{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,10,20]],"date-time":"2025-10-20T18:44:57Z","timestamp":1760985897743,"version":"3.37.3"},"reference-count":29,"publisher":"EDP Sciences","license":[{"start":{"date-parts":[[2020,4,10]],"date-time":"2020-04-10T00:00:00Z","timestamp":1586476800000},"content-version":"vor","delay-in-days":100,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Parasite"],"accepted":{"date-parts":[[2020,4,2]]},"published-print":{"date-parts":[[2020]]},"abstract":"<jats:p><jats:italic>Cyclospora cayetanensis<\/jats:italic> is an intestinal parasite responsible for the diarrheal illness, cyclosporiasis. Molecular genotyping, using targeted amplicon sequencing, provides a complementary tool for outbreak investigations, especially when epidemiological data are insufficient for linking cases and identifying clusters. The goal of this study was to identify candidate genotyping markers using a novel workflow for detection of segregating single nucleotide polymorphisms (SNPs) in <jats:italic>C. cayetanensis<\/jats:italic> genomes. Four whole <jats:italic>C. cayetanensis<\/jats:italic> genomes were compared using this workflow and four candidate markers were selected for evaluation of their genotyping utility by PCR and Sanger sequencing. These four markers covered 13 SNPs and resolved parasites from 57 stool specimens, differentiating <jats:italic>C. cayetanensis<\/jats:italic> into 19 new unique genotypes.<\/jats:p>","DOI":"10.1051\/parasite\/2020022","type":"journal-article","created":{"date-parts":[[2020,4,10]],"date-time":"2020-04-10T08:24:43Z","timestamp":1586507083000},"page":"24","source":"Crossref","is-referenced-by-count":15,"title":["Development of a workflow for identification of nuclear genotyping markers for <i>Cyclospora cayetanensis<\/i>"],"prefix":"10.1051","volume":"27","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-8272-0711","authenticated-orcid":false,"given":"Katelyn A.","family":"Houghton","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Alexandre","family":"Lomsadze","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Subin","family":"Park","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fernanda S.","family":"Nascimento","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Joel","family":"Barratt","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michael J.","family":"Arrowood","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Erik","family":"VanRoey","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eldin","family":"Talundzic","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mark","family":"Borodovsky","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Yvonne","family":"Qvarnstrom","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"250","published-online":{"date-parts":[[2020,4,10]]},"reference":[{"unstructured":"Andrews S. 2010. FastQC Quality Control tool for High Throughput Sequence Data. Available from: http:\/\/www.bioinformatics.babraham.ac.uk\/projects\/fastqc\/.","key":"R1"},{"issue":"10","key":"R2","doi-asserted-by":"crossref","first-page":"1275","DOI":"10.1017\/S0031182019000581","volume":"146","author":"Barratt","year":"2019","journal-title":"Parasitology"},{"unstructured":"CDC. 2018. Domestically acquired cases of cyclosporiasis \u2014 United States, May\u2013August 2018. Available from: https:\/\/www.cdc.gov\/parasites\/cyclosporiasis\/outbreaks\/2018\/c-082318\/index.html","key":"R3"},{"issue":"1","key":"R4","doi-asserted-by":"crossref","first-page":"611","DOI":"10.1186\/s13071-016-1896-4","volume":"9","author":"Cinar","year":"2016","journal-title":"Parasites & Vectors"},{"unstructured":"Clarke KR, Gorley RN. 2015. PRIMER v7: User manual\/tutorial. PRIMER-E Ltd.: Plymouth, United Kingdom.","key":"R5"},{"key":"R6","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1155\/2008\/619832","volume":"2008","author":"Conesa","year":"2008","journal-title":"International Journal of Plant Genomics"},{"issue":"7","key":"R7","doi-asserted-by":"crossref","first-page":"1394","DOI":"10.1101\/gr.2289704","volume":"14","author":"Darling","year":"2004","journal-title":"Genome Research"},{"issue":"3","key":"R8","doi-asserted-by":"crossref","first-page":"577","DOI":"10.1645\/0022-3395(2000)086[0577:ATEECC]2.0.CO;2","volume":"86","author":"Eberhard","year":"2000","journal-title":"Journal of Parasitology"},{"issue":"4","key":"R9","doi-asserted-by":"crossref","first-page":"371","DOI":"10.1016\/S0020-7519(99)00190-3","volume":"30","author":"Feagin","year":"2000","journal-title":"International Journal for Parasitology"},{"issue":"8","key":"R10","doi-asserted-by":"crossref","first-page":"1464","DOI":"10.3201\/eid2208.150696","volume":"22","author":"Guo","year":"2016","journal-title":"Emerging