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Molecular characterization of virulence and antibiotic resistance genes in Klebsiella pneumoniae isolated from sputum samples at a tertiary hospital in Ethiopia
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  • Published: 12 February 2026

Molecular characterization of virulence and antibiotic resistance genes in Klebsiella pneumoniae isolated from sputum samples at a tertiary hospital in Ethiopia

  • Assefa Asnakew Abebe1,2,
  • Alemayehu Godana Birhanu1 &
  • Tesfaye Sisay Tessema1 

Scientific Reports , Article number:  (2026) Cite this article

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We are providing an unedited version of this manuscript to give early access to its findings. Before final publication, the manuscript will undergo further editing. Please note there may be errors present which affect the content, and all legal disclaimers apply.

Subjects

  • Diseases
  • Medical research
  • Microbiology
  • Molecular biology

Abstract

Klebsiella pneumoniae, a Gram-negative, encapsulated rod and prominent member of the ESKAPE pathogen group, ranks among the leading causes of bacterial pneumonia worldwide. It has become increasingly problematic due to multidrug resistance (MDR) and the emergence of hypervirulent strains. In Ethiopia, there are growing reports of the increasing prevalence of MDR K. pneumoniae strains. However, molecular data on the resistance mechanisms and virulence determinants among clinical isolates remain limited. This study molecularly identified K. pneumoniae in sputum samples from patients clinically suspected of pneumonia at a tertiary hospital in Ethiopia, and evaluated their antibiotic resistance profiles, as well as molecularly characterized the isolates for key virulence and antimicrobial resistance (AMR) associated genes. A total of 182 sputum samples from pneumonia- suspected patients were collected and processed following standard microbiological procedures for bacterial isolation and antimicrobial sensitivity testing. K. pneumoniae isolates were confirmed by MALDI-TOF and PCR. Antibiotic susceptibility was assessed via the Kirby–Bauer disk diffusion method. Key virulence and AMR associated genes were detected via PCR. Among the 182 sputum samples, 32 K. pneumoniae isolates were identified, 94% of which were MDR. The predominant resistance genes detected included blaCTX-M (40.6%), blaNDM (34.4%), blaSHV (31.3%), and blaTEM (18.8%). Among the virulence genes, fimH was found in 56.3% of the isolates, mrkA in 28.1%, and rmpA in 9.4%. Additionally, the major outer membrane porin gene ompK35 and the mdtK efflux pump gene were detected in 62.6% and 28.1% of the isolates, respectively. This study reveals a high prevalence of MDR K. pneumoniae strains, and emergence of hypervirulent phenotypes posing a significant threat to therapeutic efficacy. The findings highlight complicated resistance mechanisms driven by molecular synergies, underscoring the urgent need for enhanced molecular surveillance, infection control, and antibiotic stewardship in healthcare settings.

Data availability

The datasets generated and/or analyzed during the current study are included in this published article and its supplementary information files.

References

  1. Abebe, A. A. & Birhanu, A. G. Methicillin resistant Staphylococcus aureus: molecular mechanisms underlying drug resistance development and novel strategies to combat. Infect. Drug Resist. 16, 7641–7662. https://doi.org/10.2147/idr.S428103 (2023).

    Google Scholar 

  2. Willy, C. et al. Phage therapy in Germany-Update 2023. Viruses 15(2). https://doi.org/10.3390/v15020588 (2023).

  3. WHO. Antimicrobial Resistance. https://www.who.int/news-room/fact-sheets/detail/antimicrobial-resistance (2021).

  4. Abebe, A. A., Birhanu, A. G. & Tessema, T. S. Isolation, purification, and phenotypic characterization of virulent Klebsiella pneumoniae phages from environmental samples in Addis Ababa, Ethiopia: A synergistic approach combining spot assay and streak plating. PLoS One. 20(9), e0331955. https://doi.org/10.1371/journal.pone.0331955 (2025).

    Google Scholar 

  5. WHO. WHO bacterial priority pathogens list, 2024 https://www.who.int/publications/i/item/9789240093461 (2024).

  6. Bengoechea, J. A. & Sa Pessoa, J. Klebsiella pneumoniae infection biology: living to counteract host defenses. FEMS Microbiol. Rev. 43(2), 123–144 (2019).

    Google Scholar 

  7. Murray, C. J. et al. Global burden of bacterial antimicrobial resistance in 2019: a systematic analysis. Lancet 399(10325), 629–655 (2022).

