Researchers in Britain Have Determined
The Genetic Sequence of Bubonic Plague
 Marilyn Chase / Wall Street Journal 4oct01

[Nature Science Update Article below | Nature Abstract below]

Scientists at Britain's Wellcome Trust and their colleagues have figured out the genetic blueprint of bubonic plague, also known as the "Black Death."

Plague, one of the most terrible scourges in history, has wiped out hundreds of millions people world-wide, including one-third of Europe's population in the 14th century. Lethal when untreated, plague has resurfaced as a concern in recent weeks because of its potential to be used as weapon of biological warfare.

Treatable with common antibiotics such as streptomycin, plague still sickens about 3,000 people a year world-wide. In the U.S., about a dozen people contract plague each year, mainly in the Southwest, where it is transmitted by fleas carried by small rodents such as prairie dogs, squirrels and chipmunks. In its most common form, bubonic plague is 70% fatal if untreated. More rarely, plague infects the lungs, and this form -- called pneumonic plague -- can be spread through aerosol droplets and, if untreated, is nearly 100% fatal. On Madagascar, scientists recently discovered a drug-resistant strain.

The sample of plague bacteria used in the three-year, half-million-dollar project came from an American veterinarian who died after a plague-infected cat sneezed on him as he tried to rescue it from underneath a house.

The scientific team included researchers from Wellcome Trust's Sanger Center; the Defense Science & Technology laboratory at Porton Down, Wiltshire; the London School of Hygiene & Tropical Medicine; and St. Bartholomew's Hospital and Imperial College, London. Wellcome Trust, an independent research-funding charity, said it hopes the work will lead to more and better drugs for the disease, as well as a new vaccine, which is being produced and tested by Britain's Ministry of Defense.

"This is a big announcement ... a breakthrough," said Paul Keim, professor of microbiology at Northern Arizona University, of Flagstaff, Ariz. Dr. Keim said Wellcome Trust has been sharing its plague genome as it unfolded, leading to a boom in plague research. Dr. Keim himself has used the genetic sequence to develop a high-resolution DNA fingerprinting system that he has in turn shared with the Centers for Disease Control and Prevention in Atlanta for use in rapid detection and diagnosis of plague cases. Other beneficiaries include the Pasteur Institute in Paris, where researchers are working on the genes that make plague so deadly.

"When the sequence became available, we were able to do in a day the work that previously would have taken five to 10 years," said Dr. Keim, adding he is working on plague genes that mutate rapidly and dramatically.

The research team has published the sequence both on the Internet and in Thursday's issue of the British journal Nature.

Acknowledging the fears about bioterrorism, the scientists believe the benefits of making the information public "greatly outweigh the risk of someone getting it and using it for nefarious purposes," said Rick Titball, of the British Defense Ministry's Porton Down laboratory.

Black Death's DNA
The plague bacterium joins the ranks of completed genomes
John Whitfield / Nature 4oct01

Short of the DNA of one of the four horsemen of the apocalypse, we now have the next best thing. Researchers have sequenced the plague bacterium's genome1.

The 4.65 million DNA letters will be "the basis of all future work", on plague, says Julian Parkhill of the Sanger Centre, Cambridge, UK, who led the sequencing project.

The sequence will be critical in the design of antibiotics and vaccines to treat the disease. It is a yardstick against which potential new plague threats - whether created by natural selection or as biowarfare agents - can be measured.

It will also teach us a great deal about how infectious diseases evolve. The plague bacterium Yersinia pestis is a recent descendent of the benign, gut-dwelling bug Y. pseudotuberculosis. "Two thousand years ago it gave you a mild tummy ache," says team member Brendan Wren, a geneticist at the London School of Hygiene and Tropical Medicine.

Flea jump

Within a few hundred years - an evolutionary eye blink- Y. pestis learned to leap between fleas and mammals, to live in the blood instead of the intestine, and to cause the swelling, coughing and haemorrhaging of mediaeval nightmares. It did so by kitting itself out with a new genetic wardrobe, probably pinched from other microbes.

Key to the bacterium's rapid evolution could be a tendency to shuffle chunks of its chromosome. This seems to be common in pathogens, says infectious disease researcher Mark Achtman of the Max Planck Institute for Infection Biology, Berlin.

Y. pestis carries genes for insecticidal toxins that are now deactivated but may have helped it make the first jump into fleas. Indeed the bacterium's new lifestyle left it with about 150 such pseudogenes - redundant, gene-like stretches of DNA no longer switched on in the organism. In time these may decay or be lost from the sequence altogether.

The sequence also boasts many candidate disease-causing genes, although "at this stage the evidence is only circumstantial", says Rick Titball, another member of the sequencing team, who studies plague at the UK Defence Science and Technology Laboratory, Porton Down.

To pin these genes down, researchers will need to sequence other closely related bacteria, such as Y. pseudotuberculosis, says Achtman. Looking at the plague genome in isolation reveals all sorts of changes, "but they're not necessarily linked to increased virulence," he cautions.

