{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,30]],"date-time":"2026-01-30T06:57:34Z","timestamp":1769756254737,"version":"3.49.0"},"reference-count":15,"publisher":"Oxford University Press (OUP)","issue":"1","license":[{"start":{"date-parts":[[2024,2,8]],"date-time":"2024-02-08T00:00:00Z","timestamp":1707350400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"Royal Society Te Aparangi","award":["RDF-MAU170"],"award-info":[{"award-number":["RDF-MAU170"]}]},{"DOI":"10.13039\/501100001504","name":"New Zealand Ministry of Health","doi-asserted-by":"crossref","award":["355766-02"],"award-info":[{"award-number":["355766-02"]}],"id":[{"id":"10.13039\/501100001504","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Percival Carmine Chair in Epidemiology and Public Health, Massey University"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2024,7,25]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:p>Genetic variation in Cryptosporidium, a common protozoan gut parasite in humans, is often based on marker genes containing trinucleotide repeats, which differentiate subtypes and track outbreaks. However, repeat regions have high replication slippage rates, making it difficult to discern biological diversity from error. Here, we synthesized Cryptosporidium DNA in clonal plasmid vectors, amplified them in different mock community ratios, and sequenced them using next-generation sequencing to determine the rate of replication slippage with dada2. Our results indicate that slippage rates increase with the length of the repeat region and can contribute to error rates of up to 20%.<\/jats:p>","DOI":"10.1093\/infdis\/jiae065","type":"journal-article","created":{"date-parts":[[2024,2,8]],"date-time":"2024-02-08T22:30:01Z","timestamp":1707431401000},"page":"e144-e148","source":"Crossref","is-referenced-by-count":5,"title":["Quantifying Replication Slippage Error in <i>Cryptosporidium<\/i> Metabarcoding Studies"],"prefix":"10.1093","volume":"230","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6764-6568","authenticated-orcid":false,"given":"Matthew A","family":"Knox","sequence":"first","affiliation":[{"name":"School of Veterinary Science"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0285-4101","authenticated-orcid":false,"given":"Patrick J","family":"Biggs","sequence":"additional","affiliation":[{"name":"School of Veterinary Science"},{"name":"School of Natural Sciences, Massey University , Palmerston North, Manawatu-Wanganui , New Zealand"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Juan Carlos","family":"Garcia-R","sequence":"additional","affiliation":[{"name":"School of Veterinary Science"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0087-3015","authenticated-orcid":false,"given":"David T S","family":"Hayman","sequence":"additional","affiliation":[{"name":"School of Veterinary Science"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"286","published-online":{"date-parts":[[2024,2,8]]},"reference":[{"key":"2024072520132843400_jiae065-B1","doi-asserted-by":"crossref","first-page":"2587","DOI":"10.1093\/emboj\/20.10.2587","article-title":"Replication slippage involves DNA polymerase pausing and dissociation","volume":"20","author":"Viguera","year":"2001","journal-title":"EMBO J"},{"key":"2024072520132843400_jiae065-B2","doi-asserted-by":"crossref","first-page":"97","DOI":"10.1016\/j.semcdb.2020.10.003","article-title":"Genome (in)stability at tandem repeats","volume":"113","author":"Balzano","year":"2021","journal-title":"Semin Cell Dev Biol"},{"key":"2024072520132843400_jiae065-B3","first-page":"8","article-title":"Molecular epidemiologic tools for waterborne pathogens Cryptosporidium spp. and Giardia duodenalis","author":"Xiao","year":"2017","journal-title":"Food Waterborne Parasitol"},{"key":"2024072520132843400_jiae065-B4","doi-asserted-by":"crossref","first-page":"104859","DOI":"10.1016\/j.meegid.2021.104859","article-title":"Molecular analysis of cryptosporidiosis cases in Western Australia in 2019 and 2020 supports the occurrence of two swimming pool associated outbreaks and reveals the emergence of a rare C. hominis IbA12G3 subtype","volume":"92","author":"Braima","year":"2021","journal-title":"Infect Genet Evol"},{"key":"2024072520132843400_jiae065-B5","doi-asserted-by":"crossref","first-page":"601","DOI":"10.1016\/j.ijpara.2017.03.003","article-title":"Next