Vanguard Biotech Systems
NextGenAMR turns bacterial whole-genome sequencing, within its published scope, into interpretable, traceable antimicrobial resistance interpretation — a controlled infrastructure layer for the laboratories, hospitals and surveillance networks of the genomic era. Interpretation is species-specific; the current operational scope is Escherichia coli.
NextGenAMR is a functional platform in controlled preview. Internal non-clinical testing is in progress and an independent validation programme is in preparation; no independent performance results are published. The product is not presented as an autonomous diagnostic or treatment-decision system.
Controlled preview. NextGenAMR is in internal, non-clinical testing; independent validation is in preparation. The public demonstration is an illustrative technical replay of the product's E. coli output — not a real patient or clinical sample. It is provided for illustrative purposes only, shows a model-estimated probability of resistance (never a categorical S/I/R result), and does not constitute a clinical report. NextGenAMR is not presented as an autonomous diagnostic or treatment-decision system.
| Antibiotic | Model estimate | Evidence |
|---|---|---|
| Amoxicillin–clavulanic acid | Elevated | blaTEM-1B |
| Ampicillin | Elevated | blaTEM-1B |
| Ciprofloxacin | Elevated | gyrA S83L · parC S80I |
| Ceftazidime | No marker detected | marker not detected; does not imply susceptibility |
| Gentamicin | No marker detected | marker not detected; does not imply susceptibility |
| Meropenem | No marker detected | marker not detected; does not imply susceptibility |
| Nitrofurantoin | No marker detected | marker not detected; does not imply susceptibility |
| Piperacillin–tazobactam | No marker detected | marker not detected; does not imply susceptibility |
| Trimethoprim–sulfamethoxazole | Elevated | sul1 · dfrA17 |
- AMR genes7
- Point mutations3
- Plasmid replicons2
- Mean coverage82×
- pipeline · ngamr-core@0.4.2
- db · card-2025.09 · resfinder-2025.10
- operator · lab.ops/41
- started · 2026-06-19 09:14 UTC
- Low-coverage region flagged for review.
- Marker absence ≠ susceptibility; abstains out of scope — no call emitted.
Illustrative technical replay — not a real patient sample and not a clinical diagnosis.
Genomic AMR interpretation today is often spread across disconnected scripts, databases, spreadsheets and manual judgement. Workflows composed of multiple tools can make it difficult to maintain consistent versions, provenance, handoffs and reporting across teams and runs. NextGenAMR brings that work into one auditable layer.
Fragmented today
One intelligence layer
- 1Ingest isolate WGS
- 2Interpret with evidence
- 3Trace every step
- 4Emit auditable report
One workflow instead of a fragmented toolchain spread across teams and runs.
Every result carries its evidence, versions and provenance.
Designed for access control in institutional environments.
Watch a demo isolate move through the system. Each stage checks, transforms and adds evidence — from raw reads to a structured, per-antibiotic result. This is a visual simulation of the workflow, not a live analysis.
- 01Quality control✓ donereads filtered · adapters trimmedreads passing QC 98.7%
- 02Taxonomic confirmation✓ donespecies confirmed within scopeEscherichia coli assignment 99.2%
- 03Host depletion✓ donehuman reads removedhost reads removed 0.4%
- 04Assembly & assembly QC✓ donedraft genome assembledmean coverage 82×
- 05Gene annotation✓ donecoding sequences predictedCDS predicted 4,721
- 06AMR detection✓ doneresistance markers matchedAMR genes · mutations 7 · 3
- 07Interpretation & reportrunningper-antibiotic model-estimated probability of resistanceantibiotic panel 9
Select a layer, or hover a node, to follow how evidence connects — from the genome, through the markers found in it, to the antibiotics they affect, to a per-drug interpretation, up to surveillance intelligence.
The full evidence graph.
graph online- Isolate genome→blaTEM-1B
- Isolate genome→gyrA S83L
- Isolate genome→parC S80I
- Isolate genome→sul1
- Isolate genome→dfrA17
- blaTEM-1B→Ampicillin
- gyrA S83L→Ciprofloxacin
- parC S80I→Ciprofloxacin
- sul1→Trimethoprim–sulfamethoxazole
- dfrA17→Trimethoprim–sulfamethoxazole
- Ampicillin→Interpretation
- Ciprofloxacin→Interpretation
- Trimethoprim–sulfamethoxazole→Interpretation
- Interpretation→Surveillance
Illustrative graph based on the ECOLI_DEMO_001 technical replay — not a real patient sample and not a clinical result.
