1
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Brehm JN, Sorg JA. Theophylline-based control of repA on a Clostridioides difficile plasmid for use in allelic exchange. Anaerobe 2024; 88:102858. [PMID: 38692475 DOI: 10.1016/j.anaerobe.2024.102858] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 04/16/2024] [Accepted: 04/24/2024] [Indexed: 05/03/2024]
Abstract
Historically, mutagenesis in the non-model enteropathogenic bacterium Clostridioides difficile has been challenging. Developing a versatile and reliable method of generating targeted mutations in C. difficile is important to further our understanding of its pathogenesis. Some of the most common targeted mutagenesis systems rely on allelic exchange mediated by either uracil auxotrophy combined with a toxic uracil precursor, a toxin/anti-toxin system, group II introns, or CRISPR/Cas mutagenesis. However, each of these methods suffers from its own issues. Here, we develop and test an allelic exchange strategy which better facilitates screening for integration and selecting for excision than previous systems. This is achieved by controlling plasmid replication with a theophylline-dependent riboswitch cloned upstream of repA, the gene whose product controls plasmid replication. This allows efficient mutant generation, can be performed in a wild-type strain of C. difficile, does not have the off-target effects inherent to group II introns, and alleviates the problem of testing multiple gRNA targets in CRISPR mutagenesis.
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Affiliation(s)
- Joshua N Brehm
- Department of Biology, Texas A&M University, College Station, TX, 77843, USA
| | - Joseph A Sorg
- Department of Biology, Texas A&M University, College Station, TX, 77843, USA.
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2
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Buddle JE, Thompson LM, Williams AS, Wright RCT, Durham WM, Turner CE, Chaudhuri RR, Brockhurst MA, Fagan RP. Identification of pathways to high-level vancomycin resistance in Clostridioides difficile that incur high fitness costs in key pathogenicity traits. PLoS Biol 2024; 22:e3002741. [PMID: 39146240 PMCID: PMC11326576 DOI: 10.1371/journal.pbio.3002741] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 07/09/2024] [Indexed: 08/17/2024] Open
Abstract
Clostridioides difficile is an important human pathogen, for which there are very limited treatment options, primarily the glycopeptide antibiotic vancomycin. In recent years, vancomycin resistance has emerged as a serious problem in several gram-positive pathogens, but high-level resistance has yet to be reported for C. difficile, although it is not known if this is due to constraints upon resistance evolution in this species. Here, we show that resistance to vancomycin can evolve rapidly under ramping selection but is accompanied by fitness costs and pleiotropic trade-offs, including sporulation defects that would be expected to severely impact transmission. We identified 2 distinct pathways to resistance, both of which are predicted to result in changes to the muropeptide terminal D-Ala-D-Ala that is the primary target of vancomycin. One of these pathways involves a previously uncharacterised D,D-carboxypeptidase, expression of which is controlled by a dedicated two-component signal transduction system. Our findings suggest that while C. difficile is capable of evolving high-level vancomycin resistance, this outcome may be limited clinically due to pleiotropic effects on key pathogenicity traits. Moreover, our data identify potential mutational routes to resistance that should be considered in genomic surveillance.
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Affiliation(s)
- Jessica E Buddle
- Molecular Microbiology, School of Biosciences, University of Sheffield, Sheffield, United Kingdom
| | - Lucy M Thompson
- Molecular Microbiology, School of Biosciences, University of Sheffield, Sheffield, United Kingdom
| | - Anne S Williams
- Department of Physics and Astronomy, University of Sheffield, Sheffield, United Kingdom
| | - Rosanna C T Wright
- Division of Evolution and Genomic Sciences, University of Manchester, Manchester, United Kingdom
| | - William M Durham
- Department of Physics and Astronomy, University of Sheffield, Sheffield, United Kingdom
| | - Claire E Turner
- Molecular Microbiology, School of Biosciences, University of Sheffield, Sheffield, United Kingdom
| | - Roy R Chaudhuri
- Molecular Microbiology, School of Biosciences, University of Sheffield, Sheffield, United Kingdom
| | - Michael A Brockhurst
- Division of Evolution and Genomic Sciences, University of Manchester, Manchester, United Kingdom
| | - Robert P Fagan
- Molecular Microbiology, School of Biosciences, University of Sheffield, Sheffield, United Kingdom
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3
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Cassona CP, Ramalhete S, Amara K, Candela T, Kansau I, Denève-Larrazet C, Janoir-Jouveshomme C, Mota LJ, Dupuy B, Serrano M, Henriques AO. Spores of Clostridioides difficile are toxin delivery vehicles. Commun Biol 2024; 7:839. [PMID: 38987278 PMCID: PMC11237016 DOI: 10.1038/s42003-024-06521-x] [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: 05/08/2023] [Accepted: 06/28/2024] [Indexed: 07/12/2024] Open
Abstract
Clostridioides difficile causes a wide range of intestinal diseases through the action of two main cytotoxins, TcdA and TcdB. Ingested spores germinate in the intestine establishing a population of cells that produce toxins and spores. The pathogenicity locus, PaLoc, comprises several genes, including those coding for TcdA/B, for the holin-like TcdE protein, and for TcdR, an auto-regulatory RNA polymerase sigma factor essential for tcdA/B and tcdE expression. Here we show that tcdR, tcdA, tcdB and tcdE are expressed in a fraction of the sporulating cells, in either the whole sporangium or in the forespore. The whole sporangium pattern is due to protracted expression initiated in vegetative cells by σD, which primes the TcdR auto-regulatory loop. In contrast, the forespore-specific regulatory proteins σG and SpoVT control TcdR production and tcdA/tcdB and tcdE expression in this cell. We detected TcdA at the spore surface, and we show that wild type and ΔtcdA or ΔtcdB spores but not ΔtcdR or ΔtcdA/ΔtcdB spores are cytopathic against HT29 and Vero cells, indicating that spores may serve as toxin-delivery vehicles. Since the addition of TcdA and TcdB enhance binding of spores to epithelial cells, this effect may occur independently of toxin production by vegetative cells.
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Affiliation(s)
- Carolina P Cassona
- Instituto de Tecnologia Química e Biológica, NOVA University Lisbon, Oeiras, Portugal
| | - Sara Ramalhete
- Instituto de Tecnologia Química e Biológica, NOVA University Lisbon, Oeiras, Portugal
| | - Khira Amara
- Instituto de Tecnologia Química e Biológica, NOVA University Lisbon, Oeiras, Portugal
| | - Thomas Candela
- Micalis Institute, Université Paris-Saclay, INRAE, AgroParisTech, Jouy-en-Josas, France
| | - Imad Kansau
- Micalis Institute, Université Paris-Saclay, INRAE, AgroParisTech, Jouy-en-Josas, France
| | | | | | - Luís Jaime Mota
- Associate Laboratory i4HB, Institute for Health and Bioeconomy, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
- UCIBIO, Applied Molecular Biosciences Unit, Department of Life Sciences, NOVA School of Science and Technology, NOVA University Lisbon, Caparica, Portugal
| | - Bruno Dupuy
- Institut Pasteur, Université Paris-Cité, UMR-CNRS 6047, Laboratoire Pathogenèse des Bactéries Anaérobies, F-75015, Paris, France
| | - Mónica Serrano
- Instituto de Tecnologia Química e Biológica, NOVA University Lisbon, Oeiras, Portugal
| | - Adriano O Henriques
- Instituto de Tecnologia Química e Biológica, NOVA University Lisbon, Oeiras, Portugal.
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Behlendorf C, Diwo M, Neumann-Schaal M, Fuchs M, Körner D, Jänsch L, Faber F, Blankenfeldt W. Formation of the pyruvoyl-dependent proline reductase Prd from Clostridioides difficile requires the maturation enzyme PrdH. PNAS NEXUS 2024; 3:pgae249. [PMID: 38979079 PMCID: PMC11229817 DOI: 10.1093/pnasnexus/pgae249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Accepted: 06/09/2024] [Indexed: 07/10/2024]
Abstract
Stickland fermentation, the coupled oxidation and reduction of amino acid pairs, is a major pathway for obtaining energy in the nosocomial bacterium Clostridioides difficile. D-proline is the preferred substrate for the reductive path, making it not only a key component of the general metabolism but also impacting on the expression of the clostridial toxins TcdA and TcdB. D-proline reduction is catalyzed by the proline reductase Prd, which belongs to the pyruvoyl-dependent enzymes. These enzymes are translated as inactive proenzymes and require subsequent processing to install the covalently bound pyruvate. Whereas pyruvoyl formation by intramolecular serinolysis has been studied in unrelated enzymes, details about pyruvoyl generation by cysteinolysis as in Prd are lacking. Here, we show that Prd maturation requires a small dimeric protein that we have named PrdH. PrdH (CD630_32430) is co-encoded with the PrdA and PrdB subunits of Prd and also found in species producing similar reductases. By producing stable variants of PrdA and PrdB, we demonstrate that PrdH-mediated cleavage and pyruvoyl formation in the PrdA subunit requires PrdB, which can be harnessed to produce active recombinant Prd for subsequent analyses. We further created PrdA- and PrdH-mutants to get insight into the interaction of the components and into the processing reaction itself. Finally, we show that deletion of prdH renders C. difficile insensitive to proline concentrations in culture media, suggesting that this processing factor is essential for proline utilization. Due to the link between Stickland fermentation and pathogenesis, we suggest PrdH may be an attractive target for drug development.
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Affiliation(s)
- Christian Behlendorf
- Department Structure and Function of Proteins, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Maurice Diwo
- Department Structure and Function of Proteins, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Meina Neumann-Schaal
- Leibniz-Institut DSMZ-Deutsche Sammlung von Mikroorganismen und Zellkulturen GmbH, 38124 Braunschweig, Germany
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, 38106 Braunschweig, Germany
| | - Manuela Fuchs
- Helmholtz Centre for Infection Research (HZI), Helmholtz Institute for RNA-based Infection Research (HIRI), 97080 Würzburg, Germany
- Faculty of Medicine, Institute for Molecular Infection Biology (IMIB), Julius-Maximilians-University of Würzburg (JMU), 97080 Würzburg, Germany
| | - Dominik Körner
- Cellular Proteomics, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Lothar Jänsch
- Cellular Proteomics, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - Franziska Faber
- Helmholtz Centre for Infection Research (HZI), Helmholtz Institute for RNA-based Infection Research (HIRI), 97080 Würzburg, Germany
- Faculty of Medicine, Institute for Molecular Infection Biology (IMIB), Julius-Maximilians-University of Würzburg (JMU), 97080 Würzburg, Germany
| | - Wulf Blankenfeldt
- Department Structure and Function of Proteins, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
- Institute for Biochemistry, Biotechnology and Bioinformatics, Technische Universität Braunschweig, 38106 Braunschweig, Germany
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Zhang S, Ma C, Zhang H, Zhao C, Guo R, Liu J, Wang J, Yuan J, Jia K, Wu A, Chen Y, Lei J. Toxin genotypes, antibiotic resistance and their correlations in Clostridioides difficile isolated from hospitals in Xi'an, China. BMC Microbiol 2024; 24:177. [PMID: 38783194 PMCID: PMC11112860 DOI: 10.1186/s12866-024-03327-z] [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: 04/13/2023] [Accepted: 05/10/2024] [Indexed: 05/25/2024] Open
Abstract
BACKGROUND Clostridioides difficile is the main pathogen of antimicrobial-associated diarrhoea and health care facility-associated infectious diarrhoea. This study aimed to investigate the prevalence, toxin genotypes, and antibiotic resistance of C. difficile among hospitalized patients in Xi'an, China. RESULTS We isolated and cultured 156 strains of C. difficile, representing 12.67% of the 1231 inpatient stool samples collected. Among the isolates, tcdA + B + strains were predominant, accounting for 78.2% (122/156), followed by 27 tcdA-B + strains (27/156, 17.3%) and 6 binary toxin gene-positive strains. The positive rates of three regulatory genes, tcdC, tcdR, and tcdE, were 89.1% (139/156), 96.8% (151/156), and 100%, respectively. All isolates were sensitive to metronidazole, and the resistance rates to clindamycin and cephalosporins were also high. Six strains were found to be resistant to vancomycin. CONCLUSION Currently, the prevalence rate of C. difficile infection (CDI) in Xi'an is 12.67% (156/1231), with the major toxin genotype of the isolates being tcdA + tcdB + cdtA-/B-. Metronidazole and vancomycin were still effective drugs for the treatment of CDI, but we should pay attention to antibiotic management and epidemiological surveillance of CDI.
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Affiliation(s)
- Sukai Zhang
- Clinical Medicine Class of 2019, Xi'an Jiaotong University, Xi'an, China
| | - Chen Ma
- Department of Clinical Laboratory, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Haiyue Zhang
- Clinical Medicine Class of 2019, Xi'an Jiaotong University, Xi'an, China
| | - Congcong Zhao
- Clinical Medicine Class of 2019, Xi'an Jiaotong University, Xi'an, China
| | - Ruibing Guo
- Clinical Medicine Class of 2019, Xi'an Jiaotong University, Xi'an, China
| | - Jiahao Liu
- Clinical Medicine Class of 2019, Xi'an Jiaotong University, Xi'an, China
| | - Jing Wang
- Department of Clinical Laboratory, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Jing Yuan
- Department of Clinical Laboratory, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China
| | - Kai Jia
- Xi'an Children's Hospital, Xi'an, China
| | | | - Yanjiong Chen
- Department of Immunology and Pathogenic Biology, College of Basic Medicine, Xi'an Jiaotong University Health Science Center, Xi'an, China
| | - Jin'e Lei
- Department of Clinical Laboratory, The First Affiliated Hospital of Xi'an Jiaotong University, Xi'an, China.
