Use of quantitative real-time PCR to determine viability of Streptococcus equi subspecies equi in respiratory secretions from horses with strangles

Development of a Real-Time Recombinase-Aided Amplification Method for the Rapid Detection of Streptococcus equi subsp. equi

Streptococcus equi subspecies equi (S. equi) is the causative pathogen of strangles in horses, donkeys, and other equine animals. Strangles has spread globally and causes significant losses to the horse industry. In response to the urgent need for effective disease control, this study introduces a novel nucleic acid diagnostic method known as a real-time recombinase-assisted amplification (RAA) assay, developed based on the eqbE gene, for the rapid detection of S. equi nucleic acid. The real-time RAA method employs specifically designed probes and primers targeting the eqbE gene, enhancing the overall specificity and sensitivity of the detection. After efficiency optimization, this real-time RAA method can detect 10 or more copies of nucleic acid within 20 min. The method demonstrates high specificity for S. equi and does not cross-react with other clinically relevant pathogens. Real-time RAA diagnostic performance was evaluated using 98 nasal swab samples collected from horses and compared with the real-time PCR detection method. Results revealed that 64 and 65 samples tested positive for S. equi using real-time RAA and real-time PCR, respectively. The overall agreement between the two assays was 96.94% (95/98), with a kappa value of 0.931 (p < 0.001). Further linear regression analysis indicated a significant correlation in the detection results between the two methods (R2 = 0.9012, p < 0.0001), suggesting that the real-time RAA assay exhibits a detection performance comparable to that of real-time PCR. In conclusion, the real-time RAA assay developed here serves as a highly specific and reliable diagnostic tool for the detection of S. equi in equine samples, offering a potential alternative to real-time PCR methods. In conclusion, the real-time RAA nucleic acid diagnostic method, based on the eqbE gene, offers rapid and accurate diagnosis of S. equi, with the added advantage of minimal equipment requirements, thus contributing to the efficient detection of strangles in horses.

Development of a novel real-time PCR multiplex assay for detection of Streptococcus equi subspecies equi and Streptococcus equi subspecies zooepidemicus

Strangles is a contagious bacterial disease of horses caused by Streptococcus equi subspecies equi (SEE) that occurs globally. Rapid and accurate identification of infected horses is essential for controlling strangles. Because of limitations of existing PCR assays for SEE, we sought to identify novel primers and probes that enable simultaneous detection and differentiation of infection with SEE and S. equi subsp. zooepidemicus (SEZ). Comparative genomics of U.S. strains of SEE and SEZ (n = 50 each) identified SE00768 from SEE and comB from SEZ as target genes. Primers and probes for real-time PCR (rtPCR) were designed for these genes and then aligned in silico with the genomes of strains of SEE (n = 725) and SEZ (n = 343). Additionally, the sensitivity and specificity relative to microbiologic culture were compared between 85 samples submitted to an accredited veterinary medical diagnostic laboratory. The respective primer and probe sets aligned with 99.7 % (723/725) isolates of SEE and 97.1 % (333/343) of SEZ. Of 85 diagnostic samples, 20 of 21 (95.2 %) SEE and 22 of 23 SEZ (95.6 %) culture-positive samples were positive by rtPCR for SEE and SEZ, respectively. Both SEE (n = 2) and SEZ (n = 3) were identified by rtPCR among 32 culture-negative samples. Results were rtPCR-positive for both SEE and SEZ in 21 of 44 (47.7 %) samples that were culture-positive for SEE or SEZ. The primers and probe sets reported here reliably detect SEE and SEZ from Europe and the U.S., and permit detection of concurrent infection with both subspecies.

