Antimicrobial Resistance (AMR): The Hidden Threat in the Food Chain

Introduction: A Global Food Safety Challenge

Antimicrobial resistance (AMR) is a silent but escalating threat that undermines the effectiveness of antibiotics the cornerstone of modern medicine and food safety. Once confined to clinical settings, AMR now spreads across farms, water bodies, processing units, and retail food systems. Resistant microorganisms can enter the food chain through animal products, plant-based foods, or contaminated environments, eventually reaching consumers.

AMR The World Health Organization (WHO) and FAO identify AMR as one of the top ten global public health threats, potentially causing 10 million deaths annually by 2050 if left unchecked.

At Eurofins Food Testing Laboratories, we recognize AMR not just as a health crisis but as a food safety and trade challenge. Through advanced genomics, residue analytics, and data-driven surveillance, Eurofins enables industries, regulators, and exporters to detect, manage, and mitigate AMR at every stage of the food chain.

Understanding AMR: How It Develops and Spreads

What Is Antimicrobial Resistance?

AMR occurs when microorganisms (bacteria, fungi, or parasites) evolve mechanisms that render antimicrobial agents ineffective. This results in “superbugs”—pathogens that survive treatment, persist in food systems, and transfer resistance genes to other bacteria.

Pathways of Resistance Formation

Overuse and misuse of antibiotics in livestock, poultry, and aquaculture feed as growth promoters.
Non-compliance with withdrawal periods, leading to residual antibiotics in edible products.
Cross-contamination during slaughtering, food handling, or storage.
Environmental spread via water, soil, and waste contaminated with antibiotics or resistant bacteria.

The One Health Perspective

AMR connects human health, animal health, and the environment—a “One Health” issue. Resistant bacteria and genes move seamlessly between ecosystems, meaning controlling AMR in food systems is vital to protecting both people and the planet.

The Food Chain Pathway of AMR

Stage	Source of Resistance	Path of Transmission	Example
Farm	Antibiotic overuse in animal husbandry	Feed and water contamination	Tetracycline residues in poultry
Processing	Cross-contamination in equipment	Biofilm formation, inadequate sanitation	Resistant Salmonella in meat lines
Environment	Wastewater and manure runoff	Soil and irrigation water pollution	AMR E. coli in fresh produce
Retail & Consumption	Improper cooking/storage	Resistant bacteria survive and spread	Listeria monocytogenes in RTE foods

Major Resistant Bacteria Detected in Food

Pathogen	Typical Food Source	Resistance Genes	Human Health Impact
Salmonella spp.	Poultry, meat, eggs	tetA, blaTEM, qnr	Gastroenteritis, systemic infection
E. coli (ESBL)	Meat, milk, vegetables	blaCTX-M, ampC	Urinary and bloodstream infections
Enterococcus spp.	Dairy, seafood	vanA, ermB	Hospital-acquired infections
Campylobacter spp.	Poultry, dairy	gyrA, cmeABC	Diarrheal disease
Vibrio spp.	Shrimp, fish	blaOXA, sul1	Foodborne cholera-like illness

Eurofins’ Advanced AMR Detection and Monitoring Framework

Antibiotic Residue Testing

Eurofins uses LC-MS/MS, GC-MS/MS, and UHPLC to detect antibiotic residues with precision at ppb/ppt levels.
Monitors over 120 veterinary drug classes, including sulfonamides, fluoroquinolones, macrolides, tetracyclines, β-lactams, and aminoglycosides.
Compliance with FSSAI, EU 37/2010, Codex, and FDA MRLs.
Applied in dairy, meat, seafood, and honey sectors.

Molecular Detection of Resistance Genes

PCR and multiplex PCR detect key resistance genes such as mecA, tet, blaCTX-M, vanA, and qnr.
qPCR quantification measures gene abundance and monitors reduction after mitigation steps.
Whole Genome Sequencing (WGS) identifies mutations, mobile elements, and new resistance pathways.
Eurofins uses bioinformatics pipelines to interpret genomic data and correlate it with antimicrobial usage patterns.

Metagenomics and Resistome Profiling

Eurofins is pioneering shotgun metagenomics for resistome mapping in food, feed, and environment samples.
Detects both culturable and non-culturable resistant bacteria.
Predicts risk trends based on climate, region, and production type.
Enables early warning models for emerging resistance in agriculture and aquaculture.

