Full characterization of the integrative and conjugative element carrying the metallo-β-lactamase blaSPM-1 and bicyclomycin bcr1 resistance genes found in the pandemic Pseudomonas aeruginosa clone SP/ST277

Abstract

Objectives: This study aimed to characterize the genomic context of the blaSPM-1 gene in Brazilian strains belonging to the pandemic Pseudomonas aeruginosa clone SP/ST277. Methods: WGS of clone SP/ST277 strains was performed using a Nextera paired-end library in an Illumina HiSeq 2500 sequencer. blaSPM-1 context was assessed by de novo assembly and gene prediction and annotation tools. blaSPM-1 was screened in P. aeruginosa genomes through BlastN, and comparative genomics were performed. Results: The metallo-β-lactamase blaSPM-1 has been disseminated by the pandemic Brazilian P. aeruginosa clone SP/ST277. In spite of its association with the CR4 element and with the Tn4371 element, the overall blaSPM-1 genomic context remains uncharacterized and its determination is valuable to understanding gene dispersion dynamics and the consequent emergence of carbapenem resistance. In this study, blaSPM-1 and its surrounding sequences (CR4-groEL-blaSPM-1-CR4-groEL) were found in the variable region of an ICE-like element resembling Tn4371 (where ICE stands for integrative and conjugative element). This element, named ICETn43716061, had 46 ORFs, including the bicyclomycin resistance bcr1 gene. An integrase gene and a set of conjugative transfer genes were identified. Gene content and order were shared with other Tn4371-ICEs, presenting remarkable amino acid identities. blaSPM-1 and surrounding sequences were missing in ICETn43716061 of PS600-MA, another isolate belonging to clone SP/ST277, indicating their mobilization. Eight/nine P. aeruginosa genomes assigned to clone SP/ST277, by in silico MLST, harboured blaSPM-1 inserted into ICETn43716061. Conclusions: The presence of blaSPM-1 in a Tn4371-ICE with intact integration/conjugation modules demonstrated that, besides gene dispersion by clonal expansion of the pandemic SP/ST277 lineage, blaSPM-1 may be spread through ICE conjugation.