Genomic Insight of VIM-harboring IncA Plasmid from a Clinical ST69 Escherichia coli Strain in Italy

Abstract

<i>Background</i>: VIM (Verona Integron-encoded Metallo-beta-lactamase) is a member of the Metallo-Beta-Lactamases (MBLs), and is able to hydrolyze all beta-lactams antibiotics, except for monobactams, and including carbapenems. Here we characterize a VIM-producing IncA plasmid isolated from a clinical ST69 <i>Escherichia coli</i> strain from an Italian Long-Term Care Facility (LTCF) inpatient. <i>Methods</i>: An antimicrobial susceptibility test and conjugation assay were carried out, and the transferability of the <i>bla</i>_VIM-type gene was confirmed in the transconjugant. Whole-genome sequencing (WGS) of the strain 550 was performed using the Sequel I platform. Genome assembly was performed using "Microbial Assembly". Genomic analysis was conducted by uploading the contigs to ResFinder and PlasmidFinder databases. <i>Results:</i> Assembly resulted in three complete circular contigs: the chromosome (4,962,700 bp), an IncA plasmid (p550_IncA_VIM_1; 162,608 bp), harboring genes coding for aminoglycoside resistance (<i>aac(6')-Ib4</i>, <i>ant(3″)-Ia</i>, <i>aph(3″)-Ib</i>, <i>aph(3')-XV</i>, <i>aph(6)-Id</i>), beta-lactam resistance (<i>bla</i>_SHV-12, <i>bla</i>_VIM-1), macrolides resistance (<i>mph(A)</i>), phenicol resistance (<i>catB2</i>), quinolones resistance (<i>qnrS1</i>), sulphonamide resistance (<i>sul1</i>, <i>sul2</i>), and trimethoprim resistance (<i>dfrA14</i>), and an IncK/Z plasmid (p550_IncB_O_K_Z; 100,306 bp), free of antibiotic resistance genes. <i>Conclusions:</i> The increase in reports of IncA plasmids bearing different antimicrobial resistance genes highlights the overall important role of IncA plasmids in disseminating carbapenemase genes, with a preference for the <i>bla</i>_VIM-1 gene in Italy.