London School of Hygiene & Tropical Medicine

Whole genome sequencing of 104 Vibrio cholerae isolates from Côte d’Ivoire, Ghana, Zambia and South Africa, including strains from the current pandemic, found that 96% carried resistance genes against trimethoprim and 83% against quinolones.

The sequencing was carried out by scientists trained during a 2024 five-day workshop on Oxford Nanopore Technology (ONT), organised by PulseNet Africa at the Medical Research Council Unit The Gambia at the London School of Hygiene & Tropical Medicine (MRCG at LSHTM). The workshop, attended by researchers from 14 African countries, enabled participants to bring archived, unsequenced isolates and work through the full genomic sequencing workflow.

Dr Ebenezer Foster-Nyarko, Research Fellow at LSHTM and lead author of the study, said: “The hands-on training approach, where scientists brought DNA from their own archived, unsequenced isolates and used these real samples to learn the complete workflow, proved particularly valuable. This comprehensive approach helped demystify genomic surveillance and demonstrated its immediate practical applications for public health.”

The study, published in Microbial Genomics, showed multi-drug resistance and significant genetic diversity among isolates, including several distinct local clades.

Commenting on the observed antimicrobial resistance, Dr Foster-Nyarko explained: “This pattern reflects the widespread use of trimethoprim and quinolones for decades in Africa and Asia, while azithromycin and rifampicin have been introduced more recently. It also underscores the importance of antimicrobial stewardship. We must use these remaining effective antibiotics judiciously to prevent the development and spread of resistance.”

Although limited by the lack of extensive available data, the study provided a worrying snapshot of a wider issue. Dr Foster-Nyarko emphasised: “Continued capacity building through training workshops and establishing sustained regional collaborations will be vital.”

The workshop’s success has already catalysed developments in disease surveillance across Africa. Dr Foster-Nyarko, who also serves as the Regional Coordinator for PulseNET Africa, a regional hub of PulseNET International, said: “PulseNet Africa launched feasibility studies in January 2025 to enhance genomic monitoring of PulseNet pathogens, with particular emphasis on antimicrobial resistance.”

He added: “By building local expertise in genomic surveillance, we can ensure that African countries 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.”

Publication:

Foster-Nyarko F, Able-Thomas S, Adade N E, et al. Genomic diversity and antimicrobial resistance of Vibrio cholerae isolates from Africa: a PulseNet Africa initiative using nanopore sequencing to enhance genomic surveillance. Microbial Genomics, 2025. https://doi.org/10.1099/mgen.0.001586