{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,31]],"date-time":"2025-12-31T12:10:13Z","timestamp":1767183013542,"version":"build-2238731810"},"reference-count":33,"publisher":"Public Library of Science (PLoS)","issue":"1","license":[{"start":{"date-parts":[[2022,1,14]],"date-time":"2022-01-14T00:00:00Z","timestamp":1642118400000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/publicdomain\/zero\/1.0\/"}],"funder":[{"name":"Advanced Molecular Detection Initiative at CDC"},{"DOI":"10.13039\/100006229","name":"Oak Ridge Institute for Science and Education","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100006229","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100006229","name":"Oak Ridge Institute for Science and Education","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100006229","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Williams Consulting LLC"},{"name":"CDC Foundation"}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"abstract":"<jats:p>\n                    Sequencing large numbers of individual samples is often needed for countrywide antimalarial drug resistance surveillance. Pooling DNA from several individual samples is an alternative cost and time saving approach for providing allele frequency (AF) estimates at a population level. Using 100 individual patient DNA samples of dried blood spots from a 2017 nationwide drug resistance surveillance study in Haiti, we compared codon coverage of drug resistance-conferring mutations in four\n                    <jats:italic>Plasmodium falciparum<\/jats:italic>\n                    genes (\n                    <jats:italic>crt<\/jats:italic>\n                    ,\n                    <jats:italic>dhps<\/jats:italic>\n                    ,\n                    <jats:italic>dhfr<\/jats:italic>\n                    , and\n                    <jats:italic>mdr1<\/jats:italic>\n                    ), for the same deep sequenced samples run individually and pooled. Samples with similar real-time PCR cycle threshold (Ct) values (+\/- 1.0 Ct value) were combined with ten samples per pool. The sequencing success for samples in pools were higher at a lower parasite density than the individual samples sequence method. The median codon coverage for drug resistance-associated mutations in all four genes were greater than 3-fold higher in the pooled samples than in individual samples. The overall codon coverage distribution for pooled samples was wider than the individual samples. The sample pools with &lt; 40 parasites\/\u03bcL blood showed more discordance in AF calls for\n                    <jats:italic>dhfr<\/jats:italic>\n                    and\n                    <jats:italic>mdr1<\/jats:italic>\n                    between the individual and pooled samples. This discordance in AF estimation may be due to low amounts of parasite DNA, which could lead to variable PCR amplification efficiencies. Grouping samples with an estimated \u2265 40 parasites\/\u03bcL blood prior to pooling and deep sequencing yielded the expected population level AF. Pooling DNA samples based on estimates of &gt; 40 parasites\/\u03bcL prior to deep sequencing can be used for rapid genotyping of a large number of samples for these four genes and possibly other drug resistant markers in population-based studies. As Haiti is a low malaria transmission country with very few mixed infections and continued chloroquine sensitivity, the pooled sequencing approach can be used for routine national molecular surveillance of resistant parasites.\n                  <\/jats:p>","DOI":"10.1371\/journal.pone.0262616","type":"journal-article","created":{"date-parts":[[2022,1,14]],"date-time":"2022-01-14T14:25:26Z","timestamp":1642170326000},"page":"e0262616","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":1,"title":["Evaluation of a parasite-density based pooled targeted amplicon deep sequencing (TADS) method for molecular surveillance of Plasmodium falciparum drug resistance genes in Haiti"],"prefix":"10.1371","volume":"17","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-0777-8507","authenticated-orcid":true,"given":"Swarnali","family":"Louha","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Camelia","family":"Herman","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mansi","family":"Gupta","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Dhruviben","family":"Patel","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Julia","family":"Kelley","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Je-Hoon M.","family":"OH","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Janani","family":"Guru","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jean F.","family":"Lemoine","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Michelle A.","family":"Chang","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Udhayakumar","family":"Venkatachalam","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eric","family":"Rogier","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Eldin","family":"Talundzic","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2022,1,14]]},"reference":[{"key":"pone.0262616.ref001","doi-asserted-by":"crossref","first-page":"393","DOI":"10.1186\/s12936-018-2553-5","article-title":"\u201cWherever doctors cannot reach, the sunshine can\u201d: overcoming potential barriers to malaria elimination interventions in Haiti","volume":"17","author":"T Druetz","year":"2018","journal-title":"Malaria 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2016\u20132017","volume":"26","author":"E Rogier","year":"2020","journal-title":"Emerg Infect Dis"},{"key":"pone.0262616.ref006","doi-asserted-by":"crossref","first-page":"2217","DOI":"10.4269\/ajtmh.20-0833","article-title":"Establishing a National Molecular Surveillance Program for the Detection of Plasmodium falciparum Markers of Resistance to Antimalarial Drugs in Haiti","volume":"103","author":"KES Hamre","year":"2020","journal-title":"Am J Tropical Medicine Hyg"},{"key":"pone.0262616.ref007","doi-asserted-by":"crossref","first-page":"1998","DOI":"10.1093\/infdis\/jit392","article-title":"Pooled Deep Sequencing of Plasmodium falciparum Isolates: An Efficient and Scalable Tool to Quantify Prevailing Malaria Drug-Resistance Genotypes","volume":"208","author":"SM Taylor","year":"2013","journal-title":"J Infect Dis"},{"key":"pone.0262616.ref008","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1534\/genetics.110.121012","article-title":"To Pool, or Not to 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to Accelerate Progress towards Malaria Elimination in Grande-Anse, Haiti","author":"T Druetz","year":"2021","journal-title":"J Infect Dis"}],"updated-by":[{"DOI":"10.1371\/journal.pone.0315044","type":"correction","label":"Correction","source":"publisher","updated":{"date-parts":[[2024,12,2]],"date-time":"2024-12-02T00:00:00Z","timestamp":1733097600000}}],"container-title":["PLOS ONE"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0262616","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,1,14]],"date-time":"2022-01-14T14:25:52Z","timestamp":1642170352000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0262616"}},"subtitle":[],"editor":[{"given":"Aparup","family":"Das","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2022,1,14]]},"references-count":33,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2022,1,14]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0262616","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,1,14]]}}}