Isoniazid resistance levels of Mycobacterium tuberculosis can largely be predicted by high-confidence resistance-conferring mutations

Abstract

The majority of Mycobacterium tuberculosis isolates resistant to isoniazid harbour a mutation in katG. Since these mutations cause a wide range of minimum inhibitory concentrations (MICs), largely below the serum level reached with higher dosing (15 mg/L upon 15–20 mg/kg), the drug might still remain partly active in presence of a katG mutation. We therefore investigated which genetic mutations predict the level of phenotypic isoniazid resistance in clinical M. tuberculosis isolates. To this end, the association between known and unknown isoniazid resistance-conferring mutations in whole genome sequences, and the isoniazid MICs of 176 isolates was examined. We found mostly moderate-level resistance characterized by a mode of 6.4 mg/L for the very common katG Ser315Thr mutation, and always very high MICs (≥19.2 mg/L) for the combination of katG Ser315Thr and inhA c-15t. Contrary to common belief, isolates harbouring inhA c-15t alone, partly also showed moderate-level resistance, particularly when combined with inhA Ser94Ala. No overt association between low-confidence or unknown mutations, except in katG, and isoniazid resistance (level) was found. Except for the rare katG deletion, line probe assay is thus not sufficiently accurate to predict the level of isoniazid resistance for a single mutation in katG or inhA.

<p>Association Between the Phenotype and Genotype of Isoniazid Resistance Among <em>Mycobacterium tuberculosis</em> Isolates in Thailand</p>

“…Previous studies had more than one gene mutations exhibiting a higher MIC range. 5,18,25,26 However, in our study, we detected only a single gene mutation.…”

“…26 Recent studies have shown that these uncommon gene mutations may be susceptible or have low-/high-level resistance to isoniazid. 5,26 WHO recommends that DSTs of both phenotypes and genotypes should be used for all isolates.…”

“…3 Isoniazid resistance in Mycobacterium tuberculosis (MTB) is associated with mutations of katG, inhA, ahpC promoter, and fabG1 genes. 4 However, katG is the major isoniazid-resistant gene mutation found in 40%-95% of the clinical TB isolates, [5][6][7] and katG S315T is the most frequently mutated gene found in isolates with a high level of isoniazid resistance. 8 katG gene encodes catalase/peroxidase enzymes that activate isoniazid to become an active drug.…”

“…4 Another mechanism that causes low levels of isoniazid resistance is the inhA mutation, which is found in 20%-42% of the clinical TB isolates, and results in overexpression of isoniazid's target and tends to increase the minimal inhibitory concentration (MIC). 5 It also confers resistance to second-line drugs (ethionamide and prothionamide) as they share the same target site. 9,10 WHO treatment guidelines, 2019, recommend treating patients with confirmed HR-TB with rifampicin, ethambutol, pyrazinamide, and levofloxacin (6REZ-Lfx) for 6 months.…”

Isoniazid resistance in Mycobacterium tuberculosis is a heterogeneous phenotype comprised of overlapping MIC distributions with different underlying resistance mechanisms

“…Therefore, in most settings misclassifications of double mutants would be rare compared with the increased ability to detect inhA promoter mutants with a higher clinical breakpoint. Second, the effect of these coding mutations on the INH MIC and thus clinical outcome is likely modest at worst, but more MIC data are needed for the mutations at different inhA codons (20-23). Nevertheless, it might be advisable for countries that conduct routine WGS to err on the side of caution by classifying these double mutants as high-level resistant until clinical data to the contrary are available (in practice, however, it would be challenging to conduct a sufficiently powered study to address this question as these mutations are so rare).…”