Flexible screening of infectious diseases and antibiotic resistance in poultry farming

Conventional poultry farming is particularly affected by the development of antimicrobial resistance (AMR) due to the high stocking density, the widespread use of antibiotics (AB) to prevent infectious diseases, and the associated selection pressure. Despite intensive research and efforts in recent years, the measures taken have only had a limited impact on reducing AB use in poultry. Holistic, cross-stage and integrated solutions combined with innovative processes are required to ensure resource-efficient animal husbandry, the sustainable use of AB, and high-quality animal products in line with the World Health Organization's (WHO) One Health Strategy.

The goal of MAGniFlex is to capture, analyze, and share information on poultry health, housing, and management conditions more efficiently within farms and across stakeholders in the value chain. By developing mobile rapid test methods for detecting bacterial pathogens, antimicrobial resistance (AMR) profiles, and antibiotic (AB) residues, along with a highly integrative digital data collection platform, the project aims to enable targeted preventive and intervention hygiene measures and help prevent the spread of AMR. The project focuses on the provision and combination of four key innovations:

1. Optimized sampling strategy for the enrichment of specific pathogens from complex sample matrices using phage-mediated nanosonde-based magnetic separation (NBMS).

2. Rapid on-site detection of pathogen-specific gene sequences and AMR profiles using a loop-mediated isothermal amplification (LAMP)-based magnetic method (MAGniLAMP).

3. Rapid on-site detection for qualitative and quantitative analysis of AB residues using competitive magnetic immunodetection (cMID).

4. User-friendly cloud-based data collection platform with an associated app (MAGniWARE) for cross-level data capture and analysis.

Combined, these methods aim to enable more comprehensive health monitoring of poultry flocks by efficiently linking information on AB residues, AMR, and flock health data. Potential sources of contamination and pathogen hotspots can be identified earlier, helping to prevent the spread of pathogens to healthy flocks. The methods will be demonstrated along the production and food chain—from eggs to chicks to slaughter animals—using laying hen and broiler farms for three target pathogens in test operations. Fraunhofer IME is responsible for overall coordination and is primarily involved in the development of innovative rapid test systems.