Publication Highlight: Genomic surveillance of climate-amplified cholera outbreak, Malawi, 2022-2023

A recent study by our GenPath Africa colleagues Tulio de Oliveira, Cheryl Baxter, Eduan Wilkinson and Abhinav Sharma at Stellenbosch University (SU) traced Malawi’s 2022–2023 cholera outbreak to bacteria from Pakistan and revealed how travel and climate-driven floods can fuel epidemics.

What is this publication about?

Researchers investigated Malawi’s severe cholera outbreak from 2022 to 2023, which resulted in over 59,000 cases and nearly 1,800 death. By analysing 49 full genomes of the Vibrio cholerae bacterium collected from the southern, central, and northern regions of Malawi, they discovered the outbreak did not come from local strains but from Pakistan’s 2022 cholera epidemic. This strain was likely introduced in mid-2022 through air-travel, while severe flooding in Malawi allowed the disease to spread more rapidly.

Why is this important?

This research provides the first definitive genomic evidence linking a major cholera outbreak in Africa directly to an outbreak in Asia (Pakistan), and highlights how easily infectious diseases can spread in today’s interconnected world through international travel. Addittionally, it offers clear evidence of the connection between extreme weather events and an increase in waterborne disease outbreaks, and demonstrates the power of local genomic sequencing and advanced modelling to deliver rapid, actionable insights during public health emergencies.

How can this make a difference?

This study highlights the need for surveillance systems that combine genomic, climate, and travel data to better predict and prevent outbreaks, particularly after extreme weather events, and offers strong evidence of the public health impact climate change can have. This information can guide stronger public health responses and help policymakers advocate for investing in climate-resilient health systems to better prevent future epidemics. Above all, by showing an outbreak in one country can trigger a public health crisis in another, this research underscores the importance of global health security, international data sharing, and cross-border cooperation.

Lucious Chabuka, Wonderful T. Choga, Carla N. Mavian, Monika Moir, Christian Morgenstern, Houriiyah Tegaly, Abhinav Sharma, Eduan Wilkinson, Yeshnee Naidoo, Rhys Inward, Samir Bhatt, G.R. William Wint, Kamran Khan, Isaac I. Bogoch, Moritz U.G. Kraemer, José Lourenço, Cheryl Baxter, Massimiliano Tagliamonte, Marco Salemi, Richard J. Lessells, Collins Mitambo, Ronald Chitatanga, Joseph Bitilinyu-Bango, Mabvuto Chiwaula, Yollamu Chavula, Mphatso Bukhu, Happy Manda, Moses Chitenje, Innocent Malolo, Alex Mwanyongo, Bernard Mvula, Mirrium Nyenje, Tulio de Oliveira, and Mathew Kagoli. “Genomic Surveillance of Climate-Amplified Cholera Outbreak, Malawi, 2022–2023.” Emerging Infectious Diseases, 31(6):1090-1099, June 2025. doi:10.3201/eid3106.240930.