Advance Search

Molecular typing and genetic diversity of multidrug-resistant Klebsiella pneumoniae isolated from Erbil City, Kurdistan Region, Iraq

Dashti Hadi Hamad
Department of Medical Microbiology, College of Health Sciences, Hawler Medical University, Kurdistan Region, Iraq
Salah Tofik Jalal Balaky
Department of Medical Microbiology, College of Health Sciences, Hawler Medical University, Kurdistan Region, Iraq
Keywords:
Copyright and Licensing:

Copyright (c) 2026 Dashti Hadi Hamad, Salah Tofik Jalal Balaky (Author)

Creative Commons License

This work is licensed under a Creative Commons Attribution-NonCommercial-ShareAlike 4.0 International License.

Share:
Crossref
Scopus
Google Scholar
Europe PMC

Abstract

Background and objective: Klebsiella pneumoniae, a Gram-negative encapsulated bacterium, is one of the most significant etiological agents of healthcare- or community-acquired infections worldwide. This study set out to explore the phylogenetic relationships and genetic diversity of multidrug-resistant K. pneumoniae using 16S rRNA sequencing and Multilocus Sequence Typing (MLST).

Methods: A total of 298 urine samples were analyzed from patients with symptoms of urinary tract infection. Standard biochemical tests were used for isolate identification. Resistant isolates were further analyzed by molecular diagnosis through 16S rRNA gene sequencing and Multilocus Sequence Typing (MLST), in accordance with international standards.

Results: Out of 298 urine specimens, 49 K. pneumoniae isolates were confirmed (isolation rate: 16.4%). Resistance was high: 49% to amoxicillin/clavulanic acid, 38.8% to cefazolin, 34.7% to ceftriaxone, and 12.2% to ertapenem and 16.3% to both imipenem and meropenem among the carbapenems. Multidrug resistance was detected in 65.3% of isolates (32/49), and 18.4% were extensively drug-resistant. MLST testing of 13 MDR strains identified 13 different sequence types, the most dominant (15%) being ST147, followed by ST405 and ST268 (10% each). Both the 16S rRNA sequence analysis and MLST typing showed genetic variation among the resistant isolates, with multiple alleles differing across the seven loci, indicating substantial genetic diversity in the studied isolates.

Conclusion: UTIs associated with antimicrobial-resistant K. pneumoniae pose a primary problem in this region. Genetic diversity was found within resistant isolates using molecular typing. Study limitations include the small sample size for MLST (n=13) and the absence of whole genome sequencing, which limit the epidemiological conclusions that can be drawn. Future studies with larger populations and more advanced sequencing methods (such as WGS) are needed for more comprehensive surveillance and a fuller understanding of resistance mechanisms and transmission patterns.

PDF
PDF

Metrics

Metrics Loading ...