Environmental and Feed Surveillance

Monitors antibiotic residues in water, soil, and animal feed.
Detects resistant microorganisms in effluent and biofilms.
Supports farm-level AMR audits for exporters and integrators.

Rapid Detection and On-Site Tools (RAFT™)

Eurofins’ Rapid Analytical Food Testing (RAFT™) kits allow screening of antibiotics and AMR indicators within hours at the point of sampling.
Portable and validated under FSSAI Clause 2.4 of Laboratory & Sample Analysis Regulations.
Used by Food Safety Officers, field labs, and processing facilities.

Global and Indian Regulations on AMR

The Food Safety and Standards (Contaminants, Toxins and Residues) Regulations, 2011, Version VIII (effective 01.04.2025), issued by the Food Safety and Standards Authority of India (FSSAI), establishes stringent limits on antibiotics and pharmacologically active substances in food to address antimicrobial resistance (AMR).

Section 2.3.2 sets maximum residue limits for antibiotics in seafood (e.g., Tetracycline at 0.1 mg/kg), bans specific antimicrobials like Chloramphenicol (EMRL 0.0003 mg/kg) in meat, milk, poultry, eggs, and aquaculture, and prohibits antibiotic use in honey production with Minimum Required Performance Limits (MRPLs, e.g., 0.3 µg/kg for Chloramphenicol) to detect misuse. It also specifies tolerance limits for antimicrobials in various foods to ensure safety and minimize AMR risks, aligning with global health standards. Below are the key tables summarizing these regulations:

Table 1: Antibiotics in Seafood

S.No.	Name of Antibiotics	Tolerance Limit (mg/kg or ppm)
1.	Tetracycline	0.1
2.	Oxytetracycline	0.1
3.	Trimethoprim	0.05
4.	Oxolinic acid	0.3

Table 2: Prohibited Antimicrobials and Drugs in Veterinary Practices

S.No.	Prohibited Substances
1.	Carbadox
2.	Chloramphenicol (EMRL: 0.0003 mg/kg)
3.	Chlorpromazine
4.	Clenbuterol
5.	Colistin
6.	Crystal Violet (Sum of Crystal Violet and Leucocrystal Violet)
7.	Glycopeptides
8.	Malachite Green (Sum of Malachite Green and Leucomalachite Green)
9.	Nitrofurans and its metabolites (furazolidone (AOZ), nitrofurazone (SEM), furaltadone (AMOZ), nitrofurantoin (AHD))
10.	Streptomycin and its metabolite dihydrostreptomycin
11.	Nitroimidazoles (including Dimetridazole, Ronidazole, Ipronidazole, Metronidazole, and their metabolites)
12.	Steroids
13.	Stilbenes
14.	Sulphamethoxazole
EMRL: 0.001 mg/kg for all except Chloramphenicol (0.0003 mg/kg).

Table 3: Antibiotics in Honey

Serial No.	Name of Antibiotics	Maximum Residue Performance Limit (MRPL) (µg/kg)
1.	Chloramphenicol	0.3
2.	Nitrofurans and its metabolites	1
3.	Sulphonamides and its metabolites	10 (individually or collectively)
4.	Streptomycin	10 (individually or collectively)
5.	Tetracycline	10
6(a).	Oxytetracycline	10
6(b).	Chlortetracycline	10
7.	Ampicillin	10
8.	Enrofloxacin	10
9.	Ciprofloxacin	10
10.	Erythromycin	10
11.	Tylosin	10

