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. 2024 Sep 5;13(9):851.
doi: 10.3390/antibiotics13090851.

Genomic Characterization of Extended-Spectrum β-Lactamase-Producing and Third-Generation Cephalosporin-Resistant Escherichia coli Isolated from Stools of Primary Healthcare Patients in Ethiopia

Deneke Wolde  1   2   3 , Tadesse Eguale  2   4 , Girmay Medhin  2 , Aklilu Feleke Haile  2 , Haile Alemayehu  2 , Adane Mihret  5   6 , Mateja Pirs  7 , Katja Strašek Smrdel  7 , Jana Avberšek  8 , Darja Kušar  8 , Tjaša Cerar Kišek  9 , Tea Janko  9 , Andrej Steyer  9 , Marjanca Starčič Erjavec  3
Affiliations

Genomic Characterization of Extended-Spectrum β-Lactamase-Producing and Third-Generation Cephalosporin-Resistant Escherichia coli Isolated from Stools of Primary Healthcare Patients in Ethiopia

Deneke Wolde et al. Antibiotics (Basel). .

Abstract

The global spread of antimicrobial resistance genes (ARGs) in Escherichia coli is a major public health concern. The aim of this study was to investigate the genomic characteristics of extended-spectrum β-lactamase (ESBL)-producing and third-generation cephalosporin-resistant E. coli from a previously obtained collection of 260 E. coli isolates from fecal samples of patients attending primary healthcare facilities in Addis Ababa and Hossana, Ethiopia. A total of 29 E. coli isolates (19 phenotypically confirmed ESBL-producing and 10 third-generation cephalosporin-resistant isolates) were used. Whole-genome sequencing (NextSeq 2000 system, Illumina) and bioinformatic analysis (using online available tools) were performed to identify ARGs, virulence-associated genes (VAGs), mobile genetic elements (MGEs), serotypes, sequence types (STs), phylogeny and conjugative elements harbored by these isolates. A total of 7 phylogenetic groups, 22 STs, including ST131, and 23 serotypes with different VAGs were identified. A total of 31 different acquired ARGs and 10 chromosomal mutations in quinolone resistance-determining regions (QRDRs) were detected. The isolates harbored diverse types of MGEs, with IncF plasmids being the most prevalent (66.7%). Genetic determinants associated with conjugative transfer were identified in 75.9% of the E. coli isolates studied. In conclusion, the isolates exhibited considerable genetic diversity and showed a high potential for transferability of ARGs and VAGs. Bioinformatic analyses also revealed that the isolates exhibited substantial genetic diversity in phylogenetic groups, sequence types (ST) and serogroups and were harboring a variety of virulence-associated genes (VAGs). Thus, the studied isolates have a high potential for transferability of ARGs and VAGs.

Keywords: Escherichia coli; Ethiopia; antimicrobial resistance genes; mobile genetic elements; phylogenetic groups; virulence-associated genes.

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Conflict of interest statement

The authors declare no conflicts of interest.

Figures

Figure 1
Figure 1
Phylogroups, sequence types, and serotypes of studied E. coli isolates.
Figure 2
Figure 2
Virulence-associated genes detected with prevalence greater than 10% in studied E. coli isolates from Addis Ababa and Hossana.
Figure 3
Figure 3
Number of studied E. coli isolates harboring certain plasmid types.
Figure 4
Figure 4
Number of studied E. coli isolates harboring certain types of transposable elements.
Figure 5
Figure 5
Flow diagram showing the selection of E. coli isolates for the study.
See this image and copyright information in PMC

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