Cloning and sequencing an unknown gene of Tropheryma whipplei and development of two LightCycler ® PCR assays

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Whipple’s disease is a rare infectious illness that can affect any organ system in the body. It is caused by Tropheryma whipplei, a Gram-positive rod-shaped bacterium with a high G + C content, classified within the actinobacteria. For decades, laboratory detection has been based on microscopy and the periodic acid-Schiff (PAS) staining of biopsies. Recently, PCR has become a useful tool to detect T. whipplei DNA in various clinical specimens. However, a positive PCR result does not confirm Whipple’s disease as it has been shown that asymptomatic persons can harbor T. whipplei DNA. Since there is not yet much known about the genome of T. whipplei, genome-walking represents a convenient method to determine unknown gene sequences. Starting from a RAPD fragment we have sequenced and cloned an open reading frame (ORF) of 843 bp. Two real-time PCR assays targeting the ORF fragment and the 16S rRNA gene, respectively, were developed. Compared to a conventional 16S rRNA PCR system the ORF LightCycler assay proved to be very specific (100%) but not sufficiently sensitive (62.4%). In contrast, the 16S rRNA LightCycler® assay showed a sensitivity of 95.7% and a specificity of 97.8%. Thus, the 16S rRNA gene assay but not that targeting the new ORF is a suitable alternative to conventional PCR methods.