Prevalence, Antimicrobial Susceptibility and Genotypic Characterization of <i>Escherichia coli </i>Pathotypes Isolated from Children with Diarrhoea in Meru-Kenya

Introduction: There has been a global decrease in diarrhea infections in both adults and children due to the introduction of the Rotavirus vaccine and improved water, sanitation, and hand washing interventions. Low- and middle-income countries, however, continue recording high cases of diarrhea especially among children below five years where bacterial infections are one of the main causes. Particularly, E. coli has been isolated as the major bacterial etiological agent responsible for diarrhea among children in developing countries in Africa and Asia. There is also an increasing trend in antibiotic resistance in enteric pathogens against common and locally available prescribed drugs. This study aims to determine the prevalence and antimicrobial profile of E. coli as a causal agent of diarrhea among children in Meru. Methodology: A cross-sectional study design was conducted to recruit children with diarrhea seeking medical services at Meru Teaching and Referral Hospital. A total of 210 children were recruited for the study, and stool samples were collected from them for microbiological analysis. Multiplex PCR was done to detect E. coli pathotypes and ESBL genes. The disk diffusion method was used to determine the antimicrobial susceptibility of the E. coli pathotypes. Results: Of the 210 samples collected, 150 (71.4%) samples were positive for E. coli and 68 (32.4%) were positive for at least one virulence gene. EAEC was the most predominant pathotype at 23.53% followed by EPEC at 20.59% and ETEC at 14.71%. EHEC was the fourth common pathotype at 13.24% while EIEC prevalence was 11.76%. Isolates with co-infection were also detected with EPEC + ETEC being most common at 8.82% of the isolates followed by EPEC + EAEC at 4.4% and ETEC + EAEC at 2.9%. The ages between 13 - 24 months were the most affected with DEC at 45.6% followed by the age group of 25 - 36 months at 23.6% while the least affected was the age groups of 49 - 60 months at 6%. The antimicrobial susceptibility profile of the DEC showed the highest resistance against Sulfamethoxazole/Trimethoprim at 88.2% followed by Amoxicillin/Clavulanic acid at 83.8% and Ciprofloxacillin at 38.2%. Resistance of DEC against Gentamicin was at 11.8%, and resistance against Meropenem was the lowest at 1.5%. All DEC isolates tested were susceptible to Tetracycline, and 95.6% were susceptible to Meropenem. Others were Gentamicin at 80.9%, Ciprofloxacin at 52.9% and Amoxicillin/Clavulanic acid at 16.2%. No susceptibility was observed towards Sulfamethoxazole/Trimethoprim in all the samples tested. The tested DEC pathotypes showed high carriage of ESBL with 63 (92.7%) turning positive for at least one ESBL gene. Generally, blaTEM was most common accounting for 43% while blaCTX-M accounted for 26% and blaSHV was 3%. 9% of the DEC isolates had both blaTEM and CTX-M while 3% of the isolates had all the three ESBL genes. Conclusion: This study reports predominance of Enteroagregative E. coli, high resistance to Sulfamethoxazole/Timethoprime and Amoxicillin/Clavulanic acid and ESBL carriage in DEC among the study population.