Etiologies of lower respiratory tract infections among adult patients presenting to a tertiary institution in Nairobi

Date of Award


Document Type


Degree Name

Master of Medicine (MMed)

First Supervisor/Advisor

Prof. Rodney Adam

Second Supervisor/Advisor

Dr. Jumaa Bwika


Pathology (East Africa)


Background: Lower respiratory tract infections continue to contribute significantly to morbidity and mortality across all age groups globally. Viral pathogens in isolation or as co-infections are an important cause of pneumonia and associated with several life threatening syndromes that warrant appropriate and timely lifesaving diagnosis. Many viral respiratory infections demonstrate substantial regional and seasonal variations which are poorly understood. In addition, there are very few studies in sub-Saharan Africa that have examined the role of viruses as causes of community acquired pneumonia. The availability of molecular techniques such as multiplex PCR that are much more sensitive than traditional methods and allow the simultaneous identification of multiple pathogens has improved diagnostic and surveillance capacity.

Objective: To describe the common lower respiratory tract infections among adult patients requiring hospitalization for community acquired pneumonia with an emphasis on viral diagnosis.

Methodology: A descriptive prospective study from May 2019 to March 2020 enrolled 81 adult in-patients 18 years and above with respiratory symptoms and confirmed radiographic evidence of pneumonia. Viral PCR testing was performed using the FTD respiratory pathogen-21 multiplex kit on manually extracted material from nasal/oropharyngeal and Bronchoalveolar lavage samples. Relevant additional tests performed during the patient’s hospital stay were reviewed and analyzed simultaneously.

Results: A micro-organism was identified in 71.7% including 49% viral, 18% bacterial and 3% Pneumocystis jirovecii. Nasopharyngeal swabs comprised 83.8% of the sample material used, followed by11% BAL’s and 5% Oropharyngeal swabs which yielded a positive result in 48% (30/62), 63% (5/8) and 75% (3/4) respectively. The most common disease causing viral agent was Influenza A which mostly circulated in December-January and was associated with severe clinical disease. Rhinovirus was associated with clinically varied disease and commonly found with other viral and bacterial etiologies. A few clinical characteristics were more associated with some agents, however bivariate analysis showed no statistical significance.

Conclusion: The presence of a viral pathogen is more associated with severe forms of respiratory illness and PCR is an important diagnostic tool for the detection of viral agents.

This document is available in the relevant AKU library