Whole Genome Sequencing-based Characterization of Mycobacterium tuberculosis Isolated from HIV-Seropositive Ugandans with Tuberculosis and CD4+ T-Cell Counts of 0-1150 Cells/μL

The pathogen genetic factors driving the transmission of tuberculosis in communities and drug resistance emergence are not clearly understood. We have routinely used common molecular approaches such as Restriction Fragment Length Polymorphisms (RFLP) analysis and PCR-based genotyping methods (such as Region of Difference [RD] analysis, Spoligotyping, and Mycobacterial Interspersed Repetitive Units-Variable-Number Tandem Repeats [MIRU-VNTR] analysis) for speciation of the Mycobacterium tuberculosis complex, strain identification, and inferring transmission patterns in Uganda. Through WGS analysis, we detected anti-TB drug resistance conferring mutations in all the drug resistant isolates investigated. WGS analysis can be useful in predicting resistance to all anti-TB drugs in Uganda and where applicable, it could be used to complement the conventional phenotypic and molecular susceptibility tests