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Awad MM, Suraweera CD, Vidor CJ, Ye-Lin AY, Williams GC, Mileto SJ, Barlow CK, McGowan S, Lyras D. A Clostridioides difficile endolysin modulates toxin secretion without cell lysis. Commun Biol 2024; 7:1044. [PMID: 39179651 PMCID: PMC11344133 DOI: 10.1038/s42003-024-06730-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 08/13/2024] [Indexed: 08/26/2024] Open
Abstract
The Clostridia produce and secrete Large Clostridial Glucosylating Toxins (LCGTs) responsible for disease symptoms, but the secretion mechanism is largely unknown. Recently, a holin-like protein was shown to be essential for toxin secretion. Holins, typically bacteriophage-specific proteins, are part of the holin-endo(lysin) system that releases phage progeny. To determine if the clostridia also use a lysin, we investigated two conserved putative lysins, M7404_01910 and M7404_02200, in the release of the LCGTs TcdA and TcdB from a Clostridioides difficile ribotype 027 strain, M7404. Sequence analysis and structural modelling indicates that both proteins are related to N-acetylmuramoyl-l-alanine amidases, similar to CD27L, a lysin from the C. difficile phage ΦCD27. Disruption of these genes reveal that only M7404_02200 contributes to toxin secretion and does so in a non-lytic fashion. Peptidoglycan hydrolysis assays show that recombinant M7404_02200 is an active peptidoglycan amidase, confirming its role in TcdA and TcdB secretion in C. difficile M7404.
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Affiliation(s)
- Milena M Awad
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, 3800, Australia
| | - Chathura D Suraweera
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, 3800, Australia
| | - Callum J Vidor
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, 3800, Australia
| | - Auberon Y Ye-Lin
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, 3800, Australia
| | - Galain C Williams
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, 3800, Australia
| | - Steven J Mileto
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, 3800, Australia
| | - Christopher K Barlow
- Department of Biochemistry, Biomedicine Discovery Institute, Monash University, Clayton, 3800, Australia
- Monash Proteomics & Metabolomics Platform, Monash University, Clayton, 3800, Australia
| | - Sheena McGowan
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, 3800, Australia
| | - Dena Lyras
- Department of Microbiology, Biomedicine Discovery Institute, Monash University, Clayton, 3800, Australia.
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2
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Yan Y, Xu J, Huang W, Fan Y, Li Z, Tian M, Ma J, Lu X, Liang J. Metagenomic and Culturomics Analysis of Microbial Communities within Surface Sediments and the Prevalence of Antibiotic Resistance Genes in a Pristine River: The Zaqu River in the Lancang River Source Region, China. Microorganisms 2024; 12:911. [PMID: 38792738 PMCID: PMC11124135 DOI: 10.3390/microorganisms12050911] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2024] [Revised: 04/26/2024] [Accepted: 04/28/2024] [Indexed: 05/26/2024] Open
Abstract
Microbial communities inhabiting sedimentary environments in river source regions serve as pivotal indicators of pristine river ecosystems. While the correlation between antibiotic resistome and pathogenicity with core gut bacteria in humans is well established, there exists a significant knowledge gap concerning the interaction of antibiotic resistance genes (ARGs) and human pathogenic bacteria (HPB) with specific microbes in river source basins, often referred to as "terrestrial gut". Understanding the microbial composition, including bacteria and resident genetic elements such as ARGs, HPB, Mobile Genetic Elements (MGEs), and Virulence Factors (VFs), within natural habitats against the backdrop of global change, is imperative. To address this gap, an enrichment-based culturomics complementary along with metagenomics was conducted in this study to characterize the microbial biobank and provide preliminary ecological insights into profiling the dissemination of ARGs in the Lancang River Source Basin. Based on our findings, in the main stream of the Lancang River Source Basin, 674 strains of bacteria, comprising 540 strains under anaerobic conditions and 124 under aerobic conditions, were successfully isolated. Among these, 98 species were identified as known species, while 4 were potential novel species. Of these 98 species, 30 were HPB relevant to human health. Additionally, bacA and bacitracin emerged as the most abundant ARGs and antibiotics in this river, respectively. Furthermore, the risk assessment of ARGs predominantly indicated the lowest risk rank (Rank Ⅳ) in terms of endangering human health. In summary, enrichment-based culturomics proved effective in isolating rare and unknown bacteria, particularly under anaerobic conditions. The emergence of ARGs showed limited correlation with MGEs, indicating minimal threats to human health within the main stream of the Lancang River Source Basin.
