A Planet of Viruses - Carl Zimmer (2011)

EVERYWHERE, IN ALL THINGS

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The Enemy of Our Enemy

Bacteriophages

People have known about viruses, or at least their effects, for as long as viruses have been making people sick. Scientists discovered viruses in the nineteenth century, and by the beginning of the twentieth, they had learned a few important things about them. They knew that viruses were infectious agents of unimaginably small size. They had begun to assign certain diseases, such as tobacco mosaic disease or rabies, to certain viruses. But the young science of virology was still parochial. It focused mainly on the viruses that worried people most: the ones that infect humans or the ones that infect the crops and livestock we raise for food. Virologists rarely looked beyond our little circle of experience.

A clue to the true scope of viruses came in the middle of World War I. French soldiers were dying in droves, killed not just by Germans but also by bacteria. The microbes invaded their torn flesh, their food, and their drinking water. Their path was made easier by the worldwide flu epidemic in 1918. The flu weakened the defenses of its victims, allowing bacteria to infect their lungs. The soldiers spread the flu to civilians, and ultimately fifty million people died—many of them killed by bacteria.

Today, doctors can treat all of these bacterial infections with antibiotics. But antibiotics would not be discovered until the 1930s. During World War I, doctors could only treat battlefield infections by cleaning wounds and, if that failed, amputating limbs. Their patients often died anyway.

In 1917, in the midst of this carnage, the Canadian-born physician Felix d’Herelle discovered what seemed to him a medical miracle: a powerful substance that could wipe out bacteria. It was not an antibiotic. Instead, Herelle had discovered something that no one had ever imagined before: a virus that attacked not humans, or other animals, or even plants. He found a virus that made bacteria its host.

Herelle made his discovery while investigating an outbreak of dysentery among French soldiers. As part of his analysis, he passed the stool of the soldiers through a filter. The filter’s pores were so small that not even the bacteria that caused the dysentery, known as Shigella, could slip through. Once Herelle had produced this clear, filtered fluid, he then mixed it with a fresh sample of Shigella bacteria and then spread the mixture of bacteria and clear fluid in petri dishes.

The Shigella began to grow, but within a few hours Herelle noticed strange clear spots starting to form in their colonies. He drew samples from those spots and mixed them with Shigella again. More clear spots formed in the dishes. These spots, Herelle concluded, were bacteria battlegrounds in which viruses were killing Shigella and leaving behind their translucent corpses. Herelle believed his discovery was so radical that his viruses deserved a name of their own. He dubbed them bacteriophages, meaning “eaters of bacteria.” Today, they’re known as phages for short.

The concept of bacteria-infecting viruses was so strange and so new that some scientists couldn’t believe it. Jules Bordet, a French immunologist who won the Nobel Prize in 1919, became Herelle’s most outspoken critic after he failed to find phages of his own. Instead of Shigella, Bordet used a harmless strain of Escherichia coli. He poured Ecoli–laden liquid through fine filters, and then mixed the filtered liquid with a second batch of Ecoli. The second batch died, just as they had in Herelle’s experiments. But then Bordet decided to see what would happen if he mixed the filtered liquid with the first batch of Ecoli—that is, the one he had filtered in the first place. To his surprise, the first batch of Ecoli was immune. Bordet believed that his failure to kill the bacteria meant that the filtered fluid did not contain phages. Instead, he thought, it contained a protein produced by the first Ecoli. The protein was toxic to other bacteria, but not to the ones that made it.

Herelle fought back, Bordet counterattacked, and the debate raged for years. It wasn’t until the 1940s that scientists finally found the visual proof that Herelle was right. By then, engineers had built electron microscopes powerful enough to let scientists see viruses. When they mixed bacteria-killing fluid with Ecoli and put it under the microscopes, they saw that bacteria were attacked by phages. The phages had boxlike shells in which their genes were coiled, sitting atop a set of what looked like spider legs. The phages dropped onto the surface of Ecoli like a lunar lander on the moon and then drilled into the microbe, squirting in their DNA.

