Optimizing bacteriophage engineering through an accelerated evolution platform

Favor, Andrew H.; Llanos, Carlos D.; Youngblut, Matthew D.; Bardales, Jorge A.

doi:10.1038/s41598-020-70841-1

Cited by 35 publications

(31 citation statements)

References 34 publications

(37 reference statements)

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“…Therefore, strategies to improve the characteristics of wild type phages based on random changes of the genome have been proposed. In one study, phages with improved heat stability were generated by random mutagenesis followed by a selection filter [ 24 ]. Moreover “phage training” by sequential re-propagation, and selection for advantageous mutations has been described [ 14 ].…”

Section: Introductionmentioning

confidence: 99%

ε2-Phages Are Naturally Bred and Have a Vastly Improved Host Range in Staphylococcus aureus over Wild Type Phages

Moreno¹,

Visram²,

Mutti³

et al. 2021

Pharmaceuticals

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Due to the rapid spread of antibiotic resistance, and the difficulties of treating biofilm-associated infections, alternative treatments for S. aureus infections are urgently needed. We tested the lytic activity of several wild type phages against a panel of 110 S. aureus strains (MRSA/MSSA) composed to reflect the prevalence of S. aureus clonal complexes in human infections. The plaquing host ranges (PHR) of the wild type phages were in the range of 51% to 60%. We also measured what we called the kinetic host range (KHR), i.e., the percentage of strains for which growth in suspension was suppressed for 24 h. The KHR of the wild type phages ranged from 2% to 49%, substantially lower than the PHRs. To improve the KHR and other key pharmaceutical properties, we bred the phages by mixing and propagating cocktails on a subset of S. aureus strains. These bred phages, which we termed evolution-squared (ε2) phages, have broader KHRs up to 64% and increased virulence compared to the ancestors. The ε2-phages with the broadest KHR have genomes intercrossed from up to three different ancestors. We composed a cocktail of three ε2-phages with an overall KHR of 92% and PHR of 96% on 110 S. aureus strains and called it PM-399. PM-399 has a lower propensity to resistance formation than the standard of care antibiotics vancomycin, rifampicin, or their combination, and no resistance was observed in laboratory settings (detection limit: 1 cell in 1011). In summary, ε2-phages and, in particular PM-399, are promising candidates for an alternative treatment of S. aureus infections.

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Section: Introductionmentioning

confidence: 99%

ε2-Phages Are Naturally Bred and Have a Vastly Improved Host Range in Staphylococcus aureus over Wild Type Phages

Moreno¹,

Visram²,

Mutti³

et al. 2021

Pharmaceuticals

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“…The modular build-up of phage RBP structures with recyclable building blocks responsible for the structural organization and receptor specificity, driven by intense horizontal transfers, provides an evolutionary highway for the rapid adaptation to the high diversity of K. pneumoniae capsules not necessarily constrained by taxonomic borders or different RBP architectures. With the recent maturation of synthetic biology tools for phage design (43)(44)(45)(46)(47)(48)(49), an increasing number of engineered phages can be constructed to gain further meaningful insights in the host recognition system by Klebsiella phage RBPs and the role of their domains in specificity and structural organization.…”

Section: Discussionmentioning

confidence: 99%

Engineering the Modular Receptor-Binding Proteins ofKlebsiellaPhages Switches Their Capsule Serotype Specificity

Łątka

Lemire

Grimon

et al. 2021

mBio

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The high specificity of bacteriophages is driven by their receptor-binding proteins (RBPs). Many Klebsiella bacteriophages target the capsular exopolysaccharide as the receptor and encode RBPs with depolymerase activity. The modular structure of these RBPs with an N-terminal structural module to attach the RBP to the phage tail, and a C-terminal specificity module for exopolysaccharide degradation, supports horizontal transfer as a major evolutionary driver for Klebsiella phage RBPs. We mimicked this natural evolutionary process by the construction of modular RBP chimeras, exchanging N-terminal structural modules and C-terminal specificity modules. All chimeras strictly follow the capsular serotype specificity of the C-terminal module. Transplanting chimeras with a K11 N-terminal structural RBP module in a Klebsiella phage K11 scaffold results in a capsular serotype switch and corresponding host range modification of the synthetic phages, demonstrating that horizontal transfer of C-terminal specificity modules offers Klebsiella phages an evolutionary highway for rapid adaptation to new capsular serotypes. IMPORTANCE The antimicrobial resistance crisis has rekindled interest in bacteriophage therapy. Phages have been studied over a century as therapeutics to treat bacterial infections, but one of the biggest challenges for the use of phages in therapeutic interventions remains their high specificity. In particular, many Klebsiella phages have a narrow spectrum constrained by the high diversity of exopolysaccharide capsules that shield access to the cells. In this work, we have elaborated how Klebsiella phages deal with this high diversity by exchanging building blocks of their receptor-binding proteins.

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“…For example, Kering et al 2020 were able to induce improved thermal stability of phages at elevated temperatures without affecting their lytic activity [189]. Effective methods for the rapid enhancement of additional, desired characteristics among selected phages continue to be developed as well [190].…”

Section: Phage Selection Criteria For Biocontrol and Therapymentioning

confidence: 99%

The Age of Phage: Friend or Foe in the New Dawn of Therapeutic and Biocontrol Applications?

et al. 2021

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Extended overuse and misuse of antibiotics and other antibacterial agents has resulted in an antimicrobial resistance crisis. Bacteriophages, viruses that infect bacteria, have emerged as a legitimate alternative antibacterial agent with a wide scope of applications which continue to be discovered and refined. However, the potential of some bacteriophages to aid in the acquisition, maintenance, and dissemination of negatively associated bacterial genes, including resistance and virulence genes, through transduction is of concern and requires deeper understanding in order to be properly addressed. In particular, their ability to interact with mobile genetic elements such as plasmids, genomic islands, and integrative conjugative elements (ICEs) enables bacteriophages to contribute greatly to bacterial evolution. Nonetheless, bacteriophages have the potential to be used as therapeutic and biocontrol agents within medical, agricultural, and food processing settings, against bacteria in both planktonic and biofilm environments. Additionally, bacteriophages have been deployed in developing rapid, sensitive, and specific biosensors for various bacterial targets. Intriguingly, their bioengineering capabilities show great promise in improving their adaptability and effectiveness as biocontrol and detection tools. This review aims to provide a balanced perspective on bacteriophages by outlining advantages, challenges, and future steps needed in order to boost their therapeutic and biocontrol potential, while also providing insight on their potential role in contributing to bacterial evolution and survival.

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Optimizing bacteriophage engineering through an accelerated evolution platform

Cited by 35 publications

References 34 publications

ε2-Phages Are Naturally Bred and Have a Vastly Improved Host Range in Staphylococcus aureus over Wild Type Phages

ε2-Phages Are Naturally Bred and Have a Vastly Improved Host Range in Staphylococcus aureus over Wild Type Phages

Engineering the Modular Receptor-Binding Proteins ofKlebsiellaPhages Switches Their Capsule Serotype Specificity

The Age of Phage: Friend or Foe in the New Dawn of Therapeutic and Biocontrol Applications?

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