Part One of The Bacteria Revolution begins at the 12th International Conference on Lyme Disease and Other Spirochetal and Tick-Borne Disorders in New York City, where about 350 people have gathered to review the latest information about Lyme and other tick-borne diseases.

The conference is sponsored by the Lyme Disease Foundation, headed by Karen Vanderhoof-Forschner, who was bitten by a deer tick in 1985. She didn't think much of it at the time, but upon becoming pregnant, she experienced a series of multi-system disorders, including loss of taste and smell, irregular heartbeats, and profound fatigue, although it was hard to relate these diverse symptoms to her earlier tick bite. When her son was born, however, he had evidence of a brain infection, and was later found to have Lyme disease. Forschner and her husband decided to form the foundation, hoping it would find solutions for their son. It didn't, alas: he died in 1991 at the age of 5.

Lyme disease is one of several diseases spread by insects called deer ticks. Others include human granulytic and monocytic erlichiosis, and babesiosis, which Dr. Gregory Bach of Colmar, Pennsylvania, calls the "brother of malaria". Babesiosis, he says, causes not only fatigue, but what's been called "babesiosis rage". Bach reports that one woman with babesiosis actually took a chain-saw to her furniture, and notes these exaggerated reactions have been implicated in suicides, even certain crimes.

Sorting out all the various symptoms caused by tick-borne diseases is no picnic, and both the detection and the treatment of Lyme are surrounded by controversy. As Dr. Kenneth Liegner from the New York Medical Center in Armonk, New York, points out, many academicians have staked their reputations on the view that Lyme disease is easily diagnosed and cured. However Liegner is convinced, based on many years of clinical experience, that many patients are difficult to diagnose and there may be no way of curing this infection with currently available methods.

These uncertainties are front and center at the New York conference, which is chaired by Professor James N. Miller, of the Microbiology & Molecular Genetics / Microbiology & Immunology at the University of California at Los Angeles School of Medicine. Miller agrees that there's not a clear consensus with respect to how to diagnose Lyme disease. He points out there is no unequivocally perfect test for diagnosing the disease in people without a characteristic rash. Many develop atypical rashes, or none at all, and enter into a "latent" state - which may be short or long - where there is nothing visibly happening. "Because some of the clinical manifestations in early Lyme disease can be very subtle, generalized and referable to other diseases", he says, "this makes it difficult to diagnose", adding the blood tests for Lyme have problems in terms of their specificity, sensitivity and reproducibility.

This uncertainty over the blood tests makes it hard for doctors to say whether a patient really has the infection or not. Dr. Charles Ray Jones works in pediatric and adolescent medicine in Hamden, Connecticut, with a practice of 1500 children with Lyme disease, ranging in age from 1 day to 18 years old. "Judging from the pattern of presentation, I feel that it is way under-diagnosed and way under-treated", he says, meaning that many cases are never identified by doctors. Even among those people who do receive treatment, many still go on to suffer a variety of ills, ranging from headaches and depression to arthritis, but it's not clear whether this hodge-podge of symptoms is due to the Lyme disease or something else.

Lyme disease got its name from the towns where it was first identified - Lyme and Old Lyme, Connecticut. In 1975, unusual arthritis cases were being reported in children. A type of bacteria, known scientifically as Borrelia burgdorferi, was subsequently isolated from deer ticks, and later confirmed as the cause of the illness. Recently, using high-tech DNA amplification techniques, researchers have found evidence of this bacterium dating back to Paleolithic times. Even though this agent was not even known to exist until recently, Liegner is confident it has been affecting people for millennia. The conditions it induced were called by other names, he suggests, without anyone suspecting these illnesses had an infectious cause. He adds we still don't know the range of symptoms this bacterium - and others like it - might cause.

But the notion that Lyme disease can persist in a chronic form, causing all sorts of problems for patients - even after treatment - has been hard for some researchers to accept. When Dr. Sam Donta, a leading Lyme specialist who works at Boston University's School of Medicine, first went to workshops held by early experts on the disease, he was told it only needed to be treated for two to four weeks. Yet when he saw patients start - but not finish - getting better, he looked back at the original recommendations, and discovered they were being advocated without scientific foundation.

Donta says one cannot conclude that there is no infection if blood tests are negative, and speculates the Lyme bacteria may have instead gone into hiding someplace. "People were interpreting the absence of the organism in those body fluids as meaning there wasn't any infection," he notes, "but if you think about it logically, you cannot conclude that."

Donta began comparing the standard blood tests for Lyme disease with more sophisticated tests, and soon started to question the conventional wisdom on Lyme, established by the American government's Centers for Disease Control (CDC). He began to put the picture together, and when the CDC criteria for the lab diagnosis were established, it was clear to him that those were not accurate criteria. "The shame of that now", he says, "is that physicians are still relying on a negative test as meaning that a person doesn't have Lyme disease."

