Haiti’s 2022 cholera re-emergence: what the genomes showed
Lee Katz and Andrew Page speak with CDC guests Christine Lee and Cynney Walters about Haiti’s 2022 cholera outbreak and its relationship to the outbreak that began in 2010. They discuss SNP comparisons, reference genomes and antimicrobial resistance data for Vibrio cholerae. The genomes support relatedness to earlier Haitian strains, but gaps in clinical and environmental surveillance limit conclusions about where the organism persisted.
Listen to Episode 128: Haiti cholera outbreak with Christine Lee and Cynney Walters on SoundCloud
In this episode
The CDC laboratory behind the analysis
Christine Lee introduces the LIVE Lab within CDC’s Enteric Diseases Laboratory Branch. Its remit includes Listeria, Yersinia, Vibrio and other enteric bacteria. As part of the national reference laboratories, the team supports state and local public health partners, particularly with unusual organisms and emerging patterns in foodborne illness. Christine distinguishes Vibrio cholerae found domestically in the United States from the strains responsible for major international cholera outbreaks.
Cynney Walters is the laboratory’s bioinformatician, analysing whole-genome sequencing data across these organisms. She is also a certified CLIA tester and performs wet-lab sequencing protocols. Christine explains that this patient-level testing involves requirements for data quality, reproducibility and protecting patient identifiers.
From the 2010 outbreak to re-emergence in 2022
Lee recalls joining the laboratory more than a decade earlier to investigate Haiti’s 2010 cholera outbreak. He describes it as an early, prominent use of whole-genome sequencing in outbreak investigation. The discussion briefly revisits the controversy over its origin and the phylogenetic clustering observed between Haitian and Nepalese genomes.
For the later outbreak, Christine describes disrupted water infrastructure and sociopolitical barriers to clean water. Haiti had been approaching the three years without confirmed clinical cases needed to seek cholera-free status. Working with Haiti’s National Public Health Laboratory, the CDC team received samples from multiple regions. The episode discusses Walters et al.’s paper, “Genome sequences from a reemergence of Vibrio cholerae in Haiti, 2022 reveal relatedness to previously circulating strains”.
Comparing new genomes with historical Haitian strains
Cynney describes using Lyve-SET, a tool associated with Lee’s work, to compare single nucleotide polymorphisms, or SNPs. The question was whether genomes from the re-emergence were closely related to historical Haitian strains or showed greater genetic differences that might suggest a new introduction.
The collection spanned 2010–2022, with historical isolates from years between 2010 and 2017 compared with the 2022 outbreak material. Cynney reports approximately 0–25 SNP differences between the newer and historical strains. She describes 10 SNPs as a threshold the team usually uses for very close relatedness. Their interpretation was that the re-emergent strains were related to the pre-existing strains, although relatedness did not mean all the genomes were identical. These comparisons connected the new outbreak to earlier circulation without establishing where the bacteria had persisted.
Two chromosomes, mobile elements and reference choice
Andrew asks how Vibrio cholerae’s two chromosomes affect the analysis. Lee explains that two chromosomes need not fundamentally change a SNP analysis when a suitable reference genome is available. He identifies the superintegron on the smaller second chromosome, with its transposable elements, as a complication. Lyve-SET masks regions resembling phage or other mobile elements so that SNPs in those regions do not enter the evolutionary analysis.
The team had not yet performed long-read sequencing on the new outbreak strains. Christine says they used an existing Haiti cholera reference strain, for which long-read data were available, and recalls using short-read assemblies. Lee stresses that producing that reference was a collaborative effort involving multiple partners, especially colleagues in Canada.
Antimicrobial resistance alongside SNP relatedness
Cynney also describes the antimicrobial resistance analysis reported in the paper. Three strains had AMR profiles that differed from the majority through the presence or absence of resistance genes. She interprets the overall profile similarity alongside the SNP results as further evidence that the strains were similar.
Christine names ResFinder among the methods and discusses the genes gyrase A and parC. She describes Vibrio cholerae as relatively clonal and cautions against automatically interpreting an emerging resistance pattern as evolutionary change within the strain already being followed: a different strain carrying resistance may have been introduced.
What surveillance gaps leave unresolved
The central unresolved question is whether the strain persisted in the environment or continued circulating through people without detected cases. Christine discusses another group’s molecular clock analysis and an environmental isolate related to the re-emergent strain, while emphasising the limitations of the available evidence. Without recent clinical surveillance and routine environmental sampling, the team lacked the comparisons needed to distinguish those possibilities confidently.
She also explains why environmental surveillance for Vibrio differs from wastewater surveillance for SARS-CoV-2 or polio: Vibrio already live in water. Distinguishing environmental populations from strains responsible for epidemics requires more work in bioinformatics and metagenomics. The discussion closes with the value of sustained surveillance, particularly where cholera appears close to elimination, and the potential for whole-genome sequencing to help assess whether that goal is being reached.
Highlights
- 00:01:46 — Christine introduces the LIVE Lab and its public health reference laboratory role.
- 00:05:34 — The 2010 Haiti outbreak and an early prominent application of whole-genome sequencing.
- 00:07:14 — Cholera re-emerges as Haiti approaches eligibility for cholera-free status.
- 00:09:40 — Cynney explains the Lyve-SET SNP comparison with historical Haitian strains.
- 00:11:21 — Collection years, approximately 0–25 SNP differences and interpretation of relatedness.
- 00:12:11 — Two chromosomes, the superintegron and masking mobile elements during SNP analysis.
- 00:13:23 — Possible persistence in people or the environment and evidence from molecular clock analysis.
- 00:15:49 — The existing Haiti reference strain and the status of long-read sequencing.
- 00:16:51 — AMR profiles identify three strains differing from the majority.
- 00:19:08 — Missing clinical and environmental surveillance limits source attribution.
- 00:20:02 — Global cholera resurgence and the importance of surveillance near elimination.
In their own words
So the reemergence suggests that this particular strain had been circulating either in the environment or through the population for more than a decade, right?
— Christine Lee, 00:13:23
Who is talking
- Lee Katz (host)
- Andrew Page (host)
- Christine Lee (guest, Centers for Disease Control and Prevention)
- Cynney Walters (guest, Centers for Disease Control and Prevention)
Tools and resources mentioned
Lyve-SET, ResFinder.
Questions this episode answers
Were Haiti’s 2022 cholera strains related to the earlier outbreak?
The team found approximately 0–25 SNP differences between newer and historical Haitian strains and concluded that the 2022 strains were related to previously circulating strains. The comparison used a collection spanning 2010–2022.
What software was used to analyse the Haiti cholera genomes?
Cynney describes using Lyve-SET for SNP analysis against historical strains. Christine also names ResFinder in the antimicrobial resistance analysis.
Did the analysis prove that cholera persisted in Haiti’s environment?
No. Christine says gaps in recent clinical surveillance and routine environmental sampling prevented the team from distinguishing environmental persistence from undetected circulation through people.
What did the antimicrobial resistance analysis find?
Three strains had AMR profiles that differed from the majority through resistance gene presence or absence. Cynney describes the overall similarity of the resistance profiles as consistent with the SNP evidence of relatedness.
This page was written from a machine transcript of the episode and checked against it. Listen to the episode for the whole conversation.
Show notes
Andrew and Lee talk with Christine and Cynney about the Haiti cholera outbreak
Cynney Walters: https://www.linkedin.com/in/cynney-walters-763111190
Walters et al, “Genome sequences from a reemergence of Vibrio cholerae in Haiti, 2022 reveal relatedness to previously circulating strains” https://journals.asm.org/doi/abs/10.1128/jcm.00142-23