Skip directly to site content Skip directly to page options Skip directly to A-Z link Skip directly to A-Z link Skip directly to A-Z link

Disclaimer: Early release articles are not considered as final versions. Any changes will be reflected in the online version in the month the article is officially released.

Volume 31, Number 6—June 2025

Synopsis

Genomic Surveillance of Climate-Amplified Cholera Outbreak, Malawi, 2022–2023

Lucious Chabuka1, Wonderful T. Choga1, Carla N. Mavian1Comments to Author , Monika Moir1, Christian Morgenstern1, Houriiyah Tegaly, Abhinav Sharma, Eduan Wilkinson, Yeshnee Naidoo, Rhys Inward, Samir Bhatt, G.R. WilliamWint, 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
Author affiliation: Centre for Epidemic Control and Innovation, School of Data Science and Computational Thinking, Stellenbosch University, Stellenbosch, South Africa (L. Chabuka, W.T. Choga, M. Moir, H. Tegally, E. Wilkinson, Y. Naidoo, C. Baxter, T. de Oliveira); Public Health Institute of Malawi, Lilongwe, Malawi (L. Chabuka, C. Mitambo, R. Chitatanga, J. Bitilinyu- Bango, M. Chiwaula, Y. Chavula, M. Bukhu, H. Manda, M. Chitenje, I. Malolo, A. Mwanyongo, B. Mvula, M. Nyenje, M. Kagoli); University of Florida Emerging Pathogens Institute, Gainesville, Florida, USA (C.N. Mavian, M. Tagliamonte, M. Salemi); Imperial College London, London, UK (C. Morgenstern, S. Bhatt); South African Medical Research Council Centre for Tuberculosis Research, Cape Town, South Africa (A. Sharma); University of Oxford, Oxford, UK (R. Inward, G.R. WilliamWint, M.U.G. Kraemer); Copenhagen University, Copenhagen, Denmark (S. Bhatt); Environmental Research Group Oxford, Oxford (G.R. WilliamWint); BlueDot, Toronto, Ontario, Canada (K. Khan); University of Toronto, Toronto (K. Khan, I.I. Bogoch); Pandemic Sciences Institute, University of Oxford, Oxford (M.U.G. Kraemer); Biosystems and Integrative Sciences Institute at University of Lisbon, Lisbon, Portugal (J. Lourenço); Kwazulu-Natal Research and Innovation Sequencing Platform, Durban, South Africa (R.J. Lessells, T. de Oliveira)

Main Article

Figure 2

Phylogenetic history of cholera outbreaks within Malawi shown as part of a time-scaled maximum likelihood global phylogeny of 2,778 cholera genomes. Clade branches are colored by the previous 12 introduction events involving Africa (T1–T14 and AFR15) as described by Weill et al. (9). We denote the clade containing the genomes from the 2022–2023 outbreaks in Malawi, South Africa, and Zimbabwe as the AFR15 lineage. Heat map below the tree shows continent of sample origin.

Figure 2. Phylogenetic history of cholera outbreaks within Malawi shown as part of a time-scaled maximum likelihood global phylogeny of 2,778 cholera genomes. Clade branches are colored by the previous 12 introduction events involving Africa (T1–T14 and AFR15) as described by Weill et al. (9). We denote the clade containing the genomes from the 2022–2023 outbreaks in Malawi, South Africa, and Zimbabwe as the AFR15 lineage. Heat map below the tree shows continent of sample origin.

