Whole-genome sequencing of rifampicin-resistant Mycobacterium tuberculosis strains identifies compensatory mutations in RNA polymerase genes

Abstract

Drug-resistant bacteria are emerging worldwide, despite frequently being less fit than drug-susceptible strains1. Data from model systems suggest the fitness cost of antimicrobial resistance can be mitigated by compensatory mutations2. However, current evidence that compensatory evolution plays any significant role in the success of drug-resistant bacteria in human populations is weak3–6. Here we describe a set of novel compensatory mutations in the RNA polymerase of rifampicin-resistant Mycobacterium tuberculosis, the etiologic agent of human tuberculosis (TB). M. tuberculosis strains harbouring these compensatory mutations exhibited a high competitive fitness in vitro. Moreover, these mutations were associated with high in vivo fitness as determined by their relative clinical frequency across patient populations. Importantly, in countries with the world’s highest incidence of multidrug-resistant (MDR) TB7, more than 30% of MDR clinical isolates had such a mutation. Our findings support a role for compensatory evolution in the global epidemics of MDR-TB8.

Insights into the processes that drive the evolution of drug resistance in Mycobacterium tuberculosis

“…In M. tuberculosis, data on compensatory mutations are still limited and mainly focused on isoniazid and rifampicin resistance (Comas et al., 2012; Sherman et al., 1996; Song et al., 2014; de Vos et al., 2013). Nevertheless, mechanisms of compensatory evolution were also proposed for other drug resistance genotypes (Table 3).…”

“…Therefore, it was hypothesized that the fitness cost linked to rifampicin resistance could be reduced by compensatory mutations in clinical isolates (Billington et al., 1999; Comas et al., 2012; Mariam et al., 2004; de Vos et al., 2013). Nonsynonymous mutations in the rpo A and rpo C genes that encode the α and β’ subunits of RNA polymerase, respectively, could play the role of fitness‐compensatory mutations in rifampicin‐resistant rpo B mutants (Comas et al., 2012; de Vos et al., 2013).…”

“…Therefore, it was hypothesized that the fitness cost linked to rifampicin resistance could be reduced by compensatory mutations in clinical isolates (Billington et al., 1999; Comas et al., 2012; Mariam et al., 2004; de Vos et al., 2013). Nonsynonymous mutations in the rpo A and rpo C genes that encode the α and β’ subunits of RNA polymerase, respectively, could play the role of fitness‐compensatory mutations in rifampicin‐resistant rpo B mutants (Comas et al., 2012; de Vos et al., 2013). Indeed, it was reported that part of rifampicin‐resistant isolates with a rpo B mutation also carry a nonsynonymous mutation in the rpo A or rpo C gene in South Africa (27.1%, 89/329), China (27.8%, 89/320) and Korea (39.4%, 67/170) (Comas et al., 2012; Li et al., 2016; Song et al., 2014).…”

“…Nonsynonymous mutations in the rpo A and rpo C genes that encode the α and β’ subunits of RNA polymerase, respectively, could play the role of fitness‐compensatory mutations in rifampicin‐resistant rpo B mutants (Comas et al., 2012; de Vos et al., 2013). Indeed, it was reported that part of rifampicin‐resistant isolates with a rpo B mutation also carry a nonsynonymous mutation in the rpo A or rpo C gene in South Africa (27.1%, 89/329), China (27.8%, 89/320) and Korea (39.4%, 67/170) (Comas et al., 2012; Li et al., 2016; Song et al., 2014). In addition, clinical isolates that carry mutations in the RRDR of rpo B and also in rpo A/ rpo C display higher competitive fitness in vitro and in vivo compared with laboratory‐generated rifampicin‐resistant mutants that carry only the same rpo B RRDR mutation and that belong to the same phylogenetic lineage (Brandis & Hughes, 2013; Comas et al., 2012; Song et al., 2014).…”

“…Indeed, it was reported that part of rifampicin‐resistant isolates with a rpo B mutation also carry a nonsynonymous mutation in the rpo A or rpo C gene in South Africa (27.1%, 89/329), China (27.8%, 89/320) and Korea (39.4%, 67/170) (Comas et al., 2012; Li et al., 2016; Song et al., 2014). In addition, clinical isolates that carry mutations in the RRDR of rpo B and also in rpo A/ rpo C display higher competitive fitness in vitro and in vivo compared with laboratory‐generated rifampicin‐resistant mutants that carry only the same rpo B RRDR mutation and that belong to the same phylogenetic lineage (Brandis & Hughes, 2013; Comas et al., 2012; Song et al., 2014). These data suggest that mutations in the rpo A/ rpo C genes are fitness‐compensatory mutations that alleviate the costs of rpo B mutations.…”