Use of molecular diversity of Mycoplasma gallisepticum by gene-targeted sequencing (GTS) and random amplified polymorphic DNA (RAPD) analysis for epidemiological studies

Genetic comparison of the Mycoplasma gallisepticum 6/85 vaccine strain and 6/85-like field isolates

Mycoplasma gallisepticum infection in poultry leads to disease and pathology that can reduce producer profits. Live attenuated vaccines are available that can limit or completely prevent the effects of infection. Field isolates that are genetically related to the attenuated vaccine strains have been isolated, raising the question of whether the attenuation of the vaccine strains is limited and can lead the strains to revert to more virulent forms. The 6/85 live attenuated vaccine is derived from a field isolate collected in the United States. Analysis of the genome of sequenced M. gallisepticum strains revealed a cluster of 10 6/85-like strains that group with the 6/85 vaccine strain. Four genomic regions were identified that allowed for strain differentiation. The genetic differences between strains points toward nine of the ten strains most likely being sister strains to the 6/85 vaccine strain. Insufficient differences are present in the tenth strain to make a definitive conclusion. These results suggest that most if not all strains similar to the live attenuated vaccine strain are field isolates of the parent strain used to derive the live attenuated vaccine.

Mycoplasma gallisepticum and Mycoplasma synoviae in Turkeys in Poland

The pathogenic mycoplasmas are among the bacteria causing significant losses in the poultry industry worldwide. Mycoplasma gallisepticum (MG) and M. synoviae (MS) are economically important pathogens causing chronic respiratory disease, decreased growth, egg production and hatchability rates, and significant downgrading of carcasses. Effective diagnosis of infection with these species in poultry is highly requisite considering their two routes of spreading-horizontal and vertical. Their prevalence and molecular epidemiology were investigated in 184 turkey flocks in Poland. Tracheal samples were selected from 144 broiler flocks and 40 turkey breeder flocks collected in 2015-2023. The prevalence of MG was determined by real-time PCR targeting the 16S rRNA gene and PCR targeting the mgc2 gene, and MS was determined by a 16-23S rRNA real-time PCR and a vlhA gene PCR. Further identification and molecular characterization were carried out using PCR and sequencing. M. gallisepticum and M. synoviae were found in 8.33% and 9.72% of turkey broiler flocks respectively. The phylogenetic analysis of MG isolates in most cases showed high similarity to the ts-11-like strains. MS isolates showed high similarity to strains isolated from flocks of laying hens causing EAA. Additional tests detected Ornithobacterium rhinotracheale, Gallibacterium anatis, Enterococcus faecalis and Enterococcus faecium, Staphylococcus aureus and Riemerella anatipestifer. These secondary pathogens could have significantly heightened the pathogenicity of the mycoplasma infections studied.

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.

Pathogenic bacteria associated with outbreaks of respiratory disease in Iranian broiler farms

BACKGROUND

Multi-causal respiratory infections are more commonly observed than uncomplicated cases with single agents in the commercial poultry industry. Recently, increased mortality rates associated with respiratory clinical signs have been reported in Iranian broiler farms.

OBJECTIVES

The present study aimed to determine the spectra of avian mycoplasmas (Mycoplasma gallisepticum, MG and Mycoplasma synoviae, MS) and Ornithobacterium rhinotracheale (ORT) in the broiler farms with the multi-causal respiratory disease (MCRD) from 2017 to 2020.

METHODS

Trachea and lung tissue samples were collected from 70 broiler flocks presenting increased mortality and acute respiratory disease. MG, MS, and ORT were detected by performing polymerase chain reaction with primers complementary to the 16S rRNA, vlhA, and 16S rRNA genes, respectively.

RESULTS

Genetic materials of MG, MS, and ORT were detected in five, three, and five of the 70 flocks. Based on the phylogenetic analysis of the complete mgc2 coding sequences, all MG strains formed a distinct cluster along with other Iranian MG isolates. According to the phylogenetic analysis of the partial vlhA gene of MS strains, two isolates were located along with Australian and European strains. In addition, one of them displayed an out-group association with MS isolates from Jordan. Phylogenetic analysis of Iranian ORT strains using a partial sequence of the 16S rRNA gene showed a distinct group among the other ORT strains.

CONCLUSIONS

The results indicate that MG, MS, and ORT are not predominantly responsible for the MCRD. However, continuous monitoring of poultry flocks could be significant for obtaining valuable information related to different MG, MS, and ORT strains and designing effective control strategies.

Isolation and characterization of an atypical Mycoplasma gallisepticum strain showing a new mgc2 variant

Mycoplasma gallisepticum (MG) is an important pathogen of the poultry industry able to cause chronic respiratory disease in chickens and infectious sinusitis in turkeys. Despite the application of biosecurity measures and the availability of vaccines for chickens, monitoring systems routinely applied for MG detection are still essential for infection control. Pathogen isolation is time-consuming and not suitable for rapid detection, albeit it is a compulsory step for genetic typing and antimicrobial susceptibility evaluation of single strains. The mgc2 gene is a species-specific molecular target adopted by most of the PCR protocols available for MG diagnosis, which are also included in the WOAH Terrestrial Manual. We describe the case of an atypical MG strain, isolated in 2019 from Italian turkeys, characterized by an mgc2 sequence not detectable by common endpoint PCR primers. Considering the potential risk of false negative results during diagnostic screenings with the endpoint protocol, the authors propose an alternative mgc2 PCR endpoint protocol, named MG600, which should be considered as a further diagnostic tool.

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.

The expression of GapA and CrmA correlates with the Mycoplasma gallisepticum in vitro infection process in chicken TOCs

Mycoplasma (M.) gallisepticum is the most pathogenic mycoplasma species in poultry. Infections cause mild to severe clinical symptoms associated with respiratory epithelial lesion development. Adherence, biofilm formation, and cell invasion of M. gallisepticum contribute to successful infection, immune evasion, and survival within the host. The important M. gallisepticum membrane-bound proteins, GapA and CrmA, are key factors for host cell interaction and the bacterial life-cycle, including its gliding motility, although their precise role in the individual infection step is not yet fully understood. In this study, we investigated the correlation between the host-pathogen interaction and the GapA/CrmA expression in an environment that represents the natural host's multicellular compartment. We used an in vitro tracheal organ culture (TOC) model, allowing the investigation of the M. gallisepticum variants, Rlow, RCL1, RCL2, and Rhigh, under standardised conditions. In this regard, we examined the bacterial adherence, motility and colonisation pattern, host lesion development and alterations of mucociliary clearance. Compared to low virulent RCL2 and Rhigh, the high virulent Rlow and RCL1 were more efficient in adhering to TOCs and epithelium colonisation, including faster movement from the cilia tips to the apical membrane and subsequent cell invasion. RCL2 and Rhigh showed a more localised invasion pattern, accompanied by significantly fewer lesions than Rlow and RCL1. Unrelated to virulence, comparable mucus production was observed in all M. gallisepticum infected TOCs. Overall, the present study demonstrates the role of GapA/CrmA in virulence factors from adherence to colonisation, as well as the onset and severity of lesion development in the tracheal epithelium.

