The Washington Post - USA (2020-07-28)

E4 EZ EE THE WASHINGTON POST.TUESDAY, JULY 28 , 2020

“Until 2015, we thought that plague was maybe a 3,000-year- old disease.” Scientists and archaeologists now believe, however, that the plague bacteria, which caused the medieval Black Death that killed up to half of Europe’s population, infected humans roughly 5,000 years ago in the Stone Age. The bacteria, after it had entered the bloodstream and likely killed the host, circulated into the pulp chamber of teeth, which kept its DNA insulated from millennia of environmental wear and tear. In the past decade, scientists have been able to extract and analyze that DNA.

Stone Age plague The Stone Age plague was, however, an ancestor with a slightly different genetic identity. Tracking how those differences evolve helps infectious-disease biologists better understand what causes disease and how to prepare for current outbreaks. The plague bacteria in the Stone Age, for example, lacked the genes necessary to jump from fleas to humans, which likely spread the Black Death widely. Without the flea gene, the disease probably used another ani- mal transmitter that came into contact with humans. I n 2018, a University of Copenhagen team published the first evidence, based on early data three years before, that the ancient plague bacteria, found in a Swedish

EPIDEMICS FROM E1 settlement, had the power to kill and may have threatened life in the age’s “mega-settlements” that could spread diseases quickly. “It probably was the first pandemic,” said Simon Rasmussen, a genomicist at the university and lead researcher on the plague study. In the Stone Age, also called the Neolithic period, humans made unprecedented moves to gather in large settlements with up to 10,000 people in close quarters with animals and virtually no sanitation. “It’s the textbook place of where you could have a new pathogen,” he said. Paleogenomics has also al- lowed archaeologists to fill in one of the biggest silences in the archaeological record: disease. Pathogens rarely leave traces on bones, and populations without writing could die out without any readable record of the cause. With the ability to read traces of DNA preserved in teeth, histori- ans are learning about the organ- isms inside ancient humans. Kristian Kristiansen, a Univer- sity of Copenhagen archaeologist and a co-author of the plague study, believes his group’s research illuminates the causes of a Stone Age demographic transfor- mation, called the Neolithic de- cline, which archaeologists have long studied. Settlements at the time were disappearing faster than they were appearing, and within a few hundred years, most of the population had been replaced by mi- grants from the Eurasian Steppe. Researchers had only ever hy-

pothesized that disease may have played a role in crippling the native population before it was overtaken, but now they have evidence, Kristiansen says.

Changing history “The steppe migrations would not have succeeded without the plague... and [those living in what is now Europe] would not all have spoken Indo-European languages,” Kristiansen said. “Later prehistory has been turned upside down to say the least.” In 2018, a paleogenomics team analyzed ancient teeth from Neo- lithic sites in present-day Ger- many and discovered the hepati- tis B virus stretched back at least 7,000 years. Another study the

same year extended our knowl- edge of the history of parvovirus B19 from a few hundred years to 6,900 years. Parvovirus B19 causes a mild rash in humans and leads to outbreaks in the United States every few years In February, researchers at the Massachusetts Institute of Tech- nology published evidence that types of Salmonella bacteria, which sicken about a million people in the United States every year, were afflicting humans 6,500 years ago. Microbiologist Felix Key identified Salmonella DNA in teeth recovered from burial sites near the Volga River in present-day Russia, where archaeological evidence has shown that humans began to abandon foraging for pastoral living. The

Salmonella DNA in their teeth is the first evidence, Key says, that the adoption of this lifestyle in close contact with animals may have introduced pathogens to humans. “This ancient DNA could give us the means to prove or dis- prove the hypothesis that the Neolithic revolution was the major event for introducing diseases into humans,” said Key, who is now at the Max Planck Institute for the Science of Human His- tory. “My hunch is that it did facilitate the disease, because humans and animals were co- housed.” Like many paleogenomicists, Key uses dentist tools and dons what looks like a hazmat suit that blocks possible DNA contamina- tion from teeth recovered from settlements thousands of years older than the Roman Empire.