Main Article

References
  1. Kanungo  S, Azman  AS, Ramamurthy  T, Deen  J, Dutta  S. Cholera. Lancet. 2022;399:1429–40. DOIPubMedGoogle Scholar
  2. World Health Organization. Outbreaks and other emergencies bulletin, week 30: 24–30 July 2023. 2023 [cited 2025 Feb 24]. https://www.afro.who.int/health-topics/disease-outbreaks/outbreaks-and-other-emergencies-updates
  3. World Health Organization. Disease outbreak news; cholera—global situation. 2022 Dec 16 [cited 2025 Feb 24]. https://www.who.int/emergencies/disease-outbreak-news/item/2022-DON426
  4. World Health Organization. Disease outbreak news; cholera—global situation. 2023 Feb 11. [cited 2025 Feb 24]. https://www.who.int/emergencies/disease-outbreak-news/item/2023-DON437
  5. Msyamboza  KP, Kagoli  M, M’bang’ombe  M, Chipeta  S, Masuku  HD. Cholera outbreaks in Malawi in 1998‒2012: social and cultural challenges in prevention and control. J Infect Dev Ctries. 2014;8:720–6. DOIPubMedGoogle Scholar
  6. World Health Organization African Region. Weekly regional cholera bulletin. 2024 Apr 1 [cited 2025 Feb 24]. https://iris.who.int/bitstream/handle/10665/376526/AFRO%20Cholera%20Bulletin.58.pdf
  7. World Health Organization. Disease outbreak news: cholera—Malawi. 2023 Feb 9 [cited 2025 Feb 24]. https://www.who.int/emergencies/disease-outbreak-news/item/2022-DON435
  8. Mutreja  A, Kim  DW, Thomson  NR, Connor  TR, Lee  JH, Kariuki  S, et al. Evidence for several waves of global transmission in the seventh cholera pandemic. Nature. 2011;477:462–5. DOIPubMedGoogle Scholar
  9. Weill  FX, Domman  D, Njamkepo  E, Tarr  C, Rauzier  J, Fawal  N, et al. Genomic history of the seventh pandemic of cholera in Africa. Science. 2017;358:785–9. DOIPubMedGoogle Scholar
  10. Inzaule  SC, Tessema  SK, Kebede  Y, Ogwell Ouma  AE, Nkengasong  JN. Genomic-informed pathogen surveillance in Africa: opportunities and challenges. Lancet Infect Dis. 2021;21:e281–9. DOIPubMedGoogle Scholar
  11. Chen  S, Zhou  Y, Chen  Y, Gu  J. fastp: an ultra-fast all-in-one FASTQ preprocessor. Bioinformatics. 2018;34:i884–90. DOIPubMedGoogle Scholar
  12. Li  H. A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data. Bioinformatics. 2011;27:2987–93. DOIPubMedGoogle Scholar
  13. Tonkin-Hill  G, Lees  JA, Bentley  SD, Frost  SDW, Corander  J. Fast hierarchical Bayesian analysis of population structure. Nucleic Acids Res. 2019;47:5539–49. DOIPubMedGoogle Scholar
  14. Croucher  NJ, Page  AJ, Connor  TR, Delaney  AJ, Keane  JA, Bentley  SD, et al. Rapid phylogenetic analysis of large samples of recombinant bacterial whole genome sequences using Gubbins. Nucleic Acids Res. 2015;43:e15. DOIPubMedGoogle Scholar
  15. Shen  W, Le  S, Li  Y, Hu  F. SeqKit: a cross-platform and ultrafast toolkit for FASTA/Q file manipulation. PLoS One. 2016;11:e0163962. DOIPubMedGoogle Scholar
  16. Kumar  S, Stecher  G, Li  M, Knyaz  C, Tamura  K. MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Mol Biol Evol. 2018;35:1547–9. DOIPubMedGoogle Scholar
  17. Nguyen  LT, Schmidt  HA, von Haeseler  A, Minh  BQ. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Mol Biol Evol. 2015;32:268–74. DOIPubMedGoogle Scholar
  18. Sagulenko  P, Puller  V, Neher  RA. TreeTime: maximum-likelihood phylodynamic analysis. Virus Evol. 2018;4:vex042. DOIPubMedGoogle Scholar
  19. Chaguza  C, Chibwe  I, Chaima  D, Musicha  P, Ndeketa  L, Kasambara  W, et al. Genomic insights into the 2022–2023 Vibrio cholerae outbreak in Malawi. Nat Commun. 2024;15:6291.
  20. Smith  AM, Sekwadi  P, Erasmus  LK, Lee  CC, Stroika  SG, Ndzabandzaba  S, et al. Imported cholera cases, South Africa, 2023. Emerg Infect Dis. 2023;29:1687–90. DOIPubMedGoogle Scholar
  21. Olatunji  G, Kokori  E, Moradeyo  A, Olatunji  D, Ajibola  F, Otolorin  O, et al. A perspective on the 2023 cholera outbreaks in Zimbabwe: implications, response strategies, and policy recommendations. J Epidemiol Glob Health. 2024;14:243–8. DOIPubMedGoogle Scholar
  22. Rambaut  A, Lam  TT, Max Carvalho  L, Pybus  OG. Exploring the temporal structure of heterochronous sequences using TempEst (formerly Path-O-Gen). Virus Evol. 2016;2:vew007. DOIPubMedGoogle Scholar
