Implementation of whole genome sequencing for tuberculosis diagnostics in a low-middle income, high MDR-TB burden country

Abstract

Whole genome sequencing (WGS) is revolutionary for diagnostics of TB and its mutations associated with drug-resistances, but its uptake in low- and middle-income countries is hindered by concerns of implementation feasibility. Here, we provide a proof of concept for its successful implementation in such a setting. WGS was implemented in the Kyrgyz Republic. We estimated needs of up to 55 TB-WGS per week and chose the MiSeq platform (Illumina, USA) because of its capacity of up to 60 TB-WGS per week. The project’s timeline was completed in 93-weeks. Costs of large equipment and accompanying costs were 222,065 USD and 8462 USD, respectively. The first 174 WGS costed 277 USD per sequence, but this was skewed by training inefficiencies. Based on real prices and presuming optimal utilization of WGS capacities, WGS costs could drop to 167 and 141 USD per WGS using MiSeq Reagent Kits v2 (500-cycles) and v3 (600-cycles), respectively. Five trainings were required to prepare the staff for autonomous WGS which cost 48,250 USD. External assessment confirmed excellent performance of WGS by the Kyrgyz laboratory in an interlaboratory comparison of 30 M. tuberculosis genomes showing complete agreeance of results.

Whole-Genome Sequencing Has the Potential To Improve Treatment for Rifampicin-Resistant Tuberculosis in High-Burden Settings: a Retrospective Cohort Study

“…These include cost, laboratory infrastructure and appropriate bioinformatics skills. These challenges may be feasible to overcome as demonstrated by recent experience in the Kyrgyz Republic ( 22 ). Accurate prediction of drug resistance from genomic data is also a challenge across all settings.…”

Evolution of tuberculosis diagnostics: From molecular strategies to nanodiagnostics

“…The Ion torrent was introduced in 2010 and is the most advanced gene sequencing approach. It is based on monitoring the change in pH during DNA polymerization and is coupled with a silicon detector [ 148 ]. It is relatively fast and is only applicable to smaller data sets.…”

Implementing molecular tuberculosis diagnostic methods in limited-resource and high-burden countries

“…The costs are increased when establishing a sequencing facility in low-income settings due to the costs of shipments, customs, and the eventual profit margin for local companies. Lessons learnt from implementing WGS in Kyrgyzstan show that the main cost drivers were not using library preparation and sequencing kits to their full capacity during initial training, and partly by prices charged by the regional distributor exceeding those charged to laboratories in Europe and North America [ 7 ]. In addition to hardware costs, data manipulation and analysis are done using software licensed and commercialised by companies, representing an additional cost to institutions in LICs.…”