Written by Dr. Diane Mueller
You’ve tried every protocol, every supplement stack, every hopeful detox, yet the fatigue, nerve pain, and fog still drag you down. If that sounds familiar, you’re not dealing with stubborn Lyme alone. You’re likely facing its hidden allies.
Tick bites don’t just transmit Borrelia burgdorferi; they often deliver an entire lineup of pathogens: Babesia, Bartonella, Anaplasma, and even Ehrlichia. Each one can mimic or magnify Lyme symptoms, making recovery nearly impossible without identifying the whole picture. That’s where co-infection testing becomes the real game-changer.
Relying solely on basic antibody screens like ELISA or Western Blot can leave you chasing shadows. Modern diagnostics, such as PCR panels that detect DNA fragments and next-generation sequencing (NGS) that maps multiple infections at once, are redefining how practitioners uncover the real root causes behind chronic Lyme.
If you’ve been wondering, “Where can I find a Lyme-literate doctor near me who actually understands this?”, you’re asking the right question. Choosing the right practitioner and testing strategy can mean the difference between years of guesswork and finally having a clear, targeted treatment path.
In this guide, we’ll break down every primary method so you can understand what each test reveals (and what it misses). By the end, you’ll know which diagnostics truly matter, how to interpret results through a functional medicine lens, and what next steps to take to get real answers — not just another round of uncertainty.
Testing for Lyme co-infections is critical, as over half of chronic Lyme cases involve multiple tick-borne pathogens like Babesia, Bartonella, or Anaplasma.
Standard Lyme tests, such as ELISA and Western Blot, detect only Borrelia, often missing co-infections and leading to incomplete diagnoses.
Advanced methods like PCR and Next-Generation Sequencing (NGS) improve detection by directly identifying the DNA of Lyme and co-infection pathogens.
Multiplex panels offer comprehensive testing for multiple tick-borne diseases in one run, saving time and increasing accuracy.
Functional medicine approaches pair molecular diagnostics with in-depth symptom history to create precise and personalized Lyme co-infection treatment plans.
Re-testing or seeking a second opinion is essential if symptoms persist despite negative tests or standard Lyme protocols.
Let’s paint a picture: You’ve been on antibiotics for Lyme for months, maybe years, but you’re still on the struggle bus. Sound familiar? That’s often the silent handiwork of co-infections like Babesia microti, Bartonella henselae, or Anaplasma phagocytophilum. Lyme rarely acts solo; studies show that over 50% of chronic Lyme cases harbor more than one tick-borne pathogen. That means if your doctor only tests for Borrelia, you’re rolling the dice with a half-blindfold.
Why does this matter for you? Co-infections suppress the immune system, scramble your symptoms (think profound fatigue, odd fevers, joint snaps, mental haze), and muddy up test results. Imagine trying to solve a jigsaw puzzle… except you’re missing half the pieces and the picture keeps changing.
At My Lyme Doc, we’ve seen that failing to test for co-infections is one of the biggest reasons people get stuck.
If diagnosing Lyme was simple, there wouldn’t be entire support groups devoted to head-scratching test results. Here’s what you’re up against: most co-infections, like Bartonella and Anaplasma, don’t play nicely in the blood. They’re intracellular, hiding out in your tissues, making them challenging to catch with a standard blood draw.
The plot thickens: antibiotics you’ve already taken (or steroids that tamp down your immunity) can cause a false negative Lyme test or co-infection screen. The organism load in your blood is often very low, sometimes downright ghostly, causing tests to miss active infections entirely.
Serologic testing, those classic antibody-based screens, has real blind spots. They can’t always tell if an infection is active, and your immune response might be asleep at the wheel when you need it most.
ELISA (Enzyme-linked immunosorbent assay) is usually the first stop in Lyme testing, a simple blood draw that checks for IgM and IgG antibodies to Borrelia burgdorferi. Here’s the rub: meta-analyses peg ELISA sensitivity around 59.5%. That’s a solid D grade; sometimes it plummets as low as 30%. You wouldn’t bet your mortgage on a coin toss, right?
While useful as a quick filter, the ELISA test for Lyme only looks for Borrelia (not Babesia, not Bartonella, not Anaplasma). It’s notoriously weak at flagging early or persistent infections and absolutely can’t stand alone for co-infection workups.
