Monday, March 02, 2015

Laboratory TB versus Genital TB

Tuberculosis is endemic in India , and it’s a disease which can affect practically any organ system , including the lung , bones, brain and the reproductive tract. While it's easy to "suspect" TB, it’s also extremely hard to confirm the diagnosis of tuberculosis in the lab, because it's very difficult to grow the TB bacillus in vitro.

In the past few years, it seems that practically every other infertile woman in India seems to be diagnosed as having genital tuberculosis, based on a positive endometrial TB PCR ( polymerase chain reaction) test result. The problem is that very few of them actually have tuberculosis , because the vast majority of these results are false positives. Let me explain where all these false positives come from.

Tuberculosis is a notoriously difficult diagnosis to confirm because it's very hard to grow mycobacteria in the lab. Tuberculosis is an infectious diseases , and the only way to make a definitive diagnosis of an infection is by actually growing the organism ( which is responsible  for the infection ) in the laboratory. Thus , if a patient has pneumococcal pneumonia , you can’t make the diagnosis by looking at a chest x-ray - you need to grow the pneumococci in the lab , in a petri dish. This is exactly the same principle we use in order to make a diagnosis tuberculosis , and these are called Koch's postulates. However, because mycobacterium grows very slowly in the lab, instead of insisting on a bacteriological diagnosis, even a histological diagnosis which shows tubercles or granuolomas is considered to be acceptable. In the past, to make a definitive diagnosis of genital TB , a positive mycobacterium culture or the presence of tubercles in the histopathology report ( from an endometrial biopsy  ) was required. However, what has started to happen is when doctors "clinically suspect" tuberculosis ( for example, when the endometrium remains thin, or the patient has failed multiple IVF cycles) , they send the endometrial tissue for all kinds of tests to confirm their clinical suspicion. One of the most popular tests is a PCR( polymerase chain reaction)  test for mycobacterium tuberculosis.

What is PCR ?

PCR is, in principle, a simple and rapid test for use in the detection of Mycobacterium tuberculosis because it amplifies a DNA sequence which is unique to mycobacteria. Now if the test is positive , this means that mycobacterial DNA is present in the endometrium. Isn't it then obvious that if the TB PCR is positive , this means the patient has endometrial TB  which requires treatment ? Extremely logical , but very flawed. Let's see why by starting from first principles.

Interpreting a positive PCR results

What does a positive PCR mean ? It does NOT mean the patient has genital TB ! All it tells us that a few molecules of mycobacterial DNA was found in the sample processed in the lab.

It does not provide us with any information about -
The type of mycobacteria, because the DNA sequence which is being amplified is not specific only to M tuberculosis - it is found in many other other mycobacterial species as well.
Whether the mycobacteria are alive or dead?
Where the mycobacteria came from ? ( the clinical tissue ; or as a contaminant from the OT or the lab)
How many mycobacteria are present
Most importantly, it does not provide any information on the clinical importance of the finding. Is the mycobacteria a contaminant?  or a pathogen?

More about mycobacteria

When most doctors think about mycobacteria, they refer to Mycobacterium tuberculosis which causes the disease tuberculosis ( TB) ; or , less commonly, Mycobacterium leprae which causes leprosy. However, the reality is that Mycobacteria are a diverse group of rod-shaped bacteria that include more than 100 different species. The others, which are far commoner, are called  Nontuberculous mycobacteria (NTM), environmental mycobacteria, atypical mycobacteria  and mycobacteria other than tuberculosis (MOTT). They live in the soil and water throughout the world. Because they are protected by their waxy lipid-rich cell wall, mycobacteria are resistant to disinfectants. This is why they are ubiquitous inhabitants of the hospital environment ; and frequent contaminants in hospital settings, where they are often found in the water supply and even in the solutions in which the endometrial biopsy is sent to the lab for PCR testing). The TB PCR test is highly flawed, because the DNA sequence which the PCR amplifies is common to both the mycobacterium tuberculosis as well as the other species of mycobacetria.

The problem with false positives

Since these mycobacetria are so common, when the laboratory finds a positive PCR reaction , it doesn’t know whether the mycobacterial DNA is coming from the patient or from the slide on which that sample was sent.  When a specimen is reported as being PCR positive, it is important to discriminate between true infection and contamination. The molecular cross-reaction between the ubiquitous non-pathogenic environmental mycobacteria ( which are harmless colonisers) and M tuberculosis is what creates the diagnostic dilemma. Since they have a similar DNA structure, the presence of either will provide a positive result in a PCR test. The PCR test is quite a dumb test - it's not able to determine which type of mycobacteria is providing a positive signal ! Sadly, most gynecologists and pathologists are completely clueless about the prevalence of environmental mycobacteria; and when the TB PCR test result comes back as positive, their knee jerk reaction is to assume that the patient has genital TB ( when in reality, the result is much more likely to be a false positive, because of contamination). Because environmental mycobacteria are so prevalent ( they are found practically everywhere - even in the water in the lab which is used to clean the instruments !), the chances of the PCR test being positive because of contamination by environmental bacteria is much higher than because the patient actually has genital TB !

Why doctors get fooled

Since the DNA PCR test is not specific only for mycobacterium tuberculosis,  it’s very easy for the doctor to get fooled.  Once the test is reported as positive , the doctor is happy that their clinical suspicion has been confirmed ; and the patient is happy that the doctor has finally found out why the endometrium is thin; or why the IVF cycles have failed . She is quite happy to take the anti TB treatment so that finally she can have a baby ! While a  few patients may get pregnant after starting the antiTB medicines, this doesn't mean that there was a cause and effect relationship between the treatment and the pregnancy. The tragedy is that often the PCR result was a false positive , and that she doesn’t have TB of the endometrium. She has been unnecessarily exposed to nine months of toxic drugs , which can damage her liver or kidneys ; and end up consuming a lot of time , during which her ovarian reserve and fertility will go down. This is why it’s so important that the diagnosis of endometrial tuberculosis should not be made based on the TB PCR reaction.

Unfortunately most gynecologists are not aware about the bacteriology of
mycobacteria . They get fooled by a positive PCR report. They fail to realize that a positive PCR report is very non specific , and in fact it’s because so sensitive that it gives rise to so many false positives,  which mislead both doctors and patients. Patients should insist that if the doctor suspects tuberculosis , they should establish the diagnosis either by histological examination; or by demonstrating the tubercle bacillus in the lab . The good news is there are lots of extremely effective new culture techniques to grow the bacillus, which are far better than the old techniques. And if neither the culture nor the histology shows a positive report , than treating the patient just because she has a thin endometrium with a positive PCR is not acceptable medical practice.

Environmental mycobacteria have always been around, so why wasn't this a problem in the past ? This is because modern PCR is so sensitive !  In the past, it was not easy to grow mycobacteria, which meant that even if a few contaminants were present in the specimen, these would fail to grow. However, PCR is  super-sensitive, and will pick up the presence of even a few molecules of mycobacterial DNA.

With a positive TB PCR, the odds are that a positive result ( in an asymptomatic patient) means that there is something wrong with the test, not with the patient . In fact, I think we should coin a new term for these mycobacteria which have created so much iatrogenic harm - Non pathogenic Ubiquitous Mycobacteria - NUM !

Has your doctor put you on anti TB therapy just because your TB PCR results are positive ? Please send me your medical details by filling in the form at so that I can guide you better !

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