{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,2,12]],"date-time":"2026-02-12T09:51:33Z","timestamp":1770889893970,"version":"3.50.1"},"reference-count":53,"publisher":"Public Library of Science (PLoS)","issue":"9","license":[{"start":{"date-parts":[[2015,9,3]],"date-time":"2015-09-03T00:00:00Z","timestamp":1441238400000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"DOI":"10.1371\/journal.pone.0137349","type":"journal-article","created":{"date-parts":[[2015,9,3]],"date-time":"2015-09-03T17:50:43Z","timestamp":1441302643000},"page":"e0137349","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":19,"title":["Comparison of a Real-Time Multiplex PCR and Sequetyping Assay for Pneumococcal Serotyping"],"prefix":"10.1371","volume":"10","author":[{"given":"Felix S.","family":"Dube","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Suzan P.","family":"van Mens","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lourens","family":"Robberts","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nicole","family":"Wolter","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Paul","family":"Nicol","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Joseph","family":"Mafofo","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Samantha","family":"Africa","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Heather J.","family":"Zar","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mark P.","family":"Nicol","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"340","published-online":{"date-parts":[[2015,9,3]]},"reference":[{"key":"ref1","article-title":"Global, regional, and national levels of neonatal, infant, and under-5 mortality during 1990\u20132013: a systematic analysis for the Global Burden of Disease Study 2013","author":"H Wang","year":"2014","journal-title":"Lancet"},{"key":"ref2","doi-asserted-by":"crossref","first-page":"144","DOI":"10.1016\/S1473-3099(04)00938-7","article-title":"<italic>Streptococcus pneumoniae<\/italic> colonisation: the key to pneumococcal disease","volume":"4","author":"D Bogaert","year":"2004","journal-title":"Lancet Infect Dis"},{"key":"ref3","first-page":"010401","article-title":"Epidemiology and etiology of childhood pneumonia in 2010: estimates of incidence, severe morbidity, mortality, underlying risk factors and causative pathogens for 192 countries","volume":"3","author":"I Rudan","year":"2013","journal-title":"J Glob Health"},{"key":"ref4","doi-asserted-by":"crossref","first-page":"1025","DOI":"10.1111\/j.1365-3156.2009.02331.x","article-title":"Nasopharyngeal carriage of <italic>S<\/italic>. <italic>pneumoniae<\/italic> among young children in rural Nepal","volume":"14","author":"CL Coles","year":"2009","journal-title":"Trop Med Int Health"},{"key":"ref5","doi-asserted-by":"crossref","first-page":"81","DOI":"10.1186\/1471-2334-8-81","article-title":"Molecular epidemiology of pneumococci obtained from Gambian children aged 2\u201329 months with invasive pneumococcal disease during a trial of a 9-valent pneumococcal conjugate vaccine","volume":"8","author":"M Antonio","year":"2008","journal-title":"BMC Infect Dis"},{"key":"ref6","doi-asserted-by":"crossref","first-page":"0262","DOI":"10.1371\/journal.pgen.0020031","article-title":"Genetic analysis of the capsular biosynthetic locus from all 90 pneumococcal serotypes","volume":"2","author":"SD Bentley","year":"2006","journal-title":"PLoS Genet"},{"key":"ref7","doi-asserted-by":"crossref","first-page":"27885","DOI":"10.1074\/jbc.M112.380451","article-title":"Biochemical, Genetic, and Serological Characterization of Two Capsule Subtypes among <italic>Streptococcus pneumoniae<\/italic> Serotype 20 Strains: DISCOVERY OF A NEW PNEUMOCOCCAL SEROTYPE","volume":"287","author":"JJ Calix","year":"2012","journal-title":"J Biol Chem"},{"key":"ref8","doi-asserted-by":"crossref","first-page":"e11638","DOI":"10.1371\/journal.pone.0011638","article-title":"Multiple colonization with <italic>S<\/italic>. <italic>pneumoniae<\/italic> before and after introduction of the seven-valent conjugated pneumococcal polysaccharide vaccine","volume":"5","author":"SD Brugger","year":"2010","journal-title":"PLoS One"},{"key":"ref9","doi-asserted-by":"crossref","first-page":"584","DOI":"10.1099\/jmm.0.006726-0","article-title":"Multiplex PCR reveals a high rate of nasopharyngeal pneumococcal 7-valent conjugate vaccine serotypes co-colonizing indigenous Warao children in Venezuela","volume":"58","author":"IA Rivera-Olivero","year":"2009","journal-title":"J Med Microbiol"},{"key":"ref10","doi-asserted-by":"crossref","first-page":"1784","DOI":"10.1128\/JCM.00157-11","article-title":"Improved detection of nasopharyngeal cocolonization by multiple pneumococcal serotypes by use of latex agglutination or molecular serotyping by microarray","volume":"49","author":"P Turner","year":"2011","journal-title":"J Clin Microbiol"},{"key":"ref11","first-page":"699","article-title":"The quellung reaction, a neglected microbiologic technique","volume":"43","author":"R Austrian","year":"1960","journal-title":"Mt Sinai J Med"},{"key":"ref12","doi-asserted-by":"crossref","first-page":"e1001107","DOI":"10.1371\/journal.pmed.1001107","article-title":"Effects of community-wide vaccination with PCV-7 on pneumococcal nasopharyngeal carriage in the Gambia: a cluster-randomized trial","volume":"8","author":"A Roca","year":"2011","journal-title":"PLoS Med"},{"key":"ref13","doi-asserted-by":"crossref","first-page":"1596","DOI":"10.1128\/JCM.42.4.1596-1600.2004","article-title":"Immunoblot method to detect <italic>Streptococcus pneumoniae<\/italic> and identify multiple serotypes from nasopharyngeal secretions","volume":"42","author":"MA Bronsdon","year":"2004","journal-title":"J Clin Microbiol"},{"key":"ref14","doi-asserted-by":"crossref","first-page":"4193","DOI":"10.1128\/JCM.01876-13","article-title":"Evaluation of pneumococcal serotyping by multiplex PCR and quellung reactions","volume":"51","author":"SS Richter","year":"2013","journal-title":"J Clin Microbiol"},{"key":"ref15","doi-asserted-by":"crossref","first-page":"2378","DOI":"10.1128\/JCM.41.6.2378-2384.2003","article-title":"Serotyping <italic>Streptococcus pneumoniae<\/italic> by multiplex PCR","volume":"41","author":"DA Brito","year":"2003","journal-title":"J Clin Microbiol"},{"key":"ref16","doi-asserted-by":"crossref","first-page":"124","DOI":"10.1128\/JCM.44.1.124-131.2006","article-title":"Sequential multiplex PCR approach for determining capsular serotypes of <italic>Streptococcus pneumoniae<\/italic> isolates","volume":"44","author":"R Pai","year":"2006","journal-title":"J Clin Microbiol"},{"key":"ref17","doi-asserted-by":"crossref","first-page":"2656","DOI":"10.1128\/JCM.43.6.2656-2661.2005","article-title":"Novel PCR-restriction fragment length polymorphism method for determining serotypes or serogroups of <italic>Streptococcus pneumoniae<\/italic> isolates","volume":"43","author":"SL Batt","year":"2005","journal-title":"J Clin Microbiol"},{"key":"ref18","doi-asserted-by":"crossref","first-page":"3451","DOI":"10.1128\/JCM.01368-12","article-title":"Rapid and easy identification of capsular serotypes of <italic>Streptococcus pneumoniae<\/italic> by use of fragment analysis by automated fluorescence-based capillary electrophoresis","volume":"50","author":"L Selva","year":"2012","journal-title":"J Clin Microbiol"},{"key":"ref19","doi-asserted-by":"crossref","first-page":"2018","DOI":"10.1128\/JCM.06735-11","article-title":"Concurrent