Andrzej Benkowski from Eurofins USA presented at London Calling 2023 a five-minute session on the “Practical uses of nanopore long-read sequencing in a high-throughput contract food microbiology laboratory.” They are a high-throughput contract lab specializing in food and dietary supplement investigations using the Oxford Nanopore Technologies (ONT) with the GridION. One client experienced an increase in non-confirming Listeria spp. in several food production facilities. The results could not be confirmed by traditional methods. Benkowski and team used the ONT Rapid kits and concluded that the samples were Listeria with rapid background flora growth causing confusing results. There were low levels of culturable Listeria and high levels of Enterococcus. A second case study presented was the metagenomic identification of probiotics blends. Using ONT long-read sequencing was more efficient than traditional 16S PCR. The team used the Rapid Barcoding kit for fast turnaround. Next, Benkowski spoke about identifying strains in environmental monitoring using whole genome sequencing. One example was characterizing organisms present in fermented foods. Finally, the laboratory performs spoilage investigations without the need to culture. The team sequenced lettuce microbiomes to learn about microbiome population dynamics during cold stress. Benkowski concluded that ONT long-read sequencing is a powerful tool for high-throughput contract microbiology testing along with Rapid kits and EPI2ME workflows. The use cases of ONT Rapid kits and the GridION was helpful in understanding how contract labs can use ONT for food microbiology.
