Strain-level deconvolution and phylogenomic investigation using metagenomics on commercial fermentation products allows source tracing of genetically modified microorganism contaminations

Genetically modified microorganisms (GMM) are frequently employed for the production of microbial fermentation products such as food enzymes. Although presence of the GMM or its recombinant DNA in the final product is not authorized, contaminations occur frequently, raising potential public health concerns, especially since GMM often carry antimicrobial resistance (AMR) genes. Insight into the contamination source of an unauthorized presence of a GMM is of crucial importance to allow the competent authorities to take appropriate action. The aim of the present study was to explore the feasibility of a metagenomic shotgun sequencing approach to investigate microbial contamination in fermentation products, without the need for microbial isolation. More specifically, source tracing of GMM strains using innovative strain deconvolution and phylogenomic approaches was performed. 16 commercially available food enzyme products were selected based on their contamination with one or several GMM according to qPCR. In most cases, the analysis supported finding the same GM strains with a close phylogenetic relationship between the GMM contaminations in different samples. The presence of AMR genes in the samples was strongly associated with the GMM contamination. Additionally, the results demonstrated the presence of a variety of other microbial contaminations in the samples, identifying a group of samples with a conspicuously similar microbial contamination profile, which suggested that these samples originated from the same production facility or batch. Overall, these findings emphasize the added value of metagenomics to obtain insight in the microbial contamination profiles as well as their relationships in commercial microbial fermentation products. They also highlight the need for guidelines and quality control of these products to ensure the safety of the consumers.