Molecular characterization of extended-spectrum beta-lactamase-producing Escherichia coli among children and farm animals in Agogo, Ghana

Enterobacterales such as Escherichia coli are known to produce extended-spectrum β-lactamase (ESBL) enzymes at high rates in Ghana, West Africa. However, little is known about the One Health connections that may facilitate the dissemination of these resistant bacteria. This study aimed to use whole-genome sequencing (WGS) to investigate resistance determinants, virulence genes, and associated mobile genetic elements (MGEs) of ESBL-producing E. coli isolated from stool samples of Ghanaian children under five years of age, both with and without diarrhoea, and from farm animals, including poultry and goats. A total of 117 confirmed ESBL-positive E. coli isolates recovered from stool samples of children without diarrhoea (44/117), children with diarrhoea (30/117), poultry (35/117), and goats (8/117) were subjected to WGS. Phylogenetic analyses based on multilocus sequence typing (MLST) identified 49 distinct sequence types (STs), with ST617 and ST38 among the most prevalent lineages. ESBL production was predominantly mediated by the blaCTX−M−15 gene. Overlapping resistant genes and ST profiles observed between human and animal isolates suggest shared reservoirs. In summary, the work provides region-specific genomic evidence of shared sequence types, resistance genes, virulence factors, and mobile genetic elements among ESBL-producing E. coli isolates from children and farm animals in Ghana. These findings highlight the potential dissemination of multidrug-resistant strains and fill an important knowledge gap within a One Health context. Thus, the study provides a region-specific baseline for future molecular epidemiological surveillance and One Health–focused investigations in Ghana.