    Google Scholar 

  8. Paczosa, M. K. & Mecsas, J. Klebsiella pneumoniae: going on the offense with a strong defense. Microbiol. Mol. Biol. Rev. 80(3), 629–661 (2016).

    Google Scholar 

  9. Lam, M. M. C. et al. Population genomics of hypervirulent Klebsiella pneumoniae clonal-group 23 reveals early emergence and rapid global dissemination. Nat. Commun. 9(1), 2703. https://doi.org/10.1038/s41467-018-05114-7 (2018).

    Google Scholar 

  10. Hala, S. et al. The emergence of highly resistant and hypervirulent Klebsiella pneumoniae CC14 clone in a tertiary hospital over 8 years. Genome Med. 16(1), 58. https://doi.org/10.1186/s13073-024-01332-5 (2024).

    Google Scholar 

  11. WHO. Antimicrobial Resistance, Hypervirulent Klebsiella pneumoniae - Global situation https://www.who.int/emergencies/disease-outbreak-news/item/2024-DON527 (2024).

  12. Li, Y., Kumar, S., Zhang, L., Wu, H. & Wu, H. Characteristics of antibiotic resistance mechanisms and genes of Klebsiella pneumoniae. Open. Med. (Wars). 18(1), 20230707. https://doi.org/10.1515/med-2023-0707 (2023).

    Google Scholar 

  13. Li, Y., Kumar, S. & Zhang, L. Mechanisms of antibiotic resistance and developments in therapeutic strategies to combat Klebsiella pneumoniae infection. Infect. Drug Resist. 17, 1107–1119. https://doi.org/10.2147/idr.S453025 (2024).

    Google Scholar 

  14. Li, J., Shi, Y., Song, X., Yin, X. & Liu, H. Mechanisms of antimicrobial resistance in klebsiella: advances in detection methods and clinical implications. Infect. Drug Resist. 1339–1354. (2025).

  15. Moya, C. & Maicas, S. Antimicrobial resistance in Klebsiella pneumoniae strains: mechanisms and outbreaks. In Proceedings, Vol. 66, 11 (MDPI, 2020).

  16. Navon-Venezia, S., Kondratyeva, K. & Carattoli, A. Klebsiella pneumoniae: a major worldwide source and shuttle for antibiotic resistance. FEMS Microbiol. Rev. 41(3), 252–275 (2017).

    Google Scholar 

  17. Castañeda-Barba, S., Top, E. M. & Stalder, T. Plasmids, a molecular cornerstone of antimicrobial resistance in the one health era. Nat. Rev. Microbiol. 22(1), 18–32 (2024).

    Google Scholar 

  18. Li, Y., Kumar, S., Zhang, L., Wu, H. & Wu, H. Characteristics of antibiotic resistance mechanisms and genes of Klebsiella pneumoniae. Open Med. 18(1), 20230707 (2023).

    Google Scholar 

  19. Blair, J. M., Webber, M. A., Baylay, A. J., Ogbolu, D. O. & Piddock, L. J. Molecular mechanisms of antibiotic resistance. Nat. Rev. Microbiol. 13(1), 42–51 (2015).

    Google Scholar 

  20. Fang, Y. et al. Emergence of an XDR Klebsiella pneumoniae ST5491 strain co-harboring NDM-5, MCR-1.1, tmexCD1-toprJ1, and a novel plasmid carrying CTX-M-15. Front. Microbiol. 16, 1581851. https://doi.org/10.3389/fmicb.2025.1581851 (2025).

    Google Scholar 

  21. WHO & Antimicrobial Resistance, H. Klebsiella pneumoniae - Global situation. https://www.who.int/emergencies/disease-outbreak-news/item/2024-DON527) searched in September 2024 (2024).

  22. Xu, M. et al. High prevalence of KPC-2-producing hypervirulent Klebsiella pneumoniae causing meningitis in Eastern China. Infect. Drug Resist. 641–653. (2019).

  23. Zhu, J., Wang, T., Chen, L. & Du, H. Virulence factors in hypervirulent Klebsiella pneumoniae. Front. Microbiol. 12, 642484. https://doi.org/10.3389/fmicb.2021.642484 (2021).

