Fig. 1: Maximum likelihood phylogeny of clade C Escherichia coli sequence type (ST)131 isolates, alongside the antimicrobial resistance genotype and mobile genetic element (MGE) complement. | Nature Communications

Fig. 1: Maximum likelihood phylogeny of clade C Escherichia coli sequence type (ST)131 isolates, alongside the antimicrobial resistance genotype and mobile genetic element (MGE) complement.

From: Genomic epidemiology reveals geographical clustering of multidrug-resistant Escherichia coli ST131 associated with bacteraemia in Wales

Fig. 1

Phylogeny inferred from 4142 non-recombinant orthologous biallelic core-genome single-nucleotide polymorphisms (SNPs) from 238 strains. Moderate recombination SNP density filtering in SPANDx (excluded regions with ≥3 SNPs in a 100 bp window). SNPs were derived from read mapping to the reference chromosome EC958 (GenBank: HG941718). The phylogenetic tree is rooted according to the CD306 (GenBank: CP013831) outgroup. Branch lengths represent nucleotide substitutions per site as indicated by the scale bar. Bootstrapping using 1,000 replicates demonstrates the robustness of the branches. The presence/absence analysis of loci is based on the uniform coverage at each 100 bp window size in SPANDx. Coverage is shown as a heat map where ≥80% identity is highlighted in black and ≥50% identity is highlighted in yellow. White plots indicate regions that are absent.

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