Fig. 3: Core genome characterization of E. coli isolates. | Nature Microbiology

Fig. 3: Core genome characterization of E. coli isolates.

From: Antibiotic resistance genes in the gut microbiota of mothers and linked neonates with or without sepsis from low- and middle-income countries

Fig. 3

The phylogenetic tree of 253 E. coli genomes, including 150 from BARNARDS and 103 from other studies11,12,13,14,15, is shown, using Roary (v.3.12.0)39 and FastTree40 (v.2.1.11). Isolates are coloured at the endpoint according to country and the outer ring abbreviation is labelled according to the sample source. STs for all isolates are shown in the text after the sample source. The additional two outer rings denote the presence of blaNDM and blaOXA-48-like genes. Clades containing isolates from the present study are highlighted in teal, green clades indicate E. coli neonatal sepsis isolates from other studies and pink clades relate to E. coli rectal carriage from different studies. Major STs are labelled around the phylogeny and isolates that belong to a mother–neonate pair are denoted by an orange triangle. For site acronyms, see Methods.

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