The African CDC has recently warned of a surge in cholera cases across the continent. Cholera, caused by certain strains of V. cholerae, is a waterborne infection that spreads rapidly, particularly in areas with limited access to clean water and sanitation. Africa bears the majority of the global burden of cholera, accounting for 46% of all cases and nearly 83% of all deaths. Yet, only about 1.3% of laboratories on the continent have the bacteriology capacity to confirm infections.
In 2024, representatives from 14 African countries came together for a five-day intensive workshop on a whole-genome sequencing method called Oxford Nanopore Technology (ONT) aimed at strengthening cholera surveillance capabilities across the continent. The event was organised by PulseNet Africa , a network dedicated to combating food- and waterborne diseases, and hosted at the Medical Research Council Unit the Gambia at the London School of Hygiene and Tropical Medicine (LSHTM).
"The hands-on training approach—where scientists brought DNA from their own archived, previously unsequenced isolates and used these real samples to learn the complete workflow—proved exceptionally valuable," says Dr Ebenezer Foster-Nyarko, a Research Fellow at LSHTM, Regional Co-Coordinator for PulseNet Africa and lead author of the study. "This comprehensive approach helped demystify genomic surveillance and demonstrated its immediate practical applications for public health."
The study, published in Microbial Genomics, analysed whole genome data from 104 isolates between 2010 and 2024 across Cote d'Ivoire, Ghana, Zambia, and South Africa. Findings highlight substantial genetic diversity, the presence of distinct local clades, and widespread multi-drug resistance to commonly used antibiotics, such as quinolones and trimethoprim. In contrast, resistance to azithromycin and rifampicin remains low. According to Foster-Nyarko, this pattern reflects decades of heavy reliance on trimethoprim and quinolones in Africa and Asia, whereas azithromycin and rifampicin have only recently been introduced. "This emphasises the urgent need for antimicrobial stewardship—preserving the effectiveness of remaining treatment options is critical to preventing further resistance," he notes.
Although limited by the scarcity of available genomic data, the study provides an important snapshot of a wider issue. Continued capacity building through training workshops and establishing sustained regional collaborations will be vital, says Foster-Nyarko.
The success of the 2024 workshop has already catalysed significant developments in disease surveillance across Africa; "PulseNet Africa launched feasibility studies in January 2025 to enhance genomic monitoring of PulseNet pathogens, with particular emphasis on antimicrobial resistance," says Foster-Nyarko. These efforts will expand ONT sequencing capacity beyond cholera to other foodborne diseases.
"By building local expertise in genomic surveillance, African countries will have the tools and skills needed to independently monitor and respond to cholera and other foodborne pathogens, ultimately contributing to long-term improvements in public health systems across the continent."
