A Lytic Bacteriophage Bank and Host-Range Matching Platform for Burkholderia cepacia Complex Infection in Cystic Fibrosis
Targeted to National Heart, Lung, and Blood Institute (NHLBI), R21 (Exploratory/Developmental Grant). A near-untreatable CF pathogen with scarce lytic phages — an exploratory R21 to build the bank and proof of concept.
Reviewer audit
Reviewer audit (overall 4/9).
Scores: clarity 3 · narrative 3 · structure 3 · funder alignment 4 · NIH criteria 4 · title 4 · pitfalls 3 · feasibility 5 · overall 4.
Top strengths: (1) Correctly identifies the real bottleneck — the scarcity of lytic Burkholderia phages and absence of a matching pipeline — rather than re-proving that phages can kill Bcc. (2) High clinical impact: targets a population disqualified from transplant with no antibiotic salvage, with clean NHLBI/CF-Foundation alignment. (3) Honest, mechanism-true framing of depolymerase-armed phage and an explicit eIND/IRB pathway for a vulnerable population.
Top weaknesses: (1) Thin citation base (one review) — the resubmission must add primary Bcc-phage isolation and infection-model papers. (2) Feasibility risk: lytic coverage of B. cenocepacia is historically low; the engineered-lytic fallback needs more detail and a quantitative coverage target with a real isolate panel. (3) The R21 scope is ambitious across three aims; a focused R21 (Aims 1–2) with Aim 3 as an R33/transition may score better.
What changed: tightened the Specific Aims to a measurable coverage go/no-go, foregrounded the depolymerase/re-sensitization mechanism, and made the eIND framework explicitly preparatory (not executed) to fit the exploratory mechanism.
A Lytic Bacteriophage Bank and Host-Range Matching Platform for Burkholderia cepacia Complex Infection in Cystic Fibrosis
Project Summary / Abstract
Burkholderia cepacia complex (Bcc) infection is among the most feared complications in cystic fibrosis (CF): these intrinsically multidrug-resistant Gram-negative bacteria can drive a rapid clinical decline, and chronic Bcc infection is a contraindication to lung transplantation at many centers. Antibiotic options are few and frequently fail. Lytic bacteriophages are an attractive precision alternative because they kill through a mechanism orthogonal to antibiotic resistance and can be matched to a patient's specific Burkholderia strain; some Bcc phages additionally encode depolymerases that strip the protective exopolysaccharide, potentially re-sensitizing the organism to host immunity and antibiotics. The central obstacle is supply: well-characterized, strictly lytic Burkholderia phages are far scarcer than for Pseudomonas or Staphylococcus, and the genus is genetically diverse, so rapid host-range matching and a curated bank are prerequisites for any clinical use. We will (1) assemble and genomically vet a lytic Bcc phage bank against a panel of contemporary CF Bcc isolates and define a rapid host-range matching assay; (2) establish preclinical efficacy, depolymerase activity, and phage-antibiotic synergy in infection models; and (3) build an expanded-access / emergency-IND-ready framework so matched phage can reach the patients with the fewest options. All key biological resources will be authenticated. The expected outcome is the first systematic, clinically actionable Bcc phage-matching platform — turning a transplant contraindication into a potentially manageable infection.
Specific Aims
Bcc infection in CF combines intrinsic multidrug resistance, the risk of rapid clinical deterioration, and frequent disqualification from lung transplantation, yet there is no reliable antibiotic salvage. Lytic phages offer a strain-matched, resistance-orthogonal option, but their clinical use is gated by the scarcity of characterized lytic Burkholderia phages and the absence of a rapid matching pipeline. We will close that gap.
Aim 1. Assemble and genomically vet a lytic Bcc phage bank and a rapid host-range matching assay. From environmental and clinical sources we will isolate strictly lytic phages against a panel of contemporary CF Bcc isolates (spanning the major species, including B. cenocepacia and B. multivorans), whole-genome sequence each to exclude integrase/lysogeny, toxin, and antimicrobial-resistance genes, and define a same-week host-range/match assay. Go/no-go: a banked cocktail covering ≥60% of the isolate panel with strictly lytic, genomically clean phages. [ILLUSTRATIVE coverage target]
Aim 2. Establish preclinical efficacy, depolymerase activity, and phage-antibiotic synergy. We will quantify killing and biofilm activity of matched phages and cocktails, characterize depolymerase-mediated capsule stripping and antibiotic re-sensitization, and test efficacy in Galleria and murine respiratory infection models with and without standard antibiotics.
Aim 3. Build an expanded-access / emergency-IND-ready clinical framework. We will define release criteria, a matching turnaround standard, and a correlative protocol so that, under an FDA emergency/expanded-access IND with IRB oversight, matched phage can be offered to Bcc-infected CF patients who have exhausted options, linking match quality and depolymerase activity to microbiologic and clinical readouts.
Impact. A curated, genomically vetted Bcc phage bank with rapid matching would give the most desperate CF patients a precision option where antibiotics offer almost none — and could remove chronic Bcc infection as an absolute barrier to life-saving transplantation.
