Tonight the London Calling 2023 session I watched was presented by Tiana Schwab from the Institute of Social and Preventative Medicine at the University of Bern in Switzerland. The title is “Tuberculosis drug resistance profiling from native sputum using nanopore targeted sequencing: a field application study.” Schwab is working on a Ph.D. and described the impact of drug resistant tuberculosis (TB). They noted that of those on treatment is only about 60%. In order to treat TB, you have to diagnose it. Tuberculosis drug susceptibility testing (DST) is important and time consuming for this slow-growing organism. While next-generation sequencing still requires infrastructure, it is more accessible. Further, Oxford Nanopore Technologies (ONT) portable technologies make targeted sequencing more accessible for implementation in Africa. The workflow Schwab and team developed starts with DNA extraction using the Promega Maxwell RSC system, Nucleic acid library preparation with the RBK110.96 sample prep kit, target amplification, and genotyping report creation with EPI2ME Labs. The panel was designed to learn susceptibility for fourteen drugs, developed by Nanopore. EPI2Me Labs workflows produce clean reports that are shared with physicians. The workflow is efficient and produces sequencing results <24 hrs. The project has begun in Zambia and Johannesburg. So far the sequencing protocol has been used of forty samples. The failed samples had high human DNA content. The most cost-effective sample prep would be in batches of 20+ samples. However, recruitment has been slow. Once they obtain the sample number they desire, the team will perform whole genome sequencing on the samples and also clean them up further for reanalysis. The research team is surveying the physicians to learn how useful the reports are for their work. The team will continue working in South Africa and optimizing the workflow. I am interested in how adaptable their workflow will be for other bacterial pathogens.
