Workflow: bacterial isolate sequencing

Nanopore-only microbial isolate sequencing solution (NO-MISS): a flexible and rapid approach for whole-genome sequencing of bacterial isolates

Whole-genome sequencing of microbial isolates provides valuable information for public health, clinical microbiology research, food safety, and microbial ecology. It is especially important during outbreak investigations, including detection and characterisation of antimicrobial resistance genes, virulence genes, plasmids and other mobile genetic elements, and additional genomic features that may affect the phenotypic properties of the strain. Reconstruction of complete, contiguous, high-quality microbial genomes by de novo assembly is limited with short-read sequencing. Nanopore sequencing can generate reads of unrestricted length and overcome these limitations to deliver comprehensive genome assemblies. High-accuracy nanopore sequencing shows no bias in GC-rich regions and can span repeat-rich sequences and structural variants that are inaccessible to legacy sequencing technologies. Furthermore, nanopore sequencing is a scalable solution that offers flexible sample batching and provides rapid turnaround time from sample to answer. By obtaining complete, reference-quality microbial genome sequences in one experiment and in-house, the need to outsource or use multiple techniques for validation is no longer required.

Here we present a rapid end-to-end workflow for whole-genome sequencing of bacterial isolates, using MinION Flow Cells on MinION or GridION sequencing devices and the EPI2ME analysis platform.