{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,9,29]],"date-time":"2026-09-29T15:48:48Z","timestamp":1790696928413,"version":"4.1.0"},"reference-count":41,"publisher":"Public Library of Science (PLoS)","issue":"10","license":[{"start":{"date-parts":[[2021,10,29]],"date-time":"2021-10-29T00:00:00Z","timestamp":1635465600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100004587","name":"Institute of Health Carlos III","doi-asserted-by":"crossref","award":["PI16\/00174"],"award-info":[{"award-number":["PI16\/00174"]}],"id":[{"id":"10.13039\/501100004587","id-type":"DOI","asserted-by":"crossref"}]},{"DOI":"10.13039\/501100004587","name":"Institute of Health Carlos III","doi-asserted-by":"crossref","award":["PFIS FI17\/00248"],"award-info":[{"award-number":["PFIS FI17\/00248"]}],"id":[{"id":"10.13039\/501100004587","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Catalan Agency for the Management of Grants for University Research","award":["AGAUR Grant 2017 SGR 742"],"award-info":[{"award-number":["AGAUR Grant 2017 SGR 742"]}]},{"DOI":"10.13039\/501100000805","name":"European Centre for Disease Prevention and Control","doi-asserted-by":"publisher","award":["\u2018Pertinent\u2019 project ECDC\/2015\/017"],"award-info":[{"award-number":["\u2018Pertinent\u2019 project ECDC\/2015\/017"]}],"id":[{"id":"10.13039\/501100000805","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Liliana Godia Foundation"}],"content-domain":{"domain":["www.plosone.org"],"crossmark-restriction":false},"short-container-title":["PLoS ONE"],"abstract":"<jats:sec id=\"sec001\">\n<jats:title>Purpose<\/jats:title>\n<jats:p>The purpose of this study was to characterize the nasopharyngeal microbiota of infants with possible and confirmed pertussis compared to healthy controls.<\/jats:p>\n<\/jats:sec>\n<jats:sec id=\"sec002\">\n<jats:title>Methods<\/jats:title>\n<jats:p>This prospective study included all infants &lt;1 year with microbiologically confirmed diagnosis of pertussis attended at a University Hospital over a 12-month period. For each confirmed case, up to 2 consecutive patients within the same age range and meeting the clinical case definition of pertussis but testing PCR-negative were included as possible cases. A third group of asymptomatic infants (healthy controls) were also included. Nasopharyngeal microbiota was characterized by sequencing the V3-V4 region of the 16S rRNA gene. Common respiratory DNA\/RNA viral co-infection was tested by multiplex PCR.<\/jats:p>\n<\/jats:sec>\n<jats:sec id=\"sec003\">\n<jats:title>Results<\/jats:title>\n<jats:p>Twelve confirmed cases, 21 possible cases and 9 healthy controls were included. Confirmed whooping cough was primarily driven by detection of <jats:italic>Bordetella<\/jats:italic> with no other major changes on nasopharyngeal microbiota. Possible cases had limited abundance or absence of <jats:italic>Bordetella<\/jats:italic> and a distinctive microbiota with lower bacterial richness and diversity and higher rates of viral co-infection than both confirmed cases and healthy controls. <jats:italic>Bordetella<\/jats:italic> reads determined by 16S rRNA gene sequencing were found in all 12 confirmed cases (100%), 3 out of the 21 possible cases (14.3%) but in any healthy control.<\/jats:p>\n<\/jats:sec>\n<jats:sec id=\"sec004\">\n<jats:title>Conclusion<\/jats:title>\n<jats:p>This study supports the usefulness of 16S rRNA gene sequencing for improved sensitivity on pertussis diagnosis compared to real-time PCR and to understand other microbial changes occurring in the nasopharynx in children &lt;1 year old with suspected whooping cough compared to healthy controls.<\/jats:p>\n<\/jats:sec>","DOI":"10.1371\/journal.pone.0259318","type":"journal-article","created":{"date-parts":[[2021,10,29]],"date-time":"2021-10-29T17:24:52Z","timestamp":1635528292000},"page":"e0259318","update-policy":"https:\/\/doi.org\/10.1371\/journal.pone.corrections_policy","source":"Crossref","is-referenced-by-count":4,"title":["Exploring the nasopharyngeal microbiota composition in infants with whooping cough: A test-negative case-control