{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,7,31]],"date-time":"2026-07-31T19:18:33Z","timestamp":1785525513503,"version":"3.56.0"},"reference-count":30,"publisher":"Oxford University Press (OUP)","issue":"11","license":[{"start":{"date-parts":[[2020,7,25]],"date-time":"2020-07-25T00:00:00Z","timestamp":1595635200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000865","name":"Bill and Melinda Gates Foundation","doi-asserted-by":"publisher","award":["48968"],"award-info":[{"award-number":["48968"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100010269","name":"Wellcome Trust","doi-asserted-by":"publisher","award":["098532"],"award-info":[{"award-number":["098532"]}],"id":[{"id":"10.13039\/100010269","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100008309","name":"Johns Hopkins Bloomberg School of Public Health","doi-asserted-by":"publisher","id":[{"id":"10.13039\/100008309","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Department of International Health"},{"name":"International Vaccine Access Center"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,12,6]]},"abstract":"<jats:title>Abstract<\/jats:title>\n               <jats:sec>\n                  <jats:title>Background<\/jats:title>\n                  <jats:p>An improved understanding of childhood pneumonia etiology is required to inform prevention and treatment strategies. Lung aspiration is the gold standard specimen for pneumonia diagnostics. We report findings from analyses of lung and pleural aspirates collected in the Pneumonia Etiology Research for Child Health (PERCH) study.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Methods<\/jats:title>\n                  <jats:p>The PERCH study enrolled children aged 1\u201359 months hospitalized with World Health Organization\u2013defined severe or very severe pneumonia in 7 countries in Africa and Asia. Percutaneous transthoracic lung aspiration (LA) and pleural fluid (PF) aspiration was performed on a sample of pneumonia cases with radiological consolidation and\/or PF in 4 countries. Venous blood and nasopharyngeal\/oropharyngeal swabs were collected from all cases. Multiplex quantitative polymerase chain reaction (PCR) and routine microbiologic culture were applied to clinical specimens.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Results<\/jats:title>\n                  <jats:p>Of 44 LAs performed within 3 days of admission on 622 eligible cases, 13 (30%) had a pathogen identified by either culture (5\/44) or by PCR (11\/29). A pathogen was identified in 12\/14 (86%) PF specimens tested by either culture (9\/14) or PCR (9\/11). Bacterial pathogens were identified more frequently than viruses. All but 1 of the cases with a virus identified were coinfected with bacterial pathogens. Streptococcus pneumoniae (9\/44 [20%]) and Staphylococcus aureus (7\/14 [50%]) were the predominant pathogens identified in LA and PF, respectively.<\/jats:p>\n               <\/jats:sec>\n               <jats:sec>\n                  <jats:title>Conclusions<\/jats:title>\n                  <jats:p>Bacterial pathogens predominated in this selected subgroup of PERCH participants drawn from those with radiological consolidation or PF, with S. pneumoniae and S. aureus the leading pathogens identified.<\/jats:p>\n               <\/jats:sec>","DOI":"10.1093\/cid\/ciaa1032","type":"journal-article","created":{"date-parts":[[2020,7,24]],"date-time":"2020-07-24T11:26:21Z","timestamp":1595589981000},"page":"e3788-e3796","source":"Crossref","is-referenced-by-count":19,"title":["The Etiology of Pneumonia From Analysis of Lung Aspirate and Pleural Fluid Samples: Findings From the Pneumonia Etiology Research for Child Health (PERCH) Study"],"prefix":"10.1093","volume":"73","author":[{"given":"Bernard E","family":"Ebruke","sequence":"first","affiliation":[{"name":"Medical Research Council Unit, Basse, The Gambia"},{"name":"International Foundation Against Infectious Disease in Nigeria (IFAIN), Herbert Macaulay Way Central Business District, Abuja, Nigeria"},{"name":"Department of Pediatrics, College of Medicine, University of Nebraska Medical Center, Omaha, Nebraska, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Maria","family":"Deloria Knoll","sequence":"additional","affiliation":[{"name":"Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Meredith","family":"Haddix","sequence":"additional","affiliation":[{"name":"Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Syed M A","family":"Zaman","sequence":"additional","affiliation":[{"name":"Medical Research Council Unit, Basse, The Gambia"},{"name":"London School of Hygiene and Tropical Medicine, London, United Kingdom"},{"name":"Liverpool School of Tropical Medicine, Liverpool, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Christine","family":"Prosperi","sequence":"additional","affiliation":[{"name":"Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-5154-5084","authenticated-orcid":false,"given":"Daniel R","family":"Feikin","sequence":"additional","affiliation":[{"name":"Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Laura L","family":"Hammitt","sequence":"additional","affiliation":[{"name":"Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA"},{"name":"Kenya Medical Research Institute\u2013Wellcome Trust Research Programme, Kilifi, Kenya"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Orin S","family":"Levine","sequence":"additional","affiliation":[{"name":"Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-0164-4030","authenticated-orcid":false,"given":"Katherine L","family":"O\u2019Brien","sequence":"additional","affiliation":[{"name":"Department of International Health, International Vaccine Access Center, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"David R","family":"Murdoch","sequence":"additional","affiliation":[{"name":"Department of Pathology, University of Otago, Christchurch, New Zealand"},{"name":"Microbiology Unit, Canterbury Health Laboratories, Christchurch, New Zealand"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"W Abdullah","family":"Brooks","sequence":"additional","affiliation":[{"name":"Department of International Health, Johns Hopkins Bloomberg School of Public Health, Baltimore, Maryland, USA"},{"name":"International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"J Anthony G","family":"Scott","sequence":"additional","affiliation":[{"name":"Kenya Medical Research Institute\u2013Wellcome Trust Research Programme, Kilifi, Kenya"},{"name":"Department of Infectious Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, United Kingdom"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Karen L","family":"Kotloff","sequence":"additional","affiliation":[{"name":"Department of Pediatrics, Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, Maryland, USA"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shabir A","family":"Madhi","sequence":"additional","affiliation":[{"name":"Medical Research Council, Respiratory and Meningeal Pathogens Research Unit, University of the Witwatersrand, Johannesburg, South Africa"},{"name":"Department of Science and Technology\/National Research Foundation, Vaccine Preventable Diseases Unit, University of the Witwatersrand, Johannesburg, South Africa"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-6933-1030","authenticated-orcid":false,"given":"Donald 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