A Multiplex real-time PCR for detection of Mycoplasma gallisepticum and Mycoplasma synoviae in clinical samples from Brazilian commercial poultry flocks

Mycoplasma gallisepticum and Mycoplasma synoviae in commercial poultry: current control strategies and future challenges

Mycoplasma gallisepticum (Mg) and Mycoplasma synoviae (Ms) are regarded as the most important avian mycoplasma species for today's chicken and turkey farming industry from clinical and economical perspectives. Control strategies for Mg and Ms have become more efficient due to investments in mycoplasma research over the last 70 years. These investments have contributed to the further implementation of serological and molecular testing, the development of vaccines, and the improvement of antimicrobial treatment strategies. However, the increasing spotlight on welfare, the pressure on prudent use of antimicrobials, and the expected global increase in poultry production, are going to have an impact on the future control of avian mycoplasmas in commercial poultry. In this paper a group of avian mycoplasma experts discuss the future challenges in mycoplasma control considering the background of these expected changes and the relevance for future avian mycoplasma research.

First molecular investigation to detect avian Mycoplasma species in clinical samples from laying-hen farms in Tunisia

BACKGROUND

Avian mycoplasmas are known pathogens, which cause severe economic losses in poultry flocks. PCR is a rapid, sensitive, and less expensive diagnostic tool than culture for the identification of mycoplasmas in poultry farms. The objective of this study was to determine by PCR the presence of Mycoplasma spp., Mycoplasma gallisepticum (MG), Mycoplasma synoviae (MS), and Mycoplasma pullorum (MP) in laying hens located in the Sfax region, in the South of Tunisia.

RESULTS

A total of 781 tracheal swabs were collected from 13 laying-hen farms without clinical signs at the date of sampling. MP was detected by a newly described specific PCR assay. The prevalence calculated from PCR results at the flock level was 100% for Mycoplasma spp., 0% for MG, 84.6% for MS and 61.5% for MP. The overall prevalence at the animal level was 38.7% for Mycoplasma spp., 0% for MG, 25% for MS and 6.4% for MP. The overall prevalence of 100% of avian mycoplasmas in laying-hen farms (38.7% prevalence at the animal level) shows an alarming situation.

CONCLUSIONS

These results underline the importance of monitoring the emergence and spread of Mycoplasma strains in farms in order to decrease economic losses due to mycoplasmoses.

Mycoplasmosis in Poultry: An Evaluation of Diagnostic Schemes and Molecular Analysis of Egyptian Mycoplasma gallisepticum Strains

Infections with Mycoplasma gallisepticum (MG) in poultry are associated with a wide range of disease conditions, including those affecting the respiratory and reproductive systems. The purpose of this study was to endorse the more sensitive diagnostic scheme for MG infection and identify the best molecular marker for MG phylogenetic analysis using six housekeeping genes: mgc2, mraW, atpG, ugpA, DUF31196, and lgT. For these purposes, 55 poultry flocks of different species were screened using either qRT-PCR or PCR techniques analogous to conventional culturing from non-cultured and cultured swabs on PPLO broth. The rate of MG positivity was the highest when using qRT-PCR from cultured broth (89.0%) and the lowest when using conventional culturing (34.5%). Compared to qRT-PCR from broth, statistical analysis using the Roc curve in MedCalc statistical software showed that the PCR schemes (qRT-PCR from swabs and PCR from swabs and broth) performed better than conventional culturing in terms of sensitivity, accuracy, and area under the curve (AUC), suggesting that they may be more reliable schemes. Further support was added by Cohen's kappa test, showing moderate agreement between the molecular approaches. Among the six screened genes, mgc2 and mraW had the highest detection rates (69% and 65.4%, respectively). The comparative phylogenetic analysis revealed that mgc2 or atpG gene sequences distinguished MG isolates into different clades with high discriminatory power.

A Multiplex PCR Assay for Differential Identification of Wild-type and Vaccine Strains of Mycoplasma gallisepticum

Mycoplasma gallisepticum (MG) can cause respiratory disease in chickens and result in serious economic losses in the chicken industry. The use of live vaccines has been a favorable option for the control of MG infection in multi-age commercial layers and broiler breeders. There are three live vaccines, including ts-11, 6/85, and F strain, that have been commonly used in various parts of the world, including South Korea. The definitive diagnosis of the infection, therefore, requires the differentiation of wild-type field strains of MG from the vaccine strains used. Thus, we aimed to develop a novel multiplex PCR assay to discriminate between vaccine strains (ts-11, 6/85, and F strain) and wild-type field strains of MG isolated from infected chickens. We designed four novel primer sets that are each specific to MG species, ts-11, 6/85, and F strain. The multiplex PCR assay using the primer sets differentially identified wild-type and vaccine strains of MG but did not detect other avian bacteria. The detection limit of this assay was 250 fg/μL of genomic DNA of each strain tested. In addition, this assay was applied to 36 MG strains isolated from chickens over the past 20 years in South Korea. As a result, the assay identified 22 wild-type strains and 14 vaccine strains. Consequently, the novel multiplex PCR assay can discriminate between vaccine and wild-type field strains of MG and could be a valuable tool for the diagnosis of MG infection in MG-vaccinated chicken flocks.