While Dr. Donta and his colleagues work to uncover the true extent of Lyme disease, others downplay the very notion of chronic Lyme.

The insurance industry, for example, is often reluctant to pay for better tests or lengthier courses of treatment, without clear evidence that patients are still infected. Karen Vanderhoof-Forschner says, "There is a lot of money out there to be made by having expert witnesses at trials for insurance companies say who does and who doesn't definitively have Lyme, so there is money to be made for those who feel they can clearly and easily separate those who have the infection from those who are disease wannabees."

There's no shortage of patients who have joined coalitions, like the Lyme Disease Foundation, to agitate for more research. Donta recognizes that because patients aren't dying right and left with Lyme, there isn't the support there is with AIDS, but from his perspective, Lyme is pervasive. Liegner suggests there are so many different manifestations that we're going to find that Lyme disease has a role in a lot of things that we do not yet accept or realize.

Indeed, there may be overlaps with diseases like fibromyalgia, chronic fatigue syndrome (CFS) - even Gulf War illness. Donta says "We're dealing with a whole new set of disorders, and people haven't stretched their mind to think of a different model. We've been spoiled with our antibiotics to treat acute disorders that come and go rapidly, and since there are often no objective signs [of Lyme infection], you tend to dismiss it, you say the person made it up or it's psychosomatic."

Psychosomatic illness - originating not from external influences but in the mind of the patient - is a label often used by doctors when they just can't figure out what's making somebody sick. But now that doctors have better techniques for zeroing in on hidden infections, they're finding Lyme bacteria in all kinds of patients - even those who don't show the typical symptoms of Lyme.

For example, Dr. Martin Freid recently presented evidence of infection with the Lyme germ in patients with Crohn's disease, an inflammation of the bowel which affects some 50,000 Canadians, and whose precise cause has eluded medical researchers.

Dr. Gordon Greenberg, Professor of Medicine at the University of Toronto and head of the Division of Gastroenterology at Mount Sinai, says it's not clear exactly what causes either Crohn's disease, or another inflammatory bowel disease called ulcerative colitis. He notes, "There has always been the concept that a single infectious etiology might be the cause of Crohn's or ulcerative colitis, but to date no single bacterium or virus has been linked with either disease. What is clear, however, is that bacterial flora within the gut, at least in a secondary way, perpetuate the inflammatory process in Crohn's."

Greenberg cites several lines of evidence, including studies from his own center, on the effect of specific antibiotics, which he's found to be particularly effective in helping to control the inflammation of Crohn's disease. His initial data suggest improvement or remission in up to 63% of Crohn's patients treated with antibiotics. "More and more the concept is emerging that bacteria do play an important role, and that selected antibiotics are quite helpful in the management of patients with Crohn's disease," Greenberg notes.

Dr. Freid recently saw an 8-year-old girl with blood in her stool, a typical symptom of ulcerative colitis. He prescribed medicine to calm the inflammation, but he also sent a tissue biopsy off for analysis. Surprisingly, it revealed an active Lyme infection. He put the girl on antibiotics for a month, and she made a complete recovery. "That's not the nature of ulcerative colitis, which would come back. But an infection would go away if treated properly. I thought it was fascinating."

Neither Dr. Fried nor Dr. Greenberg is sure just what's going on in their patients, but the evidence certainly points to a role for bacteria. This uncertainty over causation extends as well to mysterious problems like chronic fatigue and fibromyalgia. Some think the Lyme bug may be to blame for a lot of cases, others suspect another organism called a mycoplasma - it's going to be a while until we know for sure.

Professor Garth Nicolson, chief scientific officer at the Institute for Molecular Medicine in Huntington Beach, California, works on a variety of diseases, including CFS, fibromyalgia, Gulf War syndrome, rheumatoid arthritis, and a number of auto-immune diseases, including MS, ALS (Lou Gehrig's disease), and Graves' disease. These are for the most part interrelated disorders, Nicolson says, particularly CFS, fibromyalgia and Gulf War syndrome, but there are certain unique characteristics that typify the disorders: fibromyalgia symptoms include muscle pain, aching and tenderness all over the body, as well as a number of secondary symptoms that overlap with CFS.

The origin of these diseases has been open to speculation, with suggested causes including genetics or environmental exposure to chemicals. Nicolson and colleagues have been very interested in the role of infectious micro-organisms like mycoplasmas, and bacteria known as chlamydia, in the progression of these diseases, and have found chronic infections in the majority of patients suffering from them. For example, approximately 70% of Nicolson's fibromyalgia patients have mycoplasmal infections in their blood, which he says go deep into tissues and are responsible for much of their sickness.

