Comparative evaluation of molecular-based detection methods for drug resistant tuberculosis

Abstract

Tuberculosis (TB) is a globally problematic infectious disease and is currently one of the leading causes of death from any infectious disease worldwide. Mycobacterium tuberculosis (MTB) is notorious for developing resistance to currently available treatment, and according to the World Health Organization (WHO), 157947 cases of multidrug‐resistant tuberculosis (MDR‐TB) were reported globally in 2020. South Africa is classified as a high TB burden country and accounts for 6784 of the MDR-TB cases detected in 2020 (World Health Organization, 2021). This highlights the need for new and improved methods for TB drug resistance profiling. Sensitive, specific, and reproducible are some of the most important characteristics of an advanced molecular-based drug resistance profiling test. Firstly, a meta-analysis was performed to compare evidence for highly sensitive and specific Mycobacterium tuberculosis complex (MTBC) drug resistance profile determination. We did this to answer the question whether the Mycobacterial Growth Indicator Tube (MGIT) still serves as a good representative gold standard with all the recent advancements in molecular based diagnostics? The study outcomes were used to determine and assess sensitivity, specificity, and reproducibility of the respective drug resistance profiling kits from literature. A total of eighteen studies were identified for comparison between MTBDRplus V2.0 (n=9), MTBDRsl V2.0 (n=6) and Nipro NTM + MTBDR (n=3). Each method had related advantages. The turnaround time of the included methods are rapid compared to culture methods and the reported results yielded high accuracies especially for the MTBDR V2.0 line probe assays. Secondly, we evaluated the commercially available Hain GenoType® MTBDRplus and sl Version 2.0 kits, as well as the recently developed CapitalBio Gene Real-Time PCR Detection Kit. A total of 92 blinded and randomized MTBC DNA samples received from the Centre for Tuberculosis (CTB) at the National Institute for Communicable Diseases (NICD) and subjected to analyses by each kit. The kits were evaluated in terms of diagnostic accuracy, affordability, ease of use, turnaround time and robustness. The Hain GenoType® MTBDR V2.0 assays had the highest rates of accuracy with whole genome sequencing as reference standard. The CapitalBio Gene Real-Time PCR Detection Kit is suitable for implementation due to its affordability, rapid turnaround time and wide detection range of first-and second-line drug resistance in TB patients simultaneously, however it does require optimisation. This study determined that the Hain GenoType® MTBDR V2.0 assays are superior to the CapitalBio Gene Real-Time PCR Detection Kit when all aspects of advanced diagnostics for DR-TB in South Africa are considered.