{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,11,11]],"date-time":"2025-11-11T22:15:54Z","timestamp":1762899354669},"reference-count":41,"publisher":"American Society for Microbiology","issue":"3","license":[{"start":{"date-parts":[[2017,3,1]],"date-time":"2017-03-01T00:00:00Z","timestamp":1488326400000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"funder":[{"DOI":"10.13039\/501100007294","name":"Myndigheten f\u00f6r Samh\u00e4llsskydd och Beredskap","doi-asserted-by":"publisher","award":["2012-172"],"award-info":[{"award-number":["2012-172"]}],"id":[{"id":"10.13039\/501100007294","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100007294","name":"Myndigheten f\u00f6r Samh\u00e4llsskydd och Beredskap","doi-asserted-by":"publisher","award":["2013-1556"],"award-info":[{"award-number":["2013-1556"]}],"id":[{"id":"10.13039\/501100007294","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["J Clin Microbiol"],"published-print":{"date-parts":[[2017,3]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n          <jats:p>\n            In order to improve genotyping and epidemiological analysis of\n            <jats:named-content content-type=\"genus-species\">Cryptosporidium<\/jats:named-content>\n            spp., genomic data need to be generated directly from a broad range of clinical specimens. Utilizing a robust method that we developed for the purification and generation of amplified target DNA, we present its application for the successful isolation and whole-genome sequencing of 14 different\n            <jats:named-content content-type=\"genus-species\">Cryptosporidium hominis<\/jats:named-content>\n            patient specimens. Six isolates of subtype IbA10G2 were analyzed together with a single representative each of 8 other subtypes: IaA20R3, IaA23R3, IbA9G3, IbA13G3, IdA14, IeA11G3T3, IfA12G1, and IkA18G1. Parasite burden was measured over a range of more than 2 orders of magnitude for all samples, while the genomes were sequenced to mean depths of between 17\u00d7 and 490\u00d7 coverage. Sequence homology-based functional annotation identified several genes of interest, including the gene encoding\n            <jats:named-content content-type=\"genus-species\">Cryptosporidium<\/jats:named-content>\n            oocyst wall protein 9 (COWP9), which presented a predicted loss-of-function mutation in all the sequence subtypes, except for that seen with IbA10G2, which has a sequence identical to the\n            <jats:named-content content-type=\"genus-species\">Cryptosporidium parvum<\/jats:named-content>\n            reference Iowa II sequence. Furthermore, phylogenetic analysis showed that all the IbA10G2 genomes form a monophyletic clade in the\n            <jats:named-content content-type=\"genus-species\">C. hominis<\/jats:named-content>\n            tree as expected and yet display some heterogeneity within the IbA10G2 subtype. The current report validates the aforementioned method for isolating and sequencing\n            <jats:named-content content-type=\"genus-species\">Cryptosporidium<\/jats:named-content>\n            directly from clinical stool samples. In addition, the analysis demonstrates the potential in mining data generated from sequencing multiple whole genomes of\n            <jats:named-content content-type=\"genus-species\">Cryptosporidium<\/jats:named-content>\n            from human fecal samples, while alluding to the potential for a higher degree of genotyping within\n            <jats:named-content content-type=\"genus-species\">Cryptosporidium<\/jats:named-content>\n            epidemiology.\n          <\/jats:p>","DOI":"10.1128\/jcm.01798-16","type":"journal-article","created":{"date-parts":[[2016,12,22]],"date-time":"2016-12-22T02:02:29Z","timestamp":1482372149000},"page":"844-858","update-policy":"http:\/\/dx.doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":29,"title":["Genomic Variation in IbA10G2 and Other Patient-Derived Cryptosporidium hominis Subtypes"],"prefix":"10.1128","volume":"55","author":[{"given":"Per","family":"Sikora","sequence":"first","affiliation":[{"name":"Laboratory Medicine Core Facility, Sahlgrenska University Hospital, Gothenburg, Sweden"},{"name":"Department of Microbiology, Public Health Agency of Sweden, Solna, Sweden"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sofia","family":"Andersson","sequence":"additional","affiliation":[{"name":"Department of Microbiology, Public Health Agency of Sweden, Solna, Sweden"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jadwiga","family":"Winiecka-Krusnell","sequence":"additional","affiliation":[{"name":"Department of Microbiology, Public Health Agency of Sweden, Solna, Sweden"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Bj\u00f6rn","family":"Hallstr\u00f6m","sequence":"additional","affiliation":[{"name":"Department of Microbiology, Public Health Agency of Sweden, Solna, Sweden"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Cecilia","family":"Alsmark","sequence":"additional","affiliation":[{"name":"Department of Microbiology, National Veterinary Institute, Uppsala, Sweden"},{"name":"Division of Pharmacognosy, Department of Medicinal Chemistry, Uppsala University, Sweden"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Karin","family":"Troell","sequence":"additional","affiliation":[{"name":"Department of Microbiology, National Veterinary Institute, Uppsala, Sweden"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jessica","family":"Beser","sequence":"additional","affiliation":[{"name":"Department of Microbiology, Public Health Agency of Sweden, Solna, Sweden"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Romanico B. 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