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Gong JJ, Huang IH, Su MSW, Xie SX, Liu WY, Huang CR, Hung YP, Wu SR, Tsai PJ, Ko WC, Chen JW. Phage transcriptional regulator X (PtrX)-mediated augmentation of toxin production and virulence in Clostridioides difficile strain R20291. Microbiol Res 2024; 280:127576. [PMID: 38183754 DOI: 10.1016/j.micres.2023.127576] [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: 10/03/2023] [Revised: 11/24/2023] [Accepted: 12/13/2023] [Indexed: 01/08/2024]
Abstract
Clostridioides difficile is a Gram-positive, anaerobic, and spore-forming bacterial member of the human gut microbiome. The primary virulence factors of C. difficile are toxin A and toxin B. These toxins damage the cell cytoskeleton and cause various diseases, from diarrhea to severe pseudomembranous colitis. Evidence suggests that bacteriophages can regulate the expression of the pathogenicity locus (PaLoc) genes of C. difficile. We previously demonstrated that the genome of the C. difficile RT027 strain NCKUH-21 contains a prophage-like DNA sequence, which was found to be markedly similar to that of the φCD38-2 phage. In the present study, we investigated the mechanisms underlying the φNCKUH-21-mediated regulation of the pathogenicity and the PaLoc genes expression in the lysogenized C. difficile strain R20291. The carriage of φNCKUH-21 in R20291 cells substantially enhanced toxin production, bacterial motility, biofilm formation, and spore germination in vitro. Subsequent mouse studies revealed that the lysogenized R20291 strain caused a more severe infection than the wild-type strain. We screened three φNCKUH-21 genes encoding DNA-binding proteins to check their effects on PaLoc genes expression. The overexpression of NCKUH-21_03890, annotated as a transcriptional regulator (phage transcriptional regulator X, PtrX), considerably enhanced toxin production, biofilm formation, and bacterial motility of R20291. Transcriptome analysis further confirmed that the overexpression of ptrX led to the upregulation of the expression of toxin genes, flagellar genes, and csrA. In the ptrX-overexpressing R20291 strain, PtrX influenced the expression of flagellar genes and the sigma factor gene sigD, possibly through an increased flagellar phase ON configuration ratio.
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Affiliation(s)
- Jun-Jia Gong
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - I-Hsiu Huang
- Department of Biochemistry and Microbiology, Oklahoma State University Center for Health Sciences, Tulsa, OK 74107, USA
| | - Marcia Shu-Wei Su
- Department of Biotechnology and Laboratory Science in Medicine, National Yang Ming Chiao Tung University, Taipei, Taiwan
| | - Si-Xuan Xie
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Wei-Yong Liu
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Cheng-Rung Huang
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan
| | - Yuan-Pin Hung
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan, Taiwan; 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
| | - Shang-Rung Wu
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Institute of Oral 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; Department of Pathology, National Cheng Kung University Hospital, Tainan, Taiwan; Center for Clinical Medicine Research, National Cheng Kung University Hospital, 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
| | - Jenn-Wei Chen
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan, Taiwan; Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan, Taiwan.
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Sapa D, Brosse A, Coullon H, Péan de Ponfilly G, Candela T, Le Monnier A. A Streamlined Method to Obtain Biologically Active TcdA and TcdB Toxins from Clostridioides difficile. Toxins (Basel) 2024; 16:38. [PMID: 38251254 PMCID: PMC10821508 DOI: 10.3390/toxins16010038] [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: 09/25/2023] [Revised: 12/15/2023] [Accepted: 12/30/2023] [Indexed: 01/23/2024] Open
Abstract
The major virulence factors of Clostridioides difficile (C. difficile) are enterotoxins A (TcdA) and B (TcdB). The study of toxins is a crucial step in exploring the virulence of this pathogen. Currently, the toxin purification process is either laborious and time-consuming in C. difficile or performed in heterologous hosts. Therefore, we propose a streamlined method to obtain functional toxins in C. difficile. Two C. difficile strains were generated, each harboring a sequence encoding a His-tag at the 3' end of C. difficile 630∆erm tcdA or tcdB genes. Each toxin gene is expressed using the Ptet promoter, which is inducible by anhydro-tetracycline. The obtained purification yields were 0.28 mg and 0.1 mg per liter for rTcdA and rTcdB, respectively. In this study, we successfully developed a simple routine method that allows the production and purification of biologically active rTcdA and rTcdB toxins with similar activities compared to native toxins.
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Affiliation(s)
- Diane Sapa
- Micalis Institute, Université Paris-Saclay, INRAE, AgroParisTech, 78350 Jouy-en-Josas, France; (D.S.); (H.C.); (G.P.d.P.); (T.C.); (A.L.M.)
| | - Anaïs Brosse
- Micalis Institute, Université Paris-Saclay, INRAE, AgroParisTech, 78350 Jouy-en-Josas, France; (D.S.); (H.C.); (G.P.d.P.); (T.C.); (A.L.M.)
| | - Héloïse Coullon
- Micalis Institute, Université Paris-Saclay, INRAE, AgroParisTech, 78350 Jouy-en-Josas, France; (D.S.); (H.C.); (G.P.d.P.); (T.C.); (A.L.M.)
| | - Gauthier Péan de Ponfilly
- Micalis Institute, Université Paris-Saclay, INRAE, AgroParisTech, 78350 Jouy-en-Josas, France; (D.S.); (H.C.); (G.P.d.P.); (T.C.); (A.L.M.)
- Service de Microbiologie Clinique, GH Paris Saint-Joseph, 75674 Paris, France
| | - Thomas Candela
- Micalis Institute, Université Paris-Saclay, INRAE, AgroParisTech, 78350 Jouy-en-Josas, France; (D.S.); (H.C.); (G.P.d.P.); (T.C.); (A.L.M.)
| | - Alban Le Monnier
- Micalis Institute, Université Paris-Saclay, INRAE, AgroParisTech, 78350 Jouy-en-Josas, France; (D.S.); (H.C.); (G.P.d.P.); (T.C.); (A.L.M.)
- Service de Microbiologie Clinique, GH Paris Saint-Joseph, 75674 Paris, France
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Couturier J, Davies K, Barbut F. Ribotypes and New Virulent Strains Across Europe. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2024; 1435:151-168. [PMID: 38175475 DOI: 10.1007/978-3-031-42108-2_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/05/2024]
Abstract
Clostridioides (formerly Clostridium) difficile is a major bacterial cause of post-antibiotic diarrhoea. The epidemiology of C. difficile infections (CDIs) has dramatically changed since the early 2000s, with an increasing incidence and severity across Europe. This trend is partly due to the emergence and rapid worldwide spread of the hypervirulent and epidemic PCR ribotype 027. Profiles of patients with CDI have also evolved, with description of community-acquired (CA) infections in patients with no traditional risk factors for CDI. However, epidemiological studies indicated that some European countries have successfully controlled the dissemination of the 027 clone whereas other countries reported the emergence of other virulent or unusual strains. The aims of this review are to summarize the current European CDI epidemiology and to describe the new virulent C. difficile strains circulating in Europe, as well as other potential emerging strains described elsewhere. Standardized typing methods and surveillance programmes are mandatory for a better understanding and monitoring of CDI in Europe.
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Affiliation(s)
- Jeanne Couturier
- National Reference Laboratory for C. difficile, Hôpital Saint-Antoine, Paris, France.
- Université Paris Cité, UMR INSERM 1139, Paris, France.
| | - Kerrie Davies
- Healthcare Associated Infections Research Group, Leeds Teaching Hospitals NHS Trust and University of Leeds, Leeds, UK
- European Society of Clinical Microbiology and Infectious Diseases (ESCMID) study group for Clostridioides difficile (ESGCD), Basel, Switzerland
| | - Frédéric Barbut
- National Reference Laboratory for C. difficile, Hôpital Saint-Antoine, Paris, France
- Université Paris Cité, UMR INSERM 1139, Paris, France
- European Society of Clinical Microbiology and Infectious Diseases (ESCMID) study group for Clostridioides difficile (ESGCD), Basel, Switzerland
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9
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Lin Q, Li Z, Ke H, Fei J, Zhang T, Wang P, Chen Y. Linked mutations within the pathogenicity locus of Clostridioides difficile increase virulence. Infect Dis (Lond) 2023; 55:847-856. [PMID: 37615633 DOI: 10.1080/23744235.2023.2249551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Accepted: 08/14/2023] [Indexed: 08/25/2023] Open
Abstract
BACKGROUND The clinical manifestations of Clostridioides difficile infections range from diarrhoea to pseudomembranous colitis (PMC) and death. We evaluated the association between gene content in C. difficile clinical isolates and disease severity. METHODS Fifty-three C. difficile isolates were subjected to Sanger sequencing, clinical data were used to analyse the association of gene content with disease severity, and 83 non-duplicate isolates were collected to confirm the results. Virulence was further examined by functional in vitro and in vivo experiments. RESULTS Among the 53 C. difficile isolates, ribotypes 017 (n = 9, 17.0%) and 012 (n = 8, 15.1%) were predominant. Fifteen strains exhibited a correlation between mutations of pathogenicity locus genes (tcdB, tcdC, tcdR, and tcdE) and were named linked-mutation strains. Ribotypes are not associated with clinical PMC and Linked-mutation strains. The proportion of patients with PMC was higher in the group infected with linked-mutation strains than in the non-linked-mutation group (57.14% vs. 0%, p < 0.001). The linked-mutation rate of C. difficile was higher in patients with PMC than in patients without PMC (89.47% vs. 7.8%, p < 0.0001). Linked-mutation strains showed greater cytotoxicity in vitro and caused more severe tissue damage in a mouse model. CONCLUSIONS Linked-mutation strains are associated with high virulence and PMC development. This result will help monitor the clinical prognosis of C. difficile infection and provide key insights for developing therapeutic targets and monoclonal antibodies.
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Affiliation(s)
- Qianyun Lin
- Department of Gastroenterology, Beijing Friendship Hospital, Capital Medical University, Beijing, China
| | - Zitong Li
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Haoran Ke
- Hepatology Unit, Department of Infectious Diseases, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Jiaxi Fei
- Graceland Medical Center, the, Sixth Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Ting Zhang
- Department of Gastroenterology, the Third Affiliated Hospital of Southern Medical University, Guangzhou, China
| | - Pu Wang
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, China
| | - Ye Chen
- Guangdong Provincial Key Laboratory of Gastroenterology, Department of Gastroenterology, Nanfang Hospital, Southern Medical University, Guangzhou, China
- Integrative Microecology Center, Department of Gastroenterology, Shenzhen Hospital, Southern Medical University, Shenzhen, China
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10
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DiBenedetto NV, Oberkampf M, Cersosimo L, Yeliseyev V, Bry L, Peltier J, Dupuy B. The TcdE holin drives toxin secretion and virulence in Clostridioides difficile. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.09.16.558055. [PMID: 37745472 PMCID: PMC10516005 DOI: 10.1101/2023.09.16.558055] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Clostridioides difficile is the leading cause of healthcare associated infections. The Pathogenicity Locus (PaLoc) toxins TcdA and TcdB promote host disease. These toxins lack canonical N-terminal signal sequences for translocation across the bacterial membrane, suggesting alternate mechanisms of release, which have included targeted secretion and passive release from cell lysis. While the holin TcdE has been implicated in TcdA and TcdB release, its role in vivo remains unknown. Here, we show profound reductions in toxin secretion in ΔtcdE mutants in the highly virulent strains UK1 (epidemic ribotype 027, Clade 3) and VPI10463 (ribotype 087, Clade 1). Notably, tcdE deletion in either strain rescued highly susceptible gnotobiotic mice from lethal infection by reducing acute extracellular toxin to undetectable levels, limiting mucosal damage, and enabling long-term survival, in spite of continued toxin gene expression in ΔtcdE mutants. Our findings confirm TcdE's critical functions in vivo for toxin secretion and C. difficile virulence.
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Affiliation(s)
- N V DiBenedetto
- Massachusetts Host-Microbiome Center, Dept. Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - M Oberkampf
- Institut Pasteur, Université Paris-Cité, UMR-CNRS 6047, Laboratoire Pathogenèse des Bactéries Anaérobies, F-75015 Paris, France
| | - L Cersosimo
- Massachusetts Host-Microbiome Center, Dept. Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - V Yeliseyev
- Massachusetts Host-Microbiome Center, Dept. Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - L Bry
- Massachusetts Host-Microbiome Center, Dept. Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - J Peltier
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS, Université Paris-Saclay, Gif-sur-Yvette, France
| | - B Dupuy
- Institut Pasteur, Université Paris-Cité, UMR-CNRS 6047, Laboratoire Pathogenèse des Bactéries Anaérobies, F-75015 Paris, France
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11
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Marsh JW, Kirk C, Ley RE. Toward Microbiome Engineering: Expanding the Repertoire of Genetically Tractable Members of the Human Gut Microbiome. Annu Rev Microbiol 2023; 77:427-449. [PMID: 37339736 DOI: 10.1146/annurev-micro-032421-112304] [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] [Indexed: 06/22/2023]
Abstract
Genetic manipulation is necessary to interrogate the functions of microbes in their environments, such as the human gut microbiome. Yet, the vast majority of human gut microbiome species are not genetically tractable. Here, we review the hurdles to seizing genetic control of more species. We address the barriers preventing the application of genetic techniques to gut microbes and report on genetic systems currently under development. While methods aimed at genetically transforming many species simultaneously in situ show promise, they are unable to overcome many of the same challenges that exist for individual microbes. Unless a major conceptual breakthrough emerges, the genetic tractability of the microbiome will remain an arduous task. Increasing the list of genetically tractable organisms from the human gut remains one of the highest priorities for microbiome research and will provide the foundation for microbiome engineering.
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Affiliation(s)
- James W Marsh
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany;
| | - Christian Kirk
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany;
| | - Ruth E Ley
- Department of Microbiome Science, Max Planck Institute for Biology, Tübingen, Germany;
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12
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Dicks LMT. Biofilm Formation of Clostridioides difficile, Toxin Production and Alternatives to Conventional Antibiotics in the Treatment of CDI. Microorganisms 2023; 11:2161. [PMID: 37764005 PMCID: PMC10534356 DOI: 10.3390/microorganisms11092161] [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: 06/29/2023] [Revised: 08/16/2023] [Accepted: 08/24/2023] [Indexed: 09/29/2023] Open
Abstract
Clostridioides difficile is considered a nosocomial pathogen that flares up in patients exposed to antibiotic treatment. However, four out of ten patients diagnosed with C. difficile infection (CDI) acquired the infection from non-hospitalized individuals, many of whom have not been treated with antibiotics. Treatment of recurrent CDI (rCDI) with antibiotics, especially vancomycin (VAN) and metronidazole (MNZ), increases the risk of experiencing a relapse by as much as 70%. Fidaxomicin, on the other hand, proved more effective than VAN and MNZ by preventing the initial transcription of RNA toxin genes. Alternative forms of treatment include quorum quenching (QQ) that blocks toxin synthesis, binding of small anion molecules such as tolevamer to toxins, monoclonal antibodies, such as bezlotoxumab and actoxumab, bacteriophage therapy, probiotics, and fecal microbial transplants (FMTs). This review summarizes factors that affect the colonization of C. difficile and the pathogenicity of toxins TcdA and TcdB. The different approaches experimented with in the destruction of C. difficile and treatment of CDI are evaluated.