Table 4: Antimicrobials and Drugs in Various Foods

Serial No.	Antimicrobials and Drugs	Food	Tolerance Limit (mg/kg)
1.	Ampicillin	All edible animal tissues, Fats, Milk	0.01
		Finfish	0.05
2.	Amprolium	Cattle (Kidney, Liver, Muscle)	0.5
		Cattle (Fat)	2.0
		Poultry (Kidney, Liver)	1.0
		Poultry (Egg)	7.0
		Poultry (Muscle)	0.5
3.	Apramycin	All edible animal tissues except fish, Fats, Milk	0.01
4.	Albendazole	Species not specified (Muscle, Fat, Milk, Fish)	0.1
		Species not specified (Liver, Kidney)	5.0
5.	Amoxicillin	Cattle, Pig, Sheep (Muscle, Liver, Kidney, Fat)	0.05
		Cattle, Sheep (Milk)	0.004
		Finfish (Fillet, Muscle)	0.05
6.	Cloxacillin	All edible animal tissues, Fats	0.01
		Milk	0.03
7.	Chlortetracycline/Oxytetracycline/Tetracycline	Cattle, Pig, Poultry, Sheep (Muscle)	0.2
		Cattle, Pig, Poultry, Sheep (Liver)	0.6
		Cattle, Pig, Poultry, Sheep (Kidney)	1.2
		Cattle, Sheep (Milk)	0.1
		Poultry (Eggs)	0.4
		Giant prawn (muscle), Fish	0.2
8.	Ceftiofur	Cattle, Pig, Sheep (Muscle)	1.0
		Cattle, Pig, Sheep (Liver)	2.0
		Cattle, Pig, Sheep (Kidney)	6.0
		Cattle, Pig, Sheep (Fat)	2.0
		Cattle (Milk)	0.1 mg/l
9.	Cephapirine	All edible animal tissues except fish, Fats	0.01
		Milk	0.06
10.	Clopidol	All edible animal tissues except fish, Fats	0.01
11.	Closantel	Cattle (Muscle, Liver)	1.0
		Cattle (Kidney)	3.0
		Cattle (Fat)	3.0
		Sheep (Muscle, Liver)	1.5
		Sheep (Kidney)	5.0
		Sheep (Fat)	2.0
		Milk (Bovine)	0.045
12.	Cefphacetrile	All edible animal tissues except fish, Fats	0.01
		Milk	0.125
13.	Cephalexin	All edible animal tissues except fish, Fats	0.01
		Milk	0.1
14.	Danofloxacin	Cattle, Pig, Chicken (Muscle)	0.2 (Cattle, Chicken), 0.1 (Pig)
		Cattle, Chicken (Liver, Kidney)	0.4
		Pig (Liver)	0.05
		Pig, Chicken (Kidney)	0.2
		Cattle, Pig, Chicken (Fat)	0.1
15.	Doramectin	Cattle (Muscle)	0.01
		Cattle (Liver, Kidney)	0.1, 0.03
		Cattle (Fat)	0.15
		Cattle (Milk)	0.015
		Pig (Muscle)	0.005
		Pig (Liver, Kidney, Fat)	0.1, 0.03, 0.15
16.	Diminazene	Cattle (Muscle)	0.5
		Cattle (Liver)	12.0
		Cattle (Kidney)	6.0
		Cattle (Milk)	0.15
17.	Erythromycin	Chicken, Turkey (Muscle, Liver, Kidney, Fat)	0.1
		Chicken (Eggs)	0.05
18.	Flumequine	Cattle, Chicken, Pig, Sheep, Trout (Muscle)	0.5
		Cattle, Chicken, Pig, Sheep (Liver)	0.5
		Cattle, Chicken, Pig, Sheep (Kidney)	3.0
		Cattle, Chicken, Pig, Sheep (Fat)	1.0
19.	Flunixin	All edible animal tissues except fish, Fats, Milk	0.01
20.	Febantel/Fenbendazole/Oxyfendazole	Cattle, Pig, Sheep, Goat (Muscle, Liver, Kidney, Fat, Milk)	0.1 (Muscle, Fat, Milk), 0.5 (Liver, Kidney)
21.	Gentamicin	Cattle, Pig (Muscle, Fat)	0.1
		Cattle, Pig (Liver)	2.0
		Cattle, Pig (Kidney)	5.0
		Cattle (Milk)	0.2 mg/l
22.	Ivermectin	Cattle (Milk)	0.01
