John Burns wasn’t getting better.

Diagnosed with Lyme disease with a federally approved test near his home in Albany, N.Y. six years ago, he was treated with several courses of antibiotics. Seven months later, he was still suffering from a crippling, overwhelming fatigue.

Worried he had developed a chronic illness from the tick-borne bacteria, he saw an infectious disease specialist and received a far different diagnosis: Early stage lung cancer.

“I’m probably the only person in the world who will say he is happy he got Lyme disease,’’ said Burns, 65, a heating, ventilation and air conditioning technician. “That’s how they found the cancer early.”

Burns’ experience, along with two other cases detailed in a paper published today in JAMA Internal Medicine (a publication of the Journal of the American Medical Association) highlights the challenges – and dangers – of some Lyme disease diagnoses. The study documents three cases in which patients’ cancer diagnoses were delayed because of a Lyme misdiagnosis.

Federally approved tests don’t always detect Lyme disease, especially early on, and many symptoms of the illness can mimic dozens of other ailments. Those challenges have allowed a cottage industry to develop in which health professionals diagnose the disease using unproven tests or their own judgment. Confounding the issue is an enormous debate over whether Lyme disease can be a chronic, active infection.

In the study’s first case, from Massachusetts in 2001, a man was treated with antibiotics for Lyme disease for three years but did not get better. He was later found to have a pituitary tumor that had grown too big to be fully removed. In the second case, a North Carolina man was diagnosed with chronic Lyme disease even though he lived in an area where Lyme disease is rare. It was later discovered he had stage IV lymphoma, not Lyme, and died in 2013.

“These three cases are the tip of the iceberg,’’ said Dr. Christina Nelson, a medical officer in the US Centers for Disease Control and Prevention’s Division of Vector-Borne Diseases. She found the patients through different means: One wrote to a newspaper about his experience while another patient and one doctor contacted the CDC.

“We have heard of cases of ALS (amyotrophic lateral sclerosis), MS (multiple sclerosis) and lupus and various other conditions that were misdiagnosed,” Nelson said.

Lyme is one of the Northeast’s most insidious public health threats. Deer ticks no bigger than a poppy seed can latch onto people during outdoor activities. The parasites, while feeding on a host’s blood, can transfer the Lyme bacteria and other disease-causing pathogens. Early Lyme symptoms can mimic those of the flu and, untreated, the disease can cause arthritis, among other ailments.

A course of antibiotics tends to cure most people, but a segment of those diagnosed with Lyme using both federally approved and other methods continue to feel ill with cognitive problems, fatigue, joint pain and a host of other symptoms.

Many sick patients and some doctors believe the problems stem from an active infection that often must be treated with even more antibiotics.  But medical establishment doctors, including the CDC, remain unconvinced, and believe some patients never had Lyme to begin with or, those that did, are suffering some type of post-infection ailment. They do not recommend prolonged antibiotic treatment.

Burns’ story underscores just how confusing it can be to get at the exact cause of what is ailing patients. While the other two patients in the paper never tested positive for Lyme using federally approved methods, Burns did. He started feeling better with antibiotics, but when he went off them, he felt worse.

“I just wasn’t feeling right, it was wearing on me,’’ he said. By January of 2009, he had undergone three courses of antibiotics but there was no change in his health. He eventually went to an infectious disease specialist for presumed chronic Lyme disease.

His doctor, Sarah Elmendorf, of Upstate Infectious Disease Associates in Albany, N.Y. gave him a blood test that found a slightly elevated white blood cell count. A subsequent chest X-ray found a tiny mass in his lung.

“I had surgery but didn’t need chemo or radiation,’’ said Burns. “I’m fine now.” Complicating the matter, he said, was that he also had another tick-borne disease at the same time.

Nelson said the study should not be interpreted to mean that every patient with vague symptoms such as fatigue should be aggressively evaluated for cancer. Rather, she said, it’s a cautionary tale “not to assume these patients have chronic Lyme disease.”

A separate paper also released today in the journal PLoS ONE attempts to help resolve this controversy. Johns Hopkins University researchers report they have developed a test to measure the effectiveness of thousands of FDA-drugs on Lyme bacteria that may still be alive after initial treatment.