Epidemiology, AMR, and genomics of bacteria causing invasive human disease in The Gambia

Antimicrobial resistance (AMR) is a pressing global health crisis, with sub-Saharan Africa disproportionately affected due to high infection burdens and limited surveillance capacity. Many low-resource settings, including The Gambia, face significant data gaps on AMR prevalence, hindering effective containment strategies. This PhD research addresses these critical gaps by characterizing the resistance profiles of key bacterial pathogens responsible for infections in The Gambia. Utilizing routine, quality-assured diagnostic microbiology data, this study provides novel insights into AMR epidemiology, informs local antimicrobial stewardship, and generates evidence to guide clinical practice and public health interventions. This research pursued three core objectives: The first objective was to unravel the epidemiology of invasive community-acquired bacterial infections (CABIs) in The Gambia, producing the first comprehensive surveillance dataset in the country; The second objective was to leverage cumulative antibiogram data to develop localized antibiotic prescription guidelines, thereby promoting optimal antibiotic use in a secondary hospital; and the third objective was employing whole-genome sequencing (WGS) to investigate sequential neonatal outbreaks of Burkholderia cepacia (B. cepacia) and multidrug-resistant Klebsiella pneumoniae (K. pneumoniae), enabling the mapping of transmission pathways and informing infection prevention strategies in a tertiary hospital. The findings have significantly contributed to The Gambia’s National Action Plan (NAP) on AMR and informed global surveillance initiatives, including Global Antimicrobial Resistance and Use Surveillance System (GLASS) reporting. By establishing a scalable framework for AMR surveillance in resource-limited settings, this research demonstrates how quality-assured diagnostic data can drive evidence-based clinical decision-making and strengthen antimicrobial stewardship programs. Ultimately, this work positions The Gambia as a key player in regional AMR surveillance and containment efforts, reinforcing its role in the global fight against AMR.