Rapid diagnosis of strangles (Streptococcus equi subspecies equi) using PCR

Laboratory tools for the direct detection of bacterial respiratory infections and antimicrobial resistance: a scoping review

Rapid laboratory tests are urgently required to inform antimicrobial use in food animals. Our objective was to synthesize knowledge on the direct application of long-read metagenomic sequencing to respiratory samples to detect bacterial pathogens and antimicrobial resistance genes (ARGs) compared to PCR, loop-mediated isothermal amplification, and recombinase polymerase amplification. Our scoping review protocol followed the Joanna Briggs Institute and PRISMA Scoping Review reporting guidelines. Included studies reported on the direct application of these methods to respiratory samples from animals or humans to detect bacterial pathogens ±ARGs and included turnaround time (TAT) and analytical sensitivity. We excluded studies not reporting these or that were focused exclusively on bioinformatics. We identified 5,636 unique articles from 5 databases. Two-reviewer screening excluded 3,964, 788, and 784 articles at 3 levels, leaving 100 articles (19 animal and 81 human), of which only 7 studied long-read sequencing (only 1 in animals). Thirty-two studies investigated ARGs (only one in animals). Reported TATs ranged from minutes to 2 d; steps did not always include sample collection to results, and analytical sensitivity varied by study. Our review reveals a knowledge gap in research for the direct detection of bacterial respiratory pathogens and ARGs in animals using long-read metagenomic sequencing. There is an opportunity to harness the rapid development in this space to detect multiple pathogens and ARGs on a single sequencing run. Long-read metagenomic sequencing tools show potential to address the urgent need for research into rapid tests to support antimicrobial stewardship in food animal production.

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.

Complete genome sequencing and comparative genomic analysis of three donkey Streptococcus equi subsp. equi isolates

Introduction

Streptococcus equi subspecies equi (S. equi) is the causative agent of strangles, which is one of the most common and highly contagious respiratory infectious illnesses in horses. Streptococcus equi (S. equi) is a horse-specific pathogen that originated from the closely related zoonotic pathogen Streptococcus equi subspecies zooepidemicus (S. zooepidemicus). Despite decades of research, the movement of genetic material across host-restricted diseases remains a mystery.

Methods

Three S. equi donkey isolates (HTP133, HTP232, and HT1112) were recently isolated from a strangles epidemic on donkey farms in China's Xinjiang Province. In this study, we performed a comprehensive comparative analysis of these isolates using whole genome sequencing and compared them to the published genomic sequences of equine strain S. equi 4047 to uncover evidence of genetic events that shaped the evolution of these donkey S. equi isolates' genomes.

Results

Whole genome sequencing indicated that both strains were closely related, with comparable gene compositions and a high rate of shared core genomes (1788-2004). Our comparative genomic study indicated that the genome structure is substantially conserved across three donkey strains; however, there are several rearrangements and inversions when compared to the horse isolate S. equi 4047. The virulence factors conveyed by genomic islands and prophages, in particular, played a key role in shaping the pathogenic capacity and genetic diversity of these S. equi strains. Furthermore, we discovered that the HT133 isolate had a strong colonization ability and increased motility; the HT1112 isolates had a significantly higher ability for antimicrobial resistance and biofilm formation, and the HT232 isolate gained pathogenic specialization by acquiring a bacteriophage encoding hyaluronate lyase.

Discussion

In summary, our findings show that genetic exchange across S. equi strains influences the development of the donkey S. equi genome, offering important genetic insights for future epidemiological studies of S. equi infection.

Molecular and sequencing study and identification of novel SeM-type in beta-hemolytic streptococci involving the upper respiratory tract in Iran

BACKGROUND

Beta-hemolytic streptococci involving the upper respiratory tract cause strangles and strangles-like diseases in horses and cause severe economic damage to the equestrian club each year. Therefore, careful epidemiological study of these bacteria, evaluation of phylogenetic connections and SeM-typing can be useful to determine the source and epidemiological characteristics of the disease outbreak. Isolates were analyzed using molecular and phylogenetic methods and to determine antibiotic resistance pattern in Iranian isolates. Molecular and phylogenetic methods were used to evaluate Iranian streptococcal isolates, and the similarity of the Iranian SeM-97 sequence with other alleles was assessed using the Neighbor-joining method with the Kimura 2 Parameter statistical model. The amino acid sequence of this gene was compared with the predicted SeM-3 reference amino acid sequence (FM204883) using MEGA 7 software.

RESULTS

One type of SeM was found among streptococcal isolates. This type (SeM-97) was reported for the first time and was a new SeM. The relationship between streptococcal isolates and age, sex, race, clinical signs and geographical area was investigated. A significant relationship was observed between streptococcal isolates with age variables and clinical symptoms.