Think of the Western Blot as ELISA’s older, more sophisticated sibling. It’s a two-tiered test that looks for specific IgM and IgG bands against Borrelia. Positive? It’s considered “confirmatory” for Lyme, at least by insurance. But here’s the kicker: it’s 100% blind to Babesia, Bartonella, and Anaplasma. Only checks for Lyme, leaves the rest of the tick-borne mob undetected.
IFAs harness fluorescent dyes to light up specific antibodies in your blood, think of it as the “crime scene forensics” of Lyme co-infections. Particularly useful for Bartonella and Anaplasma, it can sometimes catch what ELISA and Western Blot miss. Still, it’s another antibody test, so if your immune system is sluggish or overworked, results may not reflect the real picture.
The blood smear test is the go-to for Babesia microti. Under a microscope, techs search for telltale Maltese cross-shaped parasites inside your red blood cells. This one shines in acute, high-parasite-load cases, think sudden fever, hemolytic anemia, and significant fatigue. In chronic disease or low-level infection, though, this test misses a lot.
Test Method | Detects Borrelia burgdorferi | Detects Babesia microti | Detects Bartonella henselae | Detects Anaplasma phagocytophilum |
|---|---|---|---|---|
ELISA | ✔ (antibodies) | – | – | – |
Western Blot | ✔ | – | – | – |
IFA | – | – | ✔ | ✔ |
Blood Smear | – | ✔ | – | – |
PCR / DNA Sequencing | ✔ | ✔ | ✔ | ✔ |
(Note: “–” means the test isn’t typically used for that bug in standard testing.)
Here’s where tech gets personal. PCR (Polymerase Chain Reaction) testing can pluck out the DNA of Borrelia, Babesia, Bartonella, or Anaplasma directly, no need to wait for your immune system to send a search party.
What’s the upside? PCR can spot current, active infections even before your antibodies show up. Whether you’re testing for Babesia microti PCR, Bartonella henselae PCR, or Anaplasma phagocytophilum PCR, you’re checking if that bug is actually present NOW, not just a ghost of infections past.
But it’s not perfect. PCR is choosy about timing and sample quality. For Borrelia in blood, sensitivity hovers around 19%, which is pretty low, since the bacteria love hiding in tissue instead. Babesia and Anaplasma are more readily found in blood, so PCR shines there.
Pro tip: PCR is powerful when paired with other methods, and clinical context always matters most. Don’t chase numbers, work with a tick-savvy doc who looks at symptoms, history, and labs as a unit.
Ever wanted a full pathogen scan, but for your blood? Next-Generation Sequencing (NGS) is about as sci-fi as it gets. These advanced panels use multiplex sequencing to look for not just Lyme, but a whole lineup: Babesia, Bartonella, Ehrlichia, and beyond. It’s like putting your blood sample through a DNA search engine.
A recent upgrade? Dual index barcoding. This technique tags dozens of samples at once, keeping results accurate while making the whole process faster and cheaper. NGS with dual index barcoding excels for chronic, atypical, or treatment-resistant Lyme cases. (If you’re reading research on IGeneX or Vibrant America, you know the lingo already.)
But, tiny asterisk, NGS is newer, so the research is still rolling in. It’s a powerhouse for finding hidden co-infections, but results ALWAYS need to be matched to your real-world symptoms. If your labs show five bugs but you feel fabulous… don’t panic. Clinical correlation is king (or queen).
NGS makes sense if you can’t crack the case, if you have stubbornly persistent symptoms, or your pattern doesn’t fit the usual playbook. The future? Probably a lot more NGS, especially for stubborn chronic cases.
If you’re tired of piecemeal testing (one bug, one bill at a time), multiplex panels offer a multipronged shortcut. Fancy labs, think IGeneX, ArminLabs, or Vibrant America, now have comprehensive tick-borne panels to screen for Lyme (Borrelia), Babesia, Bartonella, Ehrlichia, and more in a single run. (Not an endorsement, just the most active names in chronic illness groups these days.)
Here’s what these panels often cover (example schematic, actual coverage varies by lab):
Lab Panel Name | Lyme (Borrelia burgdorferi) | Babesia microti | Bartonella henselae | Anaplasma phagocytophilum | Ehrlichia chaffeensis |
|---|---|---|---|---|---|
Panel A | ✔ | ✔ | ✔ | ✔ | ✔ |
Panel B | ✔ | ✔ | – | ✔ | – |
Panel C | ✔ | – | ✔ | – | ✔ |
The perks? You get a comprehensive catch-all, not just Lyme, but the bugs that most often sneak by. It’s perfect for cases that won’t clear, mystery symptoms, or when you’re facing expensive headaches from endless test bills.
