Detection and speciation of mycobacteria in formalin-fixed, paraffin-embedded tissue sections

The ability to detect mycobacterial DNA by polymerase chain reaction (PCR)-based methodology in formalin-fixed, paraffin-embedded tissue sections is useful in several clinical scenarios. The major use of this type of assay is in those instances in which infectious disease is not clinically suspected and microbiological cultures are not performed. In these cases, the only tissue available for examination is that present in routinely prepared paraffin blocks after histologic examination. The presence of necrotizing granulomatous inflammation should result in special stains for acid-fast organisms. However, in many such cases the special stains are unsatisfactory, because the number of organisms present is very low (as in Mycobacterium tuberculosis). Thus, the tedious examination of multiple serial sections is often necessary to identify the pathogenic organism, and often no organism is found. Therefore, more sensitive detection methods are needed. PCR-based detection of mycobacterial DNA is more sensitive and can be used either to verify the presence of organisms seen on special stains or to identify an occult organism. By combining the PCR assays with restriction analyses of the products, it is often possible to speciate the pathogenic organism.