Sharma Arnav, Bansal Sherry, Moore Matthew D, Luo Yaguang, Schneider Keith R, Zhang Boce
Food Science and Human Nutrition Department, University of Florida, Gainesville, Florida, USA; email:
School of Medicine, Duke University, Durham, North Carolina, USA.
Annu Rev Food Sci Technol. 2025 Apr;16(1):219-244. doi: 10.1146/annurev-food-072023-034549. Epub 2025 Jan 13.
Foodborne illnesses are a significant global public health challenge, with an estimated 600 million cases annually. Conventional food microbiology methods tend to be laborious and time consuming, pose difficulties in real-time utilization, and can display subpar accuracy or typing capabilities. With the recent advancements in third-generation sequencing and microbial omics, nanopore sequencing technology and its long-read sequencing capabilities have emerged as a promising platform. In recent years, nanopore sequencing technology has been benchmarked for its amplicon sequencing, whole-genome and transcriptome analysis, meta-analysis, and other advanced omics approaches. This review comprehensively covers nanopore sequencing technology's current advances in food safety applications, including outbreak investigation, pathogen surveillance, and antimicrobial resistance profiling. Despite significant progress, ongoing research and development are crucial to overcoming challenges in sequencing chemistry, accuracy, bioinformatics, and real-time adaptive sampling to fully realize nanopore sequencing technology's potential in food safety and food microbiology.
食源性疾病是一项重大的全球公共卫生挑战，据估计每年有6亿例病例。传统的食品微生物学方法往往既费力又耗时，在实时应用方面存在困难，并且准确性或分型能力可能欠佳。随着第三代测序和微生物组学的最新进展，纳米孔测序技术及其长读长测序能力已成为一个有前景的平台。近年来，纳米孔测序技术已在其扩增子测序、全基因组和转录组分析、荟萃分析及其他先进的组学方法方面成为基准。本综述全面涵盖了纳米孔测序技术在食品安全应用方面的当前进展，包括疫情调查、病原体监测和抗菌药物耐药性分析。尽管取得了重大进展，但持续的研发对于克服测序化学、准确性、生物信息学和实时自适应采样方面的挑战至关重要，以便充分实现纳米孔测序技术在食品安全和食品微生物学方面的潜力。