Infectious Diseases"},{"issue":"1","key":"R11","doi-asserted-by":"crossref","first-page":"47","DOI":"10.1186\/s13071-019-3294-1","volume":"12","author":"Guo","year":"2019","journal-title":"Parasites & Vectors"},{"issue":"19","key":"R12","doi-asserted-by":"crossref","first-page":"493","DOI":"10.15585\/mmwr.mm6619a2","volume":"66","author":"Hlavsa","year":"2017","journal-title":"Morbidity and Mortality Weekly Report"},{"key":"R13","doi-asserted-by":"crossref","first-page":"3","DOI":"10.1051\/parasite\/2019004","volume":"26","author":"Hofstetter","year":"2019","journal-title":"Parasite"},{"issue":"Database issue","key":"R14","first-page":"D250","volume":"36","author":"Jensen","year":"2008","journal-title":"Nucleic Acids Research"},{"unstructured":"Kiryutin B, Souvorov A, Tatusova T. 2007. ProSplign\u2013protein to gnomic aignment tol. in: Proc. 11th Annual International Conference in Research in Computational Molecular Biology, San Fransisco, USA.","key":"R15"},{"issue":"14","key":"R16","doi-asserted-by":"crossref","first-page":"1890","DOI":"10.1017\/S0031182017001299","volume":"144","author":"Li","year":"2017","journal-title":"Parasitology"},{"issue":"1","key":"R17","doi-asserted-by":"crossref","first-page":"316","DOI":"10.1186\/s12879-018-3224-4","volume":"18","author":"Li","year":"2018","journal-title":"BMC Infectious Diseases"},{"key":"R18","doi-asserted-by":"crossref","first-page":"316","DOI":"10.1186\/s12864-016-2632-3","volume":"17","author":"Liu","year":"2016","journal-title":"BMC Genomics"},{"issue":"7","key":"R19","doi-asserted-by":"crossref","first-page":"1314","DOI":"10.3201\/eid2507.181447","volume":"25","author":"Nascimento","year":"2019","journal-title":"Emerging Infectious Disease"},{"key":"R20","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1016\/j.mimet.2016.08.020","volume":"130","author":"Nascimento","year":"2016","journal-title":"Journal of Microbiological Methods"},{"unstructured":"Nurk S, Bankevich A, Antipov D, Gurevich A, Korobeynikov A, Lapidus A, Prjibelsky A, Pyshkin A, Sirotkin A, Sirotkin Y, Stepanauskas R, McLean J, Lasken R, Clingenpeel SR, Woyke T, Tesler G, Alekseyev MA, Pevzner PA. 2013. Assembling genomes and mini-metagenomes from highly chimeric reads. Research in Computational Molecular Biology., 158\u2013170.","key":"R21"},{"issue":"7","key":"R22","doi-asserted-by":"crossref","first-page":"865","DOI":"10.1017\/S0031182017001925","volume":"145","author":"Qvarnstrom","year":"2017","journal-title":"Parasitology"},{"doi-asserted-by":"crossref","unstructured":"Qvarnstrom Y, Wei-Pridgeon Y, Li W, Nascimento FS, Bishop HS, Herwaldt BL, Moss DM, Nayak V, Srinivasamoorthy G, Sheth M, Arrowood MJ. 2015. Draft genome sequences from Cyclospora cayetanensis oocysts purified from a human stool sample. Genome Announcements, 3(6).","key":"R23","DOI":"10.1128\/genomeA.01324-15"},{"key":"R24","doi-asserted-by":"crossref","first-page":"45","DOI":"10.1186\/s13099-018-0272-7","volume":"10","author":"Qvarnstrom","year":"2018","journal-title":"Gut Pathogens"},{"unstructured":"Rozen S, Skaletsky H. 1999. Primer3 on the WWW for general users and for biologist programmers, in Bioinformatics Methods and Protocols. Methods in Molecular Bioogy. Misener S, Krawetz SA, Editor. Humana Press: Totowa, NJ. p. 365\u2013386.","key":"R25"},{"key":"R26","doi-asserted-by":"crossref","first-page":"88","DOI":"10.1186\/s13104-016-1900-2","volume":"9","author":"Schubert","year":"2016","journal-title":"BMC Research Notes"},{"issue":"4","key":"R27","doi-asserted-by":"crossref","first-page":"1040","DOI":"10.1086\/314051","volume":"31","author":"Strausbaugh","year":"2000","journal-title":"Clinical Infectious Diseases"},{"issue":"1","key":"R28","doi-asserted-by":"crossref","first-page":"358","DOI":"10.1186\/s13071-015-0966-3","volume":"8","author":"Tang","year":"2015","journal-title":"Parasites & Vectors"},{"issue":"1","key":"R29","doi-asserted-by":"crossref","first-page":"80","DOI":"10.1016\/j.exppara.2009.03.018","volume":"124","author":"Xiao","year":"2010","journal-title":"Experimental Parasitology"}],"container-title":["Parasite"],"original-title":[],"link":[{"URL":"https:\/\/www.parasite-journal.org\/10.1051\/parasite\/2020022\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,4,10]],"date-time":"2020-04-10T08:25:05Z","timestamp":1586507105000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.parasite-journal.org\/10.1051\/parasite\/2020022"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2020]]},"references-count":29,"alternative-id":["parasite190152"],"URL":"https:\/\/doi.org\/10.1051\/parasite\/2020022","relation":{},"ISSN":["1776-1042"],"issn-type":[{"type":"electronic","value":"1776-1042"}],"subject":[],"published":{"date-parts":[[2020]]}}}