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Whole-genome sequencing of Egyptian multidrug-resistant Klebsiella pneumoniae isolates: a multi-center pilot study

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Abstract

Multidrug-resistant (MDR) Klebsiella pneumoniae is a common infectious pathogen. We performed whole-genome sequencing (WGS) of 39 randomly selected, geographically diverse MDR K. pneumoniae from nine Egyptian hospitals. Clinical sources, phenotypic antibiotic resistance, and hyper-mucoviscosity were documented. WGS data were epidemiologically interpreted and tested for the presence of antibiotic resistance and virulence genes. Based on WGS data, we identified 18 classical multi-locus sequence types (MLST), the most common type being ST101 (23.1%) followed by ST147 (17.9%). Phylogenetic analyses identified small numbers of closely related isolates in a few of the centers, so we mostly documented independent nosocomial acquisition or import from public sources. The most common acquired resistance gene found was blaCTX-M-15, detected in 27 isolates (69.2%). Carbapenemase genes encountered were blaNDM-1 (n = 13), blaNDM-5 (n = 1), blaOXA-48 (n = 12), blaOXA-181 (n = 2), and blaKPC2 (n = 1). Seven strains (18%) contained more than a single carbapenemase gene. While searching for virulence-associated genes, sixteen wzi alleles were identified with wzi137, wzi64, and wzi50 most commonly found in ST101, ST147, and ST16, respectively. Yersiniabactin was the most common virulence factor (69.2%). Hyper-mucoviscosity was documented for 6 out of 39 isolates.

This is the first genomic study of MDR K. pneumoniae from Egypt. The study revealed a clear spread of well-known international clones and their associated antimicrobial resistance and (hyper)virulence traits. The clinical situation in Egypt seems to reflect the scenario documented in many other countries and requires close attention.

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Acknowledgements

We acknowledge the support of the Science and Technology Development Fund (STDF) and the staff of the Molecular Research and Sequencing Laboratory, Chemical Pathology Department, Faculty of Medicine, Cairo University, Cairo, Egypt.

Funding

The study was funded by capacity building grant number 22838 from the Science and Technology Development Fund (STDF) of the Academy of Scientific Research and Technology (ASRT) in Egypt, "Establishing a Reference Laboratory For Rapid Diagnosis of Emerging Infections and Investigation of Outbreaks,” principal investigator: Prof Amani El Kholy. Mattia Palmieri was funded by the European Union’s Horizon 2020 research and innovation program under the Marie Skłodowska-Curie Grant Agreement No. 675412 (New Diagnostics for Infectious Diseases [ND4ID]).

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Authors and Affiliations

  1. Department of Clinical Pathology, Faculty of Medicine, Cairo University, Cairo, Egypt

    May Sherif & Amani El-Kholy

  2. bioMérieux, Open Innovation and Partnerships, 3 route de Port Michaud 38390, Les Grottes, La Balme, France

    Mattia Palmieri, Caroline Mirande & Alex van Belkum

  3. Department of Clinical Pathology, National Cancer Institute, Cairo University, Cairo, Egypt

    Hadir El-Mahallawy

  4. Department of Clinical Pathology, Faculty of Medicine, Assiut University, Assiut, Egypt

    Hebatallah G. Rashed

  5. Department of Clinical Pathology, Faculty of Medicine, Fayoum University, Fayoum, Egypt

    Fadwa Abd-El-Reheem

  6. Department of Microbiology and Infection Control, Dar-Al-Fouad Hospital, 6th of October City, Egypt

    Arwa Ramadan El-Manakhly

  7. Department of Microbiology and Immunology, Faculty of Pharmacy, Russian University in Cairo, Cairo, Egypt

    Arwa Ramadan El-Manakhly

  8. Department of Clinical Pathology, Faculty of Medicine, Beni-Suef University, Beni-Suef, Egypt

    Radwa Ahmad Rabea Abdel-latif

  9. Department of Microbiology, Medical Research Institute, Alexandria University, Alexandria, Egypt

    Aliaa Gamaleldin Aboulela

  10. Department of Clinical Pathology, Faculty of Medicine, Sohag University, Sohag, Egypt

    Laila Yosef Saeed

  11. Department of Clinical Pathology, Faculty of Medicine, Banha University, Banha, Egypt

    Soheir Abdel-Rahman

  12. Department of Clinical Pathology, Faculty of Medicine, Mansoura University, Mansoura, Egypt

    Eman Elsayed

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  1. May Sherif
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Sherif, M., Palmieri, M., Mirande, C. et al. Whole-genome sequencing of Egyptian multidrug-resistant Klebsiella pneumoniae isolates: a multi-center pilot study. Eur J Clin Microbiol Infect Dis 40, 1451–1460 (2021). https://doi.org/10.1007/s10096-021-04177-7

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