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

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dc.contributor.authorAsare, P.
dc.contributor.authorOtchere, I.D.
dc.contributor.authorBedeley, E.
dc.contributor.authorBrites, D.
dc.contributor.authorLoiseau, C.
dc.contributor.authorBaddoo, N.A.
dc.contributor.authorAsante-Poku, A.
dc.contributor.authorOsei-Wusu, S.
dc.contributor.authorPrah, D.A.
dc.contributor.authorBorrell, S.
dc.contributor.authorReinhard, M.
dc.contributor.authorForson, A.
dc.contributor.authorKoram, K.A.
dc.contributor.authorGagneux, S.
dc.contributor.authorYeboah-Manu, D.
dc.date.accessioned2020-06-26T09:31:26Z
dc.date.available2020-06-26T09:31:26Z
dc.date.issued2020-05-19
dc.descriptionResearch Articleen_US
dc.description.abstractWhole 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.en_US
dc.description.sponsorshipWellcome Trust Intermediate Fellowship Grant (097134/Z/11/Z) to DY-M. Funders had no role in the study design; collection, analysis, and interpretation of data; in the writing of the report; and in the decision to submit the paper for publication. DY-M, PA, and IO had full access to all the data used in the study. PA, DY-M had the final responsibility for the decision to submit for publication.en_US
dc.identifier.citationAsare P, Otchere ID, Bedeley E, Brites D, Loiseau C, Baddoo NA, Asante-Poku A, Osei-Wusu S, Prah DA, Borrell S, Reinhard M, Forson A, Koram KA, Gagneux S and Yeboah-Manu D (2020) Whole Genome Sequencing and Spatial Analysis Identifies Recent Tuberculosis Transmission Hotspots in Ghana. Front. Med. 7:161. doi: 10.3389/fmed.2020.00161en_US
dc.identifier.otherhttps://doi.org/10.3389/fmed.2020.00161
dc.identifier.urihttp://ugspace.ug.edu.gh/handle/123456789/35364
dc.language.isoenen_US
dc.publisherFrontiers in Medicineen_US
dc.relation.ispartofseries7;161
dc.subjectMycobacterium tuberculosisen_US
dc.subjectMycobacterium africanumen_US
dc.subjectmolecular epidemiologyen_US
dc.subjectwhole genome sequenceen_US
dc.subjectrecent transmissionen_US
dc.subjectclusteren_US
dc.titleWhole Genome Sequencing and Spatial Analysis Identifies Recent Tuberculosis Transmission Hotspots in Ghanaen_US
dc.typeArticleen_US

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