Genetic Mutations Associated with Isoniazid Resistance in <i>Mycobacterium tuberculosis</i>: A Systematic Review

<div><p>Background</p><p>Tuberculosis (TB) incidence and mortality are declining worldwide; however, poor detection of drug-resistant disease threatens to reverse current progress toward global TB control. Multiple, rapid molecular diagnostic tests have recently been developed to detect genetic mutations in <i>Mycobacterium tuberculosis (Mtb)</i> genes known to confer first-line drug resistance. Their utility, though, depends on the frequency and distribution of the resistance associated mutations in the pathogen population. Mutations associated with rifampicin resistance, one of the two first-line drugs, are well understood and appear to occur in a single gene region in >95% of phenotypically resistant isolates. Mutations associated with isoniazid, the other first-line drug, are more complex and occur in multiple <i>Mtb</i> genes.</p><p>Objectives/Methodology</p><p>A systematic review of all published studies from January 2000 through August 2013 was conducted to quantify the frequency of the most common mutations associated with isoniazid resistance, to describe the frequency at which these mutations co-occur, and to identify the regional differences in the distribution of these mutations. Mutation data from 118 publications were extracted and analyzed for 11,411 <i>Mtb</i> isolates from 49 countries.</p><p>Principal Findings/Conclusions</p><p>Globally, 64% of all observed phenotypic isoniazid resistance was associated with the <i>kat</i>G315 mutation. The second most frequently observed mutation, <i>inhA</i>-15, was reported among 19% of phenotypically resistant isolates. These two mutations, <i>katG</i>315 and <i>inhA</i>-15, combined with ten of the most commonly occurring mutations in the <i>inhA</i> promoter and the <i>ahpC-oxyR</i> intergenic region explain 84% of global phenotypic isoniazid resistance. Regional variation in the frequency of individual mutations may limit the sensitivity of molecular diagnostic tests. Well-designed systematic surveys and whole genome sequencing are needed to identify mutation frequencies in geographic regions where rapid molecular tests are currently being deployed, providing a context for interpretation of test results and the opportunity for improving the next generation of diagnostics.</p></div

Performance of Xpert MTB/RIF vs AFB smear microscopy for the exclusion of NTM, using mycobacterial culture as the reference standard.

<p>Performance of Xpert MTB/RIF vs AFB smear microscopy for the exclusion of NTM, using mycobacterial culture as the reference standard.</p

Performance of Xpert MTB/RIF for the detection of RIF resistance, relative to phenotypic DST.

<p>Performance of Xpert MTB/RIF for the detection of RIF resistance, relative to phenotypic DST.</p

Performance of Xpert MTB/RIF for the detection of MTBC as stratified by smear status, using mycobacterial culture as the reference standard; In comparison with the performance of AFB smear microscopy.

<p>Performance of Xpert MTB/RIF for the detection of MTBC as stratified by smear status, using mycobacterial culture as the reference standard; In comparison with the performance of AFB smear microscopy.</p

Drug resistant specimens by phenotypic DST (n = 16).

<p>Drug resistant specimens by phenotypic DST (n = 16).</p

Performance of the Xpert MTB/RIF assay for the diagnosis of pulmonary tuberculosis and rifampin resistance in a low-incidence, high-resource setting