    Google Scholar 

  24. Monteiro, A., d., S. S., Cordeiro, S. M. & Reis, J. N. Virulence factors in Klebsiella pneumoniae: A literature review. Indian J. Microbiol. 64(2), 389–401. https://doi.org/10.1007/s12088-024-01247-0 (2024).

    Google Scholar 

  25. Tilahun, M. et al. Etiology of bacterial pneumonia and multidrug resistance pattern among pneumonia suspected patients in Ethiopia: a systematic review and meta-analysis. BMC Pulm Med. 24(1), 182. https://doi.org/10.1186/s12890-024-03000-1 (2024).

    Google Scholar 

  26. Assefa, M., Amare, A., Belachew, T. & Tigabu, A. Hypermucoviscous Klebsiella pneumoniae caused community-acquired pneumonia in Gondar, Northwest Ethiopia. Clin. Lab. 70(9). https://doi.org/10.7754/Clin.Lab.2024.240205 (2024).

  27. AAU. Black Lion Specialized Hospital https://hakimethio.org/facility/black-lion-specialized-hospital/ (2025).

  28. Monica In District Laboratory Practice in Tropical Countries, 2 ed. (ed. Cheesbrough, M.) i-ii. (Cambridge University Press, 2006).

  29. Murk, J. L. et al. Enrichment broth improved detection of extended-spectrum-beta-lactamase-producing bacteria in throat and rectal surveillance cultures of samples from patients in intensive care units. J. Clin. Microbiol. 47(6), 1885–1887. https://doi.org/10.1128/jcm.01406-08 (2009).

    Google Scholar 

  30. Nhem, S. et al. Detection of Burkholderia pseudomallei in sputum using selective enrichment Broth and Ashdown’s medium at Kampong Cham Provincial Hospital, Cambodia. F1000Res. 3, 302. https://doi.org/10.12688/f1000research.5935.2 (2014).

  31. Osman, E. A., El-Amin, N., Adrees, E. A. E., Al-Hassan, L. & Mukhtar, M. Comparing conventional, biochemical and genotypic methods for accurate identification of Klebsiella pneumoniae in Sudan. Access. Microbiol. 2(3), acmi000096. https://doi.org/10.1099/acmi.0.000096 (2020).

    Google Scholar 

  32. Belete, M. A., Demlie, T. B., Chekole, W. S. & Sisay Tessema, T. Molecular identification of diarrheagenic Escherichia coli pathotypes and their antibiotic resistance patterns among diarrheic children and in contact calves in Bahir Dar city, Northwest Ethiopia. PLoS One. 17(9), e0275229. https://doi.org/10.1371/journal.pone.0275229 (2022).

    Google Scholar 

  33. Liu, Y. et al. PCR detection of Klebsiella pneumoniae in infant formula based on 16S-23S internal transcribed spacer. Int. J. Food Microbiol. 125(3), 230–235. https://doi.org/10.1016/j.ijfoodmicro.2008.03.005 (2008).

    Google Scholar 

  34. Turton, J. F., Perry, C., Elgohari, S. & Hampton, C. V. PCR characterization and typing of Klebsiella pneumoniae using capsular type specific, variable number tandem repeat and virulence gene targets. J. Med. Microbiol. 59(Pt 5), 541–547. https://doi.org/10.1099/jmm.0.015198-0 (2010).

    Google Scholar 

  35. Fadare, F. T., Fadare, T. O. & Okoh, A. I. Prevalence, molecular characterization of integrons and its associated gene cassettes in Klebsiella pneumoniae and K. oxytoca recovered from diverse environmental matrices. Sci. Rep. 13(1), 14373. https://doi.org/10.1038/s41598-023-41591-7 (2023).

    Google Scholar 

  36. Alsanie, W. F. Molecular diversity and profile analysis of virulence-associated genes in some Klebsiella pneumoniae isolates. Practical Lab. Med. 19, e00152. https://doi.org/10.1016/j.plabm.2020.e00152 (2020).

    Google Scholar 

  37. Ahmadi, M., Ranjbar, R., Behzadi, P. & Mohammadian, T. Virulence factors, antibiotic resistance patterns, and molecular types of clinical isolates of Klebsiella pneumoniae. Expert Rev. anti-infective Therapy. 20(3), 463–472. https://doi.org/10.1080/14787210.2022.1990040 (2022).

