Phylogenetic Groups and Antibiotic Resistance Genes of Escherichia coli isolated from Food and Humans in Ouagadougou, Burkina Faso.

Escherichia coli is a major inhabitant of the intestinal tract of most mammalian species, including humans and animals. This bacterium is classified into four main phylogenetic groups (A, B1, B2, D), with pathogenic strains primarily belonging to group B2 and, to a lesser extent, group D. This study investigated the correlation between E. coli phylogenetic groups and antibiotic resistance by analyzing 144 strains (95 clinical, 49 food-derived). Species identification was confirmed via uidA gene PCR, and antimicrobial susceptibility was assessed using the Kirby-Bauer disc diffusion method. Extended-spectrum beta-lactamase (ESBL) production was determined through the double synergy test, and phylogenetic classification was performed using triplex PCR. Clinical isolates exhibited high resistance to cephalosporins (up to 56%) and fluoroquinolones (57%), whereas food-derived strains showed significantly lower resistance levels. The distribution of phylogroups differed: clinical isolates were predominantly A (35%) and B1 (44%), while food-derived strains were primarily B1 (57%) and A (23%). Resistance genes CTX-M and TEM were most prevalent in phylogroup A. These findings underscore the high levels of antimicrobial resistance observed in both clinical and foodborne E. coli strains, highlighting the urgent need for enhanced surveillance and stricter regulatory measures, particularly in developing regions such as Burkina Faso.