadata. Hierarchical clustering rapidly identifies database entries that are related at multiple levels of genetic distance, facilitating communication among researchers, clinicians and public-health officials who are combatting disease caused by C. difficile.
Collapse
Affiliation(s)
| | - Zhemin Zhou
- Warwick Medical School, University of Warwick, UK
| | - Matthias Steglich
- Leibniz Institute DSMZ, Braunschweig, Germany
- German Center for Infection Research (DZIF), Partner site Hannover-Braunschweig, Germany
| | | | | | - Thomas Riedel
- Leibniz Institute DSMZ, Braunschweig, Germany
- German Center for Infection Research (DZIF), Partner site Hannover-Braunschweig, Germany
| | - Boyke Bunk
- Leibniz Institute DSMZ, Braunschweig, Germany
| | | | - Jörg Overmann
- Leibniz Institute DSMZ, Braunschweig, Germany
- German Center for Infection Research (DZIF), Partner site Hannover-Braunschweig, Germany
- Braunschweig Integrated Center of Systems Biology (BRICS), Technical University, Braunschweig, Germany
| | - Marion Blaschitz
- AGES-Austrian Agency for Health and Food Safety, Vienna, Austria
| | - Alexander Indra
- AGES-Austrian Agency for Health and Food Safety, Vienna, Austria
| | | | - Thomas A. Kohl
- Research Center Borstel, Germany
- German Center for Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel, Germany
| | - Stefan Niemann
- Research Center Borstel, Germany
- German Center for Infection Research (DZIF), Partner site Hamburg-Lübeck-Borstel, Germany
| | | | - Frank Klawonn
- Biostatistics, Helmholtz Centre for Infection Research, Braunschweig, Germany
- Institute for Information Engineering, Ostfalia University, Wolfenbüttel, Germany
| | | | | | - Sergio García-Fernández
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
- Red Española de Investigación en Patología Infecciosa (REIPI), Madrid, Spain
| | - Rafael Cantón
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
- Red Española de Investigación en Patología Infecciosa (REIPI), Madrid, Spain
| | - Rosa del Campo
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal, and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), Madrid, Spain
- Red Española de Investigación en Patología Infecciosa (REIPI), Madrid, Spain
| | | | - Uwe Groß
- University Medical Center Göttingen, Germany
| | - Mark Achtman
- Warwick Medical School, University of Warwick, UK
| | - Ulrich Nübel
- Leibniz Institute DSMZ, Braunschweig, Germany
- German Center for Infection Research (DZIF), Partner site Hannover-Braunschweig, Germany
- Braunschweig Integrated Center of Systems Biology (BRICS), Technical University, Braunschweig, Germany
| |
Collapse
|
45
|
Molecular epidemiology and antimicrobial resistance of Clostridioides difficile detected in chicken, soil and human samples from Zimbabwe. Int J Infect Dis 2020; 96:82-87. [DOI: 10.1016/j.ijid.2020.04.026] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2020] [Revised: 04/06/2020] [Accepted: 04/07/2020] [Indexed: 01/05/2023] Open
|
46
|
Detection of C. difficile toxin as a model assay for performing fully automated high-throughput RT-PCR on clinical stool samples. J Microbiol Methods 2020; 172:105882. [DOI: 10.1016/j.mimet.2020.105882] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Revised: 02/27/2020] [Accepted: 02/27/2020] [Indexed: 01/02/2023]
|
47
|
Waker E, Ambrozkiewicz F, Kulecka M, Paziewska A, Skubisz K, Cybula P, Targoński Ł, Mikula M, Walewski J, Ostrowski J. High Prevalence of Genetically Related Clostridium Difficile Strains at a Single Hemato-Oncology Ward Over 10 Years. Front Microbiol 2020; 11:1618. [PMID: 32793147 PMCID: PMC7384382 DOI: 10.3389/fmicb.2020.01618] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 06/22/2020] [Indexed: 12/19/2022] Open
Abstract