Quality check: Look for labs with CLIA and CAP accreditation. If someone’s offering a “super-panel” for cheap but without certification, wave the red flag. Multiplex panels are a pillar of the functional medicine approach, pairing molecular diagnostics with practical, clinical insight.
Ever get a negative test and still feel “off”? Or wonder why a positive result doesn’t always mean you’re actually sick? Welcome to the wild world of sensitivity and specificity.
Sensitivity is how well a test finds disease when it’s really there. Specificity means the test nails it when you’re actually disease-free. Most serologic tests for Lyme and co-infections get tripped up on both. In early Lyme, antibody test sensitivity often clangs in at 41–58%, meaning lots of folks fall through the cracks.
False negatives haunt anyone relying on antibody-only tests, especially if your immune system is sluggish or suppressed from chronic infection, mold exposure, or antibiotics. False positives happen, too, though less commonly, especially with Lyme, thanks to cross-reactions.
Moral of the story? No test gets the whole picture. The best diagnostic accuracy Lyme warriors get comes from combining PCR vs serology, new tools like NGS, AND a detailed symptom and exposure history. You are not your lab slip: functional medicine says trust your timeline, not just your titers.
This is where the toolbox grows. Functional medicine lab tests don’t stop at “You’re positive” or “You’re negative.” Practitioners in the My Lyme Doc tradition combine mainstream tests with advanced markers, like CD57 (immune cell activity), cytokines, C-reactive protein, and even organ stress (think liver enzymes or mitochondrial markers).
Why does this matter for you? It helps map the pathways behind your illness: Are you immunosuppressed? Battling systemic inflammation? Carrying a co-infection load heavy enough to tip the scales? This broad view guides real-world solutions, not just protocols pulled from the internet.
Plus, functional medicine means you are the focus, not just your lab numbers. It’s detective work: history, symptoms, functional lab data, and a compassionate doctor who knows chronic illness isn’t solved by algorithms alone.
When should you even test? Here’s a quick gut-check list:
Ongoing symptoms (fatigue, neuro blips, joint pain)
Living in/visiting an endemic region
Recent tick bite, even if you didn’t see the bug itself
Persistent illness that ignores past treatment
A few pro tips to keep your test on track:
Avoid antibiotics before PCR; those meds can drop pathogen numbers and quietly turn up a false negative Lyme test.
If you’re doing molecular testing, use an EDTA tube and make sure the sample gets shipped fast. Delays = degraded DNA and wasted time.
Don’t let samples thaw, refreeze, or bake in the sun. Yes, this seems obvious. Yes, we’ve seen it happen.
Time your testing: Some tests work better when symptoms flare. Babesia blood smear? Acute illness is best. Serology and PCR? Chronic or relapsing disease fits the bill.
Finally, journal your exposure history, tick bites, round rashes, herx reactions, and the “weird” timeline only you know. Bring this when you visit your practitioner. (Bonus: Most Lyme-literate docs do a happy dance when you walk in with a symptom chart. It’s our version of a backstage pass.)
You may have seen “all clear” on your test report, yet something inside still screams, Not right. Should you keep testing? Sometimes, yes, it can take more than one round, actually, to spot co-infections or relapsing Lyme.
Consider a re-test or second opinion if:
Symptoms stick around even though a standard Lyme protocol is followed.
New or different symptoms crash your recovery party.
You relapse weeks or months after what felt like remission
Switching test modalities can also solve mysteries: If ELISA and Western Blot come up empty, try a PCR or NGS panel. If blood fails, some advanced cases use tissue or spinal fluid (with a specialist’s guidance).
And please, don’t settle if you hit a wall.
Find resources here → Lyme-literate doctor near me, and find a multi-pathogen experience and genuine compassion. Our own team does lots of second-opinion consults. At the end of the day, your healing journey is yours. If something feels off, keep pushing for the answers you deserve.
Getting diagnosed for Lyme and its co-infections shouldn’t be a lottery. The proper tests, not just the standard roster, plus functional medicine interpretation, can mean the difference between endless “mystery illness” and finally feeling human again.
Here’s the bottom line: Combine molecular tools (PCR, NGS), serologic screens, and a solid symptom/exposure history, and you’ll leap far beyond what standard protocols offer. At My Lyme Doc, we’ve seen the difference comprehensive diagnostics make, even for the most challenging chronic cases.
