Lyme Testing in Children - Why a Negative Test Isn't the End

Aug 16
13 min read

Updated: 2 days ago

Parent discussing Lyme testing with a child

Lyme testing in children and what a negative test does and doesn't mean

Written by Amy Patton, DNP, APRN, CPNP-PC — pediatric nurse practitioner and founder of Happy Kid Functional Medicine, Omaha.

A Lyme test is an antibody test. It measures your child's immune response to the bacteria. It does not measure the bacteria themselves. That one fact explains most of what confuses families here. It is why a negative test early on proves very little. It is also why a positive test months later can't tell you much. That test can't say whether the infection is still there.

If you're holding a result you don't believe, keep reading. You may be right. You may be wrong. Both are worth knowing for sure.

What do parents ask me most about this?

Short answers first. The full reasoning is below.

Why did my child's Lyme test come back negative?

Because standard two-tier Lyme testing looks for antibodies. Antibodies take weeks to build. Early in an infection, there is nothing yet for the test to find. So a negative result soon after a bite does not rule Lyme disease out. It mostly tells you one thing. The immune system hasn't caught up.

What does the standard Lyme test actually do?

Standard two-tier testing runs two steps on one blood sample. The first step is an EIA or an IFA. If that first step is negative, testing stops there. Is it positive or equivocal? Then the lab runs a second test on the same sample. Only the combination counts as a positive result.

What if my child has the rash?

If a child has the expanding rash of early Lyme disease, you treat it. You don't wait for a test. That rash is called erythema migrans. In a child with likely exposure, it makes the diagnosis on its own. Testing at that moment is more likely to mislead you than to help.

What about specialty labs like IGeneX?

IGeneX is a CLIA-certified specialty laboratory in Milpitas, California. Its Lyme ImmunoBlot uses recombinant proteins instead of whole-cell lysate. The company states that the test detects antibodies to nine different Borrelia species. Nine. Not 41. A "41 species" claim circulates widely online.

Are there kinds of Lyme the standard test misses?

Yes, two are worth knowing by name. Borrelia mayonii and Borrelia miyamotoi are both carried by the blacklegged tick. Both cause illness in people. Neither one is reliably picked up by standard two-tier Lyme serology.

Why did my child's Lyme test come back negative?

The size of that gap is well measured. Waddell's 2016 meta-analysis looked at two-tier testing in early stage 1 disease. Sensitivity was 46.3%. The 95% CI ran 39.1–53.7. Fewer than half of infected people test positive at that stage. Sensitivity rose to 89.7% in early disseminated disease. It reached 99.4% in late disease. Specificity stayed above 99% at every stage.

Lyme test sensitivity changes from early to later stages of infection

CDC's own authors say it just as plainly. Moore and colleagues wrote it in a 2016 paper. Their words: "sensitivity of 2-tiered testing is low (30%–40%) during early infection while the antibody response is developing." Those are CDC scientists, describing CDC's own recommended test.

Steere's 2008 prospective study makes it concrete. It followed 76 patients who had the Lyme rash in front of a doctor. Only about a third were positive on acute-phase samples. Nearly two-thirds were positive on samples drawn 3–4 weeks later. Same patients. Same infection. Different week.

So there are two common reasons a child's test comes back negative. It was drawn too early. Or your child doesn't have Lyme disease. Those are very different. The test alone cannot tell them apart. What separates them is timing and exposure. That's why my first questions are about where your child was and when. Not about the number on the page.

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What does standard Lyme testing in children actually do?

Two-tier Lyme disease testing process showing first and second blood tests

For years, the second step was a western blot. Since 2019, CDC also accepts a second EIA in place of the blot. That setup is called modified two-tier testing. Mead and colleagues put it in MMWR that year. When cleared by FDA for this purpose, EIA-based two-test formats "are acceptable alternatives for the laboratory diagnosis of Lyme disease." Those words about FDA clearance carry weight. Not every EIA pairing qualifies.

The band rules are worth knowing. Parents get handed these lists with no note on how to read them. An IgM blot counts as positive with at least 2 of 3 bands: 24 kDa (OspC), 39 kDa (BmpA), and 41 kDa (Fla). An IgG blot counts as positive with at least 5 of 10 bands: 18, 24, 28, 30, 39, 41, 45, 58, 66, and 93 kDa. Some labs print OspC as 23 kDa. It's the same band.

CDC attaches four caveats to its own test:

The assays may be falsely negative in the first 4–6 weeks of infection.
Antibody titers persist for months to years. So a positive test cannot tell you whether the infection is gone. There is no follow-up test that confirms it cleared.
False positives occur with relapsing fever, syphilis, rheumatoid arthritis, and Epstein-Barr virus.
Early antibiotic treatment can blunt the antibody response. That can make a truly infected child look negative.

