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Midani FS, Danhof HA, Mathew N, Ardis CK, Garey KW, Spinler JK, Britton RA. Emerging Clostridioides difficile ribotypes have divergent metabolic phenotypes. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.08.15.608124. [PMID: 39185189 PMCID: PMC11343193 DOI: 10.1101/2024.08.15.608124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 08/27/2024]
Abstract
Clostridioides difficile is a gram-positive spore-forming pathogen that commonly causes diarrheal infections in the developed world. Although C. difficile is a genetically diverse species, certain ribotypes are overrepresented in human infections. It is unknown if metabolic adaptations are essential for the emergence of these epidemic ribotypes. Here, we tested carbon substrate utilization by 88 C. difficile isolates and looked for differences in growth between 22 ribotypes. By profiling clinical isolates, we assert that C. difficile is a generalist species capable of growing on a variety of carbon substrates. Further, C. difficile strains clustered by phylogenetic relationship and displayed ribotype-specific and clade-specific metabolic capabilities. Surprisingly, we observed that two emerging lineages, ribotypes 023 and 255, have divergent metabolic phenotypes. In addition, although C. difficile Clade 5 is the most evolutionary distant clade and often detected in animals, it displayed more robust growth on simple dietary sugars than Clades 1-4. Altogether, our results corroborate the generalist metabolic strategy of C. difficile and demonstrate lineage-specific metabolic capabilities. In addition, our approach can be adapted to the study of additional pathogens to ascertain their metabolic niches in the gut. IMPORTANCE The gut pathogen Clostridioides difficile utilizes a wide range of carbon sources. Microbial communities can be rationally designed to combat C. difficile by depleting its preferred nutrients in the gut. However, C. difficile is genetically diverse with hundreds of identified ribotypes and most of its metabolic studies were performed with lab-adapted strains. Here, we profiled carbon metabolism by a myriad of C. difficile clinical isolates. While the metabolic capabilities of these isolates clustered by their genetic lineage, we observed surprising metabolic divergence between two emerging lineages. We also found that the most genetically distant clade grew robustly on simple dietary sugars, posing intriguing questions about the adaptation of C. difficile to the human gut. Altogether, our results underscore the importance of considering the metabolic diversity of pathogens in the study of their evolution and the rational design of therapeutic interventions.
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Freeman J, Viprey V, Ewin D, Spittal W, Clark E, Vernon J, Fawley W, Davis G, Tkalec V, Wilcox M, Rupnik M, Davies K. Antimicrobial susceptibility in Clostridioides difficile varies according to European region and isolate source. JAC Antimicrob Resist 2024; 6:dlae112. [PMID: 39045220 PMCID: PMC11264405 DOI: 10.1093/jacamr/dlae112] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Accepted: 06/29/2024] [Indexed: 07/25/2024] Open
Abstract
Objectives Clostridioides difficile epidemiology is evolving with country-associated emerging and resistant ribotypes (RT). Antimicrobial susceptibility testing of C. difficile isolated from clinical and animal samples collected across Europe in 2018 was performed to provide antimicrobial resistance data and according to C. difficile RTs and source. Methods Samples were cultured for C. difficile and isolates PCR ribotyped. Metronidazole, vancomycin, fidaxomicin, moxifloxacin, clindamycin, imipenem, tigecycline, linezolid, rifampicin and meropenem minimum inhibitory concentrations (MICs) for 280 clinical and 126 animal isolates were determined by Wilkins-Chalgren agar dilution. Results Fidaxomicin was the most active antimicrobial (all isolates geometric mean MIC = 0.03 mg/L) with no evidence of reduced susceptibility. Metronidazole MICs were elevated among RT027 (1.87 mg/L) and RT181 clinical isolates (1.03 mg/L). RT027 and RT181 had elevated geometric mean moxifloxacin MICs (14.49 mg/L, 16.88 mg/L); clindamycin (7.5 mg/L, 9.1 mg/L) and rifampicin (0.6 mg/L, 21.5 mg/L). Five isolates (RT002, RT010 and RT016) were metronidazole resistant (MIC = 8 mg/L) and 10 (RT027; RT198) had intermediate resistance (4 mg/L). Metronidazole MICs were not elevated in animal isolates. Increased geometric mean vancomycin MICs were observed among RT078, mostly isolated from animals, but there was no resistance (MIC ≥ 4 mg/L). Clinical and animal isolates of multiple RTs showed resistance to moxifloxacin and clindamycin. No resistance to imipenem or meropenem was observed. Conclusion Increased antimicrobial resistance was detected in eastern Europe and mostly associated with RT027 and related emerging RT181, while clinical isolates from northern and western Europe had the lowest general levels of resistance.
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Affiliation(s)
- Jane Freeman
- Healthcare Associated Infections Research Group, Leeds Institute of Medical Research, University of Leeds, Leeds, UK
- Department of Microbiology, Leeds Teaching Hospitals NHS Trust, Leeds, UK
- European Society of Clinical Microbiology and Infectious Diseases (ESCMID), Study Group for Clostridioides difficile (ESGCD), Basel, Switzerland
| | - Virginie Viprey
- Healthcare Associated Infections Research Group, Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - Duncan Ewin
- Healthcare Associated Infections Research Group, Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - William Spittal
- Healthcare Associated Infections Research Group, Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - Emma Clark
- Healthcare Associated Infections Research Group, Leeds Institute of Medical Research, University of Leeds, Leeds, UK
- Department of Microbiology, Leeds Teaching Hospitals NHS Trust, Leeds, UK
| | - Jon Vernon
- Healthcare Associated Infections Research Group, Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - Warren Fawley
- Department of Microbiology, Leeds Teaching Hospitals NHS Trust, Leeds, UK
- C. difficile Ribotyping Network for England and Wales, UK Health Security Agency, Leeds, UK
| | - Georgina Davis
- Healthcare Associated Infections Research Group, Leeds Institute of Medical Research, University of Leeds, Leeds, UK
| | - Valerija Tkalec
- National Laboratory for Health, Environment and Food (NLZOH), Centre for Medical Microbiology, Maribor, Slovenia
- Faculty of Medicine, University of Maribor, Maribor, Slovenia
| | - Mark Wilcox
- Healthcare Associated Infections Research Group, Leeds Institute of Medical Research, University of Leeds, Leeds, UK
- Department of Microbiology, Leeds Teaching Hospitals NHS Trust, Leeds, UK
- European Society of Clinical Microbiology and Infectious Diseases (ESCMID), Study Group for Clostridioides difficile (ESGCD), Basel, Switzerland
| | - Maja Rupnik
- European Society of Clinical Microbiology and Infectious Diseases (ESCMID), Study Group for Clostridioides difficile (ESGCD), Basel, Switzerland
- National Laboratory for Health, Environment and Food (NLZOH), Centre for Medical Microbiology, Maribor, Slovenia
- Faculty of Medicine, University of Maribor, Maribor, Slovenia
| | - Kerrie Davies
- Healthcare Associated Infections Research Group, Leeds Institute of Medical Research, University of Leeds, Leeds, UK
- Department of Microbiology, Leeds Teaching Hospitals NHS Trust, Leeds, UK
- European Society of Clinical Microbiology and Infectious Diseases (ESCMID), Study Group for Clostridioides difficile (ESGCD), Basel, Switzerland
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Spigaglia P. Clostridioides difficile and Gut Microbiota: From Colonization to Infection and Treatment. Pathogens 2024; 13:646. [PMID: 39204246 PMCID: PMC11357127 DOI: 10.3390/pathogens13080646] [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: 07/08/2024] [Revised: 07/23/2024] [Accepted: 07/29/2024] [Indexed: 09/03/2024] Open
Abstract
Clostridioides difficile is the main causative agent of antibiotic-associated diarrhea (AAD) in hospitals in the developed world. Both infected patients and asymptomatic colonized individuals represent important transmission sources of C. difficile. C. difficile infection (CDI) shows a large range of symptoms, from mild diarrhea to severe manifestations such as pseudomembranous colitis. Epidemiological changes in CDIs have been observed in the last two decades, with the emergence of highly virulent types and more numerous and severe CDI cases in the community. C. difficile interacts with the gut microbiota throughout its entire life cycle, and the C. difficile's role as colonizer or invader largely depends on alterations in the gut microbiota, which C. difficile itself can promote and maintain. The restoration of the gut microbiota to a healthy state is considered potentially effective for the prevention and treatment of CDI. Besides a fecal microbiota transplantation (FMT), many other approaches to re-establishing intestinal eubiosis are currently under investigation. This review aims to explore current data on C. difficile and gut microbiota changes in colonized individuals and infected patients with a consideration of the recent emergence of highly virulent C. difficile types, with an overview of the microbial interventions used to restore the human gut microbiota.
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Affiliation(s)
- Patrizia Spigaglia
- Department of Infectious Diseases, Istituto Superiore di Sanità, 00161 Roma, Italy
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TAKEICHI K, FUKUDA A, SHONO C, OTA N, NAKAJIMA C, SUZUKI Y, USUI M. Association of toxin-producing Clostridioides difficile with piglet diarrhea and potential transmission to humans. J Vet Med Sci 2024; 86:769-776. [PMID: 38797681 PMCID: PMC11251813 DOI: 10.1292/jvms.24-0051] [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: 01/31/2024] [Accepted: 05/09/2024] [Indexed: 05/29/2024] Open
Abstract
The pathogenicity of Clostridioides difficile in piglets remains controversial. It is unknown whether C. difficile control helps protect piglet health. To clarify the association between C. difficile presence and piglet diarrhea, isolates were obtained from piglets with and without diarrhea. In addition, to determine the genetic relationship of C. difficile from pigs and humans, we performed whole-genome sequencing (WGS) of C. difficile isolates. Diarrheal and non-diarrheal stool samples were collected from neonatal piglets from five farms in Japan in 2021. To clarify the relationship between C. difficile derived from pigs and those from human clinical cases, WGS of C. difficile isolates was performed. Toxin-positive C. difficile were significantly more prevalent in piglets with diarrhea, although the overall frequency of C. difficile did not differ between piglets with and without diarrhea. This observation indicates an association between toxin-positive C. difficile and diarrhea in piglets. However, further studies are needed to establish a direct causal relationship and to explore other contributing factors to diarrhea in piglets. WGS results showed that C. difficile sequence type (ST) 11 including the hypervirulent PCR ribotype 078 isolates derived from Japanese pigs were closely related to ST11 of overseas strains (human clinical and animal-derived) and a Japanese human clinical strain. Toxin-positive C. difficile may cause diarrhea in piglets and hypervirulent C. difficile are spreading among pigs and human populations worldwide.
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Affiliation(s)
- Kouki TAKEICHI
- Laboratory of Food Microbiology and Food Safety, School of Veterinary Medicine, Rakuno Gakuen University, Hokkaido, Japan
| | - Akira FUKUDA
- Laboratory of Food Microbiology and Food Safety, School of Veterinary Medicine, Rakuno Gakuen University, Hokkaido, Japan
| | - Chika SHONO
- Biological Science Laboratories, Kao Corporation, Tochigi, Japan
| | - Noriyasu OTA
- Biological Science Laboratories, Kao Corporation, Tochigi, Japan
| | - Chie NAKAJIMA
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Hokkaido, Japan
- International Collaboration Unit, Hokkaido University International Institute for Zoonosis Control, Hokkaido, Japan
- Institute for Vaccine Research and Development, Hokkaido University, Hokkaido, Japan
| | - Yasuhiko SUZUKI
- Division of Bioresources, Hokkaido University International Institute for Zoonosis Control, Hokkaido, Japan
- International Collaboration Unit, Hokkaido University International Institute for Zoonosis Control, Hokkaido, Japan
- Institute for Vaccine Research and Development, Hokkaido University, Hokkaido, Japan
| | - Masaru USUI
- Laboratory of Food Microbiology and Food Safety, School of Veterinary Medicine, Rakuno Gakuen University, Hokkaido, Japan
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Huang J, Li T, Zhu Y, Li Q, Kuo CJ, Guo X, Wei B, Ni P, Dong K. Molecular Characterization and Potential Host-switching of Swine Farm associated Clostridioides difficile ST11. Vet Microbiol 2024; 294:110129. [PMID: 38810364 DOI: 10.1016/j.vetmic.2024.110129] [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: 08/05/2023] [Revised: 05/19/2024] [Accepted: 05/23/2024] [Indexed: 05/31/2024]
Abstract
OBJECTIVE To conduct molecular prevalence and genetic polymorphism analysis of 24 Swine Farm associated C. difficile ST11 strains, in addition to other representative sequenced ST strains. METHODS The collected C. difficile strains underwent whole genome sequencing and bioinformatic analysis using the illumina NovaSeq platform, SPAdes, Prokka, MOB-suite, and FastTree. Virulence and antibiotic resistance genes were identified through NCBI Pathogen Database. Cytotoxicity tests were conducted on HT-29 cells and Vero cells to verify the function of toxin A and toxin B. RESULTS The most prevalent resistance genes in ST11 were found to be against β-lactamases, aminoglycosides, and tetracycline. A C. difficile isolate (strain 27) with tcdA deletion and high antibiotic resistance genes was far apart from other swine farm associated ST11 isolates in the phylogenetic branch. The remarkable genetic similarity between animal and human C. difficile strains suggests potential transmission of ST11 strains between animals and humans. The plasmid replicon sequences repUS43 were identified in all ST11 strains except one variant (strain 27), and 91.67% (22/24) of these were assessed by MOB-typer as having mobilizable plasmids. CONCLUSION Swine farm associated C. difficile ST11 carried fewer virulence genes than ST11 strains collected from NCBI database. It is critical to monitor the evolution of C. difficile strains to understand their changing characteristics, host-switching, and develop effective control and prevention strategies.
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Affiliation(s)
- Jiewen Huang
- Department of Laboratory Medicine, College of Health Science and Technology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China; Department of Animal Health and Food Safety, School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Tinghua Li
- Department of Laboratory Medicine, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yongzhang Zhu
- Department of Animal Health and Food Safety, School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Qingtian Li
- Department of Laboratory Medicine, College of Health Science and Technology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Chih-Jung Kuo
- Department of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan
| | - Xiaokui Guo
- Department of Animal Health and Food Safety, School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Beiwen Wei
- Department of Laboratory Medicine, College of Health Science and Technology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Peihua Ni
- Department of Laboratory Medicine, College of Health Science and Technology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
| | - Ke Dong
- Department of Animal Health and Food Safety, School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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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.
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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
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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.
