Revolutionizing Next-Generation Sequencing: Tools and Technologies location:Leuven, Belgium date:15-16 Januari 2015
Characterisation of bacterial isolates beyond the species and subspecies level, i.e. subtyping, is necessary for surveillance of infectious diseases and is crucial to identify a link between the origin of an infection and the human isolate in case of outbreak situations.
At the Belgian National Reference Centre (NRC) for Salmonella and Shigella, Salmonella enterica subsp. enterica serovar Typhimurium (S. Typhimurium) is currently subtyped by phage typing, multiple-locus variable-number of tandem repeats analysis (MLVA) or pulsed-field gel electrophoresis (PFGE). Although proven to have additional value for subtyping, each of these techniques has one or more aspects that do not correspond to the ideal subtyping method, which should be inexpensive, rapid, highly discriminative, robust and universally applicable in epidemiology and diagnosis.
In this study we are evaluating if whole genome sequencing could be used at the NRC as a routine subtyping method for surveillance and outbreak investigation of S. Typhimurium. Whereas data generation is feasible using e.g. an Illumina platform, data analysis and interpretation remains a bottleneck in a routine setting. Following issues are addressed: Whether the analysis should be SNP- or allele-based, how a distinct subtype should be defined, how the antibiotic resistance phenotype could be derived from the genotype and how a link with historical subtyping data could be made.