Salmonella nomenclature in the genomic era: a time for change

Abstract

Abstract Salmonella enterica nomenclature has evolved over the past one hundred years into a highly sophisticated naming convention based on the recognition of antigens by specific antibodies. This serotyping scheme has led to the definition of over 2500 serovars which are well understood, have standing in nomenclature and, for the majority, biological relevance. Therefore, it is highly desirable for any change in naming convention to maintain backwards compatibility with the information linked to these serovars. The routine use of whole genome sequencing and the well-established link between sequence types and serovars presents an opportunity to update the scheme by incorporating the phylogenetically relevant sequence data whilst preserving the best of serotyping nomenclature. Advantages include: overcoming the variability in antibody preparations; removing the need to use laboratory animals and implementing a truly universal system. However, the issue of trying to reproduce the phenotyping gold standard needs to be relaxed if we are to fully embrace the genomic era. We have used whole genome sequence data from over 46,000 isolates of Salmonella enterica subspecies enterica to define clusters in two stages: Multi Locus Sequence Typing followed by antigen prediction. Sequence type—serotype discrepancies were resolved using core SNP clustering to determine the phylogenetic groups and this was confirmed by overlaying the antigenic prediction onto the core SNP clusters and testing the separation of clusters using cgMLST Hierarchical Clustering. This allowed us to define any major antigenic clusters within an ST—here called the MAC type and written as ST-serovar. Using this method, 99.96% of Salmonella isolates reported in the UK were assigned a MAC type and linked to a serovar name taken from the Kauffmann and White scheme. We propose a change for reporting of Salmonella enterica sub-types using the ST followed by serovar.