DNA extraction methods New methods of extracting DNA that were developed for medical purposes have made paleogenomics possible in the past decade. After using dentist tools to recover and pulverize material locked inside a tooth, molecular biologists use a technique called “shotgun sequencing” to extract all genetic material without needing to know what to look for. Decrypting the data then re- quires that bioinformatic special- ists can match the genetic identi- ties to known pathogens. As the disease database grows, it be- comes easier to identify signals from noise. Archaeologists then

have the task of putting human disease into historical context. The process is expensive, and it’s dominated by labs in Europe with equipment and funding. Conducting a complete survey of teeth can cost upward of $1 million. That depends, still, on a team’s good fortune in finding enough ancient teeth that have experienced the right conditions over millennia to preserve pathogen DNA. In the study of the Salmonella bacteria, Key’s team analyzed 3,000 samples and found just eight with preserved Salmonella bacteria. Rasmussen, of the C openha- gen plague study, said that, while he is fairly certain his team’s evidence describes the oldest human pandemic, more DNA samples must be found and analyzed. The DNA used in his study come from just one small settlement in the area of modern-day Sweden. To prove a pandemic, Rasmussen said, scientists will need to find DNA evidence in some larger sites — in other parts of Europe. Even so, Stone said, paleo - genomics has shown that humans have been in “an arms race with pathogens” for thousands of years. “Periodically, pathogens jump into humans,” she said, “and it’s really easy to become compla- cent when you don’t happen to have a pathogen affecting large segments of your population at the moment. But you let those resources go at your peril, which we’re seeing right now.” [email protected]

E vidence in teeth suggests early plagues forced epoch-defining changes

ISTOCK A close-up view of a jawbone. Paleogenomics, a nascent field that studies DNA in ancient teeth, has amounted to a “revolution” in understanding disease history, a microbiologist says.

BY DIANE BERNARD

I

n March 1942, 33-year-old Anne Miller lay delirious in New Haven Hospital, death- ly ill from septicemia that she developed following a miscarriage a month before. Dur- ing her stay at the Connecticut hospital, doctors tried every cure imaginable — from sulfa drugs to blood transfusions — as her tem- perature at times spiked past 106 degrees. “She was just incurable,” Eric Lax, author of “The Mold in Dr. Florey’s Coat,” said in a phone interview. “It was like somebody today with covid-19 who is going down the tubes.” Desperate, her doctors ac- quired a tablespoon of an experi- mental drug and gave her an injection. Overnight, her temper- ature dropped. A day later, she was up and eating again. The miracle drug that saved her life? A virtually unknown substance called penicillin. As researchers around the world chase a vaccine and treat- ments for the novel coronavirus, the quest echoes the race to mass-produce penicillin in the United States and Britain during World War II. In the days before antibiotics, something as simple as a scratch or even a blister could get infected and lead to death. Before the beginning of the 20th century, the average life expectancy was 47 years, even in the industrial- ized world, according to the Na- tional Institutes of Health. Infec- tious diseases such as smallpox, cholera, diphtheria and pneumo- nia cut life short. No treatment existed for them. Scottish biologist Alexander Fleming had discovered the penicillin mold in London in 1928. Fleming attempted to extract the mold’s active substance that fought bacteria but was unsuc- cessful, and he gave up experi- mentation, according to Lax’s book. As war broke out in Europe in 1939, Australian doctor Howard Florey obtained funding from the Rockefeller Foundation in New York to study Fleming’s discovery further at the University of Ox- ford. Along with brash German emigre Ernst Chain, and meticu- lous assistant Norman Heatley, he worked to generate penicillin’s active ingredient. But in the course of their research, Florey confronted an obstacle: Extracting the active ingredient from the mold was terribly difficult. Time after time, the delicate mold would dissolve in the process of extraction, leaving scientists frustrated. The tablespoon of penicillin that cured Anne Miller represent- ed half the entire amount of the antibiotic available in the United States in 1942. To give her a full treatment, doctors had to collect her urine, extract the remaining penicillin from it at about 70 percent potency, and re-inject it, according to Lax’s book. Through trial and error, the team had discovered that penicillin was much more effective and