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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
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8
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Cersosimo LM, Worley JN, Bry L. Approaching toxigenic Clostridia from a One Health perspective. Anaerobe 2024; 87:102839. [PMID: 38552896 PMCID: PMC11180571 DOI: 10.1016/j.anaerobe.2024.102839] [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: 12/31/2023] [Revised: 02/29/2024] [Accepted: 03/17/2024] [Indexed: 04/08/2024]
Abstract
Spore-forming pathogens have a unique capacity to thrive in diverse environments, and with temporal persistence afforded through their ability to sporulate. Their prevalence in diverse ecosystems requires a One Health approach to identify critical reservoirs and outbreak-associated transmission chains, given their capacity to freely move across soils, waterways, foodstuffs and as commensals or infecting pathogens in human and animal populations. Among anaerobic spore-formers, genomic resources for pathogens including C. botulinum, C. difficile, and C. perfringens enable our capacity to identify common and unique factors that support their persistence in diverse reservoirs and capacity to cause disease. Publicly available genomic resources for spore-forming pathogens at NCBI's Pathogen Detection program aid outbreak investigations and longitudinal monitoring in national and international programs in public health and food safety, as well as for local healthcare systems. These tools also enable research to derive new knowledge regarding disease pathogenesis, and to inform strategies in disease prevention and treatment. As global community resources, the continued sharing of strain genomic data and phenotypes further enhances international resources and means to develop impactful applications. We present examples showing use of these resources in surveillance, including capacity to assess linkages among clinical, environmental, and foodborne reservoirs and to further research investigations into factors promoting their persistence and virulence in different settings.
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Affiliation(s)
- Laura M Cersosimo
- Massachusetts Host-Microbiome Center, Dept. Pathology, Brigham & Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - Jay N Worley
- Massachusetts Host-Microbiome Center, Dept. Pathology, Brigham & Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA; National Center for Biotechnology Information, NIH, Bethesda, MD, USA
| | - Lynn Bry
- Massachusetts Host-Microbiome Center, Dept. Pathology, Brigham & Women's Hospital, Harvard Medical School, Boston, MA, 02115, USA.
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O’Grady K, Hong S, Putsathit P, George N, Hemphill C, Huntington PG, Korman TM, Kotsanas D, Lahra M, McDougall R, McGlinchey A, Levy A, Moore CV, Nimmo G, Prendergast L, Robson J, Speers DJ, Waring L, Wehrhahn MC, Weldhagen GF, Wilson RM, Riley TV, Knight DR. Defining the phylogenetics and resistome of the major Clostridioides difficile ribotypes circulating in Australia. Microb Genom 2024; 10:001232. [PMID: 38717815 PMCID: PMC11165652 DOI: 10.1099/mgen.0.001232] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 03/27/2024] [Indexed: 06/13/2024] Open
Abstract
Clostridioides difficile infection (CDI) remains a significant public health threat globally. New interventions to treat CDI rely on an understanding of the evolution and epidemiology of circulating strains. Here we provide longitudinal genomic data on strain diversity, transmission dynamics and antimicrobial resistance (AMR) of C. difficile ribotypes (RTs) 014/020 (n=169), 002 (n=77) and 056 (n=36), the three most prominent C. difficile strains causing CDI in Australia. Genome scrutiny showed that AMR was uncommon in these lineages, with resistance-conferring alleles present in only 15/169 RT014/020 strains (8.9 %), 1/36 RT056 strains (2.78 %) and none of 77 RT002 strains. Notably, ~90 % of strains were resistant to MLSB agents in vitro, but only ~5.9 % harboured known resistance alleles, highlighting an incongruence between AMR genotype and phenotype. Core genome analyses revealed all three RTs contained genetically heterogeneous strain populations with limited evidence of clonal transmission between CDI cases. The average number of pairwise core genome SNP (cgSNP) differences within each RT group ranged from 23.3 (RT056, ST34, n=36) to 115.6 (RT002, ST8, n=77) and 315.9 (RT014/020, STs 2, 13, 14, 49, n=169). Just 19 clonal groups (encompassing 40 isolates), defined as isolates differing by ≤2 cgSNPs, were identified across all three RTs (RT014/020, n=14; RT002, n=3; RT056, n=2). Of these clonal groups, 63 % (12/19) comprised isolates from the same Australian State and 37 % (7/19) comprised isolates from different States. The low number of plausible transmission events found for these major RTs (and previously documented populations in animal and environmental sources/reservoirs) points to widespread and persistent community sources of diverse C. difficile strains as opposed to ongoing nationwide healthcare outbreaks dominated by a single clone. Together, these data provide new insights into the evolution of major lineages causing CDI in Australia and highlight the urgent need for enhanced surveillance, and for public health interventions to move beyond the healthcare setting and into a One Health paradigm to effectively combat this complex pathogen.
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Affiliation(s)
- Keeley O’Grady
- Centre for Biosecurity and One Health, Harry Butler Institute, Murdoch University, Murdoch, Western Australia, Australia
| | - Stacey Hong
- Communicable Disease Control Directorate, WA Department of Health, East Perth, Western Australia, Australia
| | - Papanin Putsathit
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia
| | - Narelle George
- Pathology Queensland, Royal Brisbane and Women’s Hospital, Herston, Queensland, Australia
| | | | - Peter G. Huntington
- Department of Microbiology, NSW Health Pathology, Royal North Shore Hospital, St Leonards, New South Wales, Australia
| | - Tony M. Korman
- Monash University, Monash Health, Clayton, Victoria, Australia
| | - Despina Kotsanas
- Monash Infectious Diseases, Monash Health, Monash Medical Centre, Clayton, Victoria, Australia
| | - Monica Lahra
- Department of Microbiology, The Prince of Wales Hospital, Randwick, New South Wales, Australia
| | | | | | - Avram Levy
- Department of Microbiology, PathWest Laboratory Medicine WA, Nedlands, Western Australia, Australia
| | - Casey V. Moore
- Microbiology and Infectious Diseases Laboratories, SA Pathology, Adelaide, South Australia, Australia
| | - Graeme Nimmo
- Pathology Queensland, Royal Brisbane and Women’s Hospital, Herston, Queensland, Australia
| | | | - Jennifer Robson
- Sullivan Nicolaides Pathology, Taringa, Queensland, Australia
| | - David J. Speers
- Department of Microbiology, PathWest Laboratory Medicine WA, Nedlands, Western Australia, Australia
- School of Medicine, The University of Western Australia, Nedlands, Western Australia, Australia
| | | | | | - Gerhard F. Weldhagen
- Microbiology and Infectious Diseases Laboratories, SA Pathology, Adelaide, South Australia, Australia
| | - Richard M. Wilson
- Australian Clinical Labs, Microbiology Department, Wayville, South Australia, Australia
| | - Thomas V. Riley
- Centre for Biosecurity and One Health, Harry Butler Institute, Murdoch University, Murdoch, Western Australia, Australia
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia
- Department of Microbiology, PathWest Laboratory Medicine WA, Nedlands, Western Australia, Australia
- School of Biomedical Sciences, The University of Western Australia, Nedlands, Western Australia, Australia
| | - Daniel R. Knight
- Department of Microbiology, PathWest Laboratory Medicine WA, Nedlands, Western Australia, Australia
- School of Biomedical Sciences, The University of Western Australia, Nedlands, Western Australia, Australia
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10
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Cersosimo LM, Worley JN, Bry L. Approaching pathogenic Clostridia from a One Health perspective. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.01.08.574718. [PMID: 38260382 PMCID: PMC10802438 DOI: 10.1101/2024.01.08.574718] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/24/2024]
Abstract
Spore-forming pathogens have a unique capacity to thrive in diverse environments, and with temporal persistence afforded through their ability to sporulate. These behaviors require a One Health approach to identify critical reservoirs and outbreak-associated transmission chains, given their capacity to freely move across soils, waterways, foodstuffs, and as commensals or infecting pathogens in human and veterinary populations. Among anaerobic spore-formers, genomic resources for pathogens including C. botulinum, C. difficile, and C. perfringens enable our capacity to identify common and unique factors that support their persistence in diverse reservoirs and capacity to cause disease. Publicly available genomic resources for spore-forming pathogens at NCBI's Pathogen Detection program aid outbreak investigations and longitudinal monitoring in national and international programs in public health and food safety, as well as for local healthcare systems. These tools also enable research to derive new knowledge regarding disease pathogenesis, and to inform strategies in disease prevention and treatment. As global community resources, the continued sharing of strain genomic data and phenotypes further enhances international resources and means to develop impactful applications. We present examples showing use of these resources in surveillance, including capacity to assess linkages among clinical, environmental, and foodborne reservoirs and to further research investigations into factors promoting their persistence and virulence in different settings.
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Affiliation(s)
- Laura M. Cersosimo
- Massachusetts Host-Microbiome Center, Dept. Pathology, Brigham & Women's Hospital, Harvard Medical School, Boston, MA
| | - Jay N. Worley
- Massachusetts Host-Microbiome Center, Dept. Pathology, Brigham & Women's Hospital, Harvard Medical School, Boston, MA
- National Center for Biotechnology Information, NIH, Bethesda, MD
| | - Lynn Bry
- Massachusetts Host-Microbiome Center, Dept. Pathology, Brigham & Women's Hospital, Harvard Medical School, Boston, MA
- Clinical Microbiology Laboratory, Dept. Pathology, Brigham & Women's Hospital, Boston, MA
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11
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Janezic S, Garneau JR, Monot M. Comparative Genomics of Clostridioides difficile. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1435:199-218. [PMID: 38175477 DOI: 10.1007/978-3-031-42108-2_10] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Clostridioides difficile, a Gram-positive spore-forming anaerobic bacterium, has rapidly emerged as the leading cause of nosocomial diarrhoea in hospitals. The availability of large numbers of genome sequences, mainly due to the use of next-generation sequencing methods, has undoubtedly shown their immense advantages in the determination of C. difficile population structure. The implementation of fine-scale comparative genomic approaches has paved the way for global transmission and recurrence studies, as well as more targeted studies, such as the PaLoc or CRISPR/Cas systems. In this chapter, we provide an overview of recent and significant findings on C. difficile using comparative genomic studies with implications for epidemiology, infection control and understanding of the evolution of C. difficile.
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Affiliation(s)
- Sandra Janezic
- National Laboratory for Health, Environment and Food (NLZOH), Maribor, Slovenia.
- Faculty of Medicine, University of Maribor, Maribor, Slovenia.
| | - Julian R Garneau
- Department of Fundamental Microbiology, University of Lausanne, Lausanne, Switzerland
| | - Marc Monot
- Institut Pasteur, Université Paris Cité, Plate-forme Technologique Biomics, Paris, France
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12
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Spigaglia P, Mastrantonio P, Barbanti F. Antibiotic Resistances of Clostridioides difficile. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1435:169-198. [PMID: 38175476 DOI: 10.1007/978-3-031-42108-2_9] [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
The rapid evolution of antibiotic resistance in Clostridioides difficile and the consequent effects on prevention and treatment of C. difficile infections (CDIs) are a matter of concern for public health. Antibiotic resistance plays an important role in driving C. difficile epidemiology. Emergence of new types is often associated with the emergence of new resistances, and most of the epidemic C. difficile clinical isolates is currently resistant to multiple antibiotics. In particular, it is to worth to note the recent identification of strains with reduced susceptibility to the first-line antibiotics for CDI treatment and/or for relapsing infections. Antibiotic resistance in C. difficile has a multifactorial nature. Acquisition of genetic elements and alterations of the antibiotic target sites, as well as other factors, such as variations in the metabolic pathways or biofilm production, contribute to the survival of this pathogen in the presence of antibiotics. Different transfer mechanisms facilitate the spread of mobile elements among C. difficile strains and between C. difficile and other species. Furthermore, data indicate that both genetic elements and alterations in the antibiotic targets can be maintained in C. difficile regardless of the burden imposed on fitness, and therefore resistances may persist in C. difficile population in absence of antibiotic selective pressure.
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Affiliation(s)
- Patrizia Spigaglia
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy.
| | - Paola Mastrantonio
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Fabrizio Barbanti
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
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13
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Cautivo-Reyes K, Knight DR, Bowie D, Moreira-Grez B, Whiteley AS, Riley TV. Biogeographic distribution and molecular epidemiology of Clostridioides ( Clostridium) difficile in Western Australian soils. Appl Environ Microbiol 2023; 89:e0037923. [PMID: 37823643 PMCID: PMC10617432 DOI: 10.1128/aem.00379-23] [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: 03/13/2023] [Accepted: 08/23/2023] [Indexed: 10/13/2023] Open
Abstract
Clostridioides (Clostridium) difficile is a leading cause of infectious diarrhea in humans and production animals and can be found in a variety of environmental sources. The prevalence and diversity of multi-locus sequence type clade 5 strains of C. difficile in Australian production animals suggest Australia might be the ancestral home of this lineage of One Health importance. To better understand the role of the environment in the colonization of humans and animals in Australia, it is important to investigate these endemic sources. This study describes the prevalence, molecular epidemiology, and biogeographic distribution of C. difficile in soils of Western Australia. A total of 321 soil samples from remote geographical locations across the eight health regions of Western Australia were screened for C. difficile and isolates characterized by PCR ribotyping and toxin gene profiling. C. difficile was isolated from 31.15% of samples, with the highest prevalence in the Perth Metropolitan Health Region (49.25%, n = 33/67). Overall, 52 different strains [PCR ribotypes (RTs)] were identified, with 14 being novel, and 38% (38/100) of isolates being toxigenic, the most common of which was RT014/020. Five unique novel isolates showed characteristics similar to C. difficile clade 5. This is the first study of C. difficile isolated from soils in Australia. The high prevalence and heterogeneity of C. difficile strains recovered suggest that soils play a role in the survival and environmental dissemination of this organism, and potentially its transmission among native wildlife and production animals, and in community and hospital settings.IMPORTANCEClostridium difficile is a pathogen of One Health importance. To better understand the role of the environment in human and animal colonization/infection, it is critical that autochthonous reservoirs/sources of C. difficile be investigated. This is the first study of C. difficile isolated from soils of Western Australia (WA). Here, the ecology of C. difficile in WA is described by examining the geographic distribution, molecular epidemiology, and diversity of C. difficile isolated from soils across WA.
