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

## TL;DR

This study explores how gut microbiota changes in patients colonized with antibiotic-resistant bacteria in an Egyptian hospital, highlighting risks and the need for infection control.

## Contribution

The study identifies a link between CPE colonization and gut microbiota dysbiosis, particularly Proteobacteria dominance, in a hospital setting.

## Key findings

- 22.85% of patients were colonized with carbapenemase-producing Enterobacterales (CPE).
- Proteobacteria were significantly more abundant in the gut microbiota of CPE carriers.
- blaNDM and blaOXA-48 were the most common carbapenemase genes detected.

## Abstract

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.

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.

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.

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 online version contains supplementary material available at 10.1186/s12866-025-04575-3.