Prokaryotes at the Gate

Bacteria, ancient members of the prokaryotic world, are striking back with a vengeance and we are running out of weapons to fight them.

By Mark Caldwell|Monday, August 01, 1994
Back in the early 1940s, at the dawn of the antibiotic era, many slaphappy doctors and even a few scientists thought they could scent the triumph of man over microbe. Bacteria had been around for at least 3.5 billion years, primitive relics of the Precambrian. Now they were hopelessly outclassed by their newfangled descendant, the brainy human, and ripe for sweeping off the evolutionary map. Humans had just discovered penicillin. New antibiotics were coming along in a seemingly endless procession, erasing once-lethal pathogens like so many chalk marks from a blackboard. A few Panglosses even envisioned the day when disease-causing bacteria would become a shadowy memory, like the Visigothic hordes.

Ha, answered the prokaryotes (the class of simple, usually one- celled, nucleus-free organisms to which bacteria belong). They spat on their cytoplasmic hands, got down to work, and within a few years had produced an ingenious array of weapons against the new miracle drugs. Antibiotics, they quietly reminded us, weren't originally human concoctions--they were substances the microbes themselves had evolved and were therefore quite familiar with.

Penicillin, after all, was the invention of a microbe--the Penicillium mold. In fact, as far back as the mid-1800s researchers had been lighting on evidence that bacteria were able to manufacture substances that inhibited or even killed other prokaryotes. Louis Pasteur, for example, noticed that certain soil bacteria could stifle the development of the dreaded anthrax bacillus. And the German scientist Rudolf Emmerich noted that a streptococcus infection could apparently protect guinea pigs from the cholera bacillus.

It really shouldn't have surprised anyone that if microbes could attack rival germs, they might also be able to defend themselves from attack. Many bacterial species have vied for the same ecological niches for eons, so you'd expect evolution to equip them with genes for producing suitable weaponry and defenses. In the face of continuing threat, bacteria have devised and constantly improved these genes and even passed them out among their cronies like taco chips at a beer party. "Microbes," observes microbiologist Richard Krause of the National Institutes of Health's Fogerty International Center, "have a tremendous power to shuttle genes back and forth within a species--and even between species." In other words, they are able not only to invent resistance genes but also to spread them around with alacrity.

Now, 50 years after the first human deployment of antibiotics, bacteria are putting our drugs to rout. Initially antibiotics gained us many easy victories, but their subsequent overuse also gave bacteria ample opportunity to confront our chemical weapons and find ways around them. This microbial counterattack has been so dismayingly consistent that it's tempting to attribute it to fiendish microbial guile rather than the true cause--blind but relentless evolution. Most bacteria will succumb to a powerful new antibiotic, but a few will have genes (or genetic mutations) that allow them to resist the onslaught and produce similarly resistant descendants. Thus the fittest survive to pit themselves against the next wave of souped-up drugs we throw at them; they will no doubt develop resistance to those drugs too.

And so it goes on, bugs versus drugs, in a pattern of escalating warfare. Twenty years ago, thanks to antibiotics, tuberculosis seemed a plague of the past. By the 1980s, however, TB was on the rise and showing serious resistance to several once-fail-safe antibiotics. One Florida hospital reported that 29 of its patients were diagnosed with multidrug- resistant tuberculosis in the latter half of 1989. By 1992 doomsday had arrived: strains of TB had appeared that were resistant to all of the 11 drugs in existence to treat it. And TB is by no means the only plague that's risen from the grave: although much less well publicized, pneumonia, gonorrhea, and a raft of potentially fatal hospital-borne infections have also become dangerously defiant.

"There are now organisms, still fortunately rare, resistant to every antibiotic known," says Fred Tenover, chief of the lab that analyzes such infections at the Centers for Disease Control (CDC) in Atlanta. "And we're coming to the end of the road for new antibiotic mechanisms. There are only so many ways you can attack a bacterium biochemically, and we've exhausted the majority of the simple targets. For some organisms, in fact, we're at the end of the road."

