Evaluation of a real-time quantitative polymerase chain reaction assay for detection and quantitation of virulent Rhodococcus equi

Fatal Infection in an Alpaca (Vicugna pacos) Caused by Pathogenic Rhodococcus equi

Simple Summary

Serious consequences of septicemic bacterial infections include the formation of purulent and pyogranulomatous inflammation resulting in abscesses in inner organs. Different bacteria are known to cause these infections in livestock. In this study, we report in detail on a case of a fatal Rhodococcus (R.) equi infection in an alpaca (Vicugna pacos), to our knowledge, for the first time. R. equi is a member of the actinomycetes, a bacterial group known to contain several pathogenic bacteria. R. equi primarily affects equine foals and other domestic animals, but also humans, which renders this bacterium a zoonotic agent. The rhodococcal infection of the alpaca reported herein caused septicemia, resulting in emaciation and severe lesions in the lungs and heart. The onset of infection was presumably caused by aspiration pneumonia, resulting in abscesses exclusively in the lungs. The R. equi isolate proved to be pathogenic, based on the virulence gene vapA encoding the virulence-associated protein A. Antibiotic susceptibility testing revealed a susceptibility to doxycycline, erythromycin, gentamycin, neomycin, rifampicin, trimethoprim/sulfamethoxazole, tetracycline and vancomycin. This report of an R. equi infection in an alpaca makes clear that we still have knowledge gaps about bacterial infectious diseases in alpacas and potential zoonotic impacts. Therefore, the determination of pathogenic, zoonotic bacteria in alpacas is essential for treatment and preventive measures with respect to sustaining the health, welfare and productivity of this camelid species.

Abstract

Rhodococcus (R.) equi is a pathogen primarily known for infections in equine foals, but is also present in numerous livestock species including New World camelids. Moreover, R. equi is considered an emerging zoonotic pathogen. In this report, we describe in detail a fatal rhodococcal infection in an alpaca (Vicugna pacos), to our best knowledge, for the first time. The alpaca died due to a septicemic course of an R. equi infection resulting in emaciation and severe lesions including pyogranulomas in the lungs and pericardial effusion. The onset of the infection was presumably caused by aspiration pneumonia. R. equi could be isolated from the pyogranulomas in the lung and unequivocally identified by MALDI-TOF MS analysis and partial sequencing of the 16S rRNA gene, the 16S-23S internal transcribed spacer (ITS) region and the rpoB gene. The isolate proved to possess the vapA gene in accordance with tested isolates originating from the lungs of infected horses. The R. equi isolates revealed low minimal inhibitory concentrations (MIC values) for doxycycline, erythromycin, gentamycin, neomycin, rifampicin, trimethoprim/sulfamethoxazole, tetracycline and vancomycin in antibiotic susceptibility testing. Investigations on the cause of bacterial, especially fatal, septicemic infections in alpacas are essential for adequately addressing the requirements for health and welfare issues of this New World camelid species. Furthermore, the zoonotic potential of R. equi has to be considered with regard to the One Health approach.

Novel Quantitative PCR for Rhodococcus equi and Macrolide Resistance Detection in Equine Respiratory Samples

R. equi is an important veterinary pathogen that takes the lives of many foals every year. With the emergence and spread of MDR R. equi to current antimicrobial treatment, new tools that can provide a fast and accurate diagnosis of the disease and antimicrobial resistance profile are needed. Here, we have developed and analytically validated a multiplex qPCR for the simultaneous detection of R. equi and related macrolide resistance genes in equine respiratory samples. The three sets of oligos designed in this study to identify R. equi housekeeping gene choE and macrolide resistance genes erm(46) and erm(51) showed high analytic sensitivity with a limit of detection (LOD) individually and in combination below 12 complete genome copies per PCR reaction, and an amplification efficiency between 90% and 147%. Additionally, our multiplex qPCR shows high specificity in in-silico analysis. Furthermore, it did not present any cross-reaction with normal flora from the equine respiratory tract, nor commonly encountered respiratory pathogens in horses or other genetically close organisms. Our new quantitative PCR is a trustable tool that will improve the speed of R. equi infection diagnosis, as well as helping in treatment selection.

