Genomics of Adaptation during Experimental Evolution of the Opportunistic Pathogen Pseudomonas aeruginosa

Adaptation is likely to be an important determinant of the success of many pathogens,for example when colonizing a new host species,when challenged by antibiotic treatment,or in governing the establishment and progress of long-term chronic infection. yet,the genomic basis of adaptation is poorly understood in general,and for pathogens in particular. we investigated the genetics of adaptation to cystic fibrosis-like culture conditions in the presence and absence of fluoroquinolone antibiotics using the opportunistic pathogen pseudomonas aeruginosa. whole-genome sequencing of experimentally evolved isolates revealed parallel evolution at a handful of known antibiotic resistance genes. while the level of antibiotic resistance was largely determined by these known resistance genes,the costs of resistance were instead attributable to a number of mutations that were specific to individual experimental isolates. notably,stereotypical quinolone resistance mutations in dna gyrase often co-occurred with other mutations that,together,conferred high levels of resistance but no consistent cost of resistance. this result may explain why these mutations are so prevalent in clinical quinolone-resistant isolates. in addition,genes involved in cyclic-di-gmp signalling were repeatedly mutated in populations evolved in viscous culture media,suggesting a shared mechanism of adaptation to this cf-like growth environment. experimental evolutionary approaches to understanding pathogen adaptation should provide an important complement to studies of the evolution of clinical isolates. © 2012 wong et al.