serotyping and genotyping of pneumococci by use of PCR and electrospray ionization mass spectrometry","volume":"50","author":"C Massire","year":"2012","journal-title":"J Clin Microbiol"},{"key":"ref20","article-title":"Multiplex PCR and reverse line blot hybridization assay (mPCR\/RLB)","author":"MVN O\u2019Sullivan","year":"2011","journal-title":"J Vis Exp"},{"key":"ref21","doi-asserted-by":"crossref","first-page":"647","DOI":"10.1128\/JCM.02927-12","article-title":"Sequential triplex real-time PCR assay for detecting 21 pneumococcal capsular serotypes that account for a high global disease burden","volume":"51","author":"FC Pimenta","year":"2013","journal-title":"J Clin Microbiol"},{"key":"ref22","doi-asserted-by":"crossref","first-page":"528","DOI":"10.1099\/jmm.0.071464-0","article-title":"A novel high-throughput method for molecular serotyping and serotype-specific quantification of <italic>Streptococcus pneumoniae<\/italic> using a nanofluidic real-time PCR system","volume":"63","author":"BG Dhoubhadel","year":"2014","journal-title":"J Med Microbiol"},{"key":"ref23","doi-asserted-by":"crossref","first-page":"e9282","DOI":"10.1371\/journal.pone.0009282","article-title":"Realtime PCR is more sensitive than multiplex PCR for diagnosis and serotyping in children with culture negative pneumococcal invasive disease","volume":"5","author":"C Azzari","year":"2010","journal-title":"PLoS One"},{"issue":"Suppl 4","key":"ref24","doi-asserted-by":"crossref","first-page":"S331","DOI":"10.1093\/cid\/cir048","article-title":"Interpreting assays for the detection of <italic>Streptococcus pneumoniae<\/italic>","volume":"52","author":"AJ Blaschke","year":"2011","journal-title":"Clin Infect Dis"},{"key":"ref25","doi-asserted-by":"crossref","first-page":"451","DOI":"10.4269\/ajtmh.2010.10-0225","article-title":"Enhanced determination of <italic>Streptococcus pneumoniae<\/italic> serotypes associated with invasive disease in Laos by using a real-time polymerase chain reaction serotyping assay with cerebrospinal fluid","volume":"83","author":"CE Moore","year":"2010","journal-title":"Am J Trop Med Hyg"},{"key":"ref26","doi-asserted-by":"crossref","first-page":"1042","DOI":"10.1086\/656579","article-title":"Community-acquired bacteremic pneumococcal pneumonia in children: diagnosis and serotyping by real-time polymerase chain reaction using blood samples","volume":"51","author":"M Resti","year":"2010","journal-title":"Clin Infect Dis"},{"key":"ref27","doi-asserted-by":"crossref","first-page":"2419","DOI":"10.1128\/JCM.06384-11","article-title":"Sequetyping: serotyping <italic>Streptococcus pneumoniae<\/italic> by a single PCR sequencing strategy","volume":"50","author":"MH Leung","year":"2012","journal-title":"J Clin Microbiol"},{"key":"ref28","doi-asserted-by":"crossref","first-page":"41","DOI":"10.1016\/j.mimet.2015.03.006","article-title":"Current methods for capsular typing of <italic>Streptococcus pneumoniae<\/italic>","volume":"113","author":"E Jauneikaite","year":"2015","journal-title":"J Microbiol Methods"},{"key":"ref29","article-title":"Epidemiology of invasive pneumococcal disease in the pre-conjugate vaccine era: South Africa, 2003\u20132008","author":"A Von Gottberg","year":"2013","journal-title":"Epidemiology of invasive pneumococcal disease in the pre-conjugate vaccine era: South Africa, 2003\u20132008"},{"key":"ref30","doi-asserted-by":"crossref","first-page":"1139","DOI":"10.1128\/JCM.36.4.1139-1140.1998","article-title":"Long-term survival of <italic>Streptococcus pneumoniae<\/italic> at room temperature on Dorset egg medium","volume":"36","author":"AD Wasas","year":"1998","journal-title":"J Clin Microbiol"},{"key":"ref31","doi-asserted-by":"crossref","first-page":"e95","DOI":"10.1016\/S2214-109X(14)70360-2","article-title":"Incidence