Pathotyping and Antimicrobial Susceptibility Profile of Diarrheagenic Escherichia Coli Isolated From Children in an Urban Informal Settlement, Nairobi

Abstract

Diarrhea is among the primary contributors of mortality in children less than five years old globally. Diarrheagenic Escherichia coli (DEC) is the prime causative agent of childhood diarrhea in underdeveloped nations. The distribution of DEC pathotypes varies geographically, and in informal settlements, their occurrence is driven majorly by poor hygiene and sanitation. In addition, the lack of capacity for laboratory identification and antibiotic resistance in these settings poses a great challenge to management of childhood diarrhea. Therefore, detecting the predominant pathotypes of diarrheagenic E. coli informal settlements is key for proper management of childhood diarrhea. Methodology A laboratory-based cross-sectional study was undertaken to analyze presumptive Escherichia coli isolates from children below five years old presenting with acute diarrhea in three outpatient clinics at Mukuru, Nairobi, between January 2017 and September 2018. Identification, antimicrobial susceptibility testing (AST) and detection of Extended spectrum beta-lactamase (ESBL) positive DEC were determined using Vitek 2 System. Pathotyping of DEC isolates was performed using singleplex PCR and the amplicons run through gel electrophoresis. Proportions and frequency distributions of DEC pathotypes, AST profiles and ESBL positive DEC were computed and presented in tables, charts, and graphs. Results Of the 383 bacterial isolates, 175 were identified as E. coli. Among the E. coli isolates, 27% were DEC. These comprised of; Enteroaggregative E. coli (19%; 34/175), Enterohaemorrhagic E. coli (5%; 9/175), and Enteropathogenic E. coli (3%; 5/175). Overall, DEC isolates were resistant to cefazolin (90%; 43/48), ampicillin (83%; 40/48), ampicillin-sulbactam (77%; 37/48), and trimethoprim-sulfamethoxazole (83%; 40/48) but susceptible to amikacin, tigecycline, and carbapenems (100%). Resistance to ciprofloxacin (31%; 15/48), gentamicin (14%; 7/48), ceftriaxone (8%; 4/48), and cefepime (8%; 4/48) was also reported. A total of (17%; 8/48) of these isolates were ESBL positive. Conclusion This study reports the predominance of Enteroaggregative E. coli, high resistance to penicillins and cephalosporins antibiotics and ESBL positive DEC isolates in our study population