{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,21]],"date-time":"2026-07-21T02:19:35Z","timestamp":1784600375143,"version":"3.55.0"},"reference-count":34,"publisher":"BMJ","issue":"6","funder":[{"DOI":"10.13039\/501100000024","name":"Canadian Institutes of Health Research","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100000024","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100011094","name":"Public Health Agency of Canada","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100011094","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/100013739","name":"Pfizer Canada","doi-asserted-by":"crossref","id":[{"id":"10.13039\/100013739","id-type":"DOI","asserted-by":"crossref"}]}],"content-domain":{"domain":["bmj.com"],"crossmark-restriction":true},"short-container-title":["BMJ Open"],"accepted":{"date-parts":[[2017,4,12]]},"published-print":{"date-parts":[[2017,6]]},"abstract":"<jats:sec>\n                    <jats:title>Study design<\/jats:title>\n                    <jats:p>\n                      Detection and serotyping of\n                      <jats:italic>Streptococcus pneumoniae are<\/jats:italic>\n                      important to assess the impact of pneumococcal vaccines. This study describes the diagnostic accuracy of PCR-based detection of\n                      <jats:italic>S. pneumoniae<\/jats:italic>\n                      directly from nasopharyngeal (NP) swabs collected for respiratory virus studies.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>\n                      Active surveillance for community-acquired pneumonia (CAP) in hospitalised adults was performed from December 2010 to 2013. Detection of pneumococcal CAP (CAP\n                      <jats:sub>Spn<\/jats:sub>\n                      ) was performed by urine antigen detection (UAD), identification of\n                      <jats:italic>S. pneumoniae<\/jats:italic>\n                      in sputum or blood cultures.\n                      <jats:italic>S. pneumoniae<\/jats:italic>\n                      was detected in NP swabs using\n                      <jats:italic>lytA<\/jats:italic>\n                      and\n                      <jats:italic>cpsA<\/jats:italic>\n                      real-time PCR, and serotyping was performed using conventional and real-time multiplex PCRs. For serotyping, the Quellung reaction, PCR-based serotyping or a serotype-specific UAD was used.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      NP swab results were compared against CAP cases where all pneumococcal tests were performed (n=434), or where at least one test was performed (n=1616). CAP\n                      <jats:sub>Spn<\/jats:sub>\n                      was identified in 22.1% (96\/434) and 14.9% (240\/1616), respectively. The sensitivity of NP swab PCR for the detection of\n                      <jats:italic>S. pneumoniae<\/jats:italic>\n                      was poor for CAP\n                      <jats:sub>Spn<\/jats:sub>\n                      (35.4% (34\/96) and 34.17% (82\/240)), but high specificity was observed (99.4% (336\/338) and 97.89% (1347\/1376)). Of the positive NP swabs, a serotype could be deduced by PCR in 88.2% (30\/34) and 93.9% (77\/82), respectively.\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>While further optimisation may be needed to increase the sensitivity of PCR-based detection, its high specificity suggests there is a value for pneumococcal surveillance. With many laboratories archiving specimens for influenza virus surveillance, this specimen type could provide a non-culture-based method for pneumococcal surveillance.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1136\/bmjopen-2016-015008","type":"journal-article","created":{"date-parts":[[2017,6,9]],"date-time":"2017-06-09T21:03:55Z","timestamp":1497042235000},"page":"e015008","update-policy":"https:\/\/doi.org\/10.1136\/crossmarkpolicy","source":"Crossref","is-referenced-by-count":6,"title":["Assessing the diagnostic accuracy of PCR-based detection of\n                    <i>Streptococcus pneumoniae<\/i>\n                    from nasopharyngeal swabs collected for viral studies in Canadian adults hospitalised with community-acquired pneumonia: a Serious Outcomes Surveillance (SOS) Network of the Canadian Immunization Research (CIRN) study"],"prefix":"10.1136","volume":"7","author":[{"given":"Hayley D","family":"Gillis","sequence":"first","affiliation":[{"name":"Canadian Centre for Vaccinology (CCfV), IWK Health Center, Nova Scotia Health Authority (NSHA), and Dalhousie University, Halifax, Nova Scotia, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Amanda L S","family":"Lang","sequence":"additional","affiliation":[{"name":"Canadian Centre for Vaccinology (CCfV), IWK Health Center, Nova Scotia Health Authority (NSHA), and Dalhousie University, Halifax, Nova Scotia, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"May","family":"ElSherif","sequence":"additional","affiliation":[{"name":"Canadian Centre for Vaccinology (CCfV), IWK Health Center, Nova Scotia Health Authority (NSHA), and Dalhousie University, Halifax, Nova Scotia, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Irene","family":"Martin","sequence":"additional","affiliation":[{"name":"National Microbiology Laboratory (NML), Winnipeg, Manitoba, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Todd F","family":"Hatchette","sequence":"additional","affiliation":[{"name":"Canadian Centre for Vaccinology (CCfV), IWK Health Center, Nova Scotia Health Authority (NSHA), and Dalhousie University, Halifax, Nova Scotia, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shelly A","family":"McNeil","sequence":"additional","affiliation":[{"name":"Canadian Centre for Vaccinology (CCfV), IWK Health Center, Nova Scotia Health Authority (NSHA), and Dalhousie University, Halifax, Nova Scotia, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jason J","family":"LeBlanc","sequence":"additional","affiliation":[{"name":"Canadian Centre for Vaccinology (CCfV), IWK Health Center, Nova Scotia Health Authority (NSHA), and Dalhousie University, Halifax, Nova Scotia, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"239","published-online":{"date-parts":[[2017,6,8]]},"reference":[{"key":"2025121510571973000_7.6.e015008.1","doi-asserted-by":"publisher","DOI":"10.1016\/S1473-3099(04)00938-7"},{"key":"2025121510571973000_7.6.e015008.2","doi-asserted-by":"publisher","DOI":"10.1016\/S0140-6736(09)61204-6"},{"key":"2025121510571973000_7.6.e015008.3","doi-asserted-by":"crossref","unstructured":"McNeil SA , Qizilbash N , Ye J , et al . 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