FIG 2.

Core genome SNP phylogeny of isolates in PFGE group A1. Four distinct clusters are evident in (a) the maximum-likelihood phylogeny and (b) the neighbor-joining phylogeny, supported by hierarchical Bayesian estimations of the genetic population structure (hierBAPS). Isolates were indistinguishable by PFGE, MLST, and serotype. The maximum-likelihood tree was approximated using FastTree v2.1.8 with 1,000 bootstrap replicates. Major nodes had >99% bootstrap support, with nodes and branches with <70% support colored in red. SplitsTree4 was used to infer the neighbor-joining phylogeny from the alignment of core genome SNPs produced by Snippy v2.5. Core genome content was highly conserved (>90%) across these isolates.