Genetic sequencing for surveillance of drug resistance in tuberculosis in highly endemic countries: a multi-country population-based surveillance study

Abstract

SummaryBackgroundIn many countries, regular monitoring of the emergence of resistance to anti-tuberculosis drugs is hampered by the limitations of phenotypic testing for drug susceptibility. We therefore evaluated the use of genetic sequencing for surveillance of drug resistance in tuberculosis.MethodsPopulation-level surveys were done in hospitals and clinics in seven countries (Azerbaijan, Bangladesh, Belarus, Pakistan, Philippines, South Africa, and Ukraine) to evaluate the use of genetic sequencing to estimate the resistance of Mycobacterium tuberculosis isolates to rifampicin, isoniazid, ofloxacin, moxifloxacin, pyrazinamide, kanamycin, amikacin, and capreomycin. For each drug, we assessed the accuracy of genetic sequencing by a comparison of the adjusted prevalence of resistance, measured by genetic sequencing, with the true prevalence of resistance, determined by phenotypic testing.FindingsIsolates were taken from 7094 patients with tuberculosis who were enrolled in the study between November, 2009, and May, 2014. In all tuberculosis cases, the overall pooled sensitivity values for predicting resistance by genetic sequencing were 91% (95% CI 87–94) for rpoB (rifampicin resistance), 86% (74–93) for katG, inhA, and fabG promoter combined (isoniazid resistance), 54% (39–68) for pncA (pyrazinamide resistance), 85% (77–91) for gyrA and gyrB combined (ofloxacin resistance), and 88% (81–92) for gyrA and gyrB combined (moxifloxacin resistance). For nearly all drugs and in most settings, there was a large overlap in the estimated prevalence of drug resistance by genetic sequencing and the estimated prevalence by phenotypic testing.InterpretationGenetic sequencing can be a valuable tool for surveillance of drug resistance, providing new opportunities to monitor drug resistance in tuberculosis in resource-poor countries. Before its widespread adoption for surveillance purposes, there is a need to standardise DNA extraction methods, recording and reporting nomenclature, and data interpretation.FundingBill & Melinda Gates Foundation, United States Agency for International Development, Global Alliance for Tuberculosis Drug Development.

Value of pyrazinamide for composition of new treatment regimens for multidrug-resistant Mycobacterium tuberculosis in China

“…Although the basis of this diversity is unclear, it is hypothesized that either the gene is situated in a hot spot region, or that it is a consequence of the lack of DNA mismatch repair mechanisms in MTB [32]. For the mutations in pncA, 40/61 point mutations conferring pyrazinamide resistance that we found have been reported previously [33][34][35], and to our knowledge, 21 novel mutations and all 11 frameshift changes (insertions or deletions) were first found in this study. There are also other unknown resistance mechanisms responsible for the resistance phenotype, such as mutations in rpsA gene, however, low frequency of rpsA gene mutations showed that rpsA gene mutation was not the main mechanism of pyrazinamide resistance [36,37].…”

Drug resistance mechanisms and drug susceptibility testing for tuberculosis

“…The introduction of WGS in routine diagnostics was found accurate (species identification accuracy: 99%; drug susceptibility accuracy: 96% for eight drugs) and rapid (72 h for WGS vs 28 days for DST only), allowing to replace seven different molecular assays and accelerating reporting time . WGS was also successfully used for drug resistance surveillance purposes …”

“…161,162 WGS was also successfully used for drug resistance surveillance purposes. 163,164 The advances in performances of NGS workflow (from DNA extraction to data analysis) allowed to improve WGS for 'real-time' routine diagnosis in direct clinical samples, with MTB complex detection accuracy of >97%. Prediction of DST was obtained from 62% of cases, with complete concordance with phenotypic drug susceptibility reference testing.…”

Organoids as a Powerful Model for Respiratory Diseases

“…Since its discovery by Robert Koch in 1832, Mycobacterium tuberculosis (MTB) remains a great health threat to the global population, particularly in Southeast Asian and some African countries [63]. Nearly ten million new MTB infections have been recognized annually during the past 5 years according to a WHO TB report.…”