Estimating the Sensitivity and Specificity of Real-Time Quantitative PCR of Fecal Samples for Diagnosis of Rhodococcus equi Pneumonia in Foals

Diagnosis of bacteria from the CMNR group in farm animals

The CMNR group comprises bacteria of the genera Corynebacterium, Mycobacterium, Nocardia, and Rhodococcus and share cell wall and DNA content characteristics. Many pathogenic CMNR bacteria cause diseases such as mastitis, lymphadenitis, and pneumonia in farmed animals, which cause economic losses for breeders and represent a threat to public health. Traditional diagnosis in CMNR involves isolating target bacteria on general or selective media and conducting metabolic analyses with the assistance of laboratory biochemical identification systems. Advanced mass spectrometry may also support diagnosing these bacteria in the clinic's daily routine despite some challenges, such as the need for isolated bacteria. In difficult identification among some CMNR members, molecular methods using polymerase chain reaction (PCR) emerge as reliable options for correct specification that is sometimes achieved directly from clinical samples such as tracheobronchial aspirates and feces. On the other hand, immunological diagnostics such as the skin test or Enzyme-Linked Immunosorbent Assay (ELISA) for Mycobacterium tuberculosis yield promising results in subclinical infections with no bacterial growth involved. In this review, we present the methods most commonly used to diagnose pathogenic CMNR bacteria and discuss their advantages and limitations, as well as challenges and perspectives on adopting new technologies in diagnostics.

Rhodococcus equi-What is New This Decade?

Foals become infected shortly after birth; most develop subclinical pneumonia and 20% to 30% develop clinical pneumonia that requires treatment. It is now well established that the combination of screening programs based on thoracic ultrasonography and treatment of subclinical foals with antimicrobials has led to the development of resistant Rhodococcus equi strains. Thus, targeted treatment programs are needed. Administration of R equi-specific hyperimmune plasma shortly after birth is beneficial as foals develop less severe pneumonia but does not seem to prevent infection. This article provides a summary of clinically relevant research published during this past decade.

Transfusion of hyperimmune plasma for protecting foals against Rhodococcus equi pneumonia

The bacterium Rhodococcus equi causes pneumonia in foals that is prevalent at breeding farms worldwide. In the absence of an effective vaccine, transfusion of commercial plasma from donor horses hyperimmunised against R. equi is used by many farms to reduce the incidence of pneumonia among foals at farms where the disease is endemic. The effectiveness of hyperimmune plasma for controlling R. equi pneumonia in foals has varied considerably among reports. The purposes of this narrative review are: 1) to review early studies that provided a foundational basis for the practice of transfusion of hyperimmune plasma that is widespread in the US and in many other countries; 2) to summarise current knowledge of hyperimmune plasma for preventing R. equi pneumonia; 3) to provide an interpretive summary of probable explanations for the variable results among studies evaluating the effectiveness of transfusion of hyperimmune plasma for reducing the incidence of R. equi pneumonia; 4) to review mechanisms by which hyperimmune plasma might mediate protection; and 5) to consider risks of transfusing foals with hyperimmune plasma. Although the weight of evidence supports the practice of transfusing foals with hyperimmune plasma to prevent R. equi pneumonia, many important gaps in our knowledge of this topic remain including the volume/dose of hyperimmune plasma to be transfused, the timing(s) of transfusion, and the mechanism(s) by which hyperimmune plasma mediates protection. Transfusing foals with hyperimmune plasma is expensive, labour-intensive, and carries risks for foals; therefore, alternative approaches for passive and active immunisation to prevent R. equi pneumonia are greatly needed. This article is protected by copyright. All rights reserved.

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.

Association of pneumonia with concentrations of virulent Rhodococcus equi in fecal swabs of foals before and after intrabronchial infection with virulent R. equi

Background

Intragastric administration of virulent Rhodococcus equi protects foals against subsequent experimental intrabronchial (IB) infection, but it is unknown whether R. equi naturally ingested by foals contributes to their susceptibility to pneumonia.

Hypothesis

Fecal concentration of virulent R. equi before IB infection with R. equi is positively associated with protection from pneumonia in foals.

Animals

Twenty‐one university‐owned foals.

Methods

Samples were collected from experimental studies. Five foals were gavaged with live, virulent R. equi (LVRE) at age 2 and 4 days; the remaining 16 foals were not gavaged with LVRE (controls). Fecal swabs were collected from foals at ages 28 days, immediately before IB infection. Foals were monitored for clinical signs of pneumonia, and fecal swabs were collected approximately 2 weeks after IB infection. Swabs were tested by quantitative PCR for concentration of virulent R. equi (ie, copy numbers of the virulence‐associated protein A gene [vapA] per 100 ng fecal DNA).

Results

Fecal concentrations of virulent R. equi (vapA) before IB infection were significantly (P < .05) lower in control foals (25 copies/100 ng DNA [95% CI, 5 to 118 copies/100 ng DNA) that developed pneumonia (n = 8) than in healthy control foals (n = 8; 280 copies/100 ng DNA; 95% CI, 30 to 2552 copies/100 ng DNA) or those gavaged with LVRE (707 copies/100 ng DNA, 95% CI, 54 to 9207 copies/100 ng DNA).

Conclusions and Clinical Importance

Greater natural ingestion of LVRE might contribute to protection against pneumonia among foals.

