Antimicrobial resistance (AMR) is a major public health threat in sub-Saharan Africa, including Cameroon, driven by the emergence and spread of multidrug-resistant bacteria. Extended-spectrum β-lactamase-producing Escherichia coli (ESBL-Ec) are a priority pathogen implicated in severe infections in both hospital and community settings. Data on the genetic determinants of ciprofloxacin-resistant E. coli are limited in Cameroon. This study aimed to determine the prevalence, resistance profiles, genetic mechanisms and phylogroups of multidrug-resistant E. coli recovered from clinical samples in two healthcare facilities in Yaoundé.
A cross-sectional study was performed from February to June 2025 in two healthcare facilities located in Yaoundé, Cameroon. All clinical specimens received from inpatients and outpatients during the study period were processed for bacteriological culture and identification.
Isolate identification was carried out using API20E according to the manufacturer’s instructions. Screening for extended-spectrum β-lactamase production used CHROMagar ESBL. Antimicrobial susceptibility testing was performed by the Kirby–Bauer disk diffusion method to determine resistance phenotypes, including susceptibility to third-generation cephalosporins and fluoroquinolones such as ciprofloxacin.
Polymerase chain reaction (PCR) assays were used to detect genes encoding ESBLs and plasmid-mediated quinolone resistance (PMQR) determinants. Mutations in the quinolone resistance-determining region (QRDR) of topoisomerase genes (gyrA and parC) were also investigated. The presence of resistance genes on plasmids was assessed, and horizontal plasmid transfer experiments were undertaken to evaluate mobility. Phylogroup analysis was performed to assign isolates to E. coli phylogenetic groups.
Isolates were allocated to phylogroups to infer likely ecological origins. The study reports the relative distribution of phylogroups, highlighting the predominance of commensal-associated groups among clinical isolates.
Sixty-five Escherichia coli isolates were analysed. Multidrug resistance was identified in 50.7% of isolates (33/65). All MDR isolates (33/33) were ESBL producers on CHROMagar ESBL.
Resistance to third-generation cephalosporins was universal among MDR isolates: cefotaxime and ceftriaxone resistance were both 100%. Ciprofloxacin resistance was present in 91% of MDR isolates.
PCR detection showed that the most frequent ESBL gene overall was blaTEM, found in 36.3% (12/33) of MDR isolates. Among ESBL genes detected on plasmids, blaTEM was the most prevalent plasmid-borne gene at 40%, followed by blaCTX-M at 26.7%.
Regarding quinolone resistance mechanisms, PMQR gene qnrB was detected in 16.6% (5/30) of isolates tested (denominator reported as 30 in the source). Mutations within the QRDR of the topoisomerase gene parC were identified in 36.6% (11/30) of ciprofloxacin-resistant strains. The source reports that only ESBL genes were found to be carried by plasmids, and that PMQR determinants showed chromosomal stabilization in this collection.
Phylogroup analysis revealed a predominance of phylogroup A, followed by phylogroup B, indicating a notable representation of commensal-associated E. coli lineages among clinical isolates.
This cross-sectional survey in two hospitals in Yaoundé documents a high prevalence of multidrug-resistant E. coli among clinical samples, with all MDR isolates producing extended-spectrum β-lactamases and the majority resistant to ciprofloxacin. The study highlights the dominance of blaTEM among ESBL determinants and reports that ESBL genes were disseminated via plasmids, whereas PMQR determinants were observed as chromosomally stabilized in the tested isolates. QRDR mutations in parC were present in a substantial subset of ciprofloxacin-resistant strains, supporting combined plasmid- and chromosomal-mediated mechanisms contributing to fluoroquinolone resistance.
The predominance of commensal-associated phylogroup A in clinical isolates suggests a role for the community reservoir in the circulation of resistant E. coli strains. These findings underscore the need for enhanced surveillance, including real-time genomic approaches and a One Health perspective, to track and limit the spread of plasmid-mediated ESBLs and evolving fluoroquinolone resistance mechanisms in Cameroon.
The authors conclude that urgent reinforcement of real-time One Health genomic surveillance is required in Cameroon to monitor and respond to the high burden of ESBL and fluoroquinolone resistance in clinical E. coli isolates.
Note: This report is based on the data and summary presented in the preprint; additional methodological details, full gene lists, isolate-level data, and outcomes of plasmid transfer experiments were not reported in the abstracted source text provided here.