MinION

MinION performs long-read nanopore sequencing to generate rapid, multiplexed whole-genome and plasmid assemblies for identification and characterization of foodborne pathogens.

Key Features:

• Long-Read Nanopore Sequencing: Generates long reads that resolve highly repetitive genomic regions and complex genomic arrangements, enabling closure of bacterial chromosomes and plasmids.
• Multiplexed Sequencing: Supports simultaneous sequencing of multiple genomes and plasmids in a single run to produce comprehensive genomic datasets.
• Rapid Turnaround: Can produce full-length genome assemblies from short sequencing runs (reported sequencing runs as brief as four hours) with reported average identities of 99.87% for Salmonella enterica subsp. enterica serovar Bareilly and 99.89% for Escherichia coli O157:H7 compared to MiSeq references.
• Comprehensive Data Analysis: Integrates a customized workflow that leverages publicly-available bioinformatics tools for de novo genome assembly and identification of serotype, virulence factors, and antimicrobial resistance genes from nanopore assemblies.
• Phylogenetic Inference: Enables rapid preliminary phylogenetic inference to support epidemiological analyses and outbreak investigations.

Scientific Applications:

• Public Health Surveillance: Identification and characterization of foodborne pathogens to support outbreak detection and investigation.
• Pathogen Genomics: Comprehensive sequencing of bacterial chromosomes and plasmids to determine serotype, virulence determinants, and antimicrobial resistance genes.

Methodology:

Uses a rapid, random nanopore sequencing approach coupled with de novo genome assembly within a customized workflow that leverages publicly-available bioinformatics tools; library preparation and sequencing can be completed within approximately 10 hours.