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Affiliation(s)
- Karla Cautivo-Reyes
- Biosecurity and One Health Research Center, Harry Butler Institute, Murdoch University, Western Australia, Australia
| | - Daniel R. Knight
- School of Biomedical Sciences, The University of Western Australia, Western Australia, Australia
- Department of Microbiology, PathWest Laboratory Medicine, Queen Elizabeth II Medical Center, Western Australia, Australia
| | - Deborah Bowie
- School of Agriculture and Environment Science, The University of Western Australia, Western Australia, Australia
| | - Benjamin Moreira-Grez
- School of Agriculture and Environment Science, The University of Western Australia, Western Australia, Australia
| | | | - Thomas V. Riley
- Biosecurity and One Health Research Center, Harry Butler Institute, Murdoch University, Western Australia, Australia
- School of Biomedical Sciences, The University of Western Australia, Western Australia, Australia
- Department of Microbiology, PathWest Laboratory Medicine, Queen Elizabeth II Medical Center, Western Australia, Australia
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia
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14
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Snydman DR, McDermott LA, Thorpe CM, Goldstein EJC, Schuetz AN, Johnson S, Gerding DN, Gluck L, Bourdas D, Carroll KC, Lancaster CK, Garey KW, Wang Q, Walk ST, Duperchy E. A US-based national surveillance study for the susceptibility and epidemiology of Clostridioides difficile isolates with special reference to ridinilazole: 2020-2021. Antimicrob Agents Chemother 2023; 67:e0034923. [PMID: 37728368 PMCID: PMC10583687 DOI: 10.1128/aac.00349-23] [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: 03/15/2023] [Accepted: 07/04/2023] [Indexed: 09/21/2023] Open
Abstract
We have previously reported on the susceptibility and epidemiology of Clostridioides difficile isolates from six geographically dispersed medical centers in the United States. This current survey was conducted with isolates collected in 2020-2021 from six geographically dispersed medical centers in the United States, with specific attention to susceptibility to ridinilazole as well as nine comparators. C. difficile isolates or stools from patients with C. difficile antibiotic-associated diarrhea were collected and referred to a central laboratory. After species confirmation of 300 isolates at the central laboratory, antibiotic susceptibilities were determined by the agar dilution method [M11-A9, Clinical and Laboratory Standards Institute (CLSI)] against the 10 agents. Ribotyping was performed by PCR capillary gel electrophoresis on all isolates. Ridinilazole had a minimum inhibitory concentration (MIC) 90 of 0.25 mcg/mL, and no isolate had an MIC greater than 0.5 mcg/mL. In comparison, fidaxomicin had an MIC 90 of 0.5 mcg/mL. The vancomycin MIC 90 was 2 mcg/mL with a 0.7% resistance rate [both CLSI and European Committee on Antimicrobial Susceptibility Testing (EUCAST) criteria]. The metronidazole MIC 90 was 1 mcg/mL, with none resistant by CLSI criteria, and a 0.3% resistance rate by EUCAST criteria. Among the 50 different ribotypes isolated in the survey, the most common ribotype was 014-020 (14.0%) followed by 106 (10.3%), 027 (10%), 002 (8%), and 078-126 (4.3%). Ridinilazole maintained activity against all ribotypes and all strains resistant to any other agent tested. Ridinilazole showed excellent in vitro activity against C. difficile isolates collected between 2020 and 2021 in the United States, independent of ribotype.
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Affiliation(s)
- D. R. Snydman
- Tufts Medical Center, Boston, Massachusetts, USA
- Tufts University School of Medicine and the Stuart B. Levy Center for the Integrated Management of Antimicrobial Resistance, Boston, Massachusetts, USA
| | - L. A. McDermott
- Tufts Medical Center, Boston, Massachusetts, USA
- Tufts University School of Medicine and the Stuart B. Levy Center for the Integrated Management of Antimicrobial Resistance, Boston, Massachusetts, USA
| | - C. M. Thorpe
- Tufts Medical Center, Boston, Massachusetts, USA
- Tufts University School of Medicine and the Stuart B. Levy Center for the Integrated Management of Antimicrobial Resistance, Boston, Massachusetts, USA
| | | | - A. N. Schuetz
- Mayo Clinic School of Medicine and Science, Rochester, Minnesota, USA
| | - S. Johnson
- Edward Hines, Jr. VA Hospital, Hines, Illinois, USA
- Loyola University Medical Center, Maywood, Illinois, USA
| | | | - L. Gluck
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - D. Bourdas
- Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - K. C. Carroll
- University of Houston College of Pharmacy, Houston, Texas, USA
| | | | - K. W. Garey
- Summit (Oxford) Ltd, Abingdon, United Kingdom
| | - Q. Wang
- Montana State University, Bozeman, Montana, USA
| | - S. T. Walk
- Montana State University, Bozeman, Montana, USA
| | - E. Duperchy
- Johns Hopkins Hospital, Baltimore, Maryland, USA
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15
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Abstract
Clostridioides difficile (C. difficile) infection is still a threat to many healthcare settings worldwide. Clostridioides difficile epidemiology has changed over the last 20 years, largely due to the emergence of hypervirulent and antimicrobial-resistant C. difficile strains. The excessive use of antimicrobials, the absence of optimal antibiotic policies, and suboptimal infection control practices have fueled the development of this pressing health issue. The prudent use of antimicrobials, particularly broad-spectrum agents, and simple infection control measures, such as hand hygiene, can significantly reduce C. difficile infection rates. Moreover, the early detection of these infections and understanding their epidemiological behavior using accurate laboratory methods are the cornerstone to decreasing the incidence of C. difficile infection and preventing further spread. Although there is no consensus on the single best laboratory method for the diagnosis of C. difficile infection, the use of 2 or more techniques can improve diagnostic accuracy, and it is recommended.
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Affiliation(s)
- Ibrahim A. Al-Zahrani
- From the Department of Medical Laboratory Sciences, Faculty of Applied Medical Sciences, King Abdulaziz University, and from the Special Infectious Agents Unit-Biosafety Level-3, King Fahad Medical Research Centre, King Abdulaziz University, Jeddah, Kingdom of Saudi Arabia
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16
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Abad-Fau A, Sevilla E, Martín-Burriel I, Moreno B, Bolea R. Update on Commonly Used Molecular Typing Methods for Clostridioides difficile. Microorganisms 2023; 11:1752. [PMID: 37512924 PMCID: PMC10384772 DOI: 10.3390/microorganisms11071752] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 06/26/2023] [Accepted: 07/01/2023] [Indexed: 07/30/2023] Open
Abstract
This review aims to provide a comprehensive overview of the significant Clostridioides difficile molecular typing techniques currently employed in research and medical communities. The main objectives of this review are to describe the key molecular typing methods utilized in C. difficile studies and to highlight the epidemiological characteristics of the most prevalent strains on a global scale. Geographically distinct regions exhibit distinct strain types of C. difficile, with notable concordance observed among various typing methodologies. The advantages that next-generation sequencing (NGS) offers has changed epidemiology research, enabling high-resolution genomic analyses of this pathogen. NGS platforms offer an unprecedented opportunity to explore the genetic intricacies and evolutionary trajectories of C. difficile strains. It is relevant to acknowledge that novel routes of transmission are continually being unveiled and warrant further investigation, particularly in the context of zoonotic implications and environmental contamination.
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Affiliation(s)
- Ana Abad-Fau
- Departamento de Patología Animal, Facultad de Veterinaria, Instituto Agroalimentario de Aragon-IA2-(Universidad de Zaragoza-CITA), 50013 Zaragoza, Spain
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes, Facultad de Veterinaria, Universidad de Zaragoza, 50013 Zaragoza, Spain
| | - Eloísa Sevilla
- Departamento de Patología Animal, Facultad de Veterinaria, Instituto Agroalimentario de Aragon-IA2-(Universidad de Zaragoza-CITA), 50013 Zaragoza, Spain
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes, Facultad de Veterinaria, Universidad de Zaragoza, 50013 Zaragoza, Spain
| | - Inmaculada Martín-Burriel
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes, Facultad de Veterinaria, Universidad de Zaragoza, 50013 Zaragoza, Spain
- Laboratorio de Genética Bioquímica, Facultad de Veterinaria, Instituto Agroalimentario de Aragon-IA2-(Universidad de Zaragoza-CITA), 50013 Zaragoza, Spain
| | - Bernardino Moreno
- Departamento de Patología Animal, Facultad de Veterinaria, Instituto Agroalimentario de Aragon-IA2-(Universidad de Zaragoza-CITA), 50013 Zaragoza, Spain
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes, Facultad de Veterinaria, Universidad de Zaragoza, 50013 Zaragoza, Spain
| | - Rosa Bolea
- Departamento de Patología Animal, Facultad de Veterinaria, Instituto Agroalimentario de Aragon-IA2-(Universidad de Zaragoza-CITA), 50013 Zaragoza, Spain
- Centro de Encefalopatías y Enfermedades Transmisibles Emergentes, Facultad de Veterinaria, Universidad de Zaragoza, 50013 Zaragoza, Spain
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17
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Hain-Saunders NMR, Knight DR, Bruce M, Byrne D, Riley TV. Genomic Analysis of Clostridioides difficile Recovered from Horses in Western Australia. Microorganisms 2023; 11:1743. [PMID: 37512915 PMCID: PMC10386058 DOI: 10.3390/microorganisms11071743] [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: 06/09/2023] [Revised: 06/27/2023] [Accepted: 06/29/2023] [Indexed: 07/30/2023] Open
Abstract
Clostridioides difficile poses an ongoing threat as a cause of gastrointestinal disease in humans and animals. Traditionally considered a human healthcare-related disease, increases in community-associated C. difficile infection (CDI) and growing evidence of inter-species transmission suggest a wider perspective is required for CDI control. In horses, C. difficile is a major cause of diarrhoea and life-threatening colitis. This study aimed to better understand the epidemiology of CDI in Australian horses and provide insights into the relationships between horse, human and environmental strains. A total of 752 faecal samples from 387 Western Australian horses were collected. C. difficile was isolated from 104 (30.9%) horses without gastrointestinal signs and 19 (37.8%) with gastrointestinal signs. Of these, 68 (55.3%) harboured one or more toxigenic strains, including C. difficile PCR ribotypes (RTs) 012 (n = 14), 014/020 (n = 10) and 087 (n = 7), all prominent in human infection. Whole-genome analysis of 45 strains identified a phylogenetic cluster of 10 closely related C. difficile RT 012 strains of equine, human and environmental origin (0-62 SNP differences; average 23), indicating recent shared ancestry. Evidence of possible clonal inter-species transmission or common-source exposure was identified for a subgroup of three horse and one human isolates, highlighting the need for a One Health approach to C. difficile surveillance.
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Affiliation(s)
- Natasza M R Hain-Saunders
- Centre for Biosecurity, and One Health, Harry Butler Institute, Murdoch University, Murdoch, WA 6150, Australia
| | - Daniel R Knight
- School of Biomedical Sciences, The University of Western Australia, Queen Elizabeth II Medical Centre, Nedlands, WA 6009, Australia
- PathWest Laboratory Medicine, Department of Microbiology, Queen Elizabeth II Medical Centre, Nedlands, WA 6009, Australia
| | - Mieghan Bruce
- Centre for Biosecurity, and One Health, Harry Butler Institute, Murdoch University, Murdoch, WA 6150, Australia
- School of Veterinary Medicine, Murdoch University, Murdoch, WA 6150, Australia
| | - David Byrne
- School of Veterinary Medicine, Murdoch University, Murdoch, WA 6150, Australia
| | - Thomas V Riley
- Centre for Biosecurity, and One Health, Harry Butler Institute, Murdoch University, Murdoch, WA 6150, Australia
- School of Biomedical Sciences, The University of Western Australia, Queen Elizabeth II Medical Centre, Nedlands, WA 6009, Australia
- PathWest Laboratory Medicine, Department of Microbiology, Queen Elizabeth II Medical Centre, Nedlands, WA 6009, Australia
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA 6027, Australia
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18
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Spigaglia P, Barbanti F, Faccini S, Vescovi M, Criscuolo EM, Ceruti R, Gaspano C, Rosignoli C. Clostridioides difficile in Pigs and Dairy Cattle in Northern Italy: Prevalence, Characterization and Comparison between Animal and Human Strains. Microorganisms 2023; 11:1738. [PMID: 37512910 PMCID: PMC10383565 DOI: 10.3390/microorganisms11071738] [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: 04/14/2023] [Revised: 06/21/2023] [Accepted: 06/29/2023] [Indexed: 07/30/2023] Open
Abstract
It has been observed that novel strains of Clostridioides difficile can rapidly emerge and move between animal and human hosts. The aim of this study was to investigate the prevalence of C. difficile in pigs and dairy cattle in northern Italy and to characterize and compare C. difficile animal strains with those from patients from the same geographical area. The C. difficile strains were isolated from animals from farms and slaughterhouses (cross-sectional studies) and from neonatal animals with enteric disorders in routine diagnostic investigations (passive surveillance). Samples positive for C. difficile were found in 87% of the pig farms and in 40% of the cattle farms involved in the cross-sectional studies, with a 20% prevalence among suckling piglets and 6.7% prevalence in neonatal calves, with no significant difference between animals with and without diarrheal symptoms. The prevalence of C. difficile in older animal categories was significantly lower. This result suggests that young age is an important risk factor for C. difficile colonization. In cross-sectional studies at slaughterhouses, in both the heavy pigs and dairy cows examined, only 2% of the intestinal content samples were positive for C. difficile and no contamination was found on the surface of the carcasses. Considering passive surveillance, the prevalence rates of positive samples were 29% in piglets and 1.4% in calves. Overall, 267 strains of animal origin and 97 from humans were collected. In total, 39 ribotypes (RTs) were identified, with RT 078 and RT 018 being predominant among animals and humans, respectively. Several RTs overlapped between animals and patients. In particular, RT 569 was identified as an emergent type in our country. Resistance to erythromycin and moxifloxacin was widely diffused among C. difficile strains, regardless of origin. This study supports C. difficile as a pathogen of one-health importance and highlights the need for a collaborative approach between physicians and veterinarians to control and prevent infections that are able to cross species and geographical barriers.
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Affiliation(s)
- Patrizia Spigaglia
- Dipartimento di Malattie Infettive, Istituto Superiore di Sanità, 00161 Roma, Italy
| | - Fabrizio Barbanti
- Dipartimento di Malattie Infettive, Istituto Superiore di Sanità, 00161 Roma, Italy
| | - Silvia Faccini
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "B. Ubertini", Sede Territoriale di Mantova, 46100 Mantova, Italy
| | - Mariella Vescovi
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "B. Ubertini", Sede Territoriale di Mantova, 46100 Mantova, Italy
| | | | - Rossella Ceruti
- Servizio di Medicina di Laboratorio, ASST Ospedale "Carlo Poma", 46100 Mantova, Italy
| | - Clara Gaspano
- Servizio di Medicina di Laboratorio, ASST Ospedale "Carlo Poma", 46100 Mantova, Italy
| | - Carlo Rosignoli
- Istituto Zooprofilattico Sperimentale della Lombardia e dell'Emilia Romagna "B. Ubertini", Sede Territoriale di Mantova, 46100 Mantova, Italy
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19
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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.
