Antimicrobial resistance is a recognised global health crisis that threatens to take 10 million lives per year by 2050. Antibiotic resistance genes (ARGs) spread rapidly between bacteria, plasmids and chromosomes due to the actions of different mobile genetic elements (MGEs). In a single step, their movement can increase the number of bacterial hosts carrying an ARG or alter the selective advantage associated with ARG carriage. Characterising the combinations of MGEs contributing to the dissemination of ARGs is thus crucial.

blaKPC is a highly mobile, carbapenemase-encoding ARG. We collated information from 1789 publicly available, completely assembled bacterial chromosomes and plasmids containing one blaKPCgene. Using a mathematical graphing approach, alignments between all pairs of sequences were collapsed into a ‘tree’ of shared blaKPC contexts. We annotated MGEs, ORFs and other key features in representatives of the most common blaKPC flanking sequences, and characterised relationships between representative contexts using Pangraph.

We found considerable diversity in blaKPCflanking sequences. We identified 41 unique contexts upstream of blaKPC and 35 downstream. There were 60 common combined up- and downstream blaKPCcontexts. blaKPC co-locates with other ARGs in at least 40% of sequences, including genes conferring resistance to β-lactams, aminoglycosides and sulfonamides.Tn4401, IS26, ISKpn27and Tn1722 transposable elements were highly prevalent near blaKPCgenes.

Our analysis supports the hypothesis that all observed blaKPC contexts are derived from Tn4401. Sequence similarity across the dataset abruptly breaks down at the boundaries of key transposable elements, indicating that these are both common and active in blaKPC dissemination. The methods developed are applicable to a wide range of ARGs, enabling full characterisation of the complex MGE structures responsible for dissemination. This work has applications in surveillance and control of antibiotic resistance, allowing instances of horizontal and intracellular movement of ARGs to be rapidly identified.