Complete Genome Sequences of Three Mycoplasma gallisepticum 6/85-like Isolates

Control of Mycoplasma gallisepticum infection can be accomplished through vaccination. However, virulent field strains with genetic markers identical to vaccine strains have been identified. Here, we report the sequencing of three field isolates with genetic markers identical to the M. gallisepticum 6/85 vaccine strain.

Percent positivity and phylogenetic analysis of Mycoplasma gallisepticum and Mycoplasma synoviae in commercial poultry from the different States of India

Background and Aim: The Indian and global poultry industries suffer significant economic losses due to Mycoplasma gallisepticum (MG) and Mycoplasma synoviae (MS) infections, which adversely affect egg production, hatchability, weight gain, and feed efficiency in farms, thus decreasing the overall production efficiency. This study aimed to determine the percent positivity and phylogenetic analysis of MG, MS, and co-infection of both mycoplasmas in commercial poultry farms across different states of India from 2017 to 2021. Materials and Methods: A total of 3620 tracheal or choacal swabs were collected from breeder and layer farms showing clinical signs of avian mycoplasma infections from commercial poultry farms across India, and the percent positivites for MG, MS, and co-infection of both mycoplasmas were determined by Polymerase chain reaction using the 16S rRNA and vlhA genes amplification, respectively. Phylogenetic analysis was carried out by sequencing the mgc2 and vlhA genes of 2 samples of MG and 24 samples of M. synoviae to gain insight into the genetic variability of Indian strains. The data were then compared with other Indian strains, vaccines strains, and strains from other countries. Results: Our data shows the percent positivity of MG, MS, and co-infection of both MG and MS was 6.43%, 23.61%, and 15.49%, respectively. The phylogenetic relationship between MG and MS was determined using the vlhA and mgc2 genes, revealing two samples of MG and 24 samples of MS clustered with other Indian strains. M. synoviae MSM22 and previously studied M. synoviae MGS 482 clustered with vaccine strain M. synoviae MS-H. Conclusion: Mycoplasma synoviae infections in breeder, layer, and in both is predominant compared to MG across the states investigated in India. Sequenced samples of MG and MS showed evolutionary relationships with the previously studied Indian strains of MG and MS. These findings support our view that monitoring chickens for avian mycoplasma infections are of paramount significance. It further lends credence to the contention that such information will pave the way for the development of a home-grown vaccination control program and thus safeguard the poultry sector against mycoplasma infections.

Targeted sequencing analysis of Mycoplasma gallisepticum isolates in chicken layer and breeder flocks in Thailand

Mycoplasma gallisepticum (MG) is one of the most economically important pathogens worldwide. MG affects the respiratory system and impairs growth performance in poultry. In developing countries, the most widely used technique to identify MG is the conventional PCR assay. In this study, 24 MG isolates collected from Thailand farms with unvaccinated chickens during 2002–2020 were characterized by gene-targeted sequencing (GTS), followed by phylogenetic analysis using unweighted pair group method with arithmetic mean. These 24 Thai MG isolates differed from vaccine strains, including the F, ts-11 and 6/85 strains. One isolate showed 99.5–100% genetic similarity to the F strain with 4 partial gene analyses. This result may have been due to contamination from vaccinated flocks because the F strain is the most commonly used vaccine strain in Thailand. However, the GTS analysis using the partial MG genes in this study showed that the isolates could be grouped into different patterns based on individual gene sequences. The phylogenetic analysis of partial mgc2, gapA, pvpA and lp gene sequences classified the Thai MG isolates into 7, 11, 7 and 2 groups, respectively. In conclusion, at least 2 partial MG genes, especially partial gapA and mgc2 genes, are needed to differentiate MG isolates.

Mycoplasma gallisepticum: a devastating organism for the poultry industry in Egypt

Mycoplasma gallisepticum (MG) is a worldwide ruined bacteria affecting different avian species, causing severe economic losses. Consequently, the current research sought to detect the incidence of MG among different commercial broiler, layer chickens and turkey farms, and environmental litter samples in different Egyptian governorates (Damietta, Giza, El-Qalyobia, El-Sharqia, and El-Behera) from January 2019 to December 2020. Four hundred samples (infraorbital sinus aspirates, tracheal swabs, serum from diseased birds, and organ samples; lung tissues, air sacs and tracheal bifurcation from freshly dead birds), and environmental samples (litter) were collected for MG isolation. Samples were subjected to phenotypic and molecular identification. Positive bacteriological samples were subjected for molecular identification using polymerase chain reaction (PCR) test to detect MG, then sequencing for PCR amplicon of mgc2 gene. Out of 332 samples subjected for bacteriological examination, 206 were bacteriologically positive for MG with an incidence of 62%. The highest incidence of MG was detected in turkey farms at a rate of 83%, followed by broiler chicken farms, layer chicken farms and litter samples at a percentage of 70, 40, and 40, respectively. The highest prevalence of MG in chickens and turkey was recorded during the winter and autumn seasons. Molecular identification of MG isolates revealed that 85% of isolates were positive for mgc2 gene using PCR. The Four sequenced strains in this study are closely related and placed in one group with the vaccine strain 6/85 and ts11 strain.

Cloning of cytadhesin protein gene (pvpA) and expression analysis of recombinant fusion protein of Mycoplasma gallisepticum

Chronic respiratory disease (CRD) caused by Mycoplasma gallisepticum (MG) is one of the major respiratory tract infections of the poultry, resulting in significant economic loss to the poultry farmers. Diagnosis of such ailment is highly necessary for effective control measures. In addition, promising molecular tools are warranted for efficient epidemiological tracing of the outbreaks. The study was focused on the elucidation of phase variable cytadhesin protein gene (pvpA) of MG through cloning and expression analysis. A set of primers targeting the pvpA gene of MG was designed. The complete pvpA gene was amplified and cloned into pUC-derived expression vector pRSETA. Finally, the recombinant clones were examined through colony PCR and restriction endonuclease (RE) analysis with EcoR1 and BamH1 enzymes followed by sequencing. The expression of the recombinant pvpA gene was optimized at 1.4mM/μl concentration of Isopropyl-β-D-thiogalactoside induction at 30°C. The recombinant fusion protein was purified by immobilized metal affinity chromatography and characterized by SDS-PAGE followed by confirmation of recombinant cytadhesin fusion protein through western blot analysis. The pvpA gene was successfully cloned and expressed. The deduced amino acid sequence analysis had shown the presence of two direct repeats (DR1 and DR2) along with predicted PRP motifs repeatedly with high proline encoding regions at the carboxy-terminal of pvpA gene indicating its scope for epidemiological studies.

