Supplementary Data for “Reinventing Antimicrobial Therapy: Bacteriophages, Engineered Lysins & Precision Antibacterials”
Description
This dataset comprises the supplementary material supporting the review article, “Reinventing Antimicrobial Therapy: Bacteriophages, Engineered Lysins & Precision Antibacterials.” It provides the methodological details, evidence-synthesis data, supplementary analyses, tables, and figures underlying the review. The dataset includes the full evidence-retrieval strategy, eligibility criteria, screening and study-selection procedures, and the Phage Therapy Readiness Index (PTRI) scoring protocol. It also contains the characteristics of 73 studies included in the updated evidence synthesis, together with supplementary analyses covering the bibliometric landscape of phage-therapy research, antimicrobial-resistance surveillance, bacteriophage biology and replication, historical and contemporary applications, phage-derived lytic proteins, ecological considerations, the human gut phageome, host-range engineering, and translational milestones for precision phage therapy. Supplementary tables provide consolidated information on phage-mediated transfer of antibiotic-resistance genes, phage-derived lytic enzymes against multidrug-resistant pathogens, outstanding technical and translational challenges, cross-jurisdictional regulatory frameworks, and the commercial landscape of phage therapeutics. Supplementary figures present publication trends, antimicrobial-resistance surveillance data for Neisseria gonorrhoeae, and projected translational milestones for precision phage therapy from 2025 to 2035. The deposited material is intended to provide transparency, reproducibility, and convenient access to the supporting evidence, analyses, tables, and figures cited in the associated manuscript. The evidence synthesis comprises studies identified through the stated systematic search and a subsequent focused currency update, with the scope and limitations of each component documented in the supplementary methods.
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Steps to reproduce
The evidence synthesis was conducted using a predefined eligibility framework. PubMed/MEDLINE, Web of Science Core Collection, and Scopus were searched from database inception to 30 June 2025 without language restriction. The search strategy combined three concept blocks: (i) bacteriophage-related terms, including “bacteriophage”, “phage therapy”, “endolysin”, “lysin”, “artilysin”, “innolysin”, and “engineered phage”; (ii) antimicrobial-resistance terms, including “antimicrobial resistance”, “antibiotic resistance”, “multidrug resistant”, and “ESKAPE”; and (iii) treatment and outcome terms, including “treatment”, “clinical trial”, “in vivo”, “biofilm”, and “safety”. The three blocks were combined using Boolean AND operators. Eligible records comprised peer-reviewed primary studies and reviews reporting phage or phage-derived-protein activity against bacterial pathogens, with publications from 2000–2025 prioritised and earlier seminal studies retained where they provided historical or mechanistic foundations. Records without accessible full text, studies not targeting bacteria, purely computational reports without experimental or clinical grounding, and duplicate datasets were excluded. Two reviewers independently screened titles and abstracts and subsequently assessed full texts. Disagreements were resolved through consensus, with third-reviewer adjudication where required. Reference lists of retrieved reviews were hand-searched for additional records. The original search identified 2,061 database records and 24 additional records through hand-searching. After duplicate removal, 1,474 records underwent title and abstract screening, 188 full texts were assessed, and 67 studies met the eligibility criteria. A focused currency update covering 1 July 2025–July 2026 was subsequently conducted using PubMed/MEDLINE, journal tables of contents, citation-chasing, and the ClinicalTrials.gov registry. Web of Science and Scopus were not rerun for this update. Six additional eligible studies were identified, resulting in 73 included studies overall. The update was treated as a focused currency check rather than a second complete systematic search. Study characteristics and reported outcomes were extracted into Supplementary Table S1. The quantitative component represents descriptive comparison of reported survival/mortality, bacterial-load reduction and biofilm-biomass reduction; no formal meta-analysis or statistical pooling was performed because of substantial heterogeneity among studies. The Phage Therapy Readiness Index (PTRI) was scored independently by two authors across six dimensions: efficacy, safety, manufacturability, regulatory maturity, cost/scalability, and clinical readiness. Each criterion received a score of 1–3, producing a composite score of 6–18.
Institutions
- Sher-e-Kashmir University of Agricultural Sciences and Technology of KashmirJammu and Kashmir, Srinagar