First report of chromosomal co-occurrence of blaAFM-3 and blaIMP-45 genes in a multidrug-resistant Pseudomonas aeruginosa clinical isolate

Multidrug-resistant (MDR) Pseudomonas aeruginosa, especially carbapenemase-producing strains, poses major clinical challenges due to their widespread dissemination and limited treatment options. A 65-year-old patient with intracranial infection was hospitalized. An MDR P. aeruginosa strain isolated from her cerebrospinal fluid was analyzed using MALDI-TOF mass spectrometry, antimicrobial susceptibility testing (AST), and whole genome sequencing (WGS). P. aeruginosa strain YB1 was resistant to carbapenems, cephalosporins, quinolones, and aminoglycosides, except colistin. Its genome comprised a 6.41-Mb chromosome and a 448-kb IncP-like plasmid. Six β-lactamase genes were identified on the chromosome: blaPER-1, blaOXA-1, blaIMP-45, and blaAFM-3 in the MDR region, with blaOXA-488 and blaPAO-201 located outside it. The chromosomal MDR region shared high homology with plasmid-borne Tn6485e, which originated from multiple plasmids. Specifically, the novel carbapenemase gene blaAFM-3 resided in a conserved transposon (ISCR27n3-groL-△floR-blaAFM-3-bleMBL-trpF-ISCR27n2), identical to that originally characterized in the Alcaligenes faecalis plasmid. Additionally, blaIMP-45 was located in a conserved type I integron (IntI-aac(6')-Ib-blaIMP-45-blaOXY-1-catB3-△qacE-sul1). Notably, the 3'-terminal sequence of Tn6485e (IS26-aph(3')-Ia-IS26-tet(C)-tetR(C)-IS26-IS6100), absent from the chromosomal MDR region, was found on YB1's plasmid. Moreover, IS26 flanked the 71,600-bp chromosomal fragment covering the MRD region, with a 14-bp inverted repeat (5'-GGCACTGTTGCAAA-3') on their outer sides in the same orientation, implying potential IS26-facilitated plasmid-chromosome recombination. This study first identified the coexistence of the blaAFM-3 and blaIMP-45 genes on the chromosome of P. aeruginosa. Monitoring gene transfer from plasmids to chromosomes is crucial, as it boosts bacterial survival against antibiotics and enables heritable resistance, threatening human health.