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Affiliation(s)
- Leon M T Dicks
- Department of Microbiology, Stellenbosch University, Stellenbosch 7600, South Africa
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13
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Dupuy B. Regulation of Clostridial Toxin Gene Expression: A Pasteurian Tradition. Toxins (Basel) 2023; 15:413. [PMID: 37505682 PMCID: PMC10467148 DOI: 10.3390/toxins15070413] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 06/13/2023] [Accepted: 06/19/2023] [Indexed: 07/29/2023] Open
Abstract
The alarming symptoms attributed to several potent clostridial toxins enabled the early identification of the causative agent of tetanus, botulism, and gas gangrene diseases, which belongs to the most famous species of pathogenic clostridia. Although Clostridioides difficile was identified early in the 20th century as producing important toxins, it was identified only 40 years later as the causative agent of important nosocomial diseases upon the advent of antibiotic therapies in hospital settings. Today, C. difficile is a leading public health issue, as it is the major cause of antibiotic-associated diarrhea in adults. In particular, severe symptoms within the spectrum of C. difficile infections are directly related to the levels of toxins produced in the host. This highlights the importance of understanding the regulation of toxin synthesis in the pathogenicity process of C. difficile, whose regulatory factors in response to the gut environment were first identified at the Institut Pasteur. Subsequently, the work of other groups in the field contributed to further deciphering the complex mechanisms controlling toxin production triggered by the intestinal dysbiosis states during infection. This review summarizes the Pasteurian contribution to clostridial toxin regulation studies.
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Affiliation(s)
- Bruno Dupuy
- Institut Pasteur, Université Paris-Cité, UMR-CNRS 6047, Laboratoire Pathogenèse des Bactéries Anaérobies, F-75015 Paris, France
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14
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Omorotionmwan BB, Wang H, Baker JP, Gizynski K, Yoo M, Akaluka C, Zhang Y, Minton NP. Chromosomal engineering of inducible isopropanol- butanol-ethanol production in Clostridium acetobutylicum. Front Bioeng Biotechnol 2023; 11:1218099. [PMID: 37397966 PMCID: PMC10312008 DOI: 10.3389/fbioe.2023.1218099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2023] [Accepted: 06/05/2023] [Indexed: 07/04/2023] Open
Abstract
The use of environmentally damaging petrochemical feedstocks can be displaced by fermentation processes based on engineered microbial chassis that recycle biomass-derived carbon into chemicals and fuels. The stable retention of introduced genes, designed to extend product range and/or increase productivity, is essential. Accordingly, we have created multiply marked auxotrophic strains of Clostridium acetobutylicum that provide distinct loci (pyrE, argH, purD, pheA) at which heterologous genes can be rapidly integrated using allele-coupled exchange (ACE). For each locus, ACE-mediated insertion is conveniently selected on the basis of the restoration of prototrophy on minimal media. The Clostridioides difficile gene (tcdR) encoding an orthogonal sigma factor (TcdR) was integrated at the pyrE locus under the control of the lactose-inducible, bgaR::PbgaL promoter to allow the simultaneous control of genes/operons inserted at other disparate loci (purD and pheA) that had been placed under the control of the PtcdB promoter. In control experiments, dose-dependent expression of a catP reporter gene was observed with increasing lactose concentration. At the highest doses tested (10 mM) the level of expression was over 10-fold higher than if catP was placed directly under the control of bgaR::PbgaL and over 2-fold greater than achieved using the strong Pfdx promoter of the Clostridium sporogenes ferredoxin gene. The utility of the system was demonstrated in the production of isopropanol by the C. acetobutylicum strain carrying an integrated copy of tcdR following the insertion of a synthetic acetone operon (ctfA/B, adc) at the purD locus and a gene (sadh) encoding a secondary dehydrogenase at pheA. Lactose induction (10 mM) resulted in the production of 4.4 g/L isopropanol and 19.8 g/L Isopropanol-Butanol-Ethanol mixture.
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Affiliation(s)
- Bunmi B. Omorotionmwan
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), Biodiscovery Institute, School of Life Sciences, The University of Nottingham, Nottingham, United Kingdom
| | - Hengzheng Wang
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), Biodiscovery Institute, School of Life Sciences, The University of Nottingham, Nottingham, United Kingdom
| | - Jonathan P. Baker
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), Biodiscovery Institute, School of Life Sciences, The University of Nottingham, Nottingham, United Kingdom
| | - Krzysztof Gizynski
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), Biodiscovery Institute, School of Life Sciences, The University of Nottingham, Nottingham, United Kingdom
| | - Minyeong Yoo
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), Biodiscovery Institute, School of Life Sciences, The University of Nottingham, Nottingham, United Kingdom
| | - Cynthia Akaluka
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), Biodiscovery Institute, School of Life Sciences, The University of Nottingham, Nottingham, United Kingdom
| | - Ying Zhang
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), Biodiscovery Institute, School of Life Sciences, The University of Nottingham, Nottingham, United Kingdom
| | - Nigel P. Minton
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), Biodiscovery Institute, School of Life Sciences, The University of Nottingham, Nottingham, United Kingdom
- NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham, United Kingdom
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15
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Ormsby MJ, Vaz F, Kirk JA, Barwinska-Sendra A, Hallam JC, Lanzoni-Mangutchi P, Cole J, Chaudhuri RR, Salgado PS, Fagan RP, Douce GR. An intact S-layer is advantageous to Clostridioides difficile within the host. PLoS Pathog 2023; 19:e1011015. [PMID: 37384772 PMCID: PMC10310040 DOI: 10.1371/journal.ppat.1011015] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 05/31/2023] [Indexed: 07/01/2023] Open
Abstract
Clostridioides difficile is responsible for substantial morbidity and mortality in antibiotically-treated, hospitalised, elderly patients, in which toxin production correlates with diarrhoeal disease. While the function of these toxins has been studied in detail, the contribution of other factors, including the paracrystalline surface layer (S-layer), to disease is less well understood. Here, we highlight the essentiality of the S-layer in vivo by reporting the recovery of S-layer variants, following infection with the S-layer-null strain, FM2.5. These variants carry either correction of the original point mutation, or sequence modifications which restored the reading frame, and translation of slpA. Selection of these variant clones was rapid in vivo, and independent of toxin production, with up to 90% of the recovered C. difficile population encoding modified slpA sequence within 24 h post infection. Two variants, subsequently named FM2.5varA and FM2.5varB, were selected for study in greater detail. Structural determination of SlpA from FM2.5varB indicated an alteration in the orientation of protein domains, resulting in a reorganisation of the lattice assembly, and changes in interacting interfaces, which might alter function. Interestingly, variant FM2.5varB displayed an attenuated, FM2.5-like phenotype in vivo compared to FM2.5varA, which caused disease severity more comparable to that of R20291. Comparative RNA sequencing (RNA-Seq) analysis of in vitro grown isolates revealed large changes in gene expression between R20291 and FM2.5. Downregulation of tcdA/tcdB and several genes associated with sporulation and cell wall integrity may account for the reported attenuated phenotype of FM2.5 in vivo. RNA-seq data correlated well with disease severity with the more virulent variant, FM2.5varA, showing s similar profile of gene expression to R20291 in vitro, while the attenuated FM2.5varB showed downregulation of many of the same virulence associated traits as FM2.5. Cumulatively, these data add to a growing body of evidence that the S-layer contributes to C. difficile pathogenesis and disease severity.
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Affiliation(s)
- Michael J. Ormsby
- School of Infection and Immunity, College of Medical, Veterinary & Life Sciences, University of Glasgow, Scotland, United Kingdom
| | - Filipa Vaz
- School of Infection and Immunity, College of Medical, Veterinary & Life Sciences, University of Glasgow, Scotland, United Kingdom
| | - Joseph A. Kirk
- Molecular Microbiology, School of Biosciences, University of Sheffield, England, United Kingdom
| | - Anna Barwinska-Sendra
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, England, United Kingdom
| | - Jennifer C. Hallam
- School of Infection and Immunity, College of Medical, Veterinary & Life Sciences, University of Glasgow, Scotland, United Kingdom
| | - Paola Lanzoni-Mangutchi
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, England, United Kingdom
| | - John Cole
- School of Infection and Immunity, College of Medical, Veterinary & Life Sciences, University of Glasgow, Scotland, United Kingdom
| | - Roy R. Chaudhuri
- Molecular Microbiology, School of Biosciences, University of Sheffield, England, United Kingdom
| | - Paula S. Salgado
- Biosciences Institute, Faculty of Medical Sciences, Newcastle University, England, United Kingdom
| | - Robert P. Fagan
- Molecular Microbiology, School of Biosciences, University of Sheffield, England, United Kingdom
| | - Gillian R Douce
- School of Infection and Immunity, College of Medical, Veterinary & Life Sciences, University of Glasgow, Scotland, United Kingdom
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16
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Yip C, Phan JR, Abel-Santos E. Mechanism of germination inhibition of Clostridioides difficile spores by an aniline substituted cholate derivative (CaPA). J Antibiot (Tokyo) 2023; 76:335-345. [PMID: 37016015 PMCID: PMC10406169 DOI: 10.1038/s41429-023-00612-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Revised: 02/28/2023] [Accepted: 03/07/2023] [Indexed: 04/06/2023]
Abstract
Clostridioides difficile infection (CDI) is the major identifiable cause of antibiotic-associated diarrhea and has been declared an urgent threat by the CDC. C. difficile forms dormant and resistant spores that serve as infectious vehicles for CDI. To cause disease, C. difficile spores recognize taurocholate and glycine to trigger the germination process. In contrast to other sporulating bacteria, C. difficile spores are postulated to use a protease complex, CspABC, to recognize its germinants. Since spore germination is required for infection, we have developed anti-germination approaches for CDI prophylaxis. Previously, the bile salt analog CaPA (an aniline-substituted cholic acid) was shown to block spore germination and protect rodents from CDI caused by multiple C. difficile strains and isolates. In this study, we found that CaPA is an alternative substrate inhibitor of C. difficile spore germination. By competing with taurocholate for binding, CaPA delays C. difficile spore germination and reduces spore viability, thus diminishing the number of outgrowing vegetative bacteria. We hypothesize that the reduction of toxin-producing bacterial burden explains CaPA's protective activity against murine CDI. Previous data combined with our results suggests that CaPA binds tightly to C. difficile spores in a CspC-dependent manner and irreversibly traps spores in an alternative, time-delayed, and low yield germination pathway. Our results are also consistent with kinetic data suggesting the existence of at least two distinct bile salt binding sites in C. difficile spores.
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Affiliation(s)
- Christopher Yip
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, NV, 89154, USA
| | - Jacqueline R Phan
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, NV, 89154, USA
| | - Ernesto Abel-Santos
- Department of Chemistry and Biochemistry, University of Nevada, Las Vegas, NV, 89154, USA.
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17
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Fuchs M, Lamm-Schmidt V, Lenče T, Sulzer J, Bublitz A, Wackenreuter J, Gerovac M, Strowig T, Faber F. A network of small RNAs regulates sporulation initiation in Clostridioides difficile. EMBO J 2023:e112858. [PMID: 37140366 DOI: 10.15252/embj.2022112858] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2022] [Revised: 03/23/2023] [Accepted: 03/29/2023] [Indexed: 05/05/2023] Open
Abstract
The obligate anaerobic, enteric pathogen Clostridioides difficile persists in the intestinal tract by forming antibiotic-resistant endospores that contribute to relapsing and recurrent infections. Despite the importance of sporulation for C. difficile pathogenesis, environmental cues and molecular mechanisms that regulate sporulation initiation remain ill-defined. Here, by using RIL-seq to globally capture the Hfq-dependent RNA-RNA interactome, we discovered a network of small RNAs that bind to mRNAs encoding sporulation-related genes. We show that two of these small RNAs, SpoX and SpoY, regulate translation of the master regulator of sporulation, Spo0A, in an opposing manner, which ultimately leads to altered sporulation rates. Infection of antibiotic-treated mice with SpoX and SpoY deletion mutants revealed a global effect on gut colonization and intestinal sporulation. Our work uncovers an elaborate RNA-RNA interactome controlling the physiology and virulence of C. difficile and identifies a complex post-transcriptional layer in the regulation of spore formation in this important human pathogen.
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Affiliation(s)
- Manuela Fuchs
- Helmholtz Centre for Infection Research (HZI), Helmholtz Institute for RNA-based Infection Research (HIRI), Würzburg, Germany
- Faculty of Medicine, Institute for Molecular Infection Biology (IMIB), Julius-Maximilians-University of Würzburg (JMU), Würzburg, Germany
| | - Vanessa Lamm-Schmidt
- Helmholtz Centre for Infection Research (HZI), Helmholtz Institute for RNA-based Infection Research (HIRI), Würzburg, Germany
- Faculty of Medicine, Institute for Molecular Infection Biology (IMIB), Julius-Maximilians-University of Würzburg (JMU), Würzburg, Germany
| | - Tina Lenče
- Faculty of Medicine, Institute for Molecular Infection Biology (IMIB), Julius-Maximilians-University of Würzburg (JMU), Würzburg, Germany
| | - Johannes Sulzer
- Faculty of Medicine, Institute for Molecular Infection Biology (IMIB), Julius-Maximilians-University of Würzburg (JMU), Würzburg, Germany
| | - Arne Bublitz
- Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
| | - Janet Wackenreuter
- Helmholtz Centre for Infection Research (HZI), Helmholtz Institute for RNA-based Infection Research (HIRI), Würzburg, Germany
| | - Milan Gerovac
- Faculty of Medicine, Institute for Molecular Infection Biology (IMIB), Julius-Maximilians-University of Würzburg (JMU), Würzburg, Germany
| | - Till Strowig
- Helmholtz Centre for Infection Research (HZI), Braunschweig, Germany
- German Center for Infection Research (DZIF), Hannover-Braunschweig, Germany
| | - Franziska Faber
- Helmholtz Centre for Infection Research (HZI), Helmholtz Institute for RNA-based Infection Research (HIRI), Würzburg, Germany
- Faculty of Medicine, Institute for Molecular Infection Biology (IMIB), Julius-Maximilians-University of Würzburg (JMU), Würzburg, Germany
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18
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Wang S, Ju X, Heuler J, Zhang K, Duan Z, Warnakulasuriya Patabendige HML, Zhao S, Sun X. Recombinant Fusion Protein Vaccine Containing Clostridioides difficile FliC and FliD Protects Mice against C. difficile Infection. Infect Immun 2023; 91:e0016922. [PMID: 36939332 PMCID: PMC10112125 DOI: 10.1128/iai.00169-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2022] [Accepted: 02/09/2023] [Indexed: 03/21/2023] Open
Abstract
Bacterial flagella are involved in infection through their roles in host cell adhesion, cell invasion, auto-agglutination, colonization, the formation of biofilms, and the regulation and secretion of nonflagellar bacterial proteins that are involved in the virulence process. In this study, we constructed a fusion protein vaccine (FliCD) containing the Clostridioides difficile flagellar proteins FliC and FliD. The immunization of mice with FliCD induced potent IgG and IgA antibody responses against FliCD, protected mice against C. difficile infection (CDI), and decreased the C. difficile spore and toxin levels in the feces after infection. Additionally, the anti-FliCD serum inhibited the binding of C. difficile vegetative cells to HCT8 cells. These results suggest that FliCD may represent an effective vaccine candidate against CDI.
