Fecal concentration of Rhodococcus equi determined by quantitative polymerase chain reaction of rectal swab samples to differentiate foals with pneumonia from healthy foals

BACKGROUND: Diagnostic accuracy of real‐time, quantitative PCR (qPCR) assays to quantify virulent Rhodococcus equi using rectal swab samples has not been systematically evaluated. OBJECTIVE: To evaluate the accuracy of qPCR of rectal swab samples to differentiate foals with pneumonia from healthy foals of similar age from the same environment. ANIMALS: One hundred privately owned foals born in 2021 from 2 farms in New York. METHODS: An incident case‐control study design was used. Rectal swabs were collected from all foals diagnosed with R. equi pneumonia at 2 horse‐breeding farms (n = 47). Eligible pneumonia cases (n = 39) were matched by age to up to 2 healthy (n = 53) control foals; rectal swabs were collected from control foals on the day of diagnosis of the index case. DNA was extracted from fecal swabs and the concentration of virulent R. equi (ie, copy numbers of the virulence‐associated protein A gene [vapA] per 100 ng fecal DNA) was estimated by qPCR. RESULTS: The area under the ROC curve for qPCR of fecal swabs was 83.7% (95% CI, 74.9‐92.6). At a threshold of 14 883 copies of vapA per 100 ng fecal DNA, specificity of the assay was 83.0% (95% CI, 71.7‐92.4) and sensitivity was 79.5% (95% CI, 66.7‐92.3). CONCLUSIONS AND CLINICAL IMPORTANCE: Although fecal concentrations of virulent R. equi are significantly higher in pneumonic foals than healthy foals of similar age in the same environment, qPCR of rectal swabs as reported here lacks adequate diagnostic accuracy for clinical use.