Matthew Riley - Evaluation of Nanopore Sequencing for Rapid Bacterial Identification and Complete Genome Sequencing
Nanopore Community Meeting 2017
"Nanopore sequencing technology is a rapidly evolving tool for next-generation sequencing (NGS) with a wide variety of applications in biomedical and biological threat applied research. The MinION device is capable of on-site, rapid species-level pathogen identification and genome sequencing of biothreat agents. Here, various MinION NGS applications have been investigated including rapid identification and complete genome sequencing of blinded bacterial isolates as well as presumptive antimicrobial susceptibility prediction. Isolates were sequenced either alone or in mixed populations, without barcoding, using the 1D Ligation Sequencing Kit and Rapid Sequencing Kits with minimal infrastructure and informatics workflows. Complete genome sequencing revealed 4 isolates presumptively identified via other methods to be incorrectly identified at the Genus or species level. Genome sequences generated using the MinION compared favorably against sequences generated using Illumina and PacBio technologies, and predicted antimicrobial susceptibilities matched phenotypic resistances. Novel workflows using the MinION device to rapidly identify mixed populations of up to 8 unknown bacterial isolates were able to correctly identify each isolate at the species level, and in some cases the specific strain, even without uniquely barcoding each sample. These data, workflows and results demonstrate multiple uses for the MinION device comparable to existing capabilities but with far less infrastructure, labor and overall effort. These characteristics suggest these MinION workflows could be applied in a mobile or field setting, bringing typically large laboratory capabilities for forward into field applications for biological defense."