title: Coexistence and within-host evolution of diversified lineages of hypermutable Pseudomonas aeruginosa in long-term cystic fibrosis infections.
abstract: The advent of high-throughput sequencing techniques has made it possible to follow the genomic evolution of pathogenic bacteria by comparing longitudinally collected bacteria sampled from human hosts. Such studies in the context of chronic airway infections by Pseudomonas aeruginosa in cystic fibrosis (CF) patients have indicated high bacterial population diversity. Such diversity may be driven by hypermutability resulting from DNA mismatch repair system (MRS) deficiency, a common trait evolved by P. aeruginosa strains in CF infections. No studies to date have utilized whole-genome sequencing to investigate within-host population diversity or long-term evolution of mutators in CF airways. We sequenced the genomes of 13 and 14 isolates of P. aeruginosa mutator populations from an Argentinian and a Danish CF patient, respectively. Our collection of isolates spanned 6 and 20 years of patient infection history, respectively. We sequenced 11 isolates from a single sample from each patient to allow in-depth analysis of population diversity. Each patient was infected by clonal populations of bacteria that were dominated by mutators. The in vivo mutation rate of the populations was ∼100 SNPs/year-∼40-fold higher than rates in normo-mutable populations. Comparison of the genomes of 11 isolates from the same sample showed extensive within-patient genomic diversification; the populations were composed of different sub-lineages that had coexisted for many years since the initial colonization of the patient. Analysis of the mutations identified genes that underwent convergent evolution across lineages and sub-lineages, suggesting that the genes were targeted by mutation to optimize pathogenic fitness. Parallel evolution was observed in reduction of overall catabolic capacity of the populations. These findings are useful for understanding the evolution of pathogen populations and identifying new targets for control of chronic infections.
authors.affiliation: Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), CONICET, Departamento de Química Biológica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina.
authors.forename: Sofía
authors.initials: S
authors.lastname: Feliziani
authors.affiliation: Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark.
authors.forename: Rasmus L
authors.initials: RL
authors.lastname: Marvig
authors.affiliation: Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), CONICET, Departamento de Química Biológica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina; Daphne du Maurier, Centre for Ecology and Conservation, College of Life and Environmental Sciences, University of Exeter, Cornwall Campus, Cornwall, United Kingdom.
authors.forename: Adela M
authors.initials: AM
authors.lastname: Luján
authors.affiliation: Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), CONICET, Departamento de Química Biológica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina.
authors.forename: Alejandro J
authors.initials: AJ
authors.lastname: Moyano
authors.affiliation: Estadística y Biometría, Facultad de Ciencias Agropecuarias, Universidad Nacional de Córdoba, Córdoba, Argentina.
authors.forename: Julio A
authors.initials: JA
authors.lastname: Di Rienzo
authors.affiliation: Department of Clinical Microbiology 9301, Rigshospitalet, Copenhagen University Hospital, Copenhagen, and The Novo Nordisk Foundation Centre for Biosustainability, Hørsholm, Technical University of Denmark, Denmark.
authors.forename: Helle
authors.initials: H
authors.lastname: Krogh Johansen
authors.affiliation: Department of Systems Biology, Technical University of Denmark, Lyngby, Denmark.
authors.forename: Søren
authors.initials: S
authors.lastname: Molin
authors.affiliation: Centro de Investigaciones en Química Biológica de Córdoba (CIQUIBIC), CONICET, Departamento de Química Biológica, Facultad de Ciencias Químicas, Universidad Nacional de Córdoba, Córdoba, Argentina.
authors.forename: Andrea M
authors.initials: AM
authors.lastname: Smania
mesh_terms: D005075:Biological Evolution; D003430:Cross-Sectional Studies; D003550:Cystic Fibrosis / Q000150:complications / Q000382:microbiology*; D014644:Genetic Variation; D054884:Host-Pathogen Interactions; D006801:Humans; D008137:Longitudinal Studies; D016106:Methicillin Resistance / Q000235:genetics; D059645:Mutation Rate; D020641:Polymorphism, Single Nucleotide; D011552:Pseudomonas Infections / Q000235:genetics / Q000382:microbiology*; D011550:Pseudomonas aeruginosa / Q000235:genetics* / Q000472:pathogenicity