Fig 2.

Maximum-likelihood SNP-based phylogenetic tree of 117 ESBL-E. coli isolates from humans (n = 20), poultry (n = 12), and environmental sources (n = 85) in various poultry-intensive sites in Bangladesh. The tree was constructed by trimmed reads and was assembled using Unicycler v0.50. The contigs were annotated using Bakta v1.7.0. The pangenome was calculated using Roary v3.13.0. The SNPs were extracted from the resulting multi-fasta alignment using SNP-sites v2.5.1. A tree was generated from the extracted SNPs using IQtree v2.2.0.3 with bootstrapping set to 1,000 and a standard model of substitution. The resulting SNP tree was visualized with iTOL v5. Blue and green highlights indicate a clonal relationship between isolates (<22 SNPs). Colored rings represent source (inner ring), study site (second ring from the center), phylogroup (third ring), MLST (fourth ring), and serotype (fifth ring).