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

• Published in: Journal of evolutionary biology 2022-11, Vol.35 (11), p.1475-1487
• Main Authors: Kortright, Kaitlyn E., Chan, Benjamin K., Evans, Benjamin R., Turner, Paul E.
• Format: Article
• Language: English
• Subjects: antibiotic resistance; Antibiotics; Bacteria; bacteriophage; Biosynthesis; Coevolution; Dynamics; Evolution; experimental evolution; Flagella; Gene sequencing; Genetics; Genomes; Lipopolysaccharides; Mutation; Phages; Pseudomonas aeruginosa; Sampling designs; trade‐off; Whole genome sequencing
• ISSN: 1010-061X; 1420-9101
• DOI: 10.1111/jeb.14095

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. We tested the ability for Pseudomonas aeruginosa to coevolve with phage OMKO1 during 10 passages in the laboratory. Also, we sampled these co‐evolved microbes to test occurrence of arms‐race versus fluctuating‐selection dynamics coevolution, and whether bacteria evolved a predicted phenotypic trade‐off between phage resistance and antibiotic re‐sensitivity.