Extended Data Fig. 4: Whole genome single-nucleotide polymorphisms analysis of ST405 E. coli isolates. | Nature Microbiology

Extended Data Fig. 4: Whole genome single-nucleotide polymorphisms analysis of ST405 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

Extended Data Fig. 4

Whole genome SNP analysis of ST405 E. coli (n = 24 isolates) 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, neonate (BR) rectal isolates from Pakistan Institute of Medical Sciences (PP), Islamabad. Reference, BC-MR1421-3. Dates of rectal swab collection are shown.

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