A Validation Approach of an End-to-End Whole Genome Sequencing Workflow for Source Tracking of Listeria monocytogenes and Salmonella enterica

• Published in: Frontiers in microbiology Vol. 9; p. 446
• Main Authors: Portmann, Anne-Catherine, Fournier, Coralie, Gimonet, Johan, Ngom-Bru, Catherine, Barretto, Caroline, Baert, Leen
• Format: Journal Article
• Language: English
• Published: Switzerland Frontiers Media S.A 14.03.2018
• Subjects: Listeria monocytogenes; Microbiology; phylogeny; Salmonella enterica; SNP; validation; WGS; Salmonella enterica; WGS; SNP; source tracking; Listeria monocytogenes; outbreak; phylogeny; validation
• ISSN: 1664-302X; 1664-302X
• DOI: 10.3389/fmicb.2018.00446

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 and 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 and 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 and 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 or .