As scientists got to know phages better, it became clear that the debate between Herelle and Bordet was just a case of apples and oranges. Phages do not belong to a single species, and different phage species behave differently toward their hosts. Herelle had found a vicious form, called a lytic phage, which kills its host as it multiplies. Bordet had found a more benevolent kind of virus, which came to be known as a temperate phage. Temperate phages treat bacteria much like human papillomaviruses treat our skin cells. When a temperate phage infects its host microbe, its host does not burst open with new phages. Instead, the temperate phage’s genes are joined into the host’s own DNA, and the host continues to grow and divide. It is as if the virus and its host become one.

Once in a while, however, the DNA of the temperate phage awakens. It commandeers the cell to make new phages, which burst out of the cell and invade new ones. And once a temperate phage is incorporated into a microbe, the host becomes immune from any further invasion. That’s why Bordet couldn’t kill his first batch of Ecoli with the phage—it was already infected, and thus protected.

Herelle did not wait for the debate over phages to end before he began to use them to cure his patients. During World War I, he observed that as soldiers recovered from dysentery and other diseases, the levels of phages in their stool climbed. Herelle concluded that the phages were actually killing the bacteria. Perhaps, if he gave his patients extra phages, he could eliminate diseases even faster.

Before he could test this hypothesis, Herelle first needed to be sure phages were safe. So he swallowed some to see if they made him sick. He found that he could ingest phages, as he later wrote, “without detecting the slightest malaise.” Herelle injected phages into his skin, again with no ill effects. Confident that phages were safe, Herelle began to give them to sick patients. He reported that they helped people recover from dysentery and cholera. When four passengers on a French ship in the Suez Canal came down with bubonic plague, Herelle gave them phages. All four victims recovered.

Herelle’s cures made him even more famous than before. The American writer Sinclair Lewis made Herelle’s radical research the basis of his 1925 best-selling novel Arrowsmith, which Hollywood turned into a movie in 1931. Meanwhile, Herelle developed phage-based drugs sold by the company that’s now known as L’Oreal. People used his phages to treat skin wounds and to cure intestinal infections.

But by 1940, the phage craze had come to end. The idea of using live viruses as medicine had made many doctors uneasy. When antibiotics were discovered in the 1930s, those doctors responded far more enthusiastically, because antibiotics were not alive; they were just artificial chemicals and proteins produced by fungi and bacteria. Antibiotics were also staggeringly effective, often clearing infections in a few days. Pharmaceutical companies abandoned Herelle’s phages and began to churn out antibiotics. With the success of antibiotics, investigating phage therapy seemed hardly worth the effort.

Yet Herelle’s dream did not vanish entirely when he died in 1949. On a trip to the Soviet Union in the 1920s, he had met scientists who wanted to set up an entire institute for research on phage therapy. In 1923 he helped Soviet researchers establish the Eliava Institute of Bacteriophage, Microbiology, and Virology in Tbilisi, which is now the capital of the Republic of Georgia. At its peak, the institute employed 1,200 people to produce tons of phages a year. During World War II, the Soviet Union shipped phage powders and pills to the front lines, where they were dispensed to infected soldiers.

In 1963, the Eliava Institute ran the largest trial ever conducted to see how well phages actually worked in humans, enrolling 30,769 children in Tbilisi. Once a week, about half the children swallowed a pill that contained phages against Shigella. The other half of the children got a pill made of sugar. To minimize environmental influences as much as possible, the Eliava scientists gave the phage pills only to children who lived on one side of each street, and the sugar pills to the children who lived on the other side. The scientists followed the children for 109 days. Among the children who took the sugar pill, 6.7 out of every 1,000 got dysentery. Among the children who took the phage pill, that figure dropped to 1.8 per 1,000. In other words, taking phages caused a 3.8-fold decrease in a child’s chance of getting sick.

