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

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

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...

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Bibliographic Details
Published in:European journal of clinical microbiology & infectious diseases Vol. 40; no. 7; pp. 1451 - 1460
Main Authors: Sherif, May, Palmieri, Mattia, Mirande, Caroline, El-Mahallawy, Hadir, Rashed, Hebatallah G., Abd-El-Reheem, Fadwa, El-Manakhly, Arwa Ramadan, Abdel-latif, Radwa Ahmad Rabea, Aboulela, Aliaa Gamaleldin, Saeed, Laila Yosef, Abdel-Rahman, Soheir, Elsayed, Eman, van Belkum, Alex, El-Kholy, Amani
Format: Journal Article
Language:English
Published: Berlin/Heidelberg Springer Berlin Heidelberg 01-07-2021
Springer Nature B.V
Subjects:
Antibiotic resistance
Antibiotics
Antimicrobial resistance
Biomedical and Life Sciences
Biomedicine
Carbapenemase
Drug resistance
Epidemiology
Gene sequencing
Genes
Genomes
Hospitals
Internal Medicine
Klebsiella
Klebsiella pneumoniae
Medical Microbiology
Multidrug resistance
Multidrug resistant organisms
Nosocomial infection
Original Article
Phylogeny
Virulence
Virulence factors
Whole genome sequencing
Egypt
Multi-locus sequence typing (MLST)
Multidrug resistance (MDR)
Carbapenem resistance
Whole-genome sequencing (WGS)
Klebsiella pneumoniae
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Summary: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 bla CTX-M-15 , detected in 27 isolates (69.2%). Carbapenemase genes encountered were bla NDM-1 ( n = 13), bla NDM-5 ( n = 1), bla OXA-48 ( n = 12), bla OXA-181 ( n = 2), and bla KPC2 ( 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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ISSN:0934-9723
1435-4373
DOI:10.1007/s10096-021-04177-7