One more CDC rule trips up families. Has the child been ill for more than 30 days? Then a positive IgM result should be disregarded. IgM is an early-response antibody. Months into an illness, a lone positive IgM is much more likely to be noise than signal. Say a child has been sick since spring. Someone builds a long treatment plan on an IgM band. That rule is the thing to raise.

What if my child has the rash?

Gerber's 1996 study settles this for children. It was published in the New England Journal of Medicine. He followed 201 consecutive children with Lyme disease in southeastern Connecticut. The median age was 7. Serology at presentation was positive in only 37% of the children with a single rash. Among children with multiple rashes, 89% were positive. So the diagnosis was plain to the eye. The blood test still failed nearly two-thirds of the time.

Here the mainstream position and the Lyme-literate position actually agree. Families deserve to hear that out loud. CDC and the IDSA/AAN/ACR guideline say treat the rash clinically. ILADS says treat the rash clinically. Nobody is arguing.

Gerber's outcomes are worth carrying too. All 201 children responded to treatment. 94% were free of symptoms at 4 weeks. Follow-up ran 25.4 months on average. None had chronic or recurrent Lyme disease. That is a good number to hold on a hard night.

The rash is often not a bullseye. It's easy to miss under hair. What to do after a tick bite: where to look. It also gives the timeline to watch.

What about specialty labs like IGeneX?

IGeneX is a CLIA-certified specialty laboratory in Milpitas, California. Its Lyme ImmunoBlot uses recombinant proteins instead of whole-cell lysate. The company states that the test detects antibodies to nine different Borrelia species. Nine. Not 41. A "41 species" claim circulates widely online. It is not traceable to anything IGeneX publishes about its own test. So please don't repeat it.

Getting the company's actual claims right matters. Both sides of this argument get them wrong. IGeneX states it is CLIA-certified in all 50 states, in the high-complexity category. It holds separate state licenses in California, Maryland, Pennsylvania, New York, and Rhode Island. New York State approved its Lyme ImmunoBlots. IGeneX does not claim CAP accreditation. Nobody should claim it on their behalf.

Their validation paper is Liu and colleagues in Healthcare, 2018. It ran 178 sera: 26 patients with Lyme disease and 152 without. Samples were read in a blinded fashion against both CDC criteria and IGeneX's own in-house criteria. The conclusion: the ImmunoBlot outperformed the Western blot. Two things about that study are simply facts. All six authors were IGeneX staff. The developer was also the judge. And 26 cases is a pilot. No independent replication was located.

Here is the mainstream objection, in its own words. CDC and FDA put out a joint notice in MMWR in 2005. They warned about commercial laboratories testing for Lyme disease "by using assays whose accuracy and clinical usefulness have not been adequately established." They also warned about laboratories that "interpret Western blots using criteria that have not been validated and published in peer-reviewed scientific literature." The 2020 IDSA/AAN/ACR guideline names more methods to skip. The list: nonstandard serology interpretation, urine antigen tests, DNA testing, lymphocyte transformation tests, and CD57 assays. Those "should be avoided for clinical use due to lack of systematic, independent, reproducible validation studies."

Now, the detail almost nobody includes. It is the most useful thing on this page. Fallon's 2014 study ran in Clinical Infectious Diseases. It sent sera to four laboratories. Those were one university lab, one commercial lab, and two Lyme specialty labs. The sera came from 37 patients and 40 healthy controls. The labs differed little on positive ELISA and IgG western blot results. What changed was the reading. The specialty labs applied their own in-house criteria for positivity. At one of them, specificity then dropped a lot. The problem was traced to the interpretive criteria, not the assay platform.

That is the fair version of the criticism. It also gives you something to do. "Specialty labs are unreliable" does not. Does your child have a result from one of these labs? Ask which criteria were used to call it positive. Then ask whether it would still be positive under standard criteria.

Finally, the point both camps invoke. The CSTE and CDC surveillance case definition says it in its own words. Surveillance case definitions "are not intended to be used by healthcare providers for making a clinical diagnosis or determining how to meet an individual patient's health needs." That cuts two ways. It cuts against over-reading a positive band. It also cuts against waving off a sick child for not meeting a counting rule.

Are there kinds of Lyme the standard test misses?

Yes, two are worth knowing by name. Borrelia mayonii and Borrelia miyamotoi are both carried by the blacklegged tick. Both cause illness in people. Neither one is reliably picked up by standard two-tier Lyme serology.

