Fig. 2

Single nucleotide polymorphism (SNP)-based maximum-likelihood phylogenomic tree after regions of recombination have been excluded using Gubbins [26]. Group (invasive/non-invasive) and MLST clonal complex are described for each isolate and white bars depict isolates that do not belong to any of the five named major MLST clonal complexes. Genomic regions with high frequency of recombination are mapped to the reference genome of Streptococcus agalactiae NEM316 (annotated in blue on top). Each row represents an isolate and the columns relate to bases in the reference genome. The red columns are recombinations shared by multiple isolates and occuring in the internal branches. The blue columns are recombinations in the terminal branch and represented by unique isolates