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Affiliation(s)
- Yi Yan
- School of Light Industry Science and Engineering, Beijing Technology and Business University, Beijing 100048, China; (Y.Y.); (J.X.); (W.H.); (M.T.); (J.M.)
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
| | - Jialiang Xu
- School of Light Industry Science and Engineering, Beijing Technology and Business University, Beijing 100048, China; (Y.Y.); (J.X.); (W.H.); (M.T.); (J.M.)
| | - Wenmin Huang
- School of Light Industry Science and Engineering, Beijing Technology and Business University, Beijing 100048, China; (Y.Y.); (J.X.); (W.H.); (M.T.); (J.M.)
| | - Yufeng Fan
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (Y.F.); (Z.L.)
| | - Zhenpeng Li
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (Y.F.); (Z.L.)
| | - Mingkai Tian
- School of Light Industry Science and Engineering, Beijing Technology and Business University, Beijing 100048, China; (Y.Y.); (J.X.); (W.H.); (M.T.); (J.M.)
| | - Jinsheng Ma
- School of Light Industry Science and Engineering, Beijing Technology and Business University, Beijing 100048, China; (Y.Y.); (J.X.); (W.H.); (M.T.); (J.M.)
| | - Xin Lu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China; (Y.F.); (Z.L.)
| | - Jian Liang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, Xining 810016, China
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3
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Cai X, Peng Y, Yang G, Feng L, Tian X, Huang P, Mao Y, Xu L. Populational genomic insights of Paraclostridium bifermentans as an emerging human pathogen. Front Microbiol 2023; 14:1293206. [PMID: 38029151 PMCID: PMC10665999 DOI: 10.3389/fmicb.2023.1293206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2023] [Accepted: 10/26/2023] [Indexed: 12/01/2023] Open
Abstract
Paraclostridium bifermentans (P.b) is an emerging human pathogen that is phylogenomically close to Paeniclostridium sordellii (P.s), while their populational genomic features and virulence capacity remain understudied. Here, we performed comparative genomic analyses of P.b and compared their pan-genomic features and virulence coding profiles to those of P.s. Our results revealed that P.b has a more plastic pangenome, a larger genome size, and a higher GC content than P.s. Interestingly, the P.b and P.s share similar core-genomic functions, but P.b encodes more functions in nutrient metabolism and energy conversion and fewer functions in host defense in their accessory-genomes. The P.b may initiate extracellular infection processes similar to those of P.s and Clostridium perfringens by encoding three toxin homologs (i.e., microbial collagenase, thiol-activated cytolysin, phospholipase C, which are involved in extracellular matrices degradation and membrane damaging) in their core-genomes. However, P.b is less toxic than the P.s by encoding fewer secretion toxins in the core-genome and fewer lethal toxins in the accessory-genome. Notably, P.b carries more toxins genes in their accessory-genomes, particularly those of plasmid origin. Moreover, three within-species and highly conserved plasmid groups, encoding virulence, gene acquisition, and adaptation, were carried by 25-33% of P.b strains and clustered by isolation source rather than geography. This study characterized the pan-genomic virulence features of P.b for the first time, and revealed that P. bifermentans is an emerging pathogen that can threaten human health in many aspects, emphasizing the importance of phenotypic and genomic characterizations of in situ clinical isolates.
