{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,8,3]],"date-time":"2026-08-03T11:44:56Z","timestamp":1785757496696,"version":"3.56.0"},"reference-count":35,"publisher":"MDPI AG","issue":"15","license":[{"start":{"date-parts":[[2026,8,3]],"date-time":"2026-08-03T00:00:00Z","timestamp":1785715200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Key Project of the Special Program for Technological Innovation, Application and Development of Chongqing Municipality","award":["CSTB2025TIAD-KPX0079"],"award-info":[{"award-number":["CSTB2025TIAD-KPX0079"]}]},{"name":"Agricultural Fundamental & Long-term Scientific Observation and Research","award":["MARA-ORS261-AH024"],"award-info":[{"award-number":["MARA-ORS261-AH024"]}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Animals"],"abstract":"<jats:p>Clostridium perfringens type A causes neonatal clostridial enteritis, hemorrhagic enteritis, and sudden death syndrome in cattle. This study examined a fatal outbreak at a fattening farm housing 58 adult yaks in Southwest China, with an incidence of 22.41% (13\/58) and a 100% case fatality rate. Histopathology of deceased yaks showed widespread multi-organ hemorrhage and severe hemorrhagic enteritis. A specific PCR assay amplified the alpha-toxin gene of Clostridium perfringens, while no other pathogens were detected. Clostridium perfringens was isolated from small intestinal contents using TSC agar, designated strain CQ1, and identified as type A through toxinotyping. Whole-genome sequencing revealed that strain CQ1 carries the core alpha-toxin gene along with key accessory virulence determinants (pfoA, colA, and cloSI). Phylogenomic analysis based on core single-nucleotide polymorphisms revealed that strain CQ1 is clustered into a distinct, independent evolutionary lineage with an existing historical yak isolate and a canine-origin isolate. Intraperitoneal challenge in mice confirmed its extreme lethality, causing 100% mortality within 36 h with severe intestinal necrosis. These findings provide fundamental genetic resources for understanding the virulence mechanisms and genetic background of this pathogen and offer critical insights for preventing and controlling clostridial diseases in high-altitude yak farming.<\/jats:p>","DOI":"10.3390\/ani16152391","type":"journal-article","created":{"date-parts":[[2026,8,3]],"date-time":"2026-08-03T10:24:07Z","timestamp":1785752647000},"page":"2391","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Isolation, Genomic Evolution, and Pathogenicity of Clostridium perfringens Type A Causing Hemorrhagic Enteritis in Adult Yaks in Southwest China"],"prefix":"10.3390","volume":"16","author":[{"ORCID":"https:\/\/orcid.org\/0009-0007-7136-4951","authenticated-orcid":false,"given":"Long","family":"Zhao","sequence":"first","affiliation":[{"name":"Chongqing Academy of Animal Sciences, Chongqing 402460, China"},{"name":"National Technology Innovation Center for Pigs, Chongqing 402460, China"},{"name":"Rongchang, Animal Disease, Observation and Research Station, Ministry of Agriculture and Rural Affairs, Chongqing 402460, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yongqiang","family":"Miao","sequence":"additional","affiliation":[{"name":"Chongqing Academy of Animal Sciences, Chongqing 402460, China"},{"name":"National Technology Innovation Center for Pigs, Chongqing 402460, China"},{"name":"Rongchang, Animal Disease, Observation and Research Station, Ministry of Agriculture and Rural Affairs, Chongqing 402460, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhen","family":"Yang","sequence":"additional","affiliation":[{"name":"Chongqing Academy of Animal Sciences, Chongqing 402460, China"},{"name":"National Technology Innovation Center for Pigs, Chongqing 402460, China"},{"name":"Rongchang, Animal Disease, Observation and Research Station, Ministry of Agriculture and Rural Affairs, Chongqing 402460, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Kefei","family":"Shen","sequence":"additional","affiliation":[{"name":"Chongqing Academy of Animal Sciences, Chongqing 402460, China"},{"name":"National Technology Innovation Center for Pigs, Chongqing 402460, China"},{"name":"Rongchang, Animal Disease, Observation and Research Station, Ministry of Agriculture and Rural Affairs, Chongqing 402460, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Dengfeng","family":"Xu","sequence":"additional","affiliation":[{"name":"Chongqing Academy of Animal Sciences, Chongqing 402460, China"},{"name":"National