<div><p>Performance of the Xpert MTB/RIF assay, designed to simultaneously detect <i>Mycobacterium tuberculosis</i> complex (MTBC) and rifampin (RIF) resistance, has been well documented in low-resource settings with high TB-incidence. However, few studies have assessed its accuracy in low TB incidence settings. We evaluated the performance of Xpert MTB/RIF using clinical sputum specimens routinely collected from suspect pulmonary TB patients over a 4-year time period in San Diego County, California. Xpert MTB/RIF results were compared to acid-fast bacilli (AFB) smear microscopy, mycobacterial culture, and phenotypic drug susceptibility testing (DST). Of 751 sputum specimens, 134 (17.8%) were MTBC culture-positive and 2 (1.5%) were multidrug-resistant (MDR). For the detection of MTBC, Xpert MTB/RIF sensitivity was 89.6% (97.7% and 74.5% in smear-positive and -negative sputa, respectively) and specificity was 97.2%; while AFB smear sensitivity and specificity were 64.9% and 77.8%, respectively. Xpert MTB/RIF detected 35 of 47 smear-negative culture-positive specimens, and excluded 124 of 137 smear-positive culture-negative specimens. Xpert MTB/RIF also correctly excluded 99.2% (121/122) of nontuberculous mycobacteria (NTM) specimens, including all 33 NTM false-positives by smear microscopy. For the detection of RIF resistance, Xpert MTB/RIF sensitivity and specificity were 100% and 98.3%, respectively. Our findings demonstrate that Xpert MTB/RIF is able to accurately detect MTBC and RIF resistance in routinely collected respiratory specimens in a low TB-incidence setting, with comparable performance to that achieved in high-incidence settings; and suggest that under these conditions the assay has particular utility in detecting smear-negative TB cases, excluding smear-positive patients without MTBC disease, and differentiating MTBC from NTM.</p></div

Additional file 1: Table S1. of Shedding light on the performance of a pyrosequencing assay for drug-resistant tuberculosis diagnosis

Pyrosequencing (PSQ) Success of Each Gene Target by Smear- and Culture-Status. Table S2. Proportion of Successful Pyrosequencing (PSQ) Reactions by Smear- and Culture-Status. (DOCX 18 kb

Additional file 2: of Shedding light on the performance of a pyrosequencing assay for drug-resistant tuberculosis diagnosis

Pyrosequencing (PSQ) Performance Dataset. (TXT 400 kb

Performance Comparison of Three Rapid Tests for the Diagnosis of Drug-Resistant Tuberculosis

<div><p>Background</p><p>The aim of this study was to compare the performance of several recently developed assays for the detection of multi- and extensively drug-resistant tuberculosis (M/XDR-TB) in a large, multinational field trial.</p><p>Methods</p><p>Samples from 1,128 M/XDR-TB suspects were examined by Line Probe Assay (LPA), Pyrosequencing (PSQ), and Microscopic Observation of Drug Susceptibility (MODS) and compared to the BACTEC MGIT960 reference standard to detect M/XDR-TB directly from patient sputum samples collected at TB clinics in India, Moldova, and South Africa.</p><p>Results</p><p>Specificity for all three assays was excellent: 97–100% for isoniazid (INH), rifampin (RIF), moxifloxacin (MOX) and ofloxacin (OFX) and 99–100% for amikacin (AMK), capreomycin (CAP) and kanamycin (KAN) resistance. Sensitivities were lower, but still very good: 94–100% for INH, RIF, MOX and OFX, and 84–90% for AMK and CAP, but only 48–62% for KAN. In terms of agreement, statistically significant differences were only found for detection of RIF (MODS outperformed PSQ) and KAN (MODS outperformed LPA and PSQ) resistance. Mean time-to-result was 1.1 days for LPA and PSQ, 14.3 days for MODS, and 24.7 days for MGIT.</p><p>Conclusions</p><p>All three rapid assays evaluated provide clinicians with timely detection of resistance to the drugs tested; with molecular results available one day following laboratory receipt of samples. In particular, the very high specificity seen for detection of drug resistance means that clinicians can use the results of these rapid tests to avoid the use of toxic drugs to which the infecting organism is resistant and develop treatment regiments that have a higher likelihood of yielding a successful outcome.</p></div

Sensitivity, specificity and percent agreement between three rapid drug susceptibility tests and MGIT for seven drugs: isoniazid (INH), rifampin (RIF), moxifloxacin (MOX), ofloxacin (OFX), amikacin (AMK), kanamycin (KAN), and capreomycin (CAP).

<p>Mean values and 95% confidence intervals for each comparison are represented in the figure; full data is included as a supplementary table.</p