Arms race and fluctuating selection dynamics in Pseudomonas aeruginosa bacteria coevolving with phage OMKO1

Abstract

Experimental evolution studies have examined coevolutionary dynamics between bacteria and lytic phages, where two models for antagonistic coevolution dominate: arms‐race dynamics (ARD) and fluctuating‐selection dynamics (FSD). Here, we tested the ability for Pseudomonas aeruginosa to coevolve with phage OMKO1 during 10 passages in the laboratory, whether ARD versus FSD coevolution occurred, and how coevolution affected a predicted phenotypic trade‐off between phage resistance and antibiotic sensitivity. We used a unique “deep” sampling design, where 96 bacterial clones per passage were obtained from the three replicate coevolving communities. Next, we examined phenotypic changes in growth ability, susceptibility to phage infection and resistance to antibiotics. Results confirmed that the bacteria and phages coexisted throughout the study with one community undergoing ARD, whereas the other two showed evidence for FSD. Surprisingly, only the ARD bacteria demonstrated the anticipated trade‐off. Whole genome sequencing revealed that treatment populations of bacteria accrued more de novo mutations, relative to a control bacterial population. Additionally, coevolved bacteria presented mutations in genes for biosynthesis of flagella, type‐IV pilus and lipopolysaccharide, with three mutations fixing contemporaneously with the occurrence of the phenotypic trade‐off in the ARD‐coevolved bacteria. Our study demonstrates that both ARD and FSD coevolution outcomes are possible in a single interacting bacteria‐phage system and that occurrence of predicted phage‐driven evolutionary trade‐offs may depend on the genetics underlying evolution of phage resistance in bacteria. These results are relevant for the ongoing development of lytic phages, such as OMKO1, in personalized treatment of human patients, as an alternative to antibiotics.

Coevolution with a seed bank

“…Despite the low frequency of sensitive phenotypes, phage population sizes remained high, a pattern consistent with the invasion of host range mutants that arise owing to coevolution. In support of this, we documented an increase in the frequency of mutations associated with host receptors (teichoic acids) and phage tail components, which are hallmark targets of coevolution in bacteria-phage systems (Scanlan et al 2011;Habusha et al 2019;Kortright et al 2022).…”

“…The copyright holder for this preprint this version posted February 10, 2023. ; https://doi.org/10.1101/2023.02.08.527722 doi: bioRxiv preprint associated with host receptors (teichoic acids) and phage tail components, which are hallmark targets of coevolution in bacteria-phage systems (Scanlan et al 2011;Habusha et al 2019;Kortright et al 2022).…”

“…The copyright holder for this preprint this version posted February 10, 2023. ; https://doi.org/10.1101/2023.02.08.527722 doi: bioRxiv preprint step of infection where tail like-structures of a phage particle attach to receptor molecules on the surface of the bacterial host (Scanlan et al 2011;Betts et al 2018;Kortright et al 2022). The resulting coevolutionary dynamics are dependent on the fitness costs of evolved strains as well as the maintenance of diversity, including physical or physiological refugia from phages (Schrag & Mittler 1996;Hall et al 2011;Igler 2022).…”

“…Fast generation times and large population sizes allow for rapid evolution, which can be tracked through longitudinal sampling (McDonald 2019). In such studies, bacteria and phage often coexist owing in part to arms race dynamics and negative-frequency dependent selection, which has been demonstrated with infection networks and genome sequencing (Flores et al 2011;Betts et al 2018;Kortright et al 2022). The targets of selection are typically associated with the initial step of infection where tail like-structures of a phage particle attach to receptor molecules on the surface of the bacterial host (Scanlan et al 2011;Betts et al 2018;Kortright et al 2022).…”

“…In such studies, bacteria and phage often coexist owing in part to arms race dynamics and negative-frequency dependent selection, which has been demonstrated with infection networks and genome sequencing (Flores et al 2011;Betts et al 2018;Kortright et al 2022). The targets of selection are typically associated with the initial step of infection where tail like-structures of a phage particle attach to receptor molecules on the surface of the bacterial host (Scanlan et al 2011;Betts et al 2018;Kortright et al 2022). The resulting coevolutionary dynamics are dependent on the fitness costs of evolved strains as well as the maintenance of diversity, including physical or physiological refugia from phages (Schrag & Mittler 1996;Hall et al 2011;Igler 2022).…”