Introduction

A cascading convergence of climate dynamics and agricultural biology is quietly reshaping the risk landscape for global food and feed supply chains. As NOAA forecasts a 62% probability of El Niño emerging between June and August 2026 and persisting through at least the end of the year, industry stakeholders face an urgent reality: warming temperatures, shifting rainfall patterns, and crop stress are amplifying aflatoxin contamination risks across key production regions.

For food manufacturers, feed mills, dairy processors, importers, and exporters, this is no longer a distant climate scenario — it is a near‑term compliance and operational risk. The 2025 harvest season has already demonstrated how climate variability elevates mycotoxin levels in corn and other grains across Europe and the Americas. With a medium‑to‑strong El Niño likely developing in the second half of 2026, this article examines the science behind climate‑driven aflatoxin risk, its cascading impact on supply chains, and practical multi‑layer testing strategies — including rapid screening, ELISA, and confirmatory chromatography — that empower food and feed businesses to manage uncertainty with confidence.

1. Why Aflatoxin Risk Is Increasing: The El Niño–Climate Connection

The relationship between climate patterns and mycotoxin contamination is rooted in how temperature, moisture, and crop stress influence fungal behavior and toxin production.

1.1 El Niño 2026: What the Forecasts Show

Multiple global weather models agree on the near‑term outlook. According to NOAA’s latest ENSO Diagnostic Discussion, the Pacific is transitioning toward El Niño conditions. ENSO‑neutral is favored through May–July 2026 at a 55% probability, followed by El Niño emerging in June–August at a 62% chance. The event is expected to persist through the rest of 2026, though its ultimate strength remains uncertain.

El Niño typically brings distinct regional weather impacts: drought stress in parts of Southeast Asia, Australia, and southern Africa; excess rainfall and flooding risks in South America; and altered monsoon patterns across the Indian subcontinent. These extremes — particularly drought followed by untimely rainfall — create ideal conditions for fungal proliferation.

1.2 How Warming and Moisture Drive Fungal Growth

Aflatoxins are toxic secondary metabolites produced primarily by Aspergillus flavus and Aspergillus parasiticus. Their production is directly modulated by environmental conditions. Rising temperatures, droughts, and shifting rainfall patterns increasingly favor the growth of aflatoxigenic fungi and pre‑harvest aflatoxin contamination in crops, posing growing risks to food and feed safety.

The mechanism is well understood:

• Heat stress — when daily temperatures rise into the 25–40°C range during grain filling and maturation — directly accelerates fungal metabolism and aflatoxin biosynthesis.
• Drought stress weakens crop immune responses and alters kernel structure, making plants more susceptible to invasion and toxin accumulation.
• Humidity and rainfall patterns influence the post‑harvest environment, where improper drying or storage can trigger explosive fungal growth.

A 2025 review published earlier this year reinforces that global environmental changes (increased temperature, heavy rainfalls, and droughts) are modulating factors of mold growth and mycotoxin production.

1.3 Regional Evidence: Europe, the Americas, and Beyond

The 2025 harvest season provided tangible evidence of these dynamics. Multiple industry sources confirmed that warmer weather in Southern Europe contributed to elevated aflatoxin levels in corn, while barley showed a much higher risk than wheat, averaging 6.7 mycotoxins per sample. The 2025 findings confirm that mycotoxin risk remains highly variable, region‑specific, and strongly influenced by weather and crop stress — a pattern that will likely intensify under El Niño conditions in 2026.

In Latin America, the 2025 global mycotoxin landscape was shaped by increasing pressure on raw material supply chains, with mycotoxin prevalence no longer confined to specific regions or seasons. Climate change is flattening traditional risk maps, and low‑dose, long‑term exposure is becoming the dominant concern for animal health and performance.

A peer‑reviewed European overview reached a similar conclusion: rising temperatures, droughts, and shifting rainfall patterns increasingly favor the growth of aflatoxigenic fungi and pre‑harvest aflatoxin (AF) contamination in European crops, with significant implications for agricultural stability.

