Metagenomic Assay for Identification of Microbial Pathogens in Tumor Tissues

Baldwin, Don A.; Feldman, Michael; Alwine, James C.; Robertson, Erle S.

Assay performance with tumor tissue samples. The AllPrep DNA/RNA FFPE kit provides efficient extraction of genomic DNA and total RNA from the same FFPE specimen, so this kit was tested for its ability, importantly, to extract nucleic acids from fungal cells and Gram-negative or Gram-positive bacteria, which are likely to be the most difficult microbial agents in the samples. DNA and RNA from Saccharomyces cerevisiae, Bacillus cereus, and Escherichia coli cultures were efficiently recovered using the kit (data not shown). This provided a preliminary indication that nucleic acids from eukaryotic and prokaryotic pathogens can be extracted and detected from the PathoChip tumor extraction procedure (Fig. 1C) .