{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2024,5,16]],"date-time":"2024-05-16T06:25:53Z","timestamp":1715840753052},"reference-count":25,"publisher":"American Society for Microbiology","issue":"3","license":[{"start":{"date-parts":[[2015,3,1]],"date-time":"2015-03-01T00:00:00Z","timestamp":1425168000000},"content-version":"tdm","delay-in-days":0,"URL":"https:\/\/journals.asm.org\/non-commercial-tdm-license"}],"content-domain":{"domain":["journals.asm.org"],"crossmark-restriction":true},"short-container-title":["J Clin Microbiol"],"published-print":{"date-parts":[[2015,3]]},"abstract":"<jats:title>ABSTRACT<\/jats:title>\n          <jats:p>\n            Large outbreaks of pertussis occur despite vaccination. A first step in the analyses of outbreaks is strain typing. However, the typing of\n            <jats:named-content content-type=\"genus-species\">Bordetella pertussis<\/jats:named-content>\n            , the causative agent of pertussis, is problematic because the available assays are insufficiently discriminatory, not unequivocal, time-consuming, and\/or costly. Here, we describe a single nucleotide primer extension assay for the study of\n            <jats:named-content content-type=\"genus-species\">B. pertussis<\/jats:named-content>\n            populations, SNPeX (single nucleotide primer extension), which addresses these problems. The assay is based on the incorporation of fluorescently labeled dideoxynucleotides (ddNTPs) at the 3\u2032 end of allele-specific poly(A)-tailed primers and subsequent analysis with a capillary DNA analyzer. Each single nucleotide polymorphism (SNP) primer has a specific length, and as a result, up to 20 SNPs can be determined in one SNPeX reaction. Importantly, PCR amplification of target DNA is not required. We selected 38 SNPeX targets from the whole-genome sequencing data of 74\n            <jats:named-content content-type=\"genus-species\">B. pertussis<\/jats:named-content>\n            strains collected from across the world. The SNPeX-based phylogenetic trees preserved the general tree topology of\n            <jats:named-content content-type=\"genus-species\">B. pertussis<\/jats:named-content>\n            populations based on whole-genome sequencing, with a minor loss of details. We envisage a strategy whereby SNP types (SnpTs) are quickly identified with the SNPeX assay during an outbreak, followed by whole-genome sequencing (WGS) of a limited number of isolates representing predominant SnpTs and the incorporation of novel SNPs in the SNPeX assay. The flexibility of the SNPeX assay allows the method to evolve along with the pathogen, making it a promising method for studying outbreaks of\n            <jats:named-content content-type=\"genus-species\">B. pertussis<\/jats:named-content>\n            and other pathogens.\n          <\/jats:p>","DOI":"10.1128\/jcm.02995-14","type":"journal-article","created":{"date-parts":[[2015,1,8]],"date-time":"2015-01-08T04:41:40Z","timestamp":1420692100000},"page":"838-846","update-policy":"http:\/\/dx.doi.org\/10.1128\/asmj-crossmark-policy-page","source":"Crossref","is-referenced-by-count":11,"title":["Studying Bordetella pertussis Populations by Use of SNPeX, a Simple High-Throughput Single Nucleotide Polymorphism Typing Method"],"prefix":"10.1128","volume":"53","author":[{"given":"Anne","family":"Zeddeman","sequence":"first","affiliation":[{"name":"Centre for Infectious Disease Control (CIb), National Institute of Public Health and the Environment (RIVM), Bilthoven, the Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sandra","family":"Witteveen","sequence":"additional","affiliation":[{"name":"Centre for Infectious Disease Control (CIb), National Institute of Public Health and the Environment (RIVM), Bilthoven, the Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marieke J.","family":"Bart","sequence":"additional","affiliation":[{"name":"Centre for Infectious Disease Control (CIb), National Institute of Public Health and the Environment (RIVM), Bilthoven, the Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marjolein","family":"van Gent","sequence":"additional","affiliation":[{"name":"Centre for Infectious Disease Control (CIb), National Institute of Public Health and the Environment (RIVM), Bilthoven, the Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Han G. J.","family":"van der Heide","sequence":"additional","affiliation":[{"name":"Centre for Infectious Disease Control (CIb), National Institute of Public Health and the Environment (RIVM), Bilthoven, the Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Kees