2. From Farm to Fork: How Aflatoxin Enters the Food Chain

2.1 Primary Contamination: Corn, Peanut, and Other High‑Risk Crops

Corn and peanuts are the most frequently contaminated commodities. In corn — a staple ingredient for both human food and animal feed — drought stress during kernel fill triggers a defense response that simultaneously makes the plant more permeable to Aspergillus infection. Once inside, the fungus proliferates rapidly in warm conditions.

Aflatoxin contamination continues to be a perennial issue, resulting in significant economic losses to the global peanut industry. The association between aflatoxin contamination and drought and heat stresses is well documented and of growing concern with ongoing climate change.

2.2 Feed Contamination: The Unseen Gateway

Animal feed — particularly corn‑based feed and byproducts like DDGS — acts as a concentrated pathway for aflatoxin entry into the livestock production system. Maize is just one source of mycotoxins that can contaminate feed; other grains, byproducts, and protein meals contain different mycotoxins that can increase the overall contamination level when formulating diets.

Once contaminated feed is consumed by livestock, the consequences cascade. Mycotoxin contamination damages the organism through multiple mechanisms, including oxidative stress, cellular apoptosis, and disruption of the gut‑liver axis and gut‑immune axis.

2.3 Dairy Carry‑Over: AFB1 → AFM1

This is perhaps the most consequential and least understood pathway. When dairy cattle consume AFB1‑contaminated feed, their livers metabolize a portion of the toxin into Aflatoxin M1 (AFM1), which is secreted into milk. This carry‑over occurs even when feed AFB1 levels are within regulated limits.

The economic significance cannot be overstated. A single AFM1 detection in a milk tank can trigger product recall, brand damage, and suspension from export markets. The European Union’s maximum limit for AFM1 in milk is 0.05 μg/kg — among the strictest globally. Meeting this standard requires not only testing milk at the farm gate but also upstream screening of incoming feed ingredients.

2.4 Economic Toll: The True Cost of Contamination

Mycotoxin contamination poses a significant threat to all stakeholders: farmers, feed producers, food processors, public authorities, and end consumers. Global economic losses from aflatoxin contamination — including trade rejections, medical costs, and lost productivity — are estimated to range from USD 600 million to USD 1.8 billion annually.

The 7th International Conference of Mycotoxicology and Food Security convened in Hangzhou in March 2026, where experts confirmed that with climate warming, contamination risks have shown a tendency to intensify, posing serious threats to food safety and public health. Presentations examined evolving trends of mycotoxins under climate change and their impacts on global supply chains.

3. Why Food and Feed Companies Face Rising Risks in 2026

3.1 Export Risks: Border Enforcement Is Tightening

The global trade landscape for aflatoxin‑sensitive commodities is becoming more restrictive. Recent border incidents highlight the trend:

March 2026 – Albania: Albania’s National Food Authority intercepted five shipments of animal feed corn at the Han i Hotit border crossing due to aflatoxin B1 exceeding legal limits — four shipments originating from Serbia and one from Greece.

April 2026 – EU (RASFF): German authorities notified the EU’s Rapid Alert System for Food and Feed (RASFF) that U.S.‑origin peanut shipments contained aflatoxin B1 levels at 58 ± 18 μg/kg and total aflatoxins at 66 ± 19 μg/kg, far exceeding EU allowable limits. The product was refused entry before reaching the EU market.

3.2 Regulatory Pressures: Global Standards Converging Downward

European Union: The EU maintains the strictest standards globally. Regulation (EU) 2023/915, as amended, sets maximum levels for aflatoxins in many direct‑consumption products at 2 μg/kg for AFB1 and 4 μg/kg for total aflatoxins. In July 2025, the European Commission issued Implementing Regulation (EU) 2025/1441, temporarily strengthening official controls on certain third‑country food and feed due to contamination risks, including aflatoxins. The Commission has also launched a public consultation to further amend Regulation 2023/915, aiming to refine criteria for aflatoxin levels in maize and rice.

