Unraveling Antimicrobial Resistance Phenotypes and Carriage of Extended-Spectrum Β-Lactamase Genes in Escherichia Coli Isolated From Dairy Farms in Kiambu County, Kenya
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Date
2023
Authors
Waithiru, Dan Wairimu
Journal Title
Journal ISSN
Volume Title
Publisher
kenyatta university
Abstract
Antibiotics are increasingly being used globally in livestock farming for prophylaxis and promotion of growth. Consequently, the use of antibiotics has considerably resulted in emergence and spread of antibiotic-resistant strains of bacteria in livestock. The role of livestock farming in the transmission of antibiotic resistance remains poorly studied. This study sought to establish the carriage of genes associated with anti-microbial resistance including the extended β-lactamase genes in Escherichia coli (E. coli) strain recovered from farmers and their cattle and cattle slurry in the immediate environment within Kiambu County, Kenya. Stool, hand swab, cattle dung, and slurry samples were obtained from selected farmers, their cattle, and their immediate environment. Isolation and antimicrobial susceptibility profiling were conducted. Phenotypic tests and polymerase chain reaction were carried out for determination of carriage of Extended Spectrum Beta-Lactamase (ESBL) genes and the molecular diversity of the strains. The overall number of E. coli isolated from 352 samples was 286 (81%). Results of the antimicrobial susceptibility profiles indicated that 40% (114) of the total isolates had developed resistance to at least three antimicrobial classes and were therefore classified as Multi-Drug Resistant (MDR) isolates. More specifically, 14% (40) of multidrug-resistant strains of E. coli were resistant to only three different classes of antimicrobials while 25% (71) of E. coli multidrug-resistant strains exhibited resistance encompassing antibiotics from four to seven distinct classes. Only 3 (1%) strains were resistant to 8 antimicrobial categories. A significant difference was found between the carriage of the MDR phenotype and isolates from human and non-human sources. In addition, there was no homogeneity in antimicrobial resistance profiles in these isolates. ESBL resistance was found in 15 isolates (11 from humans, 2 from cattle, and 2 from the environment). The blaCTX-M was identified in only 10 E. coli strains while blaTEM genes were identified in 15 E. coli strains. The (GTG)5 PCR analysis revealed that isolates from cattle handlers, immediate environment, and cattle dung had no absolute distinction and were dispersed across all cluster groups. The study painted a comprehensive picture of diverse antimicrobial susceptibility patterns within E. coli. It revealed a higher prevalence of MDR E. coli compared to prior studies. Additionally, the presence of extended β-lactamase genes was identified in E. coli strains resistant to third- generation cephalosporins. Notably, genetic analysis underscored significant genomic diversity with no distinct evidence of clonal lineages. The study recommends the development of a holistic approach to tackle antimicrobial resistance on dairy farms, which should encompass surveillance, responsible antibiotic use, and public awareness campaigns. Furthermore, there is a need to prioritise further research into understanding resistance mechanisms, mobility, and genomic diversity in resistant strains.
Description
A Thesis Submitted in Partial Fulfilment of the Requirements for the Award of the Degree of Master of Science in Medical Microbiology in the School of Pure and Applied Sciences of Kenyatta University
Keywords
Antimicrobial, Spectrum Β, Lactamase Genes, Escherichia Coli, Kiambu County, Kenya