Escherichia colior E.coli are harmless gut microbes, but some pathogenic strains can cause life-threatening infections, and other illnesses like UTIs. The bacteria can also cause disease in animals, leading to economic losses due to mortality and morbidity. According to the World Health Organization, E.coli has been catagorised as a priority pathogen due to its widespread antibiotic. Nairobi is the capital city in Kenya where the population is rapidly growing, and livestock are commonly kept within household compounds bringing them into close contact with people. E. coli is an ideal organism to study the spread of AMR in this complex environment since it is a ubiquitous commensal in both livestock and humans, but with a wide range of resistance phenotypes. This study focuses on the role of livestock keeping as a potentially high-risk urban interface for AMR transmission between humans and livestock in urban Nairobi.
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To better understand AMR risks due to antimicrobial use in agriculture, aquaculture and livestock, we undertake studies in selected sites into the biology, ecology, and epidemiology of infections. We use latest available technologies, such as whole genome sequencing to characterise movement of AMR genes within these ecologies and investigate drivers of AMR emergence and transmission at the human-animal-environmental interface. In addition, we conduct research on AMR occurrence and residues in food items.
Our main activities are:
- Agree and promote use of adequate study designs following epidemiological principles for genotyping research and AMR transmission dynamics studies at the human-livestock-environment interface
- Generate evidence on the extent of antimicrobial-resistant bacteria and antimicrobial residues found in livestock, fish, humans, the environment, water and food;
- Understand the transmission and genetic mechanisms of resistance in agriculture and the implications for human and animal health; and
- Develop a range of mathematical and biological models of AMR in low- and middle-income countries to understand the relative contribution of agriculturally-associated AMR to the human AMR burden and risk of drug-resistant infections in different contexts.
The case studies featured below illustrate ongoing and past research and provide insights into how AMR research is done within the CGIAR AMR hub.