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

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.

Diagnosis of tuberculosis among COVID-19 suspected cases in Ghana

“…These two samples respectively showed high and medium bacterial load when analyzed with GeneXpert MTB/RIF assay indicating that there could be a high chance of community spread of TB with such high bacterial loads detected [ 16 ]. Interestingly, these two TB positive samples from contact tracing were both from the Ayawaso sub-district which our previous studies have confirmed to be a hotspot for active TB transmission [ 17 ].…”

“…This further stresses the need to conduct frequent community screening of individuals in known hotspot communities such as Ayawaso and Ablekuma sub-districts where active TB transmission has been shown to be taking place [ 17 ]. There is therefore the need for active community case search to ensure early active TB case detection to ensure efficient management to cut any potential spread.…”

A Saudi Arabian Public Health Perspective of Tuberculosis

“…Whole Genome Sequencing (WGS) is useful in the detection of unsuspected outbreaks; therefore, it is a useful research tool and can also be part of surveillance programs to help in the tracking, monitoring, and control of TB. It also aids in the recognition of MTB strains associated with drug resistance and in the identification of hotspots [ 52 ]. Co-existence of two or more strains of mycobacteria may present with a complex challenge of misidentification of MTB.…”

Whole-Genome Sequencing Reveals Recent Transmission of Multidrug-Resistant Mycobacterium tuberculosis CAS1-Kili Strains in Lusaka, Zambia

“…Despite some reports indicating the reduced fitness as a result of drug resistance evolution [ 20 , 21 ], others have indicated emanating high fitness strains with preserved ability to spread [ 22 , 23 ]. Thus, the latter might explain the scenario in our current study.…”