Details of Studies Included in Review and Source of <i>Mycobactrium tuberculosis</i> Isolates.

<p> <b>CDC = Center for Disease Control and Prevention, Atlanta.</b></p

Evaluation of Genetic Mutations Associated with <em>Mycobacterium tuberculosis</em> Resistance to Amikacin, Kanamycin and Capreomycin: A Systematic Review

<div><h3>Background</h3><p>Rapid molecular diagnostics for detecting multidrug-resistant and extensively drug-resistant tuberculosis (M/XDR-TB) primarily identify mutations in <em>Mycobacterium tuberculosis</em> (<em>Mtb</em>) genes associated with drug resistance. Their accuracy, however, is dependent largely on the strength of the association between a specific mutation and the phenotypic resistance of the isolate with that mutation, which is not always 100%. While this relationship is well established and reliable for first-line anti-TB drugs, rifampin and isoniazid, it is less well-studied and understood for second-line, injectable drugs, amikacin (AMK), kanamycin (KAN) and capreomycin (CAP).</p> <h3>Methodology/Principal Findings</h3><p>We conducted a systematic review of all published studies evaluating <em>Mtb</em> mutations associated with resistance to AMK, KAN, CAP in order to characterize the diversity and frequency of mutations as well as describe the strength of the association between specific mutations and phenotypic resistance in global populations. Our objective was to determine the potential utility and reliability of these mutations as diagnostic markers for detecting AMK, KAN and CAP resistance. Mutation data was reviewed for 1,585 unique clinical isolates from four continents and over 18 countries. Mutations in the <em>rrs</em>, <em>tlyA</em>, <em>eis</em> promoter and <em>gidB</em> genes were associated with AMK, KAN and/or CAP resistance.</p> <h3>Conclusions/Significance</h3><p>The <em>rrs</em> A1401G mutation was present in the majority of AMK, KAN and CAP resistant <em>Mtb</em> strains reviewed, but was also found in 7% of CAP susceptible strains. The 1401 mutation alone, however, was not found with sufficient frequency to detect more than 70–80% of global <em>Mtb</em> strains resistant to AMK and CAP, and 60% of strains resistant to KAN. Additional mutations in the <em>rrs</em>, <em>eis</em> promoter, <em>tlyA</em> and <em>gidB</em> genes appear to be associated with resistance and could improve sensitivity and specificity of future diagnostics.</p> </div

Heatmap of Reviewed Studies that Evaluated <i>rrs</i> Gene Mutations in <i>Mycobacterium tuberculosis</i> isolates.

<p>Graphic shows the region of the <i>rrs</i> gene studied, the number of isolates tested in each study and the locations of the mutations found. The X-axis (nucleotide position) has a 25 base pair resolution. The numbers of isolates varies from 314 (black) to 10 (lightest grey). Red indicates that a mutation has been found in that 25 base pair region.</p

Study Selection Process and Reason for Exclusion of Studies.

<p>Study Selection Process and Reason for Exclusion of Studies.</p

Cumulative Frequencies of Selected Mutations within the <i>tlyA</i> Gene among <i>Mycobacterium tuberculosis</i> Isolates Resistant or Susceptible to Amikacin (AMK), Kanamycin (KAN) and/or Capreomycin (CAP).

*<p>Represents an amino acid change, as specific nucleotide changes were not provided for this mutation.</p><p>R = Resistant isolates.</p><p>S = Susceptible isolates.</p

Cumulative Frequencies of Multiple Mutations within the <i>rrs</i> Gene among <i>Mycobacterium tuberculosis</i> Isolates Resistant or Susceptible to Amikacin (AMK), Kanamycin (KAN) and/or Capreomycin (CAP).

<p>R = Resistant isolates.</p><p>S = Susceptible isolates.</p

Phase 2 comparative accuracy of the YD line probe assay versus Hain V1 line probe assay on sputum samples.

<p>The difference in sensitivity/specificity (Δ = YD–Hain V1) is displayed in the CIs in each plot. The horizontal axis indicates the percent difference between tests. The point in the center of each CI represents the point estimate and whiskers representing the upper and lower limit of the 95% CIs. The black vertical dotted line (where visible) indicates zero difference in sensitivity/specificity and the red vertical broken line indicates the non-inferiority margin. Non-inferiority is demonstrated for a given comparison if the lower limit of the 95%CI does not cross the red broken line (non-inferiority margin).</p

Comparative accuracy of the REBA MTB MDR and Hain MTBDR<i>plus</i> line probe assays for the detection of multidrug-resistant tuberculosis: A multicenter, non-inferiority study

<div><p>Introduction</p><p>Despite recent diagnostic advances, the majority of multidrug-resistant tuberculosis (MDR-TB) cases remain undiagnosed. Line probes assays (LiPAs) hold great promise to curb the spread of MDR-TB as they can rapidly detect MDR-TB even when laboratory infrastructure is limited, yet few of these assays are currently widely available or supported by World Health Organization (WHO) policy.</p><p>Methods</p><p>The aim of this prospective, blinded, non-inferiority study was to compare the performance of YD Diagnostics REBA MTB MDR LiPA (YD) to the WHO-endorsed Hain MTBDR<i>plus</i> V1 LiPA (Hain V1) for the detection of rifampicin and isoniazid resistance. In phase 1, YD and Hain V1 diagnostic performance was assessed with selected culture isolates and results were compared to phenotypic drug susceptibility testing (DST) results and targeted sequencing data. In phase 2, both assays were tested on processed sputum samples and results were compared to phenotypic DST results.</p><p>Results</p><p>In phase 1, YD did not achieve non-inferiority to Hain V1. For isoniazid resistance detection, Hain V1 had a sensitivity of 89% (95%CI 83.8–93%) and specificity of 99.4% (95%CI 96.9–100%). While YD had a similar sensitivity of 92% (95%CI 87.3–95.4%), the specificity was inferior at 92.6% (95%CI 87.6–96%). For rifampicin resistance detection, Hain V1 had a sensitivity of 90.2% (95%CI 84.8–94.2%) and specificity of 98.5% (95%CI 95.7–99.7%) while YD had an inferior sensitivity of 72.4% (95%CI 65.1–78.9%) and a comparable specificity of 98% (95%CI 95–99.5%). Similar results were observed in phase 2. For MDR-TB detection, the sensitivity and specificity of Hain V1 was 93.4% (95%CI 88.2–96.2%) and 96.2% (95%CI 88.2–96.8%), respectively, compared to 75.7% (95%CI 68–82.2%) and 92% (95%CI 88.2–94.9%) for YD.</p><p>Conclusions</p><p>YD did not achieve non-inferiority with Hain V1. Further improvements and repeat evaluation of YD is necessary prior to recommending its use for clinical settings.</p></div

Phase 1 comparative accuracy of the YD line probe assay versus Hain V1 line probe assay on characterized strains.

<p>Phase 1 comparative accuracy of the YD line probe assay versus Hain V1 line probe assay on characterized strains.</p

Phase 1 per-probe performance analysis on characterized strains.

<p>Phase 1 per-probe performance analysis on characterized strains.</p