Molecular detection of Mycoplasma gallisepticum in different poultry breeds of Abbottabad and Rawalpindi, Pakistan

The poultry sector in Pakistan is contributing mainly in bridging gap between demand and supply for protein. Mycoplasma gallisepticum is an emerging bacterium causing serious problems in poultry industry of Pakistan. A cross-sectional study was conducted to evaluate the M. gallisepticum load in poultry populated regions of Pakistan. Total 600 serum and 600 swab samples were collected, 200 from each broiler, layers and breeders poultry in Rawalpindi and Abbottabad districts. Serum samples were analyzed through ELISA for seroprevalence. Swabs were cultured on Frey's medium followed by PCR and partial mgc2 gene sequencing. Results of seroprevalence of M. gallisepticum showed that layers (75%, n=150) are more positive as compared to breeders (70%, n=140) and broilers (50%, n=100). Typical colonies of the M. gallisepticum were observed in breeder (26.5%), followed by layer (21%) and broilers (9%). A total of 37.1% (n=42) samples were identified positive through PCR out of total 113 cultured based positive samples. A total of six M. gallisepticum isolates of current study showed 98-99 percent similarity with previously reported isolates on the basis of mgc2 gene partial sequencing. The M. gallisepticum was found highly prevalent in different poultry breads. Results of this study would add into basic data and provide a direction for livestock sector to strengthen a control strategy for mycoplasmosis in poultry farms.

Complete Sequence-Based Genotyping of mgc2/pvpA Genes in Chicken-Derived Mycoplasma gallisepticum Isolates of Iran

Mycoplasma gallisepticum (MG) is a major pathogen of the poultry industry throughout the world. MG causes chronic respiratory disease in chickens and infectious sinusitis in turkeys. Despite constant improvements in the biosecurity of the poultry industry in Iran, MG infection still occurs and causes significant economic issues. To evaluate genetic variability, 10 Iranian MG isolates along with 17 available sequences were characterized by gene-targeted sequencing (GTS) analysis of complete mgc2/pvpA genes. According to the findings, 21 different sequence types within the sample set of 27 strains were typed by this method. The discriminatory power of this typing assay was established to be 0.97. Although no insertions and deletions of nucleotides were observed in the mgc2 gene among the Iranian strains, different lengths of pvpA genes with 1086, 1095, and 1101 nucleotides were detected within direct repeats (DRs) 1 and 2. Generally, eight tetrapeptides Pro-Arg-Pro-Met/Gln/Asn were found in the DRs of PvpA. Analysis of the carboxyl ends of PvpA proteins exhibited various repeats of prolines. In the phylogenetic tree of partial and complete mgc2/pvpA genes, all Iranian MG isolates were clustered into two distinct groups. Because this typing assay could provide a higher discriminatory power than the previously reported GTS scheme of partial mgc2/ pvpA genes, these results can be considered a blueprint for future national control and diagnostic strategies. Furthermore, consistent surveillance with larger datasets will be needed to clarify the epidemiologic characteristics of MG outbreaks in different poultry hosts.

Molecular Differentiation of Mycoplasma gallisepticum Outbreaks: A Last Decade Study on Italian Farms Using GTS and MLST

Mycoplasma gallisepticum (MG) infects many avian species and leads to significant economic losses in the poultry industry. Transmission of this pathogen occurs both horizontally and vertically, and strategies to avoid the spread of MG rely on vaccination and the application of biosecurity measures to maintain breeder groups as pathogen-free. Two live attenuated MG vaccine strains are licensed in Italy: 6/85 and ts-11. After their introduction, the implementation of adequate genotyping tools became necessary to distinguish between field and vaccine strains and to guarantee proper infection monitoring activity. In this study, 40 Italian MG isolates collected between 2010–2019 from both vaccinated and unvaccinated farms were genotyped using gene-targeted sequencing (GTS) of the cythadesin gene mgc2 and multilocus sequence typing (MLST) based on six housekeeping genes. The discriminatory power of GTS typing ensures 6/85-like strain identification, but the technique does not allow the identification ts-11 strains; conversely, MLST differentiates both vaccine strains, describing more detailed interrelation structures. Our study describes MG genetic scenario within a mixed farming context. In conclusion, the use of adequate typing methods is essential to understand the evolutionary dynamics of MG strains in a particular area and to conduct epidemiological investigations in the avian population.

Clonal dissemination of antibiotic resistance among Tunisian Mycoplasma gallisepticum isolates as revealed by gene-targeted sequencing analysis

SummaryTo date, very little is known about avian mycoplasma infections in Tunisia. Mycoplasma gallisepticum is one of the most economically significant pathogen for poultry in Tunisia and worldwide. Based on the paucity of data regarding the genetic profiles and antibacterial behavior of M. gallisepticum strains in Tunisia, the present study was conducted. Genetic typing and phylogenetic relationships of 40 M. gallisepticum strains (20 Tunisian isolates, 19 international strains collection, and S6 reference strain) were investigated by gene-targeted sequencing (GTS) using 4 loci ( pvpA , mgc2 , vlhA and the InterGenic Spacer Region (IGSR) between the 16S and the 23S rRNA genes). GTS reveals 12 STs that were found to spread over 2 clonal complexes (CC) and 5 singletons.Emergence of enrofloxacin and spiramycin resistance among M. gallisepticum local isolates have been revealed using the broth microdilution method. Causal mutations have been identified by sequencing the quinolone-resistance determining region (QRDR) and domain II and V of 23S rRNA as well as the rplD and rplV genes for enrofloxacine- and macrolide-resistant isolates, respectively. The emersion of antibiotic resistance to enrofloxacin and spiramycin has been identified as being related to a distinctive clonal complex formed by 4 different STs (ST2, ST3, ST4 and ST5) which would suggest that this phenotype was clonally disseminated.

Unraveling the Global Phylodynamic and Phylogeographic Expansion of Mycoplasma gallisepticum: Understanding the Origin and Expansion of This Pathogen in Ecuador

Mycoplasma gallisepticum (MG) is among the most significant problems in the poultry industry worldwide, representing a serious threat to international trade. Despite the fact that the mgc2 gene has been widely used for diagnostic and molecular characterization purposes, there is a lack of evidence supporting the reliability of this gene as a marker for molecular epidemiology approaches. Therefore, the current study aimed to assess the accuracy of the mgc2 gene for phylogenetic, phylodynamic, and phylogeographic evaluations. Furthermore, the global phylodynamic expansion of MG is described, and the origin and extension of the outbreak caused by MG in Ecuador were tracked and characterized. The results obtained strongly supported the use of the mgc2 gene as a reliable phylogenetic marker and accurate estimator for the temporal and phylogeographic structure reconstruction of MG. The phylodynamic analysis denoted the failures in the current policies to control MG and highlighted the imperative need to implement more sensitive methodologies of diagnosis and more efficient vaccines. Framed in Ecuador, the present study provides the first piece of evidence of the circulation of virulent field MG strains in Ecuadorian commercial poultry. The findings derived from the current study provide novel and significant insights into the origin, diversification, and evolutionary process of MG globally.

