Background Diarrheal diseases constitute a serious public health problem, particularly in developing countries and it is the second leading cause of child mortality. Self-medication and overuse of antibiotics due to the scarcity of complementary diagnostic systems can lead to the development of multi-resistant bacteria causing diarrhea. The objective of this work was to identify the bacteria responsible for diarrhea in children and to characterize their sensitivity to a panel of antibiotics used in Mali.

Methods This study involved 554 children seen in outpatient visits at the Yirimadio community health center and diagnosed with diarrhea. Yirimadio is a peripheral district area of Bamako the capital city of Mali. Stool samples were collected and analyzed by stool culture and antibiotic susceptibility was determined by the disk diffusion method on agar medium.

Results The bacteria responsible for diarrheal were Escherichia coli (31.8%) and Salmonella (2.9%). In Escherichia coli strain, amoxicillin and cotrimoxazole were the most resistant antibiotics, 93.8% and 92.6%, respectively. The Extented Spectrum Beta Lactamase resistance phenotype accounted for 39.8% in Escherichia coli. A resistance of 12.5% to cotrimoxazole and cefoxitin was found to Salmonella strains.

Conclusion This study showed that Escherichia coli is the most frequent bacteria involved in diarrhea in children under 3 years of age in Yirimadio, which are resistant to amoxicillin and co-trimoxazole, two antibiotics commonly prescribed in this setting.