When appropriately treated with long-term antibiotics, these patients can apparently recover, although this is dependent on a number of other factors, including other infections and chemicals in their systems. Nicolson and his institute have convinced the U.S. Department of Defense to conduct an $8 million clinical trial, testing the effects of various antibiotics in patients with Gulf War syndrome.

But it's going to be long time before this kind of research effort is brought to bear on patients suffering from what is thought to be chronic Lyme disease, because no one seems to be able to prove they're still infected with the Lyme bacterium.

All that may change, however, with a bombshell discovery published in the November/December 1998 issue of the prominent medical journal Infection (vol. 26, p. 364-367). In a controversial paper entitled "A Proposal for the Reliable Culture of Borrelia burgdorferi from Patients with Chronic Lyme Disease, Even from Those Previously Aggressively Treated," American researchers describe a complex technique with which they can find previously undetectable Lyme bacteria in the blood of patients with chronic disease (click here to listen to a brief audio clip of the lead author, Greenwich, Connecticut internist Dr. Steven Phillips, discussing the results of his study).

Dr. Hamid Moayad, a neurologist from Fort Worth, Texas, first heard from Phillips in 1997, through their joint association with Lida Holmes Mattman, a Wayne State University microbiologist well-known for her work on stealth pathogens, and who now runs a private lab in a suburb of Detroit. Mattman says the Infection paper developed because Moayad and Phillips both had many Lyme patients, and supplied her with blood samples, out of which she allegedly grew the Lyme bacterium in laboratory cultures, where it could be studied indefinitely.

The material used to grow the Lyme bacterium - the culture medium - has to be ingeniously designed. Lida Mattman's recipe includes sugar, starch and a variety of laboratory chemicals (along with Detroit tap water). Using this special culture medium, the Phillips research team claims to be able to grow the Lyme bacterium from the blood of patients with suspected chronic Lyme disease - patients who had been missed by the standard tests.

Culturing a disease organism from a patient is seen as the gold standard by which all other tests are judged. The publication of the Phillips paper - allegedly proving that patients with chronic Lyme disease are still infected with the Lyme bacterium - opens up a Pandora's box for patients and researchers alike. "This would actually be the gold standard for diagnosis of Lyme disease", ventures Moayad, "because if you are able to culture the bacteria, then no one can doubt the diagnosis any more, especially in the chronic late stages, which the controversy is about". This article, he says, "proves without a shadow of a doubt that it is a chronic infection - chronic Lyme means chronic infection."

But the paper has come under fire from both patients and scientists alike, who question its conclusions. Rita Stanley first contracted Lyme disease many years ago, and went on to start several support groups for Lyme patients in the Northwestern part of the U.S. She remembers the excitement that initially greeted the Phillips paper. Stanley recalls, "This is exactly what the doctor ordered - we need a test like this, but as in everything else, things aren't cut and dry, especially in science. One has to have an eagle eye to ask the question: is this valid?"

James Miller would like to see the work reproduced before he can accept it. "It was a very, very provocative study, one that is very important, but because it is so provocative and so important, it needs to be reproduced."

The problems faced by the Phillips paper represent a good illustration of the problems faced by any revolutionary finding in science - problems that have been well described by historians like Thomas Kuhn. When a paradigm-shattering discovery is presented, most people reject it because it doesn't fit with their picture of the world. But how can there be so much controversy over a paper that's appeared in an eminent, peer-reviewed, journal like Infection. It must be correct, right?

Not necessarily. Even the editor of the journal tells me he's not sure if Phillips is right, since other labs still haven't been able to reproduce the results, at least not yet. Dr. Walter Marget, speaking from Munich, says "Our reviewers are very, very skeptical, and personally, I am not very enthusiastic about this study". Marget cites experienced Lyme disease researchers in Germany who have tried to reproduce Phillips' results - but to no avail.

One of those researchers is Dr. Deiter Hassler in Heidelberg. "[To] my knowledge, nobody worldwide has found so much borrelia in culture like Phillips has," Hassler says, "and we don't know exactly why. I can't believe that so much borrelia survives, but I'm not sure, and I spoke to Dr. Marget and I told him 'we have to discuss it, we have to try it... if other work groups are able to find the same, it would be sensational.'"

You might be surprised that science articles get published before they're reproduced and verified. But publication is often an invitation to other researchers to try and duplicate the discovery; and so far no other Lyme researcher has been able to reliably cultivate the Lyme organism from the blood of patients allegedly suffering from the late stages of the disease.

A number of concerns surfaced in interviews with other prominent Lyme researchers at the New York conference, including Dr. Richard Tilton, who is medical director at Boston's BBI Clinical Laboratories, as well as serving as editor-in-chief of the Journal of Clinical Microbiology. Tilton says "If the work can be corroborated, then it is truly remarkable. However, based on the paper that was published in Infection, we will have a very difficult time repeating that work." He says he tried unsuccessfully to grow a standard laboratory strain of B. burgdorferi in the Mattman medium, but was later told he had the wrong recipe.

