Molecular characterization, population structure, transmission dynamics, antimicrobial resistance and associated factors of Shigella, EHEC and EIEC Pathogens isolated from adult dysenteric patients

PhD Candidate: Yerega Belete Alamneh
Institution: Saint Paul’s Hospital Millennium Medical College (EpiGen SPHMMC, in collaboration with Addis Ababa University and Ethiopian Public Health Institute)
Supervisors: Dr. Solomon Ali; Professor Hailemichael Desalegn; Dr. Sisay Sirgu; Dr. Alem Abrha; Dr. Kelemework Adane; Dr. Geremew Tasew; Dr. Dawit Wolday; Professor Tobias Rinke de Wit

This PhD project investigates the molecular epidemiology and antimicrobial resistance of bacterial dysentery in adult patients attending health centres in Addis Ababa, Ethiopia. It focuses on Shigella spp., enterohemorrhagic Escherichia coli (EHEC), and enteroinvasive E. coli (EIEC), which are important causes of dysentery and are increasingly associated with multidrug resistance.

The study aims to determine the magnitude of these pathogens, their antimicrobial susceptibility patterns, and associated socio-demographic and environmental risk factors among adult dysenteric patients. Stool samples will be collected from eligible patients and processed using standard culture methods, biochemical identification, and antimicrobial susceptibility testing following CLSI guidelines.

Molecular analyses using whole genome sequencing will be conducted to characterize virulence genes, antimicrobial resistance determinants (including ESBL and carbapenemase genes), and to assess population structure, serotypes, and genetic relatedness of isolates. Bioinformatics approaches, including phylogenetic analysis and MLST, will be used to explore transmission dynamics.

The study integrates clinical, epidemiological, and genomic data to generate evidence that supports improved diagnosis, antimicrobial stewardship, and surveillance of dysentery-causing bacterial pathogens in Ethiopia.