VetPathogenVeterinary Pathogen Analysis & AMR Insights
Transforming routine sequence uploads into actionable lab intelligence.
The Challenge
Antimicrobial resistance in animals threatens food security and One Health resilience. Veterinary labs face siloed, research-heavy tools that are slow to adapt to frontline cases. VetPathogen is designed to close that gap with an integrated, lab-friendly workflow.
How VetPathogen Began
VetPathogen grew out of three foundational projects that explored core ideas in computational microbiology:
- Sequence Analysis Demo — reading FASTA files, computing GC%, and translating DNA to protein.
- AMR Gene Detection — comparing bacterial sequences to resistance gene catalogues.
- VetPathogen Pipeline — orchestrating analysis and reporting workflows.
These experiments formed the building blocks of today's platform. What began as individual Jupyter notebooks became an integrated system combining Python-based analysis, FastAPI orchestration, and a Next.js interface—proof that complex bioinformatics workflows can be intuitive, transparent, and lab-friendly.
The Platform Today
- Streamlined pipeline classifies pathogens and detects AMR genes directly from FASTA uploads.
- Delivers QC metrics, alignment summaries, and exportable CSV/PDF artefacts in one interface.
- Functional demo proves the full stack — sequence parsing, alignment heuristics, AMR catalogue lookup, and reporting.
Where It's Headed
- Curated reference catalogues (NCBI / CARD) with provenance tracking and automated refreshes.
- Integrated quality controls: fastp pre-processing, contamination screening, and metadata validation.
- Evidence-based AMR risk stratification tuned to veterinary clinical breakpoints.
- Reproducible job orchestration with provenance, audit logs, and governance-friendly controls.
- Privacy-conscious deployments for veterinary labs, academic partners, and One Health networks.
About the Developer
Mehdi Khedi is a Doctor of Veterinary Medicine (DVM) passionate about computational biology and the intersection of life sciences and technology. He created VetPathogen to make antimicrobial resistance (AMR) analysis more accessible, automated, and transparent for veterinary researchers and clinicians.
Contact
Have questions or want to collaborate? Send a note and I’ll get back to you shortly.