Moayad insists the culture technique developed by Dr. Mattman is a very reliable culture for this bacteria, a technique he says took her 5 to 6 years to come up with, and he's confident it will be reproduced soon.

Other experts can't understand how the Lyme bacteria could still persist in the blood of patients who have been aggressively treated with antibiotics for months, even years.  The answer may lie in a very important idea that surrounds the work of Phillips and colleagues: disease-causing bacteria may be able to transform themselves into something that's resistant to standard treatment and invisible to the body's immune system.

Dr. Moayad says the Lyme bacteria may take a form different than the usual coiled spiral shape characteristic of the spirochete family to which it belongs. There's a lot of evidence, especially from the older syphilis literature, that suggests spirochetes - (syphilis is caused by a spirochete, like Lyme) can form what are called "cysts", containing tiny granules that may form the basis for new "daughter" spirochetes.

The discoverer of the Lyme-causing spirochete Borrelia burgdorferi is Willy Burgdorfer, after whom the spirochete is named. Dr. Burgdorfer, a microbiologist and editor-in-chief of the Journal of Spirochetal & Tick-Borne Diseases, gave the keynote address at the New York conference - The Complexity of Vector-borne Spirochetes (Borrelia spp) - which explored the idea of spirochete cysts "hiding" in the human body. Burgdorfer notes this was once called "granulation theory" and was considered as the organism's mode of reproduction. He's not sure whether the cyst forms represent a true propagative mechanism, but he is confident they represent a complex defense mechanism of the organism in a human host.

Asked what implications this way of looking at spirochetes has for the diagnosis of Lyme disease, Burgdorfer says "It's probably the answer for the difficulties we have in diagnosing Lyme and other spirochetal diseases, in that we can demonstrate these cysts by microscopy, and once they are in the tissues of the patient, we can no longer detect them. It is quite possible that this material that we cannot see by microscopy is responsible for producing prolonged and chronic disease."

Burgdorfer is asked whether he's seen the Phillips paper, which purports to have reliably identified this same "cyst" - or "bleb" material, as it's called - from the blood of late-stage Lyme patients. He hasn't seen it, but when shown a copy, responds immediately: "This is exactly what I'm talking about".

He points to the electron microscope photographs included in the paper (left). "Here you see blebs, and these are shed by the mother spirochetes, and they are thought the germinative units out of which the daughter spirochetes develop. I personally believe that the significance of these blebs as the agent responsible for prolonged and chronic disease is very important, and it may be the answer to the diagnosis of these chronic diseases such as Lyme disease - because that's what we are looking for: something that produces diseases long after the initial treatment, and then relapse occurs after several months - or years - and the question is: where did this relapse come from? Well, it may come from these surviving crystals or bleb material that is in the tissue, and it stays there until the antibiotic or immune pressure is gone, and then when the conditions are right for its further development, they develop into typical spirochetes again."

It is very difficult, he says, to see these blebs or these morphologically atypical spirochetes microscopically in tissues. "You don't see a typical long spirochete - all you see is granules, and atypical material, and to demonstrate that this is actively living material is very difficult."

Dr. Burgdorfer and I proceed back to the conference, where we bump into Moayad, one of the co-authors of the Phillips paper. Burgdorfer reminds him the notion of a spirochetal life cycle was first proposed in the syphilis literature long ago, which described how the syphilis organism

(Treponema pallidum, left) is not only present as a classical, beautiful spirochetal structure but it may also adopt "cyst-like" forms (right). Liegner notes "one couldn't even recognize these as having anything to do with syphilis or spirochetes unless one had made a very detailed study of the nature of the syphilis organism in tissues under various conditions."

In other IDEAS programs, we've heard about how the syphilis spirochete may be causing a lot of what we call "AIDS", despite remaining undetectable on blood tests (see What Causes AIDS? A Second Look , aired November 6 & 7, 1991, and éDja Vu: AIDS in Historical Perspective , aired January 9 & 10, 1996). It's possible it might elude detection by turning into these cyst-like forms. (see "Implications of the recent lyme culture technique for the diagnosis of syphilis", a paper by John Scythes and Colman Jones, presented at the Lyme conference - click here to read the press release).

James Miller, who has worked for nearly half a century with the spirochetes of both Lyme and syphilis, says "There's never been any definitive proof that the so-called cyst-like forms of T. pallidum occur in vivo, either in an animal or human." He notes that when the fluid from lymph nodes of syphilitic rabbits - in which he could not find any organisms - were injected into rabbits who had never been exposed to the disease, the newly-infected animals developed the disease, complete with classic spirochete organisms. But he can't say whether there were cyst-like forms present in the lymph nodes of the original rabbits, or simply very few spirochetes that he could not detect.

