From WGS to Safety: How to Navigate AMR Testing for EFSA Compliance

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Antimicrobial resistance (AMR) continues to pose a serious global health challenge, quietly undermining our ability to treat common infections in both humans and animals. Despite decades of monitoring and policy efforts, recent data from EFSA and ECDC reveal that bacteria resistant to key antimicrobials are still routinely detected in humans and food-producing animals across Europe.

As regulatory expectations continue to evolve, particularly regarding microbial-based products in the food and feed sectors, EFSA has strengthened its scientific framework to better assess and mitigate the risks associated with AMR. For biotech companies and innovators working with microorganisms, three critical pillars have become indispensable in AMR risk assessment: AMR gene screening, MIC (Minimum Inhibitory Concentration) testing, and antimicrobial production analysis.

AMR Gene Screening – The First Red Flag

AMR gene screening is the foundational step in characterizing a microbial strain. The presence of genes coding for or contributing to resistance against clinically relevant antimicrobials should be investigated using WGS, compared against at least two up-to-date curated databases such as CARD, ResFinder, or ARG-ANNOT.

EFSA emphasizes the importance of distinguishing intrinsic from acquired resistance genes. Any acquired resistance genes related to antimicrobials classified as critically important or highly important by the WHO or EMA must be identified. The presence of such genes may lead to a negative safety conclusion unless supported by strong scientific justification.

MIC Test – Understanding Phenotypic Resistance

While genomic data provides valuable insights into the resistance potential of a microorganism, phenotypic testing remains essential to confirm functional resistance, especially when acquired AMR genes are detected or when the function of a resistance gene is uncertain. In such cases, EFSA requires antimicrobial susceptibility testing to determine whether the gene actually confers resistance under laboratory conditions.

The MIC test, which measures the lowest concentration of an antimicrobial that prevents visible growth of the organism, plays a critical role in verifying whether the phenotypic behavior aligns with the genotypic profile of the strain. MIC values must be compared against established cut-off values provided by EFSA, EUCAST, or CLSI. Values exceeding these thresholds may indicate resistance and must be interpreted with care.

To ensure accuracy and reproducibility, MIC testing should be conducted under standardized conditions, including defined growth media, inoculum density, incubation time, and appropriate controls.

Antimicrobial Production Test – Hidden Hazards in Products

Even in the absence of identifiable AMR genes and observable phenotypic resistance, a microbial strain may still produce antimicrobial substances capable of affecting microbial communities, such as the gut microbiota, or contributing indirectly to AMR development.

EFSA recommends that the assessment of antimicrobial substance production should incorporate both WGS-based analysis and phenotypic testing. WGS can be used to detect biosynthetic gene clusters potentially involved in the production of antimicrobial compounds, while in vitro assays serve to confirm whether these genetic elements translate into functional activity. Phenotypically, the culture supernatant and/or the fermentation product should be tested for inhibitory activity against a panel of indicator organisms. The appearance of inhibition zones indicates the secretion of active antimicrobial substances—such as bacteriocins, secondary metabolites, or other bioactive agents.

If such activity is detected, further investigation is necessary to characterize the compound and assess its potential impact. This may involve chemical analysis, detailed study of biosynthetic pathways, or knockout experiments to confirm the nature and safety of the antimicrobial substance.

Final Thoughts

EFSA’s tiered approach—encompassing genotypic, phenotypic, and functional assessments—provides a robust and comprehensive evaluation of AMR risk. For companies developing microbial-based products intended for the food chain, integrating these assessments early in the development process is not only a regulatory expectation but also a proactive measure to safeguard consumer health and ensure product safety and integrity.

As AMR continues to emerge and evolve, so must our vigilance. Sound science, supported by rigorous and standardized testing, remains our strongest defense.

Want to know more?

At BaseClear, we are committed to advancing antimicrobial resistance (AMR) research through innovation, collaboration, and cutting-edge science. By integrating WGS and advanced BioIT analytics into our AMR gene screening, nature of the AMR genes (‘intrinsic’/’acquired’) demonstration, antimicrobial susceptibility testing (MIC), and antimicrobial production assessments, we deliver a comprehensive and EFSA-compliant approach to microbial safety evaluation for food and feed applications.

If you’re preparing a dossier or planning strain characterization, our regulatory expert is ready to support you. We guide you through the entire AMR risk assessment process—from genomic analysis to final dossier submission—bridging scientific excellence with EFSA’s evolving regulatory landscape.