<i>Escherichia coli</i> Pathotypes in Children with Acute Diarrhea in an Informal Settlement in Nairobi, Kenya

Abstract

Diarrhea is among the leading causes of morbidity and mortality in children aged < 5 years globally. In underdeveloped countries, diarrheagenic Escherichia coli (DEC) accounts for 30% -40% of childhood diarrhea cases. To identify the pathotypes involved in diarrheal outbreaks in Kenya, we analyzed archived E. coli isolates from children < 5 years old presenting with diarrhoea at three outpatient facilities in an informal settlement between January 2017 and September 2018. E. coli confirmation and antimicrobial susceptibility testing were done using the VITEK ® 2 instrument. Pathotype identification was performed via conventional polymerase chain reaction. Of 175 E. coli isolates, 48 (27%) were DEC pathotypes, with enteroaggregative E. coli (EAEC) predominating (71%, 34/48). Enterohemorrhagic (EHEC) and enteropathogenic E. coli (EPEC) represented 19% and 10% of isolates, respectively. Enteroinvasive and enterotoxigenic pathotypes were not identified. All DEC isolates were susceptible to amikacin, ertapenem, imipenem, meropenem and tigecycline. Conversely, most (>80%) isolates were resistant to ampicillin, ampicillin-sulbactam and sulfamethoxazole-trimethoprim. Half of all EAEC and EPEC strains were resistant to cefazolin while half of EHEC isolates were resistant to ciprofloxacin and moxifloxacin. In total, 18 resistance phenotypes were identified with "ampicillin-cefazolin-ampicillin/ sulbactam-sulfamethoxazole/trimethoprim" predominating (33%, 16/48). The majority (81%) of DEC isolates were multidrug-resistant, with extendedspectrum beta-lactamase production identified in 8% of these isolates. This