The Infectious Diseases Pathology Branch of the Centers for Disease Control and Prevention (CDC) routinely receives autopsy and biopsy tissues for diagnostic evaluation. These tissues are typically formalin-fixed, paraffin-embedded (FFPE) in nature. Initially, histological stains are employed to determine which tissues are affected and the nature of the infectious process. Along with any provided clinical information, this information is then used by the pathologist to request testing for specific pathogens, either by use of immunohistochemical or molecular techniques. As one of the molecular pathologists, my primary tools are PCR and RT-PCR assays specific to bacterial or viral agents. After agarose gel analysis of the amplicons, followed by band excision and purification, Sanger sequencing can be performed using the GenomeLab GeXP™ Genetic Analysis System. Sequences are then trimmed, contigs are created, and consensus sequences are analyzed using the Basic Local Alignment Search Tool (BLAST). Depending on the level of identity reported by the BLAST, specific diagnoses can then be made, providing clinicians, patients, and/or patient’s families with valuable insight. While the process sounds simple and straightforward, there are actually many difficulties that arise when working with FFPE tissues. However, FFPE tissues provide a convenient means to examine tissues for infectious organisms from a variety of geographical locations using multiple modalities with no biosafety risk.
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