Development of a Multilocus Sequence Typing Assay for Mycoplasma gallisepticum

Mycoplasma gallisepticum (MG) is the most pathogenic avian mycoplasma species. It affects commercial and noncommercial poultry and wild birds. Current MG sequence typing methods rely on the partial sequence of one or more surface antigen genes. Multilocus sequence typing (MLST), a widely used typing method for many human and animal pathogens, relies on conserved housekeeping genes. Recently, MLST assays have been developed for Mycoplasma synoviae (MS) and Mycoplasma iowae. Additionally, a whole genome-based core genome MLST (cgMLST) assay has been developed for MG and MS. However, cgMLST can be implemented only on pure isolates and cannot be applied to clinical samples. Here, we have developed a seven-locus-based MLST scheme for MG that can be applied directly on clinical samples without the need for isolation. The seven loci were selected from 425 genes recently used for the cgMLST assay. A total of 101 diverse MG samples, including isolates and clinical samples, were typed with the newly developed seven-locus MLST. The phylogeny and discriminatory power of the seven-locus MLST were evaluated and compared with the cgMLST and gene-targeted sequencing methods currently used for MG sequence typing. The seven-locus MLST provided optimum discriminatory power and congruent phylogeny to cgMLST. Additionally, a database for MG MLST was created and is currently available for public use online. This assay will increase accessibility to MG sequence typing and provide a stable and expandable nomenclature compatible with cgMLST. The seven-locus MLST assay represents an important tool for epidemiologic investigation of MG that can contribute to better control and eradication efforts.

Development of mismatch amplification mutation assay for the rapid differentiation of Mycoplasma gallisepticum K vaccine strain from field isolates

Mycoplasma gallisepticum causes respiratory diseases and reproduction disorders in turkeys and chickens. The infection has considerable economic impact due to reduced meat and egg production. Because elimination programmes are not feasible in a large number of poultry farms, vaccination remains the only effective measure of disease control. Differentiating vaccine strains from field isolates is necessary in the control of vaccination programmes and diagnostics. The aim of this study was to develop a polymerase chain reaction based mismatch amplification mutation assay (MAMA) for the discrimination of K vaccine strain (K 5831, Vaxxinova Japan K.K.). After determining the whole genome sequence of the K strain, primers were designed to detect seven different vaccine-specific single nucleotide polymorphisms. After evaluating preliminary results, the MAMA-K-fruA test detecting a single guanine-adenine substitution within the fruA gene (G88A) was found to be the most applicable assay to distinguish the K vaccine strain from field isolates. The detected K strain-specific single nucleotide polymorphism showed genetic stability after serial passage in vitro, but this stability test should still be evaluated in vivo as well, investigating a large number of K strain re-isolates. The MAMA-K-fruA assay was tested on a total of 280 culture and field samples. The designed assay had 10² and 10³ template copy number/µl sensitivity in melt-curve analysis based and agarose-gel based assays, respectively, and showed no cross reaction with other avian Mycoplasma species. The new MAMA provides a time- and cost-effective molecular tool for the control of vaccination programmes and for diagnostics.

Molecular detection and characterization of Mycoplasma gallisepticum and Mycoplasma synoviae strains in backyard poultry in Italy

Mycoplasma gallisepticum (MG) and Mycoplasma synoviae (MS) represent the most important avian Mycoplasma species in the poultry industry, causing considerable economic losses. In Italy, the presence of MG or MS has been investigated especially in commercial poultry farms. To our knowledge, no systematic investigations on MG or MS presence using highly specific diagnostic assays have been performed in backyard poultry. The aim of this study was to detect and molecularly characterize MG and MS strains in 11 backyard poultry flocks located in different regions of Italy. Tracheal swabs were collected and DNA was extracted. For MS, a PCR targeting a vlhA gene fragment was performed, and typing and subtyping was attempted. The presence of MG was investigated by a screening PCR, then MG typing by gene-targeted sequencing (GTS). All the amplicons were sequenced, then MG and MS dendrograms were constructed. All the flocks examined resulted Mycoplasma positive: 5 out of 11 (45.45%) were MG and MS positive, 3 (27.27%) were MG positive, and the remaining 3 (27.27%) were MS positive. The MS detections were assigned to types C, D, and F. All strains of type D belonged to subtype D1 and 2 unknown subtypes were identified. A MS sequence showed peculiar characteristics, which did not allow assignment to a known MS type or subtype. MG GTS analysis identified 6 MG strains belonging to 5 subclusters circulating in Italian backyards chicken flocks. The results of this study provide evidence of a risk for commercial poultry farms, especially in areas where backyard and commercial farms are close, suggesting the implementation of biosecurity measures.

Molecular characterisation of Mycoplasma gallisepticum isolates from Iran in the period 2012-2017

Mycoplasma gallisepticum (MG) causes chronic non-fatal diseases in the poultry industry with a remarkable decrease in feed consumption, egg production and other production indices. To study the genetic characteristics of MG isolates in commercial and backyard poultry flocks, 21 positive samples from different regions of Iran were analysed in the period 2012-2017. Typical macroscopic and histopathological lesions of the upper respiratory tract and lungs were found, similar to those reported by other researchers. A 298-361 bp part of the mgc2 gene was sequenced and analysed. Based on the phylogenetic analysis, the Iranian MG isolates fell into four distinct subgroups. The nucleotide difference between subgroups 1 and 4 was remarkable (91.6-94.9%). A 22-amino-acid insertion was present in two of the studied MG isolates, not observed in other vaccine and standard MG strains. The Iranian Veterinary Organisation (IVO) should consider the observed diversity of prevalent MG isolates from both commercial and backyard flocks in designing the strategy for controlling MG. More studies are needed to understand modifications in MG antigenicity and pathogenicity because of the observed genetic variations.

Molecular Identification and Sequencing of <I>Mycoplasma gallisepticum</I> Recovered from Broilers in Egypt

BACKGROUND AND OBJECTIVES

Avian mycoplasmosis, particularly Mycoplasma gallisepticum (MG) is one of the infectious diseases associated with economic losses in Egyptian poultry industry. Thus, this study was aimed to determine the prevalence, serological identification, molecular characterization, sequencing and minimum inhibitory concentration of M. gallisepticum isolated from diseased broilers in Egypt.

