Polymerase chain reaction amplification of bacterial 16s rRNA in biopsy samples

Abstract

TO THE EDITOR: Keay et al.1 recently reported detection of bacterial 16s rRNA in about 60% of needle biopsy samples obtained from patients with localized adenocarcinoma of the prostate using a two-step polymerase chain reaction (PCR) protocol.2,3 Application of the same PCR protocol allowed detection of bacterial DNA in 77% of transperineal prostate biopsies of patients with chronic prostatitis.4 The authors therefore conclude that the presence of bacterial 16s rRNA in prostate tissue is not specific for chronic prostatitis and localized prostate cancer. PCR analysis is a very sensitive method that allows for the detection of a single DNA target in a sample. In the past, the extremely high sensitive two-step PCR has been introduced into routine molecular diagnostics for therapeutic monitoring of patients with minimal residual leukemia.5 In contrast, two-step PCR protocols are usually not applied in microbiologic diagnostics because of the questionable clinical relevance of a positive result that may have arisen from as few as a single bacterial DNA molecule. Because of the exquisite sensitivity of PCR, precautions have to be taken to ensure that positivity indeed indicates the presence of bacterial DNA in the tissue sample and that the positive signal does not result from exogenous sources.6 Moreover, to avoid false negativity, a DNA control has to be amplified to exclude the possibility that a negative result is due to the lack of DNA in the samples (ie, failure of the DNA isolation procedure) or the presence of PCR inhibitors. Among the studies that have used the two-step PCR protocol published by Domingue et al.2 and Keay et al.,3 controversial detection rates have been reported with respect to bacterial DNA detected in samples of patients with interstitial cystitis and in those of healthy controls.2,3 Beside the possibility of false positivity resulting from exogenous contamination of the specimens during manipulation of the cystoscope,3 these differences may also be due to false negativity of PCR because neither of the investigators included a DNA control in the PCR protocol to confirm the presence of amplifiable DNA in the samples. Because one-step PCR protocols represent a useful tool to investigate the prevalence of bacteria that fail to grow in culture, we highly recommend inclusion of a DNA control (ie, amplification of the human beta-globin gene)7 in all PCR protocols to avoid false negativity of PCR in tissue biopsy samples.