and severity of childhood pneumonia in the first year of life in a South African birth cohort: the Drakenstein Child Health Study","volume":"3","author":"DM Le Roux","year":"2015","journal-title":"Lancet Glob Heal"},{"key":"ref32","doi-asserted-by":"crossref","first-page":"165","DOI":"10.1016\/j.vaccine.2013.08.062","article-title":"Standard method for detecting upper respiratory carriage of <italic>Streptococcus pneumoniae<\/italic>: updated recommendations from the World Health Organization Pneumococcal Carriage Working Group","volume":"32","author":"C Satzke","year":"2013","journal-title":"Vaccine"},{"key":"ref33","doi-asserted-by":"crossref","first-page":"e68097","DOI":"10.1371\/journal.pone.0068097","article-title":"Detection of <italic>Streptococcus pneumoniae<\/italic> from Different Types of Nasopharyngeal Swabs in Children","volume":"8","author":"FS Dube","year":"2013","journal-title":"PLoS One"},{"key":"ref34","first-page":"672","article-title":"Konemans\u2019s Color Atlas and Textbook of Diagnostic Microbiology","author":"WC Winn","year":"2006"},{"key":"ref35","doi-asserted-by":"crossref","first-page":"1989","DOI":"10.1016\/j.meegid.2011.09.002","article-title":"The adaptive potential during nasopharyngeal colonisation of <italic>Streptococcus pneumoniae<\/italic>","volume":"11","author":"MHY Leung","year":"2011","journal-title":"Infect Genet Evol"},{"key":"ref36","doi-asserted-by":"crossref","first-page":"1225","DOI":"10.1128\/JCM.02199-06","article-title":"Discovery of a new capsular serotype (6C) within serogroup 6 of <italic>Streptococcus pneumoniae<\/italic>","volume":"45","author":"IH Park","year":"2007","journal-title":"J Clin Microbiol"},{"key":"ref37","article-title":"Acquisition of <italic>Streptococcus pneumoniae<\/italic> in South African children vaccinated with 7-valent pneumococcal conjugate vaccine at 6, 14 and 40 weeks of age","author":"MC Nunes","year":"2014","journal-title":"Vaccine"},{"key":"ref38","article-title":"FastQC a quality-control tool for high-throughput sequence data","author":"S Andrews","year":"2011","journal-title":"FastQC a quality-control tool for high-throughput sequence data"},{"key":"ref39","doi-asserted-by":"crossref","first-page":"2114","DOI":"10.1093\/bioinformatics\/btu170","article-title":"Trimmomatic: a flexible trimmer for Illumina sequence data","volume":"30","author":"AM Bolger","year":"2014","journal-title":"Bioinformatics"},{"key":"ref40","doi-asserted-by":"crossref","first-page":"e30619","DOI":"10.1371\/journal.pone.0030619","article-title":"NGS QC Toolkit: a toolkit for quality control of next generation sequencing data","volume":"7","author":"RK Patel","year":"2012","journal-title":"PLoS One"},{"key":"ref41","doi-asserted-by":"crossref","first-page":"714","DOI":"10.1089\/cmb.2013.0084","article-title":"Assembling single-cell genomes and mini-metagenomes from chimeric MDA products","volume":"20","author":"S Nurk","year":"2013","journal-title":"J Comput Biol"},{"key":"ref42","doi-asserted-by":"crossref","first-page":"75","DOI":"10.1186\/1471-2164-9-75","article-title":"The RAST Server: rapid annotations using subsystems technology","volume":"9","author":"RK Aziz","year":"2008","journal-title":"BMC Genomics"},{"key":"ref43","doi-asserted-by":"crossref","first-page":"2078","DOI":"10.1093\/bioinformatics\/btp352","article-title":"The Sequence Alignment\/Map format and SAMtools","volume":"25","author":"H Li","year":"2009","journal-title":"Bioinformatics"},{"key":"ref44","doi-asserted-by":"crossref","first-page":"595","DOI":"10.1186\/1471-2105-11-595","article-title":"BIGSdb: Scalable analysis of bacterial genome variation at the population level","volume":"11","author":"KA