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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
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20
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Fettucciari K, Fruganti A, Stracci F, Spaterna A, Marconi P, Bassotti G. Clostridioides difficile Toxin B Induced Senescence: A New Pathologic Player for Colorectal Cancer? Int J Mol Sci 2023; 24:ijms24098155. [PMID: 37175861 PMCID: PMC10179142 DOI: 10.3390/ijms24098155] [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: 03/22/2023] [Revised: 04/26/2023] [Accepted: 04/28/2023] [Indexed: 05/15/2023] Open
Abstract
Clostridioides difficile (C. difficile) is responsible for a high percentage of gastrointestinal infections and its pathological activity is due to toxins A and B. C. difficile infection (CDI) is increasing worldwide due to the unstoppable spread of C. difficile in the anthropized environment and the progressive human colonization. The ability of C. difficile toxin B to induce senescent cells and the direct correlation between CDI, irritable bowel syndrome (IBS), and inflammatory bowel diseases (IBD) could cause an accumulation of senescent cells with important functional consequences. Furthermore, these senescent cells characterized by long survival could push pre-neoplastic cells originating in the colon towards the complete neoplastic transformation in colorectal cancer (CRC) by the senescence-associated secretory phenotype (SASP). Pre-neoplastic cells could appear as a result of various pro-carcinogenic events, among which, are infections with bacteria that produce genotoxins that generate cells with high genetic instability. Therefore, subjects who develop IBS and/or IBD after CDI should be monitored, especially if they then have further CDI relapses, waiting for the availability of senolytic and anti-SASP therapies to resolve the pro-carcinogenic risk due to accumulation of senescent cells after CDI followed by IBS and/or IBD.
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Affiliation(s)
- Katia Fettucciari
- Biosciences & Medical Embryology Section, Department of Medicine and Surgery, University of Perugia, 06129 Perugia, Italy
| | - Alessandro Fruganti
- School of Biosciences and Veterinary Medicine, University of Camerino, 62024 Matelica, Italy
| | - Fabrizio Stracci
- Public Health Section, Department of Medicine and Surgery, University of Perugia, 06129 Perugia, Italy
| | - Andrea Spaterna
- School of Biosciences and Veterinary Medicine, University of Camerino, 62024 Matelica, Italy
| | - Pierfrancesco Marconi
- Biosciences & Medical Embryology Section, Department of Medicine and Surgery, University of Perugia, 06129 Perugia, Italy
| | - Gabrio Bassotti
- Gastroenterology, Hepatology & Digestive Endoscopy Section, Department of Medicine and Surgery, University of Perugia, 06129 Perugia, Italy
- Gastroenterology & Hepatology Unit, Santa Maria Della Misericordia Hospital, 06129 Perugia, Italy
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21
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Zhu Q, Xu J, Chen X, Ren Y, Zhao L. Risk factors and molecular epidemiology of bloodstream infections due to carbapenem-resistant Klebsiella pneumoniae. Diagn Microbiol Infect Dis 2023; 106:115955. [PMID: 37167651 DOI: 10.1016/j.diagmicrobio.2023.115955] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2022] [Revised: 03/24/2023] [Accepted: 04/11/2023] [Indexed: 05/13/2023]
Abstract
PURPOSE Carbapenem-resistant Klebsiella pneumoniae (CRKP) is emerging as a worldwide public health concern; however, molecular epidemiological surveillance of clinical CRKP bloodstream infection (BSI) in China is limited. We conducted a retrospective observational study to assess risk factors and the molecular epidemiology of CRKP BSI. METHODS We reviewed the medical records of enrolled patients to assess risk factors of CRKP BSI. Characteristics of CRKP isolates were analyzed by whole genome sequencing and Kleborate. Evolutionary diversification in CRKP isolates was described through Single Nucleotide Polymorphisms analysis and phylogenetic tree construction. RESULTS We found that prior ICU hospitalization and use of carbapenems were independent risk factors for CRKP BSI. The main CRKP sequence type (ST) and capsular serotype were ST11 and KL64, and KPC-2 was the most prevalent enzyme type of carbapenemase-carrying Klebsiella pneumoniae. The most prevalent aerobactin and yersiniabactin of ST11-CRKP were iuc-1 and ybt9 ICEKp3, as for KL64-CRKP. Phylogenomic analysis showed that the antibacterial resistance genes on plasmids were highly consistent, but the genetic background of the chromosomes was still different. CONCLUSIONS Our findings are important for hospitals, allowing them to limit dissemination of CRKP and optimize antibiotic administration.
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Affiliation(s)
- Qiongfang Zhu
- Center of Clinical Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Jie Xu
- Center of Clinical Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Xu Chen
- Center of Clinical Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Yalu Ren
- Center of Clinical Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Lina Zhao
- Center of Clinical Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China; Department of Laboratory Medicine, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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22
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Genomic epidemiology and transmission dynamics of recurrent Clostridioides difficile infection in Western Australia. Eur J Clin Microbiol Infect Dis 2023; 42:607-619. [PMID: 36940050 PMCID: PMC10105659 DOI: 10.1007/s10096-023-04569-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 02/09/2023] [Indexed: 03/21/2023]
Abstract
Recurrent cases of Clostridioides difficile infection (rCDI) remain one of the most common and serious challenges faced in the management of CDI. The accurate distinction between a relapse (caused by infection with the same strain) and reinfection (caused by a new strain) has implications for infection control and prevention, and patient therapy. Here, we used whole-genome sequencing to investigate the epidemiology of 94 C. difficile isolates from 38 patients with rCDI in Western Australia. The C. difficile strain population comprised 13 sequence types (STs) led by ST2 (PCR ribotype (RT) 014, 36.2%), ST8 (RT002, 19.1%) and ST34 (RT056, 11.7%). Among 38 patients, core genome SNP (cgSNP) typing found 27 strains (71%) from initial and recurring cases differed by ≤ 2 cgSNPs, suggesting a likely relapse of infection with the initial strain, while eight strains differed by ≥ 3 cgSNPs, suggesting reinfection. Almost half of patients with CDI relapse confirmed by WGS suffered episodes that occurred outside the widely used 8-week cut-off for defining rCDI. Several putative strain transmission events between epidemiologically unrelated patients were identified. Isolates of STs 2 and 34 from rCDI cases and environmental sources shared a recent evolutionary history, suggesting a possible common community reservoir. For some rCDI episodes caused by STs 2 and 231, within-host strain diversity was observed, characterised by loss/gain of moxifloxacin resistance. Genomics improves discrimination of relapse from reinfection and identifies putative strain transmission events among patients with rCDI. Current definitions of relapse and reinfection based on the timing of recurrence need to be reconsidered.
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23
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Spore-Forming Clostridium ( Clostridioides) difficile in Wastewater Treatment Plants in Western Australia. Microbiol Spectr 2023; 11:e0358222. [PMID: 36475924 PMCID: PMC9927104 DOI: 10.1128/spectrum.03582-22] [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] [Indexed: 12/13/2022] Open
Abstract
There is growing evidence that shows Clostridium (Clostridioides) difficile is a pathogen of One Health importance with a complex dissemination pathway involving animals, humans, and the environment. Thus, environmental discharge and agricultural recycling of human and animal waste have been suspected as factors behind the dissemination of Clostridium difficile in the community. Here, the presence of C. difficile in 12 wastewater treatment plants (WWTPs) in Western Australia was investigated. Overall, C. difficile was found in 90.5% (114/126) of raw sewage influent, 48.1% (50/104) of treated effluent, 40% (2/5) of reclaimed irrigation water, 100% (38/38) of untreated biosolids, 95.2% (20/21) of anaerobically digested biosolids, and 72.7% (8/11) of lime-amended biosolids. Over half of the isolates (55.3% [157/284]) were toxigenic, and 97 C. difficile ribotypes (RTs) were identified, with RT014/020 the most common (14.8% [42/284]). Thirteen C. difficile isolates with the toxin gene profile A+ B+ CDT+ (positive for genes coding for toxins A and B and the binary C. difficile transferase toxin [CDT]) were found, including the hypervirulent RT078 strain. Resistance to the antimicrobials fidaxomicin, vancomycin, metronidazole, rifaximin, amoxicillin-clavulanate, meropenem, and moxifloxacin was uncommon; however, resistance to clindamycin, erythromycin, and tetracycline was relatively frequent at 56.7% (161/284), 14.4% (41/284), and 13.7% (39/284), respectively. This study revealed that toxigenic C. difficile was commonly encountered in WWTPs and being released into the environment. This raises concern about the possible spillover of C. difficile into animal and/or human populations via land receiving the treated waste. In Western Australia, stringent measures are in place to mitigate the health and environmental risk of recycling human waste; however, further studies are needed to elucidate the public health significance of C. difficile surviving the treatment processes at WWTPs. IMPORTANCE Clostridium difficile infection (CDI) is a leading cause of antimicrobial-associated diarrhea in health care facilities. Extended hospital stays and recurrences increase the cost of treatment and morbidity and mortality. Community-associated CDI (CA-CDI) cases, with no history of antimicrobial use or exposure to health care settings, are increasing. The isolation of clinically important C. difficile strains from animals, rivers, soil, meat, vegetables, compost, treated wastewater, and biosolids has been reported. The objective of this study was to characterize C. difficile in wastewater treatment plants (WWTPs) in Australia. We found that C. difficile can survive the treatment processes of WWTPs, and toxigenic C. difficile was being released into the environment, becoming a potential source/reservoir for CA-CDI.
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24
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Make It Less difficile: Understanding Genetic Evolution and Global Spread of Clostridioides difficile. Genes (Basel) 2022; 13:genes13122200. [PMID: 36553467 PMCID: PMC9778335 DOI: 10.3390/genes13122200] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 11/14/2022] [Accepted: 11/22/2022] [Indexed: 11/25/2022] Open
Abstract
Clostridioides difficile is an obligate anaerobic pathogen among the most common causes of healthcare-associated infections. It poses a global threat due to the clinical outcomes of infection and resistance to antibiotics recommended by international guidelines for its eradication. In particular, C. difficile infection can lead to fulminant colitis associated with shock, hypotension, megacolon, and, in severe cases, death. It is therefore of the utmost urgency to fully characterize this pathogen and better understand its spread, in order to reduce infection rates and improve therapy success. This review aims to provide a state-of-the-art overview of the genetic variation of C. difficile, with particular regard to pathogenic genes and the correlation with clinical issues of its infection. We also summarize the current typing techniques and, based on them, the global distribution of the most common ribotypes. Finally, we discuss genomic surveillance actions and new genetic engineering strategies as future perspectives to make it less difficile.
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25
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Tsai BY, Chien CC, Huang SH, Zheng JY, Hsu CY, Tsai YS, Hung YP, Ko WC, Tsai PJ. The emergence of Clostridioides difficile PCR ribotype 127 at a hospital in northeastern Taiwan. JOURNAL OF MICROBIOLOGY, IMMUNOLOGY, AND INFECTION = WEI MIAN YU GAN RAN ZA ZHI 2022; 55:896-909. [PMID: 35042668 DOI: 10.1016/j.jmii.2021.12.006] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 10/27/2021] [Accepted: 12/25/2021] [Indexed: 06/14/2023]
Abstract
BACKGROUND Several studies have highlighted the incidence of Clostridioides difficile infections (CDIs) in Taiwan and certain ribotypes have been related to severe clinical diseases. A study was conducted to investigate the polymerase chain reaction (PCR) ribotypes and genetic relatedness of clinical C. difficile strains collected from January 2009 to December 2015 at a hospital in northeastern Taiwan. MATERIAL AND METHODS A modified two-step typing algorithm for C. difficile was used by combining a modified 8-plex and 3'-truncated tcdA screening PCR. In addition, MLVA typing was adopted for investigation of bacterial clonality and transmission. RESULTS Among a total of 86 strains, 24 (28%) were nontoxigenic and 62 (72%) had both tcdA and tcdB (A + B+). No tcdA-negative and tcdB-positive (A-B+) strains were identified. Binary toxin (CDT)-producing (cdtA+/cdtB+) strains were started to be identified in 2013. The 21 (34%) A+B+ clinical strains with binary toxin and tcdC deletion were identified as RT127 strains, which contained both RT078-lineage markers and fluoroquinolone (FQ)-resistant mutations (Thr82Ile in gyrA). Multiple loci variable-number tandem repeat analysis (MLVA) for phylogenetic relatedness of RT127 strains indicated that 20 of 21 strains belonged to a clonal complex that was identical to a clinical strain collected from southern Taiwan in 2011, suggestive of a clonal expansion in Taiwan. CONCLUSION A two-step typing method could rapidly confirm species identification and define the toxin gene profile of C. difficile isolates. The clonal expansion of RT127 strains in Taiwan indicates monitoring and surveillance of toxigenic C. difficile isolates from human, animal, and environment are critical to develop One Health prevention strategies.
