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Cited by 32Bacteriophages and microbial interactionsCRISPR and Genetic EngineeringPlant and Fungal Interactions Research

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

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Mutalik, Vivek K., Arkin, Adam P.·2022·iScience
DOI 10.1016/j.isci.2022.104121PMC PMC8983348
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Abstract

At its current rate, the rise of antimicrobial-resistant (AMR) infections is predicted to paralyze our industries and healthcare facilities while becoming the leading global cause of loss of human life. With limited new antibiotics on the horizon, we need to invest in alternative solutions. Bacteriophages (phages)-viruses targeting bacteria-offer a powerful alternative approach to tackle bacterial infections. Despite recent advances in using phages to treat recalcitrant AMR infections, the field lacks systematic development of phage therapies scalable to different applications. We propose a Phage Foundry framework to establish metrics for phage characterization and to fill the knowledge and technological gaps in phage therapeutics. Coordinated investment in AMR surveillance, sampling, characterization, and data sharing procedures will enable rational exploitation of phages for treatments. A fully realized Phage Foundry will enhance the sharing of knowledge, technology, and viral reagents in an equitable manner and will accelerate the biobased economy.

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  • High-throughput assays mapping phage-bacterial variant interactions provide rich datasets for ML models predicting phage efficacy, host range, and resistance mechanisms.

    “High-throughput assays mapping phage–bacterial variant interactions, augmented by genetic tools such as RB-TnSeq, CRISPRi, and Dual-Barcoded Shotgun Expression Library Sequencing-(Dub-seq), provide rich datasets for ML models predicting phage efficacy, host range, and resistance mechanisms [157]”

    From Phage therapy in oncology: opportunities for cancer prevention and treatment (2026) · cites this paper as [157]

    Phage characterization levels 2 and 3 (page unavailable) describe phage-by-target killing matrices, high-throughput genetic screens of sensitivity and resistance mechanisms, and interaction datasets used to assess infection efficiency and predict susceptibility. Our copy does not say these datasets train ML models to predict efficacy, host range, and resistance mechanisms, nor does it identify the full set of genetic tools named in the citing sentence, including Dub-seq. (LLM, conf=0.85)

    Experimental — accuracy not yet measured

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Authors
Mutalik, V. K., & Arkin, A. P.
Affiliations
Lawrence Berkeley National Laboratory (US)
Corresponding author
  • Mutalik, Vivek K.
  • Arkin, Adam P.
ORCID
Venue
iScience
Publisher
Elsevier BV
Published
2022-04
Volume
25
Issue
4
Pages
104121
ISSN
2589-0042 (ISSN-L)
DOI
10.1016/j.isci.2022.104121
PMC
PMC8983348
OpenAlex
W4220735796
Cited by
32
References
3
Citations by year
2026: 10 · 2025: 4 · 2024: 10 · 2023: 4 · 2022: 4
FWCI
0.51
Type
journal article
Language
en
Open access
Licence
Locations
  • iScience (publishedVersion, cc-by-nc-nd)
  • PubMed Central (publishedVersion, cc-by-nc-nd)
  • PubMed (publishedVersion)
  • eScholarship (California Digital Library) (submittedVersion, cc-by-nc-nd)
  • OSTI OAI (U.S. Department of Energy Office of Scientific and Technical Information) (submittedVersion)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion)
Funders
  • Innovative Genomics Institute
  • U.S. Department of Energy (DE-AC02-05CH11231)
  • Office of Science
  • Laboratory Directed Research and Development
Topics
  • Physical Sciences › Environmental Science › Ecology › Bacteriophages and microbial interactions
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › CRISPR and Genetic Engineering
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Endocrinology › Plant and Fungal Interactions Research
Keywords
bacteriophages, phage therapy, antibiotic resistance, antimicrobial resistance, antimicrobial resistance surveillance, bioeconomy, viral countermeasures

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