A set of 520 genomes where serotyped with two in silico typing tools

Salmonella enterica is the second most reported cause of food-borne infections in Europe and regularly causes regional, national and cross-country outbreaks. Therefore surveillance and outbreak investigations are an important part of disease control by public health agencies. In Germany, this work is carried out by the National Reference Center for Salmonella and other bacterial enteric pathogens (NRC) at the Robert Koch-Institute. Subsequent to the implementation of whole genome-based methods, we have largely reduced classical methods for Salmonella subtyping such as Pulsed Field Gel Electrophoresis and phage typing by whole-genome-based typing methods. We still perform classical serotyping and antimicrobial resistance testing for Salmonella isolates. Recently, in silico serotyping has been adopted by other public health agencies like Public Health England and Health Canada. In this study we report on the feasibility of in silico serotyping in a German setting. We found that both, SeqSero and cgMLST gave equal results as slide agglutination for the here evaluated serotypes. However, especially SeqSero needs to be fine-tuned for reliable detection of monophasic variants, in particular monophasic S. Typhimurium, which is an epidemiologically important serotype. We conclude that with a few adjustments in silico serotyping provides a reliable substitute for the current gold standard.