    Google Scholar 

  38. Shahbandeh, M., Taati Moghadam, M., Mirnejad, R., Mirkalantari, S. & Mirzaei, M. The efficacy of AgNO3 nanoparticles alone and conjugated with Imipenem for combating extensively Drug-Resistant Pseudomonas aeruginosa. Int. J. Nanomed. 15, 6905–6916. https://doi.org/10.2147/ijn.s260520 (2020).

    Google Scholar 

  39. Poirel, L., Walsh, T. R., Cuvillier, V. & Nordmann, P. Multiplex PCR for detection of acquired carbapenemase genes. Diagn. Microbiol. Infect. Dis. 70(1), 119–123. https://doi.org/10.1016/j.diagmicrobio.2010.12.002 (2011).

    Google Scholar 

  40. Hu, X. et al. A high throughput multiplex PCR assay for simultaneous detection of seven aminoglycoside-resistance genes in Enterobacteriaceae. BMC Microbiol. 13, 58. https://doi.org/10.1186/1471-2180-13-58 (2013).

    Google Scholar 

  41. Alsanie, W. F. Molecular diversity and profile analysis of virulence-associated genes in some Klebsiella pneumoniae isolates. Practical Lab. Med. 19, e00152. https://doi.org/10.1016/j.plabm.2020.e00152 (2020).

    Google Scholar 

  42. Makhrmash, J. H., Al-Aidy, S. R. & Qaddoori, B. H. Investigation of biofilm virulence genes prevalence in Klebsiella pneumoniae isolated from the urinary tract infections. Arch. Razi Inst. 77(4), 1421–1427. https://doi.org/10.22092/ari.2022.357626.2076 (2022).

    Google Scholar 

  43. Rebelo, A. R. et al. Multiplex PCR for detection of plasmid-mediated colistin resistance determinants, mcr-1, mcr-2, mcr-3, mcr-4 and mcr-5 for surveillance purposes. Euro. Surveill. 23(6). https://doi.org/10.2807/1560-7917.Es.2018.23.6.17-00672 (2018).

  44. (https://iacld.com/UpFiles/Documents/672a1c7c-d4ad-404e-b10e-97c19e21cdce.pdf), C. Performance Standards for Antimicrobial Susceptibility Testing (2023).

  45. Magiorakos, A. P. et al. Multidrug-resistant, extensively drug-resistant and pandrug-resistant bacteria: an international expert proposal for interim standard definitions for acquired resistance. Clin. Microbiol. Infect. 18(3), 268–281. https://doi.org/10.1111/j.1469-0691.2011.03570.x (2012).

    Google Scholar 

  46. Tsai, Y. M., Wang, S., Chiu, H. C., Kao, C. Y. & Wen, L. L. Combination of modified carbapenem inactivation method (mCIM) and EDTA-CIM (eCIM) for phenotypic detection of carbapenemase-producing Enterobacteriaceae. BMC Microbiol. 20(1), 315. https://doi.org/10.1186/s12866-020-02010-3 (2020).

    Google Scholar 

  47. Fang, C. T., Chuang, Y. P., Shun, C. T., Chang, S. C. & Wang, J. T. A novel virulence gene in Klebsiella pneumoniae strains causing primary liver abscess and septic metastatic complications. J. Exp. Med. 199(5), 697–705. https://doi.org/10.1084/jem.20030857 (2004).

    Google Scholar 

  48. Gebre, A. B., Begashaw, T. A. & Ormago, M. D. Bacterial profile and drug susceptibility among adult patients with community acquired lower respiratory tract infection at tertiary hospital, Southern Ethiopia. BMC Infect. Dis. 21(1), 440. https://doi.org/10.1186/s12879-021-06151-2 (2021).

    Google Scholar 

  49. Nurahmed, N. et al. Bacterial profile and antimicrobial susceptibility patterns of lower respiratory tract infection among patients attending selected health centers of Addis Ababa, Ethiopia. Egypt. J. Chest Dis. Tuberculosis. 69(2), 399–406 (2020).

    Google Scholar 

  50. Assefa, M., Tigabu, A., Belachew, T. & Tessema, B. Bacterial profile, antimicrobial susceptibility patterns, and associated factors of community-acquired pneumonia among adult patients in Gondar, Northwest Ethiopia: A cross-sectional study. PLoS One. 17(2), e0262956. https://doi.org/10.1371/journal.pone.0262956 (2022).

