Oral Presentation Australian Society for Microbiology Annual Scientific Meeting 2023

Tn5403 promotes plasmid rearrangements and degradation of the Klebsiella pneumoniae carbapenemase (KPC) transposon Tn4401 (94010)

Anna E Sheppard 1 , Katie E Barry 2 , Hardik I Parikh 2 , Kasi Vegesana 2 , Robert Sebra 3 , Sophie George 4 , Nicholas D Sanderson 4 , David W Eyre 4 , Derrick W Crook 4 , A Sarah Walker 4 , Amy J Mathers 2
  1. School of Biological Sciences, University of Adelaide, Adelaide, SA, Australia
  2. University of Virginia Health System, Charlottesville, VA, USA
  3. Icahn School of Medicine at Mount Sinai, New York, NY, USA
  4. University of Oxford, Oxford, UK

The worldwide dissemination of antimicrobial resistance is partially driven by mobile genetic elements including plasmids and transposons. The major recognised vector for mobilisation of the Klebsiella pneumoniae carbapenemase (KPC) gene, blaKPC, is the 10 kb replicative transposon Tn4401, which has been largely stably associated with blaKPC for ~25 years.

From whole-genome sequencing of a large collection of KPC-Enterobacterales isolated from patients and the wastewater environment within a single hospital over 10 years, we identified an integration of Tn5403 into Tn4401 downstream of blaKPC. This composite structure, denoted Tn4401::Tn5403, was found in 109/1,266 (9%) KPC-positive hospital isolates. Tn4401::Tn5403 was found in 10 different bacterial species, with the most common being Raoultella ornithinolytica (n=54), Klebsiella oxytoca (n=26), and K. pneumoniae (n=10). There were multiple isolates with independent integrations of Tn4401::Tn5403 into other Tn5403 copies, with recombination between internal and external Tn5403 sequences leading to deletions and other rearrangements. Long-read sequencing of isolates from a patient with four different species carrying Tn4401::Tn5403 revealed a complex array of molecular processes involved in blaKPC mobilisation and Tn4401 rearrangements, including inter-species plasmid transfer, Tn4401::Tn5403 transposition into the chromosome or other plasmids, Tn5403- and IS26-mediated rearrangements, and IS26-mediated composite transposition. To assess the impact of Tn5403 more broadly, we queried the European Nucleotide Archive for Tn5403 presence and associations with Tn4401. This revealed that Tn5403 was widely dispersed across Enterobacterales, being found in 34% and 19% of Klebsiella and Enterobacter sequences, respectively, and has integrated into Tn4401 on multiple occasions.

Taken together, our results demonstrate an association between Tn5403 and Tn4401 that is degrading the Tn4401 structure and impacting blaKPC mobility. As well as highlighting the complexity of genomic rearrangements arising from resistance gene associations with different transposable elements, our results have important implications for resistance surveillance given the variety of mechanisms driving blaKPC dissemination.