Kimberlee Musser from the Wadsworth Center at the New York State Department of Health presented an update at the Nanopore Community Meeting Houston 2023. Wadsworth Center is the largest state public health laboratory with 750 staff! The Wadsworth Center receives CDC and NIH funding and develops new assays. Musser explained that they have their in-house LIMS. The Public Health Laboratory contributes to national surveillance, reference testing, outbreak source tracking, and assay development. Musser discussed how long-read sequencing can be used for antimicrobial resistance (AR) detection. The team is interested in identifying the genomic context of AR genes. Their first example described a carbapenem-resistant Pseudomonas aeruginosa isolate in a case from Rhode Island. In a second example, long-read sequencing help identify transfer of genetic material between bacteria. The team also analyzed a vancomycin-resistant Staphylococcus aureus (VRSA) case using long and short-read sequencing over time. The team learned about the dynamics of vanA gene as it was likely transferred from another organism to Staphylococcus and eventually integrated into the chromosome. The team also developed the NanoCLUSTWC pipeline to streamline the sequencing of isolates. Nanopore sequencing is being used for targeted sequencing of Mycobacterium tuberculosis complex (MTBC). The team developed and validated a targeted next-generation sequencing (tNGS) assay. They are using the GridION and are able to reuse flowcells several times. An example of the outcomes of this assay were the direct detection of extensively drug-resistant (XDR) MTBC. This was the first time they were able to detect an isolate like this from this type of sample. Musser concluded that the team has experienced improvements in the identification of organisms. Musser shared that they will work on wastewater surveillance and enrichment of Legionella from environmental samples using RNA baiting and NGS! I want to learn more about this approach!
