One Health — zoonosis & AMR monitoring as a service

01Overview and value chain

Markers: [EC: EU Directive 2003/99/EC + Commission Implementing Decision (EU) 2020/1729 harmonised AMR monitoring | OECD: Biotech & health | Regulator: USDA-APHIS (USA), EFSA (EU), MoA (China)]

One Health zoonosis and antimicrobial-resistance (AMR) monitoring as a service sells integrated surveillance — human, animal and environmental compartments read together — to governments, food producers and pharma supply chains that cannot run reference labs in-house. The technical core is shotgun metagenomic sequencing of environmental swabs, feces and wastewater: a single weekly run on an MGI DNBSEQ or Oxford Nanopore platform recovers both the resistome (antimicrobial-resistance genes mapped against the CARD database of more than 5,000 reference sequences) and zoonotic pathogens such as H5N1 avian influenza and African swine fever in one assay. The EU harmonises this through Directive 2003/99/EC and Commission Implementing Decision (EU) 2020/1729, which fix the bacterial panels, the indicator organisms and the breakpoints every member state must report annually. The market is consolidating fast: in March 2026 Zoetis agreed to buy Neogen’s animal-genomics business for 160 million USD, folding 5 reference labs and customers in 120-plus countries into a single commercial surveillance network. The synergy is that genomic pathogen detection, resistome profiling and AI spillover-risk scoring share one sample, one sequencing run and one LIMS, so the marginal cost of adding a second hazard to a surveillance contract is close to zero.

The key directions of One Health zoonosis & AMR monitoring are:

1. Veterinary reference diagnostics (commercial lab networks): IDEXX and Zoetis run global point-of-care and reference-lab networks; IDEXX reported 3.81 billion USD in FY2024 revenue and in May 2026 extended its Fecal Dx antigen platform to taeniid tapeworms (Taenia, Echinococcus), detecting up to twice as many intestinal parasite infections as fecal flotation alone.
2. Harmonised national AMR surveillance (policy service): EFSA’s EU Summary Report and the EARS-Vet network standardise resistance monitoring in zoonotic and indicator bacteria across all member states, with cost-optimised sampling designs (the Belgian livestock programme being a published reference case).
3. Metagenomic environmental surveillance (sentinel service): Wageningen Bioveterinary Research and the ALARUM consortium run active One Health surveillance in low- and middle-income countries using long-read nanopore metagenomics on farm manure and wastewater to predict resistance emergence.
4. Spillover early-warning at the wildlife-livestock interface: the Friedrich-Loeffler-Institut and the Harbin Veterinary Research Institute operate BSL-3 reference labs tracking avian influenza and African swine fever, feeding national notification systems before cross-species jumps.

Sectoral value chain

[sampling] ──> [sequencing] ──> [bioinformatics] ──> [risk scoring]
                                       │
                                 (resistome + pathogen)
                                       │
                                       ▼
[policy action] <─── [LIMS reporting] <┘

Value chain levels

Cross-cutting technologies of the sector:

• Shotgun metagenomic sequencing (untargeted): one library reads every genome in a sample, recovering pathogens and AMR genes without prior knowledge of the target.
• AMR resistome profiling (CARD/AMRFinderPlus): alignment of reads against curated resistance-gene databases to quantify the resistome and its mobile-element context.
• Genomic pathogen surveillance (real-time): isolate and metagenomic sequencing feeding phylogenetic outbreak tracing and trade-relevant typing.

02US

The United States runs surveillance as a federated network of federal programmes and large commercial veterinary labs, with the private sector supplying most of the diagnostic throughput.

veterinary reference labs, NARMS AMR surveillance, fecal antigen screening

• IDEXX Laboratories: a 3.81 billion USD (FY2024) veterinary diagnostics leader whose reference-lab network and VetConnect Plus software push PCR and antigen results into clinics; in May 2026 it expanded Fecal Dx to taeniid tapeworms including the zoonotic Echinococcus.
• Zoetis: the world’s largest animal-health company agreed in March 2026 to acquire Neogen’s animal-genomics unit for 160 million USD, integrating disease-resistance genomic selection (Clarifide) with pathogen monitoring across 120-plus countries.
• NARMS framework: the national antimicrobial-resistance monitoring system links human, retail-meat and animal isolates, the policy template that commercial One Health services report into.

