Application of next-generation sequencing to detect MTB resistance to first- and second-line anti-TB drugs

Application of next-generation sequencing to detect MTB resistance to first- and second-line anti-TB drugs Introduction: Drug resistance (DR) in Mycobacterium tuberculosis (MTB) is a global challenge in TB Control worldwide. Phenotypic drug susceptibility testing (DST) is sometimes inconsistent and usually takes about a month. Next-generation sequencing (NGS) is a novel approach to detecting key DR-associated mutations of MTB. Aims and Objectives: evaluating the sensitivity and specificity of NGS for detecting MTB DR compared to phenotype-based methods. Methods: 47 MTB isolates were randomly selected from the laboratory collection. The phenotypic DST was studied in the MGIT system at critical concentrations for first- and second-line anti-TB drugs. Extracted genomic DNA was prepared and then whole genome sequencing was performed using MGISEQ-200RS (BGI, China). DR was evaluated through SNP identification in resistance-associated genes (rpsL, rRNA, katG, inhA, rpoB, embB, pncA, rpsA, gyrA, gyrB, rrs, eis). Results: NGS has been shown to be a highly sensitive method for detecting mutations associated with resistance to isoniazid, rifampicin, ofloxacin, levofloxacin and moxifloxacin (100%) and streptomycin (96,7%). Sensitivity values to ethambutol and kanamycin were lower (87.5% and 88.9%). Low sensitivity was observed for pyrazinamide (29.4%), amikacin and capreomycin (60.0%). Specificity was more than 90% for all anti-TB drugs. Conclusion: NGS allows detecting DR to a wide range of anti-TB drugs with high sensitivity and specificity. This research is still ongoing.