Whole Genome Sequencing and Spatial Analysis Identifies Recent Tuberculosis Transmission Hotspots in Ghana

Frontiers in Medicine
Prince AsareDorothy Yeboah-Manu

Abstract

Whole genome sequencing (WGS) is progressively being used to investigate the transmission dynamics of Mycobacterium tuberculosis complex (MTBC). We used WGS analysis to resolve traditional genotype clusters and explored the spatial distribution of confirmed recent transmission clusters. Bacterial genomes from a total of 452 MTBC isolates belonging to large traditional clusters from a population-based study spanning July 2012 and December 2015 were obtained through short read next-generation sequencing using the illumina HiSeq2500 platform. We performed clustering and spatial analysis using specified R packages and ArcGIS. Of the 452 traditional genotype clustered genomes, 314 (69.5%) were confirmed clusters with a median cluster size of 7.5 genomes and an interquartile range of 4-12. Recent tuberculosis (TB) transmission was estimated as 24.7%. We confirmed the wide spread of a Cameroon sub-lineage clone with a cluster size of 78 genomes predominantly from the Ablekuma sub-district of Accra metropolis. More importantly, we identified a recent transmission cluster associated with isoniazid resistance belonging to the Ghana sub-lineage of lineage 4. WGS was useful in detecting unsuspected outbreaks; hence, we recommend its use no...Continue Reading

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Citations

Aug 10, 2021·Frontiers in Public Health·Prince AsareDorothy Yeboah-Manu
Dec 29, 2021·PloS One·Theophilus AfumDorothy Yeboah-Manu

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Datasets Mentioned

BETA
PRJNA616081

Methods Mentioned

BETA
genotyping

Software Mentioned

VarScan
GTR
ArcMap
ggplot2
ggtree
snpEff
Stata
molepi
Samtools
CIPRES

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