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Microorganisms
Volume 14
Issue 7
10.3390/microorganisms14071399
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Article

Identification and Genomic Localization of the cpe Gene in Clostridium perfringens Strains Associated with Foodborne Outbreaks in South Korea

by
Jaehyun Choi
,
Yeeun Kim
,
Sumin Ryu
,
Dabin Kim
,
Min Jung Lee
,
Yonghoon Kim
,
Insun Joo
and
Woojung Lee
*
Division of Food Microbiology, National Institute of Food and Drug Safety Evaluation, Ministry of Food and Drug Safety, Cheongju 28159, Republic of Korea
*
Author to whom correspondence should be addressed.
Microorganisms 2026, 14(7), 1399; https://doi.org/10.3390/microorganisms14071399 (registering DOI)
Submission received: 20 May 2026 / Revised: 23 June 2026 / Accepted: 23 June 2026 / Published: 24 June 2026
(This article belongs to the Special Issue Basic Research and Application Research of Food Microorganisms)
Versions Notes

Abstract

Clostridium perfringens is a major foodborne pathogen in which the genomic localization of the enterotoxin gene, cpe, plays an important epidemiological role. In this study, four isolates associated with independent foodborne outbreaks in South Korea were analyzed using complete genome sequencing. All isolates were cpe-positive, including three strains carrying chromosomal cpe (c-cpe) and one strain carrying plasmid-borne cpe (p-cpe). To provide a broader genomic context, complete genomes retrieved from the National Center for Biotechnology Information database were also analyzed. Most cpe-positive strains carried p-cpe, whereas c-cpe strains were relatively uncommon. Whole-genome analysis revealed a distinct separation between c-cpe and p-cpe strains based on conserved core-genome features and virulence gene profiles. In c-cpe strains, the cpe gene was consistently located between the nadA–C operon and a downstream nucleobase transporter gene and was flanked by IS1470 family transposases, suggesting a conserved chromosomal structure and a possible vertical inheritance. Conversely, p-cpe strains carried cpe on conserved pCW3-like plasmids, indicating that horizontal gene transfer mediated by a specific plasmid lineage contributes to cpe dissemination across diverse genetic backgrounds. Overall, these findings show that cpe localization is associated with distinct genomic patterns in C. perfringens.
Keywords: Clostridium perfringens; cpe gene; foodborne outbreaks; whole-genome sequencing (WGS); comparative genomics Clostridium perfringens; cpe gene; foodborne outbreaks; whole-genome sequencing (WGS); comparative genomics

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MDPI and ACS Style

Choi, J.; Kim, Y.; Ryu, S.; Kim, D.; Lee, M.J.; Kim, Y.; Joo, I.; Lee, W. Identification and Genomic Localization of the cpe Gene in Clostridium perfringens Strains Associated with Foodborne Outbreaks in South Korea. Microorganisms 2026, 14, 1399. https://doi.org/10.3390/microorganisms14071399

AMA Style

Choi J, Kim Y, Ryu S, Kim D, Lee MJ, Kim Y, Joo I, Lee W. Identification and Genomic Localization of the cpe Gene in Clostridium perfringens Strains Associated with Foodborne Outbreaks in South Korea. Microorganisms. 2026; 14(7):1399. https://doi.org/10.3390/microorganisms14071399

Chicago/Turabian Style

Choi, Jaehyun, Yeeun Kim, Sumin Ryu, Dabin Kim, Min Jung Lee, Yonghoon Kim, Insun Joo, and Woojung Lee. 2026. "Identification and Genomic Localization of the cpe Gene in Clostridium perfringens Strains Associated with Foodborne Outbreaks in South Korea" Microorganisms 14, no. 7: 1399. https://doi.org/10.3390/microorganisms14071399

APA Style

Choi, J., Kim, Y., Ryu, S., Kim, D., Lee, M. J., Kim, Y., Joo, I., & Lee, W. (2026). Identification and Genomic Localization of the cpe Gene in Clostridium perfringens Strains Associated with Foodborne Outbreaks in South Korea. Microorganisms, 14(7), 1399. https://doi.org/10.3390/microorganisms14071399

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