单一实验室评估Q20+纳米孔测序套件用于细菌疫情调查
Maria Hoffmann1, Jay Hee Jang1, Sandra M Tallent1
1Genomics Development and Applications Branch, Division of Food Safety Genomics, Office of Applied Microbiology and Technology, Office of Laboratory Operations and Applied Science, Human Foods Program, Food & Drug Administration, College Park, MD 20740, USA.
International journal of molecular sciences
|November 27, 2024
概括
牛津纳米孔技术 (ONT) Q20+测序提供了一种快速,具有成本效益的方法,用于在食物传播疫情中识别产生Shiga毒素的大肠杆菌 (STEC). 这项技术显示了近乎实时的病原体识别潜力,改善了公共卫生监测.
科学领域:
- 食品安全微生物学 食品安全微生物学
- 基因组监测是指基因组的监测.
- 下一代测序技术是下一代的测序技术.
背景情况:
- 绿叶蔬菜是与农产品相关的滋果毒素产生大肠杆菌 (STEC) 爆发的常见来源.
- 目前的FDA疫情检测方法耗时且昂贵.
研究的目的:
- 评估牛津纳米孔技术 (ONT) Q20+化学作为一种快速,具有成本效益的方法,用于识别和聚类食源性病原体.
- 评估ONT在近乎实时的病原体识别方面的潜力,包括SNP差异,血清型和抗菌素耐药性基因.
主要方法:
- 试点研究使用五种经过良好表征的食物传播病原体菌株.
- 评估两个DNA提取方法 (马克斯韦尔RSC,君主) 和两个ONT库准备协议 (结合,快速条形码).
- 对物种,基因型和毒性因子识别的测序数据的in silico分析;家族基因组聚类.
主要成果:
- 从所有提取和测序套件组合中获得了高质量的,封闭的细菌基因组.
- ONT Q20+精确识别了物种,基因型和毒性因子,与Illumina测序相似.
- 基因组聚类显示了ONT组合与参考基因组组合在一起,观察到微小的indels/SNP差异.
结论:
- 在食品传播疫情调查中,ONT Q20+纳米孔测序化学表明了快速菌株识别的潜力.
- 需要进一步的研究和优化来解决局限性,并充分实现该技术的公共卫生益处.
- 该研究为评估用于食品传播病原体监测的新技术提供了一个框架.
相关概念视频
01:30Methods to Assess Microbial Populations
Assessing microbial populations is crucial for understanding microbial roles in health, ecology, and industry. Various complementary techniques—both culture-based and molecular—enable detailed analysis of microbial abundance, diversity, and function.Viable Plate CountThe viable plate count is a traditional culture-based method used to estimate the number of living microbes in a sample. After serial dilution, the sample is spread onto nutrient agar plates. Each viable cell forms a visible...
01:19Methods to Assess Microbial Communities
Microbial communities, comprising bacteria, archaea, and eukaryotic microorganisms, inhabit diverse ecosystems and play crucial roles in environmental and biological processes. Their diversity is defined by three main parameters: species richness (the number of distinct species), species abundance (the relative quantity of each species), and species evenness (how uniformly individual species are distributed in various locations). These factors together shape the structure and ecological balance...
01:24Automated Microbial Diagnostics
Automated diagnostic analyzers have transformed clinical microbiology by providing rapid and reliable methods for pathogen identification and antibiotic susceptibility testing. Among these systems, the Vitek 2 is widely used because it automates the traditionally labor-intensive processes of microbial identification (ID) and antibiotic susceptibility testing (AST), delivering standardized and timely results that are essential for effective patient care.Microbial Identification with ID CardsThe...