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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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Edwards AN, McBride SM. The RgaS-RgaR two-component system promotes Clostridioides difficile sporulation through a small RNA and the Agr1 system. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.06.26.546640. [PMID: 37425791 PMCID: PMC10327067 DOI: 10.1101/2023.06.26.546640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/11/2023]
Abstract
The ability to form a dormant spore is essential for the survival of the anaerobic, gastrointestinal pathogen Clostridioides difficile outside of the mammalian gastrointestinal tract. The initiation of sporulation is governed by the master regulator of sporulation, Spo0A, which is activated by phosphorylation. Multiple sporulation factors control Spo0A phosphorylation; however, this regulatory pathway is not well defined in C. difficile. We discovered that RgaS and RgaR, a conserved orphan histidine kinase and orphan response regulator, function together as a cognate two-component regulatory system to directly activate transcription of several genes. One of these targets, agrB1D1, encodes gene products that synthesize and export a small quorum-sensing peptide, AgrD1, which positively influences expression of early sporulation genes. Another target, a small regulatory RNA now known as SrsR, impacts later stages of sporulation through an unknown regulatory mechanism(s). Unlike Agr systems in many organisms, AgrD1 does not activate the RgaS-RgaR two-component system, and thus, is not responsible for autoregulating its own production. Altogether, we demonstrate that C. difficile utilizes a conserved two-component system that is uncoupled from quorum-sensing to promote sporulation through two distinct regulatory pathways.
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Affiliation(s)
- Adrianne N. Edwards
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory Antibiotic Resistance Center, Atlanta, GA, USA
| | - Shonna M. McBride
- Department of Microbiology and Immunology, Emory University School of Medicine, Emory Antibiotic Resistance Center, Atlanta, GA, USA
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Shen A, Tamayo R. Editorial overview: Gene regulation mechanisms governing Clostridioides difficile physiology and virulence. Curr Opin Microbiol 2022; 67:102139. [PMID: 35231749 DOI: 10.1016/j.mib.2022.02.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Affiliation(s)
- Aimee Shen
- Department of Molecular Biology and Microbiology, Tufts University School of Medicine, Boston, MA, USA.
| | - Rita Tamayo
- Department of Microbiology and Immunology, University of North Carolina Chapel Hill School of Medicine, Chapel Hill, NC, USA.
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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] [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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