Technology Innovation Center for Pigs, Chongqing 402460, China"},{"name":"Rongchang, Animal Disease, Observation and Research Station, Ministry of Agriculture and Rural Affairs, Chongqing 402460, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Suhui","family":"Zhang","sequence":"additional","affiliation":[{"name":"Chongqing Academy of Animal Sciences, Chongqing 402460, China"},{"name":"National Technology Innovation Center for Pigs, Chongqing 402460, China"},{"name":"Rongchang, Animal Disease, Observation and Research Station, Ministry of Agriculture and Rural Affairs, Chongqing 402460, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Liu","family":"Yang","sequence":"additional","affiliation":[{"name":"Chongqing Academy of Animal Sciences, Chongqing 402460, China"},{"name":"National Technology Innovation Center for Pigs, Chongqing 402460, China"},{"name":"Rongchang, Animal Disease, Observation and Research Station, Ministry of Agriculture and Rural Affairs, Chongqing 402460, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3329-8152","authenticated-orcid":false,"given":"Lizhi","family":"Fu","sequence":"additional","affiliation":[{"name":"Chongqing Academy of Animal Sciences, Chongqing 402460, China"},{"name":"National Technology Innovation Center for Pigs, Chongqing 402460, China"},{"name":"Rongchang, Animal Disease, Observation and Research Station, Ministry of Agriculture and Rural Affairs, Chongqing 402460, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ziqi","family":"Li","sequence":"additional","affiliation":[{"name":"Chongqing Academy of Animal Sciences, Chongqing 402460, China"},{"name":"College of Veterinary Medicine, Southwest University, Chongqing 400715, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bo","family":"Lian","sequence":"additional","affiliation":[{"name":"College of Veterinary Medicine, Southwest University, Chongqing 400715, China"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yuandi","family":"Yu","sequence":"additional","affiliation":[{"name":"Chongqing Academy of Animal Sciences, Chongqing 402460, China"},{"name":"National Technology Innovation Center for Pigs, Chongqing 402460, China"},{"name":"Rongchang, Animal Disease, Observation and Research Station, Ministry of Agriculture and Rural Affairs, Chongqing 402460, China"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"1968","published-online":{"date-parts":[[2026,8,3]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"141","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. Microbes Infect."},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Grenda, T., Jarosz, A., Sapa\u0142a, M., Grenda, A., Patyra, E., and Kwiatek, K. (2023). Clostridium perfringens-Opportunistic Foodborne Pathogen, Its Diversity and Epidemiological Significance. Pathogens, 12.","DOI":"10.3390\/pathogens12060768"},{"key":"ref_3","doi-asserted-by":"crossref","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":"ref_4","doi-asserted-by":"crossref","first-page":"104898","DOI":"10.1016\/j.fm.2025.104898","article-title":"Isolation rate, genetic diversity, and toxinotyping of Clostridium perfringens isolated from French cattle, pig or poultry slaughterhouses","volume":"133","author":"Tran","year":"2026","journal-title":"Food Microbiol."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1186\/1297-9716-44-45","article-title":"The synergistic necrohemorrhagic action of Clostridium perfringens perfringolysin and alpha toxin in the bovine intestine and against bovine endothelial cells","volume":"44","author":"Verherstraeten","year":"2013","journal-title":"Vet. Res."},{"key":"ref_6","first-page":"174","article-title":"Enteritis associated with Clostridium perfringens type A in 9-month-old calves","volume":"53","author":"Savic","year":"2012","journal-title":"Can. Vet. J."},{"key":"ref_7","doi-asserted-by":"crossref","first-page":"290","DOI":"10.1016\/j.anaerobe.2004.12.004","article-title":"Clostridial abomasitis in calves: Case report and review of the literature","volume":"11","author":"Songer","year":"2005","journal-title":"Anaerobe"},{"key":"ref_8","doi-asserted-by":"crossref","unstructured":"Luo, R., Wu, D., Luo, Z., Li, Y., Zhong, Y., Li, K., Bai, Z. (2024). Alterations in the diversity and composition of the fecal microbiota of domestic yaks (Bos grunniens) with pasture alteration-induced diarrhea. BMC Vet. Res., 20.","DOI":"10.1186\/s12917-024-04196-4"},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Zhu, Y., Lu, S., Cidan, Y., Wang, H., Li, K., and Basang, W. (2024). Comparative analysis of intestinal microbiota composition between free-ranged captive yak populations in Nimu County. Front. Cell. Infect. Microbiol., 14.","DOI":"10.3389\/fcimb.2024.1420389"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"793","DOI":"10.1099\/jgv.0.001254","article-title":"First detection of bovine coronavirus in Yak (Bos grunniens) and a bovine coronavirus genome with a recombinant HE gene","volume":"100","author":"He","year":"2019","journal-title":"J. Gen. Virol."