Legacy MLST STs and numbers of entries (records) in EnteroBase (http://enterobase.warwick.ac.uk).

<p>EnteroBase has performed genomic assemblies from sequence reads that were originally submitted to ENA short-read archives or directly uploaded to EnteroBase by users. EnteroBase also contains all entries with legacy MLST genotypes based on ABI sequencing that were originally submitted to the now defunct legacy MLST website. (A) Historical release dates in EnteroBase for assembled <i>Salmonella</i> genomes and strains subjected to legacy ABI-based MLST. The curves indicate an exponential increase in the numbers of publicly released short reads over time versus only a linear increase in legacy entries. Genomes with a release date after 1 November 2017 were excluded, as were 3,012 sets of short reads that showed evidence of contamination or did not pass quality control after assembly. (B) A total of 3,929 STs were defined from 120,471 strains of <i>Salmonella</i> by ABI sequencing (left), by WGS (right), or by both approaches (overlap). A full list of the strains summarised in this figure is publicly available to registered EnteroBase users in the EnteroBase workspace at <a href="https://enterobase.warwick.ac.uk/species/senterica/search_strains?query=workspace:9113" target="_blank">https://enterobase.warwick.ac.uk/species/senterica/search_strains?query=workspace:9113</a>. Note that the number of genomes summarised here exceeds those in part (A) because we evaluated all genomes that had been assembled by 1 November 2017, including assemblies that had not yet been released, with the exception of 795 genomic assemblies in which the alleles for all seven legacy MLST loci had not been called. ABI, Applied Biosystems; ENA, European Nucleotide Archive; WGS, whole genome sequencing. For other acronyms see <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1007261#pgen.1007261.box001" target="_blank">Box 1</a>.