References

  1. Navon-Venezia S, Kondratyeva K, Carattoli A. Klebsiella pneumoniae: a major worldwide source and shuttle for antibiotic resistance. FEMS Microbiol Rev. 2017;41(3):252-75. https://doi.org/10.1093/femsre/fux013
  2. Wyres KL, Holt KE. Klebsiella pneumoniae population genomics and antimicrobial-resistant clones. Trends Microbiol. 2016;24(12):944-56. https://doi.org/10.1016/j.tim.2016.09.007
  3. Wyres KL, Holt KE. Klebsiella pneumoniae as a key trafficker of drug resistance genes from environmental to clinically important bacteria. Curr Opin Microbiol. 2021;45:131-9. https://doi.org/10.1016/j.mib.2018.04.004
  4. Butler MS, Hansford KA, Blaskovich MA, Halai R, Cooper MA. Glycopeptide antibiotics: back to the future. J Antibiot (Tokyo). 2025;78(1):15-32. https://doi.org/10.1038/s41429-024-00751-2
  5. Yang L, Chen X, Wang Y, Li M, Zhang H. Phylogenetic analysis of Klebsiella pneumoniae using clinical isolates of 16S rRNA genes identified in China. BMC Microbiol. 2024;24:156. https://doi.org/10.1186/s12866-024-03156-2
  6. Jolley KA, Bray JE, Maiden MCJ. Open-access bacterial population genomics: BIGSdb software, the PubMLST.org website and their applications. Wellcome Open Res. 2018;3:124. https://doi.org/10.12688/wellcomeopenres.14826.1
  7. Angeletti S. Matrix assisted laser desorption time of flight mass spectrometry (MALDI-TOF MS) in clinical microbiology. J Microbiol Methods. 2017;138:20-9. https://doi.org/10.1016/j.mimet.2017.04.014
  8. Faiq SO, Omer SA. Clinical and resistance pattern of coagulase negative staphylococci. Adv Med J. 2023;8(1):40-7. https://doi.org/10.56056/amj.2023.196
  9. Pasteur Institute. Klebsiella pneumoniae MLST Database [Internet]. 2025 [cited 2025 Jan]. Available from: https://bigsdb.pasteur.fr/klebsiella/
  10. Shon AS, Russo TA, Calfee DP. Hypervirulent Klebsiella pneumoniae: the next superbug? Future Microbiol. 2023;18(8):565-72. https://doi.org/10.2217/fmb-2023-0033
  11. Zuber SA, Ganjo AR. Detection of hypervirulent and classical type of Klebsiella pneumoniae and screening their resistant properties in Erbil city. Zanco J Med Sci. 2023;27(3):329-39. https://doi.org/10.15218/zjms.2023.035
  12. Kumar S, Stecher G, Tamura K. MEGA7: Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets. Mol Biol Evol. 2016;33(7):1870-4. https://doi.org/10.1093/molbev/msw054
  13. Shah M, Veeraraghavan B, Mutreja A. Carbapenem-resistant Enterobacteriaceae: global spread and containment strategies. Lancet Microbe. 2025;6(1):e58-e70. https://doi.org/10.1016/S2666-5247(24)00201-8
  14. WHO. Global antimicrobial resistance and use surveillance system (GLASS) report: 2024. Geneva: World Health Organization; 2024.
  15. Peirano G, Chen L, Kreiswirth BN, Pitout JD. Emerging antimicrobial-resistant high-risk Klebsiella pneumoniae clones ST307 and ST147. Antimicrob Agents Chemother. 2020;64(10):e01148-20. https://doi.org/10.1128/AAC.01148-20
  16. Villa L, Feudi C, Fortini D, Brisse S, Passet V, Bonnet R, et al. Diversity, virulence, and antimicrobial resistance of the KPC-producing Klebsiella pneumoniae ST307 clone. Microb Genom. 2017;3(4):e000110. https://doi.org/10.1099/mgen.0.000110
  17. Ahmad KA, Mohammed SH, Rashid ZH, Hassan BA. Antimicrobial resistance profiles and molecular characterization of Klebsiella pneumoniae isolated in hospitals, Erbil, Iraq. Kurdistan J Appl Res. 2023;8(2):45-58. https://doi.org/10.24017/kjar.2023.8.2.45
  18. Salih RM, Abdullah NK, Mahmood SS. Proportions and molecular characterization of carbapenem-resistant Klebsiella pneumoniae in hospitals in Kurdistan region, Iraq. Iraqi J Med Sci. 2024;22(1):78-89. https://doi.org/10.22578/ijms.22.1.78
  19. Miro E, Rossen JWA, Chlebowicz MA, Harmsen D, Brisse S, Glupczynski Y. Core genome multilocus sequence typing for food safety related epidemiological surveillance of Shiga toxin-producing Escherichia coli. Appl Environ Microbiol. 2020;86(9):e02916-19. https://doi.org/10.1128/AEM.02916-19
  20. Graham RM, Doyle CJ, Jennison AV. Real-time nanopore sequencing for rapid bacterial identification in clinical microbiology. Clin Microbiol Infect. 2025;31(2):145-52. https://doi.org/10.1016/j.cmi.2024.11.018
How to Cite
Hadi Hamad, D. ., & Tofik Jalal Balaky, S. . (2026). Molecular typing and genetic diversity of multidrug-resistant Klebsiella pneumoniae isolated from Erbil City, Kurdistan Region, Iraq. Zanco Journal of Medical Sciences (ZJMS), 693–709. https://doi.org/10.15218/zjms.2026.049

Send mail to Author

Send Cancel