Fig. 5

Putative physical linkage between three alleles of AMR genes in two E. coli genomes. a A path constituting an inferred MGE in the assembly graph of genome ERR178189. This plot is drawn in Bandage with a double-strand style, where the orientation of each DNA strand is indicated by an arrow-like node end. The width of each node is proportional to its read depth determined by Unicycler. Some nodes not contributing to any MGE-related path were deleted from the original assembly graph for visual conciseness. b A path constituting the other inferred MGE (following the red dashed line) in the assembly graph of genome ERR178173. This plot was drawn in the same way as panel a. c Alignment of the two Tn7 variants we identified in E. coli genomes (ERR178189 and ERR178173) to a reference Tn7 sequence (GenBank accession: KX159451, denoted by green shaded areas). Two direct repeats flanking the ISs, including inverted repeats, are denoted by green and pink boxes, respectively. Reference DNA sequences of ISKpn26 (1,196 bp) and ISEc23 (2,532 bp) were retrieved from database ISFinder [29] in January 2018. Each IS in the resolved region showed a 100% coverage and 99% nucleotide identity to its reference