Antimicrobial Susceptibility and Characterization of Extended-Spectrum β-Lactamase-Producing Escherichia coli Isolated from Stools of Primary Healthcare Patients in Ethiopia

Antimicrobial resistance of Escherichia coli is a growing problem in both developed and developing countries. This study aimed to investigate the phenotypic antimicrobial resistance of E. coli isolates (n = 260) isolated from the stool specimen of patients attending public health facilities in Addis Ababa and Hossana. This study also aimed to characterize phenotypically confirmed extended-spectrum beta-lactamase (ESBL)-producing E. coli isolates (n = 22) using whole-genome sequencing. Resistance to 18 different antimicrobials was assessed using the disc diffusion method according to the European Committee on Antimicrobial Susceptibility Testing (EUCAST) guidelines. The highest resistance rate among the E. coli isolates was found for ampicillin (52.7%), followed by trimethoprim-sulfamethoxazole (29.6%). Of all isolates, 50 (19.2%) were multidrug-resistant and 22 (8.5%) were ESBL producers. ESBL genes were detected in 94.7% of the sequenced E. coli isolates, and multiple beta-lactamase genes were detected in 57.9% of the isolates. The predominant ESBL gene identified was bla(CTX-M-15) (78.9%). The bla(TEM-1B) gene was detected in combination with other ESBL genes in 57.9% of the isolates, while only one of the sequenced isolates contained the bla(TEM-1B) gene alone. The bla(CTX-M-3) gene was detected in three isolates. The genes bla(CTX-M-15) and bla(TEM-1B) as well as bla(CTX-M-15) and bla(TEM-169) were confirmed to coexist in 52.6% and 10.5% of the sequenced E. coli isolates, respectively. In addition, bla(OXA-1) was identified together with bla(CTX-M-15) and bla(TEM-1B) in one isolate, and in one isolate, bla(TEM-169) together with bla(CTX-M-15) and bla(TEM-1B) was found. The results obtained show that measures need to be taken to reduce the spread of drug resistance and ensure the long-term use of available antimicrobials.