Detection of Viable Streptococcus equi equi Using Propidium Monoazide Polymerase Chain Reaction

There is debate around the clinical significance of Streptococcus equi subsp. equi detection in low numbers using quantitative real-time PCR (qPCR). Propidium monoazide (PMA) qPCR has been used to differentiate DNA from viable and nonviable bacterial cells. The aim of this study was to evaluate the ability of PMA eqbE SEQ2190 triplex qPCR to differentiate DNA from viable and nonviable S. equi in positive and suspect positive clinical specimens. Fifty-seven stored (frozen and refrigerated) positive (36) or suspect positive (21) clinical specimens (determined via SeeI qPCR as the gold standard) were tested using eqbE SEQ2190 triplex qPCR with (+) and without (-) PMA pretreatment. Cycle thresholds were higher when using PMA indicating a mixture of heat killed and viable cells. Number of S. equi positive specimens were as follows: 6/57 eqbE + PMA, 13/57 eqbE -PMA (Chi- squared 3.1, p = .079); 10/57 SEQ2190 +PMA, 53/57 SEQ2190 -PMA (Chi- squared 65.6, p < .0001). The mean cycle thresholds were as follows: 23.88 eqbE -PMA, 29.89 eqbE + PMA (p = .04); 24.9 SEQ2190 -PMA, 31.9 SEQ2190 +PMA (p < .0001). PMA qPCR can be used to determine S. equi viability, but testing should be performed on fresh specimens.

Detection of Mycoplasma spp. in horses with respiratory disorders

BACKGROUND

Bacteria belonging to the genus Mycoplasma are small-sized, have no cell walls and small genomes. They commonly cause respiratory disorders in their animal hosts. Three species have been found in the respiratory tract of horses worldwide, that is., Mycoplasma (M.) equirhinis, M. pulmonis and M. felis, but their role in clinical cases remains unclear.

OBJECTIVES

The aim of this study was to i) develop and validate tools to detect, isolate and identify different Mycoplasma spp. strains in clinical equine respiratory-tract specimens and ii) subsequently define the prevalence of the three species in France depending on sample types and horse characteristics (age, breed, sex).

STUDY DESIGN

Validation of a workflow for mycoplasma diagnosis and subsequent prevalence study.

METHODS

Mycoplasma-free tracheal wash samples spiked with numerated strains and DNA dilutions were used to validate the culture methods and real-time PCR (rt-PCR) assay. Isolated strains were identified by 16S rRNA gene sequencing. Prevalences were determined on a population of 616 horses with respiratory disorders, sampled in France in 2020.

RESULTS

In total, 104 horses (16.9%) were found to be positive for Mycoplasma spp. by at least one method. M. equirhinis was the predominant circulating species, accounting for 85% of the rt-PCR-positive samples and 98% of the 40 cultured strains.

MAIN LIMITATION

The proposed pre-enrichment procedure improves the sensitivity of detection but hinders the quantification of the initial mycoplasma load in the clinical specimens.

CONCLUSIONS

Prevalence of mycoplasma varied with age, breed, and type of sample.

Current and Future Advances in the Detection and Surveillance of Biosecurity-Relevant Equine Bacterial Diseases Using Loop-Mediated Isothermal Amplification (LAMP)

Horses play an important role throughout the world, whether for work, culture, or leisure, providing an ever-growing significant contribution to the economy. The increase in importation and movement of horses, both nationally and internationally, has inevitably allowed for the global equine industry to grow. Subsequently, however, the potential for transmission of fatal equine bacterial diseases has also escalated, and devasting outbreaks continue to occur. To prevent such events, disease surveillance and diagnosis must be heightened throughout the industry. Current common, or "gold-standard" techniques, have shown to be inadequate at times, thus requiring newer technology to impede outbreaks. Loop-mediated isothermal amplification (LAMP) has proven to be a reliable, rapid, and accessible tool in both diagnostics and surveillance. This review will discuss equine bacterial diseases of biosecurity relevance and their current diagnostic approaches, as well as their respective LAMP assay developments. Additionally, we will provide insight regarding newer technology and advancements associated with this technique and their potential use for the outlined diseases.

