Re: b garinii genome paper, complete - 2004 {without pictures}

Old post from Kat, found it will googleing

NOW Magazine
Toronto, Canada, June 3, 1999
http://www.nowtoronto.com/issues/18/40/News/feature.html

Bacterial Bombshell

New technologies can uncover hidden germs -- have we found the possible
cause of heart disease, M.S. and maybe even AIDS?

By COLMAN JONES

NEW YORK CITY-- At the sedate 12th International Conference On Lyme
Disease, I have one of those electrifying moments familiar only to
those who have tracked a mystery beyond the point of good sense and
then discovered some other intrepid soul on the trail just ahead.

It occurs when Willy Burgdorfer, the white-haired discoverer of the
tick-borne Lyme microbe, shuffles his papers at the podium and offers
an idea so seismically unconventional that shivers run down my spine.

Traditional medical tests, he says, often proclaim a patient cured of
Lyme disease when the bug is really still hanging around in the body.
The microbe has a shrewd capability, he says -- it can form cysts and
hide in body tissue despite the exterminating effects of antibiotics.

After a decade on the AIDS beat, I can hardly believe my ears. What
Burgdorfer is saying about Lyme is exactly what a fellow lay researcher
and I have been saying could be happening with the closely related
syphilis germ.

For years we've been obsessed by the riddle of what happened to the
estimated half a million cases of syphilis that went untreated in gay
men during the 70s and 80s. Though deemed heretics by the mainstream
AIDS community, we continue to wonder if there's a chance that the
undetected syphilitic infection could wear down the immune system over
time, resulting in the symptoms ascribed to HIV.

While there aren't many rebel researchers asking this particular
question, there are now, fortunately, many more scientists preoccupied
with bacteria and their relationship to chronic disease.

By means of new laboratory and genetic techniques, researchers are
uncovering hitherto undiscovered germs that may be responsible for a
host of conditions previously thought to be uninfectious -- from
stomach ulcers, Crohn's disease, rheumatoid arthritis and lupus to
heart disease, Alzheimer's, multiple sclerosis and cerebral palsy.

And while it's strange to think that everything from heart attacks to
bouts of depression might one day be prevented by a dose of
antibiotics, there's no question we're in the midst of a bacterial
revolution that is paving the way for a new medical paradigm for the
next millennium.

***

Bookstore owner and AIDS heretic John Scythes and I have come to this
conference inspired by the announcement of a new culturing method that
can allegedly find cyst-like forms of the Lyme bacterium (a member of
the spiral-shaped spirochete family of germs) in the blood of patients
who have supposedly been cured of the disease.

We have submitted a paper suggesting that the technique be applied to
uncover hidden syphilis spirochetes in AIDS patients. To our surprise,
our humble laypersons' offering is given the thumbs-up; it's one of
only16 papers accepted for display at this meeting.

Thus, we are allowed our poster display in the conference foyer.

We've been aware for a long time that during the 70s and 80s, syphilis
infected vast numbers of people who then went on to develop AIDS. But
we didn't have a lot of modern-day support for the idea that the
syphilis germ -- notoriously difficult to detect after the initial
infection -- might be hiding in AIDS patients in some altered form.

Until Burgdorfer. During a break in the conference proceedings, the
esteemed scientist himself walks up to look at the reproductions of
cyst-like forms of spirochetes that Scythes and I have compiled from
old syphilis texts, some of the same images he used in the overhead to
illustrate his lecture.

"We can demonstrate cysts by microscopy (in the case of Lyme), and once
they are in the tissues of the patient we can no longer detect them,"
he tells me. "It is quite possible that this material we cannot see is
responsible for producing prolonged and chronic disease," he says of
the illness carried by ticks in wooded areas of the U.S. and Canada.

Desert termites

Does he think that everything he's suggested about the Lyme spirochete
taking on cyst-like forms and escaping detection would apply to the
syphilis spirochete as well?

"Of course. The ability of T. pallidum (the syphilis spirochete) to
undergo development into cyst forms has already been proven," he tells
me.

A few days later, in her lab at the University of Massachusetts at
Amherst, biologist Lynn Margulis, more famous for her advocacy of the
Gaia hypothesis -- the Earth as a living organism -- plays me a
live-action videotape she's made of spirochetes called spirosimplokos,
which are found in the hind guts of desert termites.

I'm amazed to watch the vigorous recoiling of the organisms into little
balls, exactly the kind of behaviour described by Burgdorfer and
Moayad, only with a different species of spirochete.

"It's likely that organisms like Borrelia (Lyme) and Treponema
(syphilis) can burrow into tissue and make the same kind of resistant
bodies, and wait and come out when conditions are suitable 20 years
later. I mean, I've got a couple of years in mud, why not in human
bodies?"

***

Whether or not undetected spirochetes are wreaking havoc in AIDS
patients, the hunt for "stealth pathogens'' is in full swing, thanks in
part to new technologies enabling scientists to "see" hitherto
invisible organisms.

David Relman, professor of medicine and microbiology at Stanford
University, is one of a growing number of researchers who note that
traditional criteria for establishing infectious causes of disease may
not be adequate for finding organisms that are difficult or impossible
to cultivate in a petri dish.

One way of testing for microbes is through polymerase chain reaction
(PCR), a technique for homing in on the genetic material that makes up
a disease organism and duplicating that genetic material millions of
times. Using PCR, medical detectives have been able to find previously
undetectable microbes in all sorts of illnesses.

Gone undetected

One of these medical detectives is Garth Nicolson, scientific director
at the Institute for Molecular Medicine in Huntington Beach,
California, who studies chronic illnesses.

