{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,14]],"date-time":"2026-09-14T10:51:24Z","timestamp":1789383084350,"version":"build-2803163510"},"reference-count":21,"publisher":"Public Library of Science (PLoS)","issue":"8","license":[{"start":{"date-parts":[[2023,8,3]],"date-time":"2023-08-03T00:00:00Z","timestamp":1691020800000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"National Institute of Health","award":["1U01AI110466-01A1"],"award-info":[{"award-number":["1U01AI110466-01A1"]}]}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"abstract":"<jats:sec id=\"sec001\">\n<jats:title>Introduction<\/jats:title>\n<jats:p>Several important human pathogens that cause life-threatening infections are asymptomatically carried in the Nasopharynx\/Oropharynx (NP\/OP). DNA extraction is a prerequisite for most culture-independent techniques used to identify pathogens in the NP\/OP. However, components of DNA extraction kits differ thereby giving rise to differences in performance. We compared the DNA concentration and the detection of three pathogens in the NP\/OP using the discontinued DNeasy PowerSoil Kit (Kit DP) and the DNeasy PowerLyzer PowerSoil Kit (Kit DPP).<\/jats:p>\n<\/jats:sec>\n<jats:sec id=\"sec002\">\n<jats:title>Methods<\/jats:title>\n<jats:p>DNA was extracted from the same set of 103 NP\/OP samples using the two kits. DNA concentration was measured using the Qubit 2.0 Fluorometer. Real-time Polymerase Chain reaction (RT-PCR) was done using the QuantStudio 7-flex system to detect three pathogens: <jats:italic>S<\/jats:italic>. <jats:italic>pneumoniae<\/jats:italic>, <jats:italic>H<\/jats:italic>. <jats:italic>influenzae<\/jats:italic>, and <jats:italic>N<\/jats:italic>. <jats:italic>meningitidis<\/jats:italic>. Bland-Altman statistics and plots were used to determine the threshold cycle (Ct) value agreement for the two kits.<\/jats:p>\n<\/jats:sec>\n<jats:sec id=\"sec003\">\n<jats:title>Results<\/jats:title>\n<jats:p>The average DNA concentration from kit DPP was higher than Kit DP; 1235.6 ng\/ml (SD = 1368.3) vs 884.9 ng\/ml (SD = 1095.3), p = 0.002. Using a Ct value cutoff of 40 for positivity, the concordance for the presence of <jats:italic>S<\/jats:italic>. <jats:italic>pneumoniae<\/jats:italic> was 82% (84\/102); 94%(96\/103) for <jats:italic>N<\/jats:italic>. <jats:italic>meningitidis<\/jats:italic> and 92%(95\/103) for <jats:italic>H<\/jats:italic>. <jats:italic>influenzae<\/jats:italic>. Kit DP proportionately resulted in higher Ct values than Kit DPP for all pathogens. The Ct value bias of measurement for <jats:italic>S<\/jats:italic>. <jats:italic>pneumoniae<\/jats:italic> was +2.4 (95% CI, 1.9\u20133.0), +1.4 (95% CI, 0.9\u20131.9) for <jats:italic>N<\/jats:italic>. <jats:italic>meningitidis<\/jats:italic> and +1.4 (95% CI, 0.2\u20132.5) for <jats:italic>H<\/jats:italic>. <jats:italic>influenzae<\/jats:italic>.<\/jats:p>\n<\/jats:sec>\n<jats:sec id=\"sec004\">\n<jats:title>Conclusion<\/jats:title>\n<jats:p>The higher DNA concentration obtained using kit DPP could increase the chances of recovering low abundant bacteria. The PCR results were reproducible for more than 90% of the samples for the gram-negative <jats:italic>H<\/jats:italic>. <jats:italic>influenzae and N<\/jats:italic>. <jats:italic>meningitidis<\/jats:italic>. Ct value variations of the kits must be taken into consideration when comparing studies that have used the two kits.