Colonization with Carbapenemase producing Enterobacterales (CPE) and associated alteration in microbiota composition in a tertiary care hospital in Egypt

Theodor Bilharz Research Institute

Bibliographic Information

Authors: El-Defrawy I.; Khaled M.; El-Far A.; El-Shenawy A.; Salem D.; Gamal D.; Fam N.; Sayed H.A.; Hayek N.N.; Elrefaiy M.A.; Ray A.E.; Soliman N.S.; Soliman M.S.; El-Kholy A.A.

Journal: BMC Microbiology

Publisher: BioMed Central Ltd

Publication Date: 27 January 2026

Volume / Issue: Volume 26 / Issue 1

Article No.: 58

ISSN: 14712180

DOI: 10.1186/s12866-025-04575-3

Scopus: View on Scopus

PubMed: 41588318

Document Type: Article

Access: All Open Access; Gold Open Access; Green Open Access

Authors and Affiliations

El-Defrawy I., Microbiology Department, Theodor Bilharz Research Institute (TBRI), P.O box 12411, 30 Imbaba, Giza, Egypt; Khaled M., Microbiology Department, Theodor Bilharz Research Institute (TBRI), P.O box 12411, 30 Imbaba, Giza, Egypt; El-Far A., Microbiology Department, Theodor Bilharz Research Institute (TBRI), P.O box 12411, 30 Imbaba, Giza, Egypt; El-Shenawy A., Microbiology Department, Theodor Bilharz Research Institute (TBRI), P.O box 12411, 30 Imbaba, Giza, Egypt; Salem D., Microbiology Department, Theodor Bilharz Research Institute (TBRI), P.O box 12411, 30 Imbaba, Giza, Egypt; Gamal D., Microbiology Department, Theodor Bilharz Research Institute (TBRI), P.O box 12411, 30 Imbaba, Giza, Egypt; Fam N., Microbiology Department, Theodor Bilharz Research Institute (TBRI), P.O box 12411, 30 Imbaba, Giza, Egypt; Sayed H.A., Public Health Department, Theodor Bilharz Research Institute (TBRI), P.O box 12411, Imbaba, Giza, Egypt; Hayek N.N., Public Health Department, Theodor Bilharz Research Institute (TBRI), P.O box 12411, Imbaba, Giza, Egypt; Elrefaiy M.A., Hepatogastoentrology Department, Theodor Bilharz Research Institute (TBRI), P.O box 12411, Imbaba, Giza, Egypt; Ray A.E., Hepatogastoentrology Department, Theodor Bilharz Research Institute (TBRI), P.O box 12411, Imbaba, Giza, Egypt; Soliman N.S., Clinical and Chemical Pathology Department, Faculty of Medicine, Cairo University, 11562, Giza, 12613, Egypt; Soliman M.S., Clinical and Chemical Pathology Department, Faculty of Medicine, Cairo University, 11562, Giza, 12613, Egypt; El-Kholy A.A., Clinical and Chemical Pathology Department, Faculty of Medicine, Cairo University, 11562, Giza, 12613, Egypt

Abstract

Background: The rising incidence of carbapenemase producing Enterobacterales (CPE)s, represents an urgent health threat due to their raised morbidity and mortality consequences. Colonization of CPE represents an important vehicle for hospital acquired infections. Microbiota dysbiosis, especially in critically ill patients, is a risk factor associated with CPE-colonized infections. In this study we aimed to characterize and assess the rate of colonization with CPE, and the possibility of subsequent infection. Also, to investigate the role of microbiota dysbiosis as a potential risk factor for colonization with CPE by comparing the gut niche in colonized patients versus non-colonized patients. Methods: Rectal swabs and stools were collected from 70 patients attending Hepatogastroentrology Department at TBRI Hospital on their first 72 h of admission and during their hospital stay. Incidence of infection with CPE was followed up in the same patients with relevant clinical specimens, mainly urine culture and sensitivity. Rectal swabs were cultured on chromogenic agar media, whereas clinical specimens were cultured following microbiological methods. Species identification and antibiotic sensitivity testing were performed using Vitek-2 compact system on suspected CPE isolates, as well as detection of carbapenemase genes by conventional PCR for detection of blaNDM, blaOXA-48, blaVIM, blaKPC and blaIMP. The 16S rRNA profiling was used for identification of gut microbiota using Illumina Miseq Sequencing System (Illumina). EzBioCloud 16S rRNA database was used for taxonomic assignment. Results: CPE carriage was found in 22.85% (n = 16) of included patients. blaNDM was found predominantly in 75% (n = 12) of the isolates followed by blaOXA-48 in 62.5% (10/16). BlaVIM was found in two isolates with blaNDM and blaOXA-48, whereas blaKPC and blaIMP were not detected in all tested isolates.Urinary tract infection associated with CRE colonization was detected in 12.5% (n = 2). Significant predominance of Proteobacteria was found in stool of CPE carriers with p < 0.03. Conclusion: Our results confirm the continuous pervasiveness of carbapenem resistance in our region. Alteration in microbiota and the abundance of Proteobacteria in CPE carriers may indicate a predisposition to inflammatory states in those patients and the requirement to further studies on the associated health effect. Efficient antimicrobial stewardships, strict infection control measures, and active surveillance programs are mandatory to limit the spread and subsequent infection with CPE isolates. © The Author(s) 2026.

Keywords

48; Altered microbiota; Carbapenemase producing Enterobacterales (CPE); Carbapenemases; Multidrug resistant bacteria (MDR); NDM; OXA; Proteobacteria; VIM; Adult; Aged; Anti-Bacterial Agents; Bacterial Proteins; beta-Lactamases; Cross Infection; Dysbiosis; Egypt; Enterobacteriaceae; Enterobacteriaceae Infections; Feces; Female; Humans; Male; Microbial Sensitivity Tests; Microbiota; Middle Aged; RNA, Ribosomal, 16S; Tertiary Care Centers; amikacin; aztreonam; carbapenem; carbapenemase; cefepime; ceftazidime; ciprofloxacin; clavulanic acid; gentamicin; imipenem; meropenem; minocycline; piperacillin; RNA 16S; sulfamethoxazole; ticarcillin; tobramycin; trimethoprim; antiinfective agent; bacterial protein; beta lactamase; antibiotic sensitivity; antimicrobial stewardship; Article; Citrobacter; colonization; Enterobacter; Enterobacterales; Escherichia coli; hospitalization; human; intestine flora; Klebsiella; Klebsiella pneumoniae; microbial colonization; microflora; polymerase chain reaction; rectal swab; risk factor; Serratia (bacterium); tertiary care center; drug effect; Enterobacteriaceae infection; enzymology; epidemiology; genetics; isolation and purification; metabolism; microbial sensitivity test; microbiology

Citation Information

Scopus Citations: 1

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