Cholera bacteria colonize Haitian rivers, evolve
April 1, 2020: UF researchers uncovered evidence that the bacteria which cause cholera, Vibrio cholerae, have established an aquatic reservoir in Haitian waterways where they are now adapting and evolving. This marks the first time the pathogenic bacteria are known to have a reservoir outside of the Bay of Bengal, which is traditionally viewed as their home.
UF researchers with the Emerging Pathogens Institute have uncovered the first-ever evidence for cholera bacteria establishing in a natural water environment outside the Bay of Bengal in the northern Indian Ocean. The bacteria are also adaptively evolving within their new aquatic habitat, the researchers reported Monday in the journal PNAS.
While cholera is thought of as an age-old human disease of poverty, the bacteria that cause it — toxigenic Vibrio cholerae — are able to persist in natural water systems for extended periods of time. V. cholerae has been documented in fresh, estuarine and marine water in the Bay of Bengal area which scientific consensus asserts is their only natural home outside of human hosts. This line of thinking argues that the bay provides the only watery habitat on earth where the bacteria are established, and the only place they evolve outside of a human, because it contains the right mix of nutrients and humans to persist over time.
“I had serious doubts that cholera only survives and evolves in the Bay of Bengal,” says study author Afsar Ali, a research associate professor with UF’s Emerging Pathogens Institute and College of Public Health and Health Professions, department of environmental and global health. “In this study, we asked: does cholera persist in Haiti’s aquatic environment, and do the bacteria only evolve within infected humans, or do they also genetically evolve in aquatic reservoirs?”
The research team, which includes EPI Director J. Glenn Morris, M.D., found evidence that V. cholerae bacteria have become established in Haitian rivers and estuaries, and that they are actively mutating in ways that could increase their adaptation and fitness to a new habitat. Both findings contradict established dogma. They also point to a troubling consideration: in the future cholera may not only be a disease of poverty, but also one of environmental contamination.
The study was co-led by Carla Mavian and Taylor Paisie, who both work in the lab of the study's senior author, Marco Salemi. All three are affiliated with both the EPI and UF's College of Medicine, department of pathology, immunology, and laboratory medicine.
Scanning electron micrograph of Vibrio cholerae bacteria. Image by Darthmouth College Electron Microscope Facility, now in the public domain, and used here with no changes under a creative commons license.
“Cholera is a waterborne disease,” Ali says. “Vibrios are highly sensitive to temperature. In between waves of epidemic, there is a hypothesis that they remain in the environment as a dormant cell. Their metabolism lowers, they barely survive through the winter, and then when the temperature warms in the spring they rise up and spillover into people.”
The bacteria were accidentally introduced to Haiti by United Nations peacekeepers who came to assist in the aftermath of a devastating 7.9 magnitude earthquake in January 2010. A subsequent cholera outbreak in October sickened 665,000 people and caused more than 8,100 deaths, according to the U.S. Centers for Disease Control. Prior to the epidemic, there had been no reports of cholera in Haiti for a century. Seasonal epidemic waves followed. The particular strain that was introduced is known as V. cholerae serogroup O1 biotype Ogawa, which is traceable to the Bay of Bengal.
“Vibrio cholerae are optimized for existing in the human gut, where they have all the nutrients they need in a tight, cozy space,” says Salemi, a UF professor of pathology. “In a way, it is an ecological disaster when they are released from a human and cast out into the environment. It’s always been thought that water was essentially a dead end for them.”
The aquatic habitats of cholera bacteria are akin to nutrient deserts in comparison to the resource-enriched human gut.
Regions around the Bay of Bengal, where cholera is endemic, are accustomed to seeing seasonal epidemic waves. The bacteria persist in the water over the winter, and tend to begin replicating when temperatures warm. They then spillover into humans who consume contaminated surface water, and when human-to-human transmission establishes, an epidemic rapidly takes hold with the potential to infect hundreds of thousands of people within a few week’s time.
The bacteria proliferate in a victim’s gut and cause acute diarrhea and dehydration. Medical care with antibiotics and rehydration therapies can help an infected person recover, but the dehydration can be so fast and severe that some victims die within several hours. In areas of the world without flush toilets, the bacteria-laden stool can quickly contaminate water sources that are also used for bathing or drinking, or bacteria can cling to a person’s hands and quickly sicken another individual.
The researchers isolated environmental toxigenic V. cholerae O1 strains from rivers and estuarine sites in the Ouest department of Haiti between 2012 and 2015. They found that the abundance of aquatic V. cholerae was linked with both temperature and rainfall, which suggests that their presence was independent of fecal contamination sources.
They also isolated strains from clinical cases sampled during the same timeframe in outbreak waves in Ouest and Artibonite departments.
They found evidence that the bacteria persisted in the water in Haiti in between seasonal spillover events that produced waves of epidemics in people.
“There was one year when cholera was absent from the island,” Salemi says. “But during that year, we show that cholera was surviving completely independently in the water, in the river streams, it kept replicating and accumulating mutations outside the human body.”
The study used whole genome sequencing and a phylogenetic likelihood maximum test to analyze the environmental and clinical samples. This elucidates evolutionary relatedness and can show which V. cholerae strains begat which strains, where in the bacterial genome mutations were occurring, and if the rate of mutation was changing.
“The interesting thing is that the mutations in the environmental strains specifically affected genes in the genome that are known to be genes which help the bacteria survive better in the water,” Salemi says. “The genes that are more useful when the bacteria are replicating in humans were not affected or were shut down in these environmental samples, but the ones that give the bacteria an advantage in surviving in the environment were all accumulating new mutations.”
It makes perfect sense that the rate of mutation was higher in the genomic area associated with environmental survival, Salemi says, as the bacteria is already perfectly optimized for survival in a human gut and transforming it into a V. cholerae replicator.
“This is a game changer in terms of our understanding of the different epidemics of cholera over time,” Salemi says. “This is a story about an organism that can adapt and evolve to two different ecological niches, even one that is potentially very hostile to it.”
The results hold implications for public health measures to limit cholera epidemics. First, the authors argue that mass vaccination campaigns are a better strategy than ring vaccination efforts, which attempt to encircle an epidemic with a vaccinated populace to surgically extinguish transmission. Mass vaccination is a better strategy if the bacteria are environmentally endemic because if the waterways are contaminated with V. cholerae, then spillover events could potentially happen anywhere.
Second, Ali argues that governments with at-risk populations should track outbreaks to understand seasonal signatures and offer chorine tablets to citizens at certain times of the year to make sure that surface water be treated before consumption or drinking.
“Environments are very complex systems. I don’t think its correct to say that V. cholerae lives only in the Bay of Bengal, and that if it moves into new areas via ships or humans or any other means, it will then simply die off from that new environment,” Ali says. “That is what we show in this paper: they can persist, adapt and evolve to cause disease in that new home with potential to move to another new landscape.”
And if Vibrio cholerae can evolve and adapt in Haiti, it could potentially become endemic to other aquatic reservoirs of the planet, too.
Written by DeLene Beeland
Top photo caption and credit: Meer Alam collects a water sample in Bellevue, near Gressier, Haiti in July 2013. Alam is a biological scientist with UF's College of Public Health and Health Professions, department of environmental and global health, and an affiliate of the Emerging Pathogens Institute. (Photo by Makendy Jean Luma, a Haitian partner on the research project.)
Read the paper in PNAS here.
Read Afsar Ali’s EPI bio here.
Read Glenn Morris's bio here.
Read Marco Salemi’s EPI bio here.