Deciphering the Genetic Mechanisms Driving Carbapenem Resistance: A Multicenter Study from Seven Egyptian Governorates Using Multiplex PCR and Whole Genome Sequencing

Theodor Bilharz Research Institute

Bibliographic Information

Authors: Gad M.; Sherif M.; Essam S.; Gamal D.; El-Defrawy I.; Abdelhakeem M.; Taher O.; Abdel-Latif R.; Shoala A.; Shawky S.; Rashed H.; Gohar H.; El-Mahallawy H.; El-kholy A.

Journal: Current Microbiology

Publisher: Springer

Publication Date: 4 June 2026

Volume / Issue: Volume 83 / Issue 7

Article No.: 402

ISSN: 3438651

DOI: 10.1007/s00284-026-04960-9

Scopus: View on Scopus

PubMed: 42240856

Document Type: Article

Authors and Affiliations

Gad M., Department of Clinical and Chemical Pathology, Faculty of Medicine, Cairo University, 1 Al-Saray Str, Al-Manial, Cairo, 11559, Egypt; Sherif M., Department of Clinical and Chemical Pathology, Faculty of Medicine, Cairo University, 1 Al-Saray Str, Al-Manial, Cairo, 11559, Egypt; Essam S., Department of Clinical and Chemical Pathology, Faculty of Medicine, Cairo University, 1 Al-Saray Str, Al-Manial, Cairo, 11559, Egypt; Gamal D., Theodor Bilharz Research Institute (TBRI), Giza, Egypt; El-Defrawy I., Theodor Bilharz Research Institute (TBRI), Giza, Egypt; Abdelhakeem M., Clinical and Chemical Pathology Department, Minia University Hospitals, Minya, Egypt; Taher O., Department of Clinical and Chemical Pathology, Faculty of Medicine, Ain Shams University, Alabassya, Cairo, Egypt; Abdel-Latif R., Department of Clinical Pathology, Faculty of Medicine, Beni-Suef University, Beni-Suef, Egypt; Shoala A., Department of Critical Care Unit, National Heart Institute, Cairo, Egypt; Shawky S., Faculty of Medicine, Alexandria University, Alexandria, Egypt; Rashed H., Clinical Pathology Department, Faculty of Medicine, Assiut University Hospitals, Assiut, Egypt; Gohar H., Medical Microbiology and Immunology, Faculty of Medicine, Cairo University, Cairo, Egypt; El-Mahallawy H., Department of Clinical Pathology, National Cancer Institute, Cairo University, Cairo, Egypt; El-kholy A., Department of Clinical and Chemical Pathology, Faculty of Medicine, Cairo University, 1 Al-Saray Str, Al-Manial, Cairo, 11559, Egypt

Abstract

Carbapenem-resistant Enterobacterales (CRE) causing healthcare-associated infections (HAI) represent a growing public health threat. We conducted a large-scale multicenter study to characterize CRE isolates from ICU patients in Egypt. Non-repetitive CRE clinical isolates were collected from infected ICU patients in 10 tertiary hospitals across 7 governorates over one year. Identification and susceptibility testing were performed using VITEK-2. Carbapenemase genes were detected by multiplex PCR for blaNDM, blaOXA−48, blaVIM,blaSPM,blaGIM,blaIMP, blaKPC, blaDIM,blaSIM,and blaAIM, and whole genome sequencing (WGS) was conducted on 40 selected isolates. Of 646 CRE isolates, K. pneumoniae (86%) and E. coli (12%) predominated. High resistance rates were observed, with tigecycline showing the highest activity (78.7% susceptible). Ceftazidime-avibactam activity varied widely (2–74.2%) among hospitals. The most prevalent carbapenemase genes were blaNDM (77%) and blaOXA−48 (64%), while blaKPC was found in 4.6%. Fourteen isolates (2.2%) lacked the screened carbapenemase genes. WGS revealed four ST types among 14 E. coli isolates, mainly ST2 and ST650, while 26 K. pneumoniae isolates were dominated by ST147 (27%) and ST11 (23%). Genes linked to hypermucoviscosity (rmpA, rmpA2) were present in 31% of K. pneumoniae, alongside other carbapenem resistance mechanisms (absence of outer membrane porins, and efflux pump activation). Carbapenemase production is the main driver of CRE among ICU-HAIs in Egypt. WGS showed diverse sequence types suggesting limited local spread, frequent hypermucoviscosity, porin loss, and efflux-mediated resistance among CRE isolates. © The Author(s), under exclusive licence to Springer Science+Business Media, LLC, part of Springer Nature 2026.

Keywords

Anti-Bacterial Agents; Bacterial Proteins; beta-Lactamases; Carbapenem-Resistant Enterobacteriaceae; Carbapenems; Cross Infection; Egypt; Enterobacteriaceae Infections; Genome, Bacterial; Humans; Microbial Sensitivity Tests; Multiplex Polymerase Chain Reaction; Whole Genome Sequencing; avibactam plus ceftazidime; aztreonam; bacterial DNA; beta lactamase; beta lactamase aim; beta lactamase dim; beta lactamase gim; beta lactamase imp; beta lactamase kpc; beta lactamase ndm; beta lactamase oxa 48; beta lactamase sim; beta lactamase spm; beta lactamase vim; carbapenemase; cefepime; cefixime; ceftazidime; ceftriaxone; cefuroxime; cotrimoxazole; levofloxacin; meropenem; outer membrane protein; piperacillin; porin; rmpa protein; rmpa2 protein; temocillin; ticarcillin; tigecycline; trimethoprim; unclassified drug; antiinfective agent; bacterial protein; carbapenem derivative; abdominal infection; Article; bacterium isolation; bloodstream infection; carbapenem resistance; carbapenem resistant Enterobacterales; Egyptian; Enterobacter cloacae; Enterobacterales; Escherichia coli; genetic analysis; genetic susceptibility; healthcare associated infection; human; intensive care unit; Klebsiella oxytoca; Klebsiella pneumoniae; major clinical study; multicenter study; outer membrane; prevalence; Proteus mirabilis; Providencia; Serratia (bacterium); tertiary care center; urinary tract infection; ventilator associated pneumonia; bacterial genome; clinical trial; drug effect; Enterobacteriaceae infection; epidemiology; genetics; isolation and purification; microbial sensitivity test; microbiology

Citation Information

Scopus Citations: 0

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