Jolley","year":"2010","journal-title":"BMC Bioinformatics"},{"key":"ref45","doi-asserted-by":"crossref","first-page":"2553","DOI":"10.1016\/j.vaccine.2014.03.054","article-title":"Reduced incidence of invasive pneumococcal disease after introduction of the 13-valent conjugate vaccine in Navarre, Spain, 2001\u20132013","volume":"32","author":"M Guevara","year":"2014","journal-title":"Vaccine"},{"key":"ref46","article-title":"Impact of the 13-Valent Pneumococcal Conjugate Vaccine on Chronic Sinusitis Associated with <italic>Streptococcus pneumoniae<\/italic> in Children","author":"L Olarte","year":"2014","journal-title":"Pediatr Infect Dis J"},{"key":"ref47","doi-asserted-by":"crossref","first-page":"203","DOI":"10.1097\/INF.0b013e318275614b","article-title":"Early trends for invasive pneumococcal infections in children after the introduction of the 13-valent pneumococcal conjugate vaccine","volume":"32","author":"SL Kaplan","year":"2013","journal-title":"Pediatr Infect Dis J"},{"key":"ref48","doi-asserted-by":"crossref","first-page":"6232","DOI":"10.1016\/j.vaccine.2013.10.032","article-title":"Prompt effect of replacing the 7-valent pneumococcal conjugate vaccine with the 13-valent vaccine on the epidemiology of invasive pneumococcal disease in Norway","volume":"31","author":"A Steens","year":"2013","journal-title":"Vaccine"},{"key":"ref49","article-title":"Pneumococcal carriage in children and adults two years after introduction of the thirteen valent pneumococcal conjugate vaccine in England","author":"AJ Van Hoek","year":"2014","journal-title":"Vaccine"},{"key":"ref50","doi-asserted-by":"crossref","DOI":"10.2807\/1560-7917.ES2014.19.12.20750","article-title":"Decreasing incidence and changes in serotype distribution of invasive pneumococcal disease in persons aged under 18 years since introduction of 10-valent and 13-valent conjugate vaccines in Portugal, July 2008 to June 2012","volume":"19","author":"S Aguiar","year":"2014","journal-title":"Euro Surveill"},{"key":"ref51","first-page":"1132","article-title":"Nasopharyngeal carriage of children 6 to 60 months during the implementation of the 13-valent pneumococcal conjugate vaccine","volume":"19","author":"R Cohen","year":"2012","journal-title":"Arch Pediatr"},{"key":"ref52","doi-asserted-by":"crossref","first-page":"1611","DOI":"10.1128\/JCM.02243-09","article-title":"Revisiting pneumococcal carriage by use of broth enrichment and PCR techniques for enhanced detection of carriage and serotypes","volume":"48","author":"M Da Gloria Carvalho","year":"2010","journal-title":"J Clin Microbiol"},{"key":"ref53","doi-asserted-by":"crossref","first-page":"7841","DOI":"10.1128\/JB.00836-07","article-title":"Genetic relatedness of the <italic>Streptococcus pneumoniae<\/italic> capsular biosynthetic loci","volume":"189","author":"A Mavroidi","year":"2007","journal-title":"J Bacteriol"}],"container-title":["PLOS ONE"],"original-title":[],"language":"en","link":[{"URL":"http:\/\/dx.plos.org\/10.1371\/journal.pone.0137349","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2020,9,7]],"date-time":"2020-09-07T23:42:17Z","timestamp":1599522137000},"score":1,"resource":{"primary":{"URL":"https:\/\/dx.plos.org\/10.1371\/journal.pone.0137349"}},"subtitle":[],"editor":[{"given":"Shamala Devi","family":"Sekaran","sequence":"first","affiliation":[],"role":[{"role":"editor","vocabulary":"crossref"}]}],"short-title":[],"issued":{"date-parts":[[2015,9,3]]},"references-count":53,"journal-issue":{"issue":"9","published-online":{"date-parts":[[2015,9,3]]}},"URL":"https:\/\/doi.org\/10.1371\/journal.pone.0137349","relation":{},"ISSN":["1932-6203"],"issn-type":[{"value":"1932-6203","type":"electronic"}],"subject":[],"published":{"date-parts":[[2015,9,3]]}}}