Carbapenem-resistance determinants acquired through novel chromosomal integrations in XDR Pseudomonas aeruginosa.

Two novel bla DIM-1 or bla IMP-1 containing genomic islands (GIs) were discovered in four extensively drug-resistant (XDR) Pseudomonas aeruginosa isolated from in-patients at a tertiary hospital in Ghana by whole-genome sequence analyses. The strains were of ST234 and formed a phylogenetic clade together with ST111, recognized as a global high-risk clone. Their carbapenem resistance was encoded by Tn402-type integrons, In1592 (bla DIM-1) and In1595 (bla IMP-1), both carrying complete tni mobilization modules. In1595 was bound by conserved 25-bp inverted repeats flanked by 5-bp direct repeats, associated with target site duplication. The integrons were embedded in two GIs that contained cognate integrases and were distinguished by a lower GC-content than the chromosomal average. PAGI-97A (52.659 bp; In1592), which encoded a P4-type site-specific integrase of the tyrosine recombinase family, in its 3'-border, was integrated into tRNA-Pro(ggg) and bracketed by a 49-bp perfect direct repeat sequence created by 3'-end target duplication. GIs with the same structural features, but diverse genetic content, were identified in 41/226 completed P. aeruginosa genomes. PAGI-97B (22.636 bp; In1595), which encoded a XerC/D superfamily integrase in its 5'-border, was inserted into the sRNA PrrF1/PrrF2 locus. Specific insertions into this highly conserved locus involved in iron-dependent regulation were identified in an additional six phylogenetically unrelated P. aeruginosa genomes, all leaving PrrF1 intact. Our molecular analyses unveiled a hospital associated clonal dissemination of carbapenem-resistant ST234 P. aeruginosa where the XDR phenotype resulted from novel insertions of two GIs into specific chromosomal sites.