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Affiliation(s)
- Shaohui Wang
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Xianghong Ju
- Department of Infectious Diseases and Global Health, Tufts University Cummings School of Veterinary Medicine, North Grafton, Massachusetts, USA
| | - Joshua Heuler
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Keshan Zhang
- Department of Infectious Diseases and Global Health, Tufts University Cummings School of Veterinary Medicine, North Grafton, Massachusetts, USA
| | - Zhibian Duan
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | | | - Song Zhao
- Department of Infectious Diseases and Global Health, Tufts University Cummings School of Veterinary Medicine, North Grafton, Massachusetts, USA
| | - Xingmin Sun
- Department of Molecular Medicine, Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
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19
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Development of an efficient ClosTron system for gene disruption in Ruminiclostridium papyrosolvens. Appl Microbiol Biotechnol 2023; 107:1801-1812. [PMID: 36808278 DOI: 10.1007/s00253-023-12427-1] [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: 10/11/2022] [Revised: 01/17/2023] [Accepted: 02/07/2023] [Indexed: 02/20/2023]
Abstract
Ruminiclostridium papyrosolvens is an anaerobic, mesophilic, and cellulolytic clostridia, promising consolidated bioprocessing (CBP) candidate for producing renewable green chemicals from cellulose, but its metabolic engineering is limited by lack of genetic tools. Here, we firstly employed the endogenous xylan-inducible promoter to control ClosTron system for gene disruption of R. papyrosolvens. The modified ClosTron can be easily transformed into R. papyrosolvens and specifically disrupt targeting genes. Furthermore, a counter selectable system based on uracil phosphoribosyl-transferase (Upp) was successfully established and introduced into the ClosTron system, which resulted in plasmid curing rapidly. Thus, the combination of xylan-inducible ClosTron and upp-based counter selectable system makes the gene disruption more efficient and convenient for successive gene disruption in R. papyrosolvens. KEY POINTS: • Limiting expression of LtrA enhanced the transformation of ClosTron plasmids in R. papyrosolvens. • DNA targeting specificity can be improved by precise management of the expression of LtrA. • Curing of ClosTron plasmids was achieved by introducing the upp-based counter selectable system.
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20
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Malet-Villemagne J, Yucheng L, Evanno L, Denis-Quanquin S, Hugonnet JE, Arthur M, Janoir C, Candela T. Polysaccharide II Surface Anchoring, the Achilles' Heel of Clostridioides difficile. Microbiol Spectr 2023; 11:e0422722. [PMID: 36815772 PMCID: PMC10100865 DOI: 10.1128/spectrum.04227-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Accepted: 01/25/2023] [Indexed: 02/24/2023] Open
Abstract
Cell wall glycopolymers (CWPGs) in Gram-positive bacteria have been reported to be involved in several bacterial processes. These polymers, pillars for proteins and S-layer, are essential for the bacterial surface setup, could be essential for growth, and, in pathogens, participate most often in virulence. CWGPs are covalently anchored to peptidoglycan by proteins that belong to the LytR-CpsA-PSr (LCP) family. This anchoring, important for growth, was reported as essential for some bacteria such as Bacillus subtilis, but the reason why CWGP anchoring is essential remains unknown. We studied LcpA and LcpB of Clostridioides difficile and showed that they have a redundant activity. To delete both lcp genes, we set up the first conditional-lethal mutant method in C. difficile and showed that polysaccharide II (PSII) anchoring at the bacterial surface is essential for C. difficile survival. In the conditional-lethal mutant, C. difficile morphology was impaired, suggesting that peptidoglycan synthesis was affected. Because Lcp proteins are transferring CWPGs from the C55-undecaprenyl phosphate (also needed in the peptidoglycan synthesis process), we assumed that there was competition between PSII and peptidoglycan synthesis pathways. We confirmed that UDP-MurNAc-pentapeptide precursor was accumulated, showing that peptidoglycan synthesis was blocked. Our results provide an explanation for the essentiality of PSII anchoring in C. difficile and suggest that the essentiality of the anchoring of CWPGs in other bacteria can also be explained by the blocking of peptidoglycan synthesis. To conclude, our results suggest that Lcps are potential new targets to combat C. difficile infection. IMPORTANCE Cell wall glycopolymers (CWGPs) in Gram-positive bacteria have been reported to be involved in several bacterial processes. CWGP anchoring to peptidoglycan is important for growth and virulence. We set up the first conditional-lethal mutant method in Clostridioides difficile to study LcpA and LcpB involved in the anchoring of CWPGs to peptidoglycan. This study offers new tools to reveal the role of essential genes in C. difficile. LcpA and LcpB activity was shown to be essential, suggesting that they are potential new targets to combat C. difficile infection. In this study, we also showed that there is competition between the polysaccharide II synthesis pathway and peptidoglycan synthesis that probably exists in other Gram-positive bacteria. A better understanding of these mechanisms allows us to define the Lcp proteins as a therapeutic target for potential design of novel antibiotics against pathogenic Gram-positive bacteria.
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Affiliation(s)
| | - Liang Yucheng
- INSERM UMR-S 1138, Centre de Recherche des Cordeliers, Sorbonne Université, Université Paris Cité, Paris, France
| | - Laurent Evanno
- Biomolécules: Conception, Isolement et Synthèse (BioCIS), Université Paris-Saclay, CNRS, Orsay, France
| | | | - Jean-Emmanuel Hugonnet
- INSERM UMR-S 1138, Centre de Recherche des Cordeliers, Sorbonne Université, Université Paris Cité, Paris, France
| | - Michel Arthur
- INSERM UMR-S 1138, Centre de Recherche des Cordeliers, Sorbonne Université, Université Paris Cité, Paris, France
| | - Claire Janoir
- Micalis Institute, Université Paris-Saclay, INRAE, AgroParisTech, Jouy-en-Josas, France
| | - Thomas Candela
- Micalis Institute, Université Paris-Saclay, INRAE, AgroParisTech, Jouy-en-Josas, France
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21
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Cheng JKJ, Unnikrishnan M. Clostridioides difficile infection: traversing host-pathogen interactions in the gut. MICROBIOLOGY (READING, ENGLAND) 2023; 169. [PMID: 36848200 DOI: 10.1099/mic.0.001306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
C. difficile is the primary cause for nosocomial infective diarrhoea. For a successful infection, C. difficile must navigate between resident gut bacteria and the harsh host environment. The perturbation of the intestinal microbiota by broad-spectrum antibiotics alters the composition and the geography of the gut microbiota, deterring colonization resistance, and enabling C. difficile to colonize. This review will discuss how C. difficile interacts with and exploits the microbiota and the host epithelium to infect and persist. We provide an overview of C. difficile virulence factors and their interactions with the gut to aid adhesion, cause epithelial damage and mediate persistence. Finally, we document the host responses to C. difficile, describing the immune cells and host pathways that are associated and triggered during C. difficile infection.
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Affiliation(s)
- Jeffrey K J Cheng
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - Meera Unnikrishnan
- Division of Biomedical Sciences, Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
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22
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Nale JY, Thanki AM, Rashid SJ, Shan J, Vinner GK, Dowah ASA, Cheng JKJ, Sicheritz-Pontén T, Clokie MRJ. Diversity, Dynamics and Therapeutic Application of Clostridioides difficile Bacteriophages. Viruses 2022; 14:v14122772. [PMID: 36560776 PMCID: PMC9784644 DOI: 10.3390/v14122772] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2022] [Revised: 12/08/2022] [Accepted: 12/08/2022] [Indexed: 12/15/2022] Open
Abstract
Clostridioides difficile causes antibiotic-induced diarrhoea and pseudomembranous colitis in humans and animals. Current conventional treatment relies solely on antibiotics, but C. difficile infection (CDI) cases remain persistently high with concomitant increased recurrence often due to the emergence of antibiotic-resistant strains. Antibiotics used in treatment also induce gut microbial imbalance; therefore, novel therapeutics with improved target specificity are being investigated. Bacteriophages (phages) kill bacteria with precision, hence are alternative therapeutics for the targeted eradication of the pathogen. Here, we review current progress in C. difficile phage research. We discuss tested strategies of isolating C. difficile phages directly, and via enrichment methods from various sample types and through antibiotic induction to mediate prophage release. We also summarise phenotypic phage data that reveal their morphological, genetic diversity, and various ways they impact their host physiology and pathogenicity during infection and lysogeny. Furthermore, we describe the therapeutic development of phages through efficacy testing in different in vitro, ex vivo and in vivo infection models. We also discuss genetic modification of phages to prevent horizontal gene transfer and improve lysis efficacy and formulation to enhance stability and delivery of the phages. The goal of this review is to provide a more in-depth understanding of C. difficile phages and theoretical and practical knowledge on pre-clinical, therapeutic evaluation of the safety and effectiveness of phage therapy for CDI.
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Affiliation(s)
- Janet Y. Nale
- Centre for Epidemiology and Planetary Health, Department of Veterinary and Animal Science, Scotland’s Rural College, Inverness IV2 5NA, UK
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Anisha M. Thanki
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Srwa J. Rashid
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Jinyu Shan
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Gurinder K. Vinner
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
| | - Ahmed S. A. Dowah
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
- School of Pharmacy, University of Lincoln, Lincoln LN6 7TS, UK
| | | | - Thomas Sicheritz-Pontén
- Center for Evolutionary Hologenomics, The Globe Institute, University of Copenhagen, 1353 Copenhagen, Denmark
- Centre of Excellence for Omics-Driven Computational Biodiscovery, AIMST University, Bedong 08100, Kedah, Malaysia
| | - Martha R. J. Clokie
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, UK
- Correspondence:
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23
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A clean in-frame knockout system for gene deletion in Acetobacterium woodii. J Biotechnol 2022; 353:9-18. [PMID: 35659892 DOI: 10.1016/j.jbiotec.2022.05.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Revised: 05/27/2022] [Accepted: 05/28/2022] [Indexed: 11/24/2022]
Abstract
Acetogenic bacteria produce acetate following the fixation of CO2 via the Wood-Ljungdahl pathway. As such, they represent excellent process organisms for the production of novel chemicals and fuels from this waste greenhouse gas. Acetobacterium woodii is the model acetogen and numerous studies have been conducted investigating its biochemistry, gas consumption and use as a production chassis. However, there are a dearth of available tools for A. woodii gene modification which limits the research options available for genetic studies. Here, the previously proposed Clostridia Roadmap is implemented in A. woodii leading to the derivation of a knockout system for the generation of clean, in-frame deletions. The replicon of the Gram-positive plasmid pCD6 that originated in Clostridioides difficile was identified as being replication-defective in A. woodii, a property that was exploited to construct a pseudo-suicide knockout plasmid which was used to generate an auxotrophic, pyrE mutant. This allowed the subsequent use of a heterologous pyrE gene (from Clostridium acetobutylicum) as a counter selection marker and the deletion of a number of genes by allelic exchange. Specific mutants generated were affected in growth on glucose, fructose and ethanol as a consequence of deletion of fruA, pstG and adhE, respectively.
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24
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Vidor CJ, Hamiot A, Wisniewski J, Mathias RA, Dupuy B, Awad M, Lyras D. A Highly Specific Holin-Mediated Mechanism Facilitates the Secretion of Lethal Toxin TcsL in Paeniclostridium sordellii. Toxins (Basel) 2022; 14:toxins14020124. [PMID: 35202151 PMCID: PMC8878733 DOI: 10.3390/toxins14020124] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Revised: 02/03/2022] [Accepted: 02/04/2022] [Indexed: 12/10/2022] Open
Abstract
Protein secretion is generally mediated by a series of distinct pathways in bacteria. Recently, evidence of a novel bacterial secretion pathway involving a bacteriophage-related protein has emerged. TcdE, a holin-like protein encoded by toxigenic isolates of Clostridioides difficile, mediates the release of the large clostridial glucosylating toxins (LCGTs), TcdA and TcdB, and TpeL from C. perfringens uses another holin-like protein, TpeE, for its secretion; however, it is not yet known if TcdE or TpeE secretion is specific to these proteins. It is also unknown if other members of the LCGT-producing clostridia, including Paeniclostridium sordellii (previously Clostridium sordellii), use a similar toxin-release mechanism. Here, we confirm that each of the LCGT-producing clostridia encode functional holin-like proteins in close proximity to the toxin genes. To characterise the respective roles of these holin-like proteins in the release of the LCGTs, P. sordellii and its lethal toxin, TcsL, were used as a model. Construction and analysis of mutants of the P. sordellii tcsE (holin-like) gene demonstrated that TcsE plays a significant role in TcsL release. Proteomic analysis of the secretome from the tcsE mutant confirmed that TcsE is required for efficient TcsL secretion. Unexpectedly, comparative sample analysis showed that TcsL was the only protein significantly altered in its release, suggesting that this holin-like protein has specifically evolved to function in the release of this important virulence factor. This specificity has, to our knowledge, not been previously shown and suggests that this protein may function as part of a specific mechanism for the release of all LCGTs.
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Affiliation(s)
- Callum J. Vidor
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC 3800, Australia; (C.J.V.); (J.W.); (R.A.M.); (M.A.)
- School of Biological Sciences, Monash University, Clayton, VIC 3800, Australia
| | - Audrey Hamiot
- Laboratoire Pathogenèse des Bactéries Anaérobies, UMR-CNRS 6047, Institut Pasteur, Université de Paris, F-75015 Paris, France; (A.H.); (B.D.)
| | - Jessica Wisniewski
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC 3800, Australia; (C.J.V.); (J.W.); (R.A.M.); (M.A.)
| | - Rommel A. Mathias
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC 3800, Australia; (C.J.V.); (J.W.); (R.A.M.); (M.A.)
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Biochemistry and Molecular Biology, Monash University, Clayton, VIC 3800, Australia
| | - Bruno Dupuy
- Laboratoire Pathogenèse des Bactéries Anaérobies, UMR-CNRS 6047, Institut Pasteur, Université de Paris, F-75015 Paris, France; (A.H.); (B.D.)
| | - Milena Awad
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC 3800, Australia; (C.J.V.); (J.W.); (R.A.M.); (M.A.)
| | - Dena Lyras
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, VIC 3800, Australia; (C.J.V.); (J.W.); (R.A.M.); (M.A.)