Does Burgdorfer think that everything that he's told me about Borrelia would apply to Treponema as well? "Of course. As far the ability of T. pallidum to undergo development into cyst forms, that has already been proven."

"And of course, in the old literature, these formations of the spirochetes were considered to be a degeneration process due to the fact that spirochetes cannot survive under these conditions and therefore they will eventually die and no longer develop. But in those days all the investigators had was the ordinary microscope to investigate what the spirochetes looked like. And then once the spirochete developed into these cyst forms, they were no longer detectable by the ordinary microscope. So, for them, that was the end of the spirochetes and they called it degeneration."

"Yet there was that other group of scientists who said, 'No, all these are a phase in the complex development from a mother spirochete to a daughter spirochete'. Still today, both theories have a lot of supporters. A lot of scientists say it has nothing to do with the further development, it has nothing to do with the immune process, and these are organisms that degenerate and are no longer able and capable of reverting to actively developing daughter spirochetes. Yet there is now mounting evidence that this complex development, and the ability of the organism to withstand unfavourable conditions, that this is true."

At the University of Massachusetts at Amherst, biologist Lynn Margulis is famous as one of the leading proponents of the Gaia Hypothesis - the idea that the earth as a whole acts like a gigantic living organism. Her concepts of symbiosis - the natural co-existence and co-development of different organisms - have transformed the study of evolution.

Part of Dr. Margulis' work involves looking at microscopic spirochetes found in the natural environment. Margulis says that free living spirochetes set a precedent, in the sense that they can survive desiccation. She has gone into their natural habitat and removed muds for as long a period as a few years - muds which look to the naked eye to be dry.

"We put that mud material back into supportive media for spirochetes and we see spirochetes come out - the spirochete form; which suggests that spirochetes are hiding in a form that's not the swimming spirochete. Now, if we take those spirochetes that look fine and healthy, and we put them into any kind of media that is threatening to them, they immediately round up, they pull in their bodies.

And this is active: this is not a falling apart, like when you hit them with alcohol or something like that. It's not a lysis, it's not a falling apart, it's not immediate death like you could easily cause immediate death by lots of negative conditions, like too much acid and so on. It's not the extreme that you see in immediate death but quite the contrary: you see active cells ballooning out their membranes, actively pulling in their bodies."

A videotape of spirochetes called Spirosymplokos (found in the hindguts of desert termites) shows the vigorous recoiling of the organisms into little balls, a remarkable behaviour to watch in real time as Margulis explains what we're seeing.

"Making these membraneous structures, that is making these non-spirochetal type morphologies, is a normal part of the life history of spirochete bacteria. It's likely that organisms like Borrelia and Treponema that have been found in human tissue can burrow into tissue and make the same kind of resistant bodies, and wait and come out when conditions are suitable twenty years later. I mean, I've got a couple of years in mud, why not in human bodies?"

In a paper published in the Proceedings of the National Academy of Science ("Composite, large spirochetes from microbial mats: Spirochete structure review", Proc. Natl. Acad. Sci. USA, vol. 90, p. 6969, August 1993), Margulis and colleagues note that confusion concerning the identification of spirochetes, especially Treponema pallidum, persists even among scholars who should be better informed. A recent book exacerbates the problem: "Syphilis has long fed on an hysterical panic that has ill-served the cause of prophylaxis .... Nowadays, by contrast, syphilis feeds on the carefree disdain of the general public. Can penicillin vanquish it? Of course, but one still has to know that one is contaminated. The treponema is a tiny fragile thing, a vulgar protozoan, not even a virus. But this fragility, which has so far made it impossible to culture in vitro and thereby gain a sufficient understanding of its modes of operation, assures its survival."

In her lab just outside of Detroit, Lida Holmes Mattman, Professor Emeritus at Wayne State University, has spent many decades studying all the different forms that bacteria can take, publishing a textbook entitled Cell-Wall Deficient Forms, published by CRC Press LLC.

Mattman says the first course on microbiology teaches everyone that bacteria have only a few shapes - balls, either in ones, twos or in chains (streptococci); rods or sticks (the well-known E. coli bacteria), and snakes (spirochetes and other spiral-shaped organisms).

But Mattman has discovered there are odd forms too, including what are called "L-forms" of bacteria. "I first realized there was such a thing as an L-form when I held in my hand a test tube that was very cloudy with broth. I had put some staphylococci in there, but when I made a smear of it, and heat-fixed it, I didn't see any organisms.

Yet I could take a few drops of that and put it in fresh broth that wasn't cloudy, and in a day it would get cloudy. But I didn't get any of these gummy colonies you can see with the naked eye. Then I realized there was something there I was missing, and I have been looking at those missing things ever since."

Mattman says it's a terrific misconception that L-forms are only produced by abnormal situations. "On the contrary, this is a normal way that bacteria grow, often 10 times more this way. It's as if you only recognize a man if he has a tuxedo on! Most of them go around very casually, and without a nameplate!"

