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Published on: December 23, 2022
Complete Genome and Plasmids Sequences of a Clinical Proteus mirabilis Isolate Producing Plasmid Mediated NDM-1 from
Ibrahim Bitar1,2, Vittoria Mattioni Marchetti3, Alessandra Mercato3
1Department of Microbiology, Faculty of Medicine, and University Hospital in Pilsen, Charles University, 32300 Pilsen, Czech Republic.
Abstract:
Background: The spread of carbapenemase genes, such as blaNDM-1, in Proteus mirabilis poses a public health threat. The aim of the study was to characterize the genome and plasmids sequences of an NDM-1-positive strain (IBCRE14), which was isolated in 2019 from a catheterized patient hospitalized in Italy. Methods: Whole genome sequencing (WGS) of IBCRE14 was performed on extracted genomic DNA using Sequel I platform. Genome assembly was performed using "Microbial Assembly". Genomic analysis was conducted by uploading the contigs to ResFinder and PlasmidFinder databases from the Center for Genomic Epidemiology. Results: IBCRE14 had a genome size of 4,018,329 bp and harboured genes coding for resistance to aminoglycosides (aadA1), phenicol (cat), tetracycline (tetJ), and trimethoprim (dfrA1). A large plasmid (pIB_NDM_1) harboured antibiotic resistance genes against sulphonamide (sul1), trimethoprim (dfrA14), tetracycline (tetB), rifampicin (arr-2), aminoglycosides (aadA1, aph3-VI), and beta-lactams (blaOXA-10, blaNDM-1). Furthermore, a small plasmid (pIB_COL3M) harboured a qnrD1 gene coding for quinolone resistance. Conclusion: The ability to conjugate and the presence of a composite antibiotic resistance island suggests that pIB_NDM_1 could both acquire more resistance genes and easily disseminate. To our knowledge, this is the first report on an untypable plasmid harbouring blaNDM-1 in P. mirabilis, in Italy.
Insights
The spread of carbapenemase genes in Proteus mirabilis is a threat. This study characterized an NDM-1-positive strain from Italy, revealing multiple antibiotic resistance genes on its genome and plasmids.
Area of Science:
- Microbiology
- Genomics
- Antimicrobial Resistance
Background:
- The emergence of carbapenemase genes, like blaNDM-1, in Proteus mirabilis presents a significant public health concern.
- Proteus mirabilis is an opportunistic pathogen frequently associated with healthcare-associated infections.
Purpose of the Study:
- To perform whole genome sequencing and plasmid characterization of an NDM-1-positive Proteus mirabilis strain (IBCRE14) isolated in Italy.
- To identify antibiotic resistance genes and genetic elements associated with antimicrobial resistance in the studied strain.
Main Methods:
- Whole genome sequencing (WGS) of the Proteus mirabilis strain IBCRE14 using the Sequel I platform.
- Bioinformatic analysis including genome assembly and identification of resistance genes and plasmids using ResFinder and PlasmidFinder databases.
Main Results:
- The genome of IBCRE14 (4,018,329 bp) contained genes conferring resistance to aminoglycosides, phenicol, tetracycline, and trimethoprim.
- A large plasmid, pIB_NDM_1, harbored multiple resistance genes including blaNDM-1, blaOXA-10, aadA1, and sul1.
- A small plasmid, pIB_COL3M, carried the qnrD1 gene, conferring quinolone resistance.
Conclusions:
- The pIB_NDM_1 plasmid possesses conjugative ability and a composite antibiotic resistance island, indicating potential for acquiring further resistance and easy dissemination.
- This study reports the first untypable plasmid carrying blaNDM-1 in Proteus mirabilis in Italy, highlighting a critical public health issue.
