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This study aimed to determine the prevalence of these enteric parasites and their coinfection with <jats:italic>E. bieneusi<\/jats:italic> in diarrheic pigs in Southwest China (Chongqing and Sichuan) using nested polymerase chain reaction (nPCR)\u00a0based methods.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Results<\/jats:title>\n                <jats:p>A total of 514 fecal samples were collected from diarrheic pigs from 14 pig farms in Chongqing (five farms) and Sichuan (nine farms) Provinces. The prevalence of <jats:italic>Encephalitozoon<\/jats:italic> spp., <jats:italic>Cryptosporidium<\/jats:italic> spp. and <jats:italic>G. duodenalis<\/jats:italic> was 16.14% (83\/514), 0% (0\/514), and 8.95% (46\/514), respectively. Nested PCR revealed 305 mono-infections of <jats:italic>E. bieneusi<\/jats:italic>, six of <jats:italic>E. cuniculi<\/jats:italic>, two of <jats:italic>E. hellem<\/jats:italic>, and nine of <jats:italic>G. duodenalis<\/jats:italic> and 106 concurrent infections of <jats:italic>E. bieneusi<\/jats:italic> with the other enteric pathogens. No infections of <jats:italic>E. intestinalis<\/jats:italic> and <jats:italic>Cryptosporidium<\/jats:italic> species were detected. The highest coinfection was detected between <jats:italic>E. bieneusi<\/jats:italic> and <jats:italic>E. cuniculi<\/jats:italic> (10.5%, 54\/514), followed by <jats:italic>E. bieneusi<\/jats:italic> and <jats:italic>G. duodenalis<\/jats:italic> (5.8%, 30\/514) and <jats:italic>E. bieneusi<\/jats:italic> and <jats:italic>E. hellem<\/jats:italic> (2.9%, 15\/514). <jats:italic>E. bieneusi<\/jats:italic> was the most frequently detected enteric pathogen, followed by <jats:italic>E. cuniculi<\/jats:italic>, <jats:italic>G. duodenalis<\/jats:italic> and <jats:italic>E. hellem<\/jats:italic>. There was a significant age-related difference in the prevalence of <jats:italic>E. cuniculi<\/jats:italic> in fattening pigs (\u03c7<jats:sup>2<\/jats:sup>\u2009=\u200915.266, df\u2009=\u20093, <jats:italic>P<\/jats:italic>\u2009=\u20090.002) and <jats:italic>G. duodenalis<\/jats:italic> in suckling pigs (\u03c7<jats:sup>2<\/jats:sup>\u2009=\u200911.92, df\u2009=\u20093, <jats:italic>P<\/jats:italic>\u2009=\u20090.008) compared with the other age groups. Sequence analysis of the ITS region of <jats:italic>Encephalitozoon<\/jats:italic> species showed two genotypes (II and III) for <jats:italic>E. cuniculi<\/jats:italic> and one (TURK1B) for <jats:italic>E. hellem<\/jats:italic>. Only <jats:italic>G. duodenalis<\/jats:italic> assemblage A was identified in all nested PCR-positive samples. <jats:italic>E. bieneusi<\/jats:italic> was found more often than other enteric pathogens.<\/jats:p>\n              <\/jats:sec><jats:sec>\n                <jats:title>Conclusions<\/jats:title>\n                <jats:p>This study showed that <jats:italic>E. bieneusi, Encephalitozoon<\/jats:italic> spp. [<jats:italic>E. cuniculi<\/jats:italic> and <jats:italic>E. hellem<\/jats:italic>] and <jats:italic>G. duodenalis<\/jats:italic> were common enteric parasites in diarrheic pigs in Chongqing and Sichuan Provinces. In case of both mono-infection and coinfection, <jats:italic>E. bieneusi<\/jats:italic> was the most common enteric pathogen in diarrheic pigs. Thus, it may be a significant cause of diarrhea in pigs. Precautions should be taken to prevent the spread of these enteric parasites.<\/jats:p>\n              <\/jats:sec>","DOI":"10.1186\/s12866-023-03070-x","type":"journal-article","created":{"date-parts":[[2023,11,11]],"date-time":"2023-11-11T10:01:32Z","timestamp":1699696892000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["First identification and coinfection detection of Enterocytozoon bieneusi, Encephalitozoon spp., Cryptosporidium spp. and Giardia duodenalis in diarrheic pigs in Southwest China"],"prefix":"10.1186","volume":"23","author":[{"given":"Samson Teweldeberhan","family":"Ghebremichael","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Xianzhi","family":"Meng","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yujiao","family":"Yang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Amanuel Kidane","family":"Andegiorgish","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zongrun","family":"Wu","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jie","family":"Chen","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Junhong","family":"Wei","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tian","family":"Li","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jialing","family":"Bao","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Zeyang","family":"Zhou","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Guoqing","family":"Pan","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2023,11,11]]},"reference":[{"key":"3070_CR1","doi-asserted-by":"publisher","first-page":"172","DOI":"10.1016\/j.virusres.2015.12.004","volume":"213","author":"S Theuns","year":"2016","unstructured":"Theuns S, Vyt P, Desmarets LMB, Roukaerts IDM, Heylen E, Zeller M, et al. 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