Lung microbiome and antimicrobial resistome of bronchiectasis patients attending a clinic at a tertiary academic hospital in Pretoria, South Africa

Abstract

Bronchiectasis is a heterogeneous disease with multiple aetiologies and diverse clinical phenotypes. The pathogenesis of bronchiectasis, a growing economic health burden, is poorly understood. While culture-independent technologies have significantly increased the understanding of the lung microbiome, there is limited data on the lung microbiome, resistome and virome from bronchiectasis patients with and without HIV on the African continent. Therefore, the purpose of this study was to identify the lung microbiome, resistome and virome in bronchiectasis patients in Pretoria, South Africa, in order to determine whether HIV status affects the bacterial and viral lung composition and accompanying antimicrobial resistance (AMR) observed.