safer in fighting bacteria in animals than sulfa drugs, which were the treatment for infections at the time. Discovered by Ger- man scientists in the 1930s, sulfa drugs had severe side effects, and researchers were motivated to find an alternative. As they tried to cultivate penicillin, they began a few human tests. In late summer 1940, Albert Alexander, a 43-year-old Oxford police officer, scratched his face while working in his rose garden. The scratch became infected by streptococci and staphylococci and spread to his eyes and scalp, according to “The Mold in Dr. Florey’s Coat.” A few weeks later, he was admitted to an Oxford University hospital and given doses of a sulfa drug for a week. Not only did the drug not cure him but it gave him a terrible rash. Lax writes that Alexander was in “great pain” and “desperately and pathetically ill” for months as he lay in the hospital with no cure available. The abscesses on his face and arms were “oozing pus everywhere,” Heatley wrote in his diary, Lax notes, and Alexander’s left eye became so infected that in February 1941 it had to be re- moved. The bacteria continued eating at him and soon spread to his lungs and shoulders. Desperate, doctors gave him 200 milligrams of penicillin, the largest individu- al dose ever given at the time, and then three doses of 100 mg every three hours, according to Lax. Within 24 hours, there was a “dramatic improvement,” Heat- ley wrote. Alexander’s fever went back to normal and his appetite returned. As with Anne Miller, researchers collected his urine to extract penicillin to re-adminis- ter. By the end of February, Alexan- der’s treatment had used up the nation’s entire supply of penicillin, according to Lax. After 10 days of stability, his condition deteriorated without any more of the drug. A second course would have helped him to fully heal, but there was no more to give him. “Florey and the others watched helplessly as a flood of septicemia swept through him. On March 15, he died,” Lax writes. Heartbroken, Florey, Chain and Heatley continued to hunt for methods to produce more penicillin. Meanwhile, the Battle of Britain raged around them. From summer 1940 into the next year, thousands of civilians were killed each month in bombings on all the major cities of Britain. In fall 1940, 50 million pounds of bombs were dropped on London alone, Lax writes. Working under tremendous pressure with limited supplies, the Oxford team also realized penicillin’s urgent value in treat- ing wounded soldiers and civilians. “They knew that of the 10 million soldiers killed in World War I, about half died not from bombs or shrapnel or bullets or gas but rather from untreatable infections from often relatively

ration of war on the United States by Germany and Italy changed not only the course of the war but also the course of the develop- ment of penicillin, Lax writes. With millions of American lives now at stake, penicillin was no longer just a scientific fascination to U.S. pharmaceutical companies — it was a medical necessity. Ten days after the Pearl Harbor attack, pharmaceutical companies began escalating penicillin production for the war effort, some experimenting with a process called deep-tank fermentation to extract the drug from the mold. Instead of using bedpans and tins to grow the mold and culling penicillin off the top, as Heatley was forced to do in Ox- ford, they tried submerging the mold in deep tanks and ferment- ing it to generate larger quanti- ties of the drug. It was a major breakthrough. As war escalated throughout 1942, researcher Andrew Moyer led the USDA Peoria lab in finding the most potent penicillin mold that would hold up during fermentation extraction. Each day, he sent assistant Mary Hunt to local markets for decaying fruit or anything with fungal growth to find more-productive strains of the penicillin mold, Lax writes. Earning the nickname “Moldy Mary,” she once found a canta- loupe “with a mold so powerful that in time it became the ancestor of most of the penicillin produced in the world,” according to the American Chemical Society. Throughout 1943, penicillin production became the War De- partment’s No. 2 priority after the Manhattan Project’s drive to build a nuclear bomb. In July 1943, the War Produc- tion Board made plans for wide- spread distribution of penicillin stocks to Allied troops fighting in Europe. Then scientists worked round-the-clock to prepare for an ultimate goal: having enough to support the D-Day invasion. On June 6, 1944, 73,000 U.S. troops landed on the beaches of Normandy, boosted by millions of doses of the miracle drug. Almost three years to the day that Florey and Heatley arrived in New York, American production of penicillin had risen from 0 to 100 billion units per month using deep-tank fermentation — enough to treat every Allied casu- alty, Lax writes. Anne Miller went on to live a long and productive life in Con- necticut, dying in 1999 at age 90. The hospital chart that tracked her recovery in that long-ago penicillin experiment is now housed at the Smithsonian Insti- tution. Florey never did receive his kilo of penicillin. He waited for more than a year for the United States to deliver on its original deal. But with America now wag- ing war on two continents, it wanted every drop of the drug it could produce. [email protected]

