Data analysis associated with the use of whole genome sequencing for subtyping of pathogenic microorganisms, Salmonella Typhimurium as a case study

As the cost of bacterial whole genome sequencing (WGS) by NGS continues to decline, its application for routine (sub)typing of pathogenic microorganisms quickly becomes a reality. NGS allows to examine relationships between different bacterial isolates of the same species at the highest possible resolution, which is essential for epidemiological surveillance and outbreak detection. However, it is still a largely unresolved question how to convert WGS data into information of sufficient quality to be reliably used for epidemiological characterization and discrimination, including the identification of a link between the origin of an infection and the human isolate in case of outbreak situations.Here, we have explored the possibilities offered by single nucleotide polymorphism (SNP)-based approach implemented in three different workflows to subtype 32