study"],"prefix":"10.1371","volume":"16","author":[{"given":"Muntsa","family":"Rocafort","sequence":"first","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Desiree","family":"Henares","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pedro","family":"Brotons","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Irene","family":"Barrabeig","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Cristian","family":"Launes","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Lore","family":"Merdrignac","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Marta","family":"Valenciano","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0003-0219-1907","authenticated-orcid":true,"given":"Angela","family":"Dom\u00ednguez","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Pere","family":"Godoy","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5586-404X","authenticated-orcid":true,"given":"Carmen","family":"Mu\u00f1oz-Almagro","sequence":"additional","affiliation":[],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"340","published-online":{"date-parts":[[2021,10,29]]},"reference":[{"key":"pone.0259318.ref001","article-title":"Molecular pathogenesis, epidemiology, and clinical manifestations of respiratory infections due to Bordetella pertussis and other Bordetella subspecies","author":"S Mattoo","year":"2005","journal-title":"Clinical Microbiology Reviews"},{"key":"pone.0259318.ref002","unstructured":"Centers for Disease Control and Prevention. Pertussis: Clinical Features | CDC. [cited 15 Apr 2021]. Available: https:\/\/www.cdc.gov\/pertussis\/clinical\/features.html."},{"key":"pone.0259318.ref003","unstructured":"Centers for Disease Control and Prevention. Pertussis: Clinical Complications | CDC. [cited 15 Apr 2021]. Available: https:\/\/www.cdc.gov\/pertussis\/clinical\/complications.html."},{"key":"pone.0259318.ref004","article-title":"Clinical characteristics and pertussis costs in cases reported to epidemiological services and cases detected in household contacts in Catalonia (Spain)","author":"P Plans","year":"2016","journal-title":"Eur J Clin Microbiol Infect Dis"},{"key":"pone.0259318.ref005","first-page":"218","volume-title":"Clinical Infectious Diseases","author":"SA Mbayei","year":"2019"},{"key":"pone.0259318.ref006","article-title":"Epidemiology of pertussis in a country with high vaccination coverage","author":"I Crespo","year":"2011","journal-title":"Vaccine"},{"key":"pone.0259318.ref007","article-title":"Pertussis epidemic despite high levels of vaccination coverage with acellular pertussis vaccine","author":"MR Sala-Farr\u00e9","year":"2015","journal-title":"Enferm Infecc Microbiol Clin"},{"key":"pone.0259318.ref008","unstructured":"European Centre for Disease Prevention and Control. Pertussis\u2014Annual Epidemiological Report for 2018. [cited 15 Apr 2021]. Available: https:\/\/www.ecdc.europa.eu\/en\/publications-data\/pertussis-annual-epidemiological-report-2018."},{"key":"pone.0259318.ref009","unstructured":"European Centre for Disease Prevention and Control. EU case definitions. [cited 26 May 2021]. Available: https:\/\/www.ecdc.europa.eu\/en\/surveillance-and-disease-data\/eu-case-definitions."},{"key":"pone.0259318.ref010","article-title":"Laboratory diagnosis of pertussis","author":"A van der Zee","year":"2015","journal-title":"Clin Microbiol Rev"},{"key":"pone.0259318.ref011","doi-asserted-by":"crossref","first-page":"2330","DOI":"10.1128\/JCM.38.6.2330-2333.2000","article-title":"Recovery of Bordetella holmesii from Patients with Pertussis-Like Symptoms: Use of Pulsed-Field Gel Electrophoresis To Characterize Circulating Strains","volume":"38","author":"E Mazengia","year":"2000","journal-title":"J Clin Microbiol"},{"key":"pone.0259318.ref012","doi-asserted-by":"crossref","first-page":"1563","DOI":"10.1128\/jcm.34.6.1563-1564.1996","article-title":"Extended incubation of culture plates improves recovery of Bordetella spp","volume":"34","author":"G Katzko","year":"1996","journal-title":"J Clin 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Res"},{"key":"pone.0259318.ref023","doi-asserted-by":"crossref","first-page":"226","DOI":"10.1186\/s40168-018-0605-2","article-title":"Simple statistical identification and removal of contaminant sequences in marker-gene and metagenomics data","volume":"6","author":"NM Davis","year":"2018","journal-title":"Microbiome"},{"key":"pone.0259318.ref024","doi-asserted-by":"crossref","first-page":"e61217","DOI":"10.1371\/journal.pone.0061217","article-title":"phyloseq: An R Package for Reproducible Interactive Analysis and Graphics of Microbiome Census Data.","volume":"8","author":"PJ McMurdie","year":"2013","journal-title":"PLoS One"},{"key":"pone.0259318.ref025","article-title":"Package \u201crandomForest\u201d: Breiman and Cutler\u2019s Random Forests for Classification and Regression.","author":"Liaw Andy","year":"2018"},{"key":"pone.0259318.ref026","doi-asserted-by":"crossref","first-page":"1283","DOI":"10.1164\/rccm.201407-1240OC","article-title":"Early respiratory microbiota composition 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