Data from: Performance of TaqMan Array Card to detect TB drug resistance on direct specimens

Culture based phenotypic drug susceptibility testing (DST) for Mycobacterium tuberculosis (TB) is time consuming therefore rapid genotypic methods are increasingly being utilized. We previously developed and evaluated on TB isolates a rapid genotypic TaqMan array card (TAC) that detects mutations in several resistance-associated genes using dozens of primer pairs, probes, and high resolution melt analysis, with >96% accuracy versus Sanger sequencing. In this study we examined the performance of TAC on sputum, comparing results between 71 paired sputum and multi drug resistant TB isolates. We also adapted the TAC to include wild-type probes and broadened coverage for rpoB and gyrA mutations. TAC was 89% successful at detecting wild-type or mutations within inhA, katG, rpoB, eis, gyrA, rplC, and pncA on smear positive sputa and 33% successful on smear negative sputa. The overall accuracy of these detections as compared to the TAC results of the paired isolate was 95% ± 7 (average sensitivity 98% ± 3; specificity 92% ± 14). Accuracy of sputum TAC results versus phenotypic DST for isoniazid, rifampin, amikacin/kanamycin, ofloxacin/moxifloxacin, and pyrazinamide was 87% ± 11. This was similar to that of the paired isolate TAC results (accuracy 90% ± 12) and inaccuracies primarily reflected intrinsic genotypic-phenotypic discordance. The TAC is a rapid, modular, comprehensive, and accurate TB DST for the major first and second line TB drugs on smear positive sputum

Quantitative drug-susceptibility in patients treated for multidrug-resistant tuberculosis in Bangladesh: implications for regimen choice.

Multidrug-resistant tuberculosis (MDR-TB) treatment in Bangladesh is empiric or based on qualitative drug-susceptibility testing (DST) by comparative growth in culture media with and without a single drug concentration.Adult patients were enrolled throughout Bangladesh during the period of 2011-2013 at MDR-TB treatment initiation. Quantitative DST by minimum inhibitory concentration (MIC) testing for 12 first and second-line anti-TB drugs was compared to pretreatment clinical characteristics and treatment outcomes. MIC values at or one dilution lower than the resistance breakpoint used for qualitative DST were categorized as borderline susceptible, and MIC values one or two dilutions greater as borderline resistant.Seventy-four patients were enrolled with a mean age of 35 ± 15 years, and 51 (69%) were men. Of the rifampin isolates with MIC >1.0 μg/ml, 12 (19%) were fully susceptible or borderline susceptible to rifabutin (MIC ≤ 0.5 μg/ml). Amikacin was fully susceptible in 73 isolates (99%), but kanamycin in only 54 (75%) (p<0.001). Ofloxacin was borderline susceptible in 64%, and fully susceptible in only 14 (19%) compared to 60 (81%) of isolates fully susceptible for moxifloxacin (p<0.001). Kanamycin non-susceptibility and receipt of the WHO Category IV regimen trended with interim treatment failure: adjusted odd ratios respectively of 5.4 [95% CI 0.82-36.2] (p = 0.08) and 7.2 [0.64-80.7] (p = 0.11).Quantitative MIC testing could impact MDR-TB regimen choice in Bangladesh. Comparative trials of higher dose or later generation fluoroquinolone, within class change from kanamycin to amikacin, and inclusion of rifabutin appear warranted

Sensitivity of TAC to detect drug resistance on sputum samples.

<p>Sensitivity of TAC to detect drug resistance on sputum samples.</p

Correlation between genotypic and phenotypic drug susceptibility test.

<p>Correlation between genotypic and phenotypic drug susceptibility test.</p

Sequencing confirmation of the discordance samples between TAC and phenotypic DST.

<p>Sequencing confirmation of the discordance samples between TAC and phenotypic DST.</p

Performance of TAC to detect drug resistance on paired sputum and isolate.

<p>Performance of TAC to detect drug resistance on paired sputum and isolate.</p

Amplification Ct cut-off.

<p>For each of 71 sputum samples the average SYTO9 Ct value for each of the 11 amplicons is shown. Average Ct are organized according to whether the sputum probe result was wild-type (black -), mutant (black x), or negative. Sputum probe negative results are further stratified into whether the cultured isolate was found to be wild-type (red +), mutant (red -), or to possess an “other” mutation (green X). ROC analysis was performed to examine the optimal Ct whereby SYTO9 to interpret the probe results.</p

TB drug resistance TAC version 2.

<p>TAC tests 8 samples and compartmentalizes 48 assays per sample. Assays are grouped according to drug isoniazid (INH), rifampin (RIF), amikacin (AMK), kanamycin (KAN), ofloxacin (OFX), moxifloxacin (MXF), linezolid (LZD), and pyrazinamide (PZA). Each assay is shown on the basis of gene nucleotide or codon. Wt = wild-type. A/B indicates duplex assays.</p

Primers and probes used in the TB TAC v2.

<p>Primers and probes used in the TB TAC v2.</p