GAPDH, rhbC, and vapA gene expression in Rhodococcus equi cultured under different iron concentrations

The ability of Rhodococcus equi to survive in macrophages and cause pneumonia in foals depends on vapA and rhbC genes, which produce the virulence-associated protein A (VapA) and the rhequichelin siderophore, respectively. Virulent R. equi acquires Fe from transferrin by unknown mechanisms. Our objectives were to determine the role of GAPDH in Fe homeostasis, to further characterize GAPDH, rhbC, and vapA expression under iron homeostasis, and to document the occurrence of rhbC gene in R. equi isolates. Therefore, vapA + R. equi was cultured under excessive, physiologic, and restricted iron concentrations, and quantitative culture and gene expression were performed. The relative expression of GAPDH, rhbC, and vapA after 48 h of culture were analyzed by qPCR. To determine the rhbC occurrence, total DNA was extracted from R. equi isolated from foals with clinical rhodococcosis (n = 22), healthy horses (feces, n = 16; nasal swab, n = 9), soil (n = 6), and 2 ATCC reference strains. Conventional PCR was performed to identify genus/species, vapA, and rhbC genes. Iron restriction proportionally decreased R. equi growth rates, and induced high expression of both GAPDH and vapA. The putative role of GAPDH in R. equi iron homeostasis should be further investigated. rhbC was significantly up-regulated under both Fe excess and critical starvation. The rhbC gene was identified in all clinical isolates and soil, but it was absent in 2 isolates from healthy horses, suggesting that rhequichelin is not required for R. equi nasal and intestinal colonization.

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.

Development and evaluation of the internal-controlled real-time PCR assay for Rhodococcus equi detection in various clinical specimens

Rhodococcus equi is the causative agent of rhodococcosis in horses, resulting in significant morbidity and mortality in foals. This bacterium has also been isolated from a variety of animals and is being increasingly reported as a cause of infection in humans, mainly in immunosuppressed individuals. Laboratory diagnostics of R. equi infections based only on conventional microbiological methods shows low accuracy and can lead to misidentification. The objective of the study was to develop and evaluate a real-time PCR assay for direct detection of R. equi in various clinical specimens, including tissue samples. The species-specific region of the gene encoding R. equi cholesterol oxidase, choE, was used as a qPCR-target. The diagnostic applicability of the assay was confirmed by testing various tissue specimens obtained from horses with clinical signs of rhodoccocal infection and swine submaxillary lymph nodes. The rate of R. equi detection in clinical specimens by the developed assay was higher in comparison to the culture method (90% vs. 60.0% of positive samples) and conventional PCR (90.0% vs. 20.0% of positive samples). In case of 13 samples that were negative in the culture-based method, R. equi was detected by the developed assay. Only in one case, it gave negative result for culture-positive sample. The assay may provide a simple and rapid tool to complement the classical methods of R. equi detection based on culture and phenotypic identification of isolates, as the performed evaluation indicated a high specificity and accuracy of the results.

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

BACKGROUND

Real-time, quantitative PCR (qPCR) methods for detecting Rhodococcus equi in feces have been developed as a noninvasive, rapid diagnostic test for R. equi pneumonia, but have not been evaluated in a large population of foals.

OBJECTIVE

The objective of this study was to evaluate the clinical utility of fecal PCR as a diagnostic test for R. equi pneumonia in foals using receiver operating characteristic (ROC) methods.

ANIMALS

186 foals born in 2011 at an R. equi-endemic ranch in Texas.

METHODS

Fecal samples were collected at the time of onset of clinical signs for pneumonic foals (n = 31). Foals with pneumonia were matched by age and birth date to healthy (n = 31) and subclinical (n = 124) control foals; fecal samples were collected from these controls. DNA was extracted from feces using commercial kits and concentration of virulent R. equi in feces was determined by qPCR.

RESULTS

Concentration of R. equi in feces differed significantly (P < .05) among groups. The area under the ROC curve for fecal qPCR for diagnosis of R. equi pneumonia was 89% (95% CI, 83-99), with a sensitivity of 94% and specificity of 72%.

CONCLUSIONS AND CLINICAL IMPORTANCE

qPCR of feces can be useful as an alternative to tracheobronchial aspiration for the diagnosis of R. equi in foals with clinical signs of pneumonia. Caution should be used in extrapolating results of this study to other populations because fecal concentration of R. equi might vary by geographic location or management practices.

Development of a polymerase chain reaction assay for quantification of Lawsonia intracellularis

The objective of the present study was to develop a quantitative polymerase chain reaction (qPCR) assay using SYBR Green for quantification of Lawsonia intracellularis in cell culture and pig fecal samples. Specific primers were designed and tested using the aspartate ammonia-lyase (aspA) gene as a target. Serial 10-fold dilutions of cell culture samples and several sets of spiked feces were used for qPCR optimization. The lower limit of the linear range of the assay in cell culture was 5.1 x 10(2) L. intracellularis/ml. A concentration of between 2.55 x 10(4) and 2.55 x 10(3) L. intracellularis/g was the lower limit of the linear range when testing community DNA from spiked fecal samples. From both cell culture and fecal samples, L. intracellularis could be detected but not accurately quantified at levels approximately 1 log below the linear range. No cross-reactivity of qPCR was found when the assay was tested using the DNA extracted from 16 species of enteric bacteria commonly found in pig feces or closely related to L. intracellularis. The new qPCR assay might prove to be a sensitive, specific, precise, and accurate method for the detection and quantification of L. intracellularis in field samples.

