Browsing by Author "Okumu, Noah Okoth"

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    Epidemiology of antimicrobial resistance in non-typhoidal salmonella, and diarrhoeagenic escherichia coli from children, food and livestock in Dagoretti, Nairobi, Kenya
    (Kenyatta University, 2025-11) Okumu, Noah Okoth
    There is currently insufficient evidence regarding the risk of antimicrobial resistance (AMR) and its transmission in vulnerable weaning children, under complementary feeding. As part of the Urban Infant Foodscape project, pathogenic Escherichia coli and non-typhoidal Salmonella were isolated from children 6-24 months old, their foods, and household livestock within 585 enrolled households in the peri-urban area of Dagoretti Sub-County, Nairobi, Kenya. This study sought to elucidate the epidemiology of antimicrobial resistance carriage in these isolates. Analysis included phenotypic AMR screening and whole-genome sequencing of 82 multidrug resistant phenotypes. Household risk factors associated with AMR based on survey data were assessed. Fourteen non-typhoidal Salmonella (0.8% prevalence) and 274 (16.46% pooled prevalence) pathogenic E. coli were isolated from 540 children, 296 livestock, and 859 food samples along the value chain. The most common resistant phenotypes among children isolates were SXT, AMP and TET at 76.2% (95%CI: 68.1-82.5%), 70.8% (95%CI: 62.3-78.0%) and 45.4% (95%CI: 37.1-53.9%) respectively. The most frequently identified genotypes included mdf(A), blaTEM-1B, sul2, sul1, aph(6)-Id, aph(3’)-Ib, tet(A), tet(B), dfrA14, and dfrA8, conferring resistance to MLS (macrolide, lincosamides, streptogramin), β-lactams, sulphonamides, aminoglycosides, tetracyclines, and trimethoprim, respectively. While children isolates had a higher AMR gene carriage, there was no statistically significant difference from livestock hosts, suggesting a potential overlap and shared resistance elements between these host groups. These antimicrobial resistance patterns were significantly associated with specific dietary habits and food handling practices, on-site garbage and livestock waste disposal, as well as diarrhoeal illness within the past week. These results highlight the complex interplay between environmental, health, and antibiotic resistance factors in both children and livestock within the household. The findings of this study offer actionable insights for public health interventions and strategies (for instance water, sanitation, and hygiene-WASH, good food handling and preparation practices with respect to specific dietary habits), serving as a catalyst for further longitudinal studies essential to track changes in resistance patterns over time, accounting for variations in dietary habits, food safety practices, and health status
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    Genetic diversity and viral disease resistance of the indigenous chickens from selected areas in Kenya
    (Kenyatta University, 2016-08) Okumu, Noah Okoth
    Indigenous chickens show extensive physical diversity. However, industrialization and globalization of chicken in the 21st century has affected and limited their genetic resources to industrial breeds. Continuous selection for rapid growth and more egg production has resulted in the loss of disease resistance and overall immuno-competence hence a projected increase in disease-related costs in the future. Genetic control of disease resistance is one of the most important targets of breeding schemes in future. In India a breed of chicken resistant to most viral diseases (kuroiler) has been identified and is being crossed with improved breeds to increase disease resistance. It is not known in Kenya if there exists pockets of poultry with genes of resistance to any of the common diseases that often reduce profitability of poultry industry. It was hypothesized that the Kenyan indigenous chickens have no diversity and potential viral disease resistance genes. This study aimed at obtaining information to facilitate indigenous chicken breeding stock development, to come up with a stock that would be potentially resistant to most common viral diseases. One hundred and fifty indigenous chickens with diverse morphological features were obtained from Kenya especially in areas where it is perceived that no cross with industrial breeds has occurred and kept at InCIP-Egerton University Njoro. Eighteen microsatellite markers were used to study genetic diversity among and within populations. Presence of viral disease resistance genes: Mx1, TVB*R, TVB*S1 and TVB*S3 was investigated. Using GDA software, population genetic indices were characterized. Statistics related to genetic variation were estimated using GenALEx6. Mean percentage polymorphic loci was 96.71% and 4% AMOVA and PhiPT (fixation index) of 0.042 was seen among the eight ecotypes, p-value of 0.003 at 95% CI. MCW0123 marker had the highest variance of 13% among populations. Mean He ranged from 0.351±0.031 (SIB) to 0.434±0.022 (BM) with a grand mean of 0.399±0.011 obtained across the populations using the SSRs and grand mean He of 0.313±0.023 observed when the SNPs were used. Nei’s genetic distance ranged from 0.016 (SIB/WP) to 0.126 (NR/SIB). DARwin6.501 analysis software was used to draw the population dendrogram and two major population clusters were observed, also seen with PCoA. It also established presence of the viral disease resistance genes: 21.33% having the homozygous A and 58.67%, the heterozygous A/G allele of the Mx1 gene (potential resistance to IAV and NDV). TVB*S3 genotype seen in 24% of the samples show potential resistance to ALVE but not B and D subgroups. Sequencing of the TVB202 amplicons would show clarity of the P4, P5 and P6 possible TVB genotype combinations for strong inference of viral diseases resistance since the XbaI enzyme used failed to restrict the PCR products. Crossing the chicken types with potential resistance to ALVE, IAV and NDV with susceptible ones would enhance survival fitness of the indigenous chickens. These resistant breeds should be selected for breeding purposes