    Google Scholar 

  51. Dawson, V. A. & A Klebsiella pneumoniae https://www.ncbi.nlm.nih.gov/books/NBK519004/ (2023).

  52. Rijnink, E. C., van Veen, S. Q. & Ruys, T. A. [A man with currant jelly sputum]. Ned Tijdschr Geneeskd 165. (2021).

  53. Awoke, T. et al. High prevalence of multidrug-resistant Klebsiella pneumoniae in a tertiary care hospital in Ethiopia. Antibiot. (Basel). 10(8). https://doi.org/10.3390/antibiotics10081007 (2021).

  54. Gebremeskel, L., Teklu, T., Kasahun, G. G. & Tuem, K. B. Antimicrobial resistance pattern of Klebsiella isolated from various clinical samples in ethiopia: a systematic review and meta-analysis. BMC Infect. Dis. 23(1), 643. https://doi.org/10.1186/s12879-023-08633-x (2023).

    Google Scholar 

  55. Beshah, D. et al. Antimicrobial resistance and associated risk factors of gram-negative bacterial bloodstream infections in Tikur Anbessa specialized hospital, Addis Ababa. Infect. Drug Resist. 15, 5043–5059. https://doi.org/10.2147/idr.S371654 (2022).

    Google Scholar 

  56. Saravanan, R. & Raveendaran, V. Antimicrobial resistance pattern in a tertiary care hospital: an observational study. J. Basic. Clin. Pharm. 4(3), 56–63. https://doi.org/10.4103/0976-0105.118797 (2013).

    Google Scholar 

  57. Awoke, T. et al. High prevalence of multidrug-resistant Klebsiella pneumoniae in a tertiary care hospital in Ethiopia. Antibiotics 10(8), 1007 (2021).

    Google Scholar 

  58. Romyasamit, C., Sornsenee, P., Kawila, S. & Saengsuwan, P. Extended-spectrum beta-lactamase-producing Escherichia coli and Klebsiella pneumoniae: insights from a tertiary hospital in Southern Thailand. Microbiol. Spectr. 12(7), e0021324. https://doi.org/10.1128/spectrum.00213-24 (2024).

    Google Scholar 

  59. Poole, K. Multidrug resistance in Gram-negative bacteria. Curr. Opin. Microbiol. 4(5), 500–508 (2001).

    Google Scholar 

  60. Aurilio, C. et al. Mechanisms of action of carbapenem resistance. Antibiotics 11(3), 421 (2022).

    Google Scholar 

  61. Ghamari, M., Emaneini, M., Hemmati, S., Jabalameli, F. & Beigverdi, R. Phenotypic and genotypic evaluation of aminoglycoside resistance in Escherichia coli isolated from patients with blood stream infections in Tehran, Iran. Iran. J. Microbiol. 16(2), 187–192. https://doi.org/10.18502/ijm.v16i2.15351 (2024).

    Google Scholar 

  62. Chen, H. et al. A Klebsiella-phage cocktail to broaden the host range and delay bacteriophage resistance both in vitro and in vivo. Npj Biofilms Microbiomes. 10(1), 127. https://doi.org/10.1038/s41522-024-00603-8 (2024).

    Google Scholar 

  63. Seman, A. et al. Prevalence and molecular characterization of extended spectrum β-lactamase and carbapenemase-producing Enterobacteriaceae isolates from bloodstream infection suspected patients in Addis Ababa, Ethiopia. Infect. Drug Resist. 15, 1367–1382. https://doi.org/10.2147/idr.S349566 (2022).

    Google Scholar 

  64. Lee, C. R. et al. Global dissemination of carbapenemase-producing Klebsiella pneumoniae: Epidemiology, genetic context, treatment options, and detection methods. Front. Microbiol. 7, 895. https://doi.org/10.3389/fmicb.2016.00895 (2016).

    Google Scholar 

  65. Awoke, T. et al. Detection of Bla KPC and Bla NDM carbapenemase genes among Klebsiella pneumoniae isolates in Addis Ababa, Ethiopia: dominance of Bla NDM. PLoS ONE 17(4), e0267657. (2022).

  66. Ahmed El-Domany, R., El-Banna, T., Sonbol, F. & Abu-Sayedahmed, S. H. Coexistence of NDM-1 and OXA-48 genes in carbapenem resistant Klebsiella pneumoniae clinical isolates in Kafrelsheikh, Egypt. Afr. Health Sci. 21(2), 489–496. https://doi.org/10.4314/ahs.v21i2.2 (2021).

