Rapid, multiplexed, whole genome and plasmid sequencing of foodborne pathogens using long-read nanopore technology.

ABSTRACT: 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 a

SUBMITTER: Taylor TL 

PROVIDER: S-EPMC6841976 | biostudies-literature | 2019 Nov

REPOSITORIES: biostudies-literature