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Using genomics to track the global spread of cholera

In this video, Daryl Domman discusses his research with Josie. Daryl is a researcher studying the evolution and transmission of cholera.
I have with me here Daryl, who’s going to tell us about his research into the transmission of cholera. So Daryl, I thought cholera was a disease of the past, is it still a problem now? So you’re right in that cholera has been a scourge since at least the 1800s. So six pandemics of cholera, we’re currently in the seventh pandemic started in 1960. It’s the worst pandemics we’ve seen of cholera yet, the current situation in Yemen, where the epidemic is quickly reaching 1 million people absolutely is a reminder that cholera has a strong foothold in the modern world. So how does cholera spread?
So cholera is the classic example of a waterborne disease, so faecal contamination of water sources, and people get this by ingesting the water contaminated with the real cholera or food that’s been prepared with contaminated water. And so are there typing schemes available that allow people to track how cholera spreads. Yeah, so historically, we’ve used serotyping of the O-antigen and the presence of the cholera toxin which is actually anaphase. Other typing techniques that we’ve used our PFG or ribotyping, but really what happened with the use of all of these techniques is that there was a lot of confusion as to what was actually going on at a global level within cholera epidemiology.
And so what the whole genome sequencing has allowed us to do is actually unify all of these things into something that makes sense, like a cohesive framework for us to understand how cholera is moving across the globe and whether or not epidemics, say in Africa or Latin America are actually connected to one another. OK, so in the course, already we’ve heard about John Snow how he managed to track transmission of cholera around London using epidemiology, why do we need these tightly schemes or genomics and those kind of things you’ve just described. No discussion of cholera can be complete without John Snow.
And it was just absolutely incredible what he was able to do in London at the time, I think it was 1854. But really what we’re able to do now with molecular techniques and especially with whole genome sequencing is just have such a better picture of what’s happening with cholera. So in London, he was able to track the individual cases around the Broad Street Pump, but now we’re looking at how cholera affects individuals, to households, to communities, all the way to how cholera is spreading across a city. So really being able to link up who or where, perhaps cholera is moving and then even to a larger scale across continents and globally.
And so how is your research using genomics, how has that helped you learn about how cholera is spreading over these large distances? Yes, what we’ve been able to do is focus on the two regions most affected by cholera, historically. So that’s been Africa, which is currently the continent that has the highest burden of disease for cholera and Latin America. And so what we’ve really done is sequenced a lot of samples from both of these areas, including with additional samples from Asia and really piecing together the puzzle of how cholera is moving across the globe. So what we’ve been able to show is that cholera enters into Africa at least 11 times since the 1970s, all from strains originating in Asia.
And also in Latin America, we’ve been able to show that again, introductions of pandemic strains of cholera into Latin America were responsible for some of the largest epidemics we’ve seen, such as in Haiti in 2010, and in Peru in 1991. OK, so specifically how are these importations happening, is it via people or is it via water? Yeah, that’s a great question actually. So we do believe that it’s through human-to-human movement, primarily. Some say that large transport could happen through the releasing of ship water into different ports, but really this is mediated all by human movement. Yeah, and you wouldn’t have been able to get that from epidemiology alone, you need the typing data to answer that.
Absolutely, so through whole genome sequencing, we were able to use snips to draw a really robust phylogeny’s, which allow us to then make robust inferences on how cholera has moved throughout the globe with really high resolution. Thank you very much, Daryl. Thanks Josie.

In this video, Daryl Domman discusses his research with Josie. Daryl is a researcher studying the evolution and transmission of cholera. In this video, we will learn how Daryl uses whole genome sequences in his research, and what this has enabled him to find out about how cholera has spread across the globe in recent decades.

In Comments, can you give an example of how Daryl uses genome sequencing to help identify and track the global spread of cholera?
Why is this helpful? Can you give any examples of the use of genome sequencing to track disease in your country?

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