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

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.

doi:10.3390/microorganisms9030608

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

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²,

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^1,*

and

Penny K. Riggs

^1,*

Department of Animal Science, Texas A&M University, College Station, TX 77843-2471, USA

Texas A&M Institute for Genome Sciences and Society, MS 2470, College Station, TX 77843-2470, USA

Department of Veterinary Integrated Biosciences, Texas A&M University, College Station, TX 77843-4461, USA

Authors to whom correspondence should be addressed.

Academic Editor: Christina L. Swaggerty

Microorganisms 2021, 9(3), 608; https://doi.org/10.3390/microorganisms9030608

Received: 12 February 2021 / Revised: 4 March 2021 / Accepted: 10 March 2021 / Published: 16 March 2021

(This article belongs to the Special Issue Control and Intervention Strategies to Reduce Foodborne Pathogens in Animal Agriculture)

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Abstract

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 E. coli surrogates and a derivative group of rifampicin-resistant mutants (rif^R) 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 E. coli elements commonly associated with pathogenesis. Genetic alterations known to confer rif^R 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. View Full-Text

Keywords: bacterial surrogate; Escherichia coli; whole genome sequence; short reads; long reads; closed genome; high throughput sequencing

This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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Therrien, D.A.; Konganti, K.; Gill, J.J.; Davis, B.W.; Hillhouse, A.E.; Michalik, J.; Cross, H.R.; Smith, G.C.; Taylor, T.M.; Riggs, P.K. Complete Whole Genome Sequences of Escherichia coli Surrogate Strains and Comparison of Sequence Methods with Application to the Food Industry. Microorganisms 2021, 9, 608. https://doi.org/10.3390/microorganisms9030608

AMA Style

Therrien DA, Konganti K, Gill JJ, Davis BW, Hillhouse AE, Michalik J, Cross HR, Smith GC, Taylor TM, Riggs PK. Complete Whole Genome Sequences of Escherichia coli Surrogate Strains and Comparison of Sequence Methods with Application to the Food Industry. Microorganisms. 2021; 9(3):608. https://doi.org/10.3390/microorganisms9030608

Chicago/Turabian Style

Therrien, Dustin A., Kranti Konganti, Jason J. Gill, Brian W. Davis, Andrew E. Hillhouse, Jordyn Michalik, H. Russell Cross, Gary C. Smith, Thomas M. Taylor, and Penny K. Riggs. 2021. "Complete Whole Genome Sequences of Escherichia coli Surrogate Strains and Comparison of Sequence Methods with Application to the Food Industry" Microorganisms 9, no. 3: 608. https://doi.org/10.3390/microorganisms9030608

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