Whole Genome Sequencing to Identify Polymorphisms Associated with Discordant Results in Phenotypic and Genotypic DSTs and Map New Regions of Drug Resistance in MTB

Background and rationale: Care of patients with TB starts with Quality Assured Diagnosis. Even though Line Probe Assay (LPA) can detect mutation(s) that are most commonly identified in resistant strains, some mutations that confer resistance are outside the regions covered by the current versions of LPA. Xpert MTB/RIF only targets mutations on the hotspot 81bp RRDR within the rpoB gene. Culture-based DST, though currently the gold standard, takes long time and so delays proper patient management of active TB. Discordant results between phenotypic DST and genotypic DST have been reported for both first line (MTBDRplus) and second line (MTBDRsl). The clinical burden of such discordance is not properly understood yet the governments of Kenya lack reliable baseline data upon which to base their response. New resistant strains also continue to emerge. There is no assurance that the release of different versions of LPA will keep pace with the ability and frequency of MTB to develop resistance.

Objectives: We propose to conduct whole genome sequencing on samples with discrepant genotypic and phenotypic DSTs to identify specific SNPs associated with such discordance, and their associated clinical outcomes. The study explored discordant results between genotypic DSTs and phenotypic DSTs, and evaluate the relevance of sequencing in the management of MDR/XDR TB in the healthcare system in Kenya.

Methods: A retrospective study was done on samples which showed discordant results for RIF and INH between MTBDRplus (Hain Life Sciences, Nehren, Germany) and liquid culture-based DST using the Becton Dickinson BACTEC MGIT TM 960 machine between August 2018 and September 2021 at KEMRI/CDC laboratories. illumina was used to identify single nucleotide polymorphism (SNPs) responsible for such discordance and whether the mutation(s) confer unfavorable clinical outcome or not.

Results: Out of the 203 samples, 3.7% discordance between phenotypic DST and genotypic DST for the case of isoniazid and 3.2% discordance between phenotypic DST and genotypic DST for the case of rifampicin. The findings inform that at least 3.7% of the patients under isoniazid and another 3.2% on rifampicin were given wrong treatments pending culture results.