Multispectral Portable Fibre-Optic Reflectometer for the Classification of the Origin of Chicken Eggshells in the Case of Mycoplasma synoviae Infections

The proper classification of the origins of food products is a crucial issue all over the world nowadays. In this paper, the authors present a device-a multispectral portable fibre-optic reflectometer and signal processing patch-together with a machine-learning algorithm for the classification of the origins of chicken eggshells in the case of Mycoplasma synoviae infection. The sensor device was developed based on previous studies with a continuous spectrum in transmittance and selected spectral lines in reflectance. In the described case, the sensor is based on the integration of reflected spectral data from short spectral bands from the VIS and NIR region, which are produced by single-colour LEDs and introduced to the sample via a fibre bundle. The measurement is carried out in a sequence, and the reflected signal is pre-processed to be put in the machine learning algorithm. The support vector machine algorithm is used together with three different types of data normalization. The obtained results of the F-score factor for classification of the origins of samples show that the percentages of eggs coming from Mycoplasma synoviae infected hens are up to 87% for white and 96% for brown eggshells.

Rapid and specific detection of Mycoplasma gallisepticum and Mycoplasma synoviae infection in poultry using single and duplex PCR assays

Avian mycoplasmosis, mainly caused by Mycoplasma gallisepticum (MG) and Mycoplasma synoviae (MS), is an economically important disease of poultry industry. The present study was aimed to develop duplex PCR as a rapid, specific and economical method for accurate detection of MG and MS in poultry and its comparison with single (monoplex) MG/MS PCR. During present investigation, a total of 146 poultry flocks having clinical history of respiratory disease were screened. Pooled tissue samples (trachea, lungs and air sacs) from 4-5 birds of each flock were collected during necropsy at disease investigation laboratories, Hisar, Haryana, India. The single and duplex PCR assays were standardized using primers of intergenic spacer region (IGSR; 16S-23S rRNA) for MG and hemagglutinin vlhA gene for MS, with expected amplicon size of 812 bp and 1200 bp products, respectively. In single PCR, 6.85%, 2.74% and 2.74% tissue samples were found positive for MG, MS and both MG and MS, respectively. However, duplex PCR showed, 7.53%, 2.74% and 1.37% positivity for MG, MS and both MG and MS, respectively. Taking the results of monoplex PCR as a gold standard, sensitivity and specificity of the developed duplex PCR was found to be 94.44% and 100%, respectively. Moreover, Cohen's kappa statistic (k = 0.97) measured a 'perfect' agreement between monoplex and duplex PCR assays. The positive and negative predictive values of duplex PCR was found to be 1.0 and 0.9922, respectively at 95% confidence interval (CI), as compared to monoplex PCR. The simultaneous use of two genes in a duplex PCR was more rapid and economical than two separate single PCR reactions.

A Preliminary Assessment of the Potential Health and Genetic Impacts of Releasing Confiscated Passerines Into the Wild: A Reduced-Risk Approach

The illegal capture and trade of wild birds have long been threats to biodiversity. The rehabilitation and release of confiscated animals may be a useful conservation tool in species management. However, differences between populations regarding health (e.g., different pathogens) and adaptation (e.g., local adaptation) must be taken into account, since both can negatively impact the recipient population. In this pilot study, we used two of the most illegally trafficked Brazilian wild passerine species, namely the red-crested cardinal (Paroaria coronata) and green-winged saltator (Saltator similis) as case studies and assessed some of the health threats that the release of confiscated passerines may pose to free-living birds. We also investigated the level of difference in mitochondrial genetic structure among populations living in different ecoregions. Blood, feces, and oropharyngeal swabs from confiscated (n = 115) and free-living (n = 120) passerines from the release sites were tested for the Newcastle disease virus, Salmonella spp., and Mycoplasma gallisepticum. These are considered major avian diseases by the Brazilian National Avian Health Program. We analyzed mtDNA to study the difference in genetic structure between populations using samples from 127 free-living passerines. We found no evidence of the Newcastle disease virus or Salmonella spp. in confiscated or free-living passerines from either species. However, the levels of infection with M. galissepticum detected in our study for red-crested cardinals and green-winged saltators calls for a high degree of caution in captive release programs. The difference in genetic structure between populations occurring in different regions was low, and was not significant between those from the Pampa/Subtropical Grasslands region. These results suggest that it may be possible to establish a cost-effective and sensitive protocol for releasing confiscated songbirds, provided that further genome-wide studies indicate that the functional genetic diversity among (at least some of the) populations is also low.