MATERIALS AND METHODS

A total of 351 samples (227 tissue samples "tracheas and air sacs" and 124 tracheal swabs) and 71 sera were collected from diseased broilers. The conventional (isolation and biochemical) and molecular methods (PCR) were performed for detection of M. gallisepticum and virulence-associated gene (mgc2). The serum plate agglutination (SPA) test and enzyme-linked immunosorbent assay (ELISA) were applied on sera for determination of the presence of antibodies against M. gallisepticum. The minimal inhibitory concentration test (MIC) was used to determine the sensitivity of two sequenced M. gallisepticum strains to anti-mycoplasma agents.

RESULTS

The total recovery rate of Mycoplasma from 351 samples from broilers was 45.29% (159) in which M. gallisepticum showed a prevalence of 62.89% (100/159). Serological identification of M. gallisepticum in 71 collected sera using SPA and ELISA were 54.9 and 40.8% with the highest geometric mean titer of ELISA for M. gallisepticum (699.08 and 495.92). Molecular characterization of Mycoplasma using PCR showed that 50% (3/6) of tested isolates were identified as M. gallisepticum based on 16SrRNA. Also, the mgc2 gene was detected in 50% (3/6) M. gallisepticum isolates. Two positive PCR mgc2 specific genes of M. gallisepticum isolates were subjected to gene target sequencing (GTS) to verify that these two isolates were M. gallisepticum. The minimal inhibitory concentration test (MIC) was applied to determine the sensitivity of these two sequenced M. gallisepticum strains to anti-mycoplasma agents. The first M. gallisepticum isolate was sensitive to tilmicosin, tiamulin and spiramycin. The second M. gallisepticum isolate showed sensitivity to tiamulin, spiramycin and tilmicosin.

CONCLUSION

These results summarized the necessity of monitoring the Egyptian poultry farms for avian mycoplasmosis. Also, further studies are required for controlling of mycoplasma in all stages of the poultry industry production chain to avoid different losses in Egypt.

Molecular detection and genetic characterization of Mycoplasma gallisepticum, Mycoplama synoviae, and infectious bronchitis virus in poultry in Myanmar

BACKGROUND

In Southeast Asian countries, including Myanmar, poultry farming is a major industry. In order to manage and maintain stable productivity, it is important to establish policies for biosecurity. Infectious respiratory diseases are a major threat to poultry farming. Avian influenza and Newcastle disease have been reported in Myanmar, but no scientific information is available for other respiratory pathogens, such as mycoplasmas and infectious bronchitis virus (IBV). Identifying the genotypes and serotypes of IBVs is especially important to inform vaccination programs. In this study, we detected Mycoplasma gallisepticum (MG), M. synoviae (MS), and IBV in several poultry farms in Myanmar.

RESULTS

Samples were collected from 20 farms in three major poultry farming areas in Myanmar, and MG, MS, and IBV were detected on two, four, and eight farms, respectively, by polymerase chain reaction. Phylogenetic analysis revealed that the observed MG and MS isolates were not identical to vaccine strains. Three different genotypes of IBV were detected, but none was an unknown variant.

CONCLUSIONS

Mycoplasmas and IBV were detected on poultry farms in Myanmar. Periodic surveillance is required to establish the distribution of each pathogen, and to institute better vaccine protocols.

Development of Molecular Methods for Rapid Differentiation of Mycoplasma gallisepticum Vaccine Strains from Field Isolates

Mycoplasma gallisepticum is among the most economically significant mycoplasmas causing production losses in poultry. Seven melt-curve and agarose gel-based mismatch amplification mutation assays (MAMAs) and one PCR are provided in the present study to distinguish the M. gallisepticum vaccine strains and field isolates based on mutations in the crmA, gapA, lpd, plpA, potC, glpK, and hlp2 genes. A total of 239 samples (M. gallisepticum vaccine and type strains, pure cultures, and clinical samples) originating from 16 countries and from at least eight avian species were submitted to the presented assays for validation or in blind tests. A comparison of the data from 126 samples (including sequences available at GenBank) examined by the developed assays and a recently developed multilocus sequence typing assay showed congruent typing results. The sensitivity of the melt-MAMA assays varied between 10¹ and 10⁴ M. gallisepticum template copies/reaction, while that of the agarose-MAMAs ranged from 10³ to 10⁵ template copies/reaction, and no cross-reactions occurred with other Mycoplasma species colonizing birds. The presented assays are also suitable for discriminating multiple strains in a single sample. The developed assays enable the differentiation of live vaccine strains by targeting two or three markers/vaccine strain; however, considering the high variability of the species, the combined use of all assays is recommended. The suggested combination provides a reliable tool for routine diagnostics due to the sensitivity and specificity of the assays, and they can be performed directly on clinical samples and in laboratories with basic PCR equipment.

Genotyping Mycoplasma gallisepticum by multilocus sequence typing

Mycoplasma gallisepticum causes chronic respiratory disease and reproductive disorders in many bird species, resulting in considerable economic losses to the poultry industry. Maintenance of M. gallisepticum-free flocks is the most adequate method to control infection. To this end, monitoring systems and vaccination programs with live vaccine strains are applied worldwide. There is strong demand for efficient epidemiological investigation tools to distinguish M. gallisepticum strains in order to control disease. Up to now, multilocus sequence typing (MLST) has been regarded as gold standard for genotyping bacteria due to its good reproducibility and high discriminatory power. The aim of this study was to develop an MLST assay which can determine phylogenetic distances between M. gallisepticum strains. After analysing more than 30 housekeeping genes, six loci (atpG, dnaA, fusA, rpoB, ruvB, uvrA) were selected for the MLST assay due to their genomic location and high diversity. Examination of 130 M. gallisepticum strains with this MLST method yielded 57 unique sequence types (STs) with a 0.96 Simpson's index of diversity. Considering the large number of STs and high diversity index, this MLST method was found to be appropriate to discriminate M. gallisepticum strains. In addition, the developed method was shown to be suitable for epidemiological investigations, as it confirmed linkage between related strains from outbreaks in different farms. Besides, MLST also suggested high impact of extensive international trade on the spread of different M. gallisepticum strains. Furthermore this method can be used for differentiation among vaccine and field strains.

Chitosan-adjuvanted Mycoplasma gallisepticum bacterin via intraocular administration enhances Mycoplasma gallisepticum protection in commercial layers

Mycoplasma gallisepticum (MG) causes respiratory signs and economic losses in the poultry industry. MG vaccination is one of the effective prevention and control measures that have been used around the world. Our previous study demonstrated that chitosan-adjuvanted MG bacterin could effectively reduce pathological lesions induced by MG and that chitosan could be used as an adjuvant in MG bacterin. The present study determining the efficacy of MG bacterins against the Thai MG strain was based on vaccine programs. Seven groups (25 layers/group) were received MG bacterins containing 0.5% chitosan or a commercial bacterin via intramuscular (IM) or intraocular (IO) route at 6 and 10 wk of age. Sham-negative and sham-positive controls were groups 1 and 2, respectively. Group 3: IM route of chitosan bacterin followed by IM route of chitosan bacterin; group 4: commercial bacterin via IM route followed by chitosan bacterin via IO route; group 5: commercial bacterin via IM route followed by commercial bacterin via IM route; group 6: chitosan bacterin via IM followed by chitosan bacterin via IO route; and group 7: chitosan bacterin via IO route followed by chitosan bacterin via IO route were determined. At 16 wk of age, all groups, excluding group 1, were challenged intratracheally with 0.1 mL containing Thai MG strain 107 colony-forming unit. At 17, 18, and 20 wk of age, 5 birds in each group were bled for serological testing and swabbed at the choanal cleft for the quantitative real-time PCR assay, the euthanized and necropsied. The results showed that birds vaccinated with a commercial intramuscular bacterin followed by an intraocularly chitosan adjuvant bacterin showed the best protection against the MG challenge. The study indicated that chitosan could be the effective mucosal adjuvant and increased the effectiveness of MG bacterin.

