Abstract
Whole genome sequencing (WGS), using high throughput sequencing technology, reveals the complete sequence of the bacterial genome in a few days. WGS is increasingly being used for source tracking, pathogen surveillance and outbreak investigation due to its high discriminatory power. In the food industry, WGS used for source tracking is beneficial to support contamination investigations. Despite its increased use, no standards or guidelines are available today for the use of WGS in outbreak and/or trace-back investigations. Here we present a validation of our complete (end-to-end) WGS workflow for Listeria monocytogenes and Salmonella enterica including: subculture of isolates, DNA extraction, sequencing and bioinformatics analysis. This end-to-end WGS workflow was evaluated according to the following performance criteria: stability, repeatability, reproducibility, discriminatory power, and epidemiological concordance. The current study showed that few single nucleotide polymorphism (SNPs) were observed for L. monocytogenes and S. enterica when comparing genome sequences from five independent colonies from the first subculture and five independent colonies after the tenth subculture. Consequently, the stability of the WGS workflow for L. monocytogenes and S. enterica was demonstrated despite the few genomic variations that can occur during subculturing steps. Repeatability and reproducibility were also demonstrated. The WGS workflow was shown to have a high discriminatory power and has the ability to show genetic relatedness. Additionally, the WGS workflow was able to reproduce published outbreak investigation results, illustrating its capability of showing epidemiological concordance. The current study proposes a validation approach comprising all steps of a WGS workflow and demonstrates that the workflow can be applied to L. monocytogenes or S. enterica.
Highlights
The current study proposes a validation approach comprising all steps of a Whole genome sequencing (WGS) workflow
This study presents results on performance characteristics applied to our complete WGS workflow used for source tracking of L. monocytogenes and S. enterica
The stability of L. monocytogenes and S. enterica was evaluated by the selection of eight L. monocytogenes and eight S. enterica strains
Summary
The use of Whole genome sequencing (WGS) for outbreak investigation and pathogen source tracking has been described in several publications since a few years (Leekitcharoenphon et al, 2014; Schmid et al, 2014; Octavia et al, 2015; Wuyts et al, 2015; Dallman et al, 2016; Jackson et al, 2016; Wilson et al, 2016; Inns et al, 2017). Several public health agencies and food authorities are using WGS for outbreak investigations or pathogen source tracking (Chen et al, 2017; Inns et al, 2017; Katz et al, 2017; Moran-Gilad, 2017), and food industries are gradually evaluating or implementing the WGS technology. The development of a standard has started within the International Organization for Standardization (ISO TC34-SC9-WG25) and aims at developing an internationally harmonized WGS methodology for source tracking
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