{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,7,30]],"date-time":"2025-07-30T16:01:58Z","timestamp":1753891318416,"version":"3.41.2"},"reference-count":20,"publisher":"Frontiers Media SA","license":[{"start":{"date-parts":[[2022,11,17]],"date-time":"2022-11-17T00:00:00Z","timestamp":1668643200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100001691","name":"Japan Society for the Promotion of Science","doi-asserted-by":"publisher","award":["19K16652","22K15460"],"award-info":[{"award-number":["19K16652","22K15460"]}],"id":[{"id":"10.13039\/501100001691","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007802","name":"Institute for Fermentation, Osaka","doi-asserted-by":"publisher","award":["Y-2021-1-002"],"award-info":[{"award-number":["Y-2021-1-002"]}],"id":[{"id":"10.13039\/100007802","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100007676","name":"Asahi Group Holdings","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100007676","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["frontiersin.org"],"crossmark-restriction":true},"short-container-title":["Front. Microbiol."],"abstract":"<jats:p>A strain of <jats:italic>Clostridium perfringens<\/jats:italic> was isolated from the bile sample of a patient with emphysematous cholecystitis who underwent a laparoscopic cholecystectomy, followed by treatment with meropenem and recovery. Metagenomic analysis of the bile sample showed that 99.73% of the bile microbiota consisted of <jats:italic>C. perfringens<\/jats:italic>, indicating that <jats:italic>C. perfringens<\/jats:italic> JUM001 was the causative pathogen of acute emphysematous cholecystitis in this patient. Complete genome sequencing showed that <jats:italic>C. perfringens<\/jats:italic> JUM001 contained a circular chromosome of 3,231,023 bp and two circular plasmids, pJUM001-1 of 49,289 bp and pJUM001-2 of 47,855 bp. JUM001 was found to possess a typing toxin gene, <jats:italic>plc<\/jats:italic>, but no other typing toxin genes, indicating that its toxinotype is type A. The plasmids pJUM001-1 and pJUM001-2 belonged to the pCP13-like and pCW3-like families of plasmids, respectively, which are characteristic conjugative and archetypical plasmids of <jats:italic>C. perfringens.<\/jats:italic> Phylogenetic analysis showed that JUM001 was closely related to <jats:italic>C. perfringens<\/jats:italic> strain JXNC-DD isolated from a dog in China. To our knowledge, this is the first report of whole-genome sequences of a clinical isolate of <jats:italic>C. perfringens<\/jats:italic> causing acute emphysematous cholecystitis.<\/jats:p>","DOI":"10.3389\/fmicb.2022.1066880","type":"journal-article","created":{"date-parts":[[2022,11,17]],"date-time":"2022-11-17T12:52:50Z","timestamp":1668689570000},"update-policy":"https:\/\/doi.org\/10.3389\/crossmark-policy","source":"Crossref","is-referenced-by-count":1,"title":["Case report: Whole genome sequence of Clostridium perfringens JUM001 causing acute emphysematous cholecystitis"],"prefix":"10.3389","volume":"13","author":[{"given":"Mari","family":"Tohya","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tomohiro","family":"Otsuka","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jiro","family":"Yoshimoto","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yoichi","family":"Ishizaki","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Teruo","family":"Kirikae","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shin","family":"Watanabe","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"1965","published-online":{"date-parts":[[2022,11,17]]},"reference":[{"key":"B1","doi-asserted-by":"publisher","first-page":"403","DOI":"10.1016\/S0022-2836(05)80360-2","article-title":"Basic local alignment search tool.","volume":"215","author":"Altschul","year":"1990","journal-title":"J. Mol. Biol."},{"key":"B2","doi-asserted-by":"publisher","first-page":"4942","DOI":"10.1128\/JB.00298-06","article-title":"Functional identification of conjugation and replication regions of the tetracycline resistance plasmid pCW3 from Clostridium perfringens.","volume":"188","author":"Bannam","year":"2006","journal-title":"J. Bacteriol."},{"key":"B3","doi-asserted-by":"publisher","first-page":"852","DOI":"10.1038\/s41587-019-0209-9","article-title":"Reproducible, interactive, scalable and extensible microbiome data science using QIIME 2.","volume":"37","author":"Bolyen","year":"2019","journal-title":"Nat. Biotechnol."},{"key":"B4","doi-asserted-by":"publisher","first-page":"3483","DOI":"10.1128\/IAI.69.5.3483-3487.2001","article-title":"Enterotoxin plasmid from Clostridium perfringens is conjugative.","volume":"69","author":"Brynestad","year":"2001","journal-title":"Infect. Immun."