This isn't merely a theoretical concern. If you become a hospital patient, you now risk a potentially lethal visit from a group of bacteria pharmacologists thought they'd decked in the 1940s with penicillin--the staphylococci. Some of them live harmlessly, as a matter of course, on our skin. But others, notably Staphylococcus aureus, cause a range of diseases, from pus-producing boils, carbuncles, and abscesses to food poisoning, osteomyelitis, and toxic shock syndrome. S. aureus flourishes in hospitals, with their crowded populations of sick and vulnerable people; in this fertile environment it can turn into a monster, causing, among other potentially fatal illnesses, blood poisoning, pneumonia, and meningitis.

Certain strains of S. aureus began showing serious antibiotic resistance as early as 1944. That shocked the optimists, but it didn't surprise the more astute pioneers of the antibiotic era, such as the late René Dubos, who predicted that bacteria would find ways to counteract the new drugs. History bore him out: nowadays penicillin and its relations have a less than 1 in 20 chance of working against S. aureus. Indeed, common hospital bacteria--including the staphylococci and the enterococci--have learned to laugh at a long list of once-reliable later-generation antibiotics, including methicillin, erythromycin, tetracycline, streptomycin, and the sulfa drugs. As an additional refinement, they've become impervious to such common disinfectants as formaldehyde, chlorine, and iodine.

Even strains of bacteria that were blessedly slow to clamber onto the resistance bandwagon have begun making up for lost time--for example, another familiar bête noire, Streptococcus pneumoniae, an organism extensively studied by Alexander Tomasz, a microbiologist at Rockefeller University in New York. This bacterium is responsible for illnesses ranging from common childhood ear infections to fatal meningitis and pneumonia. For the first two decades of the antibiotic era, S. pneumoniae was quite sluggish in rallying against penicillin and similar drugs. But in the 1960s resistant strains began appearing in Australia and Papua New Guinea, and they'd become a worldwide problem by the 1980s.

Recent advances in molecular biology have allowed researchers to track the spread of such resistant strains with startling accuracy. Tomasz cites the sudden appearance of drug-resistant S. pneumoniae in Iceland in December 1988. "It was spectacular, in a way," he ruefully recalls. "It came out of the blue and rose very rapidly." Over the next few years Icelandic investigators saw a whopping increase of this penicillin- resistant strep, from 2.5 percent of the isolates they examined in 1989 to 20 percent of isolates in 1993.

Thanks to their new molecular tools, researchers in the United States and Iceland were able to trace this bacterium to its origins. "The new techniques look really deep into the bug and pick up genetic variations--even among members of the same, outwardly identical group," points out Tomasz. These techniques showed that most of the resistant bugs in Iceland were virtually identical to a well-established strain in Spain. The inference? "Spain is a favorite vacation spot for lots of families in Iceland," Tomasz observes. The resistant bacteria may have come back home on the plane with the sunburns and souvenirs.

Sometimes (and almost certainly in this case) a strain of resistant bacteria hitches a ride from one country to another; sometimes a hitherto susceptible strain may scavenge a resistance gene from who knows where. "But what's amazing," Tomasz concludes, "is how rapidly resistance spreads. It's like a reproducing pollutant, created unintentionally by a wonderful high-tech society--spreading from one hospital to another, one city to another, one continent to another."

Combating that relentless spread can be both difficult and prohibitively expensive. According to George Jacoby, an infectious-disease specialist at the Lahey Clinic in Burlington, Massachusetts, it costs about $300 million to develop a new antibiotic. Yet resistant bacteria are gobbling through antibiotics as if they were penny candy, and pharmacologists are becoming desperate for new drug strategies. For example, there is one last-resort, state-of-the-art drug--vancomycin--that works against both recalcitrant S. pneumoniae and its even more stubbornly resistant cousin S. aureus. Introduced in the late 1960s, vancomycin was the answer to clinicians' prayers because its method of attack was so unlike anything bacteria had seen before. In many hospitals plagued by defiant Staphylococcus, vancomycin became the drug of choice.

