title: Temperate phages both mediate and drive adaptive evolution in pathogen biofilms.
abstract: Temperate phages drive genomic diversification in bacterial pathogens. Phage-derived sequences are more common in pathogenic than nonpathogenic taxa and are associated with changes in pathogen virulence. High abundance and mobilization of temperate phages within hosts suggests that temperate phages could promote within-host evolution of bacterial pathogens. However, their role in pathogen evolution has not been experimentally tested. We experimentally evolved replicate populations of Pseudomonas aeruginosa with or without a community of three temperate phages active in cystic fibrosis (CF) lung infections, including the transposable phage, ɸ4, which is closely related to phage D3112. Populations grew as free-floating biofilms in artificial sputum medium, mimicking sputum of CF lungs where P. aeruginosa is an important pathogen and undergoes evolutionary adaptation and diversification during chronic infection. Although bacterial populations adapted to the biofilm environment in both treatments, population genomic analysis revealed that phages altered both the trajectory and mode of evolution. Populations evolving with phages exhibited a greater degree of parallel evolution and faster selective sweeps than populations without phages. Phage ɸ4 integrated randomly into the bacterial chromosome, but integrations into motility-associated genes and regulators of quorum sensing systems essential for virulence were selected in parallel, strongly suggesting that these insertional inactivation mutations were adaptive. Temperate phages, and in particular transposable phages, are therefore likely to facilitate adaptive evolution of bacterial pathogens within hosts.
authors.affiliation: Institute of Infection and Global Health, University of Liverpool, Liverpool L69 7ZB, United Kingdom; Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom;
authors.forename: Emily V
authors.initials: EV
authors.lastname: Davies
authors.affiliation: Institute of Infection and Global Health, University of Liverpool, Liverpool L69 7ZB, United Kingdom; School of Environment and Life Sciences, University of Salford, Manchester M5 4WT, United Kingdom;
authors.forename: Chloe E
authors.initials: CE
authors.lastname: James
authors.affiliation: Institute of Infection and Global Health, University of Liverpool, Liverpool L69 7ZB, United Kingdom; Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom;
authors.forename: David
authors.initials: D
authors.lastname: Williams
authors.affiliation: Department of Biology, University of York, York YO10 5DD, United Kingdom.
authors.forename: Siobhan
authors.initials: S
authors.lastname: O'Brien
authors.affiliation: Institute of Infection and Global Health, University of Liverpool, Liverpool L69 7ZB, United Kingdom;
authors.forename: Joanne L
authors.initials: JL
authors.lastname: Fothergill
authors.affiliation: Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom;
authors.forename: Sam
authors.initials: S
authors.lastname: Haldenby
authors.affiliation: Institute of Integrative Biology, University of Liverpool, Liverpool L69 7ZB, United Kingdom;
authors.forename: Steve
authors.initials: S
authors.lastname: Paterson
authors.affiliation: Institute of Infection and Global Health, University of Liverpool, Liverpool L69 7ZB, United Kingdom;
authors.forename: Craig
authors.initials: C
authors.lastname: Winstanley
authors.affiliation: Department of Biology, University of York, York YO10 5DD, United Kingdom michael.brockhurst@york.ac.uk.
authors.forename: Michael A
authors.identifier: 0000-0003-0362-820X
authors.initials: MA
authors.lastname: Brockhurst
mesh_terms: D000222:Adaptation, Physiological; D001435:Bacteriophages / Q000235:genetics*; D018441:Biofilms; D005075:Biological Evolution; D009154:Mutation; D011550:Pseudomonas aeruginosa / Q000235:genetics* / Q000254:growth & development; D013183:Sputum / Q000382:microbiology
keywords: Pseudomonas aeruginosa; bacteriophage; cystic fibrosis; experimental evolution; mobile genetic element