Comparative Genomics of Mycoplasma synoviae and New Targets for Molecular Diagnostics

Mycoplasma synoviae is an important pathogen of poultry, causing significant economic losses in this industry. Analysis of the unique genes and shared genes among different M. synoviae strains and among related species is helpful for studying the molecular pathogenesis of M. synoviae and provides valuable molecular diagnostic targets to facilitate the identification of M. synoviae species. We selected a total of 46 strains, including six M. synoviae strains, from 25 major animal (including avian) Mycoplasma species/subspecies that had complete genome sequences and annotation information published in GenBank, and used them for comparative genomic analysis. After analysis, 16 common genes were found in the 46 strains. Thirteen single-copy core genes and the 16s rRNA genes were used for genetic evolutionary analysis. M. synoviae was found to have a distant evolutionary relationship not only with other arthritis-causing mycoplasmas, but also with another major avian pathogen, Mycoplasma gallisepticum, that shares the major virulence factor vlhA with M. synoviae. Subsequently, six unique coding genes were identified as shared among these M. synoviae strains that are absent in other species with published genome sequences. Two of the genes were found to be located in the genetically stable regions of the genomes of M. synoviae and were determined to be present in all M. synoviae isolated strains (n = 20) and M. synoviae-positive clinical samples (n = 48) preserved in our laboratory. These two genes were used as molecular diagnostic targets for which SYBR green quantitative PCR detection methods were designed. The two quantitative PCR methods exhibited good reproducibility and high specificity when tested on positive plasmid controls and genomic DNA extracted from different M. synoviae strains, other major avian pathogenic bacteria/mycoplasmas, and low pathogenic Mycoplasma species. The detection limit for the two genes was 10 copies or less per reaction. The clinical sensitivity and specificity of the quantitative PCR methods were both 100% based on testing chicken hock joint samples with positive or negative M. synoviae infection. This research provides a foundation for the study of species-specific differences and molecular diagnosis of M. synoviae.

Genus specific PCR-RFLP and multiplex PCR for diagnosis of avian mycoplasmosis

Diagnosis of avian mycoplasmosis remains a serious problem, due to unusual nature of etiological agent. Although, many protocols for PCR are set with the published primers; they do not always yield vis-à-vis results under different existing conditions of laboratories. Therefore, the present research was aimed towards the optimization and evaluation of genus specific and multiplex PCR for molecular diagnosis of avian mycoplasmosis. The research was carried out systematically where in first DNA extraction protocol was standardized followed by optimization of PCR. Using optimized protocols, screening of 165 clinical specimens from mycoplasmosis suspected birds was carried out employing genus specific PCR-RFLP, followed by the confirmation of positive samples by multiplex PCR assay and sequencing of unidentified PCR products. Phenol chloroform isoamyl method was found superior to rapid heat freeze method for extraction of better quality and quantity of DNA. Genus specific 16S rRNA based PCR-RFLP was found sensitive and convenient method for screening large number of clinical specimens for detection of mycoplasma infection.

Rapid and sensitive detection of Mycoplasma synoviae by an insulated isothermal polymerase chain reaction-based assay on a field-deployable device

Mycoplasma synoviae (MS), causing respiratory diseases, arthritis, and eggshell apex abnormalities in avian species, is an important pathogen in the poultry industry. Implementation of a biosecurity plan is important in MS infection management. Working on a field-deployable POCKIT™ device, an insulated isothermal polymerase chain reaction (iiPCR) assay has a potential for timely MS detection on the farm. The MS iiPCR assay had limit of detection 95% of about 9 genome equivalents by testing serial dilutions of a standard DNA. The detection endpoint of the assay for detection of MS genomic DNA was comparable to a reference real-time PCR. The assay did not crossreact with other important avian pathogens, including avian reovirus, Mycoplasma gallisepticum, Staphylococcus aureus, Escherichia coli, Pasteurella multocida, and Salmonella Pullorum. When 92 synovial fluid and respiratory tract swab samples collected from chickens, turkeys, and geese suspected of MS infection were tested, the clinical performance of the MS iiPCR had 97.8% agreement (Cohen's kappa value, 0.95) with that of the reference real-time PCR. In conclusion, the MS iiPCR/POCKIT™ system, working with field-deployable manual or automatic nucleic acid extraction methods, has potential to serve as a rapid and sensitive on-site tool to facilitate timely detection of MS.

Rapid detection of Mycoplasma synoviae by loop-mediated isothermal amplification

Mycoplasma synoviae (MS) remains a serious concern in production of poultry and affects world production of chickens and turkeys. Loop-mediated isothermal amplification (LAMP) of DNA has been recently used for the identification of different economically important avian pathogens. The aim of this study was to develop LAMP for simple and inexpensive detection of MS strains in poultry using specifically designed primers targeting hemagglutin A (vlh) gene. The assay was conducted in a water bath for 1 h at 63 °C. The results were visualized after addition of SYBR Green(®) fluorescent dye. LAMP was specific exclusively for MS without cross-reactivity with other Mycoplasma species. The sensitivity of LAMP was determined as 10(-1) CFU/ml and was 1,000 times higher than MS-specific polymerase chain reaction. LAMP assay was conducted on 18 MS field strains to ensure its reliability and usefulness. This is the first report on LAMP development and application for the rapid detection of MS isolated from chickens. This simple method may be applied by diagnostic laboratories without access to expensive equipment.