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Affiliation(s)
- Bo-Yang Tsai
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
| | - Chun-Chih Chien
- Department of Laboratory Medicine, Chang Gung Memorial Hospital at Kaohsiung, Kaohsiung, Taiwan.
| | - Shu-Huan Huang
- Department of Laboratory Medicine, Chang Gung Memorial Hospital at Kee-Lung, Keelung, Taiwan.
| | - Jun-Yuan Zheng
- Division of Infectious Diseases, Department of Internal Medicine, Chang Gung Memorial Hospital at Kee-Lung, Kee-Lung, Taiwan.
| | - Chih-Yu Hsu
- Department of Medical Laboratory Science and Biotechnology, National Cheng Kung University, Tainan, Taiwan.
| | - Yau-Sheng Tsai
- Institute of Clinical Medicine, National Cheng Kung University, Tainan, Taiwan.
| | - Yuan-Pin Hung
- Departments of Internal Medicine, Tainan Hospital, Ministry of Health & Welfare, Tainan, Taiwan; Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
| | - Wen-Chien Ko
- Department of Internal Medicine, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Department of Medicine, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
| | - Pei-Jane Tsai
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Department of Medical Laboratory Science and Biotechnology, National Cheng Kung University, Tainan, Taiwan; Center of Infectious Disease and Signaling Research, National Cheng Kung University, Tainan, Taiwan; Department of Pathology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
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26
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Gu W, Li W, Jia S, Zhou Y, Yin J, Wu Y, Fu X. Antibiotic resistance and genomic features of Clostridioides difficile in southwest China. PeerJ 2022; 10:e14016. [PMID: 36093337 PMCID: PMC9454788 DOI: 10.7717/peerj.14016] [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] [Received: 04/25/2022] [Accepted: 08/15/2022] [Indexed: 01/19/2023] Open
Abstract
Background Clostridioides difficile infection (CDI) caused by toxigenic strains leads to antibiotic-related diarrhea, colitis, or even fatal pseudomembranous enteritis. Previously, we conducted a cross-sectional study on prevalence of CDI in southwest China. However, the antibiotics resistance and characteristics of genomes of these isolates are still unknown. Methods Antibiotic susceptibility testing with E-test strips and whole genome sequence analysis were used to characterize the features of these C. difficile isolates. Results Forty-nine strains of C. difficile were used in this study. Five isolates were non-toxigenic and the rest carried toxigenic genes. We have previously reported that ST35/RT046, ST3/RT001 and ST3/RT009 were the mostly distributed genotypes of strains in the children group. In this study, all the C. difficile isolates were sensitive to metronidazole, meropenem, amoxicillin/clavulanic acid and vancomycin. Most of the strains were resistant to erythromycin, gentamicin and clindamycin. The annotated resistant genes, such as macB, vanRA, vanRG, vanRM, arlR, and efrB were mostly identified related to macrolide, glycopeptide, and fluoroquinolone resistance. Interestingly, 77.55% of the strains were considered as multi-drug resistant (MDR). Phylogenetic analysis based on core genome of bacteria revealed all the strains were divided into clade 1 and clade 4. The characteristics of genome diversity for clade 1 could be found. None of the isolates showed 18-bp deletion of tcdC as RT027 strain as described before, and polymorphism of tcdB showed a high degree of conservation than tcdA gene. Conclusions Most of the C. difficile isolates in this study were resistant to macrolide and aminoglycoside antibiotics. Moreover, the MDR strains were commonly found. All the isolates belonged to clade 1 and clade 4 according to phylogenetic analysis of bacterial genome, and highly genomic diversity of clade 1 was identified for these strains.
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Affiliation(s)
- Wenpeng Gu
- Department of Acute Infectious Diseases Control and Prevention, Yunnan Provincial Centre for Disease Control and Prevention, Kunming, China
| | - Wenge Li
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Senquan Jia
- Department of Acute Infectious Diseases Control and Prevention, Yunnan Provincial Centre for Disease Control and Prevention, Kunming, China
| | - Yongming Zhou
- Department of Acute Infectious Diseases Control and Prevention, Yunnan Provincial Centre for Disease Control and Prevention, Kunming, China
| | - Jianwen Yin
- Department of Acute Infectious Diseases Control and Prevention, Yunnan Provincial Centre for Disease Control and Prevention, Kunming, China
| | - Yuan Wu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Beijing, China
| | - Xiaoqing Fu
- Department of Acute Infectious Diseases Control and Prevention, Yunnan Provincial Centre for Disease Control and Prevention, Kunming, China
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27
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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.
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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
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28
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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.
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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
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Redding LE, Tu V, Abbas A, Alvarez M, Zackular JP, Gu C, Bushman FD, Kelly DJ, Barnhart D, Lee JJ, Bittinger KL. Genetic and phenotypic characteristics of Clostridium (Clostridioides) difficile from canine, bovine, and pediatric populations. Anaerobe 2022; 74:102539. [PMID: 35217150 PMCID: PMC9359814 DOI: 10.1016/j.anaerobe.2022.102539] [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] [Received: 11/01/2021] [Revised: 02/02/2022] [Accepted: 02/17/2022] [Indexed: 12/15/2022]
Abstract
Objectives: Carriage of Clostridioides difficile by different species of animals has led to speculation that animals could represent a reservoir of this pathogen for human infections. The objective of this study was to compare C. difficile isolates from humans, dogs, and cattle from a restricted geographic area. Methods: C. difficile isolates from 36 dogs and 15 dairy calves underwent whole genome sequencing, and phenotypic assays assessing growth and virulence were performed. Genomes of animal-derived isolates were compared to 29 genomes of isolates from a pediatric population as well as 44 reference genomes. Results: Growth rates and relative cytotoxicity of isolates were significantly higher and lower, respectively, in bovine-derived isolates compared to pediatric- and canine-derived isolates. Analysis of core genes showed clustering by host species, though in a few cases, human strains co-clustered with canine or bovine strains, suggesting possible interspecies transmission. Geographic differences (e.g., farm, litter) were small compared to differences between species. In an analysis of accessory genes, the total number of genes in each genome varied between host species, with 6.7% of functional orthologs differentially present/absent between host species and bovine-derived strains having the lowest number of genes. Canine-derived isolates were most likely to be non-toxigenic and more likely to carry phages. A targeted study of episomes identified in local pediatric strains showed sharing of a methicillin-resistance plasmid with dogs, and historic sharing of a wide range of episomes across hosts. Bovine-derived isolates harbored the widest variety of antibiotic-resistance genes, followed by canine Conclusions: While C. difficile isolates mostly clustered by host species, occasional co-clustering of canine and pediatric-derived isolates suggests the possibility of interspecies transmission. The presence of a pool of resistance genes in animal-derived isolates with the potential to appear in humans given sufficient pressure from antibiotic use warrants concern.
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Affiliation(s)
- L E Redding
- Department of Clinical Studies-New Bolton Center, University of Pennsylvania, School of Veterinary Medicine, Kennett Square, PA, 19348, USA.
| | - V Tu
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, PA, 19104, USA
| | - A Abbas
- Division of Protective Immunity, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - M Alvarez
- Division of Protective Immunity, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - J P Zackular
- Division of Protective Immunity, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA; Department of Pathology and Laboratory Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - C Gu
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - F D Bushman
- Department of Microbiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - D J Kelly
- Department of Clinical Studies-New Bolton Center, University of Pennsylvania, School of Veterinary Medicine, Kennett Square, PA, 19348, USA
| | - D Barnhart
- Department of Clinical Studies-New Bolton Center, University of Pennsylvania, School of Veterinary Medicine, Kennett Square, PA, 19348, USA
| | - J J Lee
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, PA, 19104, USA
| | - K L Bittinger
- Division of Gastroenterology, Hepatology, and Nutrition, Children's Hospital of Philadelphia, PA, 19104, USA
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Perumalsamy S, Lim SC, Riley TV. Clostridioides (Clostridium) difficile isolated from paediatric patients in Western Australia 2019-2020. Pathology 2022; 54:460-465. [PMID: 35125203 DOI: 10.1016/j.pathol.2021.10.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Revised: 10/09/2021] [Accepted: 10/17/2021] [Indexed: 11/17/2022]
Abstract
Less is understood about the epidemiology of Clostridioides difficile infection (CDI) in children compared to adults, and its impact is complicated by variations in the natural development of infection in paediatric patients. The interplay of rising CDI incidence in hospitalised paediatric patients, emergence of hypervirulent strains and community associated CDI (CA-CDI) in the past decade is a potential threat in both hospital and community settings. Research in Australia regarding paediatric CDI is limited. Here, we report the molecular characterisation of C. difficile isolated from paediatric patients at a tertiary hospital in Perth, Western Australia. A total of 427 stool samples was collected from patients aged from <1 to 17 years being investigated for diarrhoea from July 2019 to June 2020. Stool specimens were cultured and isolates of C. difficile characterised by ribotyping and toxin gene profiling. Clostridioides difficile was recovered from 84/427 (19.7%) samples tested. The most prevalent PCR ribotypes (RTs) were RT 002 (12.4%), a toxigenic strain, and RT 009 (15.7%), a non-toxigenic strain. Interestingly, C. difficile RT 078 and RT 017, strains that are not endemic in Australia, were isolated from a 1- and 4-year-old child, respectively. Clostridioides difficile RT 106, a strain of emerging importance in Australia, was recovered from two cases (5.3%). Resistance to metronidazole, fidaxomicin, amoxicillin, rifaximin and meropenem was not detected, however, 45 isolates (50.6%) showed resistance to at least one agent, and multidrug resistance was observed in 13.3% of the resistant isolates (6/45). This study provides a baseline for future surveillance of paediatric CDI in Australia. Given that young children can be asymptomatically colonised with toxigenic C. difficile strains, they represent a potential reservoir of strains causing CDI in adults.
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Affiliation(s)
- Sicilia Perumalsamy
- The University of Western Australia, School of Biomedical Sciences, Queen Elizabeth II Medical Centre, Nedlands, WA, Australia
| | - Su Chen Lim
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia
| | - Thomas V Riley
- The University of Western Australia, School of Biomedical Sciences, Queen Elizabeth II Medical Centre, Nedlands, WA, Australia; School of Medical and Health Sciences, Edith Cowan University, Joondalup, WA, Australia; School of Veterinary and Life Sciences, Murdoch University, Murdoch, WA, Australia; PathWest Laboratory Medicine, Department of Microbiology, Queen Elizabeth II Medical Centre, Nedlands, WA, Australia.
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31
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A Novel Bacteriophage with Broad Host Range against Clostridioides difficile Ribotype 078 Supports SlpA as the Likely Phage Receptor. Microbiol Spectr 2022; 10:e0229521. [PMID: 35107319 PMCID: PMC8809339 DOI: 10.1128/spectrum.02295-21] [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: 01/20/2023] Open
Abstract
Bacteriophages represent a promising option for the treatment of Clostridioides difficile (formerly Clostridium difficile) infection (CDI), which at present relies on conventional antibiotic therapy. The specificity of bacteriophages should prevent dysbiosis of the colonic microbiota associated with antibiotic treatment of CDI. While numerous phages have been isolated, none have been characterized with broad host range activity toward PCR ribotype (RT) 078 strains, despite their relevance to medicine and agriculture. In this study, we isolated four novel C. difficile myoviruses: ΦCD08011, ΦCD418, ΦCD1801, and ΦCD2301. Their characterization revealed that each was comparable with other C. difficile phages described in the literature, with the exception of ΦCD1801, which exhibited broad host range activity toward RT 078, infecting 15/16 (93.8%) of the isolates tested. In order for wild-type phages to be exploited in the effective treatment of CDI, an optimal phage cocktail must be assembled that provides broad coverage against all C. difficile RTs. We conducted experiments to support previous findings suggesting that SlpA, a constituent of the C. difficile surface layer (S-layer) is the likely phage receptor. Through interpretation of phage-binding assays, our data suggested that ΦCD1801 could bind to an RT 012 strain only in the presence of a plasmid-borne S-layer cassette corresponding to the slpA allele found in RT 078. Armed with this information, efforts should be directed toward the isolation of phages with broad host range activity toward defined S-layer cassette types, which could form the basis of an effective phage cocktail for the treatment of CDI. IMPORTANCE Research into phage therapy has seen a resurgence in recent years owing to growing concerns regarding antimicrobial resistance. Phage research for potential therapy against Clostridioides difficile infection (CDI) is in its infancy, where an optimal “one size fits all” phage cocktail is yet to be derived. The pursuit thus far has aimed to find phages with the broadest possible host range. However, for C. difficile strains belonging to certain PCR ribotypes (RTs), in particular RT 078, phages with broad host range activity are yet to be discovered. In this study, we isolate four novel myoviruses, including ΦCD1801, which exerts the broadest host range activity toward RT 078 reported in the literature. Through the application of ΦCD1801 to phage-binding assays, we provide data to support the prior notion that SlpA represents the likely phage receptor on the bacterial cell surface. Our finding directs research attention toward the isolation of phages with activity toward strains possessing defined S-layer cassette types.
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Forrester JD, Cao S, Schaps D, Liou R, Patil A, Stave C, Sokolow SH, Leo GD. Influence of Socioeconomic and Environmental Determinants of Health on Human Infection and Colonization with Antibiotic-Resistant and Antibiotic-Associated Pathogens: A Scoping Review. Surg Infect (Larchmt) 2022; 23:209-225. [DOI: 10.1089/sur.2021.348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Joseph D. Forrester
- Division of General Surgery, Department of Surgery, Stanford University, Stanford, California, USA
| | - Siqi Cao
- School of Medicine, Stanford University, Stanford, California, USA
| | - Diego Schaps
- School of Medicine, Duke University, Durham, North Carolina, USA
| | - Raymond Liou
- School of Medicine, Stanford University, Stanford, California, USA
| | | | - Christopher Stave
- School of Medicine, Stanford University, Stanford, California, USA
- Lane Medical Library, Stanford University, Stanford, California, USA
| | - Susanne H. Sokolow
- Woods Institute for the Environment, Stanford University, Stanford, California, USA
- Marine Science Institute, University of California Santa Barbara, Santa Barbara, California, USA
| | - Giulio De Leo
- Woods Institute for the Environment, Stanford University, Stanford, California, USA
- Hopkins Marine Station, Stanford University, Stanford, California, USA
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33
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Hain‐Saunders N, Knight DR, Bruce M, Riley TV. Clostridioides difficile
infection and One Health: An Equine Perspective. Environ Microbiol 2022; 24:985-997. [PMID: 35001483 PMCID: PMC9304292 DOI: 10.1111/1462-2920.15898] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 01/04/2022] [Accepted: 01/05/2022] [Indexed: 11/29/2022]
Abstract
Clostridioides (Clostridium) difficile presents a significant health risk to humans and animals. The complexity of the bacterial–host interaction affecting pathogenesis and disease development creates an ongoing challenge for epidemiological studies, control strategies and prevention planning. The recent emergence of human disease caused by strains of C. difficile found in animals adds to mounting evidence that C. difficile infection (CDI) may be a zoonosis. In equine populations, C. difficile is a known cause of diarrhoea and gastrointestinal inflammation, with considerable mortality and morbidity. This has a significant impact on both the well‐being of the animal and, in the case of performance and production animals, it may have an adverse economic impact on relevant industries. While C. difficile is regularly isolated from horses, many questions remain regarding the impact of asymptomatic carriage as well as optimization of diagnosis, testing and treatment. This review provides an overview of our understanding of equine CDI while also identifying knowledge gaps and the need for a holistic One Health approach to a complicated issue.