Application of high-resolution melting-curve analysis on pvpA gene for detection and classification of Mycoplasma gallisepticum strains

Mycoplasma gallisepticum (MG) is an avian species pathogen which causes heavy economic losses in the poultry industry. The purpose of this study was to determine genomic diversity of 14 MG field strains from chicken, Chuker partridge and peacock collected during 2009-2012 in Iran by polymerase chain reaction and partial sequencing of the pvpA gene. A High-Resolution Melting (HRM) technique was also developed and applied to differentiate between field and vaccine strains. Sequencing of the pvpA gene revealed a 51 nucleotide deletion, within DR-1 and DR-2, among MG strains from chicken and partridge whilst 63 nucleotides were deleted in MG strain from peacock. One nucleotide substitution was also observed among chicken MG strains. Phylogenetic analysis of the sequences clustered all of the Iranian MG strains into two clades or phylogeny groups; the strains from chicken and partridge in one group (group 1) and the strain from peacock into another group (group 4). HRM analysis has also produced comparable outcome to those of sequencing; four distinct melting curves which correspond to the three MG strains from chicken, Chukar partridge and peacock and ts-11 vaccine strain. Overall, findings of this study point towards a single source of infection for the chicken and partridge MG strains and likelihood of the strains being native and endemic in Iran. Peacock considered as an exotic species in Iran, hence the genetic distance for the pvpA gene. MG can be transmitted easily among different avian species and this distinct peacock strain may pose a threat to poultry industry. Our findings also show that molecular variation among pvpA gene of MG strains could be revealed using the relatively rapid and affordable HRM technique.

Rapid serum agglutination, cultural isolation and PCR for detection of M. gallisepticum and M. synoviae infection in poultry

Poultry mycoplasmosis, is an infectious disease of birds distributed worldwide causing serious economic loss to the poultry industry. Diagnosis of poultry mycoplasmosis is considered to difficult task due to different aspects of etiological agent from conventional bacteria. Therefore, the present study was aimed to detect mycoplasma infection in poultry using serological, cultural and molecular techniques. The specimens included were, sera samples and choanal swabs (150 each) collected from 150 birds housed in semi arid and costal area of Maharashtra (India). Mycoplasma gallisepticum (MG) was more prevalent than Mycoplasma synoviae (MS) in mycoplasmosis detected by rapid serum agglutination test (RSA), cultural isolation and direct PCR of samples. Nucleotide sequences of three representative MG isolates with NCBI accession nos. KY467400, KY467401 and KY467403 did not show any variations in their sequences analysed and matched with published strains of MG. RSA, cultural isolation and direct PCR yielded 93 (62%), 24 (16%) and 85 (56.67%) positive cases respectively. The sensitivity of PCR and RSA was 95.83% and 83.33% respectively. Thus, RSA and PCR were better than cultural isolation in diagnosis of poultry mycoplasmosis, therefore these methods can be used for screening the flocks for detection of mycoplasma infection depending on availability of specimens and facility.

Core Genome Multilocus Sequence Typing: a Standardized Approach for Molecular Typing of Mycoplasma gallisepticum

Mycoplasma gallisepticum is the most virulent and economically important Mycoplasma species for poultry worldwide. Currently, M. gallisepticum strain differentiation based on sequence analysis of 5 loci remains insufficient for accurate outbreak investigation. Recently, whole-genome sequences (WGS) of many human and animal pathogens have been successfully used for microbial outbreak investigations. However, the massive sequence data and the diverse properties of different genes within bacterial genomes results in a lack of standard reproducible methods for comparisons among M. gallisepticum whole genomes. Here, we proposed the development of a core genome multilocus sequence typing (cgMLST) scheme for M. gallisepticum strains and field isolates. For development of this scheme, a diverse collection of 37 M. gallisepticum genomes was used to identify cgMLST targets. A total of 425 M. gallisepticum conserved genes (49.85% of M. gallisepticum genome) were selected as core genome targets. A total of 81 M. gallisepticum genomes from 5 countries on 4 continents were typed using M. gallisepticum cgMLST. Analyses of phylogenetic trees generated by cgMLST displayed a high degree of agreement with geographical and temporal information. Moreover, the high discriminatory power of cgMLST allowed differentiation between M. gallisepticum strains of the same outbreak. M. gallisepticum cgMLST represents a standardized, accurate, highly discriminatory, and reproducible method for differentiation among M. gallisepticum isolates. cgMLST provides stable and expandable nomenclature, allowing for comparison and sharing of typing results among laboratories worldwide. cgMLST offers an opportunity to harness the tremendous power of next-generation sequencing technology in applied avian mycoplasma epidemiology at both local and global levels.

Identification of Strain-Specific Sequences That Distinguish a Mycoplasma gallisepticum Vaccine Strain from Field Isolates

Despite attempts to control avian mycoplasmosis through management, vaccination, and surveillance, Mycoplasma gallisepticum continues to cause significant morbidity, mortality, and economic losses in poultry production. Live attenuated vaccines are commonly used in the poultry industry to control avian mycoplasmosis; unfortunately, some vaccines may revert to virulence and vaccine strains are generally difficult to distinguish from natural field isolates. In order to identify genome differences among vaccine revertants, vaccine strains, and field isolates, whole-genome sequencing of the M. gallisepticum vaccine strain ts-11 and several “ts-11-like” strains isolated from commercial flocks was performed using Illumina and 454 pyrosequencing and the sequenced genomes compared to the M. gallisepticum R_low reference genome. The collective contigs for each strain were annotated using the fully annotated Mycoplasma reference genome. The analysis revealed genetic differences among vlhA alleles, as well as among genes annotated as coding for a cell wall surface anchor protein (mg0377) and a hypothetical protein gene, mg0359, unique to M. gallisepticum ts-11 vaccine strain. PCR protocols were designed to target 5 sequences unique to the M. gallisepticum ts-11 strain: vlhA3.04a, vlhA3.04b, vlhA3.05, mg0377, and mg0359. All ts-11 isolates were positive for the five gene alleles tested by PCR; however, 5 to 36% of field isolates were also positive for at least one of the alleles tested. A combination of PCR tests for vlhA3.04a, vlhA3.05, and mg0359 was able to distinguish the M. gallisepticum ts-11 vaccine strain from field isolates. This method will further supplement current approaches to quickly distinguish M. gallisepticum vaccine strains from field isolates.

