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Molecular Epidemiology and In-Depth Characterization of Klebsiella pneumoniae Clinical Isolates from Armenia
Anahit Sedrakyan1, Zaruhi Gevorgyan2, Magdalina Zakharyan1
1Institute of Molecular Biology, National Academy of Sciences of RA, Yerevan 0014, Armenia.
Abstract:
The global dissemination of Klebsiella pneumoniae pathotypes with multidrug-resistant (MDR) and hypervirulent traits poses a threat to public health. The situation in Armenia is unclear, and we performed a comprehensive characterisation of 48 clinical isolates of K. pneumoniae, collected from 2018 to 2024. The majority of the isolates (64.58%) were extensively drug-resistant (XDR) and MDR. Genomic analysis of 21 isolates revealed the presence of international high-risk MDR clones (ST395, ST15, and ST307). The ST395 strains were isolated from children and resisted the first-line drugs such as beta-lactams. These isolates harboured a range of virulence determinants, from capsule polysaccharides to siderophores to regulators of the mucoid phenotype. The ST395 strains are enriched by ICEs, plasmids, and prophages, on which antimicrobial resistance (AMR) and virulence genes are located and which may lead to the convergence of MDR and hypervirulent traits. There is a widespread non-specific AMR mechanism among our K. pneumoniae strains. These are mutations in the porin genes, which reduce permeability to antimicrobials, and mutations in the regulators of efflux pumps, which lead to overexpression of drug efflux pumps such as AcrAB. These mechanisms may contribute to the elevated MICs and confer AMR to strains with no specific AMR genes.
Insights
Multidrug-resistant Klebsiella pneumoniae strains, including extensively drug-resistant and hypervirulent types, are prevalent in Armenia. Genomic analysis identified high-risk clones, highlighting a significant public health threat.
Area of Science:
- Microbiology
- Genomics
- Public Health
Background:
- The global spread of multidrug-resistant (MDR) and hypervirulent Klebsiella pneumoniae poses a significant public health risk.
- The antimicrobial resistance (AMR) and virulence profiles of K. pneumoniae in Armenia remain largely uncharacterized.
Purpose of the Study:
- To comprehensively characterize clinical isolates of K. pneumoniae from Armenia.
- To identify prevalent antimicrobial resistance patterns, high-risk clones, and virulence factors.
Main Methods:
- Phenotypic characterization of 48 clinical K. pneumoniae isolates (2018-2024).
- Genomic analysis of 21 isolates to identify sequence types (STs), resistance genes, and virulence determinants.
- Analysis of non-specific AMR mechanisms, including porin mutations and efflux pump regulation.
Main Results:
- A high prevalence of extensively drug-resistant (XDR) and MDR K. pneumoniae (64.58%) was observed.
- Genomic analysis revealed the presence of international high-risk MDR clones: ST395, ST15, and ST307.
- ST395 strains, isolated from children, exhibited resistance to first-line drugs and carried numerous virulence factors, often co-located with AMR genes on mobile genetic elements.
- Widespread non-specific AMR mechanisms, such as porin gene mutations and efflux pump overexpression, were identified.
Conclusions:
- The study highlights the emergence of XDR and hypervirulent K. pneumoniae in Armenia, driven by international high-risk clones like ST395.
- Co-selection of AMR and virulence traits on mobile genetic elements contributes to the threat.
- Non-specific resistance mechanisms play a crucial role in the overall AMR profile of these strains, underscoring the need for enhanced surveillance and control strategies.
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