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Ueda K, Kawahara K, Kimoto N, Yamaguchi Y, Yamada K, Oki H, Yoshida T, Matsuda S, Matsumoto Y, Motooka D, Kawatsu K, Iida T, Nakamura S, Ohkubo T, Yonogi S. Analysis of the complete genome sequences of Clostridium perfringens strains harbouring the binary enterotoxin BEC gene and comparative genomics of pCP13-like family plasmids. BMC Genomics 2022; 23:226. [PMID: 35321661 PMCID: PMC8941779 DOI: 10.1186/s12864-022-08453-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Accepted: 03/08/2022] [Indexed: 11/10/2022] Open
Abstract
Background BEC-producing Clostridium perfringens is a causative agent of foodborne gastroenteritis. It was first reported in 2014, and since then, several isolates have been identified in Japan and the United Kingdom. The novel binary ADP-ribosylating toxin BEC, which consists of two components (BECa and BECb), is encoded on a plasmid that is similar to pCP13 and harbours a conjugation locus, called Pcp, encoding homologous proteins of the type 4 secretion system. Despite the high in vitro conjugation frequency of pCP13, its dissemination and that of related plasmids, including bec-harbouring plasmids, in the natural environment have not been characterised. This lack of knowledge has limited our understanding of the genomic epidemiology of bec-harbouring C. perfringens strains. Results In this study, we determined the complete genome sequences of five bec-harbouring C. perfringens strains isolated from 2009 to 2019. Each isolate contains a ~ 3.36 Mbp chromosome and 1–3 plasmids of either the pCW3-like family, pCP13-like family, or an unknown family, and the bec-encoding region in all five isolates was located on a ~ 54 kbp pCP13-like plasmid. Phylogenetic and SNP analyses of these complete genome sequences and the 211 assembled C. perfringens genomes in GenBank showed that although these bec-harbouring strains were split into two phylogenetic clades, the sequences of the bec-encoding plasmids were nearly identical (>99.81%), with a significantly smaller SNP accumulation rate than that of their chromosomes. Given that the Pcp locus is conserved in these pCP13-like plasmids, we propose a mechanism in which the plasmids were disseminated by horizontal gene transfer. Data mining showed that strains carrying pCP13-like family plasmids were unexpectedly common (58/216 strains) and widely disseminated among the various C. perfringens clades. Although these plasmids possess a conserved Pcp locus, their ‘accessory regions’ can accommodate a wide variety of genes, including virulence-associated genes, such as becA/becB and cbp2. These results suggest that this family of plasmids can integrate various foreign genes and is transmissible among C. perfringens strains. Conclusion This study demonstrates the potential significance of pCP13-like plasmids, including bec-encoding plasmids, for the characterisation and monitoring of the dissemination of pathogenic C. perfringens strains. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08453-4.
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Affiliation(s)
- Kengo Ueda
- Laboratory of Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Kazuki Kawahara
- Laboratory of Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Narumi Kimoto
- Laboratory of Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yusuke Yamaguchi
- Laboratory of Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Kazuhiro Yamada
- Department of Microbiology and Medical Zoology, Aichi Prefectural Institute of Public Health, 7-6 Nagare, Tsujicho, Kita-ku, Nagoya, Aichi, 462-8576, Japan
| | - Hiroya Oki
- Department of Infection Metagenomics, Genome Information Research Center, Research Institute for Microbial Diseases (RIMD), Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Takuya Yoshida
- Laboratory of Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Shigeaki Matsuda
- Department of Bacterial Infection, Research Institute for Microbial Disease (RIMD), Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Yuki Matsumoto
- Department of Infection Metagenomics, Genome Information Research Center, Research Institute for Microbial Diseases (RIMD), Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Daisuke Motooka
- Department of Infection Metagenomics, Genome Information Research Center, Research Institute for Microbial Diseases (RIMD), Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Kentaro Kawatsu
- Division of Microbiology, Osaka Institute of Public Health, 1-3-69 Nakamichi, Higashinari-ku, Osaka, Osaka, 537-0025, Japan
| | - Tetsuya Iida
- Department of Bacterial Infection, Research Institute for Microbial Disease (RIMD), Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan.,Center for Infectious Disease Education and Research (CiDER), Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Shota Nakamura
- Department of Infection Metagenomics, Genome Information Research Center, Research Institute for Microbial Diseases (RIMD), Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan.,Center for Infectious Disease Education and Research (CiDER), Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan
| | - Tadayasu Ohkubo
- Laboratory of Biophysical Chemistry, Graduate School of Pharmaceutical Sciences, Osaka University, 1-6 Yamadaoka, Suita, Osaka, 565-0871, Japan.
