Center for Veterinary Medicine, U.S. Food and Drug Administration , Laurel, Maryland, USA.
Center for Food Safety and Applied Nutrition, U.S. Food and Drug Administration , College Park, Maryland, USA.
Microbiol Spectr. 2023 Dec 12;11(6):e0148223. doi: 10.1128/spectrum.01482-23. Epub 2023 Oct 9.
In developed countries, the human diet is predominated by food commodities, which have been manufactured, processed, and stored in a food production facility. Little is known about the application of metagenomic sequencing approaches for detecting foodborne pathogens, such as , and characterizing microbial diversity in food production ecosystems. In this work, we investigated the utility of 16S rRNA amplicon and quasimetagenomic sequencing for the taxonomic and phylogenetic classification of culture enrichments of environmental swabs collected from dairy and seafood production facilities. We demonstrated that single-nucleotide polymorphism (SNP) analyses of metagenome-assembled genomes (MAGs) from quasimetagenomic data sets can achieve similar resolution as culture isolate whole-genome sequencing. To further understand the impact of genome coverage on MAG SNP cluster resolution, an downsampling approach was employed to reduce the percentage of target pathogen sequence reads, providing an initial estimate of required MAG coverage for subtyping resolution of .
在发达国家，人类的饮食主要以食品商品为主，这些食品商品在食品生产设施中经过制造、加工和储存。关于宏基因组测序方法在检测食源性病原体（如 和 ）方面的应用，以及在食品生产生态系统中对微生物多样性进行特征描述的研究知之甚少。在这项工作中，我们研究了 16S rRNA 扩增子和拟宏基因组测序在从乳制品和海鲜生产设施采集的环境拭子的培养物富集物的分类和系统发育分类中的应用。我们证明了来自拟宏基因组数据集的宏基因组组装基因组（MAG）的单核苷酸多态性（SNP）分析可以达到与培养物分离物全基因组测序相似的分辨率。为了进一步了解基因组覆盖度对 MAG SNP 聚类分辨率的影响，采用了一种 下采样方法来降低目标病原体序列读数的百分比，为 的亚型分辨率所需的 MAG 覆盖度提供了初步估计。