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Affiliation(s)
- Natasza Hain‐Saunders
- Biosecurity and One Health Research Centre, Harry Butler Institute Murdoch University Murdoch Western Australia Australia
| | - Daniel R. Knight
- Biosecurity and One Health Research Centre, Harry Butler Institute Murdoch University Murdoch Western Australia Australia
- School of Biomedical Sciences, The University of Western Australia, Queen Elizabeth II Medical Centre Nedlands 6009 WA Australia
| | - Mieghan Bruce
- School of Veterinary Medicine, Centre for Biosecurity and One Health Murdoch University Murdoch Western Australia Australia
| | - Thomas V. Riley
- Biosecurity and One Health Research Centre, Harry Butler Institute Murdoch University Murdoch Western Australia Australia
- School of Biomedical Sciences, The University of Western Australia, Queen Elizabeth II Medical Centre Nedlands 6009 WA Australia
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia Australia
- Department of Microbiology, PathWest Laboratory Medicine, Queen Elizabeth II Medical Centre Nedlands Western Australia Australia
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34
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Rodríguez-Pallares S, Fernández-Palacios P, Jurado-Tarifa E, Arroyo F, Rodríguez-Iglesias MA, Galán-Sánchez F. Transmission of toxigenic Clostridiodes difficile between a pet dog with diarrhea and a 10-month-old infant. Anaerobe 2022; 74:102519. [DOI: 10.1016/j.anaerobe.2022.102519] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/15/2022] [Accepted: 01/18/2022] [Indexed: 11/01/2022]
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35
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Spigaglia P. Clostridioides difficile infection (CDI) during the COVID-19 pandemic. Anaerobe 2022; 74:102518. [PMID: 35063599 PMCID: PMC8767936 DOI: 10.1016/j.anaerobe.2022.102518] [Citation(s) in RCA: 32] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Revised: 01/08/2022] [Accepted: 01/14/2022] [Indexed: 02/07/2023]
Abstract
The ongoing coronavirus disease (COVID-19) pandemic has dramatically tested healthcare systems around the world, with serious repercussions on the measures of prevention and control of hospital-acquired infections (HAIs). Among HAIs, Clostridioides difficile infection (CDI) represents one of the most important global public health threats. Although the full impact of the COVID-19 pandemic on CDI remains undetermined, depending on the development of the pandemic in the coming months, in this review literature studies of the last three years have been considered in order to depict the current situation, and make some considerations about possible future developments. If on the one hand, a general reduction in CDI incidence has been reported in several settings, mainly due to the extraordinary reinforcement of infection prevention measures, on the other hand, the critical circumstances experienced in many hospitals have limited the effectiveness of these measures, particularly in the intensive care units (ICUs), increasing the possibility of the occurrence of hospital-acquired CDI (HA-CDI). New concerns have arisen from the decrease in C. difficile testing and the increased use of broad-spectrum antibiotics reported during the pandemic. In particular, overuse of antibiotics and disinfectants may lead to a selection of resistant C. difficile strains not only in hospitals but also in the community. Furthermore, patients infected with severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) and patients that have survived COVID-19 may represent a new group of frail patients potentially at a higher risk of CDI, a group that could potentially increase in size due to SARS-CoV-2 evolution. In the dramatic COVID-19 era, the multifactorial nature of CDI has emerged more clearly than before, highlighting the necessity of a strong refocus on efforts to improve prevention strategies and to integrate CDI surveillance in a One Health prospective in order to curtail the public health threat posed by this infection in the next future.
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36
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Gu W, Wang W, Li W, Li N, Wang Y, Zhang W, Lu C, Tong P, Han Y, Sun X, Lu J, Wu Y, Dai J. New ribotype Clostridioides difficile from ST11 group revealed higher pathogenic ability than RT078. Emerg Microbes Infect 2021; 10:687-699. [PMID: 33682630 PMCID: PMC8023612 DOI: 10.1080/22221751.2021.1900748] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Revised: 02/07/2021] [Accepted: 03/04/2021] [Indexed: 11/14/2022]
Abstract
Clostridioides difficile is the predominant antibiotic-associated enteropathogen associated with diarrhoea or pseudomembranous colitis in patients worldwide. Previously, we identified C. difficile RT078 isolates (CD21062) from elderly patients in China, including two new ribotype strains (CD10010 and CD12038) belonging to the ST11 group, and their genomic features were also investigated. This study compared sporulation, spore germination, toxin expression, flagellar characteristics, and adhesion among these strains in vitro and analysed their pathogenic ability in vivo using animal models. The results showed sporulation and spore germination did not significantly differ among the three C. difficile strains. CD10010 and CD12038 showed higher transcriptional levels of toxins until 48 h; thereafter, the transcriptional levels of toxins remained constant among RT078, CD10010, and CD12038. RT078 showed a loss of flagellum and its related genes, whereas CD12038 showed the highest motility in vitro. Both CD10010 and CD12038 initially showed flg phase OFF, and the flagellar switch reversed to phase ON after 48 h in swim agar. Flagellar proteins and toxins were both upregulated when flg phase OFF changed to flg phase ON status, enhancing their pathogenic ability. CD12038 showed the highest adhesion to Hep-2 cells. Histopathology and inflammation scores demonstrated that CD12038 caused the most severe tissue damage and infection in vivo. The new ribotype strains, particularly CD12038, exhibit higher pathogenic ability than the typical RT078 strain, both in vitro and in vivo. Therefore, more attention should be paid to this new C. difficile strain in epidemiological research; further studies are warranted.
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Affiliation(s)
- Wenpeng Gu
- Center of Tree Shrew Germplasm Resources, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Yunnan Innovation Team of Standardization and Application Research in Tree Shrew, Kunming, China
- Department of Acute Infectious Diseases Control and Prevention, Yunnan Provincial Centre for Disease Control and Prevention, Kunming, China
| | - Wenguang Wang
- Center of Tree Shrew Germplasm Resources, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Yunnan Innovation Team of Standardization and Application Research in Tree Shrew, Kunming, China
| | - Wenge Li
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Na Li
- Center of Tree Shrew Germplasm Resources, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Yunnan Innovation Team of Standardization and Application Research in Tree Shrew, Kunming, China
| | - Yuanyuan Wang
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Wenzhu Zhang
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Caixia Lu
- Center of Tree Shrew Germplasm Resources, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Yunnan Innovation Team of Standardization and Application Research in Tree Shrew, Kunming, China
| | - Pinfen Tong
- Center of Tree Shrew Germplasm Resources, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Yunnan Innovation Team of Standardization and Application Research in Tree Shrew, Kunming, China
| | - Yuanyuan Han
- Center of Tree Shrew Germplasm Resources, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Yunnan Innovation Team of Standardization and Application Research in Tree Shrew, Kunming, China
| | - Xiaomei Sun
- Center of Tree Shrew Germplasm Resources, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Yunnan Innovation Team of Standardization and Application Research in Tree Shrew, Kunming, China
| | - Jinxing Lu
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Yuan Wu
- State Key Laboratory of Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jiejie Dai
- Center of Tree Shrew Germplasm Resources, Institute of Medical Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Yunnan Key Laboratory of Vaccine Research and Development on Severe Infectious Diseases, Yunnan Innovation Team of Standardization and Application Research in Tree Shrew, Kunming, China
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Zhou Y, Zhou W, Xiao T, Chen Y, Lv T, Wang Y, Zhang S, Cai H, Chi X, Kong X, Zhou K, Shen P, Shan T, Xiao Y. Comparative genomic and transmission analysis of Clostridioides difficile between environmental, animal, and clinical sources in China. Emerg Microbes Infect 2021; 10:2244-2255. [PMID: 34756150 PMCID: PMC8648027 DOI: 10.1080/22221751.2021.2005453] [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] [Indexed: 11/21/2022]
Abstract
Clostridioides difficile is the most common pathogen causing antibiotic-associated diarrhea. Previous studies showed that diverse sources, aside from C. difficile infection (CDI) patients, played a major role in C. difficile hospital transmission. This study aimed to investigate relationships and transmission potential of C. difficile strains from different sources. A prospective study was conducted both in the intensive care unit (ICU) and six livestock farms in China in 2018–2019. Ninety-eight strains from CDI patients (10 isolates), asymptomatic hospitalized carriers (55), the ICU environment (12), animals (14), soil (4), and farmers (3) were collected. Sequence type (ST) 3/ribotype (RT) 001, ST35/RT046, and ST48/RT596 were dominant types, distributed widely in multiple sources. Core-genome single-nucleotide polymorphism (cgSNP) analysis showed that hospital and farm strains shared several common clonal groups (CGs, strains separated by ≤ 2 cgSNPs) (CG4/ST3/RT001, CG7/ST35/RT046, CG11/ST48/RT596). CDI patients, asymptomatic carriers, and the ICU environment strains also shared several common CGs. The number of virulence genes was not statistically different between strains from different sources. Multi-source strains in the same CG carried identical virulence gene sequences, including pathogenicity genes at the pathogenicity locus and adhesion-related genes at S-layer cassette. Resistance genes (ermB, tetM, etc.) were widespread in multiple sources, and multi-source strains in the same CG had similar resistance phenotypes and carried consistent transposons and plasmid types. The study indicated that interspecies and cross-regional transmission of C. difficile occurs between animals, the environment, and humans. Community-associated strains from both farms and asymptomatic hospitalized carriers were important reservoirs of CDI in hospitals.
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Affiliation(s)
- Yanzi Zhou
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China, 310003
| | - Wangxiao Zhou
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China, 310003
| | - Tingting Xiao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China, 310003
| | - Yunbo Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China, 310003
| | - Tao Lv
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China, 310003
| | - Yuan Wang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China, 310003
| | - Shuntian Zhang
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China, 310003
| | - Hongliu Cai
- Department of Intensive Care Unit, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China, 310003
| | - Xiaohui Chi
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China, 310003
| | - Xiaoyang Kong
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China, 310003
| | - Kai Zhou
- Shenzhen Institute of Respiratory Diseases, the First Affiliated Hospital (Shenzhen People's Hospital), Southern University of Science and Technology, and Second Clinical Medical College, Jinan University, Shenzhen, China, 518000
| | - Ping Shen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China, 310003
| | - Tongling Shan
- Department of Swine Infectious Diseases, Shanghai Veterinary Research Institute, Chinese Academy of Agricultural Sciences, Shanghai, PR China
| | - Yonghong Xiao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, China, 310003
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Cobian N, Garlet A, Hidalgo-Cantabrana C, Barrangou R. Comparative Genomic Analyses and CRISPR-Cas Characterization of Cutibacterium acnes Provide Insights Into Genetic Diversity and Typing Applications. Front Microbiol 2021; 12:758749. [PMID: 34803983 PMCID: PMC8595920 DOI: 10.3389/fmicb.2021.758749] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 10/15/2021] [Indexed: 12/18/2022] Open
Abstract
Cutibacterium acnes is an important member of the human skin microbiome and plays a critical role in skin health and disease. C. acnes encompasses different phylotypes that have been found to be associated with different skin phenotypes, suggesting a genetic basis for their impact on skin health. Here, we present a comprehensive comparative analysis of 255 C. acnes genomes to provide insights into the species genetic diversity and identify unique features that define various phylotypes. Results revealed a relatively small and open pan genome (6,240 genes) with a large core genome (1,194 genes), and three distinct phylogenetic clades, with multiple robust sub-clades. Furthermore, we identified several unique gene families driving differences between distinct C. acnes clades. Carbohydrate transporters, stress response mechanisms and potential virulence factors, potentially involved in competitive growth and host colonization, were detected in type I strains, which are presumably responsible for acne. Diverse type I-E CRISPR-Cas systems and prophage sequences were detected in select clades, providing insights into strain divergence and adaptive differentiation. Collectively, these results enable to elucidate the fundamental differences among C. acnes phylotypes, characterize genetic elements that potentially contribute to type I-associated dominance and disease, and other key factors that drive the differentiation among clades and sub-clades. These results enable the use of comparative genomics analyses as a robust method to differentiate among the C. acnes genotypes present in the skin microbiome, opening new avenues for the development of biotherapeutics to manipulate the skin microbiota.
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Affiliation(s)
- Natalia Cobian
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, United States
| | | | - Claudio Hidalgo-Cantabrana
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, United States
| | - Rodolphe Barrangou
- Department of Food, Bioprocessing and Nutrition Sciences, North Carolina State University, Raleigh, NC, United States
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Imwattana K, Rodríguez C, Riley TV, Knight DR. A species-wide genetic atlas of antimicrobial resistance in Clostridioides difficile. Microb Genom 2021; 7:000696. [PMID: 34793295 PMCID: PMC8743556 DOI: 10.1099/mgen.0.000696] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Accepted: 09/23/2021] [Indexed: 12/27/2022] Open
Abstract
Antimicrobial resistance (AMR) plays an important role in the pathogenesis and spread of Clostridioides difficile infection (CDI), the leading healthcare-related gastrointestinal infection in the world. An association between AMR and CDI outbreaks is well documented, however, data is limited to a few ‘epidemic’ strains in specific geographical regions. Here, through detailed analysis of 10 330 publicly-available C. difficile genomes from strains isolated worldwide (spanning 270 multilocus sequence types (STs) across all known evolutionary clades), this study provides the first species-wide snapshot of AMR genomic epidemiology in C. difficile . Of the 10 330 C . difficile genomes, 4532 (43.9 %) in 89 STs across clades 1–5 carried at least one genotypic AMR determinant, with 901 genomes (8.7 %) carrying AMR determinants for three or more antimicrobial classes (multidrug-resistant, MDR). No AMR genotype was identified in any strains belonging to the cryptic clades. C. difficile from Australia/New Zealand had the lowest AMR prevalence compared to strains from Asia, Europe and North America (P <0.0001). Based on the phylogenetic clade, AMR prevalence was higher in clades 2 (84.3 %), 4 (81.5 %) and 5 (64.8 %) compared to other clades (collectively 26.9 %) (P <0.0001). MDR prevalence was highest in clade 4 (61.6 %) which was over three times higher than in clade 2, the clade with the second-highest MDR prevalence (18.3 %). There was a strong association between specific AMR determinants and three major epidemic C. difficile STs: ST1 (clade 2) with fluoroquinolone resistance (mainly T82I substitution in GyrA) (P <0.0001), ST11 (clade 5) with tetracycline resistance (various tet -family genes) (P <0.0001) and ST37 (clade 4) with macrolide-lincosamide-streptogramin B (MLSB) resistance (mainly ermB ) (P <0.0001) and MDR (P <0.0001). A novel and previously overlooked tetM -positive transposon designated Tn6944 was identified, predominantly among clade 2 strains. This study provides a comprehensive review of AMR in the global C. difficile population which may aid in the early detection of drug-resistant C. difficile strains, and prevention of their dissemination worldwide.