The only way to definitely identify these odd-shaped bacteria, Dr. Mattman says, is by using very sophisticated biochemical techniques. Mattman says there's a misconception that these cell-wall deficient organisms are harmless not so, she insists.

"They're causing all sorts of problems." How does she know? "We find them in autopsies. We can also put them in animals and prove they make people sick." I ask Mattman if there is something different about this lab that allows her to see these L-forms.

"Maybe as a teacher I had a little more time than I did as a clinician, because someone was telling me how many stains he has to look at in one hour... we spend twenty minutes on one smear, so it's a matter of time."

The kind of research Mattman is doing isn't exactly familiar to most of the doctors I spoke to, who hadn't heard of this work. Garth Nicolson says much of the new molecular microbiology is not present in medical training today, and none of this was presented to physicians who received their training 10 or 20 years ago. But now, he says, there's an emerging awareness of the role of these infections in a variety of different diseases, and it will only increase with time.

Indeed, as new research is showing, there may be a lot more to bacteria than we thought. Tilton says "As we are in the midst of a revolution in information technology, I think we have a similar revolution before our eyes with regard to the role of micro-organisms in diseases of humans."

Someone who's thought a lot about diseases that may be caused by bacteria is Paul Ewald, an evolutionary biologist at Amherst College who's fascinated by how quickly conventional thinking about diseases can change. He points to the complete about-face on what causes ulcers.

Ewald says "If you open a medical text from the 1970s, you'll see almost everything listed as a cause of ulcers except infection. And now we know that it's infection that is the main culprit and that all these other factors - stress, maybe smoking, things like that - are exacerbating the problem, but they're not the primary causes. And this really does become pretty important, because it suggests to us where we should be putting most of our effort: if we are interested in reducing atherosclerosis, if we knock out the organism, maybe some of these other risk factors are not going to be particularly important, so it's very important to distinguish what is just another risk factor from what is the primary cause of the problem."

Notions about the causes of disease have changed over the course of history. In prehistoric times, ill health was a punishment of the gods, or the result of sorcery. In the Middle Ages, it was thought noxious vapors from decaying earth made people sick - malaria was attributed literally to "bad air". It wasn't until 1867, when Robert Koch showed that anthrax, a disease of sheep and cows, could be transmitted to mice, that the modern germ theory of disease became accepted. Since then, a wide array of microbes have been proven to be responsible for an equally wide array of human illness.

But there's still a long list of old chronic diseases whose causes remain a mystery: cancer, arthritis, diabetes, atherosclerosis and Alzheimer's, to name just a few. It's been impossible to show a specific bug is behind these conditions, so investigation has focused on other factors: poisons in the environment, inherited genetic mutations, and so on. While this research has yielded some important clues, the past decade has also seen other surprising discoveries that link bacteria to previously unexplained diseases, from stomach ulcers to heart disease. Some of these discoveries would never have been made using the traditional method of growing or "culturing" bacteria in the laboratory - the standard way to prove that a particular germ is making us sick.

Part Two of "The Bacteria Revolution" explores some of these new tools with the scientists who are using them, including David Relman. Relman, who teaches medicine and microbiology at Stanford University, notes that the ability to grow micro-organisms in a laboratory culture has up until recently been the only way to definitively identify them. This is because many germs look alike under the microscope, and it’s only when you can grow enough of them to observe their behaviour in culture that it’s possible to distinguish similar-looking bugs from each other.

As a result, being able to grow a microbe in culture forms part of a series of rules, or steps, originally developed by Koch to determine whether a given organism causes a given disease, called Koch's postulates. In essence, not only do you have to find the microbe in all cases of the disease, but you also have to be able to grow the organism in the lab, and then re-introduce it into a healthy animal or person and produce the disease again. Then - and only then - can you declare the germ to be the cause of the disease.

But Koch's postulates were based on bacteria, which are only one type of micro-organism that can cause disease. Relman notes that subsequent decades have since brought the recognition of an increasingly broad diversity of microbes, including viruses, which require another living cell in order to replicate. He says this complicates the picture, in some cases making it difficult, if not impossible, to fulfill Koch's original three postulates for proving causation.

Some researchers have suggested Koch's postulates are outdated, and ought to be abandoned. Others, like Richard Tilton, editor-in-chief of the Journal of Clinical Microbiology, take a more moderate stance. "Rather than abandon them, we should modify them," he says, "because it is now possible to detect the causative agent of a disease without isolating the organism."

One way of doing this is using a technique for homing in on the genetic material that makes up a disease organism and duplicating that genetic material millions of times - PCR, which stands for polymerase chain reaction. Tilton likens the technique to finding a needle in a haystack: "If there's one needle in the haystack, it's very difficult to find. However, if you can play tricks on that needle, and make a million needles, then it's very easy to detect."

