Use of genomic technologies to enhance food safety and authenticity

据估计，食品欺诈每年给英国企业造成的损失约为11亿GB。2013年第一季度发生在欧洲各地的马肉丑闻突显了食品生产供应链和审计程序的重大缺陷。报告还强调了欧洲和英国食品检测实验室在分析能力方面存在的重大问题。实时聚合酶链式反应(RTPCR)的DNA分析很快被确定为物种确定的首选方法，但只有少数英国实验室可以使用。这导致大量样品积压，因为容量很快就饱和了。在这场危机之后，该行业寻求更强大的分析技术，可以产生更准确和更全面的数据集。存在引入新技术以满足食品和饲料生产公司和零售商的需求的商机，例如UOM和PIQ实验室的合作者开发了一种基于扩增序列的诊断方法，允许在一次检测中检测所有哺乳动物物种。这项测试克服了标准的基于聚合酶链式反应的诊断方法的主要问题，即需要在单独的测试中评估每种潜在的污染物。尽管有了这一重大进步，基于扩增序列的诊断仍存在两个关键问题。通过聚合酶链式反应扩增引入的偏倚阻碍了检测的定量使用，而且通常情况下，扩增产物无法将具有商业价值的物种与其他密切相关的物种区分开来。我们试图通过从食品样本中开发基于直接的、非扩增的靶标不可知测序的元基因组学测试来克服这些问题。这将涉及开发目标数据库、编写有效和准确询问这些数据库的程序脚本以及以具有成本效益的方式执行原型测试，重点是相关的测试市场。由于每个碱基测序成本的大幅降低，加上新的低成本测序仪以及来自食品欺诈目标物种的基因组数据的增加，将元基因组学用于食品检测现在是一个现实的命题。英国生物科学的前瞻性围绕三个相互关联的主题构建。该项目的主要目标是围绕主题2。此外，农业和食品安全研究战略框架详细说明了食品安全和营养作为重点领域。通过开发NGS技术，支持评估食品真实性、特定品种的可追溯性、过敏原以及识别食品中的病原体和毒素生产者的努力，我们涵盖了改善食品安全和营养的关键目标。此外，我们还涵盖了英国生物科学展望主题1中的目标，以建设食品诊断和安全行业的能力，以利用颠覆性生物科学技术。与此直接相关的是，我们正在支持具有广泛的专业、企业和可转让技能的个人的发展，并在粮食安全部门建设具有量化、综合性和数据密集型生物科学的能力。

Food fraud is estimated to cost UK business in the region of £11 Bn per annum. The horse meat scandal that occurred across Europe in the first quarter of 2013 highlighted major deficiencies in the food production supply chain and audit procedures. It also highlighted significant issues in analytical capabilities in European and UK food testing laboratories. DNA analysis by real time PCR (RTPCR) was quickly identified as the method of choice for species determination but was available in only a handful of UK laboratories. This resulted in a major backlog of samples as capacity was quickly saturated. Following this crisis the industry has sought more robust analytical techniques which can generate more accurate and comprehensive data sets. A business opportunity existed to introduce new technology to meet the needs of the food and feed production companies and retailers alike UoM and collaborators from PiQ laboratories developed an amplicon-seq based diagnostic which allows detection of all mammalian species in a single assay. This test overcame the major issue with standard PCR based diagnostics which requires that each potential contaminant needs to be assessed in a separate test. Despite this significant advance, there are a 2 key issues with amplicon-seq based diagnostics. Bias, introduced by PCR amplification prevents the test being used in a quantitative manner and often, the amplicons are unable to differentiate commercially valuable species from other closely related species. We seek to overcome these issues by developing metagenomics testing based on direct, non-amplified target-agnostic sequencing from food samples. This will involve development of target databases, scripting of routines to efficiently and accurately interrogate these databases and implementation of the prototype test in a cost effective manner with emphasis on relevant testing markets. The use of metagenomics for food testing is now a realistic proposition due to the dramatic reduction in per base sequencing cost, coupled with new low cost sequencers and the increase in genomic data from food fraud target species.The Forward Look for UK Bioscience is structured around three interrelated themes. The primary aim of this project is centered around theme 2. In addition, the Research in Agriculture and Food Safety strategic framework details food safety and nutrition as a focus area. By developing NGS technologies that will support efforts to assess food authenticity, traceability of specific cultivars, allergens and identification of pathogens and toxin producers in foods, we cover a key objective on improving food safety and nutrition. Alongside this we cover objectives within theme 1 of the Forward Look for UK Bioscience to build capacity in the food diagnostics and safety industry to utilise disruptive bioscience technologies. Directly linked to this we are supporting the development of an individual with a breadth of professional , enterprise and transferrable skills and building capacity in the food security sector with quantitative, integrative and data-intensive bioscience.