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 withinhost 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 freefloating 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.Pseudomonas aeruginosa | cystic fibrosis | mobile genetic element | experimental evolution | bacteriophage C omparative genomics suggests that temperate phages play an important role in the evolution and genomic diversification of bacterial pathogens (1). Bacterial genomes often contain a range of intact and remnant prophage elements (1-3), and ecologically important bacterial traits are believed to be phage-derived (e.g., phage-derived bacteriocins) (4). Phage-related sequences are observed more frequently in pathogenic than nonpathogenic strains (5), and prophage acquisition can be associated with changes in pathogen virulence (6, 7). Prophages can directly contribute accessory gene functions (1, 8) or disrupt bacterial genes by insertional inactivation. Of particular note are the transposable class of temperate phages (also known as mutator phages), including D3112 of Pseudomonas aeruginosa (9, 10), which integrate throughout the chromosome disrupting existing genes and increasing the supply of mutations available to selection. Recent reports of high rates of phage mobilization within hosts (11) and high temperate phage abundance in humans (12), including at sites of chronic infection where phage particles have been observed to exceed bacterial host densities by 10-to 100-fold (13), suggests that temperate phages could play an important role in driving within-host...

Bacterial cell‐to‐cell signaling promotes the evolution of resistance to parasitic bacteriophages

“…A crucial difference between these experiments was that Davies et al. (2016) used lysogenic phages while this and previous studies by Hosseinidoust et al. (2013) and De Smet et al.…”

Ecological and Evolutionary Benefits of Temperate Phage: What Does or Doesn't Kill You Makes You Stronger

“…[43] In a recent experimental evolution study, populations of Pseudomonas aeruginosa adapted more rapidly when cocultured with temperate phages including the transposable phage, ϕ4 (related to Pseudomonas phage D3112). [44] P. aeruginosa is the most common pathogen infecting the lungs of cystic fibrosis (CF) sufferers, where it must rapidly adapt to the lung environment. These experiments modeled the CF lung environment by using a sputum-like growth medium that recapitulates the physiochemical properties of CF lung sputum.…”

“…Moreover, in populations cocultured with phages, the observed adaptive mutations in bacteria were often caused by ϕ4 insertions, which disrupted a range of functions including type-IV pilus dependent motility and quorum sensing regulators. [44] The temperate phages used in the study were all derived from the Liverpool Epidemic Strain (LES) of P. aeruginosa, a common transmissible strain infecting CF patients that is associated with higher morbidity and mortality. [45] Interestingly, these LES temperate phages remain active in the bacterial genome and capable of lysis many years after colonizing the CF airway, [46] and appear to directly contribute to the fitness and competitiveness of LES in the lung environment.…”

Bacterial Diversification in the Light of the Interactions with Phages: The Genetic Symbionts and Their Role in Ecological Speciation

“…Over time prophages will evolve through the accumulation of small deletion events, recombination with other phages the host is exposed to, and recombination with other regions of the host genome (Bobay et al, 2014). The accumulation of new genetic information or combinations of genes through recombination can lead to the emergence of diversity in the host (Lang et al, 2012;Gama et al, 2013;Bobay et al, 2014;Davies et al, 2016;Touchon et al, 2017).…”