Erin L. Young from the Department of Health and Human Services in Utah presented at the Nanopore Community Meeting in Houston on “Nanopore sequencing for enhanced antimicrobial resistance gene surveillance.” I had watched Young present previously. They spoke about using whole genome sequencing (WGS) for surveillance and its use by the Centers for Disease Control. The CDC website mentions food and pathogen surveillance. Young is a member of a regional lab that is part of the ARLAB Network. They have sequenced microbes to learn about their human health implications. The workflow starts with a colony that is isolated. DNA is extracted and sequenced with Illumina sequencing. Young explained that they assemble or reconstruct genomes to determine antimicrobial resistance (AMR) genes. Young spoke about the benefits of long-read sequencing. A slide Young presented included the benefits of Nanopore sequencing for AMR gene identification, serotyping/subtyping, outbreak detection, horizontal gene transfer event information, and a faster turnaround. One of the reservations of using Nanopore sequencing is the decrease in quality. At the UPHL, Young and the team have sequenced 375 isolates. Some have been sequenced with Nanopore sequencing. UPHL started Nanopore sequencing in 2019 and has gained interest. Young noted that the last seventy-six isolates sequenced were performed with the V14 chemistry and flow cells. Compared to Illumina, the taxonomy and AMR predictions seemed similar. Interestingly, they found that beta-lactamase genes were more likely to be identified with Oxford Nanopore. In several isolates, OXA genes were found in Oxford Nanopore sequencing runs but not Illumina. These comparisons of plasmid and AMR predictions are intriguing, and I would like to know more about the workflows used. Young is a bioinformatician and shared some information about the programs used.
