Rapid, multiplexed, whole genome and plasmid sequencing of foodborne pathogens using long-read nanopore technology.
Tonya L TaylorJeremy D VolkeningEric DeJesusMustafa SimmonsKiril M DimitrovGlenn E TillmanDavid L SuarezClaudio L AfonsoPublished in: Scientific reports (2019)
U.S. public health agencies have employed next-generation sequencing (NGS) as a tool to quickly identify foodborne pathogens during outbreaks. Although established short-read NGS technologies are known to provide highly accurate data, long-read sequencing is still needed to resolve highly-repetitive genomic regions and genomic arrangement, and to close the sequences of bacterial chromosomes and plasmids. Here, we report the use of long-read nanopore sequencing to simultaneously sequence the entire chromosome and plasmid of Salmonella enterica subsp. enterica serovar Bareilly and Escherichia coli O157:H7. We developed a rapid and random sequencing approach coupled with de novo genome assembly within a customized data analysis workflow that uses publicly-available tools. In sequencing runs as short as four hours, using the MinION instrument, we obtained full-length genomes with an average identity of 99.87% for Salmonella Bareilly and 99.89% for E. coli in comparison to the respective MiSeq references. These nanopore-only assemblies provided readily available information on serotype, virulence factors, and antimicrobial resistance genes. We also demonstrate the potential of nanopore sequencing assemblies for rapid preliminary phylogenetic inference. Nanopore sequencing provides additional advantages as very low capital investment and footprint, and shorter (10 hours library preparation and sequencing) turnaround time compared to other NGS technologies.
Keyphrases
- escherichia coli
- single cell
- single molecule
- antimicrobial resistance
- public health
- data analysis
- copy number
- electronic health record
- biofilm formation
- pseudomonas aeruginosa
- genome wide
- crispr cas
- healthcare
- klebsiella pneumoniae
- transcription factor
- high frequency
- climate change
- artificial intelligence
- social media
- deep learning
- multidrug resistant
- liquid chromatography
- machine learning
- candida albicans
- dengue virus
- circulating tumor