The patients arrive with a folder, and the folder is usually the first thing I notice. Inside are the years they have spent searching for an answer: lab reports from companies I have sometimes never heard of, the names of the six or eight doctors who came before me, a careful record of when each symptom began.
They bring the documentation because experience has taught them they will need it. Most of them already have a diagnosis by the time they sit down. It is usually chronic Lyme disease, a label mainstream medicine does not recognize, given to people who in most cases never had Lyme at all. The most delicate part of my work is the hour that follows.
Picture a patient I meet some version of nearly every week. She is in her forties. A few years ago she grew tired in a way that sleep did not fix, then her joints began to ache, then came the mental fog, the reaching for words that used to be there. She saw her primary doctor, a rheumatologist, a neurologist.
Her thyroid was normal, her scans were clean, and more than one visit ended with the suggestion, spoken or not, that the trouble might be in her head. Then a clinician ordered a test from a specialty lab, and it came back positive, and for the first time in years someone gave her a name for what she had.
The relief of that moment is hard to overstate. She was not imagining it. There was a reason, and a plan.
The clue in the blood
Here is what I have to find a way to tell her. Her blood did hold a clue, but the clue was that the test had misled her. Lyme tests do not detect the bacterium itself; they detect the antibodies the body makes against it. There are two kinds, immunoglobulin M and G (IgM and IgG).
IgM antibodies appear first, in the early days and weeks of an infection, then fade. IgG antibodies build a little later and persist for years. Her result showed IgM alone, with no IgG, several years into her illness. An infection that had truly been in her body that long would have produced abundant IgG. A lone early-type antibody this late is one of the best-described false alarms in laboratory medicine, which is why testing guidelines from the Centers for Disease Control and Prevention (CDC) say an IgM result should be disregarded once a patient has been ill for more than 30 days.
She did not have Lyme disease. She almost certainly never did.
She is not unusual. She is the rule, and her test is only one of the ways these results mislead. Another patient's report will show a Western blot, a test that looks for antibodies against several different Lyme proteins and shows each as a band on a strip.
The federal criteria require at least five of 10 IgG bands before the result counts as positive, because the proteins are not all unique to Lyme. Some closely resemble proteins on ordinary, harmless bacteria, including ones that live in the mouth and gut, so a person who never encountered Lyme can still light up a band or two.
The most common of them, a flagellin protein, turns up in nearly half of healthy people in one study, many with little or no chance of exposure. A report that reads "two bands present" can look, to a frightened patient, like partial proof. It is closer to background noise, and standard testing calls it negative for exactly that reason.
What real Lyme looks like
To see why these false signals are so easy to mistake for the real thing, it helps to know what real Lyme disease looks like, because almost all of the confusion comes from losing track of that.
Lyme is concentrated in particular places. The great majority of cases, roughly 90%, come from a handful of high-incidence states in the Northeast, mid-Atlantic, and upper Midwest. In much of the rest of the country, including here in California, it is genuinely uncommon, and the reason is partly a quirk of natural history.
In the West, immature ticks feed heavily on the western fence lizard and the alligator lizard, whose blood carries a factor that destroys the Lyme bacterium (Borrelia burgdorferi, at right) inside the feeding tick, so the tick that molts into adulthood often emerges cleansed of it. The result is that less than 2% of adult ticks in California, and under 10% of the young ones, carry the bacterium at all. Where a person lives shifts the odds before any test is run.
The disease also has a shape. Early on it can raise a slowly expanding patch of redness at the bite, and when that rash is the classic kind, a doctor should treat it on sight, without waiting for blood work; there, Lyme is a diagnosis made with the eyes.
But the rash is often not the tidy bull's-eye of the textbooks, and sometimes there is no rash at all, which cuts both ways and makes the early picture genuinely hard. Later, untreated Lyme can settle into a joint, and when it does it tends to cause dramatic swelling of a large joint, most often the knee. Many of the patients who reach me carrying a Lyme diagnosis describe something different: an ache in the small joints of the fingers, no swelling, no knee involved at all. The label and the illness do not match.
This is why how the test is ordered matters as much as how it is read. A blood test earns its keep only when the story already points to Lyme. Ordered for someone with vague, common symptoms and no real exposure, in a place where the disease is rare, it does not uncover hidden infection so much as generate false alarms, because when Lyme was unlikely to begin with, most of the positive results it returns are wrong.
A quiet contest, now settled by Washington
For most of my career, this stayed near the margins of medicine, a quiet contest between the evidence and a parallel system of belief. On May 29, that changed. At the New Hampshire State House, Health and Human Services Secretary Robert F. Kennedy Jr. announced what he called one of the most ambitious federal efforts ever mounted against Lyme disease, flanked by patients who had waited a long time to be taken seriously.
Much of it is worth applauding. Ticks are spreading, and the season is lengthening. The plan funds new tick research, sustains the federal investment in Lyme science, and puts real money toward the better diagnostic tests we badly need. It also said aloud, from a government podium, something these patients rarely hear: that their struggle is real and deserves an answer. I believe that, too. Any honest account of this disease has to start there.
One piece of the plan does something else, and it will reach my exam room.
But one piece of the plan does something else, and it will reach my exam room. Folded into the package is a federal partnership with a group called the International Lyme and Associated Diseases Society, including a clinician finder, hosted on a government website, that steers patients toward its providers. Beside it sits a new framework that files Lyme under "infection-associated chronic illness," with guidelines to be rewritten every six months, and a Medicare billing change that treats chronic Lyme as a condition to be managed and paid for over years.
This reads as compassion. In practice it places the authority of the United States behind the same path that delivered my patient to me: the test run on the wrong person, the confident wrong diagnosis, the long treatment for an illness she did not have.