United States: The FDA enforces aflatoxins through action levels — thresholds enforceable under the Federal Food, Drug, and Cosmetic Act. The action level for aflatoxin in human food (peanuts and corn) is 20 μg/kg. In 2025, 87.2% of tested corn samples fell below the FDA’s strictest fumonisin guidance level of 5 ppm — a lower compliance proportion than in 2024 (97.2%).

3.3 Supply Chain Pressure: Testing Bottlenecks in a High‑Volume World

The fundamental tension in aflatoxin risk management lies between sampling uncertainty and throughput demands. Aflatoxin contamination in a grain lot is rarely uniform — a few “hot kernels” can determine the lot’s regulatory fate. Traditional sampling plans (e.g., taking a single 1‑kg sample from a 20‑metric‑ton container) inherently risk missing localized contamination.

Compounding this, HPLC‑ and LC‑MS/MS‑based confirmatory testing — while accurate and regulatory‑compliant — is time‑consuming. Sample preparation, immunoaffinity column cleanup, and instrument analysis typically take 2–5 hours. For a high‑volume facility receiving dozens or hundreds of shipments daily, sending every sample to a contract lab is impractical.

3.4 Limited Bandwidth of Third‑Party Laboratories

Even for companies that outsource aflatoxin testing to ISO 17025‑accredited laboratories, capacity constraints are real. During harvest peaks or when climate events trigger widespread contamination (as expected under El Niño 2026), labs face backlogs. Delays of several days to over a week can occur — a timeline that conflicts with just‑in‑time inventory systems and contractual delivery obligations.

4. Traditional Mycotoxin Testing Methods: A Comparative Framework

The core challenge for food and feed businesses is selecting the right testing method for the right purpose. Each approach occupies a distinct position on the accuracy‑speed‑cost spectrum.

The practical industry standard is a tiered testing pyramid:

• Tier 1 — Rapid Screening (10–20 minutes): Performed on every incoming lot at the receiving dock. Rapid tests act as a “gatekeeper,” identifying suspect lots for further analysis and allowing immediate release of compliant lots into the production stream.
• Tier 2 — ELISA Quantitative Screening (2–3 hours): Conducted on a statistically significant subset of lots that pass rapid screening, providing numerical data for inventory management and supplier scorecards.
• Tier 3 — HPLC or LC‑MS/MS Confirmation (4–24 hours): Applied only to lots that test positive or near‑limit on ELISA, or for official export certification. This is the “gold standard” for regulatory reporting.

5. Why Rapid Screening Has Become Essential

5.1 Market Trends: The Rapid Testing Market Is Accelerating

The underlying need for rapid, decentralized mycotoxin testing is reflected in market metrics. The global aflatoxin detection kit market was valued between USD 280 million and USD 300 million in 2025 and is projected to grow at a CAGR of 6–7% through 2030, reaching approximately USD 380–420 million. The global mycotoxin ELISA rapid test kit market alone was valued at USD 519 million in 2024 and is forecast to reach USD 732 million by 2031, growing at a CAGR of 5.6%. The broader rapid food safety testing market reached USD 19.66 billion in 2025 and is projected to exceed USD 31 billion by 2030 (CAGR 9.7%).

5.2 The “First Line of Defense” Advantage

Rapid screening tests — specifically lateral flow immunoassays — provide actionable information in minutes, not hours or days. When a tanker truck of corn‑based feed ingredients arrives at your facility, a 10–20 minute test allows you to:

• Immediately release negative lots into production
• Isolate suspect lots in a separate holding area
• Prioritize which samples to send for confirmatory testing
• Document every lot’s screening result for audit trails

This reduces both holding costs (warehouse space, tied‑up capital) and compliance risk (missing a hot lot that would later be detected at the border).

5.3 Economic Justification: Screening Pays for Itself

Consider a simple example. A mid‑sized feed mill receives 50 truckloads of corn per week. Each load contains 20 metric tons of corn worth approximately USD 8,000. Sending all 50 loads to a contract lab for HPLC testing (at USD 200 per sample, 4‑day turnaround) would cost USD 10,000/week and introduce a 4‑day inventory float.