Few people outside of Georgia heard about these striking results, thanks to the secrecy of the Soviet government. Only after the Soviet Union fell in 1989 did news start to trickle out. The reports have inspired a small but dedicated group of Western scientists to investigate phage therapy and to challenge the long-entrenched reluctance in the West to use them.

These phage champions argue that we should not be worried about using live viruses as medical treatments. After all, phages swarm inside many of the foods we eat, such as yogurt, pickles, and salami. Our bodies are packed with phages too, which is not surprising when you consider that we each carry about a hundred trillion bacteria—all promising hosts for various species of phages. Every day, those phages kill vast numbers of bacteria inside our bodies without ever harming our health.

Another concern that’s been raised about phages is that their attack is too narrowly focused. Each species of phage can only attack one species of bacteria, while one antibiotic can kill off many different species at once. But it’s clear now that phage therapy can treat a wide range of infections. Doctors just have to combine many phage species into a single cocktail. Scientists at the Eliava Institute have developed a dressing for wounds that is impregnated with half a dozen different phages, capable of killing the six most common kinds of bacteria that infect skin wounds.

Skeptics have also argued that even if scientists could design an effective phage therapy, evolution would soon render it useless. In the 1940s, the microbiologists Salvador Luria and Max Delbruck observed phage resistance evolving before their own eyes. When they laced a dish of Ecoli with phages, most of the bacteria died, but a few clung to existence and then later multiplied into new colonies. Further research revealed that those survivors had acquired mutations that allowed them to resist the phages. The resistant bacteria then passed on their mutated genes to their descendants. Critics have argued that phage therapy would also foster the evolution of phage-resistant bacteria, allowing infections to rebound.

The advocates for phage therapy respond by pointing out that phages can evolve, too. As they replicate, they sometimes pick up mutations, and some of those mutations can give them new avenues for infecting resistant bacteria. Scientists can even help phages improve their attacks. They can search through collections of thousands of different phages to find the best weapon for any particular infection, for example. They can even tinker with phage DNA to create phages that can kill in new ways.

In 2008, James Collins, a biologist at Boston University, and Tim Lu of MIT published details of the first phage engineered to kill. Their new phage is especially effective because it’s tailored to attack the rubbery sheets that bacteria embed themselves in, known as biofilms. Biofilm can foil antibiotics and phages alike, because they can’t penetrate the tough goo and reach the bacteria inside. Collins and Lu searched through the scientific literature for a gene that might make phages better able to destroy biofilms. Bacteria themselves carry enzymes that they use to loosen up biofilms when it’s time for them to break free and float away to colonize new habitats. So Collins and Lu synthesized a gene for one of these biofilm-dissolving enzymes and inserted it into a phage. They then tweaked the phage’s DNA so that it would produce lots of the enzyme as soon as it entered a host microbe. When they unleashed it on biofilms of Ecoli, the phages penetrated the microbes on the top of the biofilms and forced them to make both new phages and new enzymes. The infected microbes burst open, releasing enzymes that sliced open deeper layers of the biofilms, which the phages could infect. The engineered phages can wipe 99.997 percent of the Ecoli in a biofilm, a kill rate that’s about a hundred times better than ordinary phages.

While Collins and other scientists discover how to make phages even more effective, antibiotics are now losing their luster. Doctors are grappling with a growing number of bacteria that have evolved resistance to most of the antibiotics available today. Sometimes doctors have to rely on expensive, last-resort drugs that come with harsh side effects. And there’s every reason to expect that bacteria will evolve to resist last-resort antibiotics as well. Scientists are scrambling to develop new antibiotics, but it can take over a decade to get a new drug from the lab to the marketplace. It may be hard to imagine a world before antibiotics, but now we must imagine a world where antibiotics are not the only weapon we use against bacteria. And now, ninety years after Herelle first encountered bacteriophages, these viruses may finally be ready to become a part of modern medicine.

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