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Background <p>Carbapenem-resistant <i>Enterobacterales</i> are prevalent and increasingly reported in Egyptian hospitals. Carbapenemase production is the main mechanism of carbapenem resistance that carries the risk of dissemination among different bacterial species.</p> Purpose <p>the study aimed to detect the distribution of carbapenemase genes among <i>Enterobacterales</i> and <i>Pseudomonas</i> species isolated from clinical samples in a tertiary care university hospital in Cairo, Egypt.</p> Methods <p>GeneXpert real time multiplex PCR was used for detection of carbapenemase genes in carbapenem-resistant isolates from patients admitted to Cairo University hospitals during the period from September 2021 to July 2023. Carbapenem-resistant isolates were identified by conventional antimicrobial susceptibility testing using the disc diffusion method. <i>E. coli</i> ATCC<sup>®</sup> 25922™ <i>and Pseudomonas aeruginosa</i> ATCC<sup>®</sup> 27853™ were used as quality control strains for disc diffusion. The isolates were tested for each of the following genes, <i>bla</i><sub><i>KPC</i></sub>, <i>bla</i><sub><i>NDM</i></sub>, <i>bla</i><sub><i>OXA</i></sub>, <i>bla</i><sub><i>VIM</i></sub> and <i>bla</i><sub><i>IMP</i></sub>.</p> Results <p>A total of 330 carbapenem-resistant isolates were identified. A single carbapenemase gene was detected in 106 (32.1%) of isolates, 211 (63.9%) had two genes compared to three genes in six (1.8%) of isolates. The most common resistance gene was <i>bla</i><sub><i>NDM</i></sub> (90.3%) followed by <i>bla</i><sub><i>OXA</i></sub> (68.5%).</p> Conclusion <p>The detection of carbapenemase genes using the GeneXpert Carba-R assay represents a significant advancement in combating antimicrobial resistance. This assay is easy and rapid; offering results within approximately 50&#xa0;min; thus, represents significant added value to traditional culture methods, which require 48&#xa0;h or more. Despite the advantages of GeneXpert, the assay has some limitations, as it targets only the five most common carbapenemase gene families, and may miss less common genes.</p>

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GeneXpert CARBA-R assay for molecular characterization of carbapenem-resistance in Gram-negative bacteria in a tertiary care university hospital in Cairo-Egypt

  • 期刊论文

  • 发表日期：

    2026年6月3日

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  • Heba Shawky,
  • Afaf Mohamed Samy El Banna,
  • Eiman Mohammed AbdulRahman,
  • Ahmed Mokhtar,
  • Mariam Mahmoud Balah

摘要

Background

Carbapenem-resistant Enterobacterales are prevalent and increasingly reported in Egyptian hospitals. Carbapenemase production is the main mechanism of carbapenem resistance that carries the risk of dissemination among different bacterial species.

Purpose

the study aimed to detect the distribution of carbapenemase genes among Enterobacterales and Pseudomonas species isolated from clinical samples in a tertiary care university hospital in Cairo, Egypt.

Methods

GeneXpert real time multiplex PCR was used for detection of carbapenemase genes in carbapenem-resistant isolates from patients admitted to Cairo University hospitals during the period from September 2021 to July 2023. Carbapenem-resistant isolates were identified by conventional antimicrobial susceptibility testing using the disc diffusion method. E. coli ATCC® 25922™ and Pseudomonas aeruginosa ATCC® 27853™ were used as quality control strains for disc diffusion. The isolates were tested for each of the following genes, blaKPC, blaNDM, blaOXA, blaVIM and blaIMP.

Results

A total of 330 carbapenem-resistant isolates were identified. A single carbapenemase gene was detected in 106 (32.1%) of isolates, 211 (63.9%) had two genes compared to three genes in six (1.8%) of isolates. The most common resistance gene was blaNDM (90.3%) followed by blaOXA (68.5%).

Conclusion

The detection of carbapenemase genes using the GeneXpert Carba-R assay represents a significant advancement in combating antimicrobial resistance. This assay is easy and rapid; offering results within approximately 50 min; thus, represents significant added value to traditional culture methods, which require 48 h or more. Despite the advantages of GeneXpert, the assay has some limitations, as it targets only the five most common carbapenemase gene families, and may miss less common genes.