Using rapid strip tests at a cost of USD 10–15 per test, the same 50 loads cost USD 500–750 per week — 93% less — and generate results in 20 minutes. Loads passing the rapid screen go directly into production. Suspect loads (typically 5–10% in a moderate‑risk season) are sent to the contract lab. The ROI of rapid screening is often realized in the first month.

6. Practical Testing Workflow for Climate‑Resilient Risk Management

6.1 Recommended Multi‑Tier Protocol

For an enterprise exposed to aflatoxin risk — whether a food processor, feed mill, import firm, or dairy cooperative — the following workflow integrates regulatory requirements with operational efficiency.

Step 1 — Inbound Screening (All Lots)
Method: Rapid test strip (qualitative or semi‑quantitative)
Time: 10–20 minutes
Action: Negative result → Release into production/work‑in‑progress; Positive/Detected result → Isolate lot; transfer to Step 2

Step 2 — Quantitative Measurement (Positive/High‑Risk Lots)
Method: ELISA kit (quantitative)
Time: 2–3 hours (including extraction and incubation)
Action: Result < 50% of regulatory limit → Risk‑adjusted release with documented mitigation; Result ≥ 50% of regulatory limit → Hold for Step 3

Step 3 — Confirmatory Analysis (Legal/Export Compliance)
Method: HPLC‑FLD or LC‑MS/MS (ISO 17025‑accredited)
Time: 1–5 days (depending on lab capacity)
Action: Result below regulatory limit → Issue Certificate of Analysis; Result above regulatory limit → Reject lot / Rework or divert to regulated use

6.2 Integrating Rapid Aflatoxin Test Kits into QA Programs

The product categories below correspond to the three families of rapid tests most relevant to the current risk environment.

AFT (Total Aflatoxin) Rapid Kit
Total aflatoxin detection covers the four major aflatoxin variants (B1, B2, G1, G2) in a single assay. For grain‑based ingredients — corn, wheat, rice, barley — this provides the most comprehensive initial risk assessment. Application: raw material receiving, warehouse composite sampling.

AFB1 (Aflatoxin B1) Rapid Kit
AFB1 is the most potent and carcinogenic aflatoxin subtype. European regulations set its maximum level at just 2 μg/kg in many food products — five times stricter than total aflatoxin (4 μg/kg). An AFB1‑specific rapid kit provides higher discrimination at the lowest concentration ranges, useful for raw materials destined for direct human consumption or high‑value animal feed (e.g., dairy, poultry).

AFM1 (Aflatoxin M1) Rapid Kit
This kit is specifically designed for milk and milk‑based products. AFM1 is not present in raw plant materials — it is a metabolite formed in dairy cows after ingestion of AFB1‑contaminated feed. For any facility handling liquid milk, powdered milk, or dairy‑derived ingredients, an AFM1 rapid test is the essential barrier between contaminated raw material and finished product.

In a climate‑resilient screening program, these three rapid kits operate as complementary assets: AFT for plant‑based ingredients, AFB1 for high‑resolution detection in sensitive supply chains, and AFM1 specifically for dairy.

7. Future Outlook: Industry Trends and Climate‑Driven Risk

7.1 Forecast: El Niño 2026 Will Elevate Aflatoxin Probability

The combination of NOAA’s 62% probability of El Niño emerging June–August 2026 and the typical 2–4‑month lag between weather events and harvest‑stage contamination means that the highest risk window will be Q3 and Q4 2026, extending into Q1 2027 for Southern Hemisphere exports.

Global mycotoxin averages for Q1 2026 — before the El Niño effect fully manifests — were predicted to reach approximately 6.3 ppb for aflatoxin, 812 ppb for fumonisins, 460 ppb for DON, and 73 ppb for ZEN across global feed samples. If El Niño increases aflatoxin levels by the multiples observed in prior strong El Niño years (2x to 5x in specific regions), the proportion of lots exceeding regulatory limits may double in high‑risk zones.

