Genetic Phylogeny of Diarrheagenic Escherichia coli Pathotypes and their Antibiotic Resistance Patterns among Children below Five Years Living in Close Contact with Food Animals, Kisumu County Hospital, Kenya

Abstract

Diarrheagenic Escherichia coli strains are a major cause of diarrheal infections in young children and animals. Urban settings with high population density, close interaction between humans and food animals, and environmental contamination create hotspots for the spread of infectious diseases. Children under the age of five are particularly vulnerable due to frequent exposure to these contaminated environments, making them more susceptible to infections, with diarrhea being a common manifestation. This study focused on assessing the genetic relatedness and antibiotic resistance profiles of Escherichia coli strains isolated from children under five years old living in close contact with food animals in Kisumu County, Kenya. Of the 250 stool samples, 100 food animals’ samples matched with 150 children’s samples were collected randomly from100 enrolled households. Polymerase chain reaction was used to genetically characterize the DEC strain, 23% and 20% harbored diarrheagenic E.coli (DEC) pathotypes from children and food animal samples respectively.The predominant pathotypes isolated among children samples was Enteroaggregative E.coli (EAEC) and among food animal’s samples was Enteropathogenic E.coli (EPEC). The antibiotic profiles analysed showed predominant antimicrobial resistance observed were sulfamethoxazole trimethoprim, tetracycline, Ampicillin and Amoxicillin 100%, 100%, 92% and 80% respectively in children’s samples. Food animals reported antimicrobial resistance of less than 20% among Azithromycin, Ampicillin and Amoxicillin. Diarrheagenic E.coli from children showed significantly higher resistance to almost all antibiotic compared to those from food animals. Overall, 75% of 23 DEC isolates from the two sources exhibited multidrug resistance, with multi drug index greater than 0.2 observed. The phylogenetic tree was generated using maximum likelihood model in mega software, this analysis revealed clustering together of E.Coli from children and food animal from the same household. The genetic similarities observed ranged between 100%, 90% and 80% from children and food animals shairing the same household. Bivariate analaysis using chisquare with age categories revealed E.coli prevalence being highiest among children aged 36 months (30.2%) followed by 0-12 months (18.2) (X2=13.197.P=0.004), hence age was significantly associated with E.coli infection. Children living in homesteads with cattle, pigs, goats and poultry reported prevalence of 22% compared 2% for those who lived in homes without these animals (X2= 8.788, P= 0.001). Logistic regression analysis revealed, Children who resided in homes where cattle/chicken/goats/pigs were kept were 23.62 times more likely to be infected with E-coli compared to children who came from home where no such animals were kept (RR = 23.62, 95% CI = 4.25-460.93, p=0.004).Spatial analysis ata showed DEC high density of E.coli being spotted in Arina and Ondiek estates in Kisumu County.The findings revealed a genetic similarity between Escherichia coli isolates from children and those from food animals, highlighting the need for a One Health approach. Such integrated interventions are crucial for tracing transmission pathways and ultimately reducing the incidence of diarrhea among children under five years of age.