Publication Highlight: CholeraSeq: a comprehensive genomic pipeline for cholera surveillance and near real-time outbreak investigation
A new study by GenPath Africa consortium members Abhinav Sharma, Monika Moir, Cheryl Baxter, Tulio de Oliveira, Carla N. Mavian, and Eduan Wilkinson at Stellenbosch University’s Centre for Epidemic Response and Innovation (CERI), in collaboration with the University of Florida, introduces CholeraSeq - a powerful new tool designed to speed up the global response to cholera outbreaks.
What is this publication about?
The researchers developed CholeraSeq, an end-to-end, automated genomic pipeline that processes complex DNA sequencing data to track cholera outbreaks in near real-time. The pipeline unifies multiple technical steps - including quality control, reference mapping, and variant calling - into a single, reproducible workflow. Crucially, it includes a curated database of over 4,000 global cholera genomes, allowing scientists to immediately see how a new local outbreak relates to cases documented worldwide.
Why is this important?
Cholera remains a major global threat, and turning genomic data into "actionable evidence" is often too slow, especially in resource-limited areas. CholeraSeq solves this by providing a user-friendly and high-throughput system that can run on local laptops or cloud environments. During a test case of the 2022 Haiti outbreak, the pipeline was able to confirm the origin of the strain and link it to previous years of circulation in just 85 minutes.
How can this make a difference?
By making advanced bioinformatics accessible to non-experts and researchers in the Global South, CholeraSeq helps democratize the tools needed for outbreak investigation. It enables public health officials to identify the source of an infection quickly, monitor for antimicrobial resistance, and coordinate more effective regional responses. This automated approach ensures that critical data is available to save lives while the outbreak is still happening, rather than months after it has ended.
Massimiliano S. Tagliamonte, Abhinav Sharma, Alberto Riva, Monika Moir, Marco Salemi, Cheryl Baxter, Tulio de Oliveira, Carla N. Mavian, and Eduan Wilkinson, "CholeraSeq: a comprehensive genomic pipeline for cholera surveillance and near real-time outbreak investigation." Bioinformatics, 2026; 42(1): 1–5. doi:10.1093/bioinformatics/btaf665.