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"701","DOI":"10.1099\/jgv.0.001426","article-title":"High prevalence and genomic characteristics of G6P[1] Bovine Rotavirus A in yak in China","volume":"101","author":"Yan","year":"2020","journal-title":"J. Gen. Virol."},{"key":"ref_12","doi-asserted-by":"crossref","first-page":"2017","DOI":"10.1007\/s00705-021-05047-5","article-title":"Development and use of a reverse transcription insulated isothermal PCR assay for detection and characterization of bovine torovirus in yaks","volume":"166","author":"Zhao","year":"2021","journal-title":"Arch. Virol."},{"key":"ref_13","doi-asserted-by":"crossref","first-page":"29","DOI":"10.1186\/1743-422X-11-29","article-title":"Molecular investigation of bovine viral diarrhea virus infection in yaks (Bos gruniens) from Qinghai, China","volume":"11","author":"Gong","year":"2014","journal-title":"Virol. J."},{"key":"ref_14","doi-asserted-by":"crossref","first-page":"12312","DOI":"10.1038\/s41598-026-42837-w","article-title":"Seroprevalence, isolation, comprehensive characterization, and pathogenicity of Clostridium perfringens strain from yak in Xizang, China","volume":"16","author":"Wang","year":"2026","journal-title":"Sci. Rep."},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Wu, D., Luo, R., Cao, S., and Suolang, S. (BMC Vet. Res., 2026). Complete genome sequence of Clostridium perfringens XZ-E1 isolated from yak feces in Xizang, China, BMC Vet. Res., online ahead of print.","DOI":"10.1186\/s12917-026-05698-z"},{"key":"ref_16","doi-asserted-by":"crossref","first-page":"e0079225","DOI":"10.1128\/msphere.00792-25","article-title":"Pan-genomic insights into resistance, virulence, and stress adaptation in Clostridium perfringens from the Tibetan Plateau","volume":"11","author":"Luo","year":"2026","journal-title":"mSphere"},{"key":"ref_17","doi-asserted-by":"crossref","unstructured":"Li, K., Yuan, H., Jin, C., Rahim, M.F., Luosong, X., An, T., and Li, J. (2025). Characterization and Genomic Analysis of Pasteurella multocida NQ01 Isolated from Yak in China. Animals, 15.","DOI":"10.3390\/ani15233462"},{"key":"ref_18","doi-asserted-by":"crossref","first-page":"1096","DOI":"10.1128\/JCM.36.4.1096-1100.1998","article-title":"Development of PCR assays for species and type specific identification of Pasteurella multocida isolates","volume":"36","author":"Townsend","year":"1998","journal-title":"J. Clin. Microbiol."},{"key":"ref_19","doi-asserted-by":"crossref","first-page":"35","DOI":"10.1099\/jgv.0.001172","article-title":"Detection and molecular characteristics of neboviruses in dairy cows in China","volume":"100","author":"Guo","year":"2019","journal-title":"J. Gen. Virol."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"46","DOI":"10.1186\/s44149-025-00200-y","article-title":"Ellagic acid inhibits bovine rotavirus in vitro and in vivo","volume":"5","author":"Zhao","year":"2025","journal-title":"Anim. Dis."},{"key":"ref_21","doi-asserted-by":"crossref","first-page":"108199","DOI":"10.1016\/j.micpath.2025.108199","article-title":"Identification and pathogenicity evaluation of Bacillus cereus isolated from dairy goats in China","volume":"210","author":"Li","year":"2026","journal-title":"Microb. Pathog."},{"key":"ref_22","doi-asserted-by":"crossref","first-page":"975","DOI":"10.20506\/rst.28.3.1936","article-title":"Mastitis in dairy buffalo and cattle in Egypt due to Clostridium perfringens: Prevalence, incidence, risk factors and costs","volume":"28","author":"Osman","year":"2009","journal-title":"Rev. Sci. Tech. Off. Int. \u00c9piz."},{"key":"ref_23","unstructured":"Elyazeed, H.A., Elhariri, M., Eldeen, N.E., Aziz, D.A., and Elhelw, R. (2026). Genetic diversity and phylogenetic relationships of Clostridium perfringens strains isolated from mastitis and enteritis in Egyptian dairy farms. BMC Microbiol., 24."