The 21 genomes, 26 isolates and three tissue samples analyzed in this study.

a Received from WSU = Washington State University, USA; FOI = Swedish Defence Research Agency, Umeå, Sweden; JLU = Justus-Liebig University, Giessen, Germany; IMB = Bundeswehr Institute of Microbiology, Munich, Germany; ATCC = American Type Culture Collection, USA; RIVM = National Institute for Public Health and the Environment, Utrecht, the Netherlands.b no = no amplification; MDA = multiple displacement amplification; no/MDA = no amplification used for SNP assay, MDA used for genome sequencing.c 36 bp single-end reads (Illumina). Mean insert size not applicable.d Sampled by FOI. Isolated by JLU.e 100 bp paired-end reads (Illumina). Mean insert size (standard deviation): S4; 322(145), Z349-36/94; 269(97), 2338; 478(31).f Isolated by JLU. Cultured by FOI.g Isolated by FOI [54].h 76 bp single-end reads (Illumina). Mean insert size not applicable.i 150 bp paired-end reads (Illumina). Mean insert size (standard deviation): Namibia; 297(92).j Genomic DNA was prepared on Herzberg isolate at FOI, MDA DNA was prepared from the Herzberg isolate at IMB.k ID at RIVM.