Molecular epidemiology of ESBL, AmpC-β-lactamase, and carbapenemases-producing Escherichia coli and Klebsiella spp., isolated from human, animal, environment, and drinking water in Burkina Faso

Antimicrobial resistance (AMR) poses a significant threat to global public health. Escherichia coli ( E. coli ) and Klebsiella species are currently considered as key contributors to AMR and it spread. The objective of this study was to investigate the molecular epidemiology of ESBL, AmpC-β-lactamase and carbapenemase-encoding genes in E. coli and Klebsiella isolated from animal, human, environmental and drinking water sources. E. coli and Klebsiella were isolated from a several samples sources, including humans, animals, soil, and drinking water. Molecular techniques, such as PCR, were utilised for the detection of ESBL, AmpC-β-lactamase, and carbapenemase encoding genes detection. Subsequently, resistance profiles were analysed, and a heatmap analysis and hierarchical clustering were performed to assess the relationship between genotypic and phenotypic resistance profiles using R software. Amongst 215 ESBL isolates (90.7% gene-positive), bla _CTX−M was the most prevalent gene, with a predominance in cattle ( E. coli : 67.7%, Klebsiella spp.: 20.6%). Sapone exhibited the highest prevalence of bla _CTX−M (56.3%) and triple-gene combinations (21.8%). The cluster analysis revealed two key findings: the presence of cattle-specific Klebsiella spp. and the interspecies clusters. Positive and negative correlations between bla _CTX−M and cefotaxime resistance (r = 0.48) and nalidixic acid susceptibility (r=-0.35) respectively was observed. Bla _IMP, bla _KPC, bla _OXA−48 and bla _DHA were detected with a prevalence not exceeded 1.52%. This study highlighted bla _CTX−M and bla _TEM as the most prevalent ESBL E. coli and Klebsiella -producing found in various samples. Low prevalence of AmpC-β-lactamase, and carbapenemase encoding genes were observed. These findings emphasise the critical role of livestock farming, environmental contamination, and horizontal gene transfer in the spread of antimicrobial resistance. In view of these results, ongoing One Health approach should focus on antimicrobial stewardship, environmental monitoring, and improved veterinary and healthcare practices.