  23. Gill  MS, Lemey  P, Faria  NR, Rambaut  A, Shapiro  B, Suchard  MA. Improving Bayesian population dynamics inference: a coalescent-based model for multiple loci. Mol Biol Evol. 2013;30:713–24. DOIPubMedGoogle Scholar
  24. Suchard  MA, Lemey  P, Baele  G, Ayres  DL, Drummond  AJ, Rambaut  A. Bayesian phylogenetic and phylodynamic data integration using BEAST 1.10. Virus Evol. 2018;4:vey016. DOIPubMedGoogle Scholar
  25. Baele  G, Li  WL, Drummond  AJ, Suchard  MA, Lemey  P. Accurate model selection of relaxed molecular clocks in bayesian phylogenetics. Mol Biol Evol. 2013;30:239–43. DOIPubMedGoogle Scholar
  26. Mavian  C, Paisie  TK, Alam  MT, Browne  C, Beau De Rochars  VM, Nembrini  S, et al. Toxigenic Vibrio cholerae evolution and establishment of reservoirsin aquatic ecosystems. Proceedings of the National Academy of Sciences. 2020:201918763.
  27. Mavian  CN, Tagliamonte  MS, Alam  MT, Sakib  SN, Cash  MN, Moir  M, et al. Ancestral origin and dissemination dynamic of reemerging toxigenic Vibrio cholerae, Haiti. Emerg Infect Dis. 2023;29:2072–82. DOIPubMedGoogle Scholar
  28. Yu  GC, Smith  DK, Zhu  HC, Guan  Y, Lam  TTY. GGTREE: an R package for visualization and annotation of phylogenetic trees with their covariates and other associated data. Methods Ecol Evol. 2017;8:28–36. DOIGoogle Scholar
  29. Bielejec  F, Rambaut  A, Suchard  MA, Lemey  P. SPREAD: spatial phylogenetic reconstruction of evolutionary dynamics. Bioinformatics. 2011;27:2910–2. DOIPubMedGoogle Scholar
  30. Kass  RE Raftery  AE. Bayes factors. J Am Stat Assoc. 1995;90:773–95. DOIGoogle Scholar
  31. Bhatt  S, Ferguson  N, Flaxman  S, Gandy  A, Mishra  S, Scott  JA. Semi-mechanistic Bayesian modelling of COVID-19 with renewal processes. J R Stat Soc Ser A Stat Soc. 2023;186:601–15. DOIGoogle Scholar
  32. Cori  A, Ferguson  NM, Fraser  C, Cauchemez  S. A new framework and software to estimate time-varying reproduction numbers during epidemics. Am J Epidemiol. 2013;178:1505–12. DOIPubMedGoogle Scholar
  33. Cartalis  C, Feidas  H, Glezakou  M, Proedrou  M, Chrysoulakis  N. Use of earth observation in support of environmental impact assessments: prospects and trends. Environ Sci Policy. 2000;3:287–94.
  34. Tarpanelli  A, Mondini  AC, Camici  S. Effectiveness of Sentinel-1 and Sentinel-2 for flood detection assessment in Europe. Nat Hazards Earth Syst Sci. 2022;22:2473–89. DOIGoogle Scholar
  35. Li  S, Sun  D, Goldberg  MD, Sjoberg  B, Santek  D, Hoffman  JP, et al. Automatic near real-time flood detection using Suomi-NPP/VIIRS data. Remote Sens Environ. 2018;204:672–89.
  36. Turner  B. International Air Transport Association (IATA). In: Turner B, editor. The statesman’s yearbook 2008: the politics, cultures and economies of the world. London: Palgrave Macmillan UK; 2007. p. 48.
  37. Sim  EM, Martinez  E, Blackwell  GA, Pham  D, Millan  G, Graham  RMA, et al. Genomes of Vibrio cholerae O1 serotype Ogawa associated with current cholera activity in Pakistan. Microbiol Resour Announc. 2023;12:e0088722. DOIPubMedGoogle Scholar
  38. World Health Organization Eastern Mediterranean Region. Epidemic and pandemic-prone diseases: acute watery diarrhoea/cholera updates (16–31 March 2023). 2023 [cited 2025 Feb 24]. https://www.emro.who.int/pandemic-epidemic-diseases/cholera/acute-watery-diarrhoeacholera-updates-1631-march-2023.html
  39. Jamil  H, Liaqat  A, Lareeb  I, Tariq  W, Jaykumar  V, Kumar  L, et al. Monsoon and cholera outbreaks in Pakistan: a public health concern during a climate catastrophe. IJS Global Health. 2023;6:e105.
  40. Global Task Force on Cholera Control. Ending cholera: a global roadmap to 2030. 2017 [cited https://www.gtfcc.org/wp-content/uploads/2019/10/gtfcc-ending-cholera-a-global-roadmap-to-2030.pdf

Main Article

1These authors contributed equally to this article.

Page created: May 01, 2025
Page updated: May 21, 2025
Page reviewed: May 21, 2025
The conclusions, findings, and opinions expressed by authors contributing to this journal do not necessarily reflect the official position of the U.S. Department of Health and Human Services, the Public Health Service, the Centers for Disease Control and Prevention, or the authors' affiliated institutions. Use of trade names is for identification only and does not imply endorsement by any of the groups named above.
file_external