Gopinath G R, Cinar H N, Murphy H R, Durigan M, Almeria M, Tall B D, DaSilva A J
Office of Applied Research and Safety Assessment (OARSA), Center for Food Safety and Applied Nutrition (CFSAN), US Food and Drug Administration, 8301 Muirkirk Road, Laurel, MD 2070 USA.
Gut Pathog. 2018 Apr 10;10:15. doi: 10.1186/s13099-018-0242-0. eCollection 2018.
is a coccidian parasite associated with large and complex foodborne outbreaks worldwide. Linking samples from cyclosporiasis patients during foodborne outbreaks with suspected contaminated food sources, using conventional epidemiological methods, has been a persistent challenge. To address this issue, development of new methods based on potential genomically-derived markers for strain-level identification has been a priority for the food safety research community. The absence of reference genomes to identify nucleotide and structural variants with a high degree of confidence has limited the application of using sequencing data for source tracking during outbreak investigations. In this work, we determined the quality of a high resolution, curated, public mitochondrial genome assembly to be used as a reference genome by applying bioinformatic analyses. Using this reference genome, three new mitochondrial genome assemblies were built starting with metagenomic reads generated by sequencing DNA extracted from oocysts present in stool samples from cyclosporiasis patients. Nucleotide variants were identified in the new and other publicly available genomes in comparison with the mitochondrial reference genome. A consolidated workflow, presented here, to generate new mitochondrion genomes using our reference-guided de novo assembly approach could be useful in facilitating the generation of other mitochondrion sequences, and in their application for subtyping strains during foodborne outbreak investigations.
是一种球虫寄生虫，与全球范围内大规模且复杂的食源性疾病暴发有关。使用传统流行病学方法将食源性疾病暴发期间环孢子虫病患者的样本与疑似受污染的食物来源相联系，一直是一项持续存在的挑战。为解决这一问题，基于潜在的基因组衍生标记进行菌株水平鉴定的新方法的开发一直是食品安全研究界的优先事项。缺乏能够高度可靠地识别核苷酸和结构变异的参考基因组，限制了在暴发调查期间利用测序数据进行源头追踪的应用。在这项工作中，我们通过应用生物信息学分析，确定了一个高质量、经过整理的公共线粒体基因组组装的质量，以用作参考基因组。使用这个参考基因组，从环孢子虫病患者粪便样本中存在的卵囊中提取的DNA进行测序所产生的宏基因组读数开始，构建了三个新的线粒体基因组组装。与线粒体参考基因组相比，在新的和其他公开可用的基因组中鉴定出了核苷酸变异。本文介绍的一种整合工作流程，即使用我们的参考引导从头组装方法生成新的线粒体基因组，可能有助于促进其他线粒体序列的生成，以及它们在食源性疾病暴发调查期间用于菌株分型的应用。
