Prevalence of extended spectrum beta lactamase and molecular detection of blaTEM, blaSHV and blaCTX-M genes among gram negative bacilli uropathogen isolates in Ouagadougou, Burkina Faso.

Urinary tract infections (UTIs) represent a significant public health issue. The increasing prevalence of Extended-spectrum β-lactamases (ESBLs) producing Gram-negative bacilli (GNB) significantly limit treatment options. This study investigated the phenotypic and genotypic characteristics of ESBL-producing GNB isolated from urine specimens processed across Ouagadougou, Burkina Faso. A total of 252 non-duplicate Gram-negative bacilli isolates were collected from four clinical laboratories in Ouagadougou, Burkina Faso. Antimicrobial susceptibility was assessed via disk diffusion following European committee on antimicrobial susceptibility testing (EUCAST) guidelines. ESBL production was screened using double-disk synergy testing, and polymerase chain reaction was employed to detect blaTEM, blaCTX-M, and blaSHV genes. Phenotypic ESBL production was detected in 20.6% of the 252 isolates. These ESBL-producing strains exhibited high resistance rates (greater than 85%) to β-lactams, fluoroquinolones, and folate pathway inhibitors, while imipenem and amikacin remained largely effective. The blaTEM was the most prevalent ESBL gene (48.8%), followed by blaCTX-M (42.1%) and blaSHV (11.1%). Cluster analysis identified three genotypic-resistance profiles ranging from low to high multiple antibiotic resistance (MAR) indices. This study underscores the substantial burden of ESBL-associated multidrug resistance among urinary GNB in Burkina Faso. The incorporation of molecular diagnostic tools into routine surveillance programs is critical for early detection, informed therapeutic decision-making, and effective containment of antimicrobial resistance. The data further support the need for expanded genomic research and broader geographic sampling to reinforce national antimicrobial stewardship initiatives.