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Here, we compared molecular versus conventional diagnostic methods in prospective cross-sectional surveillances in vaccinated infants in the Netherlands. Nasopharyngeal samples (n\u2009=\u20091169) from 11- and 24-month-old children, collected during autumn\/winter 2010\/2011 and 2012\/2013, were tested by conventional culture for <jats:italic>S. pneumoniae.<\/jats:italic> DNA extracted from all culture-plate growth was tested by qPCR for pneumococcal-specific genes (<jats:italic>lytA<\/jats:italic>\/<jats:italic>piaB<\/jats:italic>) and selected serotypes (including PCV13-serotypes). qPCR significantly increased the number of carriers detected compared to culture (69% vs. 57%, <jats:italic>p<\/jats:italic>\u2009&lt;\u20090.0001). qPCR assays targeting vaccine-serotypes 4 and 5 proved non-specific (results excluded). For serotypes reliably targeted by qPCR, the number of serotype-carriage events detected by qPCR (n\u2009=\u2009709) was 1.68\u00d7 higher compared to culture (n\u2009=\u2009422). There was a strong correlation (rho\u2009=\u20090.980; <jats:italic>p<\/jats:italic>\u2009&lt;\u20090.0001) between the number of serotypes detected using qPCR and by culture. This study demonstrates the high potential of molecular methods in pneumococcal surveillances, particularly for enhanced serotype detection. We found no evidence of a hidden circulation of vaccine-targeted serotypes, despite vaccine-serotypes still significantly contributing to invasive pneumococcal disease in unvaccinated individuals, supporting the presence of a substantial <jats:italic>S. pneumoniae<\/jats:italic> reservoir outside vaccinated children.<\/jats:p>","DOI":"10.1038\/srep23809","type":"journal-article","created":{"date-parts":[[2016,4,5]],"date-time":"2016-04-05T09:14:26Z","timestamp":1459847666000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":66,"title":["Molecular surveillance of nasopharyngeal carriage of Streptococcus pneumoniae in children vaccinated with conjugated polysaccharide pneumococcal vaccines"],"prefix":"10.1038","volume":"6","author":[{"given":"Anne L.","family":"Wyllie","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alienke J.","family":"Wijmenga-Monsuur","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marlies A.","family":"van Houten","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Astrid A. T. M.","family":"Bosch","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"James A.","family":"Groot","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jody","family":"van Engelsdorp Gastelaars","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jacob P.","family":"Bruin","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Debby","family":"Bogaert","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Nynke Y.","family":"Rots","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elisabeth A. 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Mucosal Immunol. 8, 176\u2013185 (2015).","journal-title":"Mucosal Immunol."}],"container-title":["Scientific Reports"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.nature.com\/articles\/srep23809.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/srep23809","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.nature.com\/articles\/srep23809.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2023,1,5]],"date-time":"2023-01-05T03:50:12Z","timestamp":1672890612000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.nature.com\/articles\/srep23809"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2016,4,5]]},"references-count":49,"journal-issue":{"issue":"1","published-online":{"date-parts":[[2016,4,29]]}},"alternative-id":["BFsrep23809"],"URL":"https:\/\/doi.org\/10.1038\/srep23809","relation":{},"ISSN":["2045-2322"],"issn-type":[{"value":"2045-2322","type":"electronic"}],"subject":[],"published":{"date-parts":[[2016,4,5]]},"assertion":[{"value":"26 January 2016","order":1,"name":"received","label":"Received","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"15 March 2016","order":2,"name":"accepted","label":"Accepted","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"5 April 2016","order":3,"name":"first_online","label":"First Online","group":{"name":"ArticleHistory","label":"Article History"}},{"value":"E.A.M.S. declares to have received research grants from Pfizer and GSK and fees paid to the institution for advisory boards and participation in independent data monitoring committees for Pfizer and GSK. K.T. has received consulting fees from Pfizer and grant support for studies on pneumococcal carriage from Pfizer. All other authors report no potential conflicts.","order":1,"name":"Ethics","group":{"name":"EthicsHeading","label":"Competing interests"}}],"article-number":"23809"}}