Bacterial and viral enterocolitis in horses: a review

Enteritis, colitis, and enterocolitis are considered some of the most common causes of disease and death in horses. Determining the etiology of these conditions is challenging, among other reasons because different causes produce similar clinical signs and lesions, and also because some agents of colitis can be present in the intestine of normal animals. We review here the main bacterial and viral causes of enterocolitis of horses, including Salmonella spp., Clostridium perfringens type A NetF-positive, C. perfringens type C, Clostridioides difficile, Clostridium piliforme, Paeniclostridium sordellii, other clostridia, Rhodococcus equi, Neorickettsia risticii, Lawsonia intracellularis, equine rotavirus, and equine coronavirus. Diarrhea and colic are the hallmark clinical signs of colitis and enterocolitis, and the majority of these conditions are characterized by necrotizing changes in the mucosa of the small intestine, colon, cecum, or in a combination of these organs. The presumptive diagnosis is based on clinical, gross, and microscopic findings, and confirmed by detection of some of the agents and/or their toxins in the intestinal content or feces.

Rhodococcus equi-specific hyperimmune plasma administration decreases faecal shedding of pathogenic R. equi in foals

Rhodococcus equi is the most common cause of pneumonia in young foals. Pneumonic foals are an important source of environmental contamination as they shed higher amounts of R. equi in their faeces than unaffected foals. As R. equi-specific hyperimmune plasma (HIP) lessens clinical pneumonia, we hypothesise that its use would result in decreased faecal shedding of R. equi by foals. Neonatal foals were either given HIP (n=12) or nothing (n=9, control) shortly after birth and were then experimentally infected with R. equi Faeces were collected before and on weeks 2, 3, 5 and 7 after infection. Presence of virulent R. equi was tested using qPCR. There was strong evidence of an association between HIP administration and a decrease in faecal shedding of virulent R. equi (P=0.031 by Pearson chi-squared test). Foals in the control shed significantly more R. equi (colony-forming units/ml) than foals that received HIP (P=0.008 by Mann-Whitney rank-sum test). While our study is the first to report this additional benefit of HIP administration, future studies are needed to evaluate the implications of its use under field conditions.

Rhodococcus equi infection: A diverse spectrum of disease

Rhodococcus equi is a gram positive bacterium most commonly presenting clinically as pneumonia, however can disseminate to cause disease in virtually any human tissue. Although it is predominantly an opportunistic pathogen, a number of case series have described infection occurring among individuals with a normal immune system. We describe two cases of Rhodococcus equi infection which highlight the diversity of disease presentations of this rare organism.

Fecal shedding of Rhodococcus equi in mares and foals after experimental infection of foals and effect of composting on concentrations of R. equi in contaminated bedding

Rhodococcus equi, a soil saprophyte, is a common cause of pneumonia in foals and a frequent opportunistic pathogen in immunosuppressed people. Because it is widespread in the environment, R. equi can be detected in the feces of most horses. However, the exact timing and rate of shedding relative to infection is unknown. The objectives of this study were to quantify shedding of R. equi in mares and foals after experimental infection of foals with 2 different inocula and to determine the effect of composting on concentrations of R. equi in contaminated bedding. Foals were infected intratracheally with virulent R. equi using inocula of 1 × 10⁷ CFU/mL (n = 16) or 1 × 10⁶ CFU/mL (n = 12) at 23 ± 2 days (range 21 to 27 days) of age. Fecal samples were collected from mares and foals prior to infection and on days 3, 7, and 14 post-infection for quantitative culture of total and virulent R. equi. Waste from the horses was composted for 7 days. Concentrations of total and virulent R. equi in foal feces were significantly higher on day 14 post-infection compared to day 0, regardless of inoculum size. Concentration of total R. equi in mare feces was significantly higher on days 3, 7 and 14 compared to day 0 regardless of inoculum size, whereas shedding of virulent R. equi only increased on day 14 post-infection. Composting for 7 days significantly decreased concentrations of total R. equi and virulent R. equi by an average of 1.08 ± 0.21 and 0.59 ± 0.26 log₁₀ CFU/g, respectively.

Use of Serial Quantitative PCR of the vapA Gene of Rhodococcus equi in Feces for Early Detection of R. equi Pneumonia in Foals

BACKGROUND

Current screening tests for Rhodococcus equi pneumonia in foals lack adequate accuracy for clinical use. Real-time, quantitative PCR (qPCR) for virulent R. equi in feces has not been systematically evaluated as a screening test.

OBJECTIVE

The objective of this study was to evaluate the accuracy of qPCR for vapA in serially collected fecal samples as a screening test for R. equi pneumonia in foals.

ANIMALS

One hundred and twenty-five foals born in 2011 at a ranch in Texas.

METHODS

Fecal samples were collected concurrently with thoracic ultrasonography (TUS) screening examinations at ages 3, 5, and 7 weeks. Affected (pneumonic) foals (n = 25) were matched by age and date-of-birth to unaffected (n = 25) and subclinical (ie, having thoracic TUS lesions but no clinical signs of pneumonia) foals (n = 75). DNA was extracted from feces using commercial kits and concentration of virulent R. equi in feces was determined by qPCR.

RESULTS

Subsequently affected foals had significantly greater concentrations of vapA in feces than foals that did not develop pneumonia (unaffected and subclinical foals) at 5 and 7 weeks of age. Accuracy of fecal qPCR, however, was poor as a screening test to differentiate foals that would develop clinical signs of pneumonia from those that would remain free of clinical signs (including foals with subclinical pulmonary lesions attributed to R. equi) using receiver operating characteristic (ROC) methods.

CONCLUSIONS AND CLINICAL IMPORTANCE

In the population studied, serial qPCR on feces lacked adequate accuracy as a screening test for clinical R. equi foal pneumonia.