 More Retropolis at washingtonpost.com/history

RETROPOLIS

In WWII, miracle drug transformed fight against infection

IMPERIAL WAR MUSEUM Scottish biologist Alexander Fleming had discovered the penicillin mold in London in 1928.

minor wounds and injuries,” Lax said. As Europe sank deeper into war, labs around the world got word of the Oxford lab’s penicillin research and began requesting samples. Florey and his team were careful not to send any to German scientists, who could have easily developed them to support the Nazi war effort, according to Lax. The Oxford team was so fearful of the drug falling into Nazi hands that as the Blitz bombings shattered England, the team rubbed their coats with the mold, knowing the spores would live for a long time on fabric, Lax said in a phone interview. That way, if any researchers were captured or had to travel in a hurry, they had it with them and could extract and regrow it. British pharmaceutical companies were interested in mass- producing penicillin, but they were overburdened by wartime demand for other drugs. Florey and Heatley began looking over-

seas for help, turning once again to the Rockefeller Foundation in New York. Florey realized that the United States, which had not entered the war yet, had many more pharmaceutical firms than Britain with much more capacity to produce penicillin on a large scale. Florey struck a deal with his Rockefeller contacts: He and Heatley would show Americans how to produce penicillin molds. In return, Americans would give Florey a kilo of the drug. This would provide the Oxford researchers with enough penicillin to complete human trials for suffering patients like Alexander. The foundation agreed. In a hazardous trip out of war-torn Europe, Florey and Heatley arrived in New York on July 2, 1941. Through Rockefeller contacts, Florey had access to major play- ers in the U.S. government to back his project — including the War Production Board and the U.S. Department of Agriculture.

A week after arriving in New Haven, Heatley and Florey traveled to the USDA’s Northern Re- gional Research Laboratory in Peoria, Ill., a farming community about 160 miles southwest of Chicago. Robert Coghill, the head of the fermentation division, agreed to help the Oxford cause if Heatley would stay on in Peoria to get the penicillin mold culture started. Leaving Heatley in Peoria, Florey visited U.S. drug companies in the hope of persuading one or more of them to brew the culture fluid and extract the mold to yield enough for his experiments, according to “The Mold on Dr. Florey’s Coat.” By the fall, Florey had persuad- ed Charles Pfizer & Co., Eli Lilly & Co., Merck and other drug firms to work on the project, and he returned to Oxford to wait for his kilo of penicillin. But then war struck the United States: The Japanese attacked U.S. Navy ships anchored in Pearl Harbor on Dec. 7, 1941. The decla-

USDA NOBEL FOUNDATION Researcher Andrew Moyer led the USDA Peoria lab in research on the mold. Australian doctor Howard Florey got funding to study Fleming’s discovery during the war. He traveled to the United States and struck deals with drug firms and the U.S. government in developing a penicillin treatment.

The Washington Post - USA (2020-07-28)

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