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. 2023 Mar 23;9(3):mgen000951. doi: 10.1099/mgen.0.000951

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Fig. 3. — Analyses of Col-R-Ec and ESBL-Ec transmission events in Thailand. All isolates from small chicken (GMF) and pig (PMF) farms for which identical STs were found in both humans and animals were selected. Seven clusters (Cl.) of isolates with identical STs were found. The core genome phylogeny of the isolates’ fully closed genomes is plotted (left side) as are the bla _ESBL and mcr genes. Pair wise core genome Single Nucleotide Variant (cgSNV) differences are shown as compared to the 'reference' (Ref.) strain in each cluster. The genomic backgrounds (G. bgrd) of the bla _ESBL and mcr genes were identified thanks to additional long-read sequencing and subsequent hybrid assembly. Hybrid assembly analyses combined with epidemiological linkage enabled the definition of transmission from humans to animals (or vice versa).