Fig. 2
Phylogenetic analysis of Cronobacter sakazakii strains isolated from spices, compared with eight representative Cronobacter species strains (marked with superscripted ‘T’ after each strain’s name). NCBI GenBank Accession numbers of type strains: C. malonaticus LMG 23826T (NZ_CP013940), C. turicensis LMG 23827T (NC_013282), C. universalis NCTC 9529T (NZ_CP012257), C. muytjensii ATCC 51329T (NZ_CP012268), C. dublinensis subsp. dublinensis LMG 23823T (NZ_CP012266), C. dublinensis subsp. lactaridi LMG 23825T (NZ_AJKX00000000), C. dublinensis subsp. lausannensis LMG 23824T (NZ_AJKY00000000), and C. condimenti LMG 26250T (NZ_CP012264). Whole genome SNP analysis was carried out using kSNP3 software [48]. The phylogenetic tree was built using neighbor-joining method [65] and the evolutionary distances were computed using the Maximum Composite Likelihood method [66] available on MEGA7 phylogenetic suite [67]. The bootstrap values obtained from 500 bootstrap replicates are reported as percentages at the nodes [68]. Sequence type (ST) information was obtained by uploading each strain’s genome assembly to the Cronobacter MLST website (http://pubmlst.org/cronobacter/) after which the ST information was manually overlaid onto the tree with different color. Note that the phylogeny among the strains followed ST evolutionary lineages. The scale bar indicates 0.10 substitutions per nucleotide position