Trouw Nutrition, in its 2025 Global Mycotoxin Review covering more than 120,000 feed ingredient and complete feed samples from 47 countries, has warned that persistent contamination in feed ingredients and changing climate patterns will require feed producers to strengthen risk management strategies in 2026. The report deploys a robust model to identify threats to manage in 2026 feed formulation and livestock production.

7.2 Prediction: Mycotoxin Testing Will Shift Left — From Lab to Field

Three structural trends are reshaping the industry:

1. Decentralized testing. The cost and time of centralized HPLC/LC‑MS/MS laboratories are driving adoption of field‑deployable rapid tests — not to replace confirmatory methods but to supplement them by performing screening at much higher frequency.
2. Multi‑toxin awareness. Feed mills and food processors increasingly recognize that aflatoxin is often accompanied by other mycotoxins (fumonisins, DON, ZEN). An integrated testing plan accounts for co‑contamination — not just single‑toxin compliance.
3. Climate‑linked risk modeling. Companies are beginning to integrate NOAA’s ENSO forecasts and seasonal weather predictions into procurement and testing plans. When El Niño is forecast, procurement teams can pre‑emptively source from lower‑risk regions, diversify supply, and pre‑position rapid tests at receiving locations.

7.3 The Strategic Imperative: Build Resilient Screening Capacity

The window between now and Q3 2026 — when El Niño’s agricultural impacts will first appear in harvests — is the ideal time to review and stress‑test aflatoxin risk management protocols. Key questions to ask:

• Are all inbound lots screened with a rapid method before entering the production system?
• Does your supplier scorecard reflect climate‑related contamination risk (e.g., past El Niño events)?
• Is your laboratory network positioned to absorb a 30–50% increase in confirmatory testing demand during peak risk periods?
• Have dairy AFM1 thresholds been aligned with upstream AFB1 screening of purchased feed ingredients?

8. Frequently Asked Questions (FAQ)

Q1: How specifically does El Niño increase aflatoxin levels in corn and peanuts?
A: El Niño triggers drought stress during critical crop growth stages (kernel fill for corn, pod maturation for peanuts). Drought weakens crop physical barriers and triggers stress responses that paradoxically make the plant more susceptible to Aspergillus infection. Simultaneously, elevated temperatures accelerate fungal metabolism and aflatoxin biosynthesis. The combined effect — stress + heat + fungal activity — increases both the percentage of contaminated kernels and the concentration of toxin per kernel.

Q2: If we already use an ISO‑accredited contract lab for HPLC testing, why do we need rapid screening at our facility?
A: For two reasons. First, timing — a 4‑day HPLC turnaround doesn’t match the 4‑hour inventory window at a receiving dock. Rapid screening provides immediate “accept/reject/suspend” information. Second, coverage — sampling plans for aflatoxin screening have high uncertainty. Testing a single 1‑kg sample from a 20‑ton container can miss contamination that’s present in 1% of kernels. Running a rapid test on a composite of multiple sub‑samples reduces the risk of “sampling error” false negatives.

Q3: Which regulatory limits apply to aflatoxins in different markets?
A: Key regulatory benchmarks for total aflatoxins (or specific variants):
- European Union (direct consumption): AFB1 max 2 μg/kg; total aflatoxins max 4 μg/kg
- European Union (milk, AFM1): 0.05 μg/kg
- United States (human food, peanuts/corn): 20 μg/kg action level
- China (GB 2761‑2017): AFB1 in corn/peanut: 20 μg/kg; total aflatoxins in milk: 0.5 μg/kg
Note: EU Regulation 2023/915 underwent multiple amendments in 2024 and 2025, and a public consultation on further revisions was launched in September 2025. Monitoring regulatory updates is essential.

