Prevalence and molecular characterization of ESBL-producing Enterobacterales in clinical samples from the Boucle du Mouhoun region in Burkina Faso

Extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli and Klebsiella pneumoniae represent a major clinical and public health concern due to their ability to confer resistance to multiple classes of antibiotics. Data on the molecular epidemiology of ESBL-producing Escherichia coli and Klebsiella pneumoniae remain limited in many regions of Burkina Faso, particularly outside the Ouagadougou and Bobo Dioulasso. This study aimed to determine the frequency of ESBL-producing Escherichia coli and Klebsiella pneumoniae and to characterize the ESBL resistance genes circulating in the Boucle du Mouhoun region. A total of 1,845 clinical samples (urine, pus, blood, and semen) collected from patients attending two major healthcare facilities in Dédougou were processed during the study period. From these samples, 247 non-duplicate Escherichia coli and Klebsiella pneumoniae isolates were recovered and identified using API 20E and confirmed by MALDI-TOF mass spectrometry. Other Enterobacterales species identified during routine culture were excluded from subsequent analyses. Antimicrobial susceptibility testing was performed using the disk diffusion method. ESBL-encoding genes and Escherichia coli phylogenetic groups were characterized by polymerase chain reaction. Among the 247 Enterobacterales isolates, Escherichia coli accounted for 78.1% (193/247) and Klebsiella pneumoniae for 21.86% (54/247). Overall, 55.0% (136/247) of the isolates were ESBL-producing, including 58.03% (112/193) of Escherichia coli and 44.44% (24/54) of Klebsiella pneumoniae. High levels of co-resistance were observed with fluoroquinolones (90.4%), trimethoprim-sulfamethoxazole (91.9%), and aminoglycosides (55.9%). Molecular analysis revealed a predominance of CTX-M-1-group genes (88.7%), followed by CTX-M-9-group genes (10.3%). Of the 112 ESBL-producing Escherichia coli isolates, 47.3% (53/112) belonged to phylogroup B2 and 42.9% (48/112) to phylogroup A. This study provides the first molecular evidence of ESBL-producing Escherichia coli and Klebsiella pneumoniae in the Boucle du Mouhoun region of Burkina Faso. The high prevalence of blaCTX-M genes underscores the urgent need to strengthen antimicrobial stewardship programs, enhance infection prevention and control measures, and implement regular regional surveillance to curb the spread of multidrug-resistant Enterobacterales.