1
|
Hussain H, Nubgan A, Rodríguez C, Imwattana K, Knight DR, Parthala V, Mullany P, Goh S. Removal of mobile genetic elements from the genome of Clostridioides difficile and the implications for the organism's biology. Front Microbiol 2024; 15:1416665. [PMID: 38966395 PMCID: PMC11222575 DOI: 10.3389/fmicb.2024.1416665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2024] [Accepted: 06/04/2024] [Indexed: 07/06/2024] Open
Abstract
Clostridioides difficile is an emerging pathogen of One Health significance. Its highly variable genome contains mobile genetic elements (MGEs) such as transposons and prophages that influence its biology. Systematic deletion of each genetic element is required to determine their precise role in C. difficile biology and contribution to the wider mobilome. Here, Tn5397 (21 kb) and ϕ027 (56 kb) were deleted from C. difficile 630 and R20291, respectively, using allele replacement facilitated by CRISPR-Cas9. The 630 Tn5397 deletant transferred PaLoc at the same frequency (1 × 10-7) as 630 harboring Tn5397, indicating that Tn5397 alone did not mediate conjugative transfer of PaLoc. The R20291 ϕ027 deletant was sensitive to ϕ027 infection, and contained two unexpected features, a 2.7 kb remnant of the mutagenesis plasmid, and a putative catalase gene adjacent to the deleted prophage was also deleted. Growth kinetics of R20291 ϕ027 deletant was similar to wild type (WT) in rich medium but marginally reduced compared with WT in minimal medium. This work indicates the commonly used pMTL8000 plasmid series works well for CRISPR-Cas9-mediated gene deletion, resulting in the largest deleted locus (56.8 kb) described in C. difficile. Removal of MGEs was achieved by targeting conjugative/integrative regions to promote excision and permanent loss. The deletants created will be useful strains for investigating Tn5397 or ϕ027 prophage contribution to host virulence, fitness, and physiology, and a platform for other mutagenesis studies aimed at functional gene analysis without native transposon or phage interference in C. difficile 630 and R20291.
Collapse
Affiliation(s)
- Haitham Hussain
- Department of Microbial Diseases, Eastman Dental Institute, University College London, London, United Kingdom
| | - Amer Nubgan
- Department of Clinical, Pharmaceutical and Biological Sciences, University of Hertfordshire, Hatfield, United Kingdom
| | - César Rodríguez
- Facultad de Microbiología and Centro de Investigación en Enfermedades Tropicales (CIET), Universidad de Costa Rica, San José, Costa Rica
| | - Korakrit Imwattana
- School of Biomedical Sciences, The University of Western Australia, Perth, WA, Australia
- Department of Microbiology, Faculty of Medicine Siriraj Hospital, Mahidol University, Salaya, Thailand
| | - Daniel R. Knight
- School of Biomedical Sciences, The University of Western Australia, Perth, WA, Australia
- Department of Microbiology, PathWest Laboratory Medicine WA, Queen Elizabeth II Medical Centre, Nedlands, WA, Australia
| | - Valerija Parthala
- Department of Clinical, Pharmaceutical and Biological Sciences, University of Hertfordshire, Hatfield, United Kingdom
| | - Peter Mullany
- Department of Microbial Diseases, Eastman Dental Institute, University College London, London, United Kingdom
| | - Shan Goh
- Department of Clinical, Pharmaceutical and Biological Sciences, University of Hertfordshire, Hatfield, United Kingdom
| |
Collapse
|
2
|
Goh S, Inal J. Membrane Vesicles of Clostridioides difficile and Other Clostridial Species. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1435:315-327. [PMID: 38175481 DOI: 10.1007/978-3-031-42108-2_14] [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
Membrane vesicles are secreted by growing bacterial cells and are important components of the bacterial secretome, with a role in delivering effector molecules that ultimately enable bacterial survival. Membrane vesicles of Clostridioides difficile likely contribute to pathogenicity and is a new area of research on which there is currently very limited information. This chapter summarizes the current knowledge on membrane vesicle formation, content, methods of characterization and functions in Clostridia and model Gram-positive species.
