Unravelling complex transposable elements surrounding bla GES-16 in a Pseudomonas aeruginosa ExoU strain.

Objectives: We characterised the complex surrounding regions of bla _GES-16 in a Pseudomonas aeruginosa exoU+ strain (P-10.226) in Brazil.
Methods: Species identification was performed by MALDI-TOF MS, and the antimicrobial susceptibility profile was determined by broth microdilution based on European Committee on Antimicrobial Susceptibility Testing (EUCAST) breakpoints. The whole genome sequencing (WGS) of P-10.226 strain was performed using both short-read paired-end sequencing on the Illumina MiSeq platform as well as the long-read Oxford Nanopore MinION.
Results: WGS analysis showed that P-10.226 carried bla _GES-16 , which was found as a gene cassette inserted into a novel class I integron, In1992 (aadB-bla _OXA-56 -bla _GES-16 -aadB-aadA6c), whose 3'-CS was truncated by a nested transposable element, IS5564::ISPa157. The structure was even more complex since IS6100-ΔIS6100 structure and a TnAs2-like harbouring the operon merRTPADE was found downstream In1992. Fragments of TnAs3 harbouring 25-bp imperfect inverted repeats were identified bordering the intl1 of In1992 and also flanking IS6100-ΔIS6100, which might be genetic marks of its previous presence in the genome. Interestingly, In1992 also shows a distinct cassette array from In581 (bla _GES-16 -dfrA22-aacA27-aadA1), which was previously reported in Serratia marcescens strains recovered in Brazil. Finally, exoU gene, which encodes a potent cytotoxin of type III secretion systems (T3SS) effector proteins from P. aeruginosa and is associated to severe infections, was also detected.
Conclusion: We described the novel In1992 carrying bla _GES-16 surrounded by complex transposition events in a XDR P. aeruginosa strain. The identification of many sets of direct repeats adjacent to TnAs3 fragments indicates a major past of transposition events that shaped the current genetic environment of In1992.
(Copyright © 2022 The Authors. Published by Elsevier Ltd.. All rights reserved.)