Q4: What is the difference between AFT, AFB1, and AFM1 rapid test kits — and when should each be used?
A:
- AFT (Total Aflatoxin) Rapid Kit: Detects AFB1, B2, G1, G2 combined. Best for broad‑spectrum grain and feed screening.
- AFB1 (Aflatoxin B1) Rapid Kit: Detects only the most toxic subtype, AFB1. Use for direct human food ingredients and dairy feed where EU’s strict AFB1 limit (2 μg/kg) applies.
- AFM1 (Aflatoxin M1) Rapid Kit: Detects the milk metabolite of AFB1. Use exclusively for liquid milk, powdered milk, and dairy‑derived ingredients. Not for plant‑based materials.

Q5: How should my company adjust its 2026 testing plan based on the El Niño forecast?
A: Recommended adjustments:
- Increase rapid screening frequency from a percentage‑of‑lots basis to 100% of lots from high‑risk origin regions (South America, Southern Africa, Southeast Asia).
- Pre‑position additional ELISA kits at internal laboratories to handle increased volume of quantitative screening for suspect lots.
- Notify third‑party contract labs of expected volume increases and negotiate priority turnaround agreements.
- Train receiving dock personnel on sampling protocols that incorporate multiple sub‑samples for composite testing.
- Review supplier contracts to include climate‑related contingency clauses (e.g., increased testing rights during El Niño‑declared periods).

Q6: Can rapid tests detect aflatoxins at EU‑compliant levels (2–4 μg/kg)?
A: Yes — but with important nuance. Modern lateral flow rapid tests are designed to detect at or below regulatory limits. However, rapid tests are screening tools, not confirmatory methods. A negative result on a well‑validated rapid test provides high confidence that the lot is below the detection threshold. A positive or borderline result must be followed up with quantitative ELISA and/or HPLC/LC‑MS/MS for regulatory compliance. This “screen → confirm” workflow is industry best practice and aligns with international guidance on mycotoxin testing.

Q7: Which regulatory bodies provide authoritative guidance on mycotoxin limits and testing?
A: Primary sources include:
- FDA — Chemical Contaminants Transparency Tool (updated March 2025), action levels for aflatoxin in food and feed
- European Commission — Regulation (EU) 2023/915 (as amended), setting maximum levels for contaminants including aflatoxins
- EFSA — Ongoing risk assessments and scientific opinions on mycotoxin health risks
- Codex Alimentarius — International maximum levels adopted by member nations
- USDA GIPSA — MycoSAM program providing mycotoxin surveillance data

9. Conclusion

The return of El Niño in 2026 is not merely a meteorological headline — it is a material risk factor for every business that sources, processes, or trades corn, peanuts, feed ingredients, or dairy products. Climate change is no longer a distant policy debate; its fingerprints are already visible in the aflatoxin levels measured across European corn harvests in 2025.

The appropriate industry response is not alarm — it is preparation. Building a climate‑resilient aflatoxin risk management program means:

• Deploying rapid screening (AFT, AFB1, AFM1 kits) at every receiving point to create a high‑frequency, low‑cost “first filter” for contamination
• Maintaining quantitative ELISA capability for high‑volume, risk‑based screening of suspect lots
• Retaining access to ISO 17025‑accredited HPLC or LC‑MS/MS confirmatory testing for regulatory compliance and export certification

The most resilient food and feed companies are those that recognize a fundamental truth: in an era of climate‑driven biological risk, the speed and quality of your first screening decision determine your exposure to liability. The 10–20 minutes invested in a rapid test at the receiving dock may be the most valuable time in your entire supply chain quality system.

For organizations seeking to upgrade their risk management infrastructure ahead of the 2026 El Niño event, a tiered testing approach — rapid screening, followed by ELISA quantitation, concluded by confirmatory chromatography — offers the optimal balance of speed, cost, and regulatory certainty.

Disclaimer: The information in this article is for educational and informational purposes only and does not constitute legal or regulatory advice. Aflatoxin testing protocols and regulatory limits vary by jurisdiction and product type. Businesses should consult with qualified food safety professionals and legal counsel to develop testing plans appropriate to their specific operations, supply chains, and target markets. Regulatory documents cited herein are current as of the publication date but are subject to amendment; readers are responsible for verifying the most updated versions.