Now even this respite seems unlikely to last. No sooner had vancomycin begun flattening S. aureus in hospital patients than another group of common hospital bacteria--the enterococci--began profiting from their increased exposure to the drug to do the unthinkable: they engineered genes to defend themselves against the wonder drug. The first resistant strain of Enterococcus faecalis turned up in 1989. Four years later the CDC reported a 20-fold increase in the percentage of vancomycin-resistant enterococci in hospitals. So far, apparently, the enterococci haven't shared their resistance genes with S. aureus. But, chillingly, lab experiments have shown that it's possible for them to do so.

Sooner or later, it's probable that free-living bacteria will repeat the experiment. Practice has made them experts. "During the first 2 or so billion years of life, microbes were alone on Earth and they worked out every trick in the genetic book," explains the NIH's Krause. By developing and exchanging useful new genes, they quickly adapted to every niche they could find, from boiling hot springs to frozen steppes. The subsequent arrival of complicated new organisms like fish and eventually land mammals and humans--organisms ideally suited to hosting a rich variety of microbes--merely broadened their horizons. "Think of microbes as swimming in a great stew in your nose, your throat, your intestines," says Krause. "This shuttling of genes is going on everywhere."

Like a cadre of cyberpunks trading useful bits of pirated software, bacteria have amassed an array of gene-swapping strategies. They can shuttle genes on mobile segments of DNA called transposons. Or they can wait for viruses called phages, which roam from bacterium to bacterium like traveling salesmen, carrying a portmanteau of useful genes to be picked over by every bug they visit. Or the bacteria can take matters into their own hands. Tomasz's S. pneumoniae, for example, has a voracious appetite for stray DNA. "The little beasts," he says, "pick up bare DNA molecules floating around them"--perhaps from debris left by background bacteria that swarm in our mouths and nasal passages.

But the workhorse of bacterial gene swapping is a tiny circle of DNA called a plasmid. Plasmids can contain hundreds of genes. They float free in the cytoplasm of many bacteria, independent of the large, tangled skein of chromosomal DNA that contains the bacteria's core of genetic information. Many of these plasmids are responsible for what's probably the most important mechanism by which bacteria trade resistance genes: sex. Driven by their plasmids, bacteria go in for several variations of conjugation, as bacteriologists demurely call the act. In the simplest version, a bacterium with a lusty plasmid uses grappling hooks to snare a plasmidless mate, and a fusion point forms between the two; the donor bacterium then copies its plasmid and passes the spare to its mate.

Thus in bacteria the purpose of conjugation isn't reproduction (which they do on their own, by duplicating their DNA and splitting in two). Rather, these conjugal acts allow them to replicate their plasmids-- which can bear all kinds of genetic information, from genes for disease- causing toxins to genes that grant resistance to antibiotics. So seductive is this prospect that bacteria pursue conjugation energetically, often in large groups. And, breaking the usual mating rules, they don't always confine their attentions to their own species: you can be welcome at the orgy no matter what your genome looks like, as long as you're a one-celled bug.

Some promiscuous plasmids even carry genes that induce their bacterial hosts to respond to substances that perfume companies are trying to bottle for humans--sexy pheromones. "The subject invariably gets people's attention," says Don Clewell, who does research on bacterial pheromones at the University of Michigan in Ann Arbor. "But really, a pheromone is just a hormone that carries a signal between two organisms." Pheromones can provoke a number of different activities, including sex. So far, sex pheromones are known in only one species of gut bacteria, Enterococcus faecalis, but Clewell suspects they're probably at work in other species as well, contributing to conjugation and the transfer of resistance genes.

How the bacteria in Clewell's lab achieve that goal is astonishing. For example, enterococci that harbor a plasmid called pAD1 have receptors that can whiff a pheromone released by bacteria lacking the plasmid. As soon as the plasmid detects the pheromone signal, it induces the bacterium it resides in to put a fuzzy material on its surface. Then, by random collision, the plasmid-bearing bacterium, or donor, hits a recipient bacterium, and they stick together. More frequently than is the case on human blind dates, conjugation follows.

The results can be dramatic. If you put bacteria containing pAD1 into a broth with enterococci that lack it, over the course of an hour or so they'll mass together into large mating clumps. Then the plasmids inside the bacteria copy themselves and give their spare copies to the plasmidless recipients. "A fusion point arises between each mating pair," Clewell says, "and a copy of the plasmid DNA transfers from the donor to the recipient." The transferred plasmids then shut down the sex pheromone production of their new hosts (no further pAD1's need apply, thank you).