Co-infection with Multiple Respiratory Pathogens Contributes to Increased Mortality Rates in Algerian Poultry Flocks

Respiratory infections are a common cause for increased mortality rates in poultry worldwide. To improve intervention strategies, circulating pathogens have to be identified and further characterized. Because of the lack of diagnostic tools, it was not known what pathogens contribute to the high mortality rates in association with respiratory disease in Algeria. Our objective was to determine if primary pathogens including Mycoplasma gallisepticum (MG), Mycoplasma synoviae (MS), avian influenza virus (AIV), infectious bronchitis virus (IBV), and avian metapneumovirus (aMPV), known to be present in neighboring countries, can also be detected in Algerian chicken and turkey flocks. Results demonstrate the circulation of the investigated pathogens in Algerian poultry flocks as multi-infections. Phylogenetic characterization of the Algerian IBV strains confirmed the circulation of nephropathogenic viruses that are different from the strains isolated in neighboring countries. This could suggest the existence of a new IBV genotype in North Africa. Additionally, we detected for the first time an aMPV subtype B field strain and avian influenza virus. Interestingly, all viral pathogens were present in co-infections with MG, which could exacerbate clinical disease. Additional pathogens may be present and should be investigated in the future. Our results suggest that multiple respiratory infections may be responsible for high mortality in Algerian poultry flocks and very probably also in other regions of the world, which demonstrates the need for the establishment of more comprehensive control strategies.

Characterization of triosephosphate isomerase from Mycoplasma gallisepticum

Triosephosphate isomerase (Tpi) is a glycolytic enzyme that is essential for efficient energy production in many pathogens. However, its function in Mycoplasma gallisepticum has not been fully elucidated. In this study, the mga0357 gene of M. gallisepticum, which encodes TpiA (MGTpiA), was amplified and expressed in Escherichia coli by IPTG induction. The purified recombinant MGTpiA protein exhibited catalytic activity that was similar to TPI from rabbit muscle, reducing NAD(+) to NADH. The MGTpiA was also found to be a surface-exposed protein by western blotting and immunofluorescence assays. In addition, cytadherence inhibition assays confirmed that the cytadherence of M. gallisepticum to the DF-1 cells was significantly inhibited by the anti-MGTpiA serum. The results of the study suggested that MGTpiA plays an important role in the metabolism and closely related to the M. gallisepticum pathogenicity.

Evaluation of the Capacity of PCR and High-Resolution Melt Curve Analysis for Identification of Mixed Infection with Mycoplasma gallisepticum Strains

Pathogenicity and presentation of Mycoplasma gallisepticum (MG) infection may differ from one strain to another and this may have implications on control measures. Infection of individual birds with more than one MG strain has been reported. A PCR followed by high resolution melt (HRM) curve analysis has been developed in our laboratory and routinely used for detection and differentiation of MG strains. However the potential of this test for identification of MG strains in a mixed specimen has not been evaluated. In the present study, the capability of PCR-HRM curve analysis technique, targeting vlhA and pvpA genes was assessed for identification of individual MG strains in a mixed population. Different DNA ratios of two MG strains from 1 to 10^-4 ng were tested with some generated conventional and normalized curves distinct from those of individual strains alone. Using genotype confidence percentages (GCP) generated from HRM curve analysis, it was found that vlhA PCR-HRM was more consistent than pvpA PCR-HRM for the detection of MG ts-11 vaccine strain mixed with any of the MG strains 6/85, F, S6 or a field isolate. The potential of vlhA PCR-HRM to detect mixed MG strains in a specimen was found to be primarily dependent on quantity and proportion of the target DNAs in the mixture. This is the first study examining the capacity of PCR-HRM technique for identification of individual MG strains in a mixed strain population.

Understanding molecular identification and polyphasic taxonomic approaches for genetic relatedness and phylogenetic relationships of microorganisms

The major proportion of earth's biological diversity is inhabited by microorganisms and they play a useful role in diversified environments. However, taxonomy of microorganisms is progressing at a snail's pace, thus less than 1% of the microbial population has been identified so far. The major problem associated with this is due to a lack of uniform, reliable, advanced, and common to all practices for microbial identification and systematic studies. However, recent advances have developed many useful techniques taking into account the house-keeping genes as well as targeting other gene catalogues (16S rRNA, rpoA, rpoB, gyrA, gyrB etc. in case of bacteria and 26S, 28S, β-tubulin gene in case of fungi). Some uncultivable approaches using much advanced techniques like flow cytometry and gel based techniques have also been used to decipher microbial diversity. However, all these techniques have their corresponding pros and cons. In this regard, a polyphasic taxonomic approach is advantageous because it exploits simultaneously both conventional as well as molecular identification techniques. In this review, certain aspects of the merits and limitations of different methods for molecular identification and systematics of microorganisms have been discussed. The major advantages of the polyphasic approach have also been described taking into account certain groups of bacteria as case studies to arrive at a consensus approach to microbial identification.

Prevalence and differentiation of diseases in Maryland backyard flocks

Several epidemiologic surveillance studies have implicated backyard flocks as a reservoir for poultry diseases; however, much debate still exists over the risk these small flocks pose. To evaluate this concern, the prevalence of Newcastle disease (ND), infectious laryngotracheitis (ILT), Mycoplasma gallisepticum (MG), and Salmonella was determined in 39 Maryland backyard flocks. Serum, tracheal, and cloacal swabs were randomly collected from 262 birds throughout nine counties in Maryland. Through PCR and ELISA analysis, disease prevalence and seroprevalence were determined in flocks, respectively, for the following: ND (0%, 23%); ILT (26%, 77%); MG (3%, 13%); and Salmonella (0%, not done). Vaccine status could not be accurately confirmed. Premise positives were further differentiated and identified by partial nucleotide sequencing. Screening of the 10 ILT premise positives showed that most were live attenuated vaccines: eight matched a tissue culture origin vaccine, one matched a chicken embryo origin (CEO) vaccine, and one was CEO related. The single MG-positive flock, also positive for the CEO-related sequence, was identified as the infectious S6 strain. The prevalence rates for these economically important poultry diseases ranged from none to relatively low, with the vast majority of sampled flocks presenting no clinical signs.