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Affiliation(s)
- Korakrit Imwattana
- School of Biomedical Sciences, University of Western Australia, Nedlands, Western Australia, Australia
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Nakhon Pathom, Thailand
| | - César Rodríguez
- Facultad de Microbiología & Centro de Investigación en Enfermedades Tropicales (CIET), Universidad de Costa Rica, San José, Costa Rica
| | - Thomas V. Riley
- School of Biomedical Sciences, University of Western Australia, Nedlands, Western Australia, Australia
- Medical, Molecular and Forensic Sciences, Murdoch University, Murdoch, Western Australia, Australia
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Western Australia, Australia
- Department of Microbiology, PathWest Laboratory Medicine, Queen Elizabeth II Medical Centre, Nedlands, Western Australia, Australia
| | - Daniel R. Knight
- School of Biomedical Sciences, University of Western Australia, Nedlands, Western Australia, Australia
- Medical, Molecular and Forensic Sciences, Murdoch University, Murdoch, Western Australia, Australia
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Worley J, Delaney ML, Cummins CK, DuBois A, Klompas M, Bry L. Genomic Determination of Relative Risks for Clostridioides difficile Infection From Asymptomatic Carriage in Intensive Care Unit Patients. Clin Infect Dis 2021; 73:e1727-e1736. [PMID: 32676661 PMCID: PMC8678446 DOI: 10.1093/cid/ciaa894] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2020] [Accepted: 06/24/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Clostridioides difficile infections (CDIs) are among the most prevalent hospital-associated infections (HAIs), particularly for intensive care unit (ICU) patients. The risks for developing active CDI from asymptomatic carriage of C. difficile are not well understood. METHODS We identified asymptomatic C. difficile carriage among 1897 ICU patients using rectal swabs from an existing ICU vancomycin-resistant enterococci (VRE) surveillance program. C. difficile isolates from VRE swabs, and from C. difficile-positive stool samples, were genome sequenced. Spatial-temporal data from hospital records assessed genomically identified clusters for potential transmission events. RESULTS Genomic analyses identified a diverse set of strains in infected patients and asymptomatic carriers. A total of 7.4% of ICU patients asymptomatically carried C. difficile; 69% of isolates carried an intact toxin locus. In contrast, 96% of C. difficile stool isolates were toxin encoding. CDI rates in asymptomatic carriers of toxin-encoding strains were 5.3% versus 0.57% in noncarriers. The relative risk for CDI with asymptomatic carriage of a toxin-encoding strain was 9.32 (95% confidence interval, 3.25-26.7). Genomic identification of clonal clusters supported analyses for asymptomatic transmission events, with spatial-temporal overlaps identified in 13 of 28 cases. CONCLUSIONS Our studies provide the first genomically confirmed assessments of CDI relative risk from asymptomatic carriage of toxin-encoding strains and highlight the complex dynamics of asymptomatic transmission in ICUs. Asymptomatic carriers are an active reservoir of C. difficile in the nosocomial environment. C. difficile screening can be implemented within existing HAI surveillance programs and has the potential to support infection-control efforts against this pathogen.
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Affiliation(s)
- Jay Worley
- Massachusetts Host-Microbiome Center, Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland, USA
| | - Mary L Delaney
- Massachusetts Host-Microbiome Center, Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Clinical Microbiology Laboratory, Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Christopher K Cummins
- Massachusetts Host-Microbiome Center, Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Andrea DuBois
- Massachusetts Host-Microbiome Center, Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Clinical Microbiology Laboratory, Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Michael Klompas
- Department of Population Medicine, Harvard Medical School and Harvard Pilgrim Health Care Institute, Boston, Massachusetts, USA
- Division of Infectious Diseases, Department of Medicine, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
| | - Lynn Bry
- Massachusetts Host-Microbiome Center, Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
- Clinical Microbiology Laboratory, Department of Pathology, Brigham and Women’s Hospital, Harvard Medical School, Boston, Massachusetts, USA
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Ahn SW, Lee SH, Kim UJ, Jang HC, Choi HJ, Choy HE, Kang SJ, Roh SW. Genomic characterization of nine Clostridioides difficile strains isolated from Korean patients with Clostridioides difficile infection. Gut Pathog 2021; 13:55. [PMID: 34530913 PMCID: PMC8447795 DOI: 10.1186/s13099-021-00451-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Accepted: 09/08/2021] [Indexed: 12/14/2022] Open
Abstract
Background Clostridioides difficile infection (CDI) is an infectious nosocomial disease caused by Clostridioides difficile, an opportunistic pathogen that occurs in the intestine after extensive antibiotic regimens. Results Nine C. difficile strains (CBA7201–CBA7209) were isolated from nine patients diagnosed with CDI at the national university hospital in Korea, and the whole genomes of these strains were sequenced to identify their genomic characteristics. Comparative genomic analysis was performed using 51 reference strains and the nine isolated herein. Phylogenetic analysis based on 16S rRNA gene sequences confirmed that all 60 C. difficile strains belong to the genus Clostridioides, while core-genome tree indicated that they were divided into five groups, which was consistent with the results of MLST clade analysis. All strains were confirmed to have a clindamycin antibiotic resistance gene, but the other antibiotic resistance genes differ depending on the MLST clade. Interestingly, the six strains belonging to the sequence type 17 among the nine C. difficile strains isolated here exhibited unique genomic characteristics for PaLoc and CdtLoc, the two toxin gene loci identified in this study, and harbored similar antibiotic resistance genes. Conclusion In this study, we identified the specific genomic characteristics of Korean C. difficile strains, which could serve as basic information for CDI prevention and treatment in Korea. Supplementary Information The online version contains supplementary material available at 10.1186/s13099-021-00451-3.
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Affiliation(s)
- Seung Woo Ahn
- Microbiology and Functionality Research Group, World Institute of Kimchi, 86, Kimchi-ro, Nam-gu, 61755, Gwangju, Republic of Korea
| | - Se Hee Lee
- Microbiology and Functionality Research Group, World Institute of Kimchi, 86, Kimchi-ro, Nam-gu, 61755, Gwangju, Republic of Korea
| | - Uh Jin Kim
- Department of Infectious Diseases, Chonnam National University Hospital, 61469, Gwangju, Republic of Korea
| | - Hee-Chang Jang
- Department of Infectious Diseases, Chonnam National University Hospital, 61469, Gwangju, Republic of Korea
| | - Hak-Jong Choi
- Microbiology and Functionality Research Group, World Institute of Kimchi, 86, Kimchi-ro, Nam-gu, 61755, Gwangju, Republic of Korea
| | - Hyon E Choy
- Department of Microbiology, Chonnam National University Medical School, 61469, Gwangju, Republic of Korea
| | - Seung Ji Kang
- Department of Infectious Diseases, Chonnam National University Hospital, 61469, Gwangju, Republic of Korea.
| | - Seong Woon Roh
- Microbiology and Functionality Research Group, World Institute of Kimchi, 86, Kimchi-ro, Nam-gu, 61755, Gwangju, Republic of Korea.
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O’Grady K, Knight DR, Riley TV. Antimicrobial resistance in Clostridioides difficile. Eur J Clin Microbiol Infect Dis 2021; 40:2459-2478. [DOI: 10.1007/s10096-021-04311-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 07/08/2021] [Indexed: 02/08/2023]
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Antimicrobial resistance progression in the United Kingdom: A temporal comparison of Clostridioides difficile antimicrobial susceptibilities. Anaerobe 2021; 70:102385. [PMID: 34048922 DOI: 10.1016/j.anaerobe.2021.102385] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2020] [Revised: 03/29/2021] [Accepted: 05/17/2021] [Indexed: 01/31/2023]
Abstract
OBJECTIVES Clostridioides difficile (CD) is widely reported as one of the most prevalent multi-drug resistant (MDR) organisms. Assessment of temporally disparate isolate collections can give valuable epidemiological data to further the understanding of antimicrobial resistance progression. METHODS A collection of 75 CD isolates (1980-86) was characterised by PCR ribotyping, cell cytotoxicity assay and susceptibility testing with a panel of 16 antimicrobials and compared to a modern surveillance collection consisting of 416 UK isolates (2012-2016). Agar-incorporation was performed to ascertain susceptibility data for vancomycin, metronidazole, rifampicin, fidaxomicin, moxifloxacin, clindamycin, imipenem, chloramphenicol, tigecycline, linezolid, ciprofloxacin, piperacillin/tazobactam, ceftriaxone, amoxicillin, tetracycline and erythromycin. Genomes were obtained using Illumina HiSeq3000 sequencing and assembled using CLC Genomics Workbench. Resistance genes were identified using the Comprehensive Antibiotic Research Database's Resistance Gene Identifier and ResFinder3.0. RESULTS Twenty-six known and one previously unobserved ribotype (RT) were detected. RT015 and RT020 dominated; 21.3% and 17.3%, respectively. Three moxifloxacin resistant (16-32 mg/L) RT027 isolates were recovered, pre-dating the earliest reports of this phenotype/genotype. Phenotypic resistance was observed to moxifloxacin (9.3% of isolates), ciprofloxacin (100%), erythromycin (17.3%), tetracycline (9.3%), linezolid and chloramphenicol (4.0%). Phenotypic comparisons with modern strains revealed increasing minimum inhibitory concentrations (MIC), with MIC50 elevations of one doubling-dilution for the majority of compounds, excluding clindamycin and imipenem. Moxifloxacin MIC90 comparisons revealed a two doubling-dilution increase between temporal isolate collections. Historical genomes revealed twenty different resistance determinants, including ermB (8.0% of isolates), tetM (9.3%), cfr (5.3%) and gyrA substitution Thr-82→Ile (9.3%). Seventeen isolates (22.7%) were resistant to ≥3 compounds (MDR), demonstrating ten different combinations. Intra-RT diversity was observed. CONCLUSIONS Antibiotic resistance in CD has increased since the early 1980s, across the majority of classes. Moxifloxacin resistance determinants may pre-date its introduction.
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Wickramage I, Spigaglia P, Sun X. Mechanisms of antibiotic resistance of Clostridioides difficile. J Antimicrob Chemother 2021; 76:3077-3090. [PMID: 34297842 DOI: 10.1093/jac/dkab231] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Clostridioides difficile (CD) is one of the top five urgent antibiotic resistance threats in USA. There is a worldwide increase in MDR of CD, with emergence of novel strains which are often more virulent and MDR. Antibiotic resistance in CD is constantly evolving with acquisition of novel resistance mechanisms, which can be transferred between different species of bacteria and among different CD strains present in the clinical setting, community, and environment. Therefore, understanding the antibiotic resistance mechanisms of CD is important to guide optimal antibiotic stewardship policies and to identify novel therapeutic targets to combat CD as well as other bacteria. Epidemiology of CD is driven by the evolution of antibiotic resistance. Prevalence of different CD strains and their characteristic resistomes show distinct global geographical patterns. Understanding epidemiologically driven and strain-specific characteristics of antibiotic resistance is important for effective epidemiological surveillance of antibiotic resistance and to curb the inter-strain and -species spread of the CD resistome. CD has developed resistance to antibiotics with diverse mechanisms such as drug alteration, modification of the antibiotic target site and extrusion of drugs via efflux pumps. In this review, we summarized the most recent advancements in the understanding of mechanisms of antibiotic resistance in CD and analysed the antibiotic resistance factors present in genomes of a few representative well known, epidemic and MDR CD strains found predominantly in different regions of the world.
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Affiliation(s)
- Ishani Wickramage
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Down Blvd, Tampa, FL 33612, USA
| | - Patrizia Spigaglia
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Xingmin Sun
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, 12901 Bruce B. Down Blvd, Tampa, FL 33612, USA
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Xu X, Bian Q, Luo Y, Song X, Lin S, Chen H, Liang Q, Wang M, Ye G, Zhu B, Chen L, Tang YW, Wang X, Jin D. Comparative Whole Genome Sequence Analysis and Biological Features of Clostridioides difficile Sequence Type 2 ‡. Front Microbiol 2021; 12:651520. [PMID: 34290677 PMCID: PMC8287029 DOI: 10.3389/fmicb.2021.651520] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 05/31/2021] [Indexed: 01/05/2023] Open
Abstract
Clostridioides difficile sequence type 2 (ST2) has been increasingly recognized as one of the major genotypes in China, while the genomic characteristics and biological phenotypes of Chinese ST2 strains remain to be determined. We used whole-genome sequencing and phylogenetic analysis to investigate the genomic features of 182 ST2 strains, isolated between 2011 and 2017. PCR ribotyping (RT) was performed, and antibiotic resistance, toxin concentration, and sporulation capacity were measured. The core genome Maximum-likelihood phylogenetic analysis showed that ST2 strains were distinctly segregated into two genetically diverse lineages [L1 (67.0% from Northern America) and L2], while L2 further divided into two sub-lineages, SL2a and SL2b (73.5% from China). The 36 virulence-related genes were widely distributed in ST2 genomes, but in which only 11 antibiotic resistance-associated genes were dispersedly found. Among the 25 SL2b sequenced isolates, RT014 (40.0%, n = 10) and RT020 (28.0%, n = 7) were two main genotypes with no significant difference on antibiotic resistance (χ2 = 0.024-2.667, P > 0.05). A non-synonymous amino acid substitution was found in tcdB (Y1975D) which was specific to SL2b. Although there was no significant difference in sporulation capacity between the two lineages, the average toxin B concentration (5.11 ± 3.20 ng/μL) in SL2b was significantly lower in comparison to those in L1 (10.49 ± 15.82 ng/μL) and SL2a (13.92 ± 2.39 ng/μL) (χ2 = 12.30, P < 0.05). This study described the genomic characteristics of C. difficile ST2, with many virulence loci and few antibiotic resistance elements. The Chinese ST2 strains with the mutation in codon 1975 of the tcdB gene clustering in SL2b circulating in China express low toxin B, which may be associated with mild or moderate C. difficile infection.