- Correspondence:
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25
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Regulation of Clostridioides difficile toxin production. Curr Opin Microbiol 2022; 65:95-100. [PMID: 34781095 PMCID: PMC8792210 DOI: 10.1016/j.mib.2021.10.018] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2021] [Revised: 10/19/2021] [Accepted: 10/25/2021] [Indexed: 02/03/2023]
Abstract
Clostridioides difficile produces toxins TcdA and TcdB during infection. Since the severity of the illness is directly correlated with the level of toxins produced, researchers have long been interested in the regulation mechanisms of toxin production. The advent of new genetics and mutagenesis technologies in C. difficile has allowed a slew of new investigations in the last decade, which considerably improved our understanding of this crucial regulatory network. The current body of work shows that the toxin regulatory network overlaps with the regulatory networks of sporulation, motility, and key metabolic pathways. This implies that toxin production is a complicated process initiated by bacteria in response to numerous host factors during infection. We summarize the existing knowledge about the toxin gene regulatory network here.
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26
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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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27
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Joseph RC, Kelley SQ, Kim NM, Sandoval NR. Metabolic Engineering and the Synthetic Biology Toolbox for
Clostridium. Metab Eng 2021. [DOI: 10.1002/9783527823468.ch16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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28
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Riedel T, Neumann-Schaal M, Wittmann J, Schober I, Hofmann JD, Lu CW, Dannheim A, Zimmermann O, Lochner M, Groß U, Overmann J. Characterization of Clostridioides difficile DSM 101085 with A-B-CDT+ Phenotype from a Late Recurrent Colonization. Genome Biol Evol 2021; 12:566-577. [PMID: 32302381 PMCID: PMC7250501 DOI: 10.1093/gbe/evaa072] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/10/2020] [Indexed: 12/29/2022] Open
Abstract
During the last decades, hypervirulent strains of Clostridioides difficile with frequent disease recurrence and increased mortality appeared. Clostridioides difficile DSM 101085 was isolated from a patient who suffered from several recurrent infections and colonizations, likely contributing to a fatal outcome. Analysis of the toxin repertoire revealed the presence of a complete binary toxin locus and an atypical pathogenicity locus consisting of only a tcdA pseudogene and a disrupted tcdC gene sequence. The pathogenicity locus shows upstream a transposon and has been subject to homologous recombination or lateral gene transfer events. Matching the results of the genome analysis, neither TcdA nor TcdB production but the expression of cdtA and cdtB was detected. This highlights a potential role of the binary toxin C. difficile toxin in this recurrent colonization and possibly further in a host-dependent virulence. Compared with the C. difficile metabolic model strains DSM 28645 (630Δerm) and DSM 27147 (R20291), strain DSM 101085 showed a specific metabolic profile, featuring changes in the threonine degradation pathways and alterations in the central carbon metabolism. Moreover, products originating from Stickland pathways processing leucine, aromatic amino acids, and methionine were more abundant in strain DSM 101085, indicating a more efficient use of these substrates. The particular characteristics of strain C. difficile DSM 101085 may represent an adaptation to a low-protein diet in a patient with recurrent infections.
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Affiliation(s)
- Thomas Riedel
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.,German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, Germany
| | - Meina Neumann-Schaal
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.,Department of Bioinformatics and Biochemistry and Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Germany
| | - Johannes Wittmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Isabel Schober
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Julia Danielle Hofmann
- Department of Bioinformatics and Biochemistry and Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Germany
| | - Chia-Wen Lu
- Institute of Infection Immunology, TWINCORE, Centre for Experimental and Clinical Infection Research, a Joint Venture between the Medical School Hannover (MHH) and the Helmholtz Centre for Infection Research (HZI), Hannover, Germany
| | - Antonia Dannheim
- Department of Bioinformatics and Biochemistry and Braunschweig Integrated Centre of Systems Biology (BRICS), Technische Universität Braunschweig, Germany
| | - Ortrud Zimmermann
- Institute of Medical Microbiology, University Medical Center Göttingen, Germany
| | - Matthias Lochner
- Institute of Infection Immunology, TWINCORE, Centre for Experimental and Clinical Infection Research, a Joint Venture between the Medical School Hannover (MHH) and the Helmholtz Centre for Infection Research (HZI), Hannover, Germany
| | - Uwe Groß
- Institute of Medical Microbiology, University Medical Center Göttingen, Germany.,Göttingen International Health Network, Göttingen, Germany
| | - Jörg Overmann
- Leibniz Institute DSMZ-German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany.,German Center for Infection Research (DZIF), Partner Site Hannover-Braunschweig, Braunschweig, Germany.,Institute of Microbiology, Technical University of Braunschweig, Germany
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29
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Abstract
Large clostridial toxins (LCTs) are a family of bacterial exotoxins that infiltrate and destroy target cells. Members of the LCT family include Clostridioides difficile toxins TcdA and TcdB, Paeniclostridium sordellii toxins TcsL and TcsH, Clostridium novyi toxin TcnA, and Clostridium perfringens toxin TpeL. Since the 19th century, LCT-secreting bacteria have been isolated from the blood, organs, and wounds of diseased individuals, and LCTs have been implicated as the primary virulence factors in a variety of infections, including C. difficile infection and some cases of wound-associated gas gangrene. Clostridia express and secrete LCTs in response to various physiological signals. LCTs invade host cells by binding specific cell surface receptors, ultimately leading to internalization into acidified vesicles. Acidic pH promotes conformational changes within LCTs, which culminates in translocation of the N-terminal glycosyltransferase and cysteine protease domain across the endosomal membrane and into the cytosol, leading first to cytopathic effects and later to cytotoxic effects. The focus of this review is on the role of LCTs in infection and disease, the mechanism of LCT intoxication, with emphasis on recent structural work and toxin subtyping analysis, and the genomic discovery and characterization of LCT homologues. We provide a comprehensive review of these topics and offer our perspective on emerging questions and future research directions for this enigmatic family of toxins.
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Ser/Thr Kinase-Dependent Phosphorylation of the Peptidoglycan Hydrolase CwlA Controls Its Export and Modulates Cell Division in Clostridioides difficile. mBio 2021; 12:mBio.00519-21. [PMID: 34006648 PMCID: PMC8262956 DOI: 10.1128/mbio.00519-21] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Cell growth and division require a balance between synthesis and hydrolysis of the peptidoglycan (PG). Inhibition of PG synthesis or uncontrolled PG hydrolysis can be lethal for the cells, making it imperative to control peptidoglycan hydrolase (PGH) activity. The synthesis or activity of several key enzymes along the PG biosynthetic pathway is controlled by the Hanks-type serine/threonine kinases (STKs). In Gram-positive bacteria, inactivation of genes encoding STKs is associated with a range of phenotypes, including cell division defects and changes in cell wall metabolism, but only a few kinase substrates and associated mechanisms have been identified. We previously demonstrated that STK-PrkC plays an important role in cell division, cell wall metabolism, and resistance to antimicrobial compounds in the human enteropathogen Clostridioides difficile In this work, we characterized a PG hydrolase, CwlA, which belongs to the NlpC/P60 family of endopeptidases and hydrolyses cross-linked PG between daughter cells to allow cell separation. We identified CwlA as the first PrkC substrate in C. difficile We demonstrated that PrkC-dependent phosphorylation inhibits CwlA export, thereby controlling hydrolytic activity in the cell wall. High levels of CwlA at the cell surface led to cell elongation, whereas low levels caused cell separation defects. Thus, we provided evidence that the STK signaling pathway regulates PGH homeostasis to precisely control PG hydrolysis during cell division.IMPORTANCE Bacterial cells are encased in a PG exoskeleton that helps to maintain cell shape and confers physical protection. To allow bacterial growth and cell separation, PG needs to be continuously remodeled by hydrolytic enzymes that cleave PG at critical sites. How these enzymes are regulated remains poorly understood. We identify a new PG hydrolase involved in cell division, CwlA, in the enteropathogen C. difficile Lack or accumulation of CwlA at the bacterial surface is responsible for a division defect, while its accumulation in the absence of PrkC also increases susceptibility to antimicrobial compounds targeting the cell wall. CwlA is a substrate of the kinase PrkC in C. difficile PrkC-dependent phosphorylation controls the export of CwlA, modulating its levels and, consequently, its activity in the cell wall. This work provides a novel regulatory mechanism by STK in tightly controlling protein export.
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A cortex-specific penicillin-binding protein contributes to heat resistance in Clostridioides difficile spores. Anaerobe 2021; 70:102379. [PMID: 33940167 PMCID: PMC8417463 DOI: 10.1016/j.anaerobe.2021.102379] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2021] [Revised: 04/12/2021] [Accepted: 04/23/2021] [Indexed: 12/15/2022]
Abstract
Background Sporulation is a complex cell differentiation programme shared by many members of the Firmicutes, the end result of which is a highly resistant, metabolically inert spore that can survive harsh environmental insults. Clostridioides difficile spores are essential for transmission of disease and are also required for recurrent infection. However, the molecular basis of sporulation is poorly understood, despite parallels with the well-studied Bacillus subtilis system. The spore envelope consists of multiple protective layers, one of which is a specialised layer of peptidoglycan, called the cortex, that is essential for the resistant properties of the spore. We set out to identify the enzymes required for synthesis of cortex peptidoglycan in C. difficile. Methods Bioinformatic analysis of the C. difficile genome to identify putative homologues of Bacillus subtilis spoVD was combined with directed mutagenesis and microscopy to identify and characterise cortex-specific PBP activity. Results Deletion of CDR20291_2544 (SpoVDCd) abrogated spore formation and this phenotype was completely restored by complementation in cis. Analysis of SpoVDCd revealed a three domain structure, consisting of dimerization, transpeptidase and PASTA domains, very similar to B. subtilis SpoVD. Complementation with SpoVDCd domain mutants demonstrated that the PASTA domain was dispensable for formation of morphologically normal spores. SpoVDCd was also seen to localise to the developing spore by super-resolution confocal microscopy. Conclusions We have identified and characterised a cortex specific PBP in C. difficile. This is the first characterisation of a cortex-specific PBP in C. difficile and begins the process of unravelling cortex biogenesis in this important pathogen. CDR20291_2544 encodes a C. difficile homologue of the B subtilis SpoVD. Mutation of spoVDCd completely prevents the formation of heat-resistant spores. The SpoVDCd PASTA domain was dispensable for its function. SpoVDCd localises to the developing spore.
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32
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Boudry P, Piattelli E, Drouineau E, Peltier J, Boutserin A, Lejars M, Hajnsdorf E, Monot M, Dupuy B, Martin-Verstraete I, Gautheret D, Toffano-Nioche C, Soutourina O. Identification of RNAs bound by Hfq reveals widespread RNA partners and a sporulation regulator in the human pathogen Clostridioides difficile. RNA Biol 2021; 18:1931-1952. [PMID: 33629931 PMCID: PMC8583004 DOI: 10.1080/15476286.2021.1882180] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Noncoding RNAs (ncRNA) have emerged as important components of regulatory networks governing bacterial physiology and virulence. Previous deep-sequencing analysis identified a large diversity of ncRNAs in the human enteropathogen Clostridioides (Clostridium) difficile. Some of them are trans-encoded RNAs that could require the RNA chaperone protein Hfq for their action. Recent analysis suggested a pleiotropic role of Hfq in C. difficile with the most pronounced effect on sporulation, a key process during the infectious cycle of this pathogen. However, a global view of RNAs interacting with C. difficile Hfq is missing. In the present study, we performed RNA immunoprecipitation high-throughput sequencing (RIP-Seq) to identify Hfq-associated RNAs in C. difficile. Our work revealed a large set of Hfq-interacting mRNAs and ncRNAs, including mRNA leaders and coding regions, known and potential new ncRNAs. In addition to trans-encoded RNAs, new categories of Hfq ligands were found including cis-antisense RNAs, riboswitches and CRISPR RNAs. ncRNA-mRNA and ncRNA-ncRNA pairings were postulated through computational predictions. Investigation of one of the Hfq-associated ncRNAs, RCd1, suggests that this RNA contributes to the control of late stages of sporulation in C. difficile. Altogether, these data provide essential molecular basis for further studies of post-transcriptional regulatory network in this enteropathogen.
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Affiliation(s)
- Pierre Boudry
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France.,Laboratoire Pathogenèses des Bactéries Anaérobies, Institut Pasteur, Université de Paris, Paris, France
| | - Emma Piattelli
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Emilie Drouineau
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Johann Peltier
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France.,Laboratoire Pathogenèses des Bactéries Anaérobies, Institut Pasteur, Université de Paris, Paris, France
| | - Anaïs Boutserin
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Maxence Lejars
- UMR8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique, Paris, France
| | - Eliane Hajnsdorf
- UMR8261, CNRS, Université de Paris, Institut de Biologie Physico-Chimique, Paris, France
| | - Marc Monot
- Laboratoire Pathogenèses des Bactéries Anaérobies, Institut Pasteur, Université de Paris, Paris, France.,Biomics Platform, C2RT, Institut Pasteur, Paris, France
| | - Bruno Dupuy
- Laboratoire Pathogenèses des Bactéries Anaérobies, Institut Pasteur, Université de Paris, Paris, France
| | - Isabelle Martin-Verstraete
- Laboratoire Pathogenèses des Bactéries Anaérobies, Institut Pasteur, Université de Paris, Paris, France.,Institut Universitaire de France (IUF), Paris, France
| | - Daniel Gautheret
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Claire Toffano-Nioche
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France
| | - Olga Soutourina
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), Gif-sur-Yvette, France.,Laboratoire Pathogenèses des Bactéries Anaérobies, Institut Pasteur, Université de Paris, Paris, France.,Institut Universitaire de France (IUF), Paris, France
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Peltier J, Hamiot A, Garneau JR, Boudry P, Maikova A, Hajnsdorf E, Fortier LC, Dupuy B, Soutourina O. Type I toxin-antitoxin systems contribute to the maintenance of mobile genetic elements in Clostridioides difficile. Commun Biol 2020; 3:718. [PMID: 33247281 PMCID: PMC7699646 DOI: 10.1038/s42003-020-01448-5] [Citation(s) in RCA: 57] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 11/03/2020] [Indexed: 12/15/2022] Open
Abstract
Toxin-antitoxin (TA) systems are widespread on mobile genetic elements and in bacterial chromosomes. In type I TA, synthesis of the toxin protein is prevented by the transcription of an antitoxin RNA. The first type I TA were recently identified in the human enteropathogen Clostridioides difficile. Here we report the characterization of five additional type I TA within phiCD630-1 (CD0977.1-RCd11, CD0904.1-RCd13 and CD0956.3-RCd14) and phiCD630-2 (CD2889-RCd12 and CD2907.2-RCd15) prophages of C. difficile strain 630. Toxin genes encode 34 to 47 amino acid peptides and their ectopic expression in C. difficile induces growth arrest that is neutralized by antitoxin RNA co-expression. We show that type I TA located within the phiCD630-1 prophage contribute to its stability and heritability. We have made use of a type I TA toxin gene to generate an efficient mutagenesis tool for this bacterium that allowed investigation of the role of these widespread TA in prophage maintenance.
