Complete Whole Genome Sequences of Escherichia coli Surrogate Strains and Comparison of Sequence Methods with Application to the Food Industry

• Published in: Microorganisms (Basel) Vol. 9; no. 3; p. 608
• Main Authors: Therrien, Dustin A, Konganti, Kranti, Gill, Jason J, Davis, Brian W, Hillhouse, Andrew E, Michalik, Jordyn, Cross, H Russell, Smith, Gary C, Taylor, Thomas M, Riggs, Penny K
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 16.03.2021; MDPI
• Subjects: Antibiotics; bacterial surrogate; Bioinformatics; closed genome; Deoxyribonucleic acid; DNA; Drug resistance; E coli; Escherichia coli; Food industry; Food processing industry; Food safety; Foodborne diseases; Gene sequencing; Genes; Genomes; Genomics; Inspection; long reads; Nucleotide sequence; Organisms; Pathogenesis; Pathogens; Platforms; Porosity; Resistant mutant; Rifampin; Safety programs; short reads; Strains (organisms); Surveillance; Virulence; whole genome sequence; Whole genome sequencing; United States > US; Texas; short reads; long reads; Escherichia coli; bacterial surrogate; whole genome sequence; high throughput sequencing; closed genome

In 2013, the U.S. Department of Agriculture Food Safety and Inspection Service (USDA-FSIS) began transitioning to whole genome sequencing (WGS) for foodborne disease outbreak- and recall-associated isolate identification of select bacterial species. While WGS offers greater precision, certain hurdle...