Environmental Heterogeneity Drives Within-Host Diversification and Evolution of Pseudomonas aeruginosa

TY - JOUR

T1 - Environmental Heterogeneity Drives Within-Host Diversification and Evolution of Pseudomonas aeruginosa

AU - Markussen, Trine

AU - Marvig, Rasmus Lykke

AU - Gómez-Lozano, María

AU - Aanæs, Kasper

AU - Burleigh, Alexandra E

AU - Høiby, Niels

AU - Johansen, Helle Krogh

AU - Molin, Søren

AU - Jelsbak, Lars

N1 - Copyright © 2014 Markussen et al.

PY - 2014/9/16

Y1 - 2014/9/16

N2 - Microbial population polymorphisms are commonly observed in natural environments, including long-term infected hosts. However, the underlying processes promoting and stabilizing diversity are difficult to unravel and are not well understood. Here, we use chronic infection of cystic fibrosis airways by the opportunistic pathogen Pseudomonas aeruginosa as a system for investigating bacterial diversification processes during the course of infection. We analyze clonal bacterial isolates sampled during a 32-year period and map temporal and spatial variations in population diversity to different infection sites within the infected host. We show that the ancestral infecting strain diverged into distinct sublineages, each with their own functional and genomic signatures and rates of adaptation, immediately after initial colonization. The sublineages coexisted in the host for decades, suggesting rapid evolution of stable population polymorphisms. Critically, the observed generation and maintenance of population diversity was the result of partitioning of the sublineages into physically separated niches in the CF airway. The results reveal a complex within-host population structure not previously realized and provide evidence that the heterogeneity of the highly structured and complex host environment promotes the evolution and long-term stability of pathogen population diversity during infection.IMPORTANCE: Within-host pathogen evolution and diversification during the course of chronic infections is of importance in relation to therapeutic intervention strategies, yet our understanding of these processes is limited. Here, we investigate intraclonal population diversity in P. aeruginosa during chronic airway infections in cystic fibrosis patients. We show the evolution of a diverse population structure immediately after initial colonization, with divergence into multiple distinct sublineages that coexisted for decades and occupied distinct niches. Our results suggest that the spatial heterogeneity in CF airways plays a major role in relation to the generation and maintenance of population diversity and emphasize that a single isolate in sputum may not represent the entire pathogen population in the infected individual. A more complete understanding of the evolution of distinct clonal variants and their distribution in different niches could have positive implications for efficient therapy.

AB - Microbial population polymorphisms are commonly observed in natural environments, including long-term infected hosts. However, the underlying processes promoting and stabilizing diversity are difficult to unravel and are not well understood. Here, we use chronic infection of cystic fibrosis airways by the opportunistic pathogen Pseudomonas aeruginosa as a system for investigating bacterial diversification processes during the course of infection. We analyze clonal bacterial isolates sampled during a 32-year period and map temporal and spatial variations in population diversity to different infection sites within the infected host. We show that the ancestral infecting strain diverged into distinct sublineages, each with their own functional and genomic signatures and rates of adaptation, immediately after initial colonization. The sublineages coexisted in the host for decades, suggesting rapid evolution of stable population polymorphisms. Critically, the observed generation and maintenance of population diversity was the result of partitioning of the sublineages into physically separated niches in the CF airway. The results reveal a complex within-host population structure not previously realized and provide evidence that the heterogeneity of the highly structured and complex host environment promotes the evolution and long-term stability of pathogen population diversity during infection.IMPORTANCE: Within-host pathogen evolution and diversification during the course of chronic infections is of importance in relation to therapeutic intervention strategies, yet our understanding of these processes is limited. Here, we investigate intraclonal population diversity in P. aeruginosa during chronic airway infections in cystic fibrosis patients. We show the evolution of a diverse population structure immediately after initial colonization, with divergence into multiple distinct sublineages that coexisted for decades and occupied distinct niches. Our results suggest that the spatial heterogeneity in CF airways plays a major role in relation to the generation and maintenance of population diversity and emphasize that a single isolate in sputum may not represent the entire pathogen population in the infected individual. A more complete understanding of the evolution of distinct clonal variants and their distribution in different niches could have positive implications for efficient therapy.

KW - Adaptation, Physiological

KW - Cloning, Molecular

KW - Cystic Fibrosis

KW - Environment

KW - Evolution, Molecular

KW - Genes, Bacterial

KW - Genetics, Population

KW - Genomics

KW - Host-Pathogen Interactions

KW - Humans

KW - Phenotype

KW - Phylogeny

KW - Polymorphism, Single Nucleotide

KW - Pseudomonas Infections

KW - Pseudomonas aeruginosa

KW - Quorum Sensing

KW - Respiratory System

KW - Sequence Analysis, DNA

KW - Sputum

U2 - 10.1128/mBio.01592-14

DO - 10.1128/mBio.01592-14

M3 - Journal article

C2 - 25227464

SN - 2161-2129

VL - 5

SP - 1

EP - 10

JO - mBio

JF - mBio

IS - 5

M1 - e01592-14

ER -