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Affiliation(s)
- Xunchao Cai
- Department of Gastroenterology and Hepatology, Shenzhen University General Hospital, Shenzhen University, Shenzhen, Guangdong, China
- Marshall Laboratory of Biomedical Engineering, Shenzhen University, Shenzhen, Guangdong, China
| | - Yao Peng
- Department of Gastroenterology and Hepatology, Shenzhen University General Hospital, Shenzhen University, Shenzhen, Guangdong, China
| | - Gongli Yang
- Department of Gastroenterology and Hepatology, Shenzhen University General Hospital, Shenzhen University, Shenzhen, Guangdong, China
| | - Lijuan Feng
- Department of Gastroenterology and Hepatology, Shenzhen University General Hospital, Shenzhen University, Shenzhen, Guangdong, China
| | - Xiaojuan Tian
- Department of Gastroenterology and Hepatology, Shenzhen University General Hospital, Shenzhen University, Shenzhen, Guangdong, China
| | - Ping Huang
- Department of Gastroenterology and Hepatology, Shenzhen University General Hospital, Shenzhen University, Shenzhen, Guangdong, China
| | - Yanping Mao
- College of Chemistry and Environmental Engineering, Shenzhen University, Shenzhen, Guangdong, China
| | - Long Xu
- Department of Gastroenterology and Hepatology, Shenzhen University General Hospital, Shenzhen University, Shenzhen, Guangdong, China
- Marshall Laboratory of Biomedical Engineering, Shenzhen University, Shenzhen, Guangdong, China
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4
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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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5
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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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6
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Revitt-Mills SA, Watts TD, Lyras D, Adams V, Rood JI. The ever-expanding tcp conjugation locus of pCW3 from Clostridium perfringens. Plasmid 2020; 113:102516. [PMID: 32526229 DOI: 10.1016/j.plasmid.2020.102516] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Revised: 04/20/2020] [Accepted: 04/26/2020] [Indexed: 12/13/2022]
Abstract
The spore-forming, anaerobic Gram positive pathogen Clostridium perfringens encodes many of its disease-causing toxins on closely related conjugative plasmids. Studies of the tetracycline resistance plasmid pCW3 have identified many of the genes involved in conjugative transfer, which are located in the tcp conjugation locus. Upstream of this locus is an uncharacterised region (the cnaC region) that is highly conserved. This study examined the importance in pCW3 conjugation of several highly conserved proteins encoded in the cnaC region. Conjugative mating studies suggested that the SrtD, TcpN and Dam proteins were required for efficient pCW3 transfer between C. perfringens cells from the same strain background. The requirement of these proteins for conjugation was amplified in matings between C. perfringens cells of different strain backgrounds. Additionally, the putative collagen adhesin protein, CnaC, was only required for the optimal transfer of pCW3 between cells of different strain backgrounds. Based on these studies we postulate that CnaC, SrtD, TcpN and Dam are involved in enhancing the transfer frequency of pCW3. These studies have led to a significant expansion of the tcp conjugation locus, which now encompasses a 19 kb region.
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Affiliation(s)
- Sarah A Revitt-Mills
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Department of Microbiology, Monash University, Victoria 3800, Australia.
| | - Thomas D Watts
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Department of Microbiology, Monash University, Victoria 3800, Australia
| | - Dena Lyras
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Department of Microbiology, Monash University, Victoria 3800, Australia
| | - Vicki Adams
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Department of Microbiology, Monash University, Victoria 3800, Australia
| | - Julian I Rood
- Infection and Immunity Program, Monash Biomedicine Discovery Institute, Department of Microbiology, Monash University, Victoria 3800, Australia
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7
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Tian S, Liu Y, Wu H, Liu H, Zeng J, Choi MY, Chen H, Gerhard R, Dong M. Genome-Wide CRISPR Screen Identifies Semaphorin 6A and 6B as Receptors for Paeniclostridium sordellii Toxin TcsL. Cell Host Microbe 2020; 27:782-792.e7. [PMID: 32302524 DOI: 10.1016/j.chom.2020.03.007] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Revised: 02/04/2020] [Accepted: 03/11/2020] [Indexed: 01/21/2023]
Abstract
The exotoxin TcsL is a major virulence factor in Paeniclostridium (Clostridium) sordellii and responsible for the high lethality rate associated with P. sordellii infection. Here, we present a genome-wide CRISPR-Cas9-mediated screen using a human lung carcinoma cell line and identify semaphorin (SEMA) 6A and 6B as receptors for TcsL. Disrupting SEMA6A/6B expression in several distinct human cell lines and primary human endothelial cells results in reduced TcsL sensitivity, while SEMA6A/6B over-expression increases their sensitivity. TcsL recognizes the extracellular domain (ECD) of SEMA6A/6B via a region homologous to the receptor-binding site in Clostridioides difficile toxin B (TcdB), which binds the human receptor Frizzled. Exchanging the receptor-binding interfaces between TcsL and TcdB switches their receptor-binding specificity. Finally, administration of SEMA6A-ECD proteins protects human cells from TcsL toxicity and reduces TcsL-induced damage to lung tissues and the lethality rate in mice. These findings establish SEMA6A and 6B as pathophysiologically relevant receptors for TcsL.
