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In China, despite the number of HIV\/AIDS patients being extremely large, only a few studies have investigated opportunistic infections caused by intestinal pathogens in this patient population. The aims of this study were to elucidate the occurrence and genetic characteristics of<jats:italic>Cryptosporidium<\/jats:italic>spp.,<jats:italic>G. duodenalis<\/jats:italic>, and<jats:italic>E. bieneusi<\/jats:italic>in HIV\/AIDS patients.<\/jats:p><\/jats:sec><jats:sec><jats:title>Methods<\/jats:title><jats:p>We collected fecal specimens from 155 HIV\/AIDS patients (one from each patient). All of the specimens were examined for the presence of the pathogens by genotyping using polymerase chain reaction and sequencing of the small subunit ribosomal RNA gene for<jats:italic>Cryptosporidium<\/jats:italic>spp.; the triosephosphate isomerase, \u03b2-giardin and glutamate dehydrogenase genes for<jats:italic>G. duodenalis<\/jats:italic>; and the internal transcribed spacer region of the rRNA gene for<jats:italic>E. bieneusi<\/jats:italic>. The<jats:italic>Cryptosporidium<\/jats:italic>-positive specimens were further subtyped by polymerase chain reacion and sequencing of the 60-kDa glycoprotein gene.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>Six (3.9%), three (1.9%), and eight (5.2%) HIV\/AIDS patients were positive for<jats:italic>Cryptosporidium<\/jats:italic>spp.,<jats:italic>G. duodenalis<\/jats:italic>, and<jats:italic>E. bieneusi<\/jats:italic>, respectively. No statistical differences were observed in occurrence rate between the groups by gender, clinical symptom (diarrhea), and CD4<jats:sup>+<\/jats:sup>cell count. Four<jats:italic>Cryptosporidium<\/jats:italic>species were identified:<jats:italic>Cryptosporidium hominis<\/jats:italic>(<jats:italic>n<\/jats:italic>\u2009=\u20092),<jats:italic>Cryptosporidium parvum<\/jats:italic>(<jats:italic>n<\/jats:italic>\u2009=\u20091),<jats:italic>Cryptosporidium meleagridis<\/jats:italic>(<jats:italic>n<\/jats:italic>\u2009=\u20091), and<jats:italic>Cryptosporidium andersoni<\/jats:italic>(<jats:italic>n<\/jats:italic>\u2009=\u20092). Furthermore, two<jats:italic>C. hominis<\/jats:italic>subtypes (IeA12G3T3 and IaA28R4) were detected. Three<jats:italic>G. duodenalis<\/jats:italic>-positive specimens were successfully amplified and sequenced at the triosephosphate isomerase and \u03b2-giardin loci, which led to the identification of assemblages C and B, respectively. Seven genotypes (D, Type IV, EbpC, Peru11, EbpD, A, and I) were identified in<jats:italic>E. bieneusi<\/jats:italic>-positive specimens.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusions<\/jats:title><jats:p>Our findings should increase awareness of AIDS-related opportunistic intestinal pathogens, and indicate the need for routine examination in clinical practice for the detection of<jats:italic>Cryptosporidium<\/jats:italic>spp.,<jats:italic>G. duodenalis<\/jats:italic>, and<jats:italic>E. bieneusi<\/jats:italic>. Homology analyses of the three intestinal pathogens at the nucleotide and\/or amino acid levels indicated their zoonotic potential.<\/jats:p><\/jats:sec><jats:sec><jats:title>Graphical Abstract<\/jats:title><\/jats:sec>","DOI":"10.1186\/s13071-023-05666-8","type":"journal-article","created":{"date-parts":[[2023,2,4]],"date-time":"2023-02-04T20:03:44Z","timestamp":1675541024000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":45,"title":["Molecular identification and genetic characteristics of Cryptosporidium spp., Giardia duodenalis, and Enterocytozoon bieneusi in human immunodeficiency virus\/acquired immunodeficiency syndrome patients in Shanghai, China"],"prefix":"10.1186","volume":"16","author":[{"given":"Yanyan","family":"Jiang","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Li","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Zhongying","family":"Yuan","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Aiqin","family":"Liu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jianping","family":"Cao","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yujuan","family":"Shen","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"297","published-online":{"date-parts":[[2023,2,4]]},"reference":[{"key":"5666_CR1","doi-asserted-by":"publisher","first-page":"1527","DOI":"10.1097\/QAD.0000000000002583","volume":"34","author":"AH Sohn","year":"2020","unstructured":"Sohn AH, Lumbiganon P, Kurniati N, Lapphra K, Law M, Do VC, et al. 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