Significance
Bcc infection is a low-incidence but high-consequence problem in CF: it disproportionately drives morbidity, can precipitate steep decline, and is a transplant contraindication at many centers precisely because no dependable therapy exists. The organisms are intrinsically resistant to most antibiotics, and combination regimens are often suppressive at best. This is exactly the niche where a resistance-orthogonal, strain-matched modality is most valuable, and where the inability to treat has the steepest human cost. Aligning with NHLBI's mission to preserve lung function in chronic pulmonary disease — and with the Cystic Fibrosis Foundation as a natural non-federal partner — this work targets a population with few or no alternatives. The principal scientific barrier is not whether phages can kill Bcc (multiple groups have shown lytic Bcc phages and efficacy in infection models) but whether a clinically usable supply and matching pipeline can be built for a genetically diverse genus. Solving that supply-and-matching problem is the rate-limiting step for translation.
Innovation
This proposal is innovative in three ways. First, it treats the scarcity of lytic Burkholderia phages as the central, addressable problem — building a genomically vetted bank and a same-week matching assay rather than assuming phage availability. Second, it foregrounds depolymerase-armed phages as a mechanism to strip the Bcc exopolysaccharide and re-sensitize the organism, an angle underexploited in Bcc. Third, it pairs bank construction with a pre-specified expanded-access/eIND framework, so that the deliverable is not just isolated phages but a clinically actionable pathway for a population that currently has none.
Approach
Aim 1 — Bank construction & rapid matching
Rationale. Clinical use requires a curated, strictly lytic, genomically clean bank plus a fast match. Experimental design. Isolate phages against a banked CF Bcc panel; sequence and annotate each (exclude lysogeny/toxin/AMR genes); define host range; build a same-week plaque/turbidity match assay. Expected outcomes. A defined multi-phage cocktail with documented coverage and safety screens. Pitfalls & alternatives. If lytic coverage is low for a species, pursue engineered-lytic derivatives and depolymerase-only constructs; expand environmental sampling.
Aim 2 — Preclinical efficacy, depolymerase & synergy
Rationale. Matching must translate to killing in vivo and ideally to antibiotic re-sensitization. Experimental design. Quantify lysis, biofilm activity, capsule stripping, and phage-antibiotic synergy in vitro; test efficacy in Galleria and murine respiratory models ± antibiotics; monitor resistance and fitness cost of escape. Expected outcomes. Cocktail and pairing rules that maximize killing and suppress resistance. Pitfalls & alternatives. If resistance emerges, use multi-receptor cocktails and steer toward capsule-loss trade-offs.
Aim 3 — eIND-ready clinical framework
Rationale. The deliverable must be usable for real patients. Experimental design. Define GMP-aligned release/quality criteria, a matching turnaround standard, and a correlative protocol; engage FDA on the emergency/expanded-access IND pathway; pre-specify microbiologic and clinical endpoints and consent for a vulnerable population. Expected outcomes. A ready framework to offer matched phage under eIND with IRB oversight. Pitfalls & alternatives. If matching fails for a patient's isolate, the bank's diversity and engineered derivatives provide fallbacks; absent a match, the framework documents the gap rather than proceeding.
Timeline
Year 1: isolate banking, sequencing, match-assay development [ILLUSTRATIVE]. Year 2: preclinical efficacy, depolymerase and synergy studies [ILLUSTRATIVE]. Year 3: quality/release criteria, eIND package, first correlative expanded-access cases [ILLUSTRATIVE].
Budget Justification
Modular R21-scale budget [ILLUSTRATIVE]: personnel (PI, phage scientist, bioinformatician, CF clinical collaborator), phage isolation/sequencing, model systems, and regulatory preparation. All figures [ILLUSTRATIVE], to be set with the institution.
Vertebrate Animals
Galleria (invertebrate) and murine respiratory infection models are proposed in Aim 2; murine work will follow IACUC-approved protocols with humane endpoints and the minimum animals required for statistical power [ILLUSTRATIVE].
Human Subjects / Clinical Trial
Aim 3 prepares — but this exploratory award does not execute — an expanded-access pathway. Any clinical administration of investigational phage would proceed under an FDA emergency/expanded-access IND (eIND) with IRB oversight and informed consent; see the regulatory pathway for context.
Team & Environment
Template roles to fill: PI (phage biology/CF microbiology); CF pulmonary/infectious-disease physician; bacteriophage genomicist/bioinformatician; GMP/quality advisor; regulatory/bioethics lead. Environment: an academic phage-isolation and CF clinical program with biobanking capacity.
References
- Lauman P, Dennis JJ. Advances in Phage Therapy: Targeting the Burkholderia cepacia Complex. Viruses. 2021;13(7):1331. https://doi.org/10.3390/v13071331
How to actually use & submit this
This proposal is CC0 / public domain — fork it, gut it, rename it, submit it. It is a starting point, not a substitute for your program officer, biostatistician, IRB, or an IND pre-submission meeting. Every budget, enrollment, and timeline figure is marked [ILLUSTRATIVE] — replace them.
Where it would go
- Best-fit home: National Heart, Lung, and Blood Institute (NHLBI), R21 (Exploratory/Developmental Grant).
- Alternates: NIAID, Cystic Fibrosis Foundation.
- Apply against a specific NOFO/FOA — never a blank mechanism. Search the NIH Guide.
What you must register / clear first
- SAM.gov (UEI) + eRA Commons; submit via Grants.gov / NIH ASSIST.
- SBIR/STTR routes also need SBIR.gov small-business eligibility.
- Phage clinical work runs under an FDA emergency/expanded-access IND (eIND) — see the regulatory pathway.
- Human subjects need IRB; animal work needs IACUC approval.
Writing your own for a different indication? Use the funder-agnostic skeleton + AI prompt library in the flagship template (Part B), adapted from eseckel/ai-for-grant-writing.