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We used 23 published Illumina sequence data sets, including six and three data sets from NA and EU countries, respectively, for analysis. Sequencing depth targeted at 3× to 554× read depth varied across the data sets and assemblies were performed using Velvet46 and SPAdes47. Only one cgMLST protocol (04041406) was identified as highly discriminatory (D > 0.90) in two of the analysed data sets (Fig. 5; Additional file 5). The overall D value for all 23 data sets was 0.955, suggesting that highly discriminatory cgMLST protocols are available. As a result, cgMLST protocols were widely used. Coverage data determined by SPAdes showed a wide variation among the data sets analysed due to the various targeted read depths. Moreover, coverage percentages showed a wider variation between the extracted genomes themselves (Additional file 5).
We assessed genetic relatedness using seven or eight loci (SeqSphere+, cgMLST and cgMLST completenesses A, B, C, D and E) of strains from USA, Germany and Japan, respectively, as reference genomes (Additional file 6). These reference strains were initially limited to two TH53 samples from Japan to reduce the computational and analytical burden of a global data analysis. The analysis showed most isolates were genetically similar to the reference strains from the US and Japan, and genetically distant from the reference strain from Germany (Fig. 6). Further, within a respective country, a closer relationship was observed than between the US, EU or Japan, even for isolates from opposite clades comprising the same patient (Fig. 6).
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