Parallel Evolution in Pseudomonas aeruginosa over 39,000 Generations In Vivo

Abstract

The Gram-negative bacterium Pseudomonas aeruginosa is a common cause of chronic airway infections in individuals with the heritable disease cystic fibrosis (CF). After prolonged colonization of the CF lung, P. aeruginosa becomes highly resistant to host clearance and antibiotic treatment; therefore, understanding how this bacterium evolves during chronic infection is important for identifying beneficial adaptations that could be targeted therapeutically. To identify potential adaptive traits of P. aeruginosa during chronic infection, we carried out global transcriptomic profiling of chronological clonal isolates obtained from 3 individuals with CF. Isolates were collected sequentially over periods ranging from 3 months to 8 years, representing up to 39,000 in vivo generations. We identified 24 genes that were commonly regulated by all 3 P. aeruginosa lineages, including several genes encoding traits previously shown to be important for in vivo growth. Our results reveal that parallel evolution occurs in the CF lung and that at least a proportion of the traits identified are beneficial for P. aeruginosa chronic colonization of the CF lung.

Evolutionary dynamics of bacteria in a human host environment

“…The striking similarity between the phenotypes of DK2 isolates sampled from different CF patients suggests that the host environments represent parallel selective conditions by which evolution is directed. Such parallelism is expected to generate parallel evolution (20), and a search for signs of independent evolution of the same traits in the isolates confirms this. In the case of two phenotypes that evolved independently in the CF173 and CF333 isolates after their early separation from CF30-1979, we were able to identify the genetic details: (i) The lost capacity of both isolates to catabolize 4-hydroxyphenylacetic acid (4-HPA), a trait identified in the Biolog phenotypic arrays, is associated with similar-but not identical-genetic changes (Fig.…”

“…3 and Table S1). Because the CF infection process is associated with the appearance of phenotypes of which many are not usually observed among environmental, wild-type isolates of this species (18)(19)(20), we predict that the immediate ancestor to the DK2 lineage entered the CF environment shortly before the first sampling in 1973. Because the original infecting DK2 strain is unavailable for analysis, we cannot precisely determine the pre-1973 events that resulted in genomic diversity among the isolates sampled in 1973.…”

The spatial profiles and metabolic capabilities of microbial populations impact the growth of antibiotic-resistant mutants

“…These organisms include known co-pathogens with P. aeruginosa as well as 17 clinical isolates of P. aeruginosa from CF patients [16]. All bacteria tested produce inhibition (table 1; electronic supplementary material, figures S14-S16 and table S2).…”

“…Pseudomonas strains P. aeruginosa (WT PA14, WT PAO1) laboratory strains clinical P. aeruginosa strains (17) cystic fibrosis isolates [16] sandgrass isolate uncharacterized environmental isolate P. fluorescens environmental isolate…”

“…P. aeruginosa strain PAO1, 17 clinical Pseudomonas isolates [16], Pseudomonas sandgrass isolate, P. fluorescens, methicillin-resistant Staphylococcus aureus Mu50 [17], Escherichia coli DH5a, Burkholderia cepacia and Dphz1/2 mutant [18] (gifts from Whiteley, UT Austin), Serratia marcescens (gift from Rasika Harshey, UT Austin) and Saccharomyces cerevisiae S288C (gift from Edward Marcotte, UT Austin).…”