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TB or not TB


my wife is undergoing TB treatment, but we have strong doubts that she has the TB. We are in Canada just to give you an idea about the medical procedures. After a routine x-ray, the physician saw a very minor dark spot in the lungs, which he said could be nothing, but sent us for a sputum test just in case. Our 1st sputum test got lost or contaminated, so they asked her to do the 2nd sputum test, and it came as TB positive. They cultured the sputum for 8 weeks, and it did grow into TB. At that point, they put my wife to home isolation and started testing drugs on her sputum.

The bacteria was resistant to 1st line of drugs, so they decided to put her in isolation in hospital. When she arrived to the hospital, they took 2 more sputum tests, and both came smear and culture negative. It takes 8 weeks for TB to culture so by the time they found out it was negative, my wife was already 2 month into taking the MDR TB treatment including IV and oral drugs. After negative sputum, they released her from isolation, but continued the treatment. The nurse visits us every day at home, and we are on an 18 months plan to take the medications.

The question is if the 2 sputum tests taken prior to treatment were smear and culture negative, how can we be certain the 1st test was good, and my wife actually had the TB ? Taking poison for 1.5 years to kill something that may not be there is not a chance we want to take.

Since I'm her husband and we are in close contact all the time, I was tested too: skin test, x-ray, and blood QuantiFERON test. Everything is negative. Which raises our doubts further.

When we brought these doubts to our doctor, she said that sputum tests are not that accurate, and it is possible the once that were negative were not good. I understand the public concerns doctors have, and better be safe than sorry mentality, but taking heavy medication with side affects for 1.5 years is a high price to pay. We also don't fall in a typical risk zone: my wife is in her 20's, lived in Europe and US all her life and didn't travel to any hot TB spots.

My main question: can we use QuantiFERON test to verify with some degree of certainty that my wife was or was not infected. Keeping in mind that we are already 4 months into the treatment. If QuantiFERON is not an option, anything else we can do for testing, or we should just bite the bullet and go through the treatment for something we almost certainly don't have.  
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