Using PCR, medical detectives have been able to find previously undetectable microbes in all sorts of illnesses. One of these medical detectives is Garth Nicolson, scientific director at the Institute for Molecular Medicine in Huntington Beach, California. Nicolson studies chronic illnesses, which strike up to 6% of the population of North America, and has found that much if this chronic illness is due to stealth bacteria that have gone undetectable.

He says "These new technologies have just come to the forefront in the last decade, and before then there was really no evidence that these types of infections were even present. Now that we can find them, we can study their role in the disease process much more thoroughly." Nicolson feels the over-reliance on Koch's postulates has slowed the process down in finding out the role of these infections. "These organisms are extremely hard to culture, but we can fulfill many of Koch's criteria by monitoring the presence of these organisms and looking at animal models."

Because identifying the precise cause of a disease has significant ramifications for treatment, it's important to be sure you have the right bug. And with the advent of these new molecular DNA techniques comes a danger: the risk of blaming diseases on newly discovered microbes without stopping to think whether something else is involved. David Relman notes, "It is much easier to detect or amplify a DNA or RNA sequence in a clinical sample than it is to attribute some important role to this putative organism with respect to disease. As we start to apply these incredibly sensitive methods, we are starting to find that the diversity and number of organisms that occupy the human body is far greater than we thought, and it really prompts us to ask: what are these things doing there?"

Garth Nicolson insists there are a number of criteria that need to be fulfilled in order to pronounce a micro-organism the cause of a disease, including finding it in sick - but not healthy - people, detecting it in the part of body where there is illness, measuring an immune response to the infection (not always present), seeing if the patient responds to therapy, at which point the agent should be eliminated. Other pieces of evidence include developing an animal model in order to reproduce similar types of illness. Injecting organisms into humans is not considered ethical anymore, he notes, but one researcher - Barry Marshal - used it to prove Helicobacter pylori as cause of ulcers. "With some of the stealth infections we deal with, one would not want to try this, because they're potentially lethal and some people have actually died of these infections and that's in the medical literature."

Relman argues that number of independent approaches are going to be required in order to prove causality, and adds that one of the most interesting things about these molecular approaches is the new concepts of disease causation that will emerge as a result. He cites the example of molecular mimicry, in which certain bacteria can fool our immune systems into attacking not just the invading organism, but our own bodies as well. This may be the case, for example, with the bacteria Chlamydia pneumoniae, which researchers recently found shares genetic sequences with our heart muscle.

On the 10th floor of the new Princess Margaret Hospital on University Avenue in Toronto, Dr. Tak Mak, of the Ontario Cancer Institute, notes, "Our immune system is set up to make very subtle differentiations between infectious agents and yourself, because for infectious agents you would like to turn your immune system all the way up to kill every one of the infectious agents, but we talking about millions of proteins that our immune system is processing, and there will be overlaps. "

"After all, don't forget we evolved from bacteria. Bacteria make proteins often to do the same work as our own proteins, and we've only been separated for several hundred million years in evolution. A lot of the proteins are still identical from a bacterium to a man, so there will still be remnants of amino acid sequences that are shared. And when you mount an immune response against a bacterial or viral protein, and they have shared codes, our immune system can go overboard and start attacking our own tissues."

Dr. Josef Penninger works in the University Avenue lab, which is funded by Amgen Canada, a division of the giant U.S. bio-pharmaceutical company. He studies how the genetic structure of microbes can mimic parts of our own body, working on mouse models of auto-immune inflammatory heart disease.

Penninger, along with his colleague Kurt Bachmaier, was able to show that a piece of the Chlamydia pneumoniae germ, bore a striking resemblance to a protein in heart muscle. He did this by lining up the genetic sequences of chlamydia and the heart muscle protein, using DNA databases he found on the Internet. He points out "we would never have found this using Koch's postulates."

For years, there's been the suspicion that bacteria were involved in heart disease, especially since some people treated with antibiotics for other reasons seemed to have fewer heart attacks. But no one had been able to definitively prove a connection between Chlamydia pneumoniae and heart disease that is, until February 1999, when Penninger and his colleagues published their findings in Science magazine. As Penninger notes, "Our paper made the first causal link to say that bacteria are not just these little innocent bugs sitting around - they can actually trigger heart disease. Our model explains lots of anecdotal data - why people with no risk factors are getting sick, why some people who are smoking, drinking, and obese never get heart disease - our model can completely explain this, and why in some circumstances antibiotic treatment helps against heart disease. As long as no one comes up with a better model, it's a fairly reasonable assumption this contributes to heart disease."

