The Project #AIR-SAMPLE
|Start:||1 January 2018|
|Keywords:||Next generation sequencing (NGS), metagenomics, method validation, diagnostics, quality assurance|
|Contact:||Gro Johannessen (NVI)|
AIR-SAMPLE: Air-sampling, A Low-Cost Screening Tool in Biosecured Broiler Production.
AIR-SAMPLE was an international multicentre collaborative project aiming at developing and validating air sampling as a low-cost and multi-purpose alternative to faecal droppings or boot swabs for surveillance, monitoring and eradication of Campylobacter in confined and biosecured broiler production.
Monitoring of Campylobacter is mandatory according to Directive 2003/99/EC. However, the current sampling techniques, e.g. faecal droppings or boot swabs are old and need modernization to adapt to automated and molecular detection techniques, reduce the cost of handling and transport, and provide faster laboratory results. Previous studies have indicated that sampling air on gelatine filters can successfully be used for the detection of Campylobacter in broiler houses (Olsen et al., 2009, Søndergaard et al., 2014). The project aimed to provide the European community (authorities and industry) with a low-cost and harmonized tool for surveillance and monitoring. Field testing of air sampling was carried out by the five partners, representing five European countries, during two seasons. The results from the field testing indicated that air sampling in combination with real-time PCR can produce fast and reliable results increasing the likelihood of detecting Campylobacter in infected flocks. In addition, the use of metagenomics (shot-gun) analysis of the air samples was tested.
Project Outputs and Outcomes
- Harmonized and multi-centre evaluated protocols for collecting air samples in broiler houses, DNA extraction from filters and real-time PCR for Campylobacter A fast and sensitive method that increased the likelihood of detecting Campylobacter in infected flocks is available. Guidelines, SOPs and an instruction video have been developed.
- Air sampling can be implemented as an alternative to other methods for sampling for screening of Campylobacter in broiler houses. The use of air samples could be expanded to include more pathogen targets thus being a simple tool for sampling for relevant organisms. Such use needs further developing and testing.
- Use of metagenomics (shot-gun) analyses of air samples to detect Campylobacter. Identified and tested a DNA extraction protocol that can be used for both real-time PCR and metagenomic studies. A pilot study using inoculated air filters was carried out to see if it was possible to identify Campylobacter using shot-gun metagenomics.
- A step towards using metagenomics for detection of pathogenic bacteria or other microorganisms in food production environments. This is an area for further research requiring cooperation across several fields.
Early detection of Campylobacter and potentially other microorganisms that can be harmful to humans and animals enables measures to be put in place to ensure the safety of the product, and animal and human health. The outcomes can be used as a step towards using metagenomics for the detection of foodborne pathogens, with its potential use for multiple purposes.
Haverkamp, T. H. A, Spilsberg, B., Johannessen, G. S., Torp, M., & Sekse, C. (2020). Detection of Campylobacter spp. in broiler production using metagenomic analysis of air samples. Poster presentation. One Health in the 21st Century conference, Oslo, Norway. 3rd November 2021. DOI: https://doi.org/10.5281/zenodo.7447353
Marotta, F., Janowicz, A., Di Marcantonio, L., Ercole, C., Di Donato, G., Garofolo, G., Di Giannatale, E., (2020). Molecular characterisation and antimicrobial susceptibility of C. jejuni isolates from Italian wild bird populations. Pathogens. 9(4), 304; DOI: https://doi.org/10.3390/pathogens9040304
Hoorfar, J., Koláčková, I., Johannessen, GS., Garofolo, G., Marotta, F., Wieczorek, K., Osek, J., Torp, M., Spilsberg, B., Sekse, C., Thornval, NR., Karpíšková, R. (2020). A multi-center proposal for a fast screening tool in biosecured chicken flocks. Foodborne Campylobacter. Applied and Environmental Microbiology,
Johannessen, GS., Garofolo, G., Di Serafino, G.,Koláčková, I.,Karpíšková, R., Wieczorek, K., Osek, J., Christensen, J., Torp, M.,Hoorfar, J. (2020) Campylobacter in chicken- Critical parameters for international, multi-centre evaluation of air sampling and detection method. Food Microbiology, 90, 1-6. DOI: https://doi.org/10.1016/j.fm.2020.103455
Wieczorek, K., Wołkowicz, T., Osek, J. (2020) MLST-based genetic relatedness of Campylobacter jejuni isolated from chickens and humans in Poland. PLOS ONE, 15(1), e0226238. DOI: https://doi.org/10.1371/journal.pone.0226238