Fig. 4.

Phylogeny of the 62 Patient #1 urine and faecal isolates. The presence or absence of typeable plasmids and antibiotic resistance genes is indicated as per the legend. Plasmid’s presence or absence was determined based on a BLASTn comparison of the assembled contigs for each strain using the complete plasmid sequences from U12A as a reference (Supplementary Fig. 2). Scale bar indicates branch length in number of single-nucleotide polymorphisms. Antibiotic classes are abbreviated as follows: TMP trimethoprim, AGLY aminoglycoside, SUL sulfonamide, TET tetracycline, MLS macrolides, BLA beta-lactams, FLQ fluoroquinolones