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

Frontiers in Medicine

article

Prince Asare¹  Sonia Borrell⁴  Miriam Reinhard⁴  Audrey Forson⁶  Kwadwo Ansah Koram¹  Sebastien Gagneux⁴  Dorothy Yeboah-Manu¹  Isaac Darko Otchere¹  Edmund Bedeley¹  Daniela Brites⁴  Chloé Loiseau⁴  Nyonuku Akosua Baddoo⁶  Adwoa Asante-Poku¹  Stephen Osei-Wusu¹  Diana Ahu Prah¹ 

[1] Noguchi Memorial Institute for Medical Research, College of Health Sciences, University of Ghana;West African Centre for Cell Biology of Infectious Pathogens, University of Ghana;Department of Biochemistry, University of Ghana;Department of Medical Parasitology and Infection Biology, Swiss Tropical and Public Health Institute;University of Basel;Department of Chest Diseases, Korle-Bu Teaching Hospital

关键词: Mycobacterium tuberculosis;    Mycobacterium africanum;    molecular epidemiology;    whole genome sequence;    recent transmission;    cluster;   

DOI  :  10.3389/fmed.2020.00161

学科分类：社会科学、人文和艺术（综合）

来源: Frontiers

【 摘 要 】

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.

【 授权许可】

CC BY