},{"key":"B5","doi-asserted-by":"publisher","DOI":"10.1155\/2015\/523402","article-title":"Intravascular hemolysis and septicemia due to Clostridium perfringens emphysematous cholecystitis and hepatic abscesses.","volume":"2015","author":"Cochrane","year":"2015","journal-title":"Case Rep. Med."},{"key":"B6","doi-asserted-by":"publisher","first-page":"965","DOI":"10.1001\/jama.2022.2350","article-title":"Acute cholecystitis: A review.","volume":"327","author":"Gallaher","year":"2022","journal-title":"JAMA"},{"key":"B7","doi-asserted-by":"publisher","first-page":"2877","DOI":"10.1093\/bioinformatics\/btv271","article-title":"kSNP3.0: SNP detection and phylogenetic analysis of genomes without genome alignment or reference genome.","volume":"31","author":"Gardner","year":"2015","journal-title":"Bioinformatics"},{"key":"B8","doi-asserted-by":"publisher","first-page":"219","DOI":"10.12659\/AJCR.895721","article-title":"Clostridium perfringens infection in a febrile patient with severe hemolytic anemia.","volume":"17","author":"Hashiba","year":"2016","journal-title":"Am. J. Case Rep."},{"key":"B9","doi-asserted-by":"publisher","DOI":"10.1038\/s41426-018-0144-8","article-title":"An update on the human and animal enteric pathogen Clostridium perfringens.","volume":"7","author":"Kiu","year":"2018","journal-title":"Emerg. Microb. Infect."},{"key":"B10","doi-asserted-by":"publisher","first-page":"54","DOI":"10.1080\/00015458.2016.1139829","article-title":"Emphysematous cholecystitis due to Clostridium perfringens successfully treated by cholecystectomy.","volume":"116","author":"Koole","year":"2016","journal-title":"Acta Chir. Belg."},{"journal-title":"Clostridial cholecystitis.","year":"2022","author":"Kowalski","key":"B11"},{"key":"B12","doi-asserted-by":"publisher","first-page":"1585","DOI":"10.1128\/JB.188.4.1585-1598.2006","article-title":"Complete sequencing and diversity analysis of the enterotoxin-encoding plasmids in Clostridium perfringens type A non-food-borne human gastrointestinal disease isolates.","volume":"188","author":"Miyamoto","year":"2006","journal-title":"J. Bacteriol."},{"key":"B13","doi-asserted-by":"publisher","first-page":"104","DOI":"10.1016\/S0966-842X(98)01430-9","article-title":"Clostridium perfringens: Toxinotype and genotype.","volume":"7","author":"Petit","year":"1999","journal-title":"Trends Microbiol."},{"key":"B14","doi-asserted-by":"publisher","first-page":"5","DOI":"10.1016\/j.anaerobe.2018.04.011","article-title":"Expansion of the Clostridium perfringens toxin-based typing scheme.","volume":"53","author":"Rood","year":"2018","journal-title":"Anaerobe"},{"key":"B15","doi-asserted-by":"publisher","first-page":"2068","DOI":"10.1093\/bioinformatics\/btu153","article-title":"Prokka: Rapid prokaryotic genome annotation.","volume":"30","author":"Seemann","year":"2014","journal-title":"Bioinformatics"},{"key":"B16","doi-asserted-by":"publisher","first-page":"1009","DOI":"10.1093\/bioinformatics\/btr039","article-title":"Easyfig: A genome comparison visualizer.","volume":"27","author":"Sullivan","year":"2011","journal-title":"Bioinformatics"},{"key":"B17","doi-asserted-by":"publisher","first-page":"37","DOI":"10.1016\/j.plasmid.2019.02.002","article-title":"pCP13, a representative of a new family of conjugative toxin plasmids in Clostridium perfringens.","volume":"102","author":"Watts","year":"2019","journal-title":"Plasmid"},{"key":"B18","article-title":"Clostridia: Sporeforming Anaerobic Bacilli","author":"Wells","year":"1996","journal-title":"Medical Microbiology"},{"key":"B19","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pcbi.1005595","article-title":"Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads.","volume":"13","author":"Wick","year":"2017","journal-title":"PLoS Comput. Biol."},{"key":"B20","doi-asserted-by":"publisher","first-page":"2390","DOI":"10.1128\/IAI.01759-14","article-title":"BEC, a novel enterotoxin of Clostridium perfringens found in human clinical isolates from acute gastroenteritis outbreaks.","volume":"82","author":"Yonogi","year":"2014","journal-title":"Infect. Immun."}],"container-title":["Frontiers in Microbiology"],"original-title":[],"link":[{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2022.1066880\/full","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,11,17]],"date-time":"2022-11-17T12:52:55Z","timestamp":1668689575000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.frontiersin.org\/articles\/10.3389\/fmicb.2022.1066880\/full"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,11,17]]},"references-count":20,"alternative-id":["10.3389\/fmicb.2022.1066880"],"URL":"https:\/\/doi.org\/10.3389\/fmicb.2022.1066880","relation":{},"ISSN":["1664-302X"],"issn-type":[{"type":"electronic","value":"1664-302X"}],"subject":[],"published":{"date-parts":[[2022,11,17]]},"article-number":"1066880"}}