But pAD1 can do more than drive its host into a clinch. It can act as a ferry for any resistance genes lurking in the host--transporting genes from passive plasmids (which can't initiate conjugation on their own) and transposons itching to jump ship. By starting the orgy, that is, pAD1 acts as a pimp for these predatory genes, escorting them from the host into a brand-new microbe. Or, as Clewell more chastely puts it, "when the pheromone causes a mating aggregate, the other guy can sneak over." In recent years, Clewell and others have found pheromone-sensing plasmids that already have resistance genes built right into them, streamlining the process even further.

One way or another, once a resistance gene appears, it can spread rapidly from bacterium to bacterium and even from species to species. But how does the gene make its new host resistant? Surprisingly, the answer lies in a relatively small number of bacterial structures and functions. Jacoby explains the underlying principle: "The reason we can use antibiotics at all is that there are some targets bacteria have that we don't." In other words, properly focused drugs can interfere with the microbes while leaving us essentially unscathed.

Jacoby cites three particularly important targets. "First, the cell wall of the bacterium, which is chemically different from anything we possess. That's where vancomycin acts, for example." So does the matriarch of antibiotics, penicillin. "Then there's the bacterial ribosome"--the submicroscopic factory where the bacterium builds the proteins it needs to function and survive. "Streptomycin, gentamicin, and the tetracyclines, among others, act there." Third and last is the folic acid pathway, a biochemical mechanism that allows bacteria to make their own folic acid, a necessary B vitamin (humans lack a folic acid pathway; we have to get the vitamin from food). "The folic acid pathway," Jacoby says, "is blocked by sulfa drugs and trimethoprim."

To keep matters simple, let's zero in on one particular target-- the bacterial cell wall--and a single broad and important category of antibiotics, the beta-lactams, a group that includes penicillin. These drugs get their name from the beta-lactam ring, the circular chemical structure that forms their business end.

Antibiotics like this attack a bacterium in the act of reproducing--just as the cell is doubling in size and starting to divide in two. To make its new walls, and to give them stability, a bacterium relies on a key enzyme. The beta-lactam ring on an antibiotic interferes with this process by grabbing the enzyme and preventing it from doing its job in the cell wall. "It's like throwing a monkey wrench into an essential machine that assures the stability of the cell wall," Jacoby explains. Sometimes the bacterium bulges in the middle, sometimes it bends, sometimes it elongates into a noodle. "I can't tell you why you get spaghetti in one case and balloons in another," Jacoby admits, but the result is the same: the bacterium fails to divide and pops apart.

How's a beleaguered microbe to react to the challenge of antibiotics? Often it acquires a resistance gene, say from a handy plasmid absorbed during conjugation, or from a traveling phage. These genes operate in a variety of ways. The gene can alter the bacterium, perhaps narrowing the openings in the cell wall so the beta-lactam can't get inside the bacterium and at its target. Or it can create a mini-revolving door that spews the antibiotic out again as soon as it has entered. Or it can change the structure of the bacterium's cell-wall-making proteins so the beta- lactam ring no longer interacts with them. But perhaps the easiest device to understand is a gene that produces a beta-lactam-zapping enzyme, called beta-lactamase.

"It's a straightforward counterattack by the bacteria to break up the antibiotic before it can reach its target," says Jacoby. The enzyme simply adds water to the beta-lactam ring to spring it open. This frees the enzyme to clobber more penicillin molecules, while the bacterium synthesizes its cell wall normally.

With some bacteria, beta-lactamase disarms the antibiotic once it's inside them; with others, the enzyme does its damage just outside the bacteria. The difference seems trivial, but it has a nasty practical consequence. "Suppose you have some streptococci that give you a sore throat," Jacoby proposes. "Normally they're exquisitely sensitive to penicillin." But then suppose you've also got lots of harmless bacteria in your throat--and they happen to produce beta-lactamase outside their cell walls. Beta-lactamase from the harmless bacteria may well disable the drug before it attacks the vicious strep. "The penicillin may fail against the streptococci because the harmless bacteria are chewing it up."

