NCM 2022: Profiling drug-resistant Mycobacterium tuberculosis with targeted nanopore sequencing

The time required to characterize Mycobacterium tuberculosis (MTB) infections can be considerable, specifically in cases involving multi-drug or extensively-drug resistant strains. Culture-based antimicrobial susceptibility testing requires weeks to complete due to MTB’s slow growth rate. However, sequencing-based assays can identify antimicrobial resistance in less time. At the Wadsworth Center at the New York State Department of Health, we have developed a targeted Next-Generation Sequencing (tNGS) assay that amplifies loci implicated in antimicrobial resistance direct from respiratory samples. These libraries are sequenced on a MinION Mk1C device from Oxford Nanopore and analysed with a bioinformatics pipeline developed in-house that generates susceptibility profiles. The ability to sequence and analyse this data in real-time via Oxford Nanopore platforms offers the potential for shorter sequencing runs and improved turnaround times. This assay for profiling MTB antimicrobial susceptibility is currently undergoing validation in a CLEP-compliant laboratory for potential application in New York State by the Wadsworth Center after undergoing validation.