“Profiling drug-resistant Mycobacterium tuberculosis with targeted nanopore sequencing” was the title of the sessionn Shannon Murphy from the Wadsworth Center – New York State Department of Health presented at the Nanopore Community Meeting 2022. Murphy spoke about how they are planning on using Nanopore sequencing to address some of the challenges of Mycobacterium tuberculosis (MTB). I did not realize that ~7800 cases were reported in 2021 in the US, with most in New York. The resistance profiles of MTB are: pan-susceptible, drug-resistant, multi-drug resistant (MDR), and extensively-drug resistant (XDR), explained Murphy. To determine MTB susceptibilities, the traditional approach is to isolate and grow on different antibiotics. However, Murphy noted that MTB grows very slowly. Murphy emphasized that “sequencing can buy us valuable time” and that this work was already being done in the New York State Department of Health. Now, Murphy noted, phenotypic growth assays are performed in select cases, and the data are used to inform and improve the sequencing models. Murphy described their workflow as a targeted sequencing method with a panel of primers that have been validated, library preparation, and sequencing with R9 flow cells and the Mk1C. The bioinformatics pipeline was developed in-house. Murphy also explained that their targeted nanopore sequencing with WGS approach was analyzed. They tested their method between whole genome sequencing of isolates and their targeted sequencing approach, obtaining 100% concordance. Their next step is to increase the number of targets and implement this approach on a GridION they received. Murphy also noted that they are using the new chemistries too. I wonder how they prepare the libraries… as this step can lead to variability and be time consuming. I appreciate the efficiency of targeted sequencing and how this approach can be used to increase throughput and reduce computational demands of whole genome sequencing of MTB.