The microbe wars are replete with tales like this, and we've barely begun to sample their inventions. "Beta-lactam antibiotics are my favorite subject," Jacoby says, "but there are plenty of other brilliant things bacteria do." Consider vancomycin. In the 1960s, pharmacologists hoped it would prove, as Jacoby phrases it, a "last resort" antibiotic, invulnerable to resistance since it attacked the bacterium's cell-wall- producing mechanism at a novel point--at a different and earlier stage than did beta-lactam antibiotics.

Fond hope. Within two decades, Jacoby notes, bacteria had engineered "an incredibly elaborate set of changes that alter the target vancomycin attaches to, and then packed them all in a genetic unit that can jump around from cell to cell." It's a Rube Goldberg system, says Jacoby, "packaged on a transposon." As Fred Tenover of the CDC explains it, "The organism has found a new way to build its cell wall minus the drug's site of action. Organisms have never been known to do this before." Yet another round to the prokaryotes.

That's not to say the fight is lost. Pharmacology is fiercely, if somewhat belatedly, at work hunting new antimicrobial strategies. Some are quick, jury-rigged fixes to existing drugs: various additives designed to neutralize beta-lactamase, for example. But others are more inventive, even visionary: exploring new bacterial targets at which antibiotics might be aimed; finding drugs that stop plasmids from replicating; and designing Trojan-horse plasmids to sneak lethal genes into bacteria. Alternatively researchers, perhaps in a tacit admission of pharmaceutical defeat, are looking into new possibilities for bacterial vaccines that might stimulate the immune system and prevent infection in the first place. Immune-boosting strategies could also be used in people who are already sick; in an experiment at the National Jewish Center for Immunology and Respiratory Medicine in Colorado, interferon gamma is being given to patients with multidrug-resistant TB.

Tomasz, however, argues that we need to rethink our whole approach to treating infectious diseases. Despite its intuitive appeal, Tomasz believes the scorched-earth, take-no-captives approach to bacteria may have backfired. "Bombing everybody who resembles a prokaryote at the gate is probably a mistake," he says. That indiscriminate practice just incites every industrious germ in the vicinity to develop and share resistance strategies. Drugs designed to combat a broad spectrum of bacteria may be cleaning out your respiratory system, but they're also furnishing the hardiest bugs a lab for experimenting with resistance. A wiser approach, Tomasz thinks, might be to spare the bacteria but neutralize their nasty effects. For example, you could aim drugs at the specific disease-causing toxins bugs produce, or at the dangerous response they provoke in the host. The result would be more-selective, lower-profile drugs that would threaten a bug's bad habits rather than its survival, making the drugs far less likely to become sitting ducks for resistance. "There's really no such thing as a bad bacterium," Tomasz concludes, "just unpleasant genes."

Still, that may be easier said than done: new drugs are expensive to develop, and if they're highly restricted in their use, they're less likely to recoup an initial investment. These market forces have been a factor in the slow development of new drugs to fight tuberculosis. Resistant strains of the TB bacillus tend to respond only to drugs that don't work on other diseases, and terrible though TB is, pharmaceutical companies haven't fallen over themselves to make a major development effort. So persuading drug companies to make highly selective drugs instead of broad-spectrum ones may prove an uphill struggle.

Scare stories aside, there's a lesson in all this. Bacteria are far more experienced in the antibiotic industry than humans are. They've been manufacturing antibiotics--and countering them--for eons. When we humans stumbled on them, we intervened in an age-old battle of yin and yang, offense and defense. But each antibiotic is merely a stopgap, its success a challenge to microbial resourcefulness. Using antibiotics carefully--a good deal more soberly than we do now--could do much to prolong their usefulness and buy us time. But even this may not prevent the eventual obsolescence of current drugs, forcing humans to match their adversaries' ingenuity with new ideas.

Specialists in the field can't help letting the sincerity of their desire for a fail-safe antibiotic give way occasionally to a note of respect for their adversaries' resilience. "The overwhelming principle for me is that bacteria are a moving target," Jacoby concludes. "No magic bullet stays magic for long."
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