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Affiliation(s)
- Songhai Tian
- Department of Urology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Surgery and Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
| | - Yang Liu
- Department of Urology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Surgery and Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA; Department of Nephrology, The First Hospital of Jilin University, Changchun 130012, China
| | - Hao Wu
- The Vascular Biology Program, Department of Surgery, Boston Children's Hospital and Harvard Medical School, MA 02115, USA
| | - Hao Liu
- Department of Urology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Surgery and Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
| | - Ji Zeng
- Department of Urology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Surgery and Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA
| | - Mei Yuk Choi
- Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, MA 02115, USA
| | - Hong Chen
- The Vascular Biology Program, Department of Surgery, Boston Children's Hospital and Harvard Medical School, MA 02115, USA
| | - Ralf Gerhard
- Institute of Toxicology, Hannover Medical School, Hannover, 30625, Germany
| | - Min Dong
- Department of Urology, Boston Children's Hospital, Boston, MA 02115, USA; Department of Surgery and Department of Microbiology, Harvard Medical School, Boston, MA 02115, USA.
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Bravo-Ojeda J, Gomez-Quintero C, Pescador-Vargas L, Suarez-Tirado J. Bacteriemia por Clostridium sordellii en paciente con neoplasia gastrointestinal. Reporte de caso y revisión de literatura. INFECTIO 2020. [DOI: 10.22354/in.v24i2.846] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
La bacteriemia por Clostridium sordellii es infrecuente y usualmente se origina a partir de infecciones de etiología generalmente ginecológica y puerperal, con unamortalidad de aproximadamente el 70%. Existen pocas herramientas para el diagnóstico rápido y oportuno, siendo así la experiencia de tratamiento para este germen muy limitada en otros escenarios, lo que probablemente sea la causa de su alta mortalidad. Presentamos una paciente con antecedente de masa abdominal expansiva de larga data, con diagnóstico por histopatología e inmunohistoquimica compatibles con tumor del estroma gastrointestinal (GIST por sus siglas en inglés) y estudios de extensión que confirman compromiso metastásico hepático, en quien se documenta bacteriemia por Clostridium sordellii.
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9
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Kuehne SA, Rood JI, Lyras D. Clostridial Genetics: Genetic Manipulation of the Pathogenic Clostridia. Microbiol Spectr 2019; 7:10.1128/microbiolspec.gpp3-0040-2018. [PMID: 31172914 PMCID: PMC11315012 DOI: 10.1128/microbiolspec.gpp3-0040-2018] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2018] [Indexed: 02/07/2023] Open
Abstract
The past 10 years have been revolutionary for clostridial genetics. The rise of next-generation sequencing led to the availability of annotated whole-genome sequences of the important pathogenic clostridia: Clostridium perfringens, Clostridioides (Clostridium) difficile, and Clostridium botulinum, but also Paeniclostridium (Clostridium) sordellii and Clostridium tetani. These sequences were a prerequisite for the development of functional, sophisticated genetic tools for the pathogenic clostridia. A breakthrough came in the early 2000s with the development of TargeTron-based technologies specific for the clostridia, such as ClosTron, an insertional gene inactivation tool. The following years saw a plethora of new technologies being developed, mostly for C. difficile, but also for other members of the genus, including C. perfringens. A range of tools is now available, allowing researchers to precisely delete genes, change single nucleotides in the genome, complement deletions, integrate novel DNA into genomes, or overexpress genes. There are tools for forward genetics, including an inducible transposon mutagenesis system for C. difficile. As the latest addition to the tool kit, clustered regularly interspaced short palindromic repeat (CRISPR)-Cas9 technologies have also been adopted for the construction of single and multiple gene deletions in C. difficile. This article summarizes the key genetic technologies available to manipulate, study, and understand the pathogenic clostridia.