		Cattle (Liver, Fat, Muscle, Kidney)	0.8, 0.4, 0.03, 0.1
		Pig, Sheep (Liver)	0.015
		Pig, Sheep (Fat)	0.02
23.	Lincomycin	Cattle (Milk)	0.15
		Chicken, Pig (Muscle)	0.2
		Chicken, Pig (Liver)	0.5
		Chicken (Kidney)	0.5
		Pig (Kidney)	1.5
		Chicken, Pig (Fat)	0.1
24.	Levamisole	Cattle, Pig, Sheep, Poultry (Muscle, Liver, Kidney, Fat)	0.01 (Muscle, Kidney, Fat), 0.1 (Liver)
25.	Monensin	Cattle, Sheep, Goat, Chicken, Turkey, Quail (Muscle, Kidney)	0.01
		Cattle, Sheep, Goat (Liver)	0.1 (Cattle), 0.02 (Sheep, Goat)
		Cattle, Sheep, Goat, Chicken, Turkey, Quail (Fat)	0.1
		Cattle (Milk)	0.002
26.	Moxidectin	Cattle (Muscle)	0.02
		Cattle, Sheep (Liver, Kidney)	0.1, 0.05
		Cattle, Sheep (Fat)	0.5
27.	Meloxicam	Bovines (Muscle)	0.02
		Bovines (Kidney, Liver)	0.065
		Bovines (Milk)	0.015
28.	Neomycin	Cattle, Chicken, Duck, Goat, Pig, Sheep, Turkey (Muscle, Liver, Fat)	0.5
		Cattle, Chicken, Duck, Goat, Pig, Sheep, Turkey (Kidney)	10
		Cattle (Milk)	1.5
		Chicken (Eggs)	0.5
29.	Nicarbazin	Chicken (Kidney, Fat or skin, Liver, Muscle)	0.2
30.	Oxybendazole	All edible animal tissues except fish, Fats	0.01
31.	Oxyclozanide	All edible animal tissues except fish, Fats, Milk	0.01
32.	Parbendazole	All edible animal tissues except fish, Fats, Milk	0.01
33.	Praziquantel	Pig (All edible tissues)	0.01
		Sheep (All edible tissues)	0.05
34.	Penicillin G/Benzylpenicillin	Pig, Chicken, Cattle (Muscle, Liver, Kidney)	0.05
		Cattle (Milk)	0.004
35.	Spectinomycin	Cattle, Chicken, Pig, Sheep (Muscle, Liver, Fat)	0.5, 2.0 (Liver), 2.0 (Fat)
		Cattle, Chicken, Pig, Sheep (Kidney)	5.0
		Cattle (Milk)	0.2 mg/l
		Chicken (Eggs)	2.0
36.	Sulfadiazine	All edible animal tissues, Fats, Milk	0.01
37.	Sulfanilamide	All edible animal tissues, Fats, Milk	0.01
38.	Sulfaquinoxaline	All edible animal tissues except fish, Fats, Milk	0.01
39.	Sulfadimidine	Cattle (Milk)	0.025
		No Specified (Muscle, Fat, Kidney, Liver)	0.1
40.	SulfaChloropyrazine	All edible animal tissues except fish, Fats, Milk	0.01
41.	Sulfamethazine	All edible animal tissues except fish, Fats	0.01
42.	Sulfadimethoxine	All edible animal tissues except fish, Fats, Milk	0.01
43.	Thiabendazole	Cattle, Pig, Sheep, Goat (Muscle, Liver, Kidney, Fat, Milk)	0.1
44.	Triclabendazole	Cattle (Muscle)	0.25
		Cattle (Liver, Kidney, Fat or skin)	0.85, 0.4, 0.1
		Sheep (Muscle, Liver, Kidney, Fat or skin)	0.2, 0.3, 0.2, 0.1
		Milk (All ruminants)	0.01
45.	Trimethoprim	All edible animal tissues except fish, Fats	0.01
		Milk	0.05
46.	Tylosin	Cattle, Pig, Sheep, Chicken (Muscle, Liver, Kidney, Fat or skin)	0.1
		Chicken (Eggs)	0.3
47.	Virginiamycin	Poultry and egg	0.01
48.	Xylazine	All edible animal tissues except fish, Fats	0.01
49.	Zinc Bacitracin	All edible animal tissues except fish, Fats	0.01
		Milk	0.1

