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Whole genome sequencing and spatial analysis identifies recent tuberculosis transmission hotspots in Ghana
- Source :
- Frontiers in Medicine, Frontiers in Medicine, Vol 7 (2020)
- Publication Year :
- 2020
- Publisher :
- Frontiers Media, 2020.
-
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 not only as a research tool but as a surveillance tool to aid in providing the necessary guided steps to track, monitor, and control TB.
- Subjects :
- 0301 basic medicine
Population
Bacterial genome size
Computational biology
recent transmission
Genome
molecular epidemiology
Mycobacterium tuberculosis
03 medical and health sciences
0302 clinical medicine
030212 general & internal medicine
education
cluster
Original Research
Whole genome sequencing
education.field_of_study
lcsh:R5-920
Mycobacterium africanum
biology
Molecular epidemiology
whole genome sequence
General Medicine
biology.organism_classification
030104 developmental biology
Mycobacterium tuberculosis complex
Medicine
lcsh:Medicine (General)
Subjects
Details
- Database :
- OpenAIRE
- Journal :
- Frontiers in Medicine, Frontiers in Medicine, Vol 7 (2020)
- Accession number :
- edsair.doi.dedup.....68d132b59bbdae429dd50722d540f07f
- Full Text :
- https://doi.org/10.5451/unibas-ep77055