The performance of a real-time PCR assay targeting the Tropheryma whipplei rpoB gene was evaluated using test strains and 1,236 clinical specimens in a national reference laboratory. The novel rpoB-PCR assay proved to be specific, revealed improved analytical sensitivity, and substantially accelerated detection of T. whipplei DNA in clinical specimens.
Laboratory diagnosis of Whipple's disease is currently based on a combination of PCR and histopathological methods (1). The emergence of real-time PCR technology has substantially improved and facilitated the molecular detection of Tropheryma whipplei, the causative agent of Whipple's disease (2, 3). In search of a specific and sensitive PCR protocol, several target genes have already been evaluated, including the 16S rRNA gene (4), the 16S-23S rRNA intergenic spacer region (5), the hsp65 gene (6), and certain repeated sequences (7). Targeting a T. whipplei-specific segment within the rpoB gene, encoding the  subunit of the RNA polymerase, has shown promising results (8, 9), but a comprehensive study, including melting curve analysis, with respect to its robustness and suitability in routine diagnostics has not been conducted. Over an 8-year period, we evaluated a novel real-time PCR assay targeting T. whipplei-specific segments within the rpoB gene on a considerable number of clinical specimens and compared the results to a conventional PCR protocol. Starting from 2012, the rpoB-PCR was used as a screening PCR.Total genomic DNA from the various clinical specimens was isolated using either the Amplicor respiratory specimen preparation kit or the MagNA Pure compact nucleic acid isolation kit I (both from Roche Diagnostics, Mannheim, Germany) according to the manufacturer's instructions. Both extraction methods use alkaline lysis that successfully disintegrated T. whipplei in cerebrospinal fluid, blood, gut biopsy specimens, and histological sections from methacrylate-or paraffin-embedded tissues (e.g., heart valves and skin samples).Conventional PCR assay. Based on a slightly modified protocol published by von Herbay et al. (10), a 267-bp fragment of the 16S rRNA gene of T. whipplei was amplified in a seminested protocol using primers TPU5 (AAACTYAAAKGAATTGACGG) (11) and whip1 and whip2 (10). Successful amplification was confirmed by agarose gel electrophoresis. The identity of PCR products of the expected size was verified by DNA sequencing on an automated capillary DNA sequencer and comparison with all currently available sequences from public databases (EMBL and GenBank) as published elsewhere (12).Real-time PCR assay. Primers TwrpoB-F4 (CTCGGTGTTGA TGTTGATCCAA) and TwrpoB-R (GCACCGCAACCTCGGAG AAA) (8) were selected to amplify a 109-bp segment of the T. whipplei rpoB gene. Real-time detection of the amplicons was achieved by hybridization probes TwrpoB-HP1 (ACGAGGTCGG ATATTATCGC-FL) (5=-3=) and TwrpoB-HP2 (Red 640-ACAAT TCGTTATCTCGCGGCC) (5=-3=). The in silico specificity of primer and probe sequences was verified by EMBL and GenBank sequence alignments.The 20-...