{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,14]],"date-time":"2026-10-14T17:42:41Z","timestamp":1791999761914,"version":"4.4.0"},"reference-count":32,"publisher":"BMJ","issue":"3","license":[{"start":{"date-parts":[[2022,3,9]],"date-time":"2022-03-09T00:00:00Z","timestamp":1646784000000},"content-version":"unspecified","delay-in-days":8,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000865","name":"Bill & Melinda Gates Foundation","doi-asserted-by":"crossref","award":["OPP1020327"],"award-info":[{"award-number":["OPP1020327"]}],"id":[{"id":"10.13039\/100000865","id-type":"DOI","asserted-by":"crossref"}]},{"name":"Medical Research Council Unit The Gambia at London School of Hygiene and Tropical Medicine"}],"content-domain":{"domain":["bmj.com"],"crossmark-restriction":true},"short-container-title":["BMJ Open"],"accepted":{"date-parts":[[2022,2,7]]},"published-print":{"date-parts":[[2022,3]]},"abstract":"<jats:sec>\n                    <jats:title>Objectives<\/jats:title>\n                    <jats:p>To determine the causes of lobar pneumonia in rural Gambia.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Design and setting<\/jats:title>\n                    <jats:p>Population-based pneumonia surveillance at seven peripheral health facilities and two regional hospitals in rural Gambia. 7-valent pneumococcal conjugate vaccine (PCV7) was introduced routinely in August 2009 and replaced by PCV13 from May 2011.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Methods<\/jats:title>\n                    <jats:p>Prospective pneumonia surveillance was undertaken among all ages with referral of suspected pneumonia cases to the regional hospitals. Blood culture and chest radiographs were performed routinely while lung or pleural aspirates were collected from selected, clinically stable patients with pleural effusion on radiograph and\/or large, dense, peripheral consolidation. We used conventional microbiology, and from 8 April 2011 to 17 July 2012, used a multiplex PCR assay on lung and pleural aspirates. We calculated proportions with pathogens, associations between coinfecting pathogens and PCV effectiveness.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Participants<\/jats:title>\n                    <jats:p>2550 patients were admitted with clinical pneumonia; 741 with lobar pneumonia or pleural effusion. We performed 181 lung or pleural aspirates and multiplex PCR on 156 lung and 4 pleural aspirates.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>\n                      Pathogens were detected in 116\/160 specimens, the most common being\n                      <jats:italic>Streptococcus pneumoniae<\/jats:italic>\n                      (n=68)\n                      <jats:italic>, Staphylococcus aureus<\/jats:italic>\n                      (n=26) and\n                      <jats:italic>Haemophilus influenzae<\/jats:italic>\n                      type b (n=11). Bacteria (n=97) were more common than viruses (n=49). Common viruses were bocavirus (n=11) and influenza (n=11). Coinfections were frequent (n=55).\n                      <jats:italic>Moraxella catarrhalis<\/jats:italic>\n                      was detected in eight patients and in every case there was coinfection with\n                      <jats:italic>S. pneumoniae<\/jats:italic>\n                      . The odds ratio of vaccine-type pneumococcal pneumonia in patients with two or three compared with zero doses of PCV was 0.17 (95% CI 0.06 to 0.51).\n                    <\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusions<\/jats:title>\n                    <jats:p>\n                      Lobar pneumonia in rural Gambia was caused primarily by bacteria, particularly\n                      <jats:italic>S. pneumoniae<\/jats:italic>\n                      and\n                      <jats:italic>S. aureus<\/jats:italic>\n                      . Coinfection was common and\n                      <jats:italic>M. catarrhalis<\/jats:italic>\n                      always coinfected with\n                      <jats:italic>S. pneumoniae<\/jats:italic>\n                      . PCV was highly efficacious against vaccine-type pneumococcal pneumonia.\n                    <\/jats:p>\n                  <\/jats:sec>","DOI":"10.1136\/bmjopen-2021-056706","type":"journal-article","created":{"date-parts":[[2022,3,10]],"date-time":"2022-03-10T11:57:00Z","timestamp":1646913420000},"page":"e056706","update-policy":"https:\/\/doi.org\/10.1136\/crossmarkpolicy","source":"Crossref","is-referenced-by-count":4,"title":["Aetiology of lobar pneumonia determined by multiplex molecular analyses of lung and pleural aspirate specimens in the Gambia: findings from population-based pneumonia surveillance"],"prefix":"10.1136","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-4994-2627","authenticated-orcid":false,"given":"Grant Austin","family":"Mackenzie","sequence":"first","affiliation":[{"name":"Disease Control and Elimination, Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Fajara, Gambia"},{"name":"Infection and Immunity, Murdoch Children's Research Institute, Melbourne, Victoria, Australia"},{"name":"Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jessica","family":"McLellan","sequence":"additional","affiliation":[{"name":"Disease Control and Elimination, Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Fajara, Gambia"},{"name":"Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Eunice","family":"Machuka","sequence":"additional","affiliation":[{"name":"Disease Control and Elimination, Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Fajara, Gambia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Malick","family":"Ndiaye","sequence":"additional","affiliation":[{"name":"Disease Control and Elimination, Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Fajara, Gambia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Jayani","family":"Pathirana","sequence":"additional","affiliation":[{"name":"Disease Control and Elimination, Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Fajara, Gambia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Augustin","family":"Fombah","sequence":"additional","affiliation":[{"name":"Disease Control and Elimination, Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Fajara, Gambia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Baderinwa","family":"Abatan","sequence":"additional","affiliation":[{"name":"Disease Control and Elimination, Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Fajara, Gambia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ilias","family":"Hossain","sequence":"additional","affiliation":[{"name":"Disease Control and Elimination, Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Fajara, Gambia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Ahmed","family":"Manjang","sequence":"additional","affiliation":[{"name":"Disease Control and Elimination, Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Fajara, Gambia"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Brian","family":"Greenwood","sequence":"additional","affiliation":[{"name":"Faculty of Infectious & Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK"}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Philip","family":"Hill","sequence":"additional","affiliation":[{"name":"Centre for International Health, University of Otago, 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Available: WorldHealthOrganization,DepartmentofVaccinesandBiologicals.http:\/\/www.who.int\/vaccinesdocuments [Accessed 5 Oct 2004]."},{"key":"2025121601110058000_12.3.e056706.16","doi-asserted-by":"publisher","DOI":"10.5588\/ijtld.10.0468"},{"key":"2025121601110058000_12.3.e056706.17","doi-asserted-by":"publisher","DOI":"10.1097\/00006454-199411000-00008"},{"key":"2025121601110058000_12.3.e056706.18","doi-asserted-by":"publisher","DOI":"10.1136\/bmj.298.6680.1061"},{"key":"2025121601110058000_12.3.e056706.19","doi-asserted-by":"crossref","first-page":"S245","DOI":"10.1093\/cid\/cix081","article-title":"Standardization of laboratory methods for the PERCH study","volume":"64","author":"Driscoll","year":"2017","journal-title":"Clin Infect Dis"},{"key":"2025121601110058000_12.3.e056706.20","unstructured":"Mackenzie GA , Hill PC , Jeffries DJ . 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