Relationship model for the demo isolate ECOLI_DEMO_001:
- Isolate genome → blaTEM-1B (genome)
- Isolate genome → gyrA S83L (genome)
- Isolate genome → parC S80I (genome)
- Isolate genome → sul1 (genome)
- Isolate genome → dfrA17 (genome)
- blaTEM-1B → Ampicillin (resistance)
- gyrA S83L → Ciprofloxacin (resistance)
- parC S80I → Ciprofloxacin (resistance)
- sul1 → Trimethoprim–sulfamethoxazole (resistance)
- dfrA17 → Trimethoprim–sulfamethoxazole (resistance)
- Ampicillin → Interpretation (clinical)
- Ciprofloxacin → Interpretation (clinical)
- Trimethoprim–sulfamethoxazole → Interpretation (clinical)
- Interpretation → Surveillance (surveillance)
The surfaces NextGenAMR produces: interpretation, provenance, access, database integrity, evidence and the professional-review boundary. Shown here as an illustrative technical replay of the product's E. coli output — not a real patient or clinical sample, for illustrative purposes only, not a clinical report.
- pipelinengamr-core@0.4.2
- dbcard-2025.09
- resfinder-2025.10
- operatorlab.ops/41
- started2026-06-19 09:14 UTC
- readsfastq.gz · paired-end
- CARD 2025.09✓ verified
- ResFinder 2025.10✓ verified
- PointFinder 2025.10✓ verified
Supports qualified laboratory professionals under human supervision. It does not replace phenotypic AST and is not an autonomous diagnosis.
NextGenAMR turns bacterial whole-genome sequencing into structured, traceable resistance interpretation, within its published scope. Every isolate is identified taxonomically, and interpretation is species-specific — each supported species with its own antibiotic panel and model set. The current operational scope is Escherichia coli, with a closed 9-antibiotic panel; additional species are in internal development.
AMR is not an abstract problem. It is measurable.
A species-specific platform
Platform architectureNextGenAMR is not built around a single organism: a species-agnostic layer identifies the isolate, and interpretation is species-specific — each supported species with its own antibiotic panel, feature space and model set. The current operational scope is Escherichia coli; additional species are in internal development, and every call is traced end to end.
Taxonomic classification of supported cultured-isolate WGS inputs (kraken2 / Bracken), gated by a species-confidence threshold.
Species-specific antibiotic panels and a six-model ML ensemble per species–antibiotic pair, emitting model-estimated probabilities of resistance.
Every call carries its evidence, versions and provenance in auditable, reproducible reports (JSON + PDF).
NextGenAMR is in internal, non-clinical validation. Outputs are model-estimated probabilities of resistance — not a categorical S/I/R result and not a clinical diagnosis.
Estimated global deaths directly attributable to bacterial antimicrobial resistance in 2019.
Estimated global deaths associated with bacterial antimicrobial resistance in 2019.
Estimated annual deaths in the EU/EEA directly caused by antimicrobial-resistant infections.
Approximate annual cost of AMR (USD PPP) across 34 OECD / EU / EEA countries, including health-system and broader economic impact.
Bacterial pathogens on the 2024 WHO Bacterial Priority Pathogens List — a priority list for R&D, not a list of species supported by NextGenAMR.
Estimated EU/EEA incidence per 100,000 population of bloodstream infections caused by third-generation cephalosporin-resistant Escherichia coli (ECDC EARS-Net).
Global AMR burden, 2019
Deaths directly attributable to bacterial AMR versus deaths associated with bacterial AMR.
Species-specific by design
NextGenAMR treats AMR interpretation as a species-specific problem: each supported bacterial species has its own antibiotic panel, feature space, model set and interpretation logic. The current published operational scope is Escherichia coli, with a closed 9-antibiotic panel; additional species are in internal development. The architecture is species-specific by design and built to expand; every isolate is identified taxonomically, and the system abstains safely where a species is outside its published scope.
- Species-specific antibiotic panels
- A model set per species–antibiotic pair
- Abstains where a species is out of scope
Increase in EU incidence of third-generation cephalosporin-resistant E. coli bloodstream infections in 2024 compared with 2019.
