To better understand the risks of antimicrobial resistance due to antimicrobial use in agriculture, aquaculture and livestock, we undertake studies on the biology, ecology and epidemiology of infections.
We use the latest technologies, such as whole genome sequencing, to characterise movement of antimicrobial resistance genes within these ecologies and investigate drivers of the emergence and transmission of antimicrobial resistance at the human–animal–environment interface.
In addition, we conduct research on antimicrobial resistance occurrence and residues in food items.
Key activities
Escherichia coli is a harmless gut micro-organism, but some pathogenic strains can cause life-threatening infections and other illnesses like urinary tract infections.
In this study researchers aimed to understand how land-use change acts as a driver of zoonotic diseases. The scientists sampled wild birds from 99 wildlife-livestock-human interfaces across Nairobi, Kenya and applied whole-genome sequencing to characterise bacterial genes. Modeling the diversity of bacterial genes encoding antimicrobial resistance against ecological forms of the urban environment, they demonstrate that communities of avian-borne bacterial genes are shaped by the habitat within which they exist.
This study investiaged the role of wildlife from urban environments as carriers of clinically relevant antimicrobial-resistant in Nairobi. In this study, scientists investigate antimicrobial resistance overlap between wildlife, humans, livestock and their shared environment across the developing city of Nairobi located in Kenya. The data was generated by random selection of households based on socioeconomic stratification. Within these, households (n=99) were randomly selected, ensuring that households with and without domestic livestock were selected. A detailed survey of household characteristics was undertaken, and faecal, environmental and other samples were collected. In all, over 2000 wildlife samples, representing 75 different wildlife species, were collected, together with similar number of livestock and human samples, and samples from the wider environment. This data has been used to examine the role of urban wildlife in the spread of clinical relevant antimicrobial resistance.
This study investigated the prevalence of AMR in household milk for human consumption in Isiolo and Marsabit Counties, Kenya. A total of 603 milk samples were randomly selected from milk-producer households. E. coli and S. aureus were isolated from 42 and 85 samples, respectively and their antimicrobial resistance profiles determined phenotypically and genetically using microbiological and molecular techniques.
This research aims to determine shared drug resistance mechanisms between multiple bacterial species including Salmonella spp, Campylobacter spp, Klebsiella sp and Proteus sp isolated in a hospital clinical environment. In this project, focussed studies on human-derived clinically relevant isolates of a range of bacterial species sharing the same phenotype (cephalosporin resistance) are being sequenced to understand if the resistance mechanisms are shared. This will have important implications for the management of antibiotics in a hospital setting in East Africa.
This study aims to identify drug resistance patterns in E. coli isolates obtained from cattle bred on mixed smallholder livestock farming systems from western Kenya. The area of study is widely representative of the Lake Victoria Crescent ecosystem which also includes areas of Uganda and Tanzania. Cattle were sampled from around 100 farms and phenotypic and genotypic characterization of E. coli isolates was performed, which included an examination of drug resistance carriage in these bacteria.