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Affiliation(s)
- S A Kuehne
- School of Dentistry and Institute for Microbiology and Infection, University of Birmingham, Birmingham, UK
| | - J I Rood
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia 3800
| | - D Lyras
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia 3800
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10
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Moore RJ, Lacey JA. Genomics of the Pathogenic Clostridia. Microbiol Spectr 2019; 7:10.1128/microbiolspec.gpp3-0033-2018. [PMID: 31215504 PMCID: PMC11257213 DOI: 10.1128/microbiolspec.gpp3-0033-2018] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2018] [Indexed: 12/12/2022] Open
Abstract
Whole-genome sequences are now available for all the clinically important clostridia and many of the lesser or opportunistically pathogenic clostridia. The complex clade structures of C. difficile, C. perfringens, and the species that produce botulinum toxins have been delineated by whole-genome sequence analysis. The true clostridia of cluster I show relatively low levels of gross genomic rearrangements within species, in contrast to the species of cluster XI, notably C. difficile, which have been found to have very plastic genomes with significant levels of chromosomal rearrangement. Throughout the clostridial phylotypes, a large proportion of the strain diversity is driven by the acquisition and loss of mobile elements, including phages, plasmids, insertion sequences, and transposons. Genomic analysis has been used to investigate the diversity and spread of C. difficile within hospital settings, the zoonotic transfer of isolates, and the emergence, origins, and geographic spread of epidemic ribotypes. In C. perfringens the clades defined by chromosomal sequence analysis show no indications of clustering based on host species or geographical location. Whole-genome sequence analysis helps to define the different survival and pathogenesis strategies that the clostridia use. Some, such as C. botulinum, produce toxins which rapidly act to kill the host, whereas others, such as C. perfringens and C. difficile, produce less lethal toxins which can damage tissue but do not rapidly kill the host. The genomes provide a resource that can be mined to identify potential vaccine antigens and targets for other forms of therapeutic intervention.
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Affiliation(s)
- Robert J Moore
- Host-Microbe Interactions Laboratory, School of Science, RMIT University, Bundoora, Victoria 3083, Australia
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
| | - Jake A Lacey
- Doherty Department, University of Melbourne at the Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria 3000, Australia
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11
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Revitt-Mills SA, Vidor CJ, Watts TD, Lyras D, Rood JI, Adams V. Virulence Plasmids of the Pathogenic Clostridia. Microbiol Spectr 2019; 7:10.1128/microbiolspec.gpp3-0034-2018. [PMID: 31111816 PMCID: PMC11257192 DOI: 10.1128/microbiolspec.gpp3-0034-2018] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2018] [Indexed: 12/12/2022] Open
Abstract
The clostridia cause a spectrum of diseases in humans and animals ranging from life-threatening tetanus and botulism, uterine infections, histotoxic infections and enteric diseases, including antibiotic-associated diarrhea, and food poisoning. The symptoms of all these diseases are the result of potent protein toxins produced by these organisms. These toxins are diverse, ranging from a multitude of pore-forming toxins to phospholipases, metalloproteases, ADP-ribosyltransferases and large glycosyltransferases. The location of the toxin genes is the unifying theme of this review because with one or two exceptions they are all located on plasmids or on bacteriophage that replicate using a plasmid-like intermediate. Some of these plasmids are distantly related whilst others share little or no similarity. Many of these toxin plasmids have been shown to be conjugative. The mobile nature of these toxin genes gives a ready explanation of how clostridial toxin genes have been so widely disseminated both within the clostridial genera as well as in the wider bacterial community.
