Genomic diversity and transmission dynamics of extended spectrum β-lactamase and carbapenemase producing enterobacteriaceae among human, animal and the environment in northwest Ethiopia

PhD Candidate: Chalachew Genet
Institution: Bahir Dar University, Institute of Biotechnology
Supervisors: Abaineh Munshea; Endalkachew Nibret; Wendemagegn Enbiale; Anna Rommerskirchen

This PhD project investigates the genomic diversity and transmission dynamics of extended spectrum β-lactamase (ESBL) and carbapenemase-producing Enterobacteriaceae, particularly Escherichia coli and Klebsiella pneumoniae, across human, animal, and environmental interfaces in northwest Ethiopia. These organisms are critical contributors to antimicrobial resistance (AMR), with increasing global public health impact due to limited treatment options.

The study applies a One Health approach and is conducted in Bahir Dar Special Zone and North Gojjam Zone. It includes samples from patients, cattle, cattle farms, hospital environments, animal clinics, raw milk, wastewater, and environmental swabs. Sociodemographic and exposure-related data are collected alongside microbiological sampling.

ESBL and carbapenemase-producing isolates will be identified using standard microbiological methods and antimicrobial susceptibility testing. A subset of isolates will undergo whole genome sequencing to characterize genetic diversity, resistance genes, virulence factors, and high-risk clones. Bioinformatics analyses, including MLST and phylogenetic reconstruction, will be used to assess transmission pathways across human, animal, and environmental reservoirs.

The study aims to generate integrated genomic and epidemiological evidence on AMR dissemination, supporting improved infection prevention and control strategies, and strengthening One Health–based antimicrobial resistance surveillance systems in Ethiopia.