Collapse
Affiliation(s)
- Shan Goh
- Department of Clinical, Pharmaceutical and Biological Sciences, School of Life and Medical Sciences, University of Hertfordshire, Hatfield, UK.
| | - Jameel Inal
- Department of Clinical, Pharmaceutical and Biological Sciences, School of Life and Medical Sciences, University of Hertfordshire, Hatfield, UK
- School of Human Sciences, London Metropolitan University, London, UK
| |
Collapse
|
3
|
Xu M, Selvaraj GK, Lu H. Environmental sporobiota: Occurrence, dissemination, and risks. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 869:161809. [PMID: 36702282 DOI: 10.1016/j.scitotenv.2023.161809] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/22/2022] [Revised: 01/03/2023] [Accepted: 01/20/2023] [Indexed: 06/18/2023]
Abstract
Spore-forming bacteria known as sporobiota are widespread in diverse environments from terrestrial and aquatic habitats to industrial and healthcare systems. Studies on sporobiota have been mainly focused on food processing and clinical fields, while a large amount of sporobiota exist in natural environments. Due to their persistence and capabilities of transmitting virulence factors and antibiotic resistant genes, environmental sporobiota could pose significant health risks to humans. These risks could increase as global warming and environmental pollution has altered the life cycle of sporobiota. This review summarizes the current knowledge of environmental sporobiota, including their occurrence, characteristics, and functions. An interaction network among clinical-, food-related, and environment-related sporobiota is constructed. Recent and effective methods for detecting and disinfecting environmental sporobiota are also discussed. Key problems and future research needs for better understanding and reducing the risks of environmental sporobiota and sporobiome are proposed.
Collapse
Affiliation(s)
- Min Xu
- Key Laboratory of Environmental Remediation and Ecological Health, Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ganesh-Kumar Selvaraj
- Department of Microbiology, St. Peter's Institute of Higher Education and Research, Chennai 600054, Tamil Nadu, India.
| | - Huijie Lu
- Key Laboratory of Environmental Remediation and Ecological Health, Ministry of Education, College of Environmental and Resource Sciences, Zhejiang University, Hangzhou 310058, China; Key Laboratory of Water Pollution Control and Environmental Safety, Zhejiang, China.
| |
Collapse
|
4
|
Kartalidis P, Skoulakis A, Tsilipounidaki K, Florou Z, Petinaki E, Fthenakis GC. Clostridioides difficile as a Dynamic Vehicle for the Dissemination of Antimicrobial-Resistance Determinants: Review and In Silico Analysis. Microorganisms 2021; 9:microorganisms9071383. [PMID: 34202117 PMCID: PMC8307371 DOI: 10.3390/microorganisms9071383] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 06/21/2021] [Accepted: 06/22/2021] [Indexed: 01/11/2023] Open
Abstract
The present paper is divided into two parts. The first part focuses on the role of Clostridioides difficile in the accumulation of genes associated with antimicrobial resistance and then the transmission of them to other pathogenic bacteria occupying the same human intestinal niche. The second part describes an in silico analysis of the genomes of C. difficile available in GenBank, with regard to the presence of mobile genetic elements and antimicrobial resistance genes. The diversity of the C. difficile genome is discussed, and the current status of resistance of the organisms to various antimicrobial agents is reviewed. The role of transposons associated with antimicrobial resistance is appraised; the importance of plasmids associated with antimicrobial resistance is discussed, and the significance of bacteriophages as a potential shuttle for antimicrobial resistance genes is presented. In the in silico study, 1101 C. difficile genomes were found to harbor mobile genetic elements; Tn6009, Tn6105, CTn7 and Tn6192, Tn6194 and IS256 were the ones more frequently identified. The genes most commonly harbored therein were: ermB, blaCDD, vanT, vanR, vanG and vanS. Tn6194 was likely associated with resistance to erythromycin, Tn6192 and CTn7 with resistance to the β-lactams and vancomycin, IS256 with resistance to aminoglycoside and Tn6105 to vancomycin.
Collapse
Affiliation(s)
- Philip Kartalidis
- Department of Clinical and Laboratory Research, Faculty of Medicine, School of Health Sciences, University of Thessaly, 41110 Larissa, Greece; (P.K.); (A.S.); (K.T.); (Z.F.); (E.P.)
| | - Anargyros Skoulakis
- Department of Clinical and Laboratory Research, Faculty of Medicine, School of Health Sciences, University of Thessaly, 41110 Larissa, Greece; (P.K.); (A.S.); (K.T.); (Z.F.); (E.P.)
| | - Katerina Tsilipounidaki
- Department of Clinical and Laboratory Research, Faculty of Medicine, School of Health Sciences, University of Thessaly, 41110 Larissa, Greece; (P.K.); (A.S.); (K.T.); (Z.F.); (E.P.)
| | - Zoi Florou
- Department of Clinical and Laboratory Research, Faculty of Medicine, School of Health Sciences, University of Thessaly, 41110 Larissa, Greece; (P.K.); (A.S.); (K.T.); (Z.F.); (E.P.)
| | - Efthymia Petinaki
- Department of Clinical and Laboratory Research, Faculty of Medicine, School of Health Sciences, University of Thessaly, 41110 Larissa, Greece; (P.K.); (A.S.); (K.T.); (Z.F.); (E.P.)
| | - George C. Fthenakis
- Veterinary Faculty, University of Thessaly, 43100 Karditsa, Greece
- Correspondence:
| |
Collapse
|