Increase in EU incidence of carbapenem-resistant Klebsiella pneumoniae bloodstream infections in 2024 compared with 2019. Epidemiological context only — K. pneumoniae is not within NextGenAMR's operational scope.
NextGenAMR platform scope
Species-specific by design: the taxonomy layer identifies the isolate, and each supported species is interpreted through its own antibiotic panel and model set. The current published operational scope is Escherichia coli; the system abstains where a species is out of scope.
Taxonomy across bacterial isolates; species-specific antibiotic panels, feature spaces and model sets. Current published scope: Escherichia coli; additional species in internal development.
Each species has its own defined, closed antibiotic panel — not a single global list.
Ensemble — logistic regression, random forest, gradient boosting, neural net, stacking and probability calibration.
From raw sequencing reads to a structured, traceable AMR report (JSON + PDF).
Designed around bacterial whole-genome sequencing of cultured isolates.
Built around provenance, controlled workflow execution and auditability.
Species-specific antibiotic panel — worked example
Antibiotic panels are species-specific. The panel below is shown for one species as a technical example — each species defines its own.
| Antibiotic | Status |
|---|---|
| Amoxicillin–clavulanic acid | Example |
| Ampicillin | Example |
| Ciprofloxacin | Example |
| Ceftazidime | Example |
| Gentamicin | Example |
| Meropenem | Example |
| Nitrofurantoin | Example |
| Piperacillin–tazobactam | Example |
| Trimethoprim–sulfamethoxazole | Example |
Validation metrics to track
Outputs are model-estimated probabilities of resistance under an internal-validation-only posture — no clinical performance metrics are published yet. Before expansion, the priority is validation, reproducibility and operational reliability.
| Metric | Current status | Why it matters |
|---|---|---|
| Number of isolates tested | Internal validation in progress | Defines the size of the validation dataset |
| Species coverage | E. coli operational · species-specific | Species-specific panels, models and interpretation; more in internal development |
| Antibiotics evaluated | Per-species panels | Each species has its own defined antibiotic panel |
| Output semantics | Model-estimated probability of resistance | Resistance probability, never a categorical S/I/R |
| Agreement with reference AST | To be reported after validation | Measures genotype–phenotype concordance |
| Major errors | To be tracked | Critical for safety analysis |
| Very major errors | To be tracked | Critical for resistant/susceptible misclassification risk |
| Failed runs | To be tracked | Measures operational reliability |
| Median runtime | To be measured across pilot samples | Shows real-world execution performance |
| Provenance completeness | Designed into workflow | Supports auditability and reproducibility |
Public-health figures are external WHO, ECDC and OECD estimates (epidemiological context, not NextGenAMR performance), catalogued with body, year and population scope in the citation source of truth (src/domain/evidence/amr-sources.ts); sources consulted 2026-07-15. Product metrics describe current NextGenAMR platform scope and should not be interpreted as clinical validation claims.
Species-specific analysis
Taxonomic identification across bacterial isolates, with species-specific AMR interpretation — each species with its own antibiotic panel and model set — and safe abstention where a species is out of scope.
AMR-focused reporting
Structured outputs designed around antimicrobial resistance evidence and readable reports.
Pipeline traceability
Designed to preserve provenance, execution metadata and reproducibility signals.
Quality control
Quality, contamination and workflow checks help identify weak or invalid inputs.
Secure architecture
Built with a security-first mindset for access control, auditability and responsible deployment.
Clinical workflow awareness
Designed with laboratories, microbiology teams and hospital environments in mind.
Fast review experience
A clean interface that helps users move quickly from results to understanding.
Expandable foundation
Species-specific by design, built to evolve across organisms, panels and institutional needs as the published scope expands.
Who's reading?
Tune the system to your context. Your choice reshapes what the page foregrounds — nothing is hidden, only re-ordered.
Select a context to tune the view. Or keep the neutral, full read.
Hospital laboratories
Support genomic AMR review and structured reporting workflows.
Discuss this scenarioMicrobiology teams
Organize resistance-related evidence in a clearer, more usable format.
Discuss this scenarioPublic health surveillance
Help transform genomic data into comparable, auditable AMR intelligence.
