Whole-genome sequencing of rifampicin-resistant Mycobacterium tuberculosis strains identifies compensatory mutations in RNA polymerase genes
- Journal name:
- Nature Genetics
- Year published:
- (2011)
- DOI:
- doi:10.1038/ng.1038
- Received
- Accepted
- Published online
Epidemics of drug-resistant bacteria emerge worldwide, even as resistant strains frequently have reduced fitness compared to their drug-susceptible counterparts1. Data from model systems suggest that the fitness cost of antimicrobial resistance can be reduced by compensatory mutations2; however, there is limited evidence that compensatory evolution has any significant role in the success of drug-resistant bacteria in human populations3, 4, 5, 6. Here we describe a set of compensatory mutations in the RNA polymerase genes of rifampicin-resistant M. tuberculosis, the etiologic agent of human tuberculosis (TB). M. tuberculosis strains harboring these compensatory mutations showed a high competitive fitness in vitro. Moreover, these mutations were associated with high fitness in vivo, as determined by examining their relative clinical frequency across patient populations. Of note, in countries with the world's highest incidence of multidrug-resistant (MDR) TB7, more than 30% of MDR clinical isolates had this form of mutation. Our findings support a role for compensatory evolution in the global epidemics of MDR TB8.
Figures at a glance
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Figure 1: Putative compensatory mutations in rpoA and rpoC of M. tuberculosis. (a,b) Mutations identified after genome sequencing of experimentally evolved strains (circle) or paired clinical isolates (triangles) are indicated above the gene diagrams of rpoA (a) and rpoC (b). Mutations identified by screening a global and a high-burden collection of MDR strains are indicated by stars below the gene diagrams. Colors indicate the respective strain lineage (blue, lineage 2; red, lineage 4; brown, lineage 5; pink, lineage 1). Some of these mutations occurred in multiple lineages or affect the same codon position.Figure 2: Putative compensatory mutations in rpoA and rpoC fall in regions encoding the interface of the RNA polymerase subunits. Amino acid substitutions identified in rifampicin-resistant experimentally evolved isolates and paired clinical isolates were mapped onto the structure of the E. coli RNA polymerase. The alterations are localized to residues of RpoA (light blue) and RpoC (orange) that are predicted to have roles in RNA polymerase subunit interaction. Residue numbers are indicated according to M. tuberculosis coordinates. RpoA (α subunit), blue; RpoB (β subunit), red; RpoC (β′ subunit), yellow; RpoD (σ subunit), green.Figure 3: Experimental and clinical relevance of putative compensatory mutations. (a) Experimental competitive fitness of ten clinical isolates that acquired rifampicin resistance over the course of treatment compared to their susceptible counterparts. The amino acid changes encoded by HCMs are indicated in the pair in which they were identified. Bar colors indicate strain lineage (blue, lineage 2; red, lineage 4). (b) Difference in relative fitness between ten rifampicin-resistant paired clinical isolates compared to laboratory-generated mutants carrying the same rifampicin resistance–conferring mutation and with the same genetic background as defined by strain lineage. Data are shown for clinical strains with or without an HCM. Horizontal lines indicate median fitness differences. (c) Time in months between the isolation of the first and the second strain of each clinical pair. Horizontal lines indicate the median time intervals. (d) Percentage of MDR strains with putative compensatory mutations in rpoA or rpoC. Gray bars, the percentage of strains carrying HCMs; black bars, strains carrying any putative compensatory mutation. Data for a global collection of strains and for regions of Abkhazia/Georgia, Uzbekistan and Kazakhstan with high MDR TB burden are shown.
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