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Affiliation(s)
- Xingxing Xu
- Department of Clinical Laboratory, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China.,School of Laboratory Medicine, Hangzhou Medical College, Hangzhou, China
| | - Qiao Bian
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, China
| | - Yun Luo
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, NSW, Australia
| | - Xiaojun Song
- Centre of Laboratory Medicine, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, China
| | - Shan Lin
- School of Laboratory Medicine, Hangzhou Medical College, Hangzhou, China
| | - Huan Chen
- Key Laboratory of Microorganism Technology and Bioinformatics Research of Zhejiang Province, Hangzhou, China.,NMPA Key Laboratory for Testing and Risk Warning of Pharmaceutical Microbiology, Hangzhou, China
| | - Qian Liang
- Key Laboratory of Microorganism Technology and Bioinformatics Research of Zhejiang Province, Hangzhou, China.,NMPA Key Laboratory for Testing and Risk Warning of Pharmaceutical Microbiology, Hangzhou, China
| | - Meixia Wang
- Key Laboratory of Microorganism Technology and Bioinformatics Research of Zhejiang Province, Hangzhou, China.,NMPA Key Laboratory for Testing and Risk Warning of Pharmaceutical Microbiology, Hangzhou, China
| | - Guangyong Ye
- Department of Clinical Laboratory, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Bo Zhu
- Department of Clinical Laboratory, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Liang Chen
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, Untied States.,Department of Medical Sciences, Hackensack Meridian School of Medicine, Nutley, NJ, Untied States
| | - Yi-Wei Tang
- Cepheid, Danaher Diagnostic Platform, Shanghai, China
| | - Xianjun Wang
- Department of Clinical Laboratory, Hangzhou First People's Hospital, Zhejiang University School of Medicine, Hangzhou, China
| | - Dazhi Jin
- School of Laboratory Medicine, Hangzhou Medical College, Hangzhou, China.,Centre of Laboratory Medicine, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, China
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Xu X, Luo Y, Chen H, Song X, Bian Q, Wang X, Liang Q, Zhao J, Li C, Song G, Yang J, Sun L, Jiang J, Wang H, Zhu B, Ye G, Chen L, Tang YW, Jin D. Genomic evolution and virulence association of Clostridioides difficile sequence type 37 (ribotype 017) in China. Emerg Microbes Infect 2021; 10:1331-1345. [PMID: 34125660 PMCID: PMC8253194 DOI: 10.1080/22221751.2021.1943538] [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: 12/27/2022]
Abstract
Clostridioides difficile sequence type (ST) 37 (ribotype 017) is one of the most prevalent genotypes circulating in China. However, its genomic evolution and virulence determinants were rarely explored. Whole-genome sequencing, phylogeographic and phylogenetic analyses were conducted for C. difficile ST37 isolates. The 325 ST37 genomes from six continents, including North America (n = 66), South America (n = 4), Oceania (n = 7), Africa (n = 9), Europe (n = 138) and Asia (n = 101), were clustered into six major lineages, with region-dependent distributions, harbouring an array of antibiotic-resistance genes. The ST37 strains from China were divided into four distinct sublineages, showing five importation times and international sources. Isolates associated with severe infections exhibited significantly higher toxin productions, tcdB mRNA levels, and sporulation capacities (P < 0.001). Kyoto Encyclopedia of Genes and Genomes analysis showed 10 metabolic pathways were significantly enriched in the mutations among isolates associated with severe CDI (P < 0.05). Gene mutations in glycometabolism, amino acid metabolism and biosynthesis virtually causing instability in protein activity were correlated positively to the transcription of tcdR and negatively to the expression of toxin repressor genes, ccpA and codY. In summary, our study firstly presented genomic insights into genetic characteristics and virulence association of C. difficile ST37 in China. Gene mutations in certain important metabolic pathways are associated with severe symptoms and correlated with higher virulence in C. difficile ST37 isolates.
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Affiliation(s)
- Xingxing Xu
- Department of Clinical Laboratory, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, People's Republic of China.,School of Laboratory Medicine, Hangzhou Medical College, Hangzhou, People's Republic of China
| | - Yuo Luo
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Huan Chen
- Key Laboratory of Microorganism technology and bioinformatics research of Zhejiang Province, Hangzhou, People's Republic of China.,NMPA Key Laboratory For Testing and Risk Warning of Pharmaceutical Microbiology, Hangzhou, People's Republic of China
| | - Xiaojun Song
- Centre of Laboratory Medicine, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, People's Republic of China
| | - Qiao Bian
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, People's Republic of China
| | - Xianjun Wang
- Department of Laboratory Medicine, Hangzhou First People's Hospital, Hangzhou, People's Republic of China
| | - Qian Liang
- Key Laboratory of Microorganism technology and bioinformatics research of Zhejiang Province, Hangzhou, People's Republic of China.,NMPA Key Laboratory For Testing and Risk Warning of Pharmaceutical Microbiology, Hangzhou, People's Republic of China
| | - Jianhong Zhao
- Department of Clinical Microbiology, Second Hospital of Hebei Medical University, Hebei Provincial Center for Clinical Laboratories, Shijiazhuang, People's Republic of China
| | - Chunhui Li
- Infection Control Center, Xiangya Hospital of Central South University, Changsha, People's Republic of China
| | - Guangzhong Song
- School of Laboratory Medicine, Hangzhou Medical College, Hangzhou, People's Republic of China
| | - Jun Yang
- School of Laboratory Medicine, Hangzhou Medical College, Hangzhou, People's Republic of China
| | - Lingli Sun
- Key Laboratory of Microorganism technology and bioinformatics research of Zhejiang Province, Hangzhou, People's Republic of China.,NMPA Key Laboratory For Testing and Risk Warning of Pharmaceutical Microbiology, Hangzhou, People's Republic of China
| | - Jianmin Jiang
- Zhejiang Provincial Center for Disease Control and Prevention, Hangzhou, People's Republic of China
| | - Huanying Wang
- Key Laboratory of Microorganism technology and bioinformatics research of Zhejiang Province, Hangzhou, People's Republic of China.,NMPA Key Laboratory For Testing and Risk Warning of Pharmaceutical Microbiology, Hangzhou, People's Republic of China
| | - Bo Zhu
- Department of Clinical Laboratory, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, People's Republic of China
| | - Guangyong Ye
- Department of Clinical Laboratory, Women's Hospital, Zhejiang University School of Medicine, Hangzhou, People's Republic of China
| | - Liang Chen
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA.,Department of Medical Sciences, Hackensack Meridian School of Medicine, Nutley, NJ, USA
| | - Yi-Wei Tang
- Cepheid, Danaher Diagnostic Platform, Shanghai, People's Republic of China
| | - Dazhi Jin
- School of Laboratory Medicine, Hangzhou Medical College, Hangzhou, People's Republic of China.,Centre of Laboratory Medicine, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, People's Republic of China
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Knight DR, Imwattana K, Kullin B, Guerrero-Araya E, Paredes-Sabja D, Didelot X, Dingle KE, Eyre DW, Rodríguez C, Riley TV. Major genetic discontinuity and novel toxigenic species in Clostridioides difficile taxonomy. eLife 2021; 10:64325. [PMID: 34114561 PMCID: PMC8241443 DOI: 10.7554/elife.64325] [Citation(s) in RCA: 41] [Impact Index Per Article: 13.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2020] [Accepted: 06/08/2021] [Indexed: 12/17/2022] Open
Abstract
Clostridioides difficile infection (CDI) remains an urgent global One Health threat. The genetic heterogeneity seen across C. difficile underscores its wide ecological versatility and has driven the significant changes in CDI epidemiology seen in the last 20 years. We analysed an international collection of over 12,000 C. difficile genomes spanning the eight currently defined phylogenetic clades. Through whole-genome average nucleotide identity, and pangenomic and Bayesian analyses, we identified major taxonomic incoherence with clear species boundaries for each of the recently described cryptic clades CI–III. The emergence of these three novel genomospecies predates clades C1–5 by millions of years, rewriting the global population structure of C. difficile specifically and taxonomy of the Peptostreptococcaceae in general. These genomospecies all show unique and highly divergent toxin gene architecture, advancing our understanding of the evolution of C. difficile and close relatives. Beyond the taxonomic ramifications, this work may impact the diagnosis of CDI.
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Affiliation(s)
- Daniel R Knight
- Medical, Molecular and Forensic Sciences, Murdoch University, Murdoch, Australia.,School of Biomedical Sciences, the University of Western Australia, Nedlands, Australia
| | - Korakrit Imwattana
- School of Biomedical Sciences, the University of Western Australia, Nedlands, Australia.,Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Brian Kullin
- Department of Pathology, University of Cape Town, Cape Town, South Africa
| | - Enzo Guerrero-Araya
- Microbiota-Host Interactions and Clostridia Research Group, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile.,Millenium Nucleus in the Biology of Intestinal Microbiota, Santiago, Chile
| | - Daniel Paredes-Sabja
- Microbiota-Host Interactions and Clostridia Research Group, Facultad de Ciencias de la Vida, Universidad Andrés Bello, Santiago, Chile.,Millenium Nucleus in the Biology of Intestinal Microbiota, Santiago, Chile.,Department of Biology, Texas A&M University, College Station, United States
| | - Xavier Didelot
- School of Life Sciences and Department of Statistics, University of Warwick, Coventry, United Kingdom
| | - Kate E Dingle
- Nuffield Department of Clinical Medicine, University of Oxford, National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
| | - David W Eyre
- Big Data Institute, Nuffield Department of Population Health, University of Oxford, National Institute for Health Research (NIHR) Oxford Biomedical Research Centre, John Radcliffe Hospital, Oxford, United Kingdom
| | - César Rodríguez
- Facultad de Microbiología & Centro de Investigación en Enfermedades Tropicales (CIET), Universidad de Costa Rica, San José, Costa Rica
| | - Thomas V Riley
- Medical, Molecular and Forensic Sciences, Murdoch University, Murdoch, Australia.,School of Biomedical Sciences, the University of Western Australia, Nedlands, Australia.,Department of Microbiology, PathWest Laboratory Medicine, Queen Elizabeth II Medical Centre, Nedlands, Australia.,School of Medical and Health Sciences, Edith Cowan University, Joondalup, Australia
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48
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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.
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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
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49
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Frentrup M, Thiel N, Junker V, Behrens W, Münch S, Siller P, Kabelitz T, Faust M, Indra A, Baumgartner S, Schepanski K, Amon T, Roesler U, Funk R, Nübel U. Agricultural fertilization with poultry manure results in persistent environmental contamination with the pathogen Clostridioides difficile. Environ Microbiol 2021; 23:7591-7602. [PMID: 33998128 DOI: 10.1111/1462-2920.15601] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 05/13/2021] [Indexed: 11/30/2022]
Abstract
During a field experiment applying broiler manure for fertilization of agricultural land, we detected viable Clostridioides (also known as Clostridium) difficile in broiler faeces, manure, dust and fertilized soil. A large diversity of toxigenic C. difficile isolates was recovered, including PCR ribotypes common from human disease. Genomic relatedness of C. difficile isolates from dust and from soil, recovered more than 2 years after fertilization, traced their origins to the specific chicken farm that had delivered the manure. We present evidence of long-term contamination of agricultural soil with manure-derived C. difficile and demonstrate the potential for airborne dispersal of C. difficile through dust emissions during manure application. Clostridioides genome sequences virtually identical to those from manure had been recovered from chicken meat and from human infections in previous studies, suggesting broiler-associated C. difficile are capable of zoonotic transmission.
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Affiliation(s)
- Martinique Frentrup
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Nadine Thiel
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Vera Junker
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Wiebke Behrens
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Steffen Münch
- Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg, Germany
| | - Paul Siller
- Institute for Animal Hygiene and Environmental Health (ITU), Free University Berlin, Berlin, Germany
| | - Tina Kabelitz
- Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Potsdam, Germany
| | - Matthias Faust
- Leibniz-Institute for Tropospheric Research (TROPOS), Leipzig, Germany
| | - Alexander Indra
- AGES-Austrian Agency for Health and Food Safety, Vienna, Austria.,Paracelsus Medical University of Salzburg, Salzburg, Austria
| | | | | | - Thomas Amon
- Institute for Animal Hygiene and Environmental Health (ITU), Free University Berlin, Berlin, Germany.,Leibniz Institute for Agricultural Engineering and Bioeconomy (ATB), Potsdam, Germany
| | - Uwe Roesler
- Institute for Animal Hygiene and Environmental Health (ITU), Free University Berlin, Berlin, Germany
| | - Roger Funk
- Leibniz Centre for Agricultural Landscape Research (ZALF), Müncheberg, Germany
| | - Ulrich Nübel
- Leibniz-Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.,German Center for Infection Research (DZIF), Partner Site Braunschweig-Hannover, Braunschweig, Germany.,Braunschweig Integrated Center of Systems Biology (BRICS), Technical University, Braunschweig, Germany
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50
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Imwattana K, Putsathit P, Knight DR, Kiratisin P, Riley TV. Molecular Characterization of, and Antimicrobial Resistance in, Clostridioides difficile from Thailand, 2017-2018. Microb Drug Resist 2021; 27:1505-1512. [PMID: 33956520 DOI: 10.1089/mdr.2020.0603] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
Antimicrobial resistance (AMR) plays an important role in the pathogenesis and spread of Clostridioides difficile infection (CDI). Many antimicrobials, such as fluoroquinolones, have been associated with outbreaks of CDI globally. This study characterized AMR among clinical C. difficile strains in Thailand, where antimicrobial use remains inadequately regulated. Stool samples were screened for tcdB and positives were cultured. C. difficile isolates were characterized by toxin profiling and PCR ribotyping. Antimicrobial susceptibility testing was performed by agar incorporation, and whole-genome sequencing and AMR genotyping were performed on a subset of strains. There were 321 C. difficile strains isolated from 326 stool samples. The most common toxigenic ribotype (RT) was RT 017 (18%), followed by RTs 014 (12%) and 020 (7%). Resistance to clindamycin, erythromycin, moxifloxacin, and rifaximin was common, especially among RT 017 strains. AMR genotyping revealed a strong correlation between resistance genotype and phenotype for moxifloxacin and rifaximin. The presence of erm-class genes was associated with high-level clindamycin and erythromycin resistance. Point substitutions in the penicillin-binding proteins were not sufficient to confer meropenem resistance, but a Y721S substitution in PBP3 was associated with a 4.37-fold increase in meropenem minimal inhibitory concentration. No resistance to metronidazole, vancomycin, or fidaxomicin was observed.
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Affiliation(s)
- Korakrit Imwattana
- School of Biomedical Sciences, The University of Western Australia, Nedlands, Australia.,Faculty of Medicine Siriraj Hospital, Mahidol University, Bangkok, Thailand
| | - Papanin Putsathit
- School of Medical and Health Sciences, Edith Cowan University, Joondalup, Australia
| | - Daniel R Knight
- School of Biomedical Sciences, The University of Western Australia, Nedlands, Australia.,Medical, Molecular and Forensic Sciences, Murdoch University, Murdoch, Australia
| | | | - Thomas V Riley
- School of Biomedical Sciences, The University of Western Australia, Nedlands, Australia.,School of Medical and Health Sciences, Edith Cowan University, Joondalup, Australia.,Medical, Molecular and Forensic Sciences, Murdoch University, Murdoch, Australia.,Department of Microbiology, PathWest Laboratory Medicine, Queen Elizabeth II Medical Centre, Nedlands, Australia
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