Nasopharyngeal Microbiomes in Donkeys Shedding Streptococcus equi Subspecies equi in Comparison to Healthy Donkeys

Streptococcus equi subsp. equi (S. equi) is the pathogen causing strangles, a highly infectious disease that can affect equids including donkeys of all ages. It can persistently colonize the upper respiratory tract of animals asymptomatically for years, which serves as a source of infection. Several strangles outbreaks have been reported in the donkey industry in China in the last few years and pose a great threat to health, production, and the welfare of donkeys. Nasopharyngeal swab samples for culture and PCR are used widely in strangles diagnosis. Additionally, microbiomes within and on the body are essential to host homoeostasis and health. Therefore, the microbiome of the equid nasopharynx may provide insights into the health of the upper respiratory tract in animals. There has been no study investigating the nasopharyngeal microbiome in healthy donkeys, nor in donkeys shedding S. equi. This study aimed to compare nasopharyngeal microbiomes in healthy and carrier donkeys using 16S rRNA gene sequencing. Nasopharyngeal samples were obtained from 16 donkeys recovered from strangles (group S) and 14 healthy donkeys with no history of strangles exposure (group H). Of those sampled, 7 donkeys were determined to be carriers with positive PCR and culture results in group S. In group H, all 14 donkeys were considered free of strangles based on the history of negative exposure, negative results of PCR and culture. Samples from these 21 donkeys were used for microbial analysis. The nasopharyngeal microbiome composition was compared between the two groups. At the phylum level, relative abundance of Proteobacteria was predominantly higher in the S. equi carrier donkeys than in healthy donkeys (P < 0.01), while Firmicutes and Actinobacteria were significantly less abundant in the S. equi carrier donkeys than in healthy donkeys (P < 0.05). At the genus level, Nicoletella was detected in the upper respiratory tract of donkeys for the first time and dominated in carrier donkeys. It is suspected to suppress other normal flora of URT microbiota including Streptococcus spp., Staphylococcus spp., and Corynebacterium spp. We concluded that the nasopharyngeal microbiome in S. equi carrier donkeys still exhibited microbial dysbiosis, which might predispose them to other airway diseases.

Investigation of a 24-Hour Culture Step to Determine the Viability of Streptococcus equi Subspecies equi Via Quantitative Polymerase Chain Reaction in Nasal Secretions From Horses With Suspected Strangles

Polymerase chain reaction (PCR)-based detection assays for Streptococcus equi subspecies equi often overestimate the prevalence of samples containing viable organisms. The objective of this study was to determine if viability could be determined using genome quantitation and detection of messenger RNA (mRNA) transcripts for the SeM gene of S. equi in pre- and post-cultured samples. Nasal secretions collected from 42 horses with suspected strangles were tested by culture and by quantitative PCR (qPCR) before and 24 hours after a culture step. Viable S. equi was determined based on the detection of S. equi via culture, the detection of mRNA transcripts for the SeM gene of S. equi by qPCR, and/or an increase in absolute number of SeM target genes of S. equi between pre- and post-cultured samples. Viability was determined in 28/42 samples based on isolation of S. equi (11 samples), the presence of mRNA transcripts for the SeM gene of S. equi (25), and/or an increase in absolute quantitation of the SeM gene of S. equi between pre- and post-culture (17). The overall agreement between culture alone and the three criteria to determine viability was 59%. The overall agreement for the detection of mRNA transcripts and increase in absolute target genes was 88% and 74%, respectively. The combination of mRNA transcripts and increase in absolute target genes was able to determine the viability status in all 42 samples. In the absence of a culture-positive result for S. equi, the determination of viability can be achieved by using molecular strategies applied to samples undergoing a 24-hour culture step.

Development of a nested PCR assay for detection of Streptococcus equi subspecies equi in clinical equine specimens and comparison with a qPCR assay

