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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 (rifR) 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 rifR 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.

“Dark-cutting” meat in beef carcasses can result from conditions such as long-term stress and depleted glycogen stores, but some aspects of the physiological mechanisms that cause dark-cutting phenotypes remain poorly understood. Certain responses to stress factors in fully developed tissues are known to be regulated by specific microRNAs. We investigated microRNA expression in Longissimus lumborum biopsies from carcasses derived from a contemporary group of 78 steers from which a high incidence of dark-cutting meat occurred. Our objective was to identify any potential microRNA signatures that reflect the impact of environmental factors and stresses on genetic signaling networks and result in dark-cutting beef (also known as dark, firm, and dry, or DFD) in some animals. MicroRNA expression was quantified by Illumina NextSeq small RNA sequencing. When RNA extracts from DFD muscle biopsy samples were compared with normal, non-DFD (NON) samples, 29 differentially expressed microRNAs were identified in which expression was at least 20% different in the DFD samples (DFD/NON fold ratio ≤0.8 or ≥1.2). When correction for multiple testing was applied, a single microRNA bta-miR-2422 was identified at a false discovery probability (FDR) of 5.4%. If FDR was relaxed to 30%, additional microRNAs were differentially expressed (bta-miR-10174-5p, bta-miR-1260b, bta-miR-144, bta-miR-142-5p, bta-miR-2285at, bta-miR-2285e, bta-miR-3613a). These microRNAs may play a role in regulating aspects of stress responses that ultimately result in dark-cutting beef carcasses.

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