Extended Data Fig. 5: Whole genome single-nucleotide polymorphisms analysis of ST11 and ST15 K. pneumoniae isolates.
a) SNP analysis of ST11 Klebsiella pneumoniae (n = 12 isolates) collected during this study and K. pneumoniae GCF_001462965, GCF_006351115 and GCF_900607955 (see SourceData for Enterobacter sp. trees) using snippy v4.6.0 on paired end fastq, gubbins v2.3.4 to remove recombination and IQ-tree v2.0 to construct the phylogeny. iTOL v4 was used to visualise the phylogenetic tree. BCBR/BCMR, neonate (BR)/mother (MR) rectal isolates from Bangladesh, Chittagong Maa-O-Shishu Hospital, Chattogram (BC). BKBR/BKMR, neonate (BR)/mother (MR) rectal isolates from Bangladesh, Kumudini Women’s Medical College, Mirzapur (BK). PPBR/PPMR, neonate (BR)/mother (MR) rectal isolates from Pakistan Institute of Medical Sciences (PP), Islamabad. Reference, PP-BR254-2. Dates of rectal swab collection are shown. b) SNP analysis of ST15 K. pneumoniae (n = 25 isolates; BARN) collected during this study and other K. pneumoniae isolates’ genome assemblies available in GeneBank (see SourceData for Klebsiella pneumoniae trees) using snippy v4.6.0 on paired end fastq, gubbins v2.3.4 to remove recombination and IQ-tree v2.0 to construct the phylogeny. iTOL v4 was used to visualise the phylogenetic tree. PPBR/PPMR, neonate (BR)/mother (MR) rectal isolates from Pakistan Institute of Medical Sciences (PP), Islamabad. Reference, PP-BR737-1. Dates of rectal swab collection are shown.
