In silico evaluation of WHO-endorsed molecular methods to detect drug resistant tuberculosis

Abstract

Universal drug susceptibility testing (DST) for tuberculosis is a major goal of the END TB strategy. PCR-based molecular diagnostic tests have been instrumental in increasing DST globally and several assays have now been endorsed by the World Health Organization (WHO) for use in the diagnosis of drug resistance. These endorsed assays, however, each interrogate a limited number of mutations associated with resistance, potentially limiting their sensitivity compared to sequencing-based methods. We applied an in silico method to compare the sensitivity and specificity of WHO-endorsed molecular based diagnostics to the mutation set identified by the WHO mutations catalogue using phenotypic DST as the reference. We found that, in silico, the mutation sets used by probe-based molecular diagnostic tests to identify rifampicin, isoniazid, pyrazinamide, levofloxacin, moxifloxacin, amikacin, capreomycin and kanamycin resistance produced similar sensitivities and specificities to the WHO mutation catalogue. PCR-based diagnostic tests were most sensitive for drugs where mechanisms of resistance are well established and localised to small genetic regions or a few prevalent mutations. Approaches using sequencing technologies can provide advantages for drugs where our knowledge of resistance is limited, or where complex resistance signatures exist.

Figure 1

Sensitivity and specificity of WHO catalogue mutations and mutations detected by molecular diagnostic tests for predicting resistance to first-line antitubercular drugs. Error bars show 95% confidence intervals and point plots indicate performance of the molecular diagnostic test in clinical trials, these values are listed in Table 3. A full table of results is presented in Table S3. Drug acronyms: RIF rifampicin, INH isoniazid, PZA pyrazinamide.

Figure 2

Sensitivity and specificity of WHO catalogue mutations and mutations detected by molecular diagnostic tests for predicting resistance to antitubercular drugs not used in first-line treatment. Error bars show 95% confidence intervals and point plots indicate performance of molecular diagnostic tests in clinical trials, these values are listed in Table 3. A full table of results is presented in Table S3. Drug acronyms: ETH ethionamide, LEV levofloxacin, MXF moxifloxacin, AMI amikacin, CAP capreomycin, KAN kanamycin.