How to Train Your Phage: The Recent Efforts in Phage Training

Abstract

Control of pathogenic bacteria by deliberate application of predatory phages has potential as a powerful therapy against antibiotic-resistant bacteria. The key advantages of phage biocontrol over antibacterial chemotherapy are: (1) an ability to self-propagate inside host bacteria, (2) targeted predation of specific species or strains of bacteria, (3) adaptive molecular machinery to overcome resistance in target bacteria. However, realizing the potential of phage biocontrol is dependent on harnessing or adapting these responses, as many phage species switch between lytic infection cycles (resulting in lysis) and lysogenic infection cycles (resulting in genomic integration) that increase the likelihood of survival of the phage in response to external stress or host depletion. Similarly, host range will need to be optimized to make phage therapy medically viable whilst avoiding the potential for deleteriously disturbing the commensal microbiota. Phage training is a new approach to produce efficient phages by capitalizing on the evolved response of wild-type phages to bacterial resistance. Here we will review recent studies reporting successful trials of training different strains of phages to switch into lytic replication mode, overcome bacterial resistance, and increase their host range. This review will also highlight the current knowledge of phage training and future implications in phage applications and phage therapy and summarize the recent pipeline of the magistral preparation to produce a customized phage for clinical trials and medical applications.

Isolation and Characterization of Bacteriophage ZCSE6 against Salmonella spp.: Phage Application in Milk

“…The dynamic process of isolating novel phages with complete characterization from isolation to application enriches our knowledge about the phage world. In addition, it provides information about its evolution and helps to determine the most suitable application according to its characteristics [31,49]. Nowadays, several phages that target Salmonella in foodstuff are found in the market, including PhageGuard S™ that reduces the bacteria in beef meat [50].…”

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

“…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 ).…”

“…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 ).…”

Recent Advances in the Application of Bacteriophages against Common Foodborne Pathogens

“…In a relatively short time after phage penetration, new virions are assembled and released to the environment. This sequence of molecular events naturally leads to lysis of the bacterial cell [ 17 ]. Bacteriophages amplifying with the lytic cycle are called lytic or virulent phages [ 18 ].…”