    Google Scholar 

  67. Gondal, A. J., Saleem, S., Jahan, S., Choudhry, N. & Yasmin, N. Novel carbapenem-resistant Klebsiella pneumoniae ST147 coharboring Bla (NDM-1), Bla (OXA-48) and extended-spectrum β-lactamases from Pakistan. Infect. Drug Resist. 13, 2105–2115. https://doi.org/10.2147/idr.S251532 (2020). From NLM.

    Google Scholar 

  68. Sánchez-Urtaza, S. et al. Coexistence of Bla NDM-1, Bla OXA-23, Bla OXA-64, Bla PER-7 and Bla ADC-57 in a clinical isolate of Acinetobacter baumannii from Alexandria, Egypt. Int. J. Mol. Sci. 24(15), 12515 (2023).

    Google Scholar 

  69. Fuchs, F. et al. Coexistence of seven different carbapenemase producers in a single hospital admission screening confirmed by whole-genome sequencing. J. Glob Antimicrob. Resist. 39, 184–188. https://doi.org/10.1016/j.jgar.2024.09.005 (2024).

    Google Scholar 

  70. Pishtiwan, A. H. & Khadija, K. M. Prevalence of blaTEM, blaSHV, and blaCTX-M genes among ESBL-producing Klebsiella pneumoniae and Escherichia coli isolated from thalassemia patients in Erbil, Iraq. Mediterr. J. Hematol. Infect. Dis. 11(1), e2019041. https://doi.org/10.4084/mjhid.2019.041 (2019).

    Google Scholar 

  71. Onduru, O. G., Mkakosya, R. S., Aboud, S. & Rumisha, S. F. Genetic determinants of resistance among ESBL-producing enterobacteriaceae in community and hospital settings in east, central, and southern Africa: A systematic review and meta‐analysis of prevalence. Can. J. Infect. Dis. Med. Microbiol. 2021(1), 5153237. (2021).

  72. Bora, A. et al. Prevalence of blaTEM, BlaSHV and blaCTX-M genes in clinical isolates of Escherichia coli and Klebsiella pneumoniae from Northeast India. Indian J. Pathol. Microbiol. 57(2), 249–254 (2014).

    Google Scholar 

  73. Ugbo, E. et al. Prevalence of blaTEM, blaSHV, and blaCTX-M genes among extended spectrum beta-lactamase-producing Escherichia coli and Klebsiella pneumoniae of clinical origin. Gene Rep. 21, 100909 (2020).

    Google Scholar 

  74. Salvador-Oke, K. T. et al. Molecular epidemiology of carbapenemase-producing Klebsiella pneumoniae in Gauteng South Africa. Sci. Rep. 14(1), 27337. https://doi.org/10.1038/s41598-024-70910-9 (2024).

    Google Scholar 

  75. Zhang, X. et al. High-Level aminoglycoside resistance in human clinical Klebsiella pneumoniae complex isolates and characteristics of armA-Carrying IncHI5 plasmids. Front. Microbiol. 12, 636396. https://doi.org/10.3389/fmicb.2021.636396 (2021).

    Google Scholar 

  76. Ma, L. et al. Widespread dissemination of aminoglycoside resistance genes arma and RmtB in Klebsiella pneumoniae isolates in Taiwan producing CTX-M-type extended-spectrum beta-lactamases. Antimicrob. Agents Chemother. 53(1), 104–111. https://doi.org/10.1128/aac.00852-08 (2009).

    Google Scholar 

  77. Fu, Y. et al. Specific patterns of GyrA mutations determine the resistance difference to Ciprofloxacin and Levofloxacin in Klebsiella pneumoniae and Escherichia coli. BMC Infect. Dis. 13, 8. https://doi.org/10.1186/1471-2334-13-8 (2013).

    Google Scholar 

  78. Hussein, R. A., Al-Kubaisy, S. H. & Al-Ouqaili, M. T. S. The influence of efflux pump, outer membrane permeability and β-lactamase production on the resistance profile of multi, extensively and pandrug resistant Klebsiella pneumoniae. J. Infect. Public. Health. 17(11), 102544. https://doi.org/10.1016/j.jiph.2024.102544 (2024).

    Google Scholar 

  79. Dulanto Chiang, A. & Dekker, J. P. Efflux pump-mediated resistance to new beta lactam antibiotics in multidrug-resistant gram-negative bacteria. Commun. Med. 4(1), 170. https://doi.org/10.1038/s43856-024-00591-y (2024).

