Comparison of respiratory pathogen yields from nasopharyngeal/oropharyngeal swabs and sputum specimens collected from hospitalized adults in rural Western Kenya

Bryan O Nyawanda, Henry N Njuguna, Clayton O Onyango, Caroline Makokha, Shirley Lidechi, Barry Fields, Jonas M Winchell, Jim S Katieno, Jeremiah Nyaundi, Fredrick Ade, Gideon O Emukule, Joshua A Mott, Nancy Otieno, Marc-Alain Widdowson, Sandra S Chaves

Research output: Contribution to journalA1: Web of Science-article

Abstract

Molecular diagnostic methods are becoming increasingly available for assessment of acute lower respiratory illnesses (ALRI). 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 ≥18 years hospitalized with ALRI in rural Western Kenya. Specimens were tested for 30 pathogens using TaqMan Array Cards (TAC) and results compared using McNemar's test. The agreement for pathogen detection between NP/OP and sputum specimens ranged between 85-100%. More viruses were detected from NP/OP specimens whereas Klebsiella pneumoniae and Mycobacterium tuberculosis 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.

Original languageEnglish
JournalScientific Reports
Volume9
Issue number1
Pages (from-to)11237
ISSN2045-2322
DOIs
Publication statusPublished - 2019

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