Evolution of Antibiotic Tolerance Shapes Resistance Development in Chronic Pseudomonas aeruginosa Infections

Abstract

The widespread use of antibiotics promotes the evolution and dissemination of resistance and tolerance mechanisms. To assess the relevance of tolerance and its implications for resistance development, we used in vitro evolution and analyzed the inpatient microevolution of Pseudomonas aeruginosa, an important human pathogen causing acute and chronic infections. We show that the development of tolerance precedes and promotes the acquisition of resistance in vitro, and we present evidence that similar processes shape antibiotic exposure in human patients. Our data suggest that during chronic infections, P. aeruginosa first acquires moderate drug tolerance before following distinct evolutionary trajectories that lead to high-level multidrug tolerance or to antibiotic resistance. Our studies propose that the development of antibiotic tolerance predisposes bacteria for the acquisition of resistance at early stages of infection and that both mechanisms independently promote bacterial survival during antibiotic treatment at later stages of chronic infections. IMPORTANCE Over the past decades, pan-resistant strains of major bacterial pathogens have emerged and have rendered clinically available antibiotics ineffective, putting at risk many of the major achievements of modern medicine, including surgery, cancer therapy, and organ transplantation. A thorough understanding of processes leading to the development of antibiotic resistance in human patients is thus urgently needed. We show that drug tolerance, the ability of bacteria to survive prolonged exposure to bactericidal antibiotics, rapidly evolves in the opportunistic human pathogen Pseudomonas aeruginosa upon recurrent exposures to antibiotics. Our studies show that tolerance protects P. aeruginosa against different classes of antibiotics and that it generally precedes and promotes resistance development. The rapid evolution of tolerance during treatment regimens may thus act as a strong driving force to accelerate antibiotic resistance development. To successfully counter resistance, diagnostic measures and novel treatment strategies will need to incorporate the important role of antibiotic tolerance.

Novel Daptomycin Tolerance and Resistance Mutations in Methicillin-Resistant Staphylococcus aureus from Adaptive Laboratory Evolution

“…Indeed, consistent with previous in vitro evolution studies in E. coli ( 18 ) and Pseudomonas aeruginosa ( 61 ) which reported that tolerance precedes resistance, we also observed that a tolerant mutant (TOL2) appeared in an earlier cycle than a resistant mutant (RES2) in lineage 2 ( Fig. 1b and c ).…”

Coming from the Wild: Multidrug Resistant Opportunistic Pathogens Presenting a Primary, Not Human-Linked, Environmental Habitat

“…Different conditions, compounds and modes of growth that may take place during the infection process might transiently increase the resistance of this opportunistic pathogen to several antimicrobial treatments, thus hindering the eradication of the infecting bacterial population. Further, recent work has shown that the early appearance of tolerance mutations facilitates the evolution of AR [ 110 ], a feature of particular relevance in the case of chronic P. aeruginosa infections [ 111 ].…”

Polymicrobial Interactions in the Cystic Fibrosis Airway Microbiome Impact the Antimicrobial Susceptibility of Pseudomonas aeruginosa

“…Genes associated with QS, iron acquisition, phenazine biosynthesis, and multidrug efflux were shown to have mutated to promote survival and progression to chronic infection [62]. Chronic colonisation is associated with genotypic and phenotypic changes, such as reduced QS [63], metabolism [64], and motility [65] and overproduction of alginate [66] and increased antibiotic resistance [67,68]. During the chronic colonisation stage, P. aeruginosa changes from a non-mucoid motile phenotype to a mucoid biofilm former that is capable of evading host responses and antibiotics, at which point it becomes very difficult to eradicate.…”