Fig 1.
Bio-Neighbor Joining tree of the 41 Kazakhstan strains collected in 2017–2018.
SNPs (32318) were called by mapping on reference genome Z2491 assembly accession GCF_000009105. Coloring reflects region of origin. Strains are labeled with strain Id and MLST7 ST. Four strains recovered from CSF are boxed in light red.
Table 1.
Genetic and antigenic characteristics of isolated strains N. meningitidis.
Fig 2.
Comparison of the ST11 invasive strain NmKZ-33 from Kazakhstan with 14 PubMLST nearest neighbors.
A representative subset among strains with a cgMLST distance lower than 150 to Kazakhstan strain NmKZ-33 is shown. 1153 SNPs were called by mapping on genome M07149 assembly accession GCF_001697425. The size of the resulting maximum parsimony tree is 1162. Branch lengths above 10 SNPs are indicated. Strains are labeled with strain Id, year of isolation and country, and colored according to country of origin. Recombination-filtered inset: 157 SNPs are retained after filtration with Gubbins [17]. The inset shows the associated Maximum Parsimony Tree (tree size 157).
Fig 3.
Eighteen strains were assigned to the newly described ST-16025. Strains are colored according to region of origin. Two invasive strains are boxed in light red. SNPs (3635) were called by mapping on reference genome Z2491 assembly accession GCF_000009105. The size of the resulting Maximum Parsimony Tree is 3644. Branch lengths are indicated. “Recombination filtered” inset: 176 SNPs are kept after filtering of clustered SNPs by Gubbins. No homoplasia in the Maximum Parsimony tree.
Fig 4.
Seven strains were assigned to ST-767 (cc167). Strains are colored according to region of origin. SNPs (1069) were called by mapping on reference genome Z2491 assembly accession GCF_000009105. The size of the resulting Maximum Parsimony Tree is 1069 (no homoplasia). Branch lengths are indicated. “Recombination filtered” inset: 80 SNPs are kept after filtering of clustered SNPs by Gubbins, Maximum Parsimony tree size, 81.