https://www.fssai.gov.in/upload/uploadfiles/files/Comp_Contaminants_Regulations_2_4_2025_VIII.pdf

Global and National AMR Regulations

Jurisdiction	Regulation / Standard	Key Requirements / Objectives
FSSAI (India)	Food Safety and Standards (Contaminants, Toxins and Residues) First Amendment Regulations, 2024 (Effective April 1, 2025)	Bans 14 antibiotics (e.g., chloramphenicol, colistin) in meat, milk, poultry, aquaculture, and honey. Sets residue limits (≤0.001 mg/kg) and aligns with Muscat Manifesto to reduce antimicrobial use by 30–50% by 2030.
MoHFW (India)	National Action Plan on AMR (NAP-AMR II, 2024–2029)	Enforces One Health surveillance, regulates antibiotic sales, and aligns with FSSAI’s antibiotic limits.
EU	Council Recommendation on AMR (2023) and Regulation (EU) 2024/580	Limits livestock antibiotic use, bans growth-promoter antibiotics, and requires residue reporting to EFSA.
USFDA	Five-Year Antimicrobial Stewardship Plan (2024–2028)	Promotes careful antimicrobial use in food animals, bans medically important antibiotics for growth, and enhances dairy/meat residue monitoring.
WHO (Global)	WHO Global Action Plan on AMR (Updated 2024)	Targets 30–50% reduction in agrifood antimicrobial use by 2030, strengthens surveillance, and supports Muscat commitments.
Muscat Ministerial Manifesto (2022)	Third Global High-Level Ministerial Conference on AMR	Aims for 30–50% antimicrobial use reduction, bans medically important antibiotics for growth, and ensures 60% of human antibiotic use from WHO “Access Group” by 2030.

Eurofins’ Contribution to AMR Mitigation

Area	Eurofins Initiative	Outcome
Surveillance Programs	Partnered with national AMR task forces & WHO initiatives	Harmonized monitoring in food and feed
Technology Innovation	Deployed WGS and AI-based resistome analytics	Early detection of emerging resistance
Training & Awareness	Workshops for FBOs, FSOs, and QA managers	Strengthened industry capacity
Digital Integration	SmartLIMS™ platform for AMR data capture and trend visualization	Real-time compliance tracking
Sustainability Support	Farm-to-fork antibiotic stewardship audits	Reduced misuse and environmental discharge

Case Study 1: AMR Management in Poultry Exports

A large poultry processor faced export rejections due to antibiotic residues and resistant E. coli.
Eurofins intervention:

Performed LC-MS/MS residue profiling and resistance gene screening.
Implemented withdrawal compliance verification and hygiene audits.
Outcome: Rejection rates dropped by 75% within 3 months, with zero AMR detections in export batches.

Case Study 2: Aquaculture AMR Surveillance in Shrimp

Shrimp ponds showed recurring oxytetracycline resistance in Vibrio spp.
Eurofins approach:

Water and feed analysis for antibiotic residues.
Metagenomic analysis of pond microbiota to identify resistance sources.
Implementation of probiotics and feed reformulation.
Result: AMR levels in export samples reduced below detectable limits, restoring EU market access.

Capacity Building and Knowledge Transfer

Eurofins actively supports government and industry through:

AMR training modules for food safety officers and lab analysts.
Technical workshops on LC-MS/MS method validation and PCR-based AMR detection.
Joint studies with FSSAI, NCDC, and ICAR to map resistance in Indian agri-food systems.

Future of AMR Testing at Eurofins

Innovation	Description
AI-Based AMR Prediction	Machine learning models forecast risk based on climate, antimicrobial usage, and supply chain data.
Blockchain Traceability	Integration with SmartLIMS™ for transparent farm-to-export audit trails.
Resistome Data Sharing	Global AMR data exchange with WHO & EFSA partners for policy alignment.
Eco-toxicological Studies	Assess the impact of antibiotic discharge on soil and aquatic biodiversity.

Why Choose Eurofins

Global AMR expertise with harmonized methods across 900+ labs.
ISO/IEC 17025 and NABL accredited testing network.
Proprietary technologies like RAFT™, SmartLIMS™, and AI-based surveillance tools.
Integrated multi-matrix testing—food, water, feed, and environment.
Expert advisory services for exporters, regulators, and policymakers.

Antimicrobial resistance is not just a clinical problem it’s a food safety, trade, and sustainability challenge. Eurofins provides scientific, data-driven solutions that empower industries to detect, monitor, and mitigate AMR effectively.

Safeguard your supply chain from AMR risks Partner with Eurofins for world-class testing, compliance, and insight.

Enquire now: https://www.eurofins.in/food-testing/enquire-now/