Nonmutational compensation of the fitness cost of antibiotic resistance in mycobacteria by overexpression of tlyA rRNA methylase

Abstract

Several studies over the last few decades have shown that antibiotic resistance mechanisms frequently confer a fitness cost and that these costs can be genetically ameliorated by intra- or extragenic second-site mutations, often without loss of resistance. Another, much less studied potential mechanism by which the fitness cost of antibiotic resistance could be reduced is via a regulatory response where the deleterious effect of the resistance mechanism is lowered by a physiological alteration that buffers the mutational effect. In mycobacteria, resistance to the clinically used tuberactinomycin antibiotic capreomycin involves loss-of-function mutations in rRNA methylase TlyA or point mutations in 16S rRNA (in particular the A1408G mutation). Both of these alterations result in resistance by reducing drug binding to the ribosome. Here we show that alterations of tlyA gene expression affect both antibiotic drug susceptibility and fitness cost of drug resistance. In particular, we demonstrate that the common resistance mutation A1408G is accompanied by a physiological change that involves increased expression of the tlyA gene. This gene encodes an enzyme that methylates neighboring 16S rRNA position C1409, and as a result of increased TlyA expression the fitness cost of the A1408G mutation is significantly reduced. Our findings suggest that in mycobacteria, a nonmutational mechanism (i.e., gene regulatory) can restore fitness to genetically resistant bacteria. Our results also point to a new and clinically relevant treatment strategy to combat evolution of resistance in multidrug-resistant tuberculosis. Thus, by utilizing antagonistic antibiotic interactions, resistance evolution could be reduced.

Using genomics to understand the origin and dispersion of multidrug and extensively drug resistant tuberculosis in Portugal

“…Interestingly, the microevolutionary trajectory of M. tuberculosis Lisboa3 strains is set down a path that favoured the acquisition of mutations in eis promoter region and, in one sub-branch, resistance to CAP has emerged subsequently by a tlyA frameshift mutation due to a binucleotidic insertion. Increased TlyA levels are proposed to comprise a new resistance compensation mechanism upon development of rrs mutations associated with resistance to SLIDs 53 . Contrarily to a second eis G-10A sub-branch in the Lisboa3 clade, where at least one isolate was found to have acquired a rrs A1401G mutation that potentially leads to higher KAN/AMK resistance levels and CAP resistance, this was never observed for isolates which bear the tlyA Ins755GT.…”

In vivo virulence of Beijing genotype Mycobacterium tuberculosis

“…Включенные в исследование клинические штаммы генотипа Beijing обладали схожим профилем фенотипической и генетической лекарственной устойчивости, что позволило минимизировать диспропорцию в экспериментальных данных, вызванную снижением жизнеспособности лекарственно-устойчивых бактерий. В частности, в модельных экспериментах на морских свинках было продемонстрировано снижение вирулентности у изониазид-устойчивых штаммов [9,33], схожие закономерности были найдены в случае устойчивости к рифампицину [16,24], аминогликозидам [15,34] и фторхинолонам [31].…”

Whole genome sequencing for drug resistance profile prediction inMycobacterium tuberculosis

“…Furthermore, the strain genetic background [24], non-mutational mechanisms (e.g. modulation of gene expression) [25], as well as drug efflux mechanisms [26] may contribute to the variability in increase of the MIC conferred by resistance mutations.…”

“…In addition, non-mutational processes (e.g. alteration of gene expression) may compensate for fitness costs of drug resistance and at the same time alter the MIC for the drug [25]. This has not been demonstrated for streptomycin resistance in M. tuberculosis , but it seems possible that compensation of fitness costs in MDR phenotypes might alter the MIC for streptomycin [30], considering that streptomycin is not part of the current standard treatment regimen and selection for high-level streptomycin resistance is relaxed.…”