The lab that did the analysis, at McMaster University in Ontario, is well-known for extracting DNA from fossils many thousands of years old, such as woolly mammoth bones.
The team, led by geneticist Hendrik Poinar, was not so sure about finding cholera from less than 200 years ago.
The microbe, formally called Vibrio cholerae, infects only the intestines, causing severe diarrhea, and does not show up in a victim's bones. So unless someone had made a point of storing some of the soft tissue in a jar, the scientists were out of luck.
Care to guess who had something like that sitting on a shelf?
Right the first time. The Mütter Museum of the College of Physicians of Philadelphia has at least six intestines from cholera victims in 1849.
"Our wet specimens are very well inventoried," said curator Anna Dhody, a coauthor of the DNA study. "We know pretty much exactly what we have and where it is."
Still unclear was whether the bacterial DNA would be too degraded to decipher, but the situation was promising, Dhody said. The tissue was preserved in alcohol, and the bottles appeared to have been unopened since 1849. Most were sealed off with an elaborate four-layer covering: a lead disk, a piece of pig's bladder, a scrap of parchmentlike material, and finally a coating of black pitch.
The researchers used scalpels to extract six tissue bits the size of postage stamps - a procedure museum officials allowed after deciding it could yield valuable information.
The team was indeed able to recover cholera DNA from one sample - though it was highly fragmented, its average length fewer than 50 base pairs, said lead author Alison Devault, a Ph.D. candidate in McMaster's anthropology department. To put that in perspective, V. cholerae's entire genome measures about four million base pairs, while the human genome is three billion pairs.
The scientists used a series of chemical and computer techniques to fish out fragments that appeared to be from the 1849 bacteria, matching them as best they could to the framework of a known cholera genome from the mid-20th century.
The patient's intestine contained fragments from the DNA of multiple cholera-causing cells, so the scientists had multiple copies of each fragment - a good thing, for many were damaged. By looking at many versions of each fragment, they could guard against errors - almost like looking at multiple damaged versions of the same jigsaw puzzle.
The analysis revealed the 1849 version of the bacteria was 95 to 97 percent similar to the "classical" mid-20th-century variety, the authors reported. The version now present in parts of Africa, Asia, and the Caribbean, called "El Tor" after the Egyptian city where it was found, is somewhat less similar.
Jun "Jay" Zhu, associate professor of microbiology at the University of Pennsylvania's Perelman School of Medicine, praised the study.
Until now, scientists have not known for sure what form of the bacteria caused the 19th-century outbreaks in Philadelphia and other cities, said Zhu, who studies the genetics of modern cholera.
"We always suspected that the classical strain caused all those pandemics," Zhu said. "This is the first clue."
The modern version of cholera is somewhat milder than the 1849 and other classical varieties, as it contains only one copy of a genetic recipe for the toxin that causes diarrhea, he said. The classic type, with multiple copies, killed people so fast that it had not as much chance to spread.
Among them was the Mütter Museum patient identified only as 3090.13. The McMaster genetic analysis determined that he had African ancestry. In their study, the authors said such specimens needed to be handled with respect and sensitivity, noting that in the 19th century it was common for specimens to be taken from minority and poor patients without consent.
George M. Wohlreich, the College of Physicians' chief executive officer, said the study shows that such collections are more than museum exhibits.
The intestine samples were collected by prominent 19th-century physician John Neill, before the field of medicine knew the disease was caused by bacteria. Now, 165 years later, we have its DNA.
"One can use the dead to inform the living," Wohlreich said, "and hopefully to prepare for the future."