Ribosomal RNA sequences of Clostridium piliforme isolated from rodent and rabbit: re-examining the phylogeny of the Tyzzer's disease agent and development of a diagnostic polymerase chain reaction assay.

We used polymerase chain reaction (PCR) technology to amplify the 16S rRNA gene, the intergenic spacer, and most of the 23S rRNA gene from 6 isolates (2 mice, 1 hamster, 1 rat, and 2 rabbit isolates) of the Tyzzer's disease agent (Clostridium piliforme) and C. colinum. Sequence similarity searches of GenBank identified 45 closely related bacteria, which we used for phylogenetic analysis by parsimony and maximum-likelihood methods using Escherichia coli to root the resulting phylogram. Microorganisms identified as C. piliforme form 3 clusters within a single clade; the nearest related distinguishable species is C. colinum. Other bacterial clades closely related to C. piliforme are clostridia previously identified by molecular methods in the bovine, porcine, and human gastrointestinal tracts. DNA sequence alignment highlighting sequence differences were used to design a rodent and rabbit C. piliforme-specific PCR assay, which targets a 639-basepair region at the 3' end of the 16S rRNA gene and the 5' end of the intergenic spacer. We used this PCR assay to examine 4 rat fecal samples from C. piliformeseropositive rats and reexamine 2 rabbit fecal samples previously identified as containing DNA sequences consistent with C. piliforme infection by 16S PCR assay. Our new assay did not detect the presence of C. piliforme DNA sequences in either the rat or rabbit fecal DNA samples, consistent with the absence of clinical disease in the colonies evaluated.