title: Recombination is a key driver of genomic and phenotypic diversity in a Pseudomonas aeruginosa population during cystic fibrosis infection.
abstract: The Cystic Fibrosis (CF) lung harbors a complex, polymicrobial ecosystem, in which Pseudomonas aeruginosa is capable of sustaining chronic infections, which are highly resistant to multiple antibiotics. Here, we investigate the phenotypic and genotypic diversity of 44 morphologically identical P. aeruginosa isolates taken from a single CF patient sputum sample. Comprehensive phenotypic analysis of isolates revealed large variances and trade-offs in growth, virulence factors and quorum sensing (QS) signals. Whole genome analysis of 22 isolates revealed high levels of intra-isolate diversity ranging from 5 to 64 SNPs and that recombination and not spontaneous mutation was the dominant driver of diversity in this population. Furthermore, phenotypic differences between isolates were not linked to mutations in known genes but were statistically associated with distinct recombination events. We also assessed antibiotic susceptibility of all isolates. Resistance to antibiotics significantly increased when multiple isolates were mixed together. Our results highlight the significant role of recombination in generating phenotypic and genetic diversification during in vivo chronic CF infection. We also discuss (i) how these findings could influence how patient-to-patient transmission studies are performed using whole genome sequencing, and (ii) the need to refine antibiotic susceptibility testing in sputum samples taken from patients with CF.
authors.affiliation: School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, U.K.
authors.forename: Sophie E
authors.initials: SE
authors.lastname: Darch
authors.affiliation: Pathogen Research Group, Nottingham Trent University, Nottingham, U.K.
authors.forename: Alan
authors.initials: A
authors.lastname: McNally
authors.affiliation: School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, U.K.
authors.forename: Freya
authors.initials: F
authors.lastname: Harrison
authors.affiliation: Department of Mathematics and Statistics, University of Helsinki, Finland.
authors.forename: Jukka
authors.initials: J
authors.lastname: Corander
authors.affiliation: Division of Respiratory Medicine, Nottingham City Hospital, Nottingham, NG5 1PB, U.K.
authors.forename: Helen L
authors.initials: HL
authors.lastname: Barr
authors.affiliation: College of Life and Environmental Sciences, University of Exeter, Exeter.
authors.forename: Konrad
authors.initials: K
authors.lastname: Paszkiewicz
authors.affiliation: Department of Clinical Microbiology, Nottingham University NHS Trust, U.K.
authors.forename: Stephen
authors.initials: S
authors.lastname: Holden
authors.affiliation: Division of Epidemiology &Public Health, Nottingham City Hospital, Nottingham, NG5 1PB, U.K.
authors.forename: Andrew
authors.initials: A
authors.lastname: Fogarty
authors.affiliation: 1] School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, U.K. [2] Department of Clinical Microbiology, Nottingham University NHS Trust, U.K.
authors.forename: Shanika A
authors.initials: SA
authors.lastname: Crusz
authors.affiliation: School of Life Sciences, University of Nottingham, Nottingham, NG7 2RD, U.K.
authors.forename: Stephen P
authors.initials: SP
authors.lastname: Diggle
mesh_terms: D000900:Anti-Bacterial Agents / Q000494:pharmacology; D003550:Cystic Fibrosis / Q000382:microbiology*; D004352:Drug Resistance, Microbial / Q000187:drug effects / Q000235:genetics; D019143:Evolution, Molecular; D005260:Female; D014644:Genetic Variation; D016680:Genome, Bacterial; D005838:Genotype; D060005:Genotyping Techniques; D006801:Humans; D008826:Microbial Sensitivity Tests; D009154:Mutation / Q000235:genetics; D010641:Phenotype; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D011552:Pseudomonas Infections / Q000382:microbiology*; D011550:Pseudomonas aeruginosa / Q000235:genetics* / Q000254:growth & development / Q000302:isolation & purification / Q000502:physiology*; D053038:Quorum Sensing / Q000187:drug effects; D011995:Recombination, Genetic / Q000187:drug effects; D016415:Sequence Alignment; D013183:Sputum / Q000382:microbiology; D055815:Young Adult
chemical_list: D000900:Anti-Bacterial Agents