Comparison of metagenomics and classical microbiology for the characterization of the microflora of surfaces, hands and foodstuffs in different type of community kitchens. (METAGECO)

Institutional catering is legally subjected to hygiene controls by the FASFC and certification bodies. These controls are based on visual observation supplemented by sampling and classical microbiological analysis. These microbiological analyses still have certain shortcomings, however. Metagenomic analysis may possibly provide better information on the contaminants and their sources. The objective of the ‘Metageco’ project is to research better performing methods for surface sampling in institutional kitchens. Another goal is to test the relevance of metagenomic analysis for the characterization of microflora sampled during hygiene controls.

The project has ended. We started with an inspection checklist, together with the design of a reproducible protocol for the sampling of surfaces, hands and finished products in institutional kitchens. Subsequently, this sampling protocol has been applied in 4 types of kitchens: schools, child-care centers, hospitals and nursing homes. ILVO has done the sampling campaign in Flanders, while the university of Liège did the same in Wallonia. We have performed classical microbiological and metagenomic analysis on all samples. Last, the protocol has been consulted with the FASFC.

From a comparison of the different types of institutional kitchens, it seems that the child-care centers score the lowest for hygiene. In all kitchens, the sink is the most contaminated and can thus be regarded as the dirtiest place. Cutting boards are also a point of attention because Enterobacteriaceae are found on them from time to time even after cleaning. Metagenetics is able to produce a wealth of interesting and detailed information on the presence and dynamics of the microbiota in institutional kitchens, provided that sufficient amount of DNA can be prepared from the sampled surfaces. Nevertheless, the technique seems to be less sensitive for detection of pathogens in comparison to specific cultivation methods. On the basis of the extensive sampling campaign in this project, it is proposed that metagenetics could be used as a tool in the 2nd line but not to replace the targeted classical microbiological analysis in routine hygiene control of institutional kitchens. The results have been presented at various international congresses; scientific publications are planned. The results will also take part of the PhD thesis of Evelyne Duthoo.