Borrelia mayonii is a Lyme-group species. Mayo Clinic and CDC researchers described it in 2016. They found it in 6 patients out of 100,545 clinical specimens tested by PCR. They later found it in ticks. Those ticks came from Minnesota and Wisconsin. The rash is what stands out. 4 of those 6 patients had diffuse or focal rashes. They did not have one classic expanding bullseye. Five had fever. The CSTE and CDC case definition adds the footnote that matters here. There are currently no serologic tests available specifically for B. mayonii. Cross-reactivity with B. burgdorferi testing may occur.

Be clear about geography before this becomes a worry. B. mayonii is an Upper Midwest organism. Exposure means travel to Minnesota, Wisconsin, or North Dakota. It is not a Nebraska question. I cover the local picture in ticks in Nebraska and Iowa.

Borrelia miyamotoi is different. It's a relapsing-fever species, not a Lyme-group one. The same Ixodes tick carries it. Molloy's 2015 case series is the largest US description. It ran in Annals of Internal Medicine. There were 97 PCR-confirmed cases out of 11,515 patients tested. The illness presented with high fever and chills. It also brought marked headache and muscle and joint pain. Rash is not a defining feature. 24% were hospitalized.

Here is the testing number that matters. Only 16% of those patients were seropositive at presentation. On convalescent samples drawn later, 78% were. Diagnosis was made by PCR on blood in acutely sick, seronegative patients. Standard two-tier Lyme serology does not reliably detect B. miyamotoi. CDC's testing page lists relapsing fever, but not as something the test is meant to find. It lists it as a cause of false-positive cross-reaction in Lyme serology.

A negative standard Lyme panel answers a question about B. burgdorferi. It doesn't answer every question a tick can raise. Say your child had a fever after a tick bite. The Lyme panel came back negative. That is a reason to ask about the other organisms. It is not a reason to stop asking.

How I think about a Lyme test in my practice

Plenty of children come in with fatigue and brain fog. I don't order a Lyme test on every one of them. I want to tell you why. The reason is not that I doubt the child.

Two reasons. First, the infection is uncommon here. Outside endemic areas, a positive result is more likely to be a false positive. Nebraska DHHS states that local acquisition in eastern Nebraska is now demonstrated. It also states that Nebraska "will likely remain a low prevalence state." Both are true at once. Second, a test I can't act on doesn't help your family. It adds a number to worry about and a bill to pay.

What changes my mind is the exposure story. Where was your child, and which summer? Was there a tick, or a rash nobody photographed? What happened in the weeks after? Picture a child who spent July at a lake house in Wisconsin. That child came home with a fever and a limp. Now picture a child with three years of fatigue and no exposure history. Those are two different conversations. The story moves the test from noise to signal.

I treat a Lyme test as one piece of a picture, never the whole picture. And I'd rather send a family to infectious disease with an objective finding. That beats starting a long antibiotic course on a borderline band. An objective finding means a documented rash or a swollen joint. It can also mean a facial palsy or a clean positive result. It gets a child taken seriously in the next room. A borderline band gets an argument.

One honest note on the guidelines. Some children come in with developmental, behavioral, or psychiatric disorders alone. Nothing else about them points to Lyme disease. The 2020 IDSA/AAN/ACR guideline recommends against routine Lyme testing in that group. I follow that in most cases. I also want you to know how the guideline grades its own advice here. It calls that recommendation weak, based on low-quality evidence. A weak recommendation is a default, not a wall. If the exposure story is strong, I say so, and I test. These questions do overlap. To read where, see Lyme, PANS and PANDAS and the PANS and PANDAS guide.

What this means for your child

Was your child's test negative, and you don't believe it? Start with the calendar. Draw a test inside the first few weeks. It catches fewer than half of true early cases. That is Waddell's 46.3% figure. A repeat draw 3–4 weeks later is often the single most useful next step. Steere's data is why.

Was the test positive at a specialty lab, and your pediatrician waved it off? Ask one question instead of ten. Which criteria were used to call it positive? Fallon's four-lab comparison showed where the specificity problem lives. It is in the interpretive criteria, not the platform. A result that holds up under standard criteria is much harder to wave off.

And if your child has an expanding rash right now, that isn't a testing question. That's a treatment question. Both sides of this argument agree on it.

You are not being difficult by asking for a clear answer about your own child. You're being a parent. Want another set of eyes on a result nobody has explained to you? The Lyme disease and tick-borne illness hub is a good place to start. You can also reach me through my contact page.

Book My Free 15-Minute Call - get clarity and learn more.

Free. No obligation. Not a sales call. Or call or text me directly at 402-988-1873.