Kim Musser, Clinical Director, Wadsworth Center, David Axelrod Institute, presented at ESCMID Global on the use of nanopore sequencing in public health investigations. The title of the session was “Implementing next generation sequencing for rapid diagnostics and public health investigations.” Musser spoke about using nanopore sequencing for antimicrobial sequencing for antibiotic resistant bacteria to characterize mobile genetic elements and whether they are on the chromosome or plasmids. With long-read sequencing using Oxford Nanopore Technologies (ONT), plasmid-mediated antimicrobial resistance is easier to analyze. Musser spoke about an investigation to detect plasmid transfer across bacterial species. They had numerous patients in Maine. Isolates were sequenced to identify transmission of the antimicrobial gene sequences on a plasmid. Musser spoke about using ONT to analyze a vancomycin-resistant Staphylococcus aureus (VRSA). The last example was a stuy to analyze a strain of Pserudomonas aeruginosa with a unique bla resistance. Musser then spoke about the use of a Nanopore targeted next generation sequencing (tNGS) assay for M. tuberculosis analyses. The Wadsworth Center in New York obtains samples and then processes them using an automated EZ1 QIAGEN extraction. Targets are amplified across two PCR pools. Amplicons range from 1,000 to 3,700 bp. With this assay, the average improvement is fifteen days for primary speciments! The cost, Musser explained, is less than $100 when batched once a week. With this assay and a secondary more sensitive version, the team can detect antimicrobial resistance panels. Musser shared their mycobacteriology testing algorithm emphasizing that their tNGS assay workflow will allow quicker detection.
