Antimicrobial resistance (AMR) genes are carried by plasmids, which can also interchange genetic material with other structures, aiding in the spread of AMR. There is no trustworthy method for determining whether AMR genes are transferred between plasmids. This is mostly because plasmids exhibit high DNA sequence variability and there is no way to determine their phylogenetic distance. Determining and measuring this type of transfer can offer new perspectives on how resistant plasmid regions and tiny mobile elements contribute to the spread of antimicrobial resistance.
The authors created SHIP, a brand-new technique that uses the dynamics of plasmid evolution to quantify plasmid similarity. This demonstrated lateral transfer by enabling us to identify conserved segments carrying AMR genes in phylogenetically distant and structurally distinct plasmids. According to our findings, integrons, transposons, and recombination events can all be used to highly mobilise areas containing AMR genes between plasmids, which aids in the spread of AMR. A region encoding tetracycline resistance transmitted through recombination in Enterococcus faecalis and a multi-resistant complex class 1 integron in Escherichia coli and Klebsiella pneumoniae are two examples of identified transferred fragments.
You may get the code used in this work at https://github.com/AbeelLab/plasmidHGT
Reference:
Marco T. et.al. (2023) SHIP: identifying antimicrobial resistance gene transfer between plasmids. Bioinformatics 39(10): btad612