Quasi-metagenomic Analysis of Salmonella from Food and Environmental Samples.

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ID: 48853
2018
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Abstract
Quasi-metagenomics sequencing refers to the sequencing-based analysis of modified microbiomes of food and environmental samples. In this protocol, microbiome modification is designed to concentrate genomic DNA of a target foodborne pathogen contaminant to facilitate the detection and subtyping of the pathogen in a single workflow. Here, we explain and demonstrate the sample preparation steps for the quasi-metagenomics analysis of Salmonella enterica from representative food and environmental samples including alfalfa sprouts, ground black pepper, ground beef, chicken breast and environmental swabs. Samples are first subjected to the culture enrichment of Salmonella for a shortened and adjustable duration (4-24 h). Salmonella cells are then selectively captured from the enrichment culture by immunomagnetic separation (IMS). Finally, multiple displacement amplification (MDA) is performed to amplify DNA from IMS-captured cells. The DNA output of this protocol can be sequenced by high throughput sequencing platforms. An optional quantitative PCR analysis can be performed to replace sequencing for Salmonella detection or assess the concentration of Salmonella DNA before sequencing.
Reference Key
hyeon2018quasimetagenomicjournal Use this key to autocite in the manuscript while using SciMatic Manuscript Manager or Thesis Manager
Authors Hyeon, Ji-Yeon;Mann, David A;Townsend, Anna M;Deng, Xiangyu;
Journal Journal of visualized experiments : JoVE
Year 2018
DOI
10.3791/58612
URL
Keywords
next-generation sequencing transcriptome pneumonia mechanical ventilation lower respiratory tract infection

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