Survival Comes at a Cost: A Coevolution of Phage and Its Host Leads to Phage Resistance and Antibiotic Sensitivity of Pseudomonas aeruginosa Multidrug Resistant Strains

Abstract

The increasing ineffectiveness of traditional antibiotics and the rise of multidrug resistant (MDR) bacteria have necessitated the revival of bacteriophage (phage) therapy. However, bacteria might also evolve resistance against phages. Phages and their bacterial hosts coexist in nature, resulting in a continuous coevolutionary competition for survival. We have isolated several clinical strains of Pseudomonas aeruginosa and phages that infect them. Among these, the PIAS (Phage Induced Antibiotic Sensitivity) phage belonging to the Myoviridae family can induce multistep genomic deletion in drug-resistant clinical strains of P. aeruginosa, producing a compromised drug efflux system in the bacterial host. We identified two types of mutant lines in the process: green mutants with SNPs (single nucleotide polymorphisms) and smaller deletions and brown mutants with large (∼250 kbp) genomic deletion. We demonstrated that PIAS used the MexXY-OprM system to initiate the infection. P. aeruginosa clogged PIAS phage infection by either modifying or deleting these receptors. The green mutant gaining phage resistance by SNPs could be overcome by evolved PIASs (E-PIASs) with a mutation in its tail-fiber protein. Characterization of the mutant phages will provide a deeper understanding of phage-host interaction. The coevolutionary process continued with large deletions in the same regions of the bacterial genomes to block the (E-)PIAS infection. These mutants gained phage resistance via either complete loss or substantial modifications of the phage receptor, MexXY-OprM, negating its essential role in antibiotic resistance. In vitro and in vivo studies indicated that combined use of PIAS and antibiotics could effectively inhibit P. aeruginosa growth. The phage can either eradicate bacteria or induce antibiotic sensitivity in MDR-resistant clinical strains. We have explored the potential use of combination therapy as an alternative approach against MDR P. aeruginosa infection.

Resistance of Dickeya solani strain IPO 2222 to lytic bacteriophage ΦD5 results in fitness tradeoffs for the bacterium during infection

“…It is hypothesized that the stable coexistence of phage-resistant and phage-susceptible bacterial populations occurs because bacteria pay a cost for phage resistance, irrespective of whether the viruses are present in the environment or not 17 – 20 . The altered fitness of resistant bacteria is usually manifested by reduced competitiveness for resources and/or reduced virulence or both 21 , 22 . However, it should also be highlighted that not all strains that have evolved phage resistance suffer such costs 23 , 24 .…”

Evolutionary Dynamics between Phages and Bacteria as a Possible Approach for Designing Effective Phage Therapies against Antibiotic-Resistant Bacteria

“…Alterations in porins, which are phage-binding receptors, are associated with the reduction in antibiotic resistance in phage-resistant bacteria [ 30 , 205 ]. The genomic deletions in antibiotic biotic-resistant bacteria are induced by PIAS, leading to compromised efflux pump systems [ 20 , 206 ]. The loss of outer membrane- and efflux-associated antibiotic resistance is attributed to the modification of phage-binding receptors such as MexAB, MexCD, MexEF, and MexXY [ 20 ].…”

“…Phages contribute to the diversity of bacterial communities in terms of the coevolutionary fitness dynamics [ 18 , 19 ]. Recently, phages have gained revived attention as alternative antibacterial agents over conventional antibiotics [ 20 , 21 , 22 , 23 ]. In Europe, phages have been used for therapeutic and prophylactic purposes, with a less adverse effect on normal microbial flora and no side effects [ 22 , 24 ].…”

“…The emergence of phage resistance is a major concern for the use of phage therapy in terms of the coevolutionary arms races between phages and bacteria [ 28 , 29 ]. The competitive interactions between phages and bacteria are evolutionary processes, ongoing defense strategies and counterstrategies, for survival in nature [ 20 ]. Bacteria evolve phage resistance under selection pressure, resulting in the coincidental changes in bacterial fitness and virulence [ 4 , 30 ].…”

Resistance of Dickeya solani strain IPO 2222 to lytic bacteriophage vB_Dsol_D5 (ΦD5) results in fitness tradeoffs for the bacterium during infection

“…It is hypothesized that the stable coexistence of phage-resistant and phage-susceptible bacterial populations occurs because bacteria pay constant costs of phage resistance despite whether the viruses are present or not in the environment (Stern and Sorek, 2011; Bradde et al, 2017; Burmeister and Turner, 2020; Naureen et al, 2020). Such costs are primarily linked with the altered fitness of resistant bacteria and are usually manifested by reduced competitiveness for resources and/or reduced virulence or both (Labrie et al, 2010; Koderi Valappil et al, 2021). However, it should also be highlighted that not all evolved phage resistance traits suffer costs (Lythgoe and Chao, 2003; Mizoguchi et al, 2003), as well as that the costs may also depend on the environmental context and the mechanism of phage resistance itself (Lennon et al, 2007; Vale et al, 2015).…”