Comparison of multiple genes and 16S-23S rRNA intergenic space region for their capacity in high resolution melt curve analysis to differentiate Mycoplasma gallisepticum vaccine strain ts-11 from field strains

Mycoplasma gallisepticum (MG) is an important avian pathogen causing significant economic losses in the global poultry industry. In an attempt to compare and evaluate existing genotyping methods for differentiation of MG strains/isolates, high resolution melt (HRM) curve analysis was applied to 5 different PCR methods targeting vlhA, pvpA, gapA, mgc2 genes and 16S-23S rRNA intergenic space region (IGSR). To assess the discriminatory power of PCR-HRM of examined genes and IGSR, MG strains ts-11, F, 6/85 and S6, and, initially, 8 field isolates were tested. All MG strains/isolates were differentiated using PCR-HRM curve analysis and genotype confidence percentage (GCP) values of vlhA and pvpA genes, while only 0, 3 and 4 out of 12 MG strains/isolates were differentiated using gapA, mgc2 genes and IGSR, respectively. The HRM curve analysis of vlhA and pvpA genes was found to be highly correlated with the genetic diversity of the targeted genes confirmed by sequence analysis of amplicons generated from MG strains. The potential of the vlhA and pvpA genes was also demonstrated for genotyping of 12 additional MG strains from Europe and the USA. Results from this study provide a direct comparison between genes previously used in sequencing-based genotyping methods for MG strain identification and highlight the usefulness of vlhA and pvpA HRM curve analyses as rapid and reliable tools specially for diagnosis and differentiation of MG strains used here.

The development and application of a Mycoplasma gallisepticum sequence database

Molecular analysis was conducted on 36 Mycoplasma gallisepticum DNA extracts from tracheal swab samples of commercial poultry in seven South African provinces between 2009 and 2012. Twelve unique M. gallisepticum genotypes were identified by polymerase chain reaction and sequence analysis of the 16S-23S rRNA intergenic spacer region (IGSR), M. gallisepticum cytadhesin 2 (mgc2), MGA_0319 and gapA genetic regions. The DNA sequences of these genotypes were distinct from those of M. gallisepticum isolates in a database composed of sequences from other countries, vaccine and reference strains. The most prevalent genotype (SA-WT#7) was detected in samples from commercial broilers, broiler breeders and layers in five provinces. South African M. gallisepticum sequences were more similar to those of the live vaccines commercially available in South Africa, but were distinct from that of F strain vaccine, which is not registered for use in South Africa. The IGSR, mgc2 or MGA_0319 sequences of three South African genotypes were identical to those of the ts-11 vaccine strain, necessitating a combination of mgc2 and IGSR targeted sequencing to differentiate South African wild-type genotypes from ts-11 vaccine. To identify and differentiate all 12 wild-types, mgc2, IGSR and MGA_0319 sequencing was required. Sequencing of gapA was least effective at strain differentiation. This research serves as a model for the development of an M. gallisepticum sequence database, and illustrates its application to characterize M. gallisepticum genotypes, select diagnostic tests and better understand the epidemiology of M. gallisepticum.

Characterization of a ts-1-like Mycoplasma galisepticum isolate from commercial broiler chickens

Several commercial broiler flocks in northeastern Georgia that were the progeny of the same parent flock (Flock 40) were diagnosed as Mycoplasma gallisepticum (MG) positive by serology, culture, and PCR. Flock 40 had been vaccinated with ts-11 live MG vaccine. Several isolates were obtained from the MG-positive broiler flocks, and these isolates were indistinguishable from the ts-11 vaccine strain by the molecular strain differentiation methods used. A pathogenicity study was performed to compare the virulence of one of the isolates, K6216D, to the ts-11 vaccine strain. K6216D elicited a significantly stronger antibody response and significantly increased colonization of the tracheas and air sacs. K6216D also elicited significantly greater air sac and tracheal lesions than the ts-11 vaccine strain at 10 and 21 days postinoculation (P < or = 0.05). This is the first report of a field case of the apparent reversion to virulence and vertical transmission of the ts-11 vaccine.

Ultrafast evolution and loss of CRISPRs following a host shift in a novel wildlife pathogen, Mycoplasma gallisepticum

Measureable rates of genome evolution are well documented in human pathogens but are less well understood in bacterial pathogens in the wild, particularly during and after host switches. Mycoplasma gallisepticum (MG) is a pathogenic bacterium that has evolved predominantly in poultry and recently jumped to wild house finches (Carpodacus mexicanus), a common North American songbird. For the first time we characterize the genome and measure rates of genome evolution in House Finch isolates of MG, as well as in poultry outgroups. Using whole-genome sequences of 12 House Finch isolates across a 13-year serial sample and an additional four newly sequenced poultry strains, we estimate a nucleotide diversity in House Finch isolates of only ∼2% of ancestral poultry strains and a nucleotide substitution rate of 0.8-1.2×10(-5) per site per year both in poultry and in House Finches, an exceptionally fast rate rivaling some of the highest estimates reported thus far for bacteria. We also found high diversity and complete turnover of CRISPR arrays in poultry MG strains prior to the switch to the House Finch host, but after the invasion of House Finches there is progressive loss of CRISPR repeat diversity, and recruitment of novel CRISPR repeats ceases. Recent (2007) House Finch MG strains retain only ∼50% of the CRISPR repertoire founding (1994-95) strains and have lost the CRISPR-associated genes required for CRISPR function. Our results suggest that genome evolution in bacterial pathogens of wild birds can be extremely rapid and in this case is accompanied by apparent functional loss of CRISPRs.

Characterization of in vivo-acquired resistance to macrolides of Mycoplasma gallisepticum strains isolated from poultry

The macrolide class of antibiotics, including tylosin and tilmicosin, is widely used in the veterinary field for prophylaxis and treatment of mycoplasmosis. In vitro susceptibility testing of 50 strains of M. gallisepticum isolated in Israel during the period 1997-2010 revealed that acquired resistance to tylosin as well as to tilmicosin was present in 50% of them. Moreover, 72% (13/18) of the strains isolated from clinical samples since 2006 showed acquired resistance to enrofloxacin, tylosin and tilmicosin. Molecular typing of the field isolates, performed by gene-target sequencing (GTS), detected 13 molecular types (I-XIII). Type II was the predominant type prior to 2006 whereas type X, first detected in 2008, is currently prevalent. All ten type X strains were resistant to both fluoroquinolones and macrolides, suggesting selective pressure leading to clonal dissemination of resistance. However, this was not a unique event since resistant strains with other GTS molecular types were also found. Concurrently, the molecular basis for macrolide resistance in M. gallisepticum was identified. Our results revealed a clear-cut correlation between single point mutations A2058G or A2059G in domain V of the gene encoding 23S rRNA (rrnA, MGA_01) and acquired macrolide resistance in M. gallisepticum. Indeed, all isolates with MIC ≥ 0.63 μg/mL to tylosin and with MIC ≥ 1.25 μg/mL to tilmicosin possess one of these mutations, suggesting an essential role in decreased susceptibility of M. gallisepticum to 16-membered macrolides.