But why do so many people infected with Chlamydia pneumoniae - 1 in 2, according to most statistics - escape its effects? Penninger says it has to do with how white blood cells detect the presence of foreign organisms, which they do in association with a molecule called MHC (Major Histocompatibility Complex), a part of the immune system's built-in control mechanism.

It's the MHC molecule that picks up little parts of chlamydia to show to red blood cells, but these MHC molecules differ from person to person. "If I'm unlucky, and my MHC molecules shows this part which looks like my heart to the immune system, then they are tricked. But the next person might pick up another part of chlamydia, so their immune system kills chlamydia but never attacks the heart. But you still have to explain why treatment works for some and not others."

The answer may have to with when someone takes antibiotics. If the auto-immune reaction produced by chlamydia has already started, it may keep on going even after the bugs are killed off. "We think the bug is probably the trigger but once auto-immunity is established, it is self-maintaining." He says this explains why some people report antibiotics are working - "you probably hit Chlamydia infection very early."

But this business of molecular mimicry is only one mechanism bacteria use to make us sick. Relman notes there are also examples of disease where an organism may die and yet still persist in the form of pieces which may be sufficient to induce disease. Others may release a toxin capable of causing disease, or may be lurking in an anatomic site one would never think to go looking at. He favours the idea of embarking on a search using broad methods, which are not necessarily specific to any one bacterium. "There is going to be no one study which is going to give everyone the answer - it's really going to be an incremental process."

The idea that we have been using dangerously outdated methods to find infections is one shared by evolutionary biologist Paul Ewald, who has been thinking a lot about various infections and the diseases they might cause.

Ewald says "People have worked on the misunderstanding that any fewer diseases are caused by infection than really are caused by infection. The way to evaluate whether this has in fact been the case is to look at the track record, which is that, over the last hundred years, really, we have a steadily increasing number of diseases that we accept as being caused by infection."

Ewald has put forward the radical idea, dubbed "The New Germ Theory of Disease", that says that most of our chronic killers - from heart disease to Alzheimer's to cancer - must be due to infection. "If diseases have strong negative effect on the survival and reproduction of humans, and if they're pretty common, it's very unlikely that these diseases will be caused strictly by bad genes, because those bad genes would be lost through time, because of the negative effects that the disease has on the people who would harbour those genes for the disease."

A good example is the epidemic of infertility among women in the 1970s, which mystified researchers at the time. "Let's say they had some sort of bad gene", Ewald hypothesizes. "Think what would happen over next few generations: those genes would be lost in quite short order. The fertility problem decreases fitness so much it would disappear" (as it turns out, the epidemic of infertility was caused by an epidemic of Chlamydia trachomatis).

The notion that infections are at the root of most chronic diseases is surprising for some people, Ewald admits, because we supposedly "know" about the genetic basis for diseases like Alzheimer's or atherosclerosis. "But one has to be careful", he warns, "because often that genetic basis that you identify may be a genetic vulnerability to some other cause." Pointing to recent studies, such as Penninger's, he notes "the genetic basis for those diseases is really a genetic basis for vulnerability to an infectious agent, that then starts the whole disease process rolling, and then all the other risk factors exacerbate the progression of the infection and the disease that results from that."

Professor Ewald's ideas have their critics. Dr. Tak Mak in Toronto isn't sure that genetic mutations might still not be responsible for certain diseases, especially those like cancer, which strike most people well past their reproductive age. He says, "The major problem is that we, as a race, reproduce earlier than the incidence of most cancer. Most of us develop cancer starting from our 40s and 50s - by that time most of us have already reproduced, so the natural selection in a Darwinian way is not there. Therefore we are going to develop cancer for many billions of years."

Ewald responds that because chronic conditions like cancer and Alzheimer's are so common, they actually have more of a fitness cost than one might think. "The real problem in calculating how much of a negative effect they have on our survival and reproduction is that it's very difficult to know how important the effects of people - who are no longer reproducing themselves - can be on grandchildren. Older people may have a strong positive effect on their fitness if they're healthy by influencing the survival of grandchildren even if they're not actually reproducing themselves."

He adds, "The fact that where so many other chronic diseases that are having negative effects on fitness are turning out be infectious certainly should encourage us to look and see whether or not some of these other diseases, that aren't having such strong negative effects on fitness, might be caused by infection."

Microbiology has evolved into a very sophisticated science since the days of Robert Koch. When you compare Koch's simple methods for culturing bacteria to the incredible range of detection techniques available today, it's no wonder we're in the midst of a bacteria revolution - the technology we use governs the way we look at the world. Before the invention of the telescope, we had no way of seeing deep into the cosmos. Likewise, in the microbial universe: these new diagnostic tools are bringing a whole range of previously unknown disease-causing entities into sharp focus. Correctly interpreting the world of information these tools provide will be a challenge for medicine in the new millennium.

From: http://www.radio.cbc.ca/programs/ideas/shows/bacteria/bacteria.html