{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,3,21]],"date-time":"2026-03-21T07:54:28Z","timestamp":1774079668657,"version":"3.50.1"},"reference-count":0,"publisher":"American Society of Tropical Medicine and Hygiene","issue":"4","content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2022,4,6]]},"abstract":"<jats:title>ABSTRACT.<\/jats:title>\n<jats:p>The role of microbial coinfection in the pathogenesis of pneumonia in children is not well known. The aim of this work was to describe the prevalence of microorganism co-detection in nasopharyngeal samples (NPS) of pneumonia cases and control subjects and to study the potential association between nasopharyngeal microorganism co-detection and pneumonia. A case-control study was carried out from 2010 to 2014 in nine study sites located in low- or middle-income countries. The data from 888 children under 5 years of age with pneumonia (cases) and 870 children under 5 without pneumonia (controls) were analyzed. Nasopharyngeal samples were collected; reverse transcription polymerase chain reaction (RT-PCR) enabled the detection of five bacteria and 19 viruses. Multiple, mixed-effects logistic regression modeling was undertaken to evaluate the association between microorganism co-detection and pneumonia. A single <jats:italic>Streptococcus pneumoniae<\/jats:italic> colonization was observed in 15.2% of the controls and 10.1% of the cases (<jats:italic>P<\/jats:italic>\u2009=\u20090.001), whereas <jats:italic>S. pneumoniae<\/jats:italic> and a single virus co-detection was observed in 33.3% of the cases and in 14.6% of the controls (<jats:italic>P<\/jats:italic>\u2009&lt;\u20090.001). Co-detections with rhinovirus, respiratory syncytial virus, parainfluenza virus, human metapneumovirus, and influenza virus were more frequent in the cases compared with the controls (<jats:italic>P<\/jats:italic>\u2009&lt;\u20090.001) and were significantly associated with pneumonia in multiple regression analysis. The proportion of single virus detection without bacterial co-detection was not different between cases and controls (13.6% versus 11.3%, <jats:italic>P<\/jats:italic>\u2009=\u20090.13). This study suggests that coinfection of <jats:italic>S. pneumoniae<\/jats:italic> and certain viruses may play a role in the pathophysiology of pneumonia in children.<\/jats:p>","DOI":"10.4269\/ajtmh.21-0980","type":"journal-article","created":{"date-parts":[[2022,2,7]],"date-time":"2022-02-07T15:49:57Z","timestamp":1644248997000},"page":"1086-1093","source":"Crossref","is-referenced-by-count":3,"title":["Nasopharyngeal Viral and Bacterial Co-Detection among Children from Low- and Middle-Income Countries with and without Pneumonia"],"prefix":"10.4269","volume":"106","author":[{"given":"C\u00e9dric","family":"Dananch\u00e9","sequence":"first","affiliation":[{"name":"1CIRI, Centre International de Recherche en Infectiologie (team Public Health, Epidemiology and Evolutionnary Ecology of Infectious Diseases (PHE3ID)), Univ Lyon, Inserm, U1111, Universit\u00e9 Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France;"},{"name":"2Infection Control and Epidemiology Department, Hospices Civils de Lyon, Lyon, France;"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gl\u00e1ucia","family":"Paranhos-Baccal\u00e0","sequence":"additional","affiliation":[{"name":"3M\u00e9rieux Foundation, Lyon, France;"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"M\u00e9lina","family":"Messaoudi","sequence":"additional","affiliation":[{"name":"3M\u00e9rieux Foundation, Lyon, France;"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mariam","family":"Sylla","sequence":"additional","affiliation":[{"name":"4Gabriel Tour\u00e9 Hospital, Bamako, Mali;"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shally","family":"Awasthi","sequence":"additional","affiliation":[{"name":"5Chatrapati Shahu Ji Maharaj Medical University, Lucknow, India;"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Ashish","family":"Bavdekar","sequence":"additional","affiliation":[{"name":"6KEM Hospital Research Center, Pune, India;"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jean-William","family":"Pape","sequence":"additional","affiliation":[{"name":"7Centres GHESKIO (Groupe Ha\u00eftien d'Etude du Sarcome de Kaposi et des Infections Opportunistes), Port-au-Prince, Haiti;"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Vanessa","family":"Rouzier","sequence":"additional","affiliation":[{"name":"7Centres GHESKIO (Groupe Ha\u00eftien d'Etude du Sarcome de Kaposi et des Infections Opportunistes), Port-au-Prince, Haiti;"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jianwei","family":"Wang","sequence":"additional","affiliation":[{"name":"8MOH Key Laboratory of