03CN

China centres surveillance on state veterinary research institutes and agricultural universities, coupling genomic pathogen labs with a national AMR-containment programme.

avian-influenza & ASF reference labs, livestock AMR governance, environmental microbiomes

• Harbin Veterinary Research Institute (CAAS): the leading state R&D centre for avian influenza and African swine fever, operating BSL-3/ABSL-3 facilities to model cross-species transmission.
• China Agricultural University: runs AMR surveillance across livestock and environmental microbiomes and underpins cross-sectoral synergy governance for AMR control in China.
• National containment plan: the MoA-coordinated programme drives genomic surveillance of resistant organisms across the live-animal and food chain.

04EU

The EU operates the most harmonised system, with legally fixed monitoring panels and a continent-wide veterinary surveillance network alongside accredited commercial testing.

harmonised AMR reporting, EARS-Vet network, metagenomic sentinel surveillance

• EFSA & the EU Summary Report: EFSA compiles AMR in zoonotic and indicator bacteria from humans, animals and food under Directive 2003/99/EC and Decision (EU) 2020/1729, the binding reporting backbone.
• Friedrich-Loeffler-Institut (Germany): the federal animal-health institute is the national reference lab for avian influenza, issuing the monthly Radar Bulletin and feeding the TSIS notification system.
• Wageningen Bioveterinary Research & ALARUM: active One Health surveillance using long-read nanopore metagenomics to monitor and predict AMR, extended to low- and middle-income settings.

05Leading companies and research institutes

06Tech stack and innovations

The service stack is built on untargeted sequencing, curated reference databases and accredited reporting pipelines that turn one sample into multi-hazard intelligence.

1. Shotgun metagenomic sequencing (untargeted):
   • Host-DNA depletion then tagmentation libraries sequenced on MGI DNBSEQ or Oxford Nanopore platforms, recovering pathogens and resistance genes in one run.
   • Long-read nanopore data (the ALARUM and WBVR approach) resolves AMR genes together with their mobile genetic-element context, which short reads miss.
2. Resistome and pathogen bioinformatics (CARD + Kraken2):
   • Reads are taxonomically classified in Kraken2 and aligned against the CARD database of 5,000-plus resistance-gene references to quantify the resistome.
   • Isolate genomes feed phylogenetic outbreak tracing and breakpoint comparison against the EU harmonised panels.
3. AI spillover-risk scoring & LIMS reporting (ISO 17025):
   • Pathogen and AMR profiles are scored for cross-species spillover risk (for example H5N1 at the poultry interface) and trended over time.
   • Accredited LIMS dashboards emit EFSA- and NARMS-format reports, closing the loop to stewardship and trade decisions.

07Value chains and production pipelines

Industrial pipeline of weekly metagenomic AMR & zoonosis surveillance on a one-million-bird poultry complex (ISO 17025 / cGLP)

┌───────────────────────────┐      ┌───────────────────────────┐
│ 1. Environmental sampling │ ───> │ 2. Host-DNA depletion     │
└───────────────────────────┘      └───────────────────────────┘
                                                 │
                                                 ▼
┌───────────────────────────┐      ┌───────────────────────────┐
│ 4. Shotgun sequencing     │ <─── │ 3. Metagenomic library    │
└───────────────────────────┘      └───────────────────────────┘
              │
              ▼
┌───────────────────────────┐      ┌───────────────────────────┐
│ 5. Bioinformatic calling  │ ───> │ 6. Risk scoring & alert   │
└───────────────────────────┘      └───────────────────────────┘

Stage 1: Environmental sampling

Weekly boot-swabs, litter and feces are collected across the houses of a one-million-bird layer complex, barcoded and cold-chained to preserve nucleic acids for sequencing.

Stage 2: Host-DNA depletion

Enzymatic depletion removes avian host DNA so that the bacterial and viral fraction dominates the library, raising the effective sensitivity for low-abundance pathogens and AMR genes.

Stage 3: Metagenomic library preparation

Tagmentation builds shotgun libraries from the depleted extract, with unique dual indices so that dozens of samples are multiplexed on a single flow cell.

Stage 4: Shotgun sequencing

Libraries are sequenced on an MGI DNBSEQ or Oxford Nanopore device; a single weekly run recovers both the resistome and zoonotic agents such as H5N1 in one untargeted assay.

Stage 5: Bioinformatic calling

Reads are classified in Kraken2 and aligned against the CARD database of 5,000-plus resistance references, producing a taxonomic profile, a resistome and virulence-gene calls.

Stage 6: Risk scoring and alert

An AI model scores spillover risk and resistance trends, and the accredited LIMS issues EFSA/NARMS-format alerts to operators and competent authorities for stewardship and outbreak response.