Carbapenem resistance determinants acquired through novel chromosomal integrations in extensively drug-resistant pseudomonas aeruginosa

Abstract

Two novel bla_DIM-1- or bla<SUB>IMP-1</SUB>-containing genomic islands (GIs) were discovered by whole-genome sequence analyses in four extensively drug-resistant (XDR) <i>Pseudomonas aeruginosa</i> isolates from inpatients at a tertiary hospital in Ghana. The strains were of sequence type 234 (ST234) and formed a phylogenetic clade together with ST111, which is recognized as a global high-risk clone. Their carbapenem resistance was encoded by two Tn<i>402</i>-type integrons, In1592 (<i>bla</i>_DIM-1) and In1595 (<i>bla</i>_IMP-1), both carrying complete <i>tni</i> mobilization modules. In1595 was bound by conserved 25-bp inverted repeats (IRs) flanked by 5-bp direct repeats (DRs) 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 DR created by 3′-end target duplication. GIs with the same structural features, but diverse genetic content, were identified in 41/226 completed <i>P. aeruginosa</i> genomes. PAGI-97B (22,636 bp; In1595), which encoded an XerC/D superfamily integrase in its 5′ border, was inserted into the small RNA (sRNA) PrrF1/PrrF2 locus. Specific insertions into this highly conserved locus involved in iron-dependent regulation, all leaving PrrF1 intact, were identified in an additional six phylogenetically unrelated <i>P. aeruginosa</i> genomes. Our molecular analyses unveiled a hospital-associated clonal dissemination of carbapenem-resistant ST234 <i>P. aeruginosa</i> in which the XDR phenotype resulted from novel insertions of two GIs into specific chromosomal sites.