Abstract:
Chronic obstructive pulmonary disease (COPD) is characterised by the occurrence of exacerbations
triggered by infections. The aim of this study was to determine the composition of the lung
microbiome and lung virome in patients with COPD in an African setting and to compare their
composition between the stable and exacerbated states. Twenty-four adult COPD patients were
recruited from three hospitals. Sputum was collected and bacterial DNA was extracted. Targeted
metagenomics was performed to determine the microbiome composition. Viral DNA and RNA were
extracted from selected samples followed by cDNA conversion. Shotgun metagenomics sequencing
was performed on pooled DNA and RNA. The most abundant phyla across all samples were Firmicutes
and Proteobacteria. The following genera were most prevalent: Haemophilus and Streptococcus. There
were no considerable diferences for alpha and beta diversity measures between the disease states.
However, a diference in the abundances between disease states was observed for: (i) Serratia (3%
lower abundance in exacerbated state), (ii) Granulicatella (2.2% higher abundance in exacerbated
state), (iii) Haemophilus (5.7% higher abundance in exacerbated state) and (iv) Veillonella (2.5%
higher abundance in exacerbated state). Virome analysis showed a high abundance of the BeAn 58058
virus, a member of the Poxviridae family, in all six samples (90% to 94%). This study is among the frst
to report lung microbiome composition in COPD patients from Africa. In this small sample set, no
diferences in alpha or beta diversity between stable and exacerbated disease state was observed, but
an unexpectedly high frequency of BeAn 58058 virus was observed. These observations highlight the
need for further research of the lung microbiome of COPD patients in African settings.
