FIG 1.

Phylogenetic branch of K. pneumoniae containing the South African isolates (n = 18). Global phylogeny from genome assembly data sets (n = 1,148) downloaded from the PATRIC database (https://www.patricbrc.org/) was revealed by rapid core genome multialignment (https://github.com/marbl/parsnp) and metadata (isolation country and MLST) coupled with the use of Phandango (https://github.com/jameshadfield/phandango/wiki). The selected branch shows the isolate assembly identifier (ID) for the downloaded samples (lilac) and isolate ID for the samples from this study (yellow), for which subgroup (I, II, or III) and carbapenemase-encoding determinants are indicated. Color codes show isolation country and MLST for each isolate.