Systematic review of allelic exchange experiments aimed at identifying mutations that confer drug resistance in Mycobacterium tuberculosis

Abstract

This systematic review highlights those mutations that have been shown to causally change phenotypic resistance in M. tuberculosis and brings attention to a notable lack of allelic exchange data for several of the genes known to be associated with drug resistance.

Predicting Extensively Drug-Resistant Mycobacterium tuberculosis Phenotypes with Genetic Mutations

“…In contrast to the established low-MIC SNPs described above, the rpoB 531TCG¡TTG and 526CAC¡TAC/526CAC¡CGC SNPs that we observed are documented to be high-MIC mutations in both solid and liquid media (29,31,33). The single instances of these mutations we observed occurring in two isolates designated susceptible by MGIT 960 DST (Table 4) were possibly the result of DST errors.…”

“…It is important to note, however, that not all rpoB SNPs confer the same level of resistance. Certain rpoB mutations, such as the 516GAC¡TAC and 526CAC¡AAC mutations that we observed, appear to confer low-level resistance, as measured by the low MICs of the isolates (29). These MICs are usually just below or distributed across the WHO critical concentration for liquid DST, which means these isolates can go undetected by MGIT 960 DST and appear to be susceptible (31)(32)(33).…”

“…However, the interpretation of these data is complicated by the complex phenotypes that have been observed in isolates with these mutations. It has been well documented that most SNPs in the 81-bp resistancedetermining region (RDR) of the rpoB gene confer phenotypic RIF r (28,29). Thus, molecular diagnostics that detect rpoB mutations, such as the LPAs and the GeneXpert assay, have demonstrated high sensitivities and specificities as tools for predicting phenotypic RIF r in clinical samples (9,30).…”

Gyrase Mutations Are Associated with Variable Levels of Fluoroquinolone Resistance in Mycobacterium tuberculosis

“…We found the gyrA mutations A90V and D94A to have a smaller effect on the moxifloxacin MIC than the gyrA D94G mutation, but we did not observe a similar difference for ofloxacin. Previous studies have also found gyrA A90V to have a weaker effect on moxifloxacin resistance, including allelic exchange experiments, where the ofloxacin MIC was found to be in the 2-to 4-mg/liter range and the moxifloxacin MIC was consistently Յ1 mg/liter and sensitive by current WHO standards (36)(37)(38). We could not find any experimental or allelic exchange data on the effect of D94A on fluoroquinolone resistance, but this mutation is regarded as a canonical cause for any fluoroquinolone resistance in MTB (38)(39)(40).…”

Evaluation of Pyrosequencing for Detecting Extensively Drug-Resistant Mycobacterium tuberculosis among Clinical Isolates from Four High-Burden Countries

“…However, the SNPs detected in these isolates are well documented to impart only lowlevel resistance (Ͻ1 g/ml), which means that these isolates may appear RIF susceptible by MGIT 960 DST but could appear resistant on solid culture. The clinical relevance of these mutations is still unclear (17,31,32). For this reason, these isolates were not considered test discordant but rather "genotypically indeterminate" and were excluded from our specificity calculation.…”