Parallel evolution of tobramycin resistance across species and environments

Abstract

AbstractAn important problem in evolution is identifying the genetic basis of how different species adapt to similar environments. Understanding how various bacterial pathogens evolve in response to antimicrobial treatment is a pressing example of this problem, where discovery of molecular parallelism could lead to clinically useful predictions. Evolution experiments with pathogens in environments containing antibiotics combined with periodic whole population genome sequencing can be used to characterize the evolutionary dynamics of the pathways to antimicrobial resistance. We separately propagated two clinically relevant Gram-negative pathogens,Pseudomonas aeruginosaandAcinetobacter baumannii, in increasing concentrations of tobramycin in two different environments each: planktonic and biofilm. Independent of the pathogen, populations adapted to tobramycin selection by parallel evolution of mutations infusA1, encoding elongation factor G, andptsP, encoding phosphoenolpyruvate phosphotransferase. As neither gene is a direct target of this aminoglycoside, both are relatively novel and underreported causes of resistance. Additionally, both species acquired antibiotic-associated mutations that were more prevalent in the biofilm lifestyle than planktonic, in electron transport chain components inA. baumanniiand LPS biosynthesis enzymes inP. aeruginosapopulations. Using existing databases, we discovered bothfusA1andptsPmutations to be prevalent in antibiotic resistant clinical isolates. Additionally, we report site-specific parallelism offusA1mutations that extend across several bacterial phyla. This study suggests that strong selective pressures such as antibiotic treatment may result in high levels of predictability in molecular targets of evolution despite differences between organisms’ genetic background and environment.