Polymerase chain reaction amplification of bacterial 16S rRNA genes from cold-cup biopsy forceps

Purpose: In looking for a possible infectious cause for interstitial cystitis (IC), we previously determined that bladder tissue specimens from both IC patients and controls were uniformly positive by polymerase chain reaction assay (PCR) for bacterial 16S ribosomal RNA genes from various genera including Escherichia, Propionobacterium, Acinetobacter, and Salmonella. We therefore determined whether the biopsy forceps might be contaminated with bacterial DNA. Materials and Methods: A total of 23 samples were obtained following disinfection of 6 cold-cup bladder biopsy forceps (2 to 5 specimens from each forceps over a period of 19 months). DNA was extracted from each sample, and PCR performed using nested primers from a highly conserved region of the bacterial 16S rRNA gene. Amplified DNA was purified and sequenced, and the sequences obtained were compared with bacterial rRNA gene sequences recorded in GenBank. Results: Thirteen of 23 forceps specimens were positive by PCR for bacterial DNA, including at least one rinse from each of the 6 forceps. In comparison,none of 9 negative control specimens (sterile distilled water put into tubes and processed in the same manner as forceps rinses) had detectable bacterial DNA. Sequence data indicated the presence of a predominant organism in 12 of the 13 positive specimens, with > 95% homology to DNA from several different genera of bacteria including Escherichia, Propionobacterium, Stenotrophomonas and Pseudomonas. Conclusions: These data indicate that reusable bladder biopsy forceps are frequently contaminated with bacterial DNA. Tissue specimens procured with such instruments therefore are inappropriate sources to look for the presence of bacterial pathogens by PCR.