generation sequencing uncovers within-host differences in the genetic diversity of Cryptosporidium gp60 subtypes","volume":"47","author":"Zahedi","year":"2017","journal-title":"Int J Parasitol"},{"key":"2024072520132843400_jiae065-B6","doi-asserted-by":"crossref","first-page":"938","DOI":"10.3390\/pathogens11080938","article-title":"Evaluation of next-generation sequencing applied to Cryptosporidium parvum and Cryptosporidium hominis epidemiological study","volume":"11","author":"Bailly","year":"2022","journal-title":"Pathogens"},{"key":"2024072520132843400_jiae065-B7","doi-asserted-by":"crossref","first-page":"974","DOI":"10.1093\/nar\/gkg178","article-title":"Taq DNA polymerase slippage mutation rates measured by PCR and quasi-likelihood analysis: (CA\/GT)n and (A\/T)n microsatellites","volume":"31","author":"Shinde","year":"2003","journal-title":"Nucleic Acids Res"},{"key":"2024072520132843400_jiae065-B8"},{"key":"2024072520132843400_jiae065-B9","doi-asserted-by":"crossref","first-page":"581","DOI":"10.1038\/nmeth.3869","article-title":"DADA2: high-resolution sample inference from Illumina amplicon data","volume":"13","author":"Callahan","year":"2016","journal-title":"Nat Methods"},{"key":"2024072520132843400_jiae065-B10","doi-asserted-by":"crossref","first-page":"686","DOI":"10.1093\/infdis\/jiab417","article-title":"TIDE analysis of Cryptosporidium infections by gp60 typing reveals obscured mixed infections","volume":"225","author":"Dettwiler","year":"2022","journal-title":"J Infect Dis"},{"key":"2024072520132843400_jiae065-B11","doi-asserted-by":"crossref","first-page":"2123","DOI":"10.1093\/molbev\/msg228","article-title":"The relationship between microsatellite slippage mutation rate and the number of repeat units","volume":"20","author":"Lai","year":"2003","journal-title":"Mol Biol Evol"},{"key":"2024072520132843400_jiae065-B12","doi-asserted-by":"crossref","first-page":"e0132253","DOI":"10.1371\/journal.pone.0132253","article-title":"Nested PCR biases in interpreting microbial community structure in 16S rRNA gene sequence datasets","volume":"10","author":"Yu","year":"2015","journal-title":"PLoS One"},{"key":"2024072520132843400_jiae065-B13","doi-asserted-by":"crossref","first-page":"1231","DOI":"10.1111\/1755-0998.13512","article-title":"Strategies for sample labelling and library preparation in DNA metabarcoding studies","volume":"22","author":"Bohmann","year":"2022","journal-title":"Mol Ecol Resour"},{"key":"2024072520132843400_jiae065-B14","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1038\/s41598-019-48546-x","article-title":"Understanding PCR processes to draw meaningful conclusions from environmental DNA studies","volume":"9","author":"Kelly","year":"2019","journal-title":"Sci Rep"},{"key":"2024072520132843400_jiae065-B15","doi-asserted-by":"crossref","first-page":"e166814","DOI":"10.1172\/JCI166814","article-title":"Specific Cryptosporidium antigens associate with reinfection immunity and protection from cryptosporidiosis","volume":"133:","author":"Gilchrist","year":"2023","journal-title":"J Clin Invest"}],"container-title":["The Journal of Infectious Diseases"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/jid\/advance-article-pdf\/doi\/10.1093\/infdis\/jiae065\/56797352\/jiae065.pdf","content-type":"application\/pdf","content-version":"am","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/jid\/article-pdf\/230\/1\/e144\/58649833\/jiae065.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/jid\/article-pdf\/230\/1\/e144\/58649833\/jiae065.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2024,7,25]],"date-time":"2024-07-25T20:18:21Z","timestamp":1721938701000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/jid\/article\/230\/1\/e144\/7603955"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2024,2,8]]},"references-count":15,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2024,2,8]]},"published-print":{"date-parts":[[2024,7,25]]}},"URL":"https:\/\/doi.org\/10.1093\/infdis\/jiae065","relation":{},"ISSN":["0022-1899","1537-6613"],"issn-type":[{"value":"0022-1899","type":"print"},{"value":"1537-6613","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2024,7,15]]},"published":{"date-parts":[[2024,2,8]]}}}