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
• ISSN: 2076-2607; 2076-2607
• DOI: 10.3390/microorganisms9030608

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 hurdles must be overcome before widespread application within the food industry is plausible. Challenges include diversity of sequencing platform outputs and lack of standardized bioinformatics workflows for data analyses. We sequenced DNA from USDA-FSIS approved, non-pathogenic surrogates and a derivative group of rifampicin-resistant mutants (rif ) via both Oxford Nanopore MinION and Illumina MiSeq platforms to generate and annotate complete genomes. Genome sequences from each clone were assembled separately so long-read, short-read, and combined sequence assemblies could be directly compared. The combined sequence data approach provides more accurate completed genomes. The genomes from these isolates were verified to lack functional key elements commonly associated with pathogenesis. Genetic alterations known to confer rif were also identified. As the food industry adopts WGS within its food safety programs, these data provide completed genomes for commonly used surrogate strains, with a direct comparison of sequence platforms and assembly strategies relevant to research/testing workflows applicable for both processors and regulators.