},{"key":"ref_24","doi-asserted-by":"crossref","first-page":"104485","DOI":"10.1016\/j.fm.2024.104485","article-title":"Prevalence, toxin-genotype distribution, and transmission of Clostridium perfringens from the breeding and milking process of dairy farms","volume":"120","author":"Jiang","year":"2024","journal-title":"Food Microbiol."},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"735","DOI":"10.1292\/jvms.24-0403","article-title":"Emphysematous rumenitis in a Japanese black calf caused by Clostridium perfringens with secondary Balantidium coli infection","volume":"87","author":"Hegazy","year":"2025","journal-title":"J. Vet. Med. Sci."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"e5431","DOI":"10.1002\/vetr.5431","article-title":"Comparing diarrhoeic grades and pathogens present in faecal samples obtained from Danish calves infected with one or more pathogens","volume":"197","author":"Olsen","year":"2025","journal-title":"Vet. Rec."},{"key":"ref_27","doi-asserted-by":"crossref","first-page":"60","DOI":"10.1051\/parasite\/2024059","article-title":"Molecular characterization of common zoonotic protozoan parasites and bacteria causing diarrhea in dairy calves in Ningxia Hui Autonomous Region, China","volume":"31","author":"Zhao","year":"2024","journal-title":"Parasite"},{"key":"ref_28","doi-asserted-by":"crossref","first-page":"1593","DOI":"10.1292\/jvms.21-0129","article-title":"Bacteriological and molecular typing of Clostridium perfringens strains isolated in retail beef in Beijing, China","volume":"83","author":"Jiang","year":"2021","journal-title":"J. Vet. Med. Sci."},{"key":"ref_29","doi-asserted-by":"crossref","first-page":"7558","DOI":"10.1038\/s41598-019-43773-8","article-title":"Transcriptome profiles revealed the mechanisms underlying the adaptation of yak to high-altitude environments","volume":"9","author":"Xin","year":"2019","journal-title":"Sci. Rep."},{"key":"ref_30","doi-asserted-by":"crossref","first-page":"skac295","DOI":"10.1093\/jas\/skac295","article-title":"Effect of a molasses-based liquid supplement on gastrointestinal tract barrier function, inflammation, and performance of newly received feedlot cattle before and after a transport stress","volume":"101","author":"Silva","year":"2023","journal-title":"J. Anim. Sci."},{"key":"ref_31","doi-asserted-by":"crossref","first-page":"110857","DOI":"10.1016\/j.ygeno.2024.110857","article-title":"A conjoint analysis of renal structure and omics characteristics reveal new insight to yak high-altitude hypoxia adaptation","volume":"116","author":"Ding","year":"2024","journal-title":"Genomics"},{"key":"ref_32","doi-asserted-by":"crossref","first-page":"1361","DOI":"10.1128\/AAC.01581-12","article-title":"Quantitative contributions of target alteration and decreased drug accumulation to Pseudomonas aeruginosa fluoroquinolone resistance","volume":"57","author":"Bruchmann","year":"2013","journal-title":"Antimicrob. Agents Chemother."},{"key":"ref_33","doi-asserted-by":"crossref","unstructured":"Espinoza, N., Rojas, J., Pollett, S., Meza, R., Pati\u00f1o, L., Leiva, M., Cami\u00f1a, M., Bernal, M., Reynolds, N.D., and Maves, R. (2020). Validation of the T86I mutation in the gyrA gene as a highly reliable real time PCR target to detect Fluoroquinolone-resistant Campylobacter jejuni. BMC Infect. Dis., 20.","DOI":"10.1186\/s12879-020-05202-4"},{"key":"ref_34","doi-asserted-by":"crossref","first-page":"7719","DOI":"10.1128\/JB.01573-07","article-title":"Characterization of genes regulated directly by the VirR\/VirS system in Clostridium perfringens","volume":"190","author":"Kayo","year":"2008","journal-title":"J. Bacteriol."},{"key":"ref_35","doi-asserted-by":"crossref","first-page":"5","DOI":"10.1016\/j.anaerobe.2016.06.003","article-title":"Gene regulation by the VirS\/VirR system in Clostridium perfringens","volume":"41","author":"Ohtani","year":"2016","journal-title":"Anaerobe"}],"container-title":["Animals"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2076-2615\/16\/15\/2391\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,8,3]],"date-time":"2026-08-03T10:54:14Z","timestamp":1785754454000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2076-2615\/16\/15\/2391"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,8,3]]},"references-count":35,"journal-issue":{"issue":"15","published-online":{"date-parts":[[2026,8]]}},"alternative-id":["ani16152391"],"URL":"https:\/\/doi.org\/10.3390\/ani16152391","relation":{},"ISSN":["2076-2615"],"issn-type":[{"value":"2076-2615","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,8,3]]}}}