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Affiliation(s)
- Johann Peltier
- Laboratoire Pathogenèse des Bactéries Anaérobies, CNRS-2001, Institut Pasteur, Université de Paris, 75015, Paris, France
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
| | - Audrey Hamiot
- Laboratoire Pathogenèse des Bactéries Anaérobies, CNRS-2001, Institut Pasteur, Université de Paris, 75015, Paris, France
- UMR UMET, INRA, CNRS, Univ. Lille 1, 59650, Villeneuve d'Ascq, France
| | - Julian R Garneau
- Faculty of Medicine and Health Sciences, Department of Microbiology and Infectious Diseases, Université de Sherbrooke, 3201 rue Jean Mignault, Sherbrooke, QC, J1E 4K8, Canada
| | - Pierre Boudry
- Laboratoire Pathogenèse des Bactéries Anaérobies, CNRS-2001, Institut Pasteur, Université de Paris, 75015, Paris, France
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette Cedex, France
| | - Anna Maikova
- Laboratoire Pathogenèse des Bactéries Anaérobies, CNRS-2001, Institut Pasteur, Université de Paris, 75015, Paris, France
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France
- Center of Life Sciences, Skolkovo Institute of Science and Technology, Moscow, 143028, Russia
- Peter the Great St. Petersburg Polytechnic University, Saint Petersburg, 195251, Russia
| | - Eliane Hajnsdorf
- Institut de Biologie Physico-Chimique, UMR8261, CNRS, Université de Paris, 13 rue Pierre et Marie Curie, 75005, Paris, France
| | - Louis-Charles Fortier
- Faculty of Medicine and Health Sciences, Department of Microbiology and Infectious Diseases, Université de Sherbrooke, 3201 rue Jean Mignault, Sherbrooke, QC, J1E 4K8, Canada
| | - Bruno Dupuy
- Laboratoire Pathogenèse des Bactéries Anaérobies, CNRS-2001, Institut Pasteur, Université de Paris, 75015, Paris, France
| | - Olga Soutourina
- Laboratoire Pathogenèse des Bactéries Anaérobies, CNRS-2001, Institut Pasteur, Université de Paris, 75015, Paris, France.
- Université Paris-Saclay, CEA, CNRS, Institute for Integrative Biology of the Cell (I2BC), 91198, Gif-sur-Yvette, France.
- Institut Universitaire de France (IUF), Paris, France.
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Kodori M, Ghalavand Z, Yadegar A, Eslami G, Azimirad M, Krutova M, Abadi A, Zali MR. Molecular characterization of pathogenicity locus (PaLoc) and tcdC genetic diversity among tcdA +B +Clostridioides difficile clinical isolates in Tehran, Iran. Anaerobe 2020; 66:102294. [PMID: 33181348 DOI: 10.1016/j.anaerobe.2020.102294] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2020] [Revised: 10/28/2020] [Accepted: 11/01/2020] [Indexed: 12/11/2022]
Abstract
Clostridioides difficile is the main cause of healthcare-associated diarrhea worldwide. It is proposed that certain C. difficile toxinotypes with distinct pathogenicity locus (PaLoc) variants are associated with disease severity and outcomes. Additionally, few studies have described the common C. difficile toxinotypes, and also little is known about the tcdC variants in Iranian isolates. We characterized the toxinotypes and the tcdC genotypes from a collection of Iranian clinical C. difficile tcdA+B+ isolates with known ribotypes (RTs). Fifty C. difficile isolates with known RTs and carrying the tcdA and tcdB toxin genes were analyzed. Toxinotyping was carried out based on a PCR-RFLP analysis of a 19.6 kb region encompassing the PaLoc. Genetic diversity of the tcdC gene was determined by the sequencing of the gene. Of the 50 C. difficile isolates investigated, five distinct toxinotypes were recognized. Toxinotypes 0 (33/50, 66%) and V (11/50, 22%) were the most frequently found. C. difficile isolates of the toxinotype 0 mostly belonged to RT 001 (12/33, 36.4%), whereas toxinotype V consisted of RT 126 (9/11, 81.8%). The tcdC sequencing showed six variants (35/50, 70%); tcdC-sc3 (24%), tcdC-A (22%), tcdC-sc9 (18%), tcdC-B (2%), tcdC-sc14 (2%), and tcdC-sc15 (2%). The remaining isolates were wild-types (15/50, 30%) in the tcdC gene. The present study demonstrates that the majority of clinical tcdA+B+ isolates of C. difficile frequently harbor tcdC genetic variants. We also found that the RT 001/toxinotype 0 and the RT 126/toxinotype V are the most common types among Iranian isolates. Further studies are needed to investigate the putative association of various tcdC genotypes with CDI severity and its recurrence.
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Affiliation(s)
- Mansoor Kodori
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran; Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Zohreh Ghalavand
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Abbas Yadegar
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Gita Eslami
- Department of Microbiology, School of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Masoumeh Azimirad
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Marcela Krutova
- Department of Medical Microbiology, Charles University, 2nd Faculty of Medicine, Motol University Hospital, Prague, Czech Republic; European Society of Clinical Microbiology and Infectious Diseases (ESCMID) Study Group for Clostridioides Difficile (ESGCD), Basel, Switzerland
| | - Alireza Abadi
- Department of Health & Community Medicine, Faculty of Medicine, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Reza Zali
- Gastroenterology and Liver Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
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Oliveira Paiva AM, de Jong L, Friggen AH, Smits WK, Corver J. The C-Terminal Domain of Clostridioides difficile TcdC Is Exposed on the Bacterial Cell Surface. J Bacteriol 2020; 202:JB.00771-19. [PMID: 32868401 PMCID: PMC7585056 DOI: 10.1128/jb.00771-19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 08/25/2020] [Indexed: 02/04/2023] Open
Abstract
Clostridioides difficile is an anaerobic Gram-positive bacterium that can produce the large clostridial toxins toxin A and toxin B, encoded within the pathogenicity locus (PaLoc). The PaLoc also encodes the sigma factor TcdR, which positively regulates toxin gene expression, and TcdC, which is a putative negative regulator of toxin expression. TcdC is proposed to be an anti-sigma factor; however, several studies failed to show an association between the tcdC genotype and toxin production. Consequently, the TcdC function is not yet fully understood. Previous studies have characterized TcdC as a membrane-associated protein with the ability to bind G-quadruplex structures. The binding to the DNA secondary structures is mediated through the oligonucleotide/oligosaccharide binding fold (OB-fold) domain present at the C terminus of the protein. This domain was previously also proposed to be responsible for the inhibitory effect on toxin gene expression, implicating a cytoplasmic localization of the OB-fold. In this study, we aimed to obtain topological information on the C terminus of TcdC and demonstrate that the C terminus of TcdC is located extracellularly. In addition, we show that the membrane association of TcdC is dependent on a membrane-proximal cysteine residue and that mutating this residue results in the release of TcdC from the bacterial cell. The extracellular location of TcdC is not compatible with the direct binding of the OB-fold domain to intracellular nucleic acid or protein targets and suggests a mechanism of action that is different from that of the characterized anti-sigma factors.IMPORTANCE The transcription of C. difficile toxins TcdA and TcdB is directed by the sigma factor TcdR. TcdC has been proposed to be an anti-sigma factor. The activity of TcdC has been mapped to its C terminus, and the N terminus serves as the membrane anchor. Acting as an anti-sigma factor requires a cytoplasmic localization of the C terminus of TcdC. Using cysteine accessibility analysis and a HiBiT-based system, we show that the TcdC C terminus is located extracellularly, which is incompatible with its role as anti-sigma factor. Furthermore, mutating a cysteine residue at position 51 resulted in the release of TcdC from the bacteria. The codon-optimized version of the HiBiT (HiBiTopt) extracellular detection system is a valuable tool for topology determination of membrane proteins, increasing the range of systems available to tackle important aspects of C. difficile development.
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Affiliation(s)
- Ana M Oliveira Paiva
- Department of Medical Microbiology, Section Experimental Bacteriology, Leiden University Medical Center, Leiden, The Netherlands
- Center for Microbial Cell Biology, Leiden, The Netherlands
| | - Leen de Jong
- Department of Medical Microbiology, Section Experimental Bacteriology, Leiden University Medical Center, Leiden, The Netherlands
| | - Annemieke H Friggen
- Department of Medical Microbiology, Section Experimental Bacteriology, Leiden University Medical Center, Leiden, The Netherlands
- Center for Microbial Cell Biology, Leiden, The Netherlands
| | - Wiep Klaas Smits
- Department of Medical Microbiology, Section Experimental Bacteriology, Leiden University Medical Center, Leiden, The Netherlands
- Center for Microbial Cell Biology, Leiden, The Netherlands
| | - Jeroen Corver
- Department of Medical Microbiology, Section Experimental Bacteriology, Leiden University Medical Center, Leiden, The Netherlands
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Diverse Energy-Conserving Pathways in Clostridium difficile: Growth in the Absence of Amino Acid Stickland Acceptors and the Role of the Wood-Ljungdahl Pathway. J Bacteriol 2020; 202:JB.00233-20. [PMID: 32967909 DOI: 10.1128/jb.00233-20] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 07/23/2020] [Indexed: 12/21/2022] Open
Abstract
Clostridium difficile is the leading cause of hospital-acquired antibiotic-associated diarrhea and is the only widespread human pathogen that contains a complete set of genes encoding the Wood-Ljungdahl pathway (WLP). In acetogenic bacteria, synthesis of acetate from 2 CO2 molecules by the WLP functions as a terminal electron accepting pathway; however, C. difficile contains various other reductive pathways, including a heavy reliance on Stickland reactions, which questions the role of the WLP in this bacterium. In rich medium containing high levels of electron acceptor substrates, only trace levels of key WLP enzymes were found; therefore, conditions were developed to adapt C. difficile to grow in the absence of amino acid Stickland acceptors. Growth conditions were identified that produce the highest levels of WLP activity, determined by Western blot analyses of the central component acetyl coenzyme A synthase (AcsB) and assays of other WLP enzymes. Fermentation substrate and product analyses, enzyme assays of cell extracts, and characterization of a ΔacsB mutant demonstrated that the WLP functions to dispose of metabolically generated reducing equivalents. While WLP activity in C. difficile does not reach the levels seen in classical acetogens, coupling of the WLP to butyrate formation provides a highly efficient system for regeneration of NAD+ "acetobutyrogenesis," requiring only low flux through the pathways to support efficient ATP production from glucose oxidation. Additional insights redefine the amino acid requirements in C. difficile, explore the relationship of the WLP to toxin production, and provide a rationale for colocalization of genes involved in glycine synthesis and cleavage within the WLP operon.IMPORTANCE Clostridium difficile is an anaerobic, multidrug-resistant, toxin-producing pathogen with major health impacts worldwide. It is the only widespread pathogen harboring a complete set of Wood-Ljungdahl pathway (WLP) genes; however, the role of the WLP in C. difficile is poorly understood. In other anaerobic bacteria and archaea, the WLP can operate in one direction to convert CO2 to acetic acid for biosynthesis or in either direction for energy conservation. Here, conditions are defined in which WLP levels in C. difficile increase markedly, functioning to support metabolism of carbohydrates. Amino acid nutritional requirements were better defined, with new insight into how the WLP and butyrate pathways act in concert, contributing significantly to energy metabolism by a mechanism that may have broad physiological significance within the group of nonclassical acetogens.
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Redefining the Clostridioides difficile σ B Regulon: σ B Activates Genes Involved in Detoxifying Radicals That Can Result from the Exposure to Antimicrobials and Hydrogen Peroxide. mSphere 2020; 5:5/5/e00728-20. [PMID: 32938698 PMCID: PMC7494833 DOI: 10.1128/msphere.00728-20] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
In many Gram-positive bacteria, the general stress response is regulated at the transcriptional level by the alternative sigma factor sigma B (σB). In C. difficile, σB has been implicated in protection against stressors such as reactive oxygen species (ROS) and antimicrobial compounds. Here, we used an anti-σB antibody to demonstrate time-limited overproduction of σB in C. difficile despite its toxicity at higher cellular concentrations. This toxicity eventually led to the loss of the plasmid used for anhydrotetracycline-induced σB gene expression. Inducible σB overproduction uncouples σB expression from its native regulatory network and allows for the refinement of the previously proposed σB regulon. At least 32% of the regulon was found to consist of genes involved in the response to reactive radicals. Direct gene activation by C. difficile σB was demonstrated through in vitro runoff transcription of specific target genes (cd0350, cd3614, cd3605, and cd2963). Finally, we demonstrated that different antimicrobials and hydrogen peroxide induce these genes in a manner dependent on this sigma factor, using a plate-based luciferase reporter assay. Together, our work suggests that lethal exposure to antimicrobials may result in the formation of toxic radicals that lead to σB-dependent gene activation.IMPORTANCE Sigma B is the alternative sigma factor governing stress response in many Gram-positive bacteria. In C. difficile, a sigB mutant shows pleiotropic transcriptional effects. Here, we determine genes that are likely direct targets of σB by evaluating the transcriptional effects of σB overproduction, provide biochemical evidence of direct transcriptional activation by σB, and show that σB-dependent genes can be activated by antimicrobials. Together, our data suggest that σB is a key player in dealing with toxic radicals.