    Google Scholar 

  80. Meletis, G., Exindari, M., Vavatsi, N., Sofianou, D. & Diza, E. Mechanisms responsible for the emergence of carbapenem resistance in Pseudomonas aeruginosa. Hippokratia 16(4), 303 (2012).

    Google Scholar 

  81. Mahamoud, A., Chevalier, J., Alibert-Franco, S., Kern, W. V. & Pagès, J. M. Antibiotic efflux pumps in Gram-negative bacteria: the inhibitor response strategy. J. Antimicrob. Chemother. 59(6), 1223–1229 (2007).

    Google Scholar 

  82. Wasfi, R., Elkhatib, W. F. & Ashour, H. M. Molecular typing and virulence analysis of multidrug resistant Klebsiella pneumoniae clinical isolates recovered from Egyptian hospitals. Sci. Rep. 6(1), 38929 (2016).

    Google Scholar 

  83. Ferreira, R. L. et al. High prevalence of multidrug-resistant Klebsiella pneumoniae harboring several virulence and β-lactamase encoding genes in a Brazilian intensive care unit. Front. Microbiol. 9, 3198. https://doi.org/10.3389/fmicb.2018.03198 (2018).

    Google Scholar 

  84. Muhsin, E. Prevalence of efflux pump and porin-related antimicrobial resistance in clinical Klebsiella pneumoniae in Baghdad, Iraq. Arch. Razi Inst. 77(2), 785 (2022).

    Google Scholar 

  85. Hussein, R. A., Al-Kubaisy, S. H. & Al-Ouqaili, M. T. The influence of efflux pump, outer membrane permeability and β-lactamase production on the resistance profile of multi, extensively and pandrug resistant Klebsiella pneumoniae. J. Infect. Public Health. 17(11), 102544 (2024).

    Google Scholar 

  86. Tsai, Y. K. et al. Klebsiella pneumoniae outer membrane porins OmpK35 and OmpK36 play roles in both antimicrobial resistance and virulence. Antimicrob. Agents Chemother. 55(4), 1485–1493. https://doi.org/10.1128/aac.01275-10 (2011).

    Google Scholar 

  87. Sugawara, E., Kojima, S. & Nikaido, H. Klebsiella pneumoniae major porins OmpK35 and OmpK36 allow more efficient diffusion of β-lactams than their Escherichia coli homologs OmpF and OmpC. J. Bacteriol. 198(23), 3200–3208. https://doi.org/10.1128/jb.00590-16 (2016).

    Google Scholar 

  88. Wong, J. L. C. et al. OmpK36-mediated carbapenem resistance attenuates ST258 Klebsiella pneumoniae in vivo. Nat. Commun. 10(1), 3957. https://doi.org/10.1038/s41467-019-11756-y (2019).

    Google Scholar 

  89. Zhu, J., Wang, T., Chen, L. & Du, H. Virulence factors in hypervirulent Klebsiella pneumoniae. Front. Microbiol. 12, 642484 (2021).

    Google Scholar 

  90. Guo, Y. et al. Microbiological and clinical characteristics of hypermucoviscous Klebsiella pneumoniae isolates associated with invasive infections in China. Front. Cell. Infect. Microbiol. 7, 24 (2017).

    Google Scholar 

  91. Yu, W. L. et al. Association between RmpA and MagA genes and clinical syndromes caused by Klebsiella pneumoniae in Taiwan. Clin. Infect. Dis. 42(10), 1351–1358. https://doi.org/10.1086/503420 (2006).

    Google Scholar 

  92. Soltani, E. et al. Virulence characterization of Klebsiella pneumoniae and its relation with ESBL and AmpC beta-lactamase associated resistance. Iran. J. Microbiol. 12(2), 98–106 (2020).

    Google Scholar 

  93. Khattab, M. A. & Hager, R. Detection of RmpA and MagA genes in hypervirulent Klebsiella pneumoniae isolates from tertiary care hospitals. Egypt. J. Med. Microbiol. 31(3), 43–50 (2022).

    Google Scholar 

  94. Dingiswayo, L. et al. Hypervirulent Klebsiella pneumoniae in a South African tertiary hospital-clinical profile, genetic determinants, and virulence in Caenorhabditis elegans. Front. Microbiol. 15, 1385724. https://doi.org/10.3389/fmicb.2024.1385724 (2024).

