Genetic relatedness of diarrheagenic Escherichia coli pathotypes isolated from children under five years of age and food animals in Kisumu County, Kenya

Abstract

Background: Diarrheal disease remains one of the leading causes of deaths in children below five years of age. The risk factors associated with diarrhea include poor hygiene practices such as open defecation and consumption of contaminated water and food. However, exposure of domestic animal is equally a potential risk factor for diarrhea disease in children. Methodology: We characterized animal-related exposures in a subset of households (n=73) by collecting faecal samples from 150 children with diarrhoea and 100 food animals (30 cattle, 30 chicken, 25 goats and 15 pigs). Escherichia coli was isolated from the faecal samples and biochemically confirmed using conventional micro- biological techniques. The deoxyribonucleic acid (DNA) of each E. coli isolate was extracted and amplified by multiplex PCR to identify three diarrheagenic E. coli pathotypes. The amplified products were sequenced, and genetic relatedness of the isolates was determined through phylogenetic analysis. Results: We isolated and identified a total of 32 (12.8%) diarrheagenic E. coli (DEC) from the 250 faecal samples, 26 (17.3%) of which were from the 150 children with diarrhea while 6 (6.0%) were from the 100 food animals (OR=3.285, 95% CI=1.299-8.305, p=0.011). Three DEC pathotypes were confirmed by PCR in 16 DEC strains, with 9 enteroaggregative E. coli (EAEC), 2 enterotoxigenic E. coli (ETEC), 2 enteropathogenic E. coli (EPEC), 1 EAEC/ETEC, 1 EAEC/EPEC and 1 ETEC/EPEC mixed strains. The phylogenetic analysis showed that 6 DEC isolates had genetic similarity ranging between 31% to 90%. Isolates S04 originating from animal and S02 from a child with diarrhoea of the same household were closely related, with 55% similarity. Moreover, isolate S05 from animal origin and S06 of diarrheic child origin were closely related, with similarity degree as high as 82% even though they were not paired. Twenty four of the 26 (92.3%) DEC isolates from diarrhoeic children showed multidrug resistance (MDR) pattern to antibiotics but none of the 6 isolates from food animals was multi-drug resistant. Conclusion: The high degree of genetic relationship between DEC isolate S04 and S02 from animal and human origin indicated the high potency of zoonotic transmission. Further studies investigating animal husbandry practices and zoonotic transmission of DEC are needed. Keywords: Diarrhoea; Zoonotic; Genetic relatedness; Multiplex PCR; Sequencing