Tuberculosis Pathogen Dynamics, Drug Susceptibility Detected With Nanopore Sequencing

Investigators at the European Bioinformatics Institute's European Molecular Biology Laboratory and elsewhere consider the feasibility of Oxford Nanopore long-read sequencing to study the spread and drug susceptibility of tuberculosis-causing Mycobacterium tuberculosis pathogens. As they report in The Lancet Microbe, the researchers set the SNP clusters and drug sensitivity predictions found with MinION or GridION whole-genome sequencing on 151 M. tuberculosis isolates collected over time in Madagascar, South Africa, and England with Oxford Nanopore platforms against those identified with Illumina short-read sequencing platforms. Along with drug sensitivity testing on the isolates, the authors put together high-quality PacBio-based assemblies for a subset of the isolates. Their results pointed to similar performance for the Nanopore and Illumina sequences and corresponding analytical pipelines, with the Illumina platform showing slightly higher median SNP identification precision and recall and picking up a handful of extra SNP clusters. "Our analysis shows that it is now possible to obtain high-precision SNP calls in M. tuberculosis with current Nanopore data, with only a small decrease in recall," the authors write, adding that the study "provides evidence to support the adoption of Nanopore sequencing, along with open access data and software, which we hope will be of wide use."