The suffering is real, the infection is not
None of this means that everyone recovers cleanly. Most people treated for Lyme do get fully better, but a minority are left with lingering fatigue, pain, or trouble concentrating after the bacteria are gone, and we do not yet have a proven treatment for it.
This is not unique to Lyme. Many infections, viral and bacterial, can leave a tail of symptoms behind once the microbe itself has cleared, an aftermath that seems to live in the immune system's slow return to normal rather than in any surviving germ.
CDC / James Gathany, William L. Nicholson
There are hints at how that might work: in Lyme arthritis, fragments of the dead bacterium's cell wall can linger in the joint and keep provoking inflammation long after the live spirochete—another name for the spiral shaped bacterium—is gone. Repeated, careful searches for living Lyme bacteria in these patients have not found them.
The suffering is real. The hidden, ongoing infection is not, and that distinction is the whole game. The chronic Lyme world treats persistent symptoms as proof of a lingering infection that more antibiotics can clear. But the people filling its clinics are mostly not that small group of genuinely post-Lyme patients. They are people like the woman with the folder, who never had Lyme in the first place.
Whenever anyone counts, the same pattern appears. When French researchers carefully evaluated roughly 300 patients referred for presumed Lyme disease, less than 10% actually had it. More than 80% had a condition other than Lyme, most of them firmly diagnosed and many serious but treatable: depression, multiple sclerosis, thyroid and autoimmune disease, and, in a number of cases, cancer.
A wrong diagnosis is not a harmless placeholder. It is the thing standing between a patient and the right answer.
When the treatment is the danger
A wrong diagnosis would matter less if the treatment were safe. It is not. In 2017, the CDC, working with physicians in my own division at Stanford University, described five patients gravely harmed by treatment for chronic Lyme disease.
A woman in her late 30s, told she had chronic Lyme and two other infections, had a catheter threaded into a deep vein to deliver months of intravenous antibiotics; it seeded her bloodstream with bacteria, she went into shock, and she died. Another spent months treated for chronic Lyme and two invented infections while her real illness, ALS (“Lou Gehrig’s disease”), went unaddressed, and the antibiotics handed her a severe intestinal infection along the way.
A separate report found patients whose cancers were blamed on chronic Lyme for months or years, until the chance to treat the cancer had passed.
This is the system the new federal finder points toward. Surveys of chronic Lyme clinics have found consultation fees in the thousands, fewer than half staffed by physicians, and treatment menus that mix long antibiotic courses with herbs, infusions, and ozone.
A separate report found patients whose cancers were blamed on chronic Lyme for months or years, until the chance to treat the cancer had passed.
This “treatment” approach has one feature that makes it nearly impossible to escape. When a patient feels worse, the decline is recast as proof the treatment is working, a toxic release to push through. Improvement confirms the diagnosis, and so does deterioration. A system in which every outcome proves the original answer is not medicine, and the government has now built it a front door.
The vaccine RFK Jr doesn’t mention
The plan's most telling feature is what it left out. Two months before the announcement, Pfizer and Valneva reported that their Lyme vaccine had passed its final major trial, cutting confirmed cases by about 73% in people aged five years and older. Company officials said they would seek approval this year.
It would be the first Lyme vaccine available here since 2002. An effort billed as the most ambitious ever waged against Lyme, unveiled weeks after the first effective Lyme vaccine in a generation crossed the finish line, did not mention it. The silence fits Kennedy's long record against vaccines, and it shapes the prevention plan he offered instead, which leans on cutting ticks on deer.
Deer feed the adult ticks, but they are not where the bacterium lives; in the Northeast it is kept alive mostly in white-footed mice. Culling deer can lower tick numbers, but only at impractically low deer densities, and it does little to touch the reservoir that keeps infecting them. A plan that promotes a blunt tick measure while ignoring a vaccine that just proved itself has its priorities reversed.
A familiar machine
I wrote in these pages in March about a reconstituted federal advisory committee that built an entire scheme of diagnostic codes and treatment centers around a COVID vaccine–related syndrome whose estimated frequency spanned a 300-fold range and whose own recommended tests were, by the document's admission, unvalidated.
The machinery here is the same. A real but uncertain thing—lingering symptoms after Lyme disease—is being folded into a federal category of infection-associated chronic illness alongside long COVID and vaccine injury, wrapped in guidelines that change twice a year and tied to a billing code, well ahead of the science that would justify any of it. The framing is always humility before complexity.
The effect is to lower the bar of evidence for everything it touches, so that a contested syndrome can be treated, and paid for, as settled disease.
What taking her seriously looks like
So I think about the woman with the folder, and about what taking her seriously actually asks of me. It does not mean handing her the answer that comes fastest and hurts least. It means the slower work of looking for the real cause of her symptoms, the treatable one that the Lyme label would have buried.
Sometimes I find it. Sometimes I cannot, and I have to sit with her in the honesty of not yet knowing, which is its own form of respect, and which the marketplace will never offer her, because it always has something to sell.
A federal seal on the path that failed her is not the help it claims to be.
Believing a patient is not the same as agreeing with what she has been told. The cruelest thing I could do is nod along with a wrong diagnosis because it is the kind thing to say, and let her spend the next several years, and her health, chasing a cure for a disease she does not have.
She deserved better the first time. A federal seal on the path that failed her is not the help it claims to be.
Dr. Scott is a Clinical Associate Professor of Infectious Diseases at Stanford University School of Medicine and a co-author of “Updated Evidence for Covid-19, RSV, and Influenza Vaccines for 2025-2026“ in the New England Journal of Medicine.
The opinions voiced in CIDRAP Op-Ed pieces are the authors’ own and do not necessarily represent the official position of CIDRAP.