RHODOCOCCUS EQUI

RESUMO Rhodococcus equi é uma importante causa de broncopneumonia em potros com menos de seis meses de idade, sendo responsável pela mortalidade de eqüinos no mundo inteiro. É um microrganismo intracelular capaz de sobreviver e se multiplicar no interior de macrófagos. Apresenta três níveis de virulência de acordo com os diferentes antígenos expressos em sua superfície. Cepas virulentas apresentam um plasmídeo que codifica a proteína de superfície VapA e são isoladas principalmente de potros com pneumonia e de alguns pacientes humanos. Cepas com virulência intermediária expressam a proteína VapB e predominam em suínos e humanos com AIDS. Cepas avirulentas não expressam antígenos de superfície e são encontradas principalmente no ambiente e em pacientes humanos. Um dos fatores responsáveis pela ampla distribuição da enfermidade em potros é a imaturidade do sistema imunológico dos animais acometidos pela infecção, que pode se tornar endêmica em alguns criatórios. Em humanos, as formas de infecção são ainda desconhecidas, mas o contato com eqüinos é relatado em um terço dos casos. Devido à importância clínica da doença, são necessários métodos diagnósticos que promovam sua identificação precoce, facilitando e aumentando as chances de sucesso com o tratamento. Os métodos mais utilizados atualmente são o cultivo microbiológico, testes sorológicos para detecção de anticorpos séricos nos animais e técnicas de PCR que detectam a região 16S do rDNA e o fragmento do gene vapA do microrganismo.

Multiplex PCR assay for identification of Corynebacterium pseudotuberculosis from pure cultures and for rapid detection of this pathogen in clinical samples

Corynebacterium pseudotuberculosis is the aetiological agent of caseous lymphadenitis (CLA), a debilitating disease of sheep and goats. Accurate diagnosis of CLA primarily relies on microbiological examination, followed by biochemical identification of isolates. In an effort to facilitate C. pseudotuberculosis detection, a multiplex PCR (mPCR) assay was developed targeting three genes of this bacterium: the 16S rRNA gene, rpoB and pld. This method allowed efficient identification of 40 isolates of this bacterium that had been identified previously by biochemical testing. Analysis of taxonomically related species did not generate the C. pseudotuberculosis mPCR amplification profile, thereby demonstrating the assay's specificity. As little as 1 pg of C. pseudotuberculosis genomic DNA was detected by this mPCR assay, demonstrating the sensitivity of the method. The detection limit in clinical samples was estimated to be 10(3) c.f.u. C. pseudotuberculosis could be detected directly in pus samples from infected sheep and goats (n=56) with a high diagnostic sensitivity (94.6 %). The developed assay significantly improves rapid C. pseudotuberculosis detection and could supersede bacteriological culture for microbiological and epidemiological diagnosis of CLA.

Internally controlled real-time PCR method for quantitative species-specific detection and vapA genotyping of Rhodococcus equi

We developed a novel quantitative real-time PCR (Q-PCR) method for the soil actinomycete Rhodococcus equi, an important horse pathogen and emerging human pathogen. Species-specific quantification was achieved by targeting the chromosomal monocopy gene choE, universally conserved in R. equi. The choE Q-PCR included an internal amplification control (IAC) for identification of false negatives. A second Q-PCR targeted the virulence plasmid gene vapA, carried by most horse isolates but infrequently found in isolates from other sources. The choE-IAC and vapA assays were 100% sensitive and specific as determined using 178 R. equi isolates, 77 nontarget bacteria, and a panel of 60 R. equi isolates with known vapA+ and vapA-negative (including vapB+) plasmid genotypes. The vapA+ frequency among isolate types was as follows: horse, 85%; human, 20%; bovine and pig, 0%; others, 27%. The choE-IAC Q-PCR could detect up to one genome equivalent using R. equi DNA or 100 bacteria/ml using DNA extracted from artificially contaminated horse bronchoalveolar lavage (BAL) fluid. Quantification was linear over a 6-log dynamic range down to approximately 10 target molecules (or 1,000 CFU/ml BAL fluid) with PCR efficiency E of >0.94. The vapA assay had similar performance but appeared unsuitable for accurate (vapA+) R. equi quantification due to variability in target gene or plasmid copy number (1 to 9). The dual-reaction Q-PCR system here reported offers a useful tool to both medical and veterinary diagnostic laboratories for the quantitative detection of R. equi and (optional) vapA+ "horse-pathogenic" genotype determination.