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The pathogen detectives: sourcing the post-earthquake cholera outbreak in Haiti

The views expressed are those of the author and are not necessarily those of Scientific American.


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Natural disasters such as earthquakes can have far-reaching effects beyond the damage caused on the day they occur. The 2010 earthquake in Haiti damaged the already limited sanitation systems leading to areas without adequate toilet and washing facilities; perfect for the spread of infection diseases. Sure enough 9 months following the quake there was an outbreak of cholera which quickly spread across the whole country.

Cholera exists in the environment in a non-pathogenic form, which becomes dangerous when it picks up the genes for the cholera toxin. These genes are found within bacteriophages (viruses that infect bacteria) and these bacteriophages can spread the toxin genes through a cholera population, mobilising them to their pathogenic forms. Since 1817 there have been 7 major cholera pandemics, each caused by a different subgroup of the Cholera toxin. However none of these pandemics had ever before reached Haiti.

The evolution of cholera pandemics. Bacteriophage deliver the genes for toxicity which are incorporated into the bacterial genome. The bacteria from each pandemic can be identified by specific "genomic islands". Image from reference 1.

There were two possibilities for the source of the outbreak in Haiti. One was that local non-pathogenic cholera had picked up the toxicity from bacteriophages. The other was that it had come from external sources, namely aid workers and United Nations troops. The first reported case of cholera was in the town of Mirebalais, which is directly downriver from a United Nations camp of troops from Nepal.

Various different types of evidence were put together to work out the source of the infection. News reporters found improper sewerage drainage at the UN camp was leading to waste ending up in the river.  There was an cholera outbreak in Nepal shortly before the troops were deployed and as none of them showed cholera symptoms during the pre-deployment medical, no follow-up tests for the disease were done (cholera can be carried asymptomatically). The spread of the disease also followed the waterway, along rivers downstream of the camp.

The genetic big-guns of whole genome sequencing were used to determine exactly what strain of cholera was causing the epidemic. The strains causing the disease in Haiti were shown to be identical clones, suggesting a single infectious source. Comparing DNA at specific genetic islands showed the Haiti strain was in the same subgroup as strains found in Eastern Asia, but not in the Americas. The Haiti bacteria were shown to be in the same subgroup as bacteria from Nepal and Bangladesh and most closely related to the Nepalese bacteria.

Transmission electron microscope image of V. cholerae. Image credit below.

It took about three years of research before it was finally an accepted consensus: the outbreak had been caused by UN troops stationed in Haiti and was not a local strain gone rogue. Whole gene sequencing proved a vital tool in solving the mystery, and in the reference the authors point out at had this been used as a first response, rather than only being pulled out in the later stages of the investigation, it could have been solved a lot quicker. Another limiting factor was that there is no single public database of the genome sequences of recurring pathogens from different geographical locations. The development of such a database, along with cheaper and quicker whole genome sequencing, would make it far easier in future to trace the source of epidemics as they arose.

Reference 1: Orata FD, Keim PS, Boucher Y (2014) The 2010 Cholera Outbreak in Haiti: How Science Solved a Controversy. PLoS Pathog 10(4): e1003967. doi:10.1371/journal.ppat.1003967

Credit for image 2: Dartmouth Electron Microscope Facility.

S.E. Gould About the Author: A biochemist with a love of microbiology, the Lab Rat enjoys exploring, reading about and writing about bacteria. Having finally managed to tear herself away from university, she now works for a small company in Cambridge where she turns data into manageable words and awesome graphs. Follow on Twitter @labratting.

The views expressed are those of the author and are not necessarily those of Scientific American.





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  1. 1. tuned 10:48 am 04/6/2014

    What is not being said is that those U.N. troops could not have been following proper sanitary procedures.

    Link to this
  2. 2. YangHui 7:09 pm 04/7/2014

    It actually does say that:

    “News reporters found improper sewerage drainage at the UN camp was leading to waste ending up in the river”

    It’s still a point worth mentioning though. It’s definitely not something limited to the UN, but all aid workers should keep in mind that they need to help build sanitation systems, and especially for their own camps or others holding foreigners, not because the lives and comfort of foreigners are more valuable than those of locals but because they are most likely to carry dangerous infectious diseases.

    Link to this
  3. 3. aminatakone 8:53 am 07/2/2014

    We all know that the Minustah troops were involved in the spread of cholera, but it is important to keep in mind that only good sanitary infrastructures and sensitazion campaigns will end the spread of the disease. In this respect, since 2010, a think tank (Global Alliance Against Cholera) has been created. The GAAC is composed of senior representatives from public, private and international organisations, they pool their skills and energy for an efficient and sustainable fight against cholera in the African continent as well as the Caribbean.
    A collective action is most likely the key to overcome the transmission of cholera and to reduce the death pool. However, the financial support granted by the United Nations is not sufficient, thus it is essential to gather more money from international donors and public authorities in order to support the program for the elimination of cholera.

    See more at: http://en.choleraalliance.org/

    Link to this

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