Details of Illumina read sets used in this study are provided in Table 1 and Table 2. Data tables specifying the expected STs of each read set, summarised from published papers, are given in Additional file 1 [35 ].

Data sets used to assess accuracy of SRST2

SpeciesCitationN (isolates)PopulationSequencing centreAverage read depthRead length (bp)
Staphylococcus aureus[36 (link)]134Clonal, ST22Sanger, UK24×55
Staphylococcus aureus[37 ]128Clonal, ST239Sanger, UK60×65
Streptococcus pneumoniae[38 (link)]113Clonal, ST81Sanger, UK30×55
Salmonella enterica Typhimurium[39 (link)]44Clonal, ST313Sanger, UK34×76
Shigella (E. coli)[40 (link)]81Clonal, S. sonneiSanger, UK25×55
Enterococcus faecium[41 (link)]43Diverse, dominated by ST203, ST17Melbourne, Australia658×101
Listeria monocytogenesThis paper231DiverseMelbourne, Australia36×152

Data sets used to demonstrate utility of SRST2 in the hospital setting

SpeciesCitationN (isolates)Average read depthRead length (bp)
Enterococcus faecium (Figure 7a-c)[41 (link)]43658×101
Hospital outbreak investigations (Figure 8a-b)[15 (link)]2036×151
K. pneumoniae, E. coli[42 (link)]69, 7434×101
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