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

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

doi:10.1038/s41598-019-47713-4

Bryan O Nyawanda, Jeremiah Nyaundi + Show 13 more

Open Access

https://doi.org/10.1038/s41598-019-47713-4

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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.

Highlights

Molecular diagnostic methods are becoming increasingly available for assessment of acute lower respiratory illnesses (ALRI)
We found good agreement (85–100%) in the detection of respiratory pathogens between NP/OP swabs and sputum specimens when using TaqMan Array Cards (TAC)
There was no overall benefit of using sputum over NP/OP swab specimens for etiologic assessment of respiratory illness, except that we found improved detection of Mycobacterium tuberculosis and Klebsiella pneumoniae from sputum specimens compared to NP/OP

Summary

Introduction

Molecular diagnostic methods are becoming increasingly available for assessment of acute lower respiratory illnesses (ALRI). 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. With availability of multi-pathogen molecular diagnostic methods, and increasing recognition of viruses in cases of ALRI, the use of nasopharyngeal (NP) and oropharyngeal (OP) swab specimens to identify pathogens associated with ALRI has increased[2,3,4]. On the other hand, have been considered a more representative sample of the lower respiratory tract[5], but have not been extensively explored, especially in tropical countries

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