KONSERVE-AB study: Protocol for Investigating Antimicrobial Resistance in Enterobacterales Across Human, Animal, and Environmental Samples Using a One Health Approach v1

This protocol details the methodology for a cross-sectional study investigating antimicrobial resistance (AMR) patterns in Enterobacterales across human, animal, and environmental samples within Kisii, Kenya, emphasizing a One Health approach. The study aims to elucidate the prevalence of AMR in gastrointestinal pathogens, specifically Escherichia coli, Salmonella spp., Klebsiella spp., and Shigella spp., in human stool, animal feces, drinking water, and soil samples. Specimens are meticulously collected from patients with gastrointestinal symptoms at Kisii Teaching and Referral Hospital, their surrounding environment, and animal sources within households. Sample collection adheres to stringent protocols to ensure accuracy and minimize contamination. Microbiological analysis involves culturing on selective media, followed by antimicrobial susceptibility testing using the disk diffusion method, based on the Clinical and Laboratory Standards Institute (CLSI) guidelines. Molecular characterization of extended-spectrum beta-lactamase (ESBL) and carbapenemase-producing Enterobacterales is conducted using PCR and electrophoresis to detect key resistance genes, including blaTEM, blaOXA-48, blaCTX-M, and blaVIM. The study’s objective is to investigate the transmission pathways of resistant strains within the human-animal-environment interface and to determine the association between resistance patterns in different sample types. The findings will contribute to understanding the local dynamics of AMR, informing more effective diagnostic, treatment, and preventive strategies in Kenya. Furthermore, it aims to support the integration of AMR surveillance into a One Health framework for future interventions.