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
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.
Microorganisms. 2021 Mar 16;9(3):608. 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.
2013年，美国农业部食品安全检验局（USDA-FSIS）开始转向使用全基因组测序（WGS）来鉴定特定细菌物种，以应对食源性疾病暴发和召回相关的分离株。虽然WGS提供了更高的精确度，但在食品行业广泛应用之前，必须克服某些障碍。挑战包括测序平台输出的多样性以及缺乏用于数据分析的标准化生物信息学工作流程。我们通过牛津纳米孔MinION和Illumina MiSeq平台对USDA-FSIS批准的非致病性替代菌株以及一组衍生的耐利福平突变体（rif）的DNA进行测序，以生成和注释完整基因组。每个克隆的基因组序列单独组装，以便直接比较长读长、短读长和组合序列组装。组合序列数据方法可提供更准确的完整基因组。已证实这些分离株的基因组缺乏通常与致病机制相关的功能关键元件。还鉴定出了已知赋予耐利福平特性的基因改变。随着食品行业在其食品安全计划中采用WGS，这些数据为常用替代菌株提供了完整基因组，并直接比较了与适用于加工商和监管机构的研究/测试工作流程相关的序列平台和组装策略。