Comparisons between the three plague strains should also help. Each strain is associated with a particular pandemic. Antiqua caused the first recorded plague between 500 and 700 AD; Medievalis caused the mediaeval Black Death and the Great Plague of seventeenth-century London, among others. Orientalis, the dominant modern strain, is the one that has now been sequenced.

Plague's youth as a disease may explain its drastic symptoms. Many researchers believe that evolution pacifies pathogens, in order to reduce hosts' immune response. Many damaging infectious diseases - tuberculosis, anthrax and typhoid - seem to have originated in the past few millennia.

But the main drive in Y. pestis' evolution is probably to move better between rodents and their fleas, which bite humans only as a last resort. "The plague is only a sideshow to what Y. pestis is really doing," says Parkhill.

Lying low

These days, bubonic plague - cause of the characteristic underarm swellings - can be treated with antibiotics if diagnosed early enough. Public hygiene can prevent its flea-borne spread.

But the disease still kills about 2,000 people each year, mostly in Africa and Asia, and the incidence is rising. A recent case in Madagascar was resistant to multiple antibiotics. "It's a worrying trend," says Titball.

In a small percentage of cases, bubonic plague reaches the lungs, becoming pneumonic plague, with mortality close to 100%. No one knows what causes this transition.

Pneumonic plague also spreads through the air; it is thought to have caused the major historical pandemics. Today an unsuspecting carrier on a plane from an infected area could trigger a severe outbreak.

Titball's team has a plague vaccine currently in clinical trials. Even if it works, there's no telling how long the vaccine will be effective he says: "New vaccines, antibiotics and diagnostic tools are urgently needed." Because the bacterium can lurk in animals, it is unlikely that we will ever eradicate it.

Weapon of war

Plague is the original biological weapon. In 1347, the Tartars, laying siege to the Genoese-controlled Black Sea port of Caffa, hurled the bodies of their plague victims over the city walls. When infected Genoese sailors returned to Italy, the Black Death killed one third of Europe's population between 1347 and 1351.

There are concerns that governments or terrorists could spread plague again. Scientists defecting from the former Soviet Union claimed to have developed an antibiotic-resistant strain of Y. pestis, for example.

It would be a complex challenge for a terrorist group to release it into the air Rick Titball, UK Defence Science and Technology Laboratory

Plague still kills about 2000 people each year.

This has led to a debate about whether releasing genomic information for virulent diseases, such as plague or smallpox, might aid malicious science. Titball believes in openness. "The information available is of much greater advantage to people defending against biological warfare than to those intending to use it," he says.

Besides, Titball adds, "it's not a difficult organism to culture, but it would be a complex challenge for a terrorist group to release it into the air".

"These are pretty dreadful diseases already," Titball points out. "We should focus on fighting them in the form they're already in, rather than worrying about theoretical future threats."

References

Parkhill, J. et al. Genome sequence of Yerisina pestis, the causative agent of plague. Nature, 413, 523 - 527, (2001).

Genome sequence of Yersinia pestis, the causative agent of plague
Nature, 413, 523 - 527, 4oct01

J. PARKHILL*, B. W. WREN†, N. R. THOMSON*, R. W. TITBALL‡, M. T. G. HOLDEN*, M. B. PRENTICE§, M. SEBAIHIA*, K. D. JAMES*, C. CHURCHER*, K. L. MUNGALL*, S. BAKER*, D. BASHAM*, S. D. BENTLEY*, K. BROOKS*, A. M. CERDEÑO-TÁRRAGA*, T. CHILLINGWORTH*, A. CRONIN*, R. M. DAVIES*, P. DAVIS*, G. DOUGAN^II, T. FELTWELL*, N. HAMLIN*, S. HOLROYD*, K. JAGELS*, A. V. KARLYSHEV†, S. LEATHER*, S. MOULE*, P. C. F. OYSTON‡, M. QUAIL*, K. RUTHERFORD*, M. SIMMONDS*, J. SKELTON*, K. STEVENS*, S. WHITEHEAD* & B. G. BARRELL*

* The Sanger Centre, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK
† Department of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London WC1E 7HT, UK
‡ Chemical and Biological Sciences, Dstl, Porton Down, Salisbury, Wiltshire SP4 0JQ, UK
§ Department of Medical Microbiology, St Bartholomew's and the Royal London School of Medicine and Dentistry, London EC1A 7BE, UK
^II Centre for Molecular Microbiology and Infection, Department of Biological Sciences, Imperial College of Science, Technology and Medicine, London SW7 2AZ, UK

Correspondence and requests for materials should be addressed to J.P. (e-mail: parkhill@sanger.ac.uk) or B.W.W. (e-mail: brendan.wren@lshtm.ac.uk). The sequences have been submitted to EMBL under the accession numbers AL590842 (chromosome), AL109969 (pPCP1), AL117189 (pCD1) and AL117211 (pMT1).