Fig. 5: Core genome characterization of K. pneumoniae isolates. | Nature Microbiology

Fig. 5: Core genome characterization of K. pneumoniae 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. 5

The phylogenetic tree of 268 K. pneumoniae genomes, including 161 from BARNARDS and 107 from other studies12,13,14,15,16,17,18,19,20, is shown, using Roary (v.3.12.0)55 and FastTree (v.2.1.11)56. 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 K. pneumoniae neonatal sepsis isolates from other studies and pink K. pneumoniae 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. Any carriage isolates sequenced in the present study that are genetically similar to the isolate recovered from the corresponding neonatal blood culture10 are denoted by a yellow star. For site acronyms, see Methods.

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