Re-emergence of cholera in Haiti linked to environmental V. cholerae O1 Ogawa strains

BACKGROUND On September 25th, 2022, cholera re-emerged in Haiti. OBJECTIVES/METHODS Toxigenic Vibrio cholerae O1 Ogawa were isolated on October 3rd & 4th, 2022, from cholera case patients in Port-au-Prince. The two new genomes were compared with genomes from 2,129 V. cholerae O1 isolated worldwide, including 292 Haitian strains from 2010-2018. RESULTS Phylogenies conclusively show the 2022 strains clustering within the Haitian monophyletic clade dating back to the 2010 outbreak. Strains shared a most recent common ancestor with a 2018 Haitian Ogawa strain isolated from the aquatic ecosystem, and cluster with the Ogawa clade that was circulating in 2015-2016. CONCLUSIONS Re-emergence of cholera in Haiti is the likely result of a spill-over event at the aquatic-human interface related to persistence of V. cholerae O1 in the environment. One-Sentence Summary We analyzed the full genome of two V. cholerae strains isolated from Haitian patients infected during the early days of the current 2022 epidemic, with data indicating that they originated from strains that have been circulating undetected at sub-epidemic levels in the aquatic environment. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement Funding for these studies was provided in part by grants from the National Institute of Allergy and Infectious Diseases (R01AI128750; R01AI123657; R01AI097405) award to JGMJ. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: University of Florida Institutional Review Board gave ethical approval for this work I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines and uploaded the relevant EQUATOR Network research reporting checklist(s) and other pertinent material as supplementary files, if applicable. Yes The genomic sequences have been deposited with NCBI under Sequence Read Archive (SRA) under BioProject ID: PRJNA900623. All other data are available in the Supplementary Information. Xml, global maximal likelihood and MCC trees are available at .