Metagenomics as a Public Health Risk Assessment Tool in a Study of Natural Creek Sediments Influenced by Agricultural and Livestock Runoff: Potential and Limitations

作者：Brittany Suttner, Eric R. Johnston, Luis H. Orellana, Luis M. Rodriguez‐R, Janet K. Hatt, Diana Carychao, Michelle Qiu Carter, Michael B. Cooley, Konstantinos T. Konstantinidis · 发表于：Applied and Environmental Microbiology · 年份：2020 · DOI：10.1128/aem.02525-19 · 被引用次数：44 · 研究领域：Gut microbiota and health、Microbial Community Ecology and Physiology、Fecal contamination and water quality

Current agricultural and livestock practices contribute to fecal contamination in the environment and the spread of food- and waterborne disease and antibiotic resistance genes (ARGs). Traditionally, the level of pollution and risk to public health are assessed by culture-based tests for the intestinal bacterium Escherichia coli . However, the accuracy of these traditional methods (e.g., low accuracy in quantification, and false-positive signal when PCR based) and their suitability for sediments remain unclear. We collected sediments for a time series metagenomics study from one of the most highly productive agricultural regions in the United States in order to assess how agricultural runoff affects the native microbial communities and if the presence of Shiga toxin-producing Escherichia coli (STEC) in sediment samples can be detected directly by sequencing. Our study provided important information on the potential for using metagenomics as a tool for assessment of public health risk in natural environments.