    Google Scholar 

  95. Muraya, A. et al. Antimicrobial resistance and virulence characteristics of Klebsiella pneumoniae isolates in Kenya by Whole-Genome sequencing. Pathogens 11(5). https://doi.org/10.3390/pathogens11050545 (2022).

  96. Yadav, B., Mohanty, S. & Behera, B. Occurrence and genomic characteristics of hypervirulent Klebsiella pneumoniae in a Tertiary Care Hospital, Eastern India. Infect. Drug Resist. 16, 2191–2201. https://doi.org/10.2147/idr.S405816 (2023).

    Google Scholar 

  97. WHO2024. Antimicrobial Resistance, Hypervirulent Klebsiella pneumoniae - Global situation (https://www.who.int/emergencies/disease-outbreak-news/item/2024-DON527).

  98. Zhang, J. et al. Prevalence of hypervirulent Klebsiella pneumoniae strains in COVID-19 patients with bacterial coinfections. Front. Microbiol. 16, 1535893. https://doi.org/10.3389/fmicb.2025.1535893 (2025).

    Google Scholar 

  99. Altayb, H. N. et al. Genomic analysis of multidrug-resistant hypervirulent (Hypermucoviscous) Klebsiella pneumoniae strain lacking the hypermucoviscous regulators (rmpA/rmpA2). Antibiot. (Basel). 11(5). https://doi.org/10.3390/antibiotics11050596 (2022).

  100. Caneiras, C., Lito, L., Melo-Cristino, J. & Duarte, A. Community- and hospital-acquired Klebsiella pneumoniae urinary tract infections in portugal: virulence and antibiotic resistance. Microorganisms 7(5). https://doi.org/10.3390/microorganisms7050138 (2019).

  101. Jagnow, J. & Clegg, S. Klebsiella pneumoniae MrkD-mediated biofilm formation on extracellular matrix- and collagen-coated surfaces. Microbiology 149(Pt 9), 2397–2405. https://doi.org/10.1099/mic.0.26434-0 (2003).

    Google Scholar 

  102. Devanga Ragupathi, N. K. et al. Evaluation of mrkD, PgaC and WcaJ as biomarkers for rapid identification of K. pneumoniae biofilm infections from endotracheal aspirates and bronchoalveolar lavage. Sci. Rep. 14(1), 23572. https://doi.org/10.1038/s41598-024-69232-7 (2024).

    Google Scholar 

  103. Rêgo, A. T. et al. Crystal structure of the MrkD1P receptor binding domain of Klebsiella pneumoniae and identification of the human collagen V binding interface. Mol. Microbiol. 86(4), 882–893. https://doi.org/10.1111/mmi.12023 (2012).

    Google Scholar 

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Authors and Affiliations

  1. Biotechnology Research Center, Addis Ababa University, Addis Ababa, Ethiopia

    Assefa Asnakew Abebe, Alemayehu Godana Birhanu & Tesfaye Sisay Tessema

  2. Unit of Molecular Biology, Department of Medical Laboratory Sciences, Institute of Health, Bule Hora University, Bule Hora, Ethiopia

    Assefa Asnakew Abebe

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  1. Assefa Asnakew Abebe
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  2. Alemayehu Godana Birhanu
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  3. Tesfaye Sisay Tessema
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Contributions

AAA performed the conceptualization, sample collection, laboratory work, data curation, analysis, and visualization. AGB contributed to the validation, supervision, and critical review of the manuscript. TST was involved in conceptualization, validation, resource provision, supervision, and manuscript reviewing. All authors reviewed and approved the final manuscript.

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Correspondence to Assefa Asnakew Abebe.

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Abebe, A.A., Birhanu, A.G. & Tessema, T.S. Molecular characterization of virulence and antibiotic resistance genes in Klebsiella pneumoniae isolated from sputum samples at a tertiary hospital in Ethiopia. Sci Rep (2026). https://doi.org/10.1038/s41598-026-39069-3

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  • Received: 15 October 2025

  • Accepted: 02 February 2026

  • Published: 12 February 2026

  • DOI: https://doi.org/10.1038/s41598-026-39069-3

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Keywords

  • Molecular characterization
  • Virulence genes
  • Multidrug resistance
  • Hypervirulent
  • Efflux pump
  • Outer membrane porin
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