CONCLUSIONS

In our study, a Streptococcus equi subsp. equi genotype was identified. The 97 allele of this gene has not been officially reported anywhere and is only registered in the Public databases for molecular typing and microbial genome diversity (PubMLST)-SeM database by Katy Webb. This was the first isolate reported and registered in the mentioned database. The isolate (Tabriz61) had the SeM-97 allele with clinical signs including mucopurulent discharge, abnormal sounds in lung hearing, warmth and enlargement or discharge and abscess of retropharyngeal lymph node and fever. This isolate was sensitive to penicillin, meropenem, ampicillin, cefotaxime, tetracycline, erythromycin, azithromycin, chloramphenicol, enrofloxacin and ciprofloxacin antibiotics and resistant to trimethoprim-sulfamethoxazole and gentamicin antibiotics.

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.

Strangles in equines: An overview

Strangles, caused by Streptococcus equi subspecies equi, is a highly infectious respiratory disease affecting horses and other equines. The disease is economically important and compromises the productivity of equine farm significantly. The disease is characterized by pyrexia, mucopurulent nasal discharge, and abscess formation in the lymph nodes of the head and neck of horses. The disease transmission occurs either directly by coming in contact with infectious exudates or indirectly via fomite transmission. Besides this, carrier animals are the primary and most problematic source of disease infection. The organism not only initiates outbreaks but also makes the control and prevention of the disease difficult. The diagnosis of strangles is best done by isolating and characterizing the bacteria from nasal discharge, pus from abscesses, and lymphoid tissues or by using PCR. ELISA can also be used to detect serum protein M (SeM) antibodies for diagnosis. The most popular treatment for strangles is with penicillin; however, the treatment is affected by the stage, feature and severity of the disease. Prevention and control of strangles can be achieved through vaccination and good hygiene practices. Basically, this review describes the global prevalence of S. equi, as well as general aspects of the disease, like pathogenesis, diagnosis, treatment, prevention, control and management of the disease.

Molecular Features and Antimicrobial Susceptibilities of Streptococcus equi ssp. equi Isolates from Strangles Cases in Indonesia

Strangles, caused by Streptococcus equi ssp. equi (S. equi equi), is a highly infectious and frequent disease of equines worldwide. No data are available regarding the molecular epidemiology of strangles in Indonesia. This study aimed to characterize S. equi equi isolates obtained from suspected strangles cases in Indonesia in 2018. Isolates originated from seven diseased horses on four different farms located in three provinces of Indonesia. Whole genome sequences of these isolates were determined and used for seM typing, multilocus sequence typing (MLST), and core genome MLS typing (cgMLST). Genomes were also screened for known antimicrobial resistance genes and genes encoding for the recombinant antigens used in the commercial Strangvac^® subunit vaccine. All seven S. equi equi isolates from Indonesia belonged to ST179 and carried seM allele 166. Isolates differed from each other by only 2 to 14 cgSNPs and built an exclusive sub-cluster within the Bayesian Analysis of Population Structure (BAPS) cluster 2 (BAPS-2) of the S. equi equi cgMLST scheme. All isolates revealed predicted amino acid sequence identity to seven and high similarity to one of the eight antigen fragments contained in Strangvac^®. Furthermore, all isolates were susceptible to beta-lactam antibiotics penicillin G, ampicillin, and ceftiofur. Our data suggest that the horses from this study were affected by strains of the same novel sublineage within globally distributed BAPS-2 of S. equi equi. Nevertheless, penicillin G can be used as a first-choice antibiotic against these strains and Strangvac^® may also be protective against Indonesian strains.

Prospective bacterial and fungal sources of hyaluronic acid: A review

The unique biological and rheological properties make hyaluronic acid a sought-after material for medicine and cosmetology. Due to very high purity requirements for hyaluronic acid in medical applications, the profitability of streptococcal fermentation is reduced. Production of hyaluronic acid by recombinant systems is considered a promising alternative. Variations in combinations of expressed genes and fermentation conditions alter the yield and molecular weight of produced hyaluronic acid. This review is devoted to the current state of hyaluronic acid production by recombinant bacterial and fungal organisms.

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.

Pathogenicity and drug resistance of animal streptococci responsible for human infections

Bacteria of the genus Streptococcus, earlier considered typically animal, currently have also been causing infections in humans. It is necessary to make clinicians aware of the emergence of new species that may cause the development of human diseases. There is an increasing frequency of isolation of streptococci such as S. suis, S. dysgalactiae, S. iniae and S. equi from people. Isolation of Streptococcus bovis/Streptococcus equinus complex bacteria has also been reported. The streptococcal species described in this review are gaining new properties and virulence factors by which they can thrive in new environments. It shows the potential of these bacteria to changes in the genome and the settlement of new hosts. Information is presented on clinical cases that concern streptococcus species belonging to the groups Bovis, Pyogenic and Suis. We also present the antibiotic resistance profiles of these bacteria. The emerging resistance to β-lactams has been reported. In this review, the classification, clinical characteristics and antibiotic resistance of groups and species of streptococci considered as animal pathogens are summarized.

Novel seM-types of Streptococcus equi subsp. equi identified in isolates circulating in Argentina

BACKGROUND

Strangles is a worldwide infectious disease caused by Streptococcus equi subsp. equi that affects the upper respiratory tract of horses. Streptococcus equi subsp. equi characterisation by seM-typing is internationally used for epidemiological studies and comparison of isolates.

OBJECTIVES

To identify and to compare the seM-types of Argentinian isolates of Streptococcus equi subsp. equi.

