title: Environmental heterogeneity drives within-host diversification and evolution of Pseudomonas aeruginosa.
abstract: 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.
  
  
  OBJECTIVE
  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.
authors.affiliation: Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark.
authors.forename: Trine
authors.initials: T
authors.lastname: Markussen
authors.affiliation: Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark.
authors.forename: Rasmus Lykke
authors.initials: RL
authors.lastname: Marvig
authors.affiliation: Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark.
authors.forename: María
authors.initials: M
authors.lastname: Gómez-Lozano
authors.affiliation: Department of Otorhinolaryngology, Head and Neck Surgery, Rigshospitalet and Faculty of Health Sciences, Copenhagen, Denmark.
authors.forename: Kasper
authors.initials: K
authors.lastname: Aanæs
authors.affiliation: Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark.
authors.forename: Alexandra E
authors.initials: AE
authors.lastname: Burleigh
authors.forename: Niels
authors.initials: N
authors.lastname: Høiby
authors.affiliation: Department of Clinical Microbiology, University Hospital, Rigshospitalet, Copenhagen, Denmark.
authors.forename: Helle Krogh
authors.initials: HK
authors.lastname: Johansen
authors.affiliation: Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark lj@bio.dtu.dk sm@bio.dtu.dk.
authors.forename: Søren
authors.initials: S
authors.lastname: Molin
authors.affiliation: Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark lj@bio.dtu.dk sm@bio.dtu.dk.
authors.forename: Lars
authors.initials: L
authors.lastname: Jelsbak
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics*; D003001:Cloning, Molecular; D003550:Cystic Fibrosis / Q000382:microbiology; D004777:Environment; D019143:Evolution, Molecular; D005798:Genes, Bacterial; D005828:Genetics, Population; D023281:Genomics; D054884:Host-Pathogen Interactions / Q000235:genetics*; D006801:Humans; D010641:Phenotype; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D011552:Pseudomonas Infections / Q000382:microbiology; D011550:Pseudomonas aeruginosa / Q000145:classification / Q000235:genetics* / Q000302:isolation & purification; D053038:Quorum Sensing / Q000502:physiology; D012137:Respiratory System; D017422:Sequence Analysis, DNA; D013183:Sputum / Q000382:microbiology