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Whole genome sequencing and spatial analysis identifies recent tuberculosis transmission hotspots in Ghana

Asare, Prince and Otchere, Isaac Darko and Bedeley, Edmund and Brites, Daniela and Loiseau, Chloé and Baddoo, Nyonuku Akosua and Asante-Poku, Adwoa and Osei-Wusu, Stephen and Prah, Diana Ahu and Borrell, Sonia and Reinhard, Miriam and Forson, Audrey and Koram, Kwadwo Ansah and Gagneux, Sebastien and Yeboah-Manu, Dorothy. (2020) Whole genome sequencing and spatial analysis identifies recent tuberculosis transmission hotspots in Ghana. Frontiers in medicine, 7. p. 161.

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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.
Faculties and Departments:09 Associated Institutions > Swiss Tropical and Public Health Institute (Swiss TPH)
09 Associated Institutions > Swiss Tropical and Public Health Institute (Swiss TPH) > Department of Medical Parasitology and Infection Biology (MPI) > Tuberculosis Research (Gagneux)
UniBasel Contributors:Brites, Daniela and Loiseau, Chloé Marie and Borrell, Sonia and Reinhard, Miriam and Gagneux, Sebastien
Item Type:Article, refereed
Article Subtype:Research Article
Publisher:Frontiers Media
ISSN:2296-858X
Note:Publication type according to Uni Basel Research Database: Journal article
Language:English
Identification Number:
Last Modified:17 Jun 2020 10:22
Deposited On:17 Jun 2020 10:22

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