The Precision Genomics session at the Nanopore Community Meeting in Boston included a session by Julie Haendiges from the U.S. Food and Drug Administration. They explained that they are tasked with safeguarding more than $1.5 trillion worth of food, cosmetics, and dietary supplements. Haendiges spoke about how they are modernizing and optimizing methods. They explained that in the U.S. alone, $10 billion is spent on bacterial illness. The FDA started sequencing for outbreak investigations. Long-read sequencing is now being used and can help “close genomes.” The FDA has closed over 1,000 closed genomes to the Reference Genomes Submission at NCBI. With this information, the FDA can increase AMR surveillance and work with partners. Haendiges explained that they are doing training sessions nationally and internationally. They have a partnership with Mexico and offer training sessions. The microbial pathways of interest include heavy metal, disinfectant, chlorine, and many more resistance profiles. The team is also doing RNASeq and moving to long-read sequencing. Haendiges noted that they are also looking at methylation patterns of bacteria to better understand persistence. Haendiges described an experiment they did filtering 100 liters of irrigation water. In this metagenomic experiment, they tested several ONT library prep systems and noticed that the rapid kit suffered from inhibition. They optimized the pre-enrichment step and did spike-in experiments. They obtained limit of detection information and the number of reads needed to close the genome for E. coli O157H7. They performed similar experiments with powdered infant formula (PIF) to learn about the detection limits of specific bacteria in that matrix. This session emphasized the transition of the FDA to new techniques and approaches for analyzing outbreaks and food safety through sequencing.
