Identification and Characterization of Genetic Determinants of Isoniazid and Rifampicin Resistance in Mycobacterium tuberculosis in Southern India

Abstract

Drug-resistant tuberculosis (TB), one of the leading causes of death worldwide, arises mainly from spontaneous mutations in the genome of Mycobacterium tuberculosis . There is an urgent need to understand the mechanisms by which the mutations confer resistance in order to identify new drug targets and to design new drugs. Previous studies have reported numerous mutations that confer resistance to anti-TB drugs, but there has been little systematic analysis to understand their genetic background and the potential impacts on the drug target stability and/or interactions. Here, we report the analysis of whole-genome sequence data for 98 clinical M. tuberculosis isolates from a city in southern India. The collection was screened for phenotypic resistance and sequenced to mine the genetic mutations conferring resistance to isoniazid and rifampicin. The most frequent mutation among isoniazid and rifampicin isolates was S315T in katG and S450L in rpoB respectively. The impacts of mutations on protein stability, protein-protein interactions and protein-ligand interactions were analysed using both statistical and machine-learning approaches. Drug-resistant mutations were predicted not only to target active sites in an orthosteric manner, but also to act through allosteric mechanisms arising from distant sites, sometimes at the protein-protein interface.

The mismatch repair system (mutS and mutL) in Acinetobacter baylyi ADP1

“…Drug-resistant mutations in rpoB were mostly located in the 81-bp region of rpoB (rifampicin resistance determining region, RRDR). These rpoB mutations often come with fitness costs [20]. In this study, we reported the fitness cost of 14 types of rpoB base substitution and one type of 12-bp insertion.…”

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

“…A previous report found a high prevalence of the katG S315T gene mutation among HR-TB/MDR-TB/XDR-TB strains (58.7%-68.6%) in Thailand. 16,17 The prevalence of katG S315T varied according to the geographic region: Southeast Asia (78.4%), 18 Vietnam (85.3%), 19 Myanmar (61.2%), 20 Taiwan (29.3%), 6 Japan (25%), 10 India (67.6%), 21 Sri Lanka (67.8%), 22 Romania (52.8%), 23 Cameroon (64%), 24 and the United States (38%). 8 The different ranges of MIC found for each mutation gene can be explained by gene variation.…”

Genomics, Computational Biology and Drug Discovery for Mycobacterial Infections: Fighting the Emergence of Resistance

“…Mutations in the KatG and InhA are responsible for the mechanism of resistance to INH. We have mapped the resistance mutations in KatG and InhA onto their protein structures and predicted the effects on protein stability, protein-protein interactions and protein-drug interactions using SDM and mCSM (Munir et al, 2019).…”

“…These mutations were also found to alter the interactions either with the drug or the surrounding residues, and were predicted by mCSM-lig to decrease the affinity of the drug toward the protein. We also analyzed the impact of four mutations (L516P, N416T, V483G, and I491T) on RpoC, which are located at the interfaces with other subunits in RNA polymerase complex (Munir et al, 2019). These mutations were predicted to have a destabilizing impact on protein stability and protein-protein interactions.…”

“…However, the fact that these drugs must be taken for 6 months often leads to non-compliance, resulting in further spread of the disease and the development of drug resistance. In the case of tuberculosis multidrug-resistant (MDR)-TB (resistant to INH and rifampin) and extensive-drug-resistant (XDR)-TB strains require the use of second-line drugs that are much more toxic and expensive (Wallis et al, 2016;Munir et al, 2019). This has been further complicated by the HIV over the past four decades.…”