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Potential etiological relevance for gastroenteric disorders including diarrhea has been assigned to <i>Arcobacter butzleri</i>. However, standard routine diagnostic algorithms for stool samples of patients with diarrhea are rarely adapted to the detection of this pathogen and so, <i>A. butzleri</i> is likely to go undetected unless it is specifically addressed, e.g., by applying pathogen-specific molecular diagnostic approaches. In the study presented here, we compared three real-time PCR assays targeting the genes <i>hsp60</i>, <i>rpoB/C</i> (both hybridization probe assays) and <i>gyrA</i> (fluorescence resonance energy transfer assay) of <i>A. butzleri</i> in a test comparison without a reference standard using a stool sample collection with a high pretest probability from the Ghanaian endemicity setting. Latent class analysis was applied with the PCR results obtained with a collection of 1495 stool samples showing no signs of PCR inhibition to assess the real-time PCR assays’ diagnostic accuracy. Calculated sensitivity and specificity were 93.0% and 96.9% for the <i>hsp60</i>-PCR, 100% and 98.2% for the <i>rpoB/C</i>-PCR, as well as 12.7% and 99.8% for the <i>gyrA</i>-PCR, respectively. The calculated <i>A. butzleri</i> prevalence within the assessed Ghanaian population was 14.7%. As indicated by test results obtained with high-titer spiked samples, cross-reactions of the <i>hsp60</i>-assay and <i>rpoB/C</i>-assay with phylogenetically related species such as <i>A. cryaerophilus</i> can occur but are less likely with phylogenetically more distant species like, e.g., <i>A. lanthieri</i>. In conclusion, the <i>rpoB/C</i>-assay showed the most promising performance characteristics as the only assay with sensitivity >95%, albeit associated with a broad 95%-confidence interval. In addition, this assay showed still-acceptable specificity of >98% in spite of the known cross-reactivity with phylogenetically closely related species such as <i>A. cryaerophilus</i>. If higher certainty is desired, the <i>gyrA</i>-assay with specificity close to 100% can be applied for confirmation testing with samples showing positive <i>rpoB/C</i>-PCR results. However, in case of a negative result in the <i>gyrA</i>-assay, this cannot reliably exclude the detection of <i>A. butzleri</i> in the <i>rpoB/C</i>-assay due to the <i>gyrA</i>-assay’s very low sensitivity.