Metataxonomic Surveillance of Contamination Pathways in Food Processing Environments: From Observational Studies to Practical Applications

Metataxonomics represents a user-friendly omics tech- nique for culture-independent characterisation of microbiota composi- tion. Although it is a well-established approach applied for a decade in medical and environmental microbiology, most of the studies in food science are only observational and its practical implementation in the food industry seems still far away. Purpose: Therefore, we aimed to assay the pros and cons of using metataxonomic surveillance (MS) to characterise contamination pathways in food processing establishments and discover MS-based biomarkers of pathogen and spoilage bacteria presence. Over 700 environmental and food samples were collected from cattle slaughterhouses, a poultry abattoir, and a baby food facility. The 16S rRNA amplicon-based sequencing outputs were com- pared to the targeted detection of microbes by counts, enrichment, and quantitative PCR (RT-qPCR). Results: Cattle slaughterhouses’ microbial biogeography showed that resident bacteria varied between premises as a function of temperatures and longitudinally along temporal phases of cleaning/sanitising. Moreover, selective bacterial inactivation by the cleaning/sanitising was only detected through MS. Contamination patterns plotted in the poultry abattoir showed that resident microbiota mainly originated from broilers’ skin, in which Arcobacter butzleri was largely present. Targeted detection confirmed the high environmental persistence of this pathogen and flocks› cross-contaminations conveyed by carcass transport lines. In the baby food processing plant, the fluctuation of biodiversity and the succession of resident communities along a one year period were strongly influenced by the type and the microbiota composition of incoming raw materials. The parallel detection of alive spore-forming pathogens by RT-qPCR significantly correlated with low biodiversity and the presence of specific taxa. Our studies have shown that MS is a valid approach to defining contamination patterns in the processing plant, from the environment to the food products and back. As demonstrated by the benchmark with targeted cultural methods, the time for MS integration in microbiology quality control of food industries has now come.