{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,26]],"date-time":"2026-07-26T18:15:18Z","timestamp":1785089718572,"version":"3.55.0"},"reference-count":83,"publisher":"The Royal Society","issue":"9","license":[{"start":{"date-parts":[[2017,9,1]],"date-time":"2017-09-01T00:00:00Z","timestamp":1504224000000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"},{"start":{"date-parts":[[2017,9,1]],"date-time":"2017-09-01T00:00:00Z","timestamp":1504224000000},"content-version":"tdm","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"name":"National Institute of Public Health and the Environmen"},{"name":"Wilhelmina Children's hospital of UMC Utrecht"}],"content-domain":{"domain":["royalsocietypublishing.org"],"crossmark-restriction":true},"short-container-title":["Open Biol."],"published-print":{"date-parts":[[2017,9]]},"abstract":"<jats:p>\n            The vast majority of streptococci colonizing the human upper respiratory tract are commensals, only sporadically implicated in disease. Of these, the most pathogenic is Mitis group member,\n            <jats:italic>Streptococcus pneumoniae<\/jats:italic>\n            . Phenotypic and genetic similarities between streptococci can cause difficulties in species identification. Using ribosomal S2-gene sequences extracted from whole-genome sequences published from 501 streptococci, we developed a method to identify streptococcal species. We validated this method on non-pneumococcal isolates cultured from cases of severe streptococcal disease (\n            <jats:italic>n<\/jats:italic>\n            = 101) and from carriage (\n            <jats:italic>n<\/jats:italic>\n            = 103), and on non-typeable pneumococci from asymptomatic individuals (\n            <jats:italic>n<\/jats:italic>\n            = 17) and on whole-genome sequences of 1157 pneumococcal isolates from meningitis in the Netherlands. Following this, we tested 221 streptococcal isolates in molecular assays originally assumed specific for\n            <jats:italic>S. pneumoniae<\/jats:italic>\n            , targeting\n            <jats:italic>cpsA<\/jats:italic>\n            ,\n            <jats:italic>lytA<\/jats:italic>\n            ,\n            <jats:italic>piaB<\/jats:italic>\n            ,\n            <jats:italic>ply<\/jats:italic>\n            , Spn9802,\n            <jats:italic>zmpC<\/jats:italic>\n            and capsule-type-specific genes. Cluster analysis of S2-sequences showed grouping according to species in line with published phylogenies of streptococcal core genomes. S2-typing convincingly distinguished pneumococci from non-pneumococcal species (99.2% sensitivity, 100% specificity). Molecular assays targeting regions of\n            <jats:italic>lytA<\/jats:italic>\n            and\n            <jats:italic>piaB<\/jats:italic>\n            were 100% specific for\n            <jats:italic>S. pneumoniae<\/jats:italic>\n            , whereas assays targeting\n            <jats:italic>cpsA<\/jats:italic>\n            ,\n            <jats:italic>ply<\/jats:italic>\n            , Spn9802,\n            <jats:italic>zmpC<\/jats:italic>\n            and selected serotype-specific assays (but not capsular sequence typing) showed a lack of specificity. False positive results were over-represented in species associated with carriage, although no particular confounding signal was unique for carriage isolates.\n          <\/jats:p>","DOI":"10.1098\/rsob.170074","type":"journal-article","created":{"date-parts":[[2017,9,20]],"date-time":"2017-09-20T09:10:14Z","timestamp":1505898614000},"update-policy":"https:\/\/doi.org\/10.1098\/crossmark-policy","source":"Crossref","is-referenced-by-count":32,"title":["Sequencing of the variable region of\n            <i>rpsB<\/i>\n            to discriminate between\n            <i>Streptococcus pneumoniae<\/i>\n            and other streptococcal species"],"prefix":"10.1098","volume":"7","author":[{"ORCID":"https:\/\/orcid.org\/0000-0001-6015-0279","authenticated-orcid":false,"given":"Anne L.","family":"Wyllie","sequence":"first","affiliation":[{"name":"Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, the Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Yvonne","family":"Pannekoek","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology, Academic Medical Center, Amsterdam, the Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Sandra","family":"Bovenkerk","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology, Academic Medical Center, Amsterdam, the Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jody","family":"van Engelsdorp Gastelaars","sequence":"additional","affiliation":[{"name":"Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, the Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Bart","family":"Ferwerda","sequence":"additional","affiliation":[{"name":"Department of Neurology, Academic Medical Center, Amsterdam Neuroscience, Amsterdam, the Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Diederik","family":"van de Beek","sequence":"additional","affiliation":[{"name":"Department of Neurology, Academic Medical Center, Amsterdam Neuroscience, Amsterdam, the Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Elisabeth A. M.","family":"Sanders","sequence":"additional","affiliation":[{"name":"Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, the Netherlands"},{"name":"Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Krzysztof","family":"Trzci\u0144ski","sequence":"additional","affiliation":[{"name":"Department of Paediatric Immunology and Infectious Diseases, Wilhelmina Children's Hospital, University Medical Center Utrecht, Utrecht, the Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Arie","family":"van der Ende","sequence":"additional","affiliation":[{"name":"Department of Medical Microbiology, Academic Medical Center, Amsterdam, the Netherlands"},{"name":"The Netherlands Reference Laboratory for Bacterial Meningitis, Academic Medical Center, Amsterdam, the Netherlands"}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"175","published-online":{"date-parts":[[2017,9,20]]},"reference":[{"key":"e_1_3_5_2_2","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.68.3.1374-1382.2000"},{"key":"e_1_3_5_3_2","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.01490-14"},{"key":"e_1_3_5_4_2","doi-asserted-by":"publisher","DOI":"10.1128\/AAC.01357-12"},{"key":"e_1_3_5_5_2","doi-asserted-by":"publisher","DOI":"10.1128\/CMR.15.4.613-630.2002"},{"key":"e_1_3_5_6_2","doi-asserted-by":"publisher","DOI":"10.1099\/ijsem.0.001433"},{"key":"e_1_3_5_7_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0002683"},{"key":"e_1_3_5_8_2","doi-asserted-by":"publisher","DOI":"10.1186\/1741-7007-7-3"},{"key":"e_1_3_5_9_2","doi-asserted-by":"publisher","DOI":"10.1128\/9781555816537.ch1"},{"key":"e_1_3_5_10_2","doi-asserted-by":"publisher","DOI":"10.1086\/600045"},{"key":"e_1_3_5_11_2","doi-asserted-by":"publisher","DOI":"10.1093\/infdis\/jit481"},{"key":"e_1_3_5_12_2","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.01844-16"},{"key":"e_1_3_5_13_2","doi-asserted-by":"publisher","DOI":"10.1128\/CVI.00647-14"},{"key":"e_1_3_5_14_2","first-page":"CD000422","article-title":"Vaccines for preventing pneumococcal infection in adults","volume":"1","author":"Moberley S","year":"2013","unstructured":"Moberley S, Holden J, Tatham DP, Andrews RM. 2013 Vaccines for preventing pneumococcal infection in adults. 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