A multi-component genomic risk assessment tool for Listeria monocytogenes. GIF integrates virulence (V), persistence (P), clonality (C) and antimicrobial resistance (R) into a single 0–100 score and classifies each isolate by trophic strategy (nosotroph, amphitroph, saprotroph).
Reference implementation accompanying the methodological and clinical-validation manuscripts listed in the Citation section. Both manuscripts are currently available as bioRxiv preprints.
git clone https://github.com/jgamboa-biotecno/GIF-Framework.git
cd GIF-Framework
pip install -e .docker build -t gif-framework .
docker run --rm -v $(pwd):/data gif-framework score /data/genome.fasta --output /data/results/GIF requires the following bioinformatics tools to be available in PATH:
| Tool | Purpose | Install |
|---|---|---|
| BLAST+ | Sequence alignment | conda install -c bioconda blast |
| chewBBACA | cgMLST typing | conda install -c bioconda chewbbaca |
| mlst | 7-gene MLST | conda install -c bioconda mlst |
| ABRicate | AMR / virulence gene detection | conda install -c bioconda abricate |
# Single genome
gif score genome.fasta
# Directory of FASTAs
gif score /data/genomes/ --output /data/results/
# From NCBI accessions
gif score --accession GCA_000026945.2 --output results/
# From a BioProject
gif score --bioproject PRJNA422580 --output results/
# Calibration context (default: industrial)
gif score genome.fasta --context clinical
# Output format
gif score genome.fasta --format tsv # default
gif score genome.fasta --format json
gif score genome.fasta --format report # markdownRun gif --help for the complete option list.
GIF computes four orthogonal components and integrates them into a weighted score on a 0–100 scale.
| Component | Industrial weight | Clinical weight | Description |
|---|---|---|---|
| V Virulence | 0.30 | 0.40 | Clonal complex classification, LIPI islands, InlA truncation status |
| P Persistence | 0.40 | 0.20 | Genetic persistence markers (SSI-1, SSI-2, BcrABC, qac) and temporal recurrence |
| C Clonality | 0.20 | 0.30 | cgMLST allelic distance to reference clusters and cluster expansion |
| R Resistance | 0.10 | 0.10 | AMR determinants and regional prevalence weighting |
| Strategy | V-Score | P-Score | Interpretation |
|---|---|---|---|
| Nosotroph | > 65 | < 35 | Pathogenic-niche specialist |
| Amphitroph | ≥ 35 | ≥ 40 | Dual-niche: virulence and persistence |
| Saprotroph | < 30 | > 45 | Industrial-niche specialist |
| Unassigned | other | other | Intermediate profile |
The methodological basis for the trophic classification is described in the first manuscript listed in the Citation section.
If you use GIF in your work, please cite the following preprints:
-
Gamboa J. (2026). Amphitrophic Listeria monocytogenes: multi-dimensional genomic profiling reveals a third ecological strategy that challenges the virulence-persistence trade-off paradigm. bioRxiv. https://doi.org/10.64898/2026.03.23.713700
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Gamboa J. (2026). Amphitrophic Listeria monocytogenes causes one-third of invasive listeriosis yet remains undetected by clonal complex-based risk classification. bioRxiv. https://doi.org/10.64898/2026.03.28.715028
Additional preprints describing pathogen-specific applications and the regulatory context:
-
Gamboa J. (2026). Beyond Outbreak Detection: Mandatory Genomic Surveillance in the EU as an Opportunity to Quantify Metal-Mediated Co-Selection of Antimicrobial Resistance from a One Health Perspective. Preprints.org. https://doi.org/10.20944/preprints202604.0573.v1
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Gamboa J. (2026). From Serogroup to Genome: The Unfinished Transition in EU Food Safety Criteria for Shiga Toxin-Producing Escherichia coli. Preprints.org. https://doi.org/10.20944/preprints202604.0508.v1
A machine-readable citation file is provided in CITATION.cff.
Apache License 2.0. See LICENSE for the full text.