Aims: Clostridium difficile (C. difficile) infection (CDI) is the main cause of healthcare-associated infectious diarrhea. We used whole-genome sequencing (WGS) to measure the prevalence and genetic variability of C. difficile at a single hemato-oncology ward over a 10 year period. Methods: Between 2008 and 2018, 2077 stool samples were obtained from diarrheal patients hospitalized at the Department of Lymphoma; of these, 618 were positive for toxin A/B. 140 isolates were then subjected to WGS on Ion Torrent PGM sequencer. Results: 36 and 104 isolates were recovered from 36 to 46 patients with single and multiple CDIs, respectively. Of these, 131 strains were toxigenic. Toxin gene profiles tcdA(+);tcdB(+);cdtA/cdtB(+) and tcdA(+);tcdB(+);cdtA/cdtB(-) were identified in 122 and nine strains, respectively. No isolates showed reduced susceptibility to metronidazole and vancomycin. All tested strains were resistant to ciprofloxacin, and 72.9, 42.9, and 72.9% of strains were resistant to erythromycin, clindamycin, or moxifloxacin, respectively. Multi-locus sequence typing (MLST) identified 23 distinct sequence types (STs) and two unidentified strains. Strains ST1 and ST42 represented 31 and 30.1% of all strains tested, respectively. However, while ST1 was detected across nearly all years studied, ST42 was detected only from 2009 to 2011. Conclusion: The high proportion of infected patients in 2008-2011 may be explained by the predominance of more transmissible and virulent C. difficile strains. Although this retrospective study was not designed to define outbreaks of C. difficile, the finding that most isolates exhibited high levels of genetic relatedness suggests nosocomial acquisition.
Collapse
Affiliation(s)
- Edyta Waker
- Department of Clinical Microbiology, Maria Skłodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Filip Ambrozkiewicz
- Department of Genetics, Maria Skłodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Maria Kulecka
- Department of Genetics, Maria Skłodowska-Curie National Research Institute of Oncology, Warsaw, Poland
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre for Postgraduate Medical Education, Warsaw, Poland
| | - Agnieszka Paziewska
- Department of Genetics, Maria Skłodowska-Curie National Research Institute of Oncology, Warsaw, Poland
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre for Postgraduate Medical Education, Warsaw, Poland
| | - Karolina Skubisz
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre for Postgraduate Medical Education, Warsaw, Poland
| | - Patrycja Cybula
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre for Postgraduate Medical Education, Warsaw, Poland
| | - Łukasz Targoński
- Department of Lymphoproliferative Diseases, Maria Skłodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Michał Mikula
- Department of Genetics, Maria Skłodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Jan Walewski
- Department of Lymphoproliferative Diseases, Maria Skłodowska-Curie National Research Institute of Oncology, Warsaw, Poland
| | - Jerzy Ostrowski
- Department of Genetics, Maria Skłodowska-Curie National Research Institute of Oncology, Warsaw, Poland
- Department of Gastroenterology, Hepatology and Clinical Oncology, Centre for Postgraduate Medical Education, Warsaw, Poland
- *Correspondence: Jerzy Ostrowski,
| |
Collapse
|
48
|
Eyre DW, Peto TEA, Crook DW, Walker AS, Wilcox MH. Hash-Based Core Genome Multilocus Sequence Typing for Clostridium difficile. J Clin Microbiol 2019; 58:e01037-19. [PMID: 31666367 PMCID: PMC6935933 DOI: 10.1128/jcm.01037-19] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 10/24/2019] [Indexed: 12/27/2022] Open
Abstract
Pathogen whole-genome sequencing has huge potential as a tool to better understand infection transmission. However, rapidly identifying closely related genomes among a background of thousands of other genomes is challenging. Here, we describe a refinement to core genome multilocus sequence typing (cgMLST) in which alleles at each gene are reproducibly converted to a unique hash, or short string of letters (hash-cgMLST). This avoids the resource-intensive need for a single centralized database of sequentially numbered alleles. We test the reproducibility and discriminatory power of cgMLST/hash-cgMLST compared to those of mapping-based approaches in Clostridium difficile, using repeated sequencing of the same isolates (replicates) and data from consecutive infection isolates from six English hospitals. Hash-cgMLST provided the same results as standard cgMLST, with minimal performance penalty. Comparing 272 replicate sequence pairs using reference-based mapping, there were 0, 1, or 2 single-nucleotide polymorphisms (SNPs) between 262 (96%), 5 (2%), and 1 (<1%) of the pairs, respectively. Using hash-cgMLST, 218 (80%) of replicate pairs assembled with SPAdes had zero gene differences, and 31 (11%), 5 (2%), and 18 (7%) pairs had 1, 2, and >2 differences, respectively. False gene differences were clustered in specific genes and associated with fragmented assemblies, but were reduced using the SKESA assembler. Considering 412 pairs of infections with ≤2 SNPS, i.e., consistent with recent transmission, 376 (91%) had ≤2 gene differences and 16 (4%) had ≥4. Comparing a genome to 100,000 others took <1 min using hash-cgMLST. Hash-cgMLST is an effective surveillance tool for rapidly identifying clusters of related genomes. However, cgMLST/hash-cgMLST generate more false variants than mapping-based approaches. Follow-up mapping-based analyses are likely required to precisely define close genetic relationships.
Collapse
Affiliation(s)
- David W Eyre
- Big Data Institute, University of Oxford, Oxford, United Kingdom
- National Institute for Health Research Oxford Biomedical Research Centre, Oxford, United Kingdom
| | - Tim E A Peto
- National Institute for Health Research Oxford Biomedical Research Centre, Oxford, United Kingdom
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- National Institutes of Health Research Health Protection Unit on Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, United Kingdom
| | - Derrick W Crook
- National Institute for Health Research Oxford Biomedical Research Centre, Oxford, United Kingdom
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- National Institutes of Health Research Health Protection Unit on Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, United Kingdom
| | - A Sarah Walker
- National Institute for Health Research Oxford Biomedical Research Centre, Oxford, United Kingdom
- Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- National Institutes of Health Research Health Protection Unit on Healthcare Associated Infections and Antimicrobial Resistance, University of Oxford, Oxford, United Kingdom
| | - Mark H Wilcox
- Healthcare Associated Infections Research Group, University of Leeds, Leeds, United Kingdom
| |
Collapse
|
49
|
Janezic S, Rupnik M. Development and Implementation of Whole Genome Sequencing-Based Typing Schemes for Clostridioides difficile. Front Public Health 2019; 7:309. [PMID: 31709221 PMCID: PMC6821651 DOI: 10.3389/fpubh.2019.00309] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Accepted: 10/08/2019] [Indexed: 12/21/2022] Open
Abstract
Clostridioides difficile is an important nosocomial pathogen increasingly observed in the community and in different non-human reservoirs. The epidemiology and transmissibility of C. difficile has been studied using a variety of typing methods, including more recently developed whole-genome sequence (WGS) analysis that is becoming used routinely for bacterial typing worldwide. Here we review the schemes for WGS-based typing methods available for C. difficile and their applications in the field of human C. difficile infection (CDI). The two main approaches to discover genomic variations are single nucleotide variant (SNV) analysis and methods based on gene-by-gene comparisons (frequently called core genome or whole genome MLST, cgMLST, or wgMLST). SNV analysis currently provides the ultimate resolution, however, typing nomenclature and standardized methodology are missing. On the other hand, gene-by-gene approaches allow portability and standardized nomenclature, and are therefore becoming increasingly popular in bacterial epidemiology and outbreak investigation. Two commercial software packages (BioNumerics and Ridom SeqSphere+) and an open source database (EnteroBase) for allele and sequence type determination for C. difficile are currently available. Proof-of-concept WGS studies have already enabled advances in the investigation of the population structure of C. difficile species, microevolution within the epidemic strains, intercontinental transmission over time and in tracking of transmission events. WGS of clinical C. difficile isolates demonstrated a considerable genetic diversity suggesting diverse reservoirs for CDI. WGS was also shown to aid in resolving relapses and reinfections in recurrent CDI and has potential for use as a tool for assessing hospital infection prevention and control performance.