Discuss this scenarioResearch groups
Accelerate exploratory AMR analysis with a focused, reproducible workflow.
Discuss this scenarioPilot programs
Deploy a controlled platform for institutional evaluation and AMR innovation projects.
Discuss this scenarioEvery result should be explainable, every action traceable, every deployment controlled. Trust is not a badge on this page — it is how the system is built. States below are honest: what is designed in, what is an enforced boundary, and what is still on the roadmap.
NextGenAMR is in internal, non-clinical validation. It carries no regulatory certification (CE-IVD, IVDR, ISO 13485, FDA); its technical documentation is being prepared with future IVDR requirements in mind. Audit integrity is tamper-evident — changes are detectable, not prevented — and the software does not replace phenotypic AST or a clinician's judgement.
Vanguard Biotech Systems (VBS) is a biotech software company building secure bioinformatics infrastructure for genomic antimicrobial resistance. Its conviction: AMR interpretation should not stay trapped between fragmented tools, slow workflows and processes no one can audit. NextGenAMR is VBS's first product — a species-aware, controlled layer where bioinformatics, machine-learning interpretation, security-aware design and traceability come together — and the foundation the company is building on toward broader bacterial-genomics and surveillance workflows.
We are not building another dashboard. We are building the operating layer for AMR intelligence.
Minimal by design. Rigorous by default. Systems that look simple because the complexity has been controlled.
Juan Manuel Gómez Vargas founded Vanguard Biotech Systems to build NextGenAMR — infrastructure that turns bacterial whole-genome sequencing into traceable antimicrobial resistance interpretation. His focus: rigorous bioinformatics, security-aware design and honest, auditable interpretation over hype.
Read the founder profileWhat is NextGenAMR?
NextGenAMR is a species-specific software platform by Vanguard Biotech Systems that turns bacterial whole-genome sequencing (WGS), within its published scope, into interpretable, traceable antimicrobial resistance (AMR) interpretation — from quality control and taxonomy through species-specific AMR interpretation (each supported species with its own antibiotic panel and model set) to auditable reporting. Its current operational scope is Escherichia coli.
Who is NextGenAMR built for?
Clinical microbiology laboratories, hospitals, research institutions and public-health / AMR surveillance networks that work with bacterial genomic data and need structured, traceable resistance interpretation.
Is NextGenAMR clinically validated?
No. NextGenAMR produces outputs for professional review, not a clinical diagnosis and not a regulatory-cleared medical device. It is in active development and internal, non-clinical validation; public demonstrations are illustrative technical replays of the product's E. coli output — not real patient samples. It carries no CE/IVDR/ISO certification, does not replace phenotypic antibiogram (AST), and clinical judgement remains with qualified professionals.
Does NextGenAMR replace clinical judgement?
No. It structures and traces genomic evidence to support experts; interpretation and clinical decisions stay with the responsible clinicians and microbiologists.
What organisms are currently in scope?
NextGenAMR is species-specific by design: its taxonomy layer identifies the isolate, and AMR interpretation is species-specific — each supported species with its own antibiotic panel, feature space and model set. The current published operational scope is Escherichia coli, with a closed 9-antibiotic panel; additional species are in internal development and not yet available. Where a species is outside the published scope, the system abstains safely. Public demonstrations are illustrative technical replays of the product's output — not real patient samples — with Escherichia coli as the worked example.
How can an institution get in touch?
We open non-clinical evaluations case by case. Institutions can reach us through the contact page; every request is reviewed for institutional fit and non-clinical evaluation readiness.
NextGenAMR is in internal, non-clinical validation. We are opening conversations with clinical, research and surveillance institutions interested in future controlled, non-clinical evaluation. Tell us your context — every request is reviewed manually for institutional fit and evaluation readiness.
- vanguardbiotechsystems@gmail.com
- Location
- Granada, Spain
- Focus
- AMR · WGS · Clinical bioinformatics
We open controlled, non-clinical evaluations case by case. Tell us your context from the contact page — we do not ask for patient data, samples, sequences or results.
This project would not exist without the people behind it. To the team — Ángel, Alejandro, Juan Carlos and Irene — for the work, the care and the long hours. To José Luis, for believing in it when it was only an idea. To my family, and above all to my parents, for everything. And to everyone who, directly or indirectly, made NextGenAMR possible — thank you, always.