If you’re nodding along, tired of old answers, or ready to get off the symptom merry-go-round once and for all? Precision matters. It changes lives, I’ve seen it and lived it.
Remember, you’re not just searching for a positive test, but for your path back to health. And that’s something worth every ounce of perseverance (and more than a few blood draws).
No single test can identify every Lyme co-infection with perfect accuracy, but molecular-based diagnostics currently lead the field. PCR (Polymerase Chain Reaction) and Next-Generation Sequencing (NGS) tests are considered the most precise because they detect the actual DNA of pathogens like Borrelia burgdorferi, Babesia microti, Bartonella henselae, and Anaplasma phagocytophilum.
While antibody-based tests such as ELISA and Western Blot can help screen for exposure, they depend on your immune response — which may be suppressed in chronic infection. For comprehensive accuracy, many functional and Lyme-literate practitioners combine PCR, serology, and NGS panels to minimize false negatives and capture active infections.
No. Traditional Lyme tests including the ELISA and Western Blot only look for antibodies to Borrelia burgdorferi, the bacteria that causes Lyme disease. They do not detect co-infections such as Babesia (a malaria-like parasite) or Bartonella (a fastidious intracellular bacterium).
To diagnose these co-infections, you need targeted tests like IFA (Immunofluorescence Assay), PCR, or specialized multi-pathogen tick-borne panels offered by advanced laboratories. These can identify the unique DNA or antibodies of each organism for a more complete diagnostic picture.
Lyme and co-infection tests often show false negatives because of low bacterial load, intracellular hiding, or a weakened immune response. In chronic cases, the immune system may not produce enough antibodies for detection, especially after antibiotic treatment. Additionally, improper sample handling and timing of testing (too early or too late after infection) can further skew results.
DNA sequencing, particularly Next-Generation Sequencing (NGS), is an advanced molecular method that scans a blood or tissue sample for genetic material from multiple pathogens at once. Instead of testing for one infection at a time, NGS can detect known and emerging tick-borne microbes even when traditional tests miss them. Using techniques like dual-index barcoding, labs can process dozens of samples simultaneously with exceptional precision. This makes NGS an invaluable tool for uncovering hidden co-infections in patients with persistent or treatment-resistant Lyme-like symptoms.
Testing for Lyme co-infections is crucial because over half of chronic Lyme disease cases involve additional tick-borne pathogens like Babesia, Bartonella, or Anaplasma. Missing these co-infections can lead to lingering symptoms and incomplete treatment, so accurate diagnosis guides effective and personalized care.
You should consider re-testing or seeking a second opinion if symptoms persist despite treatment, new symptoms develop, or if standard Lyme tests are inconclusive. Utilizing different testing methods or consulting a Lyme-literate specialist can help uncover overlooked co-infections.
LymeDisease.org. (2014). Study finds coinfections in Lyme disease common. https://www.lymedisease.org/lymepolicywonk-study-finds-coinfections-in-lyme-disease-common-2/
Bonnet, S., Jouglin, M., Malandrin, L., & Becker, N. S. A. (2025). Seroprevalence of Borrelia, Anaplasma, Bartonella, Toxoplasma, and Neospora in horses from Normandy, France. Pathogens, 14(1), Article 96. https://doi.org/10.3390/pathogens14010096
Ornstein, K., & Bergström, S. (2002). A quantitative PCR method for the detection of Borrelia burgdorferi DNA in human blood. Journal of Clinical Microbiology, 40(9), 3532–3535. https://pmc.ncbi.nlm.nih.gov/articles/PMC496808/
Cook, M. J., & Puri, B. K. (2017). The accuracy of diagnostic tests for Lyme disease in humans, a systematic review and meta-analysis of North American research. PLoS ONE, 12(3), Article e0168613. https://journals.plos.org/plosone/article?id=10.1371/journal.pone.0168613
Leeflang, M. M. G., Ang, C. W., Berkhout, M. J. G., Bijlmer, H. A., van Bortel, W., Brienen, E. A. T., Kats, E., Melsert, R., Molijn, A. C., van Pelt, W., & Bossuyt, P. M. M. (2016). Commercial test kits for detection of Lyme borreliosis: A meta-analysis of test accuracy. International Journal of General Medicine, 9, 425–440. https://doi.org/10.2147/IJGM.S122313
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