Collapse
Affiliation(s)
- Sandra Janezic
- National Laboratory for Health, Environment and Food, Maribor, Slovenia.,Medical Faculty, University of Maribor, Maribor, Slovenia
| | - Maja Rupnik
- National Laboratory for Health, Environment and Food, Maribor, Slovenia.,Medical Faculty, University of Maribor, Maribor, Slovenia
| |
Collapse
|
50
|
Berger FK, Mellmann A, von Müller L, Bischoff M, Gärtner BC. Quality assurance for genotyping and resistance testing of Clostridium (Clostridioides) difficile isolates - Experiences from the first inter-laboratory ring trial in four German speaking countries. Anaerobe 2019; 61:102093. [PMID: 31494260 DOI: 10.1016/j.anaerobe.2019.102093] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2019] [Revised: 08/29/2019] [Accepted: 08/29/2019] [Indexed: 01/05/2023]
Abstract
Clostridium (Clostridioides) difficile is a major cause of nosocomial diarrhoea. A first inter-laboratory ring trial was performed in four European countries to evaluate the genotyping and antibiotic susceptibility testing (AST) accuracy. Six C. difficile isolates representing the epidemiologic important ribotypes (RT), RT001, RT002, RT010, RT014, RT027, and RT078 were blinded and send to 21 participating laboratories. Participants tested the samples with their genotyping and AST methods in use for concordance with reference. A total of 21 genotyping- and 14 antimicrobial susceptibility data sets were obtained. Ribotyping (11 participants) correctly identified most RTs (median 91% concordance rate) except for RT002, which was misidentified in 4/11 reports. However, this isolate was correctly asserted to RT002 after an update of a publicly available ribotyping database. Multilocus sequence typing, surface layer sequence typing, DNA microarray based genotyping, and whole genome sequencing, which were used by 1-3 participants, identified all six isolates correctly. AST was done by epsilometry by the participants and compared to agar dilution data determined by the coordinating reference centre. Susceptibilities against metronidazole, moxifloxacin, and vancomycin were correctly identified in 235 of 237 cases and in accordance to agar dilution as the gold standard. Genotyping of the C. difficile test strains revealed a remarkable high concordance on the level of ribotypes with a wide variety of methods. Epsilometry appears to be a reliable method for AST of C. difficile isolates in routine clinical microbiology laboratories.
Collapse
Affiliation(s)
- Fabian K Berger
- German National Reference Center for Clostridioides (Clostridium) difficile, Germany; Institute of Medical Microbiology and Hygiene, University of Saarland, Kirrberger Straße, Building 43, 66424, Homburg/Saar, Germany.
| | - Alexander Mellmann
- German National Reference Center for Clostridioides (Clostridium) difficile, Germany; Institute of Hygiene, University Hospital Münster, Robert-Koch-Straße 41, 48149, Münster, Germany
| | - Lutz von Müller
- German National Reference Center for Clostridioides (Clostridium) difficile, Germany; Institute of Medical Microbiology and Hygiene, University of Saarland, Kirrberger Straße, Building 43, 66424, Homburg/Saar, Germany; Institute for Laboratory Medicine, Microbiology and Hygiene, Christophorus Kliniken, Südwall 22, 48653, Coesfeld, Germany
| | - Markus Bischoff
- German National Reference Center for Clostridioides (Clostridium) difficile, Germany; Institute of Medical Microbiology and Hygiene, University of Saarland, Kirrberger Straße, Building 43, 66424, Homburg/Saar, Germany
| | - Barbara C Gärtner
- German National Reference Center for Clostridioides (Clostridium) difficile, Germany; Institute of Medical Microbiology and Hygiene, University of Saarland, Kirrberger Straße, Building 43, 66424, Homburg/Saar, Germany
| | | |
Collapse
|