STUDY DESIGN

Investigation of bacterial isolates using molecular and phylogenetic approaches.

METHODS

A total of 59 Argentinian isolates of Streptococcus equi subsp. equi obtained between 2007 and 2019 were studied by seM-typing. The sequence similarity of Argentinian seM-types and the other alleles available on the seM database was determined using BLAST and phylogenetic analysis was performed using the Neighbour-Joining algorithm. The amino acid sequences were predicted and compared with the predicted amino acid sequence of the reference strain 4047 using the MEGA 7 software and PROVEAN tool.

RESULTS

Eight seM-types were found among the isolates. Only one of them (seM-61) has been previously reported and the other seven alleles (seM-129, seM-130, seM-131, seM-132, seM-133, seM-134 and seM-135) were novel seM sequences. High genetic similarity was observed among the Argentinian seM-types, with the exception of seM-130. No functional effects of amino acid differences were predicted.

MAIN LIMITATIONS

The number of related and unrelated isolates per year.

CONCLUSIONS

Seven novel seM-types and seM-61 that were previously reported in Brazil were circulating in Argentina which were identified as circulating in Argentinian horses between 2007 and 2019. The high genetic similarity among the Argentinian and Brazilian seM-types suggests that there is a geographical distribution of strain types. The geographical restriction of strains is likely to reflect the movement of horses between different equine disciplines and neighbouring countries.

Failure of serological testing for antigens A and C of Streptococcus equi subspecies equi to identify guttural pouch carriers

BACKGROUND

Serology is commonly used as a means of identifying horses that might be chronic and silent carriers of S. equi but its sensitivity is rarely examined.

OBJECTIVES

The study was designed to investigate the sensitivity of serological testing for antibodies against S. equi antigens A and C to detect guttural pouch carriers of S. equi.

STUDY DESIGN

Retrospective clinical study.

METHODS

As part of routine surveillance and quarantine procedures horses arriving at a welfare charity quarantine unit were subject to both microbiological sampling of guttural pouches and also serological testing for antibodies directed at S. equi antigens A and C. Laboratory results and endoscopic findings were examined to determine associations between serological results and guttural pouch carriage of S. equi.

RESULTS

Of 287 included horses, 9 (3.1%) were found to be guttural pouch carriers. There was no significant association between serological status and guttural pouch carriage of S. equi Only one of the nine carriers (11%) was seropositive using a cut-off of OD ≥ 0.5, and only three of nine (33%) using a cut-off of OD ≥ 0.3.

MAIN LIMITATIONS

Horses examined in this study were new arrivals at a welfare centre rather than from a general, well-managed, equid population. As a retrospective clinical study, the laboratory test results could not be repeated for further confirmation.

CONCLUSIONS

Caution is advised when relying on seronegativity to antigens A and C in order to discount the possibility of chronic carriage of S. equi in guttural pouches.

Novel Streptococcus equi strains causing strangles outbreaks in Arabian horses in Egypt

Strangles displays a major challenge to veterinary medicine worldwide. However, no data on Streptococcus equi subsp. equi (S. equi) M protein alleles have been reported so far from Arabian horses. We report here for the first time the S. equi SeM alleles causing strangles in Arabian horses, and the associated risk factors for the disease. Duplicate samples from one hundred Arabian horses with acute strangles in confirmed outbreaks and sporadic cases were analysed by phenotypic methods and multiplex polymerase chain reaction (PCR) targeting streptokinase precursor, seeI and sodA genes. PCR and sequencing of S. equi SeM gene were employed for strains typing, and the four superantigens were determined among the allelic variants. Direct-sample PCR confirmed and highly positively correlated (r = .85) with the phenotypic results, and detected S. equi in five samples more than the conventional culture. A combination of multiplex PCR from samples and culture could successfully identify S. equi (92%), S. zooepidemicus (5%) and S. equisimilis (3%). SeM typing demonstrated five SeM alleles, including four previously unidentified alleles that were deposited in the PubMLST-SeM database. SeM-139 and SeM-141 are related to some strains that were recently recovered from donkeys in China. SeM-140 and SeM-199 are related to a group of alleles from horses in Europe. Variation in the presence of seeM, seeH and seeL superantigens was found across the four novel alleles without interference with the severity of strangles and clinical presentation seen in different outbreaks. Horse age was the most important factor in developing strangles, followed by seasonality and the diagnosis of strangles in the previous year. These new findings comprise a significant contribution to the horse industry through the identification of novel S. equi SeM types that may bolster measures for strangles control as the identified SeM alleles will certainly help in the development of SeM-containing vaccine.

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.

Ocular Manifestations of Systemic Disease in the Horse

Many systemic diseases have ocular manifestations. In some cases, ocular abnormalities are the most obvious or first recognized sign of disease that prompts veterinary evaluation. In other cases, the systemic disease leads to secondary ocular changes that might lead to loss of vision or globe if not addressed. Therefore, recognition of ocular abnormalities that might result from systemic diseases is an essential skill for the equine practitioner. This article provides practitioners with information regarding the most common systemic diseases of horses in North America that have ocular manifestations, organized by ocular signs.