Phenotypic and genotypic characterisation of diarrhoeagenic escherichia coli isolated from children in Mukuru Informal Settlement, Nairobi County, Kenya

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Kinankau, Kiunga Virginiah
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Kenyatta University
Diarrhoeal diseases in Kenya are among the five main causes of mortality in children younger than five years. Bacterial diarrhoea has been reported to account for up to 30 % of all cases of infantile diarrhoea. Among children of age five years and below, diarrhoeagenic E. coli (DEC) such as enterotoxigenic E. coli (ETEC), enteropathogenic E. coli (EPEC), enteroaggregative E. coli (EAEC) are the most important enteric pathogens and are responsible for 30 to 40 % of all the diarrhoeal episodes in developing countries. The circulation of different pathogenic E. coli is an important problem in developing countries enhanced by many factors, for example, climatic adversities, poor sanitation, malnutrition and AIDS related immunosuppression among others. Additionally, antibiotic susceptibility profiles vary from time to time. This makes it necessary to carry out susceptibility testing frequently to ensure that the right medication is given. The objectives of this study were to characterize at molecular level the different strains of E. coli isolated from diarrhoea children under the age of 5 years in Mukuru Kwa Njenga and Mukuru Kwa Reuben slums in Nairobi, Kenya. Bacteria isolated between May, 2013 and July, 2013 and archived in KEMRI-CMR were used in this study. Biochemical tests were used to confirm identity of the revived samples. The study also evaluated the resistance of the identified strains to different antibiotics (ciprofloxacin 5μg, nalidixic acid 30 μg, tetracycline 30 μg, streptomycin 10 μg, chloramphenicol 30 μg, gentamicin 10 μg , ceftazidine 30 μg, amoxicillin clavulanic acid 20/10μg, sulfamethoxazole trimethoprim1.25/23.75μg , Ampicillin 10μg and cefepime 30μg ) using Kirby Bauer technique. Multiplex PCR was used to identify DEC pathotypes through detection of various virulence genes. Data was entered using Excel (Microsoft) and checked for integrity and consistency. Statistical analysis was performed with statistical package for social sciences (SPSS) version 21.0. Categorical variables were analyzed using frequency distributions. The study found out that the isolates registered high resistance against SXT (62.18%) followed by tetracycline (47.44%), ampicilin (46.15%), AMC (18.6%), Streptomycin (14.7 %), nalidixic acid (13.5%) and ciprofloxacin (10.35%). Isolates were highly susceptible to ceftazidine (96.2 %), Cefepime (96.8 %), gentamicin (93.6%) and Chloramphenicol (92.9%). Multi drug resistance was also evident in that 43.59 % of isolates were resistant to at least three antibiotics. The results of one way ANOVA showed that there was no statistical significant difference between antibiotic susceptibility profiles of E. coli isolates from male and female children. However, isolates from male children showed higher resistance to cefepime, ceftazidine and streptomycinwhereas isolates from female children showed high resistance to the other eight antibiotics. The findings of the study also revealed that isolates from children in Mukuru kwa Reuben (MR) showed high rate of resistance against most of the antibiotics. However, the differences between susceptibility profiles of isolates from the two locations were not statistically significant. Antibiotic susceptibility profiles did not vary significantly among isolates from children of different ages for most antibiotics apart from SXT and tetracycline (P=0.03 and P=0.05 at P<0.05, respectively). The findings of the study showed that reserve antibiotics are the best treatment of childhood diarrhoea for children in Mukuru slums. The study also recommended that Sulphamethaxazole/Trimethoprim, ampicilin and tetracycline use should be minimized since they are not effective in diarrhoea treatment.
A thesis submitted in partial fulfillment of the requirements for the award of the degree of Master of Science (microbiology) in the School of Pure and Applied Sciences of Kenyatta University. June, 2016