Characterization and genomic analysis of antibiotic resistance plasmids in clinical isolates of Klebsiella pneumoniae from hospital-acquired infections

Project Abstract

Klebsiella pneumoniae remains a major cause of hospital-acquired infections worldwide, driven in part by the rapid dissemination of antibiotic resistance plasmids that encode multi-drug resistance determinants and extended-spectrum beta-lactamases. This study undertakes a comprehensive characterization and genomic analysis of antibiotic resistance plasmids isolated from clinical strains of K. pneumoniae obtained from diverse hospital wards over a 24-month period. A combination of phenotypic antimicrobial susceptibility testing, plasmid profiling, and whole-genome sequencing was employed to elucidate the diversity, structure, and evolutionary dynamics of resistance plasmids and their host genomes. Phenotypic profiling revealed a high prevalence of resistance to third-generation cephalosporins, fluoroquinolones, aminoglycosides, and carbapenems in a subset of isolates, with resistance patterns correlating to the presence of multiple plasmid-borne resistance genes. Plasmid extraction and sequencing allowed the delineation of Inc groups, with IncFII, IncA/C, and IncN replicons predominating among the study isolates. Bioinformatic analyses identified a repertoire of resistance determinants, including blaCTX-M, blaSHV, blaKPC, blaNDM, and qnr, aac, and sul genes, organized within complex integrons, transposons, and operon structures that facilitate horizontal gene transfer. Comparative genomics revealed plasmid conjugation modules and transferability mechanisms, as well as mosaic plasmids arising from recombination events between disparate replicons, underscoring active plasmid evolution in the clinical setting. Chromosomal integration events and compensatory mutations were examined to assess fitness impacts on host strains, highlighting a balance between resistance maintenance and metabolic burden. Phylogenomic analyses positioned resistance plasmids within a global context, indicating importation and local diversification, with evidence of clonal expansion in certain hospital units. The study further assessed the plasmid burden on virulence-associated traits by correlating plasmid carriage with capsule production, biofilm formation, and siderophore activity, revealing context-dependent effects on pathogenic potential. Metagenomic and plasmidome reconstruction demonstrated the co-existence of multiple resistance plasmids within single isolates, suggesting cumulative risks for horizontal transfer within the hospital microbiome. Our findings emphasize the significance of routine plasmid surveillance as an adjunct to isolate-based resistance monitoring and infection control strategies. The data generate a curated plasmid resistance map for the clinical K. pneumoniae isolates studied and reveal critical plasmid features—such as transferable conjugative systems, maintenance genes, and recombination hotspots—that warrant targeted interventions to mitigate AMR spread. In conclusion, the study provides a granular view of the plasmid-mediated resistome in hospital-associated K. pneumoniae and offers a framework for tracking, predicting, and interrupting the dissemination of resistance determinants through plasmid networks in clinical environments.

Project Overview

What This Project Is About

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A straightforward, beginner-friendly look at how certain bacteria carry resistance to antibiotics, and how scientists study these resistance genes carried on small DNA circles called plasmids in hospital-associated Klebsiella pneumoniae.

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The Problem It Addresses

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Antibiotic-resistant infections are harder to treat and spread quickly in hospitals. This project investigates why some Klebsiella pneumoniae strains resist drugs, focusing on plasmids that pass resistance between bacteria, to understand how resistance develops and spreads.

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Objectives of the Project

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1. Identify the types of plasmids found in clinical Klebsiella pneumoniae isolates.
2. Describe the resistance genes carried by these plasmids.
3. Explore how plasmids are transferred between bacteria in the lab models available.
4. Compare plasmid content across different patient isolates to spot common patterns.
5. Summarize how genomic data helps explain observed resistance.

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What You Will Do Step by Step

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1. Collect clinical Klebsiella pneumoniae samples (with appropriate approvals).
2. Isolate plasmid DNA from bacterial cells.
3. Identify resistance genes using simple genomic analysis tools.
4. Characterize plasmids by size, type, and compatibility groups.
5. Compare plasmid genes across isolates to find shared traits.
6. Summarize findings and discuss their implications for treatment and infection control.

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Expected Outcome

Clear map of which plasmids carry resistance in the studied strains, basic explanations of how these plasmids spread, and practical takeaways for monitoring and reducing antibiotic resistance in hospitals.