J.","family":"Heuvelman","sequence":"additional","affiliation":[{"name":"Centre for Infectious Disease Control (CIb), National Institute of Public Health and the Environment (RIVM), Bilthoven, the Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Leo M.","family":"Schouls","sequence":"additional","affiliation":[{"name":"Centre for Infectious Disease Control (CIb), National Institute of Public Health and the Environment (RIVM), Bilthoven, the Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Frits R.","family":"Mooi","sequence":"additional","affiliation":[{"name":"Centre for Infectious Disease Control (CIb), National Institute of Public Health and the Environment (RIVM), Bilthoven, the Netherlands"}],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"235","reference":[{"key":"e_1_3_3_2_2","doi-asserted-by":"publisher","DOI":"10.1111\/j.1469-0691.1996.tb00193.x"},{"key":"e_1_3_3_3_2","doi-asserted-by":"publisher","DOI":"10.1186\/1742-5573-2-10"},{"key":"e_1_3_3_4_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.meegid.2009.10.007"},{"key":"e_1_3_3_5_2","doi-asserted-by":"publisher","DOI":"10.1093\/molbev\/msq245"},{"key":"e_1_3_3_6_2","doi-asserted-by":"publisher","DOI":"10.1128\/mBio.01074-14"},{"key":"e_1_3_3_7_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0020340"},{"key":"e_1_3_3_8_2","doi-asserted-by":"publisher","DOI":"10.1099\/00221287-148-7-2011"},{"key":"e_1_3_3_9_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.02036-12"},{"key":"e_1_3_3_10_2","doi-asserted-by":"publisher","DOI":"10.1007\/s100960050455"},{"key":"e_1_3_3_11_2","doi-asserted-by":"publisher","DOI":"10.1128\/JCM.40.6.1994-2001.2002"},{"key":"e_1_3_3_12_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.186.16.5496-5505.2004"},{"key":"e_1_3_3_13_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.mimet.2009.06.019"},{"key":"e_1_3_3_14_2","doi-asserted-by":"publisher","DOI":"10.1099\/jmm.0.049585-0"},{"key":"e_1_3_3_15_2","doi-asserted-by":"publisher","DOI":"10.1099\/jmm.0.05515-0"},{"key":"e_1_3_3_16_2","doi-asserted-by":"publisher","DOI":"10.1128\/IAI.66.2.670-675.1998"},{"key":"e_1_3_3_17_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.pone.0046407"},{"key":"e_1_3_3_18_2","doi-asserted-by":"publisher","DOI":"10.1093\/infdis\/jis178"},{"key":"e_1_3_3_19_2","doi-asserted-by":"publisher","DOI":"10.1017\/S0950268813000071"},{"key":"e_1_3_3_20_2","volume-title":"PHYLIP version 3.6","author":"Felsenstein J","year":"2005","unstructured":"Felsenstein J. 2005. PHYLIP version 3.6. Department of Genome Sciences, University of Washington, Seattle, WA."},{"key":"e_1_3_3_21_2","doi-asserted-by":"publisher","DOI":"10.1186\/1471-2164-9-311"},{"key":"e_1_3_3_22_2","doi-asserted-by":"publisher","DOI":"10.3201\/eid1508.081511"},{"key":"e_1_3_3_23_2","doi-asserted-by":"publisher","DOI":"10.1007\/s00414-004-0428-5"},{"key":"e_1_3_3_24_2","doi-asserted-by":"publisher","DOI":"10.1371\/journal.ppat.0010045"},{"key":"e_1_3_3_25_2","doi-asserted-by":"publisher","DOI":"10.1016\/j.meegid.2012.01.001"},{"key":"e_1_3_3_26_2","doi-asserted-by":"publisher","DOI":"10.1128\/JB.01820-14"}],"container-title":["Journal of Clinical Microbiology"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/JCM.02995-14","content-type":"application\/pdf","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/journals.asm.org\/doi\/pdf\/10.1128\/JCM.02995-14","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,3,5]],"date-time":"2022-03-05T12:07:39Z","timestamp":1646482059000},"score":1,"resource":{"primary":{"URL":"https:\/\/journals.asm.org\/doi\/10.1128\/JCM.02995-14"}},"subtitle":[],"editor":[{"given":"M. J.","family":"Loeffelholz","sequence":"additional","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2015,3]]},"references-count":25,"journal-issue":{"issue":"3","published-print":{"date-parts":[[2015,3]]}},"alternative-id":["10.1128\/JCM.02995-14"],"URL":"https:\/\/doi.org\/10.1128\/jcm.02995-14","relation":{},"ISSN":["0095-1137","1098-660X"],"issn-type":[{"value":"0095-1137","type":"print"},{"value":"1098-660X","type":"electronic"}],"subject":[],"published":{"date-parts":[[2015,3]]},"assertion":[{"value":"2014-10-20","order":0,"name":"received","label":"Received","group":{"name":"publication_history","label":"Publication History"}},{"value":"2014-12-28","order":1,"name":"accepted","label":"Accepted","group":{"name":"publication_history","label":"Publication History"}},{"value":"2015-02-19","order":2,"name":"published","label":"Published","group":{"name":"publication_history","label":"Publication History"}}]}}