Culture Shock: Reviving Ancient Cholera

Sequencing the DNA of ancient pathogens can offer clues to the evolution of their modern descendants -- and it's cool science, too.

  • by North American Correspondent, MedPage Today

Vibrio cholerae has, on the face of it, very little in common with Mammuthus subplaniforms.

The first item -- the pathogen that causes cholera -- is about a micron wide and couple of microns long and it's everywhere. The second -- also known as the woolly mammoth -- stood up to 11 feet tall at the shoulder and weighed up to 6.6 tons. And the beast is extinct.

But there's some neat science that links them, according to Hendrik Poinar, PhD, principal investigator at the Ancient DNA Centre at McMaster University in Hamilton, Ontario, west of Toronto.

Poinar's lab made the news this week when he and his colleagues reported (in the New England Journal of Medicine) that they had reconstructed the genetic sequence of the V. cholerae bacteria that swept through Philadelphia in 1849.

They previously have sequenced ancient DNA of Yersinia pestis, recovered from bones of victims of the Black Death. And, Poinar told me this week, they are "very close" to having a complete genome for the woolly mammoth.

You might ask why, and I would have to admit there doesn't seem to be a lot of relevance to day-to-day life in the clinic or on the street.

But it's very cool science -- and in the case of cholera, it just might help science deal with a pathogen that, while mostly controlled, still causes thousands of deaths a year. (Y. pestis, by the way, is still a worrisome bug, and agencies such as the CDC advise keeping a wary eye on its rodent reservoirs.)

Cholera swept out of India in the early 1800s and has been responsible for several pandemics since, including the one that caused the Philly outbreak in 1849.

It can still be pretty hard to deal with, as the current outbreak in Haiti attests.

But has the pathogen changed over time? Well, yes. We know that the so-called classical biotype has been largely replaced by the El Tor biotype, the one now affecting Haiti.

That happened about the 1950s, Poinar told me, and no one really understands why. But knowing what earlier forms of the bacterium looked like genetically might offer clues.

And that, in turn, might help science understand the toxicity and virulence of cholera and give hints as to what could happen next.

Unfortunately, old DNA from V. cholerae is hard to find. The bug is enteric and tends to be excreted dramatically, eventually causing death by dehydration. Most of what lingers in the victim is in soft tissues, which degrade pretty quickly after death.

Enter the Mütter Museum in Philadelphia, which has kept specimens collected in 1849 by Dr. John Neill and colleagues in order to examine how cholera affected the intestinal lining.

Working with the museum, Poinar and colleagues took about 4 years to recover enough V. cholerae DNA from one intestinal sample to reconstitute the pathogen's genome.

Dubbed PA1849, it is 95% to 97% identical to the modern classical biotype, Poinar and colleagues found. The differences are 203 single-nucleotide polymorphisms, the absence of three genomic islands, and an increased number of tandem cholera toxin prophage (CTX) arrays.

In other words, it's "pretty close" to the modern classical strain, Poinar said, but sometime between 1849 and the 1950s, the classical V. cholerae acquired three chunks of DNA and lost some CTX arrays.

The latter, for those who don't speak genomic, are the elements that give the pathogen its virulence. The modern classical strain has only one; the El Tor strain has more.

"It's possible that the reduction in those repeats," Poinar said, "has something to do with the attenuation of the classical strain" and the increased success of the El Tor biotype.

That's speculation, but it's now testable, he said.

The study has a couple of interesting sidelights, one ethical and the other practical.

On the ethical front: Neill left little data on the "donors" of the tissue, and it's very likely they came from members of poor and marginalized groups without benefit of informed consent.

Indeed, analysis of the host DNA in this study shows the tissue came from a man and suggests he was black -- his mitochondrial DNA has a pattern that today is found in sub-Saharan Africa.

It's remotely possible that the man still has relatives close enough that genetic investigation might affect them, Poinar noted, so he and his colleagues decided they had to get -- and did get -- an ethical upcheck.

The practical issue: There are likely similar samples on dusty shelves all around the world. It's not a huge stretch to imagine busy administrators deciding to junk them in order to use the space for something more up to date.

Poinar said he hopes that highlighting the historical and scientific value of the Philadelphia specimens will act as a sort of post facto recognition of their unknown donors, and also as a reminder that some of those dusty museum shelves might contain scientific gold.

But what about the mammoth, I hear you ask? Well, there are probably no ethical issues and it's unlikely to help us understand human disease. For my money, it's just wicked cool.