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Affiliation(s)
- Sarah A Revitt-Mills
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
| | - Callum J Vidor
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
| | - Thomas D Watts
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
| | - Dena Lyras
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
| | - Julian I Rood
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
| | - Vicki Adams
- Infection and Immunity Program, Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
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Vidor CJ, Bulach D, Awad M, Lyras D. Paeniclostridium sordellii and Clostridioides difficile encode similar and clinically relevant tetracycline resistance loci in diverse genomic locations. BMC Microbiol 2019; 19:53. [PMID: 30832583 PMCID: PMC6399922 DOI: 10.1186/s12866-019-1427-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 02/25/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND With the current rise of antibiotic resistance in bacteria, it is important to monitor the efficacy of antimicrobials in clinical use. Paeniclostridium sordellii (previously Clostridium sordellii) is a bacterial pathogen that causes human uterine infection after spontaneous or medically induced abortion, for which mortality rates approach 100%. Prophylactic antibiotics have been recommended for individuals undergoing medically-induced abortion, one of which is doxycycline, a member of the tetracycline antibiotic family. However, tetracycline resistance had not been well characterized in P. sordellii. This study therefore aimed to determine the levels of tetracycline resistance in P. sordellii isolates, and to identify associated loci and their genomic locations. RESULTS Using a MIC assay, five of 24 P. sordellii isolates were found to be resistant to tetracycline, minocycline, and importantly, doxycycline. Analysis of genome sequence data from 46 isolates found that phenotypically resistant isolates encoded a variant of the Clostridium perfringens tetracycline resistance determinant Tet P. Bioinformatic analysis and comparison of the regions surrounding these determinants found variation in the genomic location of Tet P among P. sordellii isolates. The core genome comparison of the 46 isolates revealed genetic diversity and the absence of dominant genetic types among the isolates. There was no strong association between geographic location of isolation, animal host or Tet P carriage with isolate genetic type. Furthermore, the analysis of the Tet P genotype revealed that Tet P is encoded chromosomally, or on one of two, novel, small plasmids, all consistent with multiple acquisition and recombination events. BLAST analysis of Clostridioides difficile draft genome sequences also identified a Tet P locus, the genomic location of which demonstrated an evolutionary relationship with the P. sordellii locus. CONCLUSIONS The Tet P determinant is found in variable genomic locations within diverse human and animal isolates of P. sordellii and C. difficile, which suggests that it can undergo horizontal transfer, and may disseminate tetracycline resistance between clostridial species. Doxycycline is a suggested prophylactic treatment for P. sordellii infections, however, a small sub-set of the isolates tested are resistant to this antibiotic. Doxycycline may therefore not be an appropriate prophylactic treatment for P. sordellii infections.
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Affiliation(s)
- Callum J Vidor
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Dieter Bulach
- Melbourne Bioinformatics, The University of Melbourne, Melbourne, Victoria, Australia
| | - Milena Awad
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia
| | - Dena Lyras
- Infection and Immunity Program, Monash Biomedicine Discovery Institute and Department of Microbiology, Monash University, Clayton, Victoria, Australia.
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pCP13, a representative of a new family of conjugative toxin plasmids in Clostridium perfringens. Plasmid 2019; 102:37-45. [DOI: 10.1016/j.plasmid.2019.02.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 02/12/2019] [Accepted: 02/15/2019] [Indexed: 12/11/2022]
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In silico Identification of Novel Toxin Homologs and Associated Mobile Genetic Elements in Clostridium perfringens. Pathogens 2019; 8:pathogens8010016. [PMID: 30699957 PMCID: PMC6471305 DOI: 10.3390/pathogens8010016] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2018] [Revised: 01/16/2019] [Accepted: 01/24/2019] [Indexed: 01/05/2023] Open
Abstract
Clostridium perfringens causes a wide range of diseases in a variety of hosts, due to the production of a diverse set of toxins and extracellular enzymes. The C. perfringens toxins play an important role in pathogenesis, such that the presence and absence of the toxins is used as a typing scheme for the species. In recent years, several new toxins have been discovered that have been shown to be essential or highly correlated to diseases; these include binary enterotoxin (BecAB), NetB and NetF. In the current study, genome sequence analysis of C. perfringens isolates from diverse sources revealed several putative novel toxin homologs, some of which appeared to be associated with potential mobile genetic elements, including transposons and plasmids. Four novel toxin homologs encoding proteins related to the pore-forming Leukocidin/Hemolysin family were found in type A and G isolates. Two novel toxin homologs encoding proteins related to the epsilon aerolysin-like toxin family were identified in Type A and F isolates from humans, contaminated food and turkeys. A novel set of proteins related to clostridial binary toxins was also identified. While phenotypic characterisation is required before any of these homologs can be established as functional toxins, the in silico identification of these novel homologs on mobile genetic elements suggests the potential toxin reservoir of C. perfringens may be much larger than previously thought.
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