Nicolson has found that much long-term sickness is due to stealth
bacteria that have gone undetected. "Without these new technologies, it
would not be possible to detect these infections," he says.

Relman adds that one of the most interesting things about these
molecular approaches is the new concepts of causality they give rise
to.

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 is the case, for example, with the bacteria Chlamydia pneumoniae,
which researchers at Princess Margaret Hospital recently found shares
genetic sequences with our heart muscle.

Josef Penninger, whose findings linking heart disease with chlamydia
infection were published a few months ago in the pages of Science
magazine, tells me he discovered the similarity between the bacterium
and heart muscle by logging on to the Net and entering their DNA codes
into online databases.

***

Establishing new procedures for making visible what was formerly deemed
nonexistent has its challenges.

Take the case of the new culturing method developed by a team under
Greenwich, Connecticut, internist Steven Phillips aimed at locating
Lyme spirochetes in patients who are supposed to be cured. The
publication of his paper in the European journal Infection opens up a
Pandora's box for patients and researchers alike.

Many are doubtful that the test does what it says it does. Says Lyme
researcher Deiter Hassler from Heidleberg, Germany, "To my knowledge,
nobody worldwide has found as much (Lyme bacteria) in culture as
Phillips has, and we don't know exactly why. I can't believe that so
much survives, but I'm not sure."

Walter Marget, editor of Infection, declares from Munich that "our
reviewers are very, very skeptical. I'm not very enthusiastic about
this study."

But the Phillips team is insistent that its finding will forever alter
concepts about Lyme, a disease that can take many forms from fatigue to
arthritis.

Hamid Moayad, a neurologist from Fort Worth, Texas, and co-author of
the paper, says, "This would actually be the gold standard for
diagnosis of Lyme disease, 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 paper
proves without a shadow of a doubt that it is a chronic infection."

Sam Donta, a leading Lyme specialist who works at Boston University's
school of medicine, concurs that you can't conclude there is no
infection if blood tests are negative.

Donta has compared the standard blood tests for Lyme disease with more
sophisticated tests, and now questions the criteria for the lab
diagnosis of Lyme established by the U.S. Centers for Disease Control.
He notes with concern that "physicians are still relying on a negative
test as meaning that a person does not have Lyme disease."

Also banking on negative tests are U.S. insurance companies. Karen
Vanderhoof-Forschner, who chairs the board of directors of the Lyme
Disease Foundation (sponsors of the New York conference), notes, "There
is a lot of money out there to be made by having expert witnesses at
trials for insurance companies who feel they can clearly and easily
separate those who have the infection from those who are disease
wannabes."

At bottom, if Phillips and team are correct, Lyme disease may prove
itself much more widespread than was previously thought. "Given the
flaws in currently accepted diagnostic criteria, it is likely that Lyme
is vastly underdiagnosed," warns the Phillips paper.

***

Now that doctors have better techniques for zeroing in on hidden
infections, they're finding spirochetes in all kinds of patients --
even those who don't show the typical symptoms of Lyme.

For example, a doctor from New Jersey, Martin Freid, tells me he has
found infection with the Lyme germ in at least two of his patients with
Crohn's disease, an inflammation of the bowel that affects some 50,000
Canadians and whose precise cause has eluded medical researchers.

Gordon Greenberg, professor of medicine at the University of Toronto
and head of the gastroenterology division at Mount Sinai, says it's not
clear exactly what causes either Crohn's disease or ulcerative colitis,
another inflammatory bowel disease.

"There has always been the concept that a single infectious etiology
might be the cause of Crohn's or ulcerative colitis," he notes, "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 centre, on the effect of specific antibiotics 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 per cent 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.

Lida Mattman, professor emeritus of microbiology at Wayne State
University, has spent many decades studying all the different forms
bacteria can take and has written two editions of a textbook entitled
Cell-Wall Deficient Forms.

Mattman continues to find odd-shaped bacteria in the blood of patients
with all sorts of chronic diseases, at a facility I've come to visit
just outside Detroit.

"I would like a neurologist to tell me why he can't believe that
multiple sclerosis (MS) is due to a spirochete," she insists, pounding
her fist on the table, "when all you have to do is take a drop of
spinal fluid and look at it and you can see them. You don't even have
to concentrate it," she says, citing the work of German pathologists
published in the scientific literature.

"Look at the people having trouble with MS, and no research being done
on this -- it's criminal."

The kind of research Mattman is doing isn't exactly familiar to most
doctors. Nicolson says much of the new molecular microbiology is not
taught in medical schools today, and none of it was presented to
physicians trained 10 or 20 years ago.

But now, he says, there's growing awareness of the role of these
infections in a variety of different diseases, and this awareness will
only increase with time.

Paul Ewald, an evolutionary biologist at Amherst College in Amherst,
Massachusetts, has advanced the radical idea, dubbed the "new germ
theory of disease," that most of our chronic killers -- from heart
disease to Alzheimer's to cancer -- must be due to infection.

Negative effect

"If diseases have strong negative effect on the survival and
reproduction of humans, and they're common, it's unlikely that they
have a genetic cause."

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 the next few generations. Those genes
would be lost in quite short order. The fertility problem decreases
fitness so much that it would disappear." (As it turns out, the
epidemic of infertility was caused by an epidemic of Chlamydia
trachomatis.)

Ewald notes how quickly conventional thinking about diseases can
change. He points to the complete about-face on what causes ulcers.

"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 are not the primary causes."

Obviously, identifying the main culprits in chronic diseases is
important, Ewald says, because it suggests 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."

.

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