Taxonomy of the canine Mollicutes by 16S rRNA gene and 16S/23S rRNA intergenic spacer region sequence comparison

The Impact of Microorganisms on Canine Semen Quality

Various microorganisms, including Mycoplasma spp., have been reported in canine ejaculate. The impact of these microorganisms on semen quality remains unclear. This study included 63 male intact healthy dogs aged 1-8 years. One dog exhibited azoospermia, indicating a relatively low incidence of this condition. Interestingly, 36.5% of the examined dogs tested negative for both aerobic bacteria and mycoplasmas, while 12.7% tested positive for bacterial presence. Additionally, 60.3% of the dogs tested positive for Mycoplasma spp. using PCR, with most carrying 1-2 Mycoplasma species. We found no significant difference in semen characteristics between Mycoplasma-positive and -negative dogs. The detection of Mycoplasma was not significantly linked to the presence of bacteria in semen. All the microorganisms identified were classified as saprophytic flora. Our findings indicate that Mycoplasma spp. is common in canine ejaculate. Semen quality parameters were not correlated with the presence of Mycoplasma spp. in semen. Mycoplasma HRC689 was the most common species. Some dogs exhibited no presence of aerobic bacteria or mycoplasmas in their semen. Our study highlights the common presence of Mycoplasma spp. in canine ejaculate. Semen quality shows no correlation with Mycoplasma presence. Some canine ejaculate is sterile. Our findings suggest the existence of undescribed species of canine mycoplasmas, necessitating advanced diagnostic techniques like NGS for their identification.

The lack of the influence of various species of Mycoplasma spp. on canine semen quality

Mycoplasmas colonize fish, reptiles, birds and mammals, being commensals or causing diseases, sometimes severe in ruminants, swine, poultry, or wildlife animals. So far, 15 species of canine Mycoplasma spp. have been described. Conflicting results have been presented regarding the pathogenicity of Mycoplasma spp. Although many virulence factors of these bacteria have been described, they still require attention. The main aim of our study was to evaluate the presence of known canine Mycoplasmas in the male reproductive tract of clinically healthy dogs. The second aim was to check if Mycoplasma spp. cause any abnormalities in semen quality that could have further consequences and to propose the schemes for managing the carriers. 83.3% of examined dogs were Mycoplasma spp. -positive dogs, and most of them were the carriers of more than one species. Six dogs had azoospermic ejaculates. The total spermatozoa numbers were similar in Mycoplasma -positive and negative groups. Motility was slightly higher in Mycoplasma spp.-negative group, but the difference was not statistically significant. There was no significant difference in semen characteristics between the carriers and Mycoplasma spp.-negative dogs. Neither the individual species nor the number of species strains had a significant effect on sperm morphological parameters as well as viability. Semen quality parameters are not correlated with the species found on the prepuce. Over 70% Mycoplasma spp.- positive dogs have more than one species of this bacteria. Despite finding mycoplasmas in azoospermic dogs, we suggest that they were not the cause of infertility. Mycoplasma spp. could be a part of normal microbiota in canine prepuce in individuals without any clinical signs.

Characterization of the semen microbiota of healthy stud dogs using 16S RNA sequencing

The reproductive microbiota of male dogs has never been investigated using culture-independent sequencing techniques. The purpose of the present study was to get seminal knowledge on the microbiota of the ejaculate. Specifically, factors as the fraction of the ejaculate, the sperm quality (normospermia, teratozoospermia), and the living environment were evaluated. The sperm-rich and the prostatic fractions of the ejaculate were collected from healthy stud dogs. Following the sperm analysis, samples from twenty animals (normospermic n = 10 and teratozoospermic n = 10) were stored at - 80 °C until further processing including DNA extraction and 16S rRNA sequencing. Alpha- (Shannon index) and beta- (Bray-Curtis, Unweighted UniFrac) diversities were assessed and compared (PERMANOVA) based on the group of samples (biological samples from the ejaculate and controls), the fraction of the ejaculate (sperm-rich and prostatic fractions), the animal group (normospermia and teratozoospermia), and the living environment of the animal (kennel or pet living in-house). The most abundant bacterial phyla in canine semen samples were Proteobacteria, Firmicutes, and Actinobacteria. Overall, the dominant bacterial family was that of Pasteurellaceae The genus Mycoplasma was never detected. No differences in terms of bacterial composition were found based on the fraction of the ejaculate and based on the animal group (P > 0.05). On the other hand, differences in alpha and beta diversities were highlighted based on the living environment (P = 0.001). Overall, the results of the present study provide preliminary insights on dog semen microbiota, opening a new chapter in the field of canine andrology. Our results suggest that the environment may play a role in influencing the reproductive microbiota of male dogs and that the prostatic fraction of the ejaculate can be used for further research as a representative of the semen microbiota.

Detection of Mