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However, nasopharyngeal\/oropharyngeal (NP\/OP) swabs may not accurately reflect etiologic agents from the lower respiratory tract where sputum specimens are considered as a more representative sample. The pathogen yields from NP\/OP against sputum specimens have not been extensively explored, especially in tropical countries. We compared pathogen yields from NP\/OP swabs and sputum specimens from patients \u226518 years hospitalized with ALRI in rural Western Kenya. Specimens were tested for 30 pathogens using TaqMan Array Cards (TAC) and results compared using McNemar\u2019s test. The agreement for pathogen detection between NP\/OP and sputum specimens ranged between 85\u2013100%. More viruses were detected from NP\/OP specimens whereas <jats:italic>Klebsiella pneumoniae<\/jats:italic> and <jats:italic>Mycobacterium tuberculosis<\/jats:italic> were more common in sputum specimens. There was no clear advantage in using sputum over NP\/OP specimens to detect pathogens of ALRI in adults using TAC in the context of this tropical setting.<\/jats:p>","DOI":"10.1038\/s41598-019-47713-4","type":"journal-article","created":{"date-parts":[[2019,8,2]],"date-time":"2019-08-02T11:19:54Z","timestamp":1564744794000},"update-policy":"https:\/\/doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":11,"title":["Comparison of respiratory pathogen yields from Nasopharyngeal\/Oropharyngeal swabs and sputum specimens collected from hospitalized adults in rural Western Kenya"],"prefix":"10.1038","volume":"9","author":[{"ORCID":"https:\/\/orcid.org\/0000-0003-0069-1473","authenticated-orcid":false,"given":"Bryan O.","family":"Nyawanda","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Henry N.","family":"Njuguna","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Clayton O.","family":"Onyango","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Caroline","family":"Makokha","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Shirley","family":"Lidechi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Barry","family":"Fields","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jonas M.","family":"Winchell","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jim S.","family":"Katieno","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Jeremiah","family":"Nyaundi","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Fredrick","family":"Ade","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Gideon O.","family":"Emukule","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Joshua A.","family":"Mott","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Nancy","family":"Otieno","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Marc-Alain","family":"Widdowson","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Sandra S.","family":"Chaves","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2019,8,2]]},"reference":[{"key":"47713_CR1","doi-asserted-by":"publisher","first-page":"1","DOI":"10.1186\/s12879-015-1251-y","volume":"15","author":"A Lagare","year":"2015","unstructured":"Lagare, A., Ma\u00efnassara, H. 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