Streptococcus equi subsp. equi is a Gram positive bacterial pathogen commonly associated with strangles in horses, a respiratory disease characterized by abscessation of submandibular and retropharyngeal lymph nodes which can lead to obstruction of the airway. Several real-time PCR (qPCR) assays have been developed for detection of S. equi from horses with many targeting conserved regions of the S. equi cell wall-associated M-protein (SeM), a major virulence factor and immunogen of S. equi. Our objective was to develop a nested PCR (nPCR) targeting SeM and an 18S rRNA internal control gene for detection of S. equi from horses with potential improvement in detection sensitivity compared to a qPCR. Primers and probes from the Kansas State Veterinary Diagnostic Laboratory (KSVDL) S. equi clinical testing assay were utilized for all qPCR testing. Primers flanking the SeM qPCR target region were selected for an initial end-point PCR step of the nested assay; PCR product from the end-point reaction then served as template for the qPCR reaction step of the nested assay. Sample nucleic acid was also tested directly with qPCR to allow for assay comparison. Nucleic acid from clinical specimens (n = 188) submitted to KSVDL were tested in parallel with each assay. The nPCR and qPCR assays identified 22.9% (43/188) and 13.3% (25/188) of samples positive for S. equi, respectively. None of the samples positive by qPCR were negative by nPCR. The PCR products from all positive samples were submitted for DNA sequencing. Each of the 25 samples positive by both assays had a high nucleotide identity match (>96%) to the SeM gene. Among the samples positive by nPCR but negative by qPCR, 17 of 18 were sequence confirmed for SeM at greater than 96% nucleotide identity. Based on the nPCR Ct (37.8) of the one sequence un-confirmed case, it is likely that the S. equi bacterial load in this sample was below the necessary concentration for successful sequencing. Limit of detection (LOD) for the nPCR was established at a Ct of 37, and based both on the LOD of the qPCR assay (Ct of 37), as determined by standard curve data, and on the highest nPCR Cts (~37) of clinical samples able to result in SeM sequence-confirmation. As demonstrated by sequencing confirmation, the nPCR assay targeting the SeM gene is highly specific to S. equi. The increased sensitivity of the nPCR, compared to the qPCR, may reduce the number of false negative sample results in clinical testing and provide a superior detection method during low bacterial shedding periods.

Survival of Streptococcus equi subsp. equi in Normal Saline Versus Phosphate-Buffered Saline and at Two Different Temperatures

Streptococcus equi subsp. equi causes strangles in horses. Sampling to detect carriers is important for the control of the disease, and maximizing the sensitivity of this procedure is necessary. To provide a basis for the choice of sampling solution and transport temperature for samples, comparisons were made between the survival of Streptococcus equi subsp. equi in normal saline versus phosphate-buffered saline and at two different temperatures (cold and room temperature). At present, normal saline is used to sample the nasopharynx as well as the guttural pouches, and the sampling solution is transported without special cooling. The results revealed no significant difference in bacterial concentration levels between the two sampling solutions, but a significantly higher concentration of viable bacteria in the samples kept cold compared with room temperature. Hence, a change of sampling solution is not warranted, but maintaining the cold chain during storage and transport to the laboratory may be important for clinical samples.

Long term silent carriers of Streptococcus equi ssp. equi following strangles; carrier detection related to sampling site of collection and culture versus qPCR

After strangles outbreaks, Streptococcus equi ssp. equi (S. equi) can persist in clinically normal silent carriers for months to years. Two naturally occurring outbreaks of strangles with 53 and 100% morbidity, respectively, were followed longitudinally to assess occurrence of carrier state and optimal detection methods Outbreak A involved 98 yearling warmbloods, and outbreak B 38 mature Icelandic horses. Fully recovered horses were sampled at least 6 months after index cases using nasal swabs (one sampling occasion only) nasopharyngeal lavage and guttural pouch visualisation and lavages for culture and qPCR to S. equi. Any horse with at least a single sample positive was deemed a carrier. Descriptive statistics and sensitivity and negative predictive values were calculated. Comparisons were made with McNemars and Fishers exact tests. Carrier rates in outbreak A were 3% based on culture and 15% based on qPCR and for outbreak B 13% based on culture and 37% based on qPCR. All culture positives were also qPCR positive. One carrier culture negative sampled after an additional 8 months was culture positive to S. equi, indicating that qPCR positives should be suspected to carry live bacteria. Findings indicate that reliance on guttural pouch sampling and appearance does not capture all silent carriers. All culture positives were identified by qPCR and even horses positive by qPCR but culture negative should be suspected carriers of live bacteria.