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Genetic basis of antimicrobial resistance, virulence features and phylogenomics of carbapenem-resistant Acinetobacter baumannii clinical isolates

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Abstract

Purpose

The worldwide emergence and clonal spread of carbapenem-resistant Acinetobacter baumannii (CRAB) is of great concern. In the present study, we determined the mechanisms of antimicrobial resistance, virulence gene repertoire and genomic relatedness of CRAB isolates circulating in Serbian hospitals.

Methods

CRAB isolates were analyzed using whole-genome sequencing (WGS) for the presence of antimicrobial resistance-encoding genes, virulence factors-encoding genes, mobile genetic elements and genomic relatedness. Antimicrobial susceptibility testing was done by disk diffusion and broth microdilution methods.

Results

Eleven isolates exhibited an MDR resistance phenotype, while four of them were XDR. MIC90 for meropenem and imipenem were > 64 µg/mL and 32 µg/mL, respectively. While all CRABs harbored blaOXA−66 variant of blaOXA−51 gene, those assigned to STPas2, STPas636 and STPas492 had blaADC−73,blaADC−74 and blaADC−30 variants, respectively. The following acquired carbapenemases-encoding genes were found: blaOXA−72 (n = 12), blaOXA−23 (n = 3), and blaNDM−1(n = 5), and were mapped to defined mobile genetic elements. MLST analysis assigned the analyzed CRAB isolates to three Pasteur sequence types (STs): STPas2, STPas492, and STPas636. The Majority of strains belonged to International Clone II (ICII) and carried tested virulence-related genes liable for adherence, biofilm formation, iron uptake, heme biosynthesis, zinc utilization, serum resistance, stress adaptation, intracellular survival and toxin activity.

Conclusion

WGS elucidated the resistance and virulence profiles of CRABs isolated from clinical samples in Serbian hospitals and genomic relatedness of CRAB isolates from Serbia and globally distributed CRABs.

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Data availability

All data generated or analysed during this study are included in this published article.

Abbreviations

Acb complex:

Acinetobacter calcoaceticus-baumannii complex

ACD:

Ambler Class C

CLSI:

Clinical and Laboratory Standards Institute

CRAB:

Carbapenem-resistant A. baumannii

ICs:

International Clones

ICUs:

Intensive Care Units

MBLs:

Metallo-β-Lactamases

MDR:

Multidrug-Resistant

MICs:

Minimum Inhibitory Concentrations

MLST:

Multilocus Sequence Typing

NCBI:

National Center for Biotechnology Information

PDR:

Pandrug-Resistant

OXAs:

Oxacillinases

SNP:

Single-Nucleotide Polymorphisms

STs:

Sequence Types

WGS:

Whole Genome Sequencing

XDR:

Extensively Drug-Resistant

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Funding

This work was supported by the Ministry of Education, Science and Technological Development of the Republic of Serbia [Grant No. 451-03-68/2022-14/200110 and Grant No. 451-03-47/2023-01/ 200178 and Grant No. 451-03-47/2023-01/ 200007], and Science Fund of the Republic of Serbia [Grant No. 7042, Tracking antimicrobial resistance in diverse ecological niches - one health perspective- TRACE].

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Authors

Contributions

BL conceptualized the study, performed experiments and wrote the manuscript. JK carried out the experiments, performed bioinformatic analysis, and visualized obtained data. MD performed bioinformatic analysis and visualized obtained data. SK performed bioinformatic analysis. ID carried out the experiments. BJ criticaly reviewed of the manuscript. IG designed the study, visualized obtained data, revised the manuscript. All authors have read and agreed with the final version of the manuscript.

Corresponding author

Correspondence to Bojana Lukovic.

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The study was approved by the ethical committee of the Medical Faculty, University of Belgrade (1550/II-4).

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The authors declare no competing interests.

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Lukovic, B., Kabic, J., Dragicevic, M. et al. Genetic basis of antimicrobial resistance, virulence features and phylogenomics of carbapenem-resistant Acinetobacter baumannii clinical isolates. Infection (2024). https://doi.org/10.1007/s15010-024-02316-8

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