| | - Shinya Yonogi
- Department of Bacterial Infection, Research Institute for Microbial Disease (RIMD), Osaka University, 3-1 Yamadaoka, Suita, Osaka, 565-0871, Japan. .,Division of Microbiology, Osaka Institute of Public Health, 1-3-69 Nakamichi, Higashinari-ku, Osaka, Osaka, 537-0025, Japan.
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Matsuda A, Aung MS, Urushibara N, Kawaguchiya M, Sumi A, Nakamura M, Horino Y, Ito M, Habadera S, Kobayashi N. Prevalence and Genetic Diversity of Toxin Genes in Clinical Isolates of Clostridium perfringens: Coexistence of Alpha-Toxin Variant and Binary Enterotoxin Genes ( bec/ cpile). Toxins (Basel) 2019; 11:toxins11060326. [PMID: 31174364 PMCID: PMC6628447 DOI: 10.3390/toxins11060326] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2019] [Revised: 05/30/2019] [Accepted: 06/04/2019] [Indexed: 01/20/2023] Open
Abstract
Clostridium perfringens (C. perfringens) is responsible for food-borne gastroenteritis and other infectious diseases, and toxins produced by this bacterium play a key role in pathogenesis. Although various toxins have been described for C. perfringens isolates from humans and animals, prevalence of individual toxins among clinical isolates has not yet been well explored. In the present study, a total of 798 C. perfringens clinical isolates were investigated for prevalence of eight toxin genes and their genetic diversity by PCR, nucleotide sequencing, and phylogenetic analysis. Besides the alpha-toxin gene (plc) present in all the isolates, the most common toxin gene was cpe (enterotoxin) (34.2%), followed by cpb2 (beta2 toxin) (1.4%), netB (NetB) (0.3%), and bec/cpile (binary enterotoxin BEC/CPILE) (0.1%), while beta-, epsilon-, and iota-toxin genes were not detected. Genetic analysis of toxin genes indicated a high level of conservation of plc, cpe, and netB. In contrast, cpb2 was revealed to be considerably divergent, containing at least two lineages. Alpha-toxin among 46 isolates was classified into ten sequence types, among which common types were distinct from those reported for avian isolates. A single isolate with bec/cpile harbored a plc variant containing an insertion of 834-bp sequence, suggesting its putative origin from chickens.
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Affiliation(s)
- Asami Matsuda
- Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo 060-8556, Japan.
| | - Meiji Soe Aung
- Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo 060-8556, Japan.
| | - Noriko Urushibara
- Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo 060-8556, Japan.
| | - Mitsuyo Kawaguchiya
- Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo 060-8556, Japan.
| | - Ayako Sumi
- Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo 060-8556, Japan.
| | | | - Yuka Horino
- Sapporo Clinical Laboratory, Inc., Sapporo 060-0005, Japan.
| | - Masahiko Ito
- Sapporo Clinical Laboratory, Inc., Sapporo 060-0005, Japan.
| | | | - Nobumichi Kobayashi
- Department of Hygiene, Sapporo Medical University School of Medicine, Sapporo 060-8556, Japan.
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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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