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.
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.
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.