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Abstract
Although the gastrointestinal tract is regarded as mainly anoxic, low O2 tension is present in the gut and tends to increase following antibiotic-induced disruption of the host microbiota. Two decreasing O2 gradients are observed, a longitudinal one from the small to the large intestine and a second one from the intestinal epithelium toward the colon lumen. Thus, O2 concentration fluctuations within the gastrointestinal tract are a challenge for anaerobic bacteria such as C. difficile. This enteropathogen has developed efficient strategies to detoxify O2. In this work, we identified reverse rubrerythrins and flavodiiron proteins as key actors for O2 tolerance in C. difficile. These enzymes are responsible for the reduction of O2 protecting C. difficile vegetative cells from associated damages. Original and complex detoxification pathways involving O2-reductases are crucial in the ability of C. difficile to tolerate O2 and survive to O2 concentrations encountered in the gastrointestinal tract. Clostridioides difficile is a major cause of diarrhea associated with antibiotherapy. After germination of C. difficile spores in the small intestine, vegetative cells are exposed to low oxygen (O2) tensions. While considered strictly anaerobic, C. difficile is able to grow in nonstrict anaerobic conditions (1 to 3% O2) and tolerates brief air exposure indicating that this bacterium harbors an arsenal of proteins involved in O2 detoxification and/or protection. Tolerance of C. difficile to low O2 tensions requires the presence of the alternative sigma factor, σB, involved in the general stress response. Among the genes positively controlled by σB, four encode proteins likely involved in O2 detoxification: two flavodiiron proteins (FdpA and FdpF) and two reverse rubrerythrins (revRbr1 and revRbr2). As previously observed for FdpF, we showed that both purified revRbr1 and revRbr2 harbor NADH-linked O2- and H2O2-reductase activities in vitro, while purified FdpA mainly acts as an O2-reductase. The growth of a fdpA mutant is affected at 0.4% O2, while inactivation of both revRbrs leads to a growth defect above 0.1% O2. O2-reductase activities of these different proteins are additive since the quadruple mutant displays a stronger phenotype when exposed to low O2 tensions compared to the triple mutants. Our results demonstrate a key role for revRbrs, FdpF, and FdpA proteins in the ability of C. difficile to grow in the presence of physiological O2 tensions such as those encountered in the colon.
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Oatley P, Kirk JA, Ma S, Jones S, Fagan RP. Spatial organization of Clostridium difficile S-layer biogenesis. Sci Rep 2020; 10:14089. [PMID: 32839524 PMCID: PMC7445750 DOI: 10.1038/s41598-020-71059-x] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Accepted: 08/09/2020] [Indexed: 12/29/2022] Open
Abstract
Surface layers (S-layers) are protective protein coats which form around all archaea and most bacterial cells. Clostridium difficile is a Gram-positive bacterium with an S-layer covering its peptidoglycan cell wall. The S-layer in C. difficile is constructed mainly of S-layer protein A (SlpA), which is a key virulence factor and an absolute requirement for disease. S-layer biogenesis is a complex multi-step process, disruption of which has severe consequences for the bacterium. We examined the subcellular localization of SlpA secretion and S-layer growth; observing formation of S-layer at specific sites that coincide with cell wall synthesis, while the secretion of SlpA from the cell is relatively delocalized. We conclude that this delocalized secretion of SlpA leads to a pool of precursor in the cell wall which is available to repair openings in the S-layer formed during cell growth or following damage.
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Affiliation(s)
- Peter Oatley
- Department of Molecular Biology and Biotechnology, Florey Institute, University of Sheffield, Sheffield, S10 2TN, UK.
- School of Medicine, University of Central Lancashire, Preston, PR1 7BH, UK.
| | - Joseph A Kirk
- Department of Molecular Biology and Biotechnology, Florey Institute, University of Sheffield, Sheffield, S10 2TN, UK
| | - Shuwen Ma
- Department of Chemistry, University of Sheffield, Sheffield, S3 7HF, UK
| | - Simon Jones
- Department of Chemistry, University of Sheffield, Sheffield, S3 7HF, UK
| | - Robert P Fagan
- Department of Molecular Biology and Biotechnology, Florey Institute, University of Sheffield, Sheffield, S10 2TN, UK.
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Chromosomal Resistance to Metronidazole in Clostridioides difficile Can Be Mediated by Epistasis between Iron Homeostasis and Oxidoreductases. Antimicrob Agents Chemother 2020; 64:AAC.00415-20. [PMID: 32457109 DOI: 10.1128/aac.00415-20] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 05/21/2020] [Indexed: 12/17/2022] Open
Abstract
Chromosomal resistance to metronidazole has emerged in clinical Clostridioides difficile isolates, but the genetic mechanisms remain unclear. This is further hindered by the inability to generate spontaneous metronidazole-resistant mutants in the lab to interpret genetic variations in clinical isolates. We therefore constructed a mismatch repair mutator in nontoxigenic ATCC 700057 to survey the mutational landscape for de novo resistance mechanisms. In separate experimental evolutions, the mutator adopted a deterministic path to resistance, with truncation of the ferrous iron transporter FeoB1 as a first-step mechanism of low-level resistance. Deletion of feoB1 in ATCC 700057 reduced the intracellular iron content, appearing to shift cells toward flavodoxin-mediated oxidoreductase reactions, which are less favorable for metronidazole's cellular action. Higher-level resistance evolved from sequential acquisition of mutations to catalytic domains of pyruvate-ferredoxin/flavodoxin oxidoreductase (PFOR; encoded by nifJ), a synonymous codon change to putative xdh (xanthine dehydrogenase; encoded by CD630_31770), likely affecting mRNA stability, and last, frameshift and point mutations that inactivated the iron-sulfur cluster regulator (IscR). Gene silencing of nifJ, xdh, or iscR with catalytically dead Cas9 revealed that resistance involving these genes occurred only when feoB1 was inactivated; i.e., resistance was seen only in the feoB1 deletion mutant and not in the isogenic wild-type (WT) parent. Interestingly, metronidazole resistance in C. difficile infection (CDI)-associated strains carrying mutations in nifJ was reduced upon gene complementation. This observation supports the idea that mutation in PFOR is one mechanism of metronidazole resistance in clinical strains. Our findings indicate that metronidazole resistance in C. difficile is complex, involving multigenetic mechanisms that could intersect with iron-dependent and oxidoreductive metabolic pathways.
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Jiang Y, Fu Y, Ren Z, Gou H, Xu C. Screening and application of inducible promoters in Ruminiclostridium papyrosolvens. Lett Appl Microbiol 2020; 71:428-436. [PMID: 32649779 DOI: 10.1111/lam.13352] [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: 04/21/2020] [Revised: 07/05/2020] [Accepted: 07/06/2020] [Indexed: 11/27/2022]
Abstract
Ruminiclostridium papyrosolvens is a promising candidate for producing renewable green chemicals from cellulose due to its cellulolytic and ethanologenic capabilities. It is of significance to screen effective, and convenient-to-use inducible promoters that can be used for regulating the gene expression in R. papyrosolvens. We characterized two endogenous inducible promoters and investigated another two exogenous ones on the adaptability in R. papyrosolvens. Both of the endogenous xylan-inducible promoter Pxyl and exogenous lactose-inducible promoter Plac are found of high specificity and stringency. Pxyl has a short time to be induced while Plac has a low concentration of inducer. With these findings, a mazF-based counter selectable system has been constructed for promoting the efficiency of mutant screening via plasmid curing. The inducible gene expression systems provided novel tools for enhancing the capability of genetic manipulation in engineering R. papyrosolvens. SIGNIFICANCE AND IMPACT OF THE STUDY: Four inducible promoters from Clostridia were characterized in R. papyrosolvens. Xylan-inducible promoter Pxyl was found of a short time while lactose-inducible promoter Plac needs a low concentration of inducer to induce. Employing them, we successfully construct a mazF-based counter selectable system, which would be used to increase the mutant screening efficiency via induction of plasmid curing. The inducible gene expression systems provided novel tools for enhancing the capability of genetic manipulation in engineering R. papyrosolvens.
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Affiliation(s)
- Y Jiang
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, China
| | - Y Fu
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, China
| | - Z Ren
- Institute of Applied Chemistry, Shanxi University, Taiyuan, China
| | - H Gou
- Shenzhen Digital Life Institute, Shenzhen, China
| | - C Xu
- Key Laboratory of Chemical Biology and Molecular Engineering of Ministry of Education, Institute of Biotechnology, Shanxi University, Taiyuan, China
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Martínez-Meléndez A, Morfin-Otero R, Villarreal-Treviño L, Baines SD, Camacho-Ortíz A, Garza-González E. Molecular epidemiology of predominant and emerging Clostridioides difficile ribotypes. J Microbiol Methods 2020; 175:105974. [PMID: 32531232 DOI: 10.1016/j.mimet.2020.105974] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 06/05/2020] [Accepted: 06/05/2020] [Indexed: 12/18/2022]
Abstract
There has been an increase in the incidence and severity of Clostridioides difficile infection (CDI) worldwide, and strategies to control, monitor, and diminish the associated morbidity and mortality have been developed. Several typing methods have been used for typing of isolates and studying the epidemiology of CDI; serotyping was the first typing method, but then was replaced by pulsed-field gel electrophoresis (PFGE). PCR ribotyping is now the gold standard method; however, multi locus sequence typing (MLST) schemes have been developed. New sequencing technologies have allowed comparing whole bacterial genomes to address genetic relatedness with a high level of resolution and discriminatory power to distinguish between closely related strains. Here, we review the most frequent C. difficile ribotypes reported worldwide, with a focus on their epidemiology and genetic characteristics.
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Affiliation(s)
- Adrián Martínez-Meléndez
- Universidad Autónoma de Nuevo León, Facultad de Ciencias Químicas, Pedro de Alba S/N, Ciudad Universitaria, CP 66450 San Nicolás de los Garza, Nuevo Leon, Mexico
| | - Rayo Morfin-Otero
- Hospital Civil de Guadalajara "Fray Antonio Alcalde" e Instituto de Patología Infecciosa y Experimental, Centro Universitario de Ciencias de la Salud, Universidad de Guadalajara. Sierra Mojada 950, Col. Independencia, CP 44350 Guadalajara, Jalisco, Mexico
| | - Licet Villarreal-Treviño
- Universidad Autónoma de Nuevo León, Facultad de Ciencias Biológicas, Departamento de Microbiología e Inmunología, Pedro de Alba S/N, Ciudad Universitaria, CP 66450 San Nicolás de los Garza, Nuevo Leon, Mexico
| | - Simon D Baines
- University of Hertfordshire, School of Life and Medical Sciences, Department of Biological and Environmental Sciences, Hatfield AL10 9AB, UK
| | - Adrián Camacho-Ortíz
- Universidad Autónoma de Nuevo León, Hospital Universitario "Dr. José Eleuterio González", Servicio de Infectología. Av. Francisco I. Madero Pte. S/N y Av. José E. González. Col. Mitras Centro, CP 64460 Monterrey, Nuevo Leon, Mexico
| | - Elvira Garza-González
- Universidad Autónoma de Nuevo León, Hospital Universitario "Dr. José Eleuterio González", Servicio de Infectología. Av. Francisco I. Madero Pte. S/N y Av. José E. González. Col. Mitras Centro, CP 64460 Monterrey, Nuevo Leon, Mexico.
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Abstract
Understanding the underlying biology of pathogens is essential to develop novel treatment options. To drive this understanding, genetic tools are essential. In recent years, the genetic toolbox available to Clostridioides difficile researchers has expanded significantly but still requires the conjugal transfer of DNA from a donor strain into C. difficile. Here we describe an electroporation-based transformation protocol that was effective at introducing existing genetic tools into different C. difficile strains. An important risk factor for acquiring Clostridioides difficile infection is antibiotic use. Therefore, a detailed knowledge of the physiology and the virulence factors can help drive the development of new diagnostic tools and nonantibiotic therapeutic agents to combat these organisms. Several genetic systems are available to study C. difficile in the laboratory environment, and all rely on stably replicating or segregationally unstable plasmids. Currently, the transfer of plasmids into C. difficile can only be performed by conjugation using Escherichia coli or Bacillus subtilis as conjugal donors. Here we report a method to introduce plasmid DNA into C. difficile using electroporation and test factors that might contribute to higher transformation efficiencies: osmolyte used to stabilize weakened cells, DNA concentration, and recovery time postelectroporation. Depending on the C. difficile strain and plasmid used, this transformation protocol achieves between 20 and 200 colonies per microgram of DNA and is mostly influenced by the recovery time postelectroporation. Based on our findings, we recommend that each strain be tested for the optimum recovery time in each lab. IMPORTANCE Understanding the underlying biology of pathogens is essential to develop novel treatment options. To drive this understanding, genetic tools are essential. In recent years, the genetic toolbox available to Clostridioides difficile researchers has expanded significantly but still requires the conjugal transfer of DNA from a donor strain into C. difficile. Here we describe an electroporation-based transformation protocol that was effective at introducing existing genetic tools into different C. difficile strains.
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44
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Wen Z, Li Q, Liu J, Jin M, Yang S. Consolidated bioprocessing for butanol production of cellulolytic Clostridia: development and optimization. Microb Biotechnol 2020; 13:410-422. [PMID: 31448546 PMCID: PMC7017829 DOI: 10.1111/1751-7915.13478] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Revised: 08/02/2019] [Accepted: 08/04/2019] [Indexed: 12/20/2022] Open
Abstract
Butanol is an important bulk chemical, as well as a promising renewable gasoline substitute, that is commonly produced by solventogenic Clostridia. The main cost of cellulosic butanol fermentation is caused by cellulases that are required to saccharify lignocellulose, since solventogenic Clostridia cannot efficiently secrete cellulases. However, cellulolytic Clostridia can natively degrade lignocellulose and produce ethanol, acetate, butyrate and even butanol. Therefore, cellulolytic Clostridia offer an alternative to develop consolidated bioprocessing (CBP), which combines cellulase production, lignocellulose hydrolysis and co-fermentation of hexose/pentose into butanol in one step. This review focuses on CBP advances for butanol production of cellulolytic Clostridia and various synthetic biotechnologies that drive these advances. Moreover, the efforts to optimize the CBP-enabling cellulolytic Clostridia chassis are also discussed. These include the development of genetic tools, pentose metabolic engineering and the improvement of butanol tolerance. Designer cellulolytic Clostridia or consortium provide a promising approach and resource to accelerate future CBP for butanol production.
