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. 2017 May 22;12(5):e0178040. doi: 10.1371/journal.pone.0178040

Fig 3. Whole genome core SNV maximum likelihood phylogenetic tree of 137 Streptococcus pneumoniae serotype 22F isolates collected in Canada from 2005–2015.

Fig 3

The maximum likelihood phylogenetic tree is rooted on the reference genome of S. pneumoniae R6 (GenBank accession no. NC_003098.1) and the scale bar represents the estimated evolutionary divergence between isolates on the basis of average genetic distance between strains (estimated number of substitutions in the sample / total number of high quality SNVs). Clades A through F identified by cluster analysis are denoted with shading. Coloured columns in the right side heatmap represent: year of isolation (Year); province or territory isolated (Prov); patient age group (Age); clinical isolation source (Source); multi-locus sequence type (MLST); and antimicrobial susceptibilities to erythromycin (ERY), clindamycin (CLI), penicillin (PEN), cefepime (CFM), cefotaxime (CEF), ceftriaxone (CRO), meropenem (MER), trimethoprim/sulfamethoxazole (SXT) and tetracycline (TET).