Files
Abstract
Quasimetagenomics refers to the sequencing of a modified food microbiome to facilitate combined detection and strain-level subtyping of targeted pathogens in a single workflow. Through quasimetagenomic sequencing, pathogens are detected and identified in a shortened time frame compared to traditional culture enrichment and whole genome sequencing-based analyses. While this method was previously used to detect and subtype Salmonella enterica from chicken, iceberg lettuce, and black pepper, it has not been applied to investigate several pathogens in one workflow. A quasimetagenomic method to concertedly detect and subtype Salmonella enterica and Escherichia coli O157:H7 from artificially contaminated fresh produce in a single workflow was developed. The majority of quasimetagenomic samples were serotyped after 12 hours of co-enrichment in a nonselective medium. SNP typing was achievable for some initial pathogen inoculum levels as low as 0.1 CFU/g, suggesting that this method can be used for concerted detection and identification of bacterial pathogens.