Mitigation of evolved bacterial resistance to phage therapy

Variable effects on virulence of bacteriophage resistance mechanisms in extraintestinal pathogenicEscherichia coli

“…Replacing phage therapy in a broader context of phage-bacteria coevolution could provide opportunities for each phage included in a cocktail to become at some point the most efficient phage (21).…”

“…Intense research has revealed several novel phage-defense systems that target virtually all steps of the phage life cycle from adsorption to lysis (19,20). Therefore, emergence of bacterial resistance to phages is possibly a critical factor, that could lead to treatment failure (21,22). Interestingly, while phage resistance has been shown to develop rapidly in vitro, studies in humans have yielded discrepant results, reporting either the presence (23) or the absence (24) of phage resistance.…”

A Phage Foundry Framework to Systematically Develop Viral Countermeasures to Combat Antibiotic-Resistant Bacterial Pathogens

“…Phages are readily identified in the environment through sequencing, and the evolutionary patterns of the Red-Queen warfare between target pathogen and phages could possibly be tracked via sequencing as well, thereby identifying the genetic bases of the mechanisms of resistance and counter resistance ( Hussain et al., 2021 ; LeGault et al., 2021 ). The ability of phages to rapidly evolve to evade target pathogen resistance can be exploited using in vitro directed evolution to “train” libraries of phages against panels of targets to create banks of complementary phage antimicrobial agents for cocktails ( Rohde et al., 2018 ; Burrowes et al., 2019 ; Abdelsattar et al., 2021 ; Borin et al., 2021 ; Eskenazi et al., 2022 ; Torres-Barceló et al., 2022 ). The small genomic size of phages enable both full genome synthesis and possibly “booting” (producing viable phage particles from synthetic DNA) when isolation is difficult as well as efficient engineering of designed genetic changes ( Chan et al., 2005 ; Ando et al., 2015 ; Pires et al., 2016 , 2021a , 2021b ; Kilcher et al., 2018 ; Lemire et al., 2018 ; Dunne et al., 2019 ; Kilcher and Loessner, 2019 ; Weynberg and Jaschke, 2020 ; Lenneman et al., 2021 ).…”

“…However, application of phages in therapy and biocontrol present challenges as well, and many of these challenges share a substantial overlap with AMR knowledge gaps listed in Figure 1 . Although there is great progress in the technologies per se for characterizing and engineering phages, there is still lack of progress in our ability to rationally and predictably design a phage formulation to effectively eliminate a target pathogen and to ensure it works robustly across the spectrum of the population variation of a given pathogen in its natural or real-world environmental matrices ( Meaden and Koskella, 2013 ; Young and Gill, 2015 ; Koskella and Taylor, 2018 ; Brüssow, 2019 ; Caflisch et al., 2019 ; Dąbrowska and Abedon, 2019 ; Hesse and Adhya, 2019 ; Kortright et al., 2019 ; Górski et al., 2020 ; Luong et al., 2020b ; Federici et al., 2021 ; Hatfull et al., 2021 ; Pirnay et al., 2021 ); For example, despite the recent progress made in phage-target pathogen matching methods ( Henry et al., 2012 ; Estrella et al., 2016 ), it remains difficult to rapidly and economically identify phages/phage-antibiotic combinations to which a patient’s infections are susceptible or predict which multiple phages in a phage collection (“phage bank”) may be synergetic (or not) in their antimicrobial activity due to independent mechanisms of interaction, cross-resistance, and infectivity profile with the target pathogen ( Wright et al., 2021 ; Segall, et al., 2019 ; Gu Liu et al., 2020 ; Al-Anany et al., 2021 ; Gordillo Altamirano and Barr, 2021 ; Markwitz et al., 2022 ; Torres-Barceló et al., 2022 ). There are currently no guidelines for the delivery and dosing of phages that guarantee access to appropriate target infection sites in sufficient numbers so that a self-sustaining replicative cycle can be established.…”

“…Assessment of phage safety, toxicity, and stability is performed along with tests for cross-reactivity, antigenicity, immunomodulation, persistence, and impact on environment to define optimal treatment parameters under the conditions of intended use ( Balogh et al., 2010 ; Chan, et al., 2013 ; McCallin et al., 2018 ; Hernandez and Koskella, 2019 ; Jault et al., 2019 ; Wang et al., 2019 ; Liu et al., 2021 ; Nale and Clokie, 2021 ; Popescu et al., 2021 ). Rapid ALE experimental platforms are established to carry out phage training against new conditions, host variants, link genotype-phenotype relationships, and coevolution of phages and host to uncover allelic level specificity (for example, see refs ( Burrowes et al., 2019 ; Favor et al., 2020 ; Russ et al., 2020 ; Abdelsattar et al., 2021 ; Borin et al., 2021 ; Eskenazi et al., 2022 ; Torres-Barceló et al., 2022 )). Experiments are carried out to identify biomolecular substructures within a panel of bacterial hosts, leading to interaction among different combinations of phages and antibiotic to better predict CR/CS and evolutionary traps ( Pál et al., 2015 ; Scanlan et al., 2015b ; Imamovic et al., 2018 ; Scortti et al., 2018 ; Burmeister and Turner, 2020 ; Maltas et al., 2020 ; Mangalea and Duerkop, 2020 ).…”