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Affiliation(s)
- Zhiqiang Wen
- School of Environmental and Biological EngineeringNanjing University of Science and TechnologyNanjing210094China
| | - Qi Li
- College of Life SciencesSichuan Normal UniversityLongquan, Chengdu610101China
| | - Jinle Liu
- Key Laboratory of Synthetic BiologyCAS Center for Excellence in Molecular Plant SciencesShanghai Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghai200032China
| | - Mingjie Jin
- School of Environmental and Biological EngineeringNanjing University of Science and TechnologyNanjing210094China
| | - Sheng Yang
- Key Laboratory of Synthetic BiologyCAS Center for Excellence in Molecular Plant SciencesShanghai Institute of Plant Physiology and EcologyChinese Academy of SciencesShanghai200032China
- Huzhou Center of Industrial BiotechnologyShanghai Institutes of Biological SciencesChinese Academy of SciencesShanghai200032China
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Strain-Dependent RstA Regulation of Clostridioides difficile Toxin Production and Sporulation. J Bacteriol 2020; 202:JB.00586-19. [PMID: 31659010 DOI: 10.1128/jb.00586-19] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 10/21/2019] [Indexed: 02/04/2023] Open
Abstract
The anaerobic spore former Clostridioides difficile causes significant diarrheal disease in humans and other mammals. Infection begins with the ingestion of dormant spores, which subsequently germinate within the host gastrointestinal tract. There, the vegetative cells proliferate and secrete two exotoxins, TcdA and TcdB, which cause disease symptoms. Although spore formation and toxin production are critical for C. difficile pathogenesis, the regulatory links between these two physiological processes are not well understood and are strain dependent. Previously, we identified a conserved C. difficile regulator, RstA, that promotes sporulation initiation through an unknown mechanism and directly and indirectly represses toxin and motility gene transcription in the historical isolate 630Δerm To test whether perceived strain-dependent differences in toxin production and sporulation are mediated by RstA, we created an rstA mutant in the epidemic ribotype 027 strain R20291. RstA affected sporulation and toxin gene expression similarly but more robustly in R20291 than in 630Δerm In contrast, no effect on motility gene expression was observed in R20291. Reporter assays measuring transcriptional regulation of tcdR, the sigma factor gene essential for toxin gene expression, identified sequence-dependent effects influencing repression by RstA and CodY, a global nutritional sensor, in four diverse C. difficile strains. Finally, sequence- and strain-dependent differences were evident in RstA negative autoregulation of rstA transcription. Altogether, our data suggest that strain-dependent differences in RstA regulation contribute to the sporulation and toxin phenotypes observed in R20291. Our data establish RstA as an important regulator of C. difficile virulence traits.IMPORTANCE Two critical traits of Clostridioides difficile pathogenesis are toxin production, which causes disease symptoms, and spore formation, which permits survival outside the gastrointestinal tract. The multifunctional regulator RstA promotes sporulation and prevents toxin production in the historical strain 630Δerm Here, we show that RstA exhibits stronger effects on these phenotypes in an epidemic isolate, R20291, and additional strain-specific effects on toxin and rstA expression are evident. Our data demonstrate that sequence-specific differences within the promoter for the toxin regulator TcdR contribute to the regulation of toxin production by RstA and CodY. These sequence differences account for some of the variability in toxin production among isolates and may allow strains to differentially control toxin production in response to a variety of signals.
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Regulation and Anaerobic Function of the Clostridioides difficile β-Lactamase. Antimicrob Agents Chemother 2019; 64:AAC.01496-19. [PMID: 31611350 DOI: 10.1128/aac.01496-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 10/07/2019] [Indexed: 01/05/2023] Open
Abstract
Clostridioides difficile causes severe antibiotic-associated diarrhea and colitis. C. difficile is an anaerobic, Gram-positive sporeformer that is highly resistant to β-lactams, the most commonly prescribed antibiotics. The resistance of C. difficile to β-lactam antibiotics allows the pathogen to replicate and cause disease in antibiotic-treated patients. However, the mechanisms of β-lactam resistance in C. difficile are not fully understood. Our data reinforce prior evidence that C. difficile produces a β-lactamase, which is a common β-lactam resistance mechanism found in other bacterial species. Here, we characterize the C. difficile bla operon that encodes a lipoprotein of unknown function and a β-lactamase that was greatly induced in response to several classes of β-lactam antibiotics. An in-frame deletion of the operon abolished β-lactamase activity in C. difficile strain 630Δerm and resulted in decreased resistance to the β-lactam ampicillin. We found that the activity of this β-lactamase, BlaCDD, is dependent upon the redox state of the enzyme. In addition, we observed that transport of BlaCDD out of the cytosol and to the cell surface is facilitated by an N-terminal signal sequence. Our data demonstrate that a cotranscribed lipoprotein, BlaX, aids in BlaCDD activity. Further, we identified a conserved BlaRI regulatory system and demonstrated via insertional disruption that BlaRI controls transcription of the blaXCDD genes in response to β-lactams. These results provide support for the function of a β-lactamase in C. difficile antibiotic resistance and reveal the unique roles of a coregulated lipoprotein and reducing environment in C. difficile β-lactamase activity.
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Saito R, Usui Y, Ayibieke A, Nakajima J, Prah I, Sonobe K, Aiso Y, Ito S, Itsui Y, Hadano Y, Nukui Y, Koike R, Tohda S. Hypervirulent clade 2, ribotype 019/sequence type 67 Clostridioides difficile strain from Japan. Gut Pathog 2019; 11:54. [PMID: 31700548 PMCID: PMC6827173 DOI: 10.1186/s13099-019-0336-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/27/2019] [Accepted: 10/25/2019] [Indexed: 12/12/2022] Open
Abstract
Background Clostridioides difficile ribotype (RT) 019/sequence type (ST) 67 strains belong to a hypervirulent lineage closely related to RT027/ST1; however, limited data are available for hypervirulent clade 2 lineages in Japan. Herein, we report the draft genome of a C. difficile strain B18-123 belonging to clade 2, RT019/ST67 for the first time in Japan. Results The pathogenicity locus carried by B18-123 (19.6 kb) showed higher homology (97.29% nucleotide identity) with strain R20291 (RT027/ST1) than the reference strain 630 (RT012/ST54), and B18-123 harbored 8-nucleotide substitutions in tcdC. However, it did not contain an 18-base pair (bp) deletion or a single-bp deletion at position 117 in tcdC, which was identified in the previous strain R20291. A cytotoxicity assay revealed similar cytotoxicity levels between strains B18-123 and ATCC BAA-1870 (RT027/ST1). The B18-123 strain was found to be susceptible to metronidazole and vancomycin. Conclusion Our findings contribute to the further understanding of the characteristics of hypervirulent clade 2 including RT019/ST67 lineages.
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Affiliation(s)
- Ryoichi Saito
- 1Department of Molecular Microbiology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan.,2Department of Infection Control and Prevention, Tokyo Medical and Dental University Medical Hospital, Tokyo, Japan
| | - Yukino Usui
- 1Department of Molecular Microbiology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Alafate Ayibieke
- 1Department of Molecular Microbiology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Jun Nakajima
- 2Department of Infection Control and Prevention, Tokyo Medical and Dental University Medical Hospital, Tokyo, Japan.,3Department of Clinical Laboratory, Tokyo Medical and Dental University Medical Hospital, Tokyo, Japan
| | - Isaac Prah
- 1Department of Molecular Microbiology, Graduate School of Medical and Dental Sciences, Tokyo Medical and Dental University, Tokyo, Japan
| | - Kazunari Sonobe
- 2Department of Infection Control and Prevention, Tokyo Medical and Dental University Medical Hospital, Tokyo, Japan.,3Department of Clinical Laboratory, Tokyo Medical and Dental University Medical Hospital, Tokyo, Japan
| | - Yoshibumi Aiso
- 2Department of Infection Control and Prevention, Tokyo Medical and Dental University Medical Hospital, Tokyo, Japan
| | - Shiori Ito
- 4Department of Gastroenterology and Hepatology, Tokyo Medical and Dental University Medical Hospital, Tokyo, Japan
| | - Yasuhiro Itsui
- 4Department of Gastroenterology and Hepatology, Tokyo Medical and Dental University Medical Hospital, Tokyo, Japan
| | - Yoshiro Hadano
- 2Department of Infection Control and Prevention, Tokyo Medical and Dental University Medical Hospital, Tokyo, Japan
| | - Yoko Nukui
- 2Department of Infection Control and Prevention, Tokyo Medical and Dental University Medical Hospital, Tokyo, Japan
| | - Ryuji Koike
- 2Department of Infection Control and Prevention, Tokyo Medical and Dental University Medical Hospital, Tokyo, Japan
| | - Shuji Tohda
- 3Department of Clinical Laboratory, Tokyo Medical and Dental University Medical Hospital, Tokyo, Japan
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48
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Shen A, Edwards AN, Sarker MR, Paredes-Sabja D. Sporulation and Germination in Clostridial Pathogens. Microbiol Spectr 2019; 7:10.1128/microbiolspec.GPP3-0017-2018. [PMID: 31858953 PMCID: PMC6927485 DOI: 10.1128/microbiolspec.gpp3-0017-2018] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2018] [Indexed: 12/14/2022] Open
Abstract
As obligate anaerobes, clostridial pathogens depend on their metabolically dormant, oxygen-tolerant spore form to transmit disease. However, the molecular mechanisms by which those spores germinate to initiate infection and then form new spores to transmit infection remain poorly understood. While sporulation and germination have been well characterized in Bacillus subtilis and Bacillus anthracis, striking differences in the regulation of these processes have been observed between the bacilli and the clostridia, with even some conserved proteins exhibiting differences in their requirements and functions. Here, we review our current understanding of how clostridial pathogens, specifically Clostridium perfringens, Clostridium botulinum, and Clostridioides difficile, induce sporulation in response to environmental cues, assemble resistant spores, and germinate metabolically dormant spores in response to environmental cues. We also discuss the direct relationship between toxin production and spore formation in these pathogens.
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Affiliation(s)
- Aimee Shen
- Department of Molecular Biology and Microbiology, Tufts University Medical School, Boston, MA
| | - Adrianne N Edwards
- Department of Microbiology and Immunology, Emory University School of Medicine, Atlanta, GA
| | - Mahfuzur R Sarker
- Department of Microbiology, College of Science, Oregon State University, Corvallis, OR
- Department of Biomedical Sciences, College of Veterinary Medicine, Oregon State University, Corvallis, OR
| | - Daniel Paredes-Sabja
- Department of Gut Microbiota and Clostridia Research Group, Departamento de Ciencias Biolo gicas, Facultad de Ciencias Biologicas, Universidad Andres Bello, Santiago, Chile
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49
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Woods C, Humphreys CM, Rodrigues RM, Ingle P, Rowe P, Henstra AM, Köpke M, Simpson SD, Winzer K, Minton NP. A novel conjugal donor strain for improved DNA transfer into Clostridium spp. Anaerobe 2019; 59:184-191. [PMID: 31269456 PMCID: PMC6866869 DOI: 10.1016/j.anaerobe.2019.06.020] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2019] [Revised: 06/27/2019] [Accepted: 06/29/2019] [Indexed: 12/29/2022]
Abstract
Clostridium encompasses species which are relevant to human and animal disease as well as species which have industrial potential, for instance, as producers of chemicals and fuels or as tumour delivery vehicles. Genetic manipulation of these target organisms is critical for advances in these fields. DNA transfer efficiencies, however, vary between species. Low efficiencies can impede the progress of research efforts. A novel conjugal donor strain of Escherichia coli has been created which exhibits a greater than 10-fold increases in conjugation efficiency compared to the traditionally used CA434 strain in the three species tested; C. autoethanogenum DSM 10061, C. sporogenes NCIMB 10696 and C. difficile R20291. The novel strain, designated 'sExpress', does not methylate DNA at Dcm sites (CCWGG) which allows circumvention of cytosine-specific Type IV restriction systems. A robust protocol for conjugation is presented which routinely produces in the order of 105 transconjugants per millilitre of donor cells for C. autoethanogenum, 106 for C. sporogenes and 102 for C. difficile R20291. The novel strain created is predicted to be a superior conjugal donor in a wide range of species which possess Type IV restriction systems.
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Affiliation(s)
- Craig Woods
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, The University of Nottingham, Nottingham, NG7 2RD, UK
| | - Christopher M Humphreys
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, The University of Nottingham, Nottingham, NG7 2RD, UK
| | - Raquel Mesquita Rodrigues
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, The University of Nottingham, Nottingham, NG7 2RD, UK
| | - Patrick Ingle
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, The University of Nottingham, Nottingham, NG7 2RD, UK
| | - Peter Rowe
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, The University of Nottingham, Nottingham, NG7 2RD, UK
| | - Anne M Henstra
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, The University of Nottingham, Nottingham, NG7 2RD, UK
| | - Michael Köpke
- LanzaTech Inc., 8045 Lamon Avenue, Suite 400, Skokie, IL, USA
| | - Sean D Simpson
- LanzaTech Inc., 8045 Lamon Avenue, Suite 400, Skokie, IL, USA
| | - Klaus Winzer
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, The University of Nottingham, Nottingham, NG7 2RD, UK
| | - Nigel P Minton
- Clostridia Research Group, BBSRC/EPSRC Synthetic Biology Research Centre (SBRC), School of Life Sciences, The University of Nottingham, Nottingham, NG7 2RD, UK; NIHR Nottingham Biomedical Research Centre, Nottingham University Hospitals NHS Trust and the University of Nottingham, Nottingham NG7 2RD, UK.
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50
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Using an Endogenous CRISPR-Cas System for Genome Editing in the Human Pathogen Clostridium difficile. Appl Environ Microbiol 2019; 85:AEM.01416-19. [PMID: 31399410 DOI: 10.1128/aem.01416-19] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 08/06/2019] [Indexed: 12/19/2022] Open
Abstract
The human enteropathogen Clostridium difficile constitutes a key public health issue in industrialized countries. Many aspects of C. difficile pathophysiology and adaptation inside the host remain poorly understood. We have recently reported that this bacterium possesses an active CRISPR-Cas system of subtype I-B for defense against phages and other mobile genetic elements that could contribute to its success during infection. In this paper, we demonstrate that redirecting this endogenous CRISPR-Cas system toward autoimmunity allows efficient genome editing in C. difficile We provide a detailed description of this newly developed approach and show, as a proof of principle, its efficient application for deletion of a specific gene in reference strain 630Δerm and in epidemic C. difficile strain R20291. The new method expands the arsenal of the currently limiting set of gene engineering tools available for investigation of C. difficile and may serve as the basis for new strategies to control C. difficile infections.IMPORTANCE Clostridium difficile represents today a real danger for human and animal health. It is the leading cause of diarrhea associated with health care in adults in industrialized countries. The incidence of these infections continues to increase, and this trend is accentuated by the general aging of the population. Many questions about the mechanisms contributing to C. difficile's success inside the host remain unanswered. The set of genetic tools available for this pathogen is limited, and new developments are badly needed. C. difficile has developed efficient defense systems that are directed against foreign DNA and that could contribute to its survival in phage-rich gut communities. We show how one such defense system, named CRISPR-Cas, can be hijacked for C. difficile genome editing. Our results also show a great potential for the use of the CRISPR-Cas system for the development of new therapeutic strategies against C. difficile infections.
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