the Systems Biology of Pathogens and Dr. Christophe M\u00e9rieux Laboratory, Fondation M\u00e9rieux, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China;"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sonali","family":"Sanghavi","sequence":"additional","affiliation":[{"name":"6KEM Hospital Research Center, Pune, India;"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Souleymane","family":"Diallo","sequence":"additional","affiliation":[{"name":"9Centre d\u2019Infectiologie Charles M\u00e9rieux, Bamako, Mali;"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Monidarin","family":"Chou","sequence":"additional","affiliation":[{"name":"10Faculty of Pharmacy, University of Health Sciences, Phnom Penh, Cambodia;"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Tekchheng","family":"Eap","sequence":"additional","affiliation":[{"name":"11Department of Pneumology, National Pediatric Hospital, Phnom Penh, Cambodia;"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Mala","family":"Rakoto-Andrianarivelo","sequence":"additional","affiliation":[{"name":"12Fondation M\u00e9rieux, Centre d'Infectiologie Charles M\u00e9rieux, Antananarivo, Madagascar;"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Hubert","family":"Endtz","sequence":"additional","affiliation":[{"name":"3M\u00e9rieux Foundation, Lyon, France;"},{"name":"13Department of Clinical Microbiology & Infectious Diseases, Erasmus MC, Rotterdam, The Netherlands;"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Lili","family":"Ren","sequence":"additional","affiliation":[{"name":"8MOH Key Laboratory of the Systems Biology of Pathogens and Dr. Christophe M\u00e9rieux Laboratory, Fondation M\u00e9rieux, Institute of Pathogen Biology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China;"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Budragchaagiin","family":"Dash-Yandag","sequence":"additional","affiliation":[{"name":"14Bayanzurkh District General Hospital, Ulaanbaatar, Mongolia;"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Rosa","family":"Guillen","sequence":"additional","affiliation":[{"name":"15Instituto de Investigaciones en Ciencias de la Salud, National University of Asunci\u00f3n, Asunci\u00f3n, Paraguay;"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Pagbajabyn","family":"Nymadawa","sequence":"additional","affiliation":[{"name":"16Mongolian Academy of Medical Sciences, Ulaanbaatar, Mongolia;"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Graciela","family":"Russomando","sequence":"additional","affiliation":[{"name":"15Instituto de Investigaciones en Ciencias de la Salud, National University of Asunci\u00f3n, Asunci\u00f3n, Paraguay;"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Florence","family":"Komurian-Pradel","sequence":"additional","affiliation":[{"name":"3M\u00e9rieux Foundation, Lyon, France;"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Philippe","family":"Vanhems","sequence":"additional","affiliation":[{"name":"1CIRI, Centre International de Recherche en Infectiologie (team Public Health, Epidemiology and Evolutionnary Ecology of Infectious Diseases (PHE3ID)), Univ Lyon, Inserm, U1111, Universit\u00e9 Claude Bernard Lyon 1, CNRS, UMR5308, ENS de Lyon, F-69007, Lyon, France;"},{"name":"2Infection Control and Epidemiology Department, Hospices Civils de Lyon, Lyon, France;"},{"name":"17Inserm, F-CRIN, R\u00e9seau Innovative Clinical Research in Vaccinology (I-REIVAC), Lyon center, France"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Valentina S\u00e1nchez","family":"Picot","sequence":"additional","affiliation":[{"name":"3M\u00e9rieux Foundation, Lyon, France;"}],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"_","family":"_","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"2795","container-title":["The American Journal of Tropical Medicine and Hygiene"],"original-title":[],"link":[{"URL":"https:\/\/www.ajtmh.org\/view\/journals\/tpmd\/106\/4\/article-p1086.xml","content-type":"text\/html","content-version":"vor","intended-application":"text-mining"},{"URL":"https:\/\/www.ajtmh.org\/downloadpdf\/journals\/tpmd\/106\/4\/article-p1086.xml","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2022,4,6]],"date-time":"2022-04-06T12:38:18Z","timestamp":1649248698000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.ajtmh.org\/view\/journals\/tpmd\/106\/4\/article-p1086.xml"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2022,4,6]]},"references-count":0,"journal-issue":{"issue":"4"},"URL":"https:\/\/doi.org\/10.4269\/ajtmh.21-0980","relation":{},"ISSN":["0002-9637","1476-1645"],"issn-type":[{"value":"0002-9637","type":"print"},{"value":"1476-1645","type":"electronic"}],"subject":[],"published":{"date-parts":[[2022,4,6]]}}}