<\/jats:p>\n<\/jats:sec>","DOI":"10.1371\/journal.pone.0289557","type":"journal-article","created":{"date-parts":[[2023,8,3]],"date-time":"2023-08-03T17:43:35Z","timestamp":1691084615000},"page":"e0289557","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":3,"title":["Comparison of DNA concentration and bacterial pathogen PCR detection when using two DNA extraction kits for nasopharyngeal\/oropharyngeal samples"],"prefix":"10.1371","volume":"18","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-9834-8686","authenticated-orcid":true,"given":"Dam","family":"Khan","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shola-Able","family":"Thomas","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Peggy-Estelle","family":"Tientcheu","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sambou M. 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Ero\u011flu","year":"2018","journal-title":"Mikrobiyol Bul"},{"key":"pone.0289557.ref014","unstructured":"World Health Organization & Centers for Disease Control and Prevention (\u200eU.S.)\u200e. (\u200e2011)\u200e. Laboratory methods for the diagnosis of meningitis caused by neisseria meningitidis, streptococcus pneumoniae, and haemophilus influenzae: WHO manual, 2nd ed. World Health Organization."},{"issue":"1","key":"pone.0289557.ref015","doi-asserted-by":"crossref","first-page":"8373","DOI":"10.1038\/s41598-020-65399-x","article-title":"Re-evaluation of Streptococcus pneumoniae carriage in Portuguese elderly by qPCR increases carriage estimates and unveils an expanded pool of serotypes","volume":"10","author":"ST Almeida","year":"2020","journal-title":"Scientific Reports"},{"key":"pone.0289557.ref016","unstructured":"Pneumonia Fact Sheet World Health Organisation2019 [cited 2021 15\/07\/2021]. Available from: https:\/\/www.who.int\/news-room\/fact-sheets\/detail\/pneumonia."},{"issue":"1","key":"pone.0289557.ref017","doi-asserted-by":"crossref","first-page":"e85001","DOI":"10.1371\/journal.pone.0085001","article-title":"Pneumococcal carriage in sub-Saharan Africa\u2014a systematic review","volume":"9","author":"E Usuf","year":"2014","journal-title":"PloS one"},{"issue":"4","key":"pone.0289557.ref018","first-page":"397","article-title":"Antimicrobial resistance of bacterial agents of the upper respiratory tract of school children in Buea, Cameroon","volume":"26","author":"RN Ndip","year":"2008","journal-title":"J Health Popul Nutr"},{"issue":"1","key":"pone.0289557.ref019","doi-asserted-by":"crossref","first-page":"59","DOI":"10.1097\/INF.0b013e31814da70c","article-title":"The descriptive epidemiology of Streptococcus pneumoniae and Haemophilus influenzae nasopharyngeal carriage in children and adults in Kilifi district, Kenya","volume":"27","author":"O Abdullahi","year":"2008","journal-title":"Pediatr Infect Dis J"},{"issue":"6","key":"pone.0289557.ref020","doi-asserted-by":"crossref","first-page":"e0198772","DOI":"10.1371\/journal.pone.0198772","article-title":"Global etiology of bacterial meningitis: A systematic review and meta-analysis","volume":"13","author":"AM Oordt-Speets","year":"2018","journal-title":"PLoS One"},{"issue":"2","key":"pone.0289557.ref021","doi-asserted-by":"crossref","first-page":"297","DOI":"10.3390\/microorganisms9020297","article-title":"Comparative Study of Eleven Mechanical Pretreatment Protocols for Cryptosporidium parvum DNA Extraction from Stool Samples","volume":"9","author":"L Claudel","year":"2021","journal-title":"Microorganisms"}],"container-title":["PLOS ONE"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0289557","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,8,3]],"date-time":"2023-08-03T17:43:53Z","timestamp":1691084633000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0289557"}},"subtitle":[],"editor":[{"given":"Haitham Mohamed","family":"Amer","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"editor"}]}],"short-title":[],"issued":{"date-parts":[[2023,8,3]]},"references-count":21,"journal-issue":{"issue":"8","published-online":{"date-parts":[[2023,8,3]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0289557","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2023,8,3]]}}}