Occurrence and Antimicrobial Resistance Profiles of ESBL-Producing Escherichia coli and Klebsiella pneumoniae from Poultry Stool and Raw Meat in Rural and Urban Burkina Faso

Livestock contributes substantially to global food systems and livelihoods, particularly in low-income countries such as Burkina Faso. However, intensified poultry production has been associated with increased antibiotic use and the emergence of antimicrobial resistance (AMR). This study assessed the occurrence and antimicrobial resistance profiles of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli and Klebsiella pneumoniae isolated from poultry stool and raw meat samples collected in rural and urban areas of Burkina Faso. This cross-sectional study was conducted between February 2022 and December 2024 in Ouagadougou and Nouna. A total of 374 samples were collected, and the isolates were identified using biochemical testing and the VITEK 2 Compact system. ESBL production was confirmed using the combined-disk method according to EUCAST, 2022 guidelines. ESBL-producing E. coli and K. pneumoniae were detected in 70 (18.7%; 95% CI: 15.0–23.1) and 25 (6.7%; 95% CI: 4.5–9.8) samples, respectively. Among poultry stool samples, ESBL-producing E. coli were detected at similar frequencies in Ouagadougou and Nouna (Holm-adjusted p = 0.250), whereas ESBL-producing K. pneumoniae were detected significantly more frequently in Ouagadougou (Holm-adjusted p = 0.004). E. coli showed high resistance to ampicillin (100%), tetracycline (90.0%), cefuroxime (84.3%), and ceftriaxone (81.4%). All K. pneumoniae isolates were resistant to ampicillin, tetracycline, cefuroxime, ceftriaxone, and cotrimoxazole (100% each). Multidrug resistance was observed in 98.6% of E. coli and 100% of K. pneumoniae isolates. The detection of these organisms in the poultry production system and raw meat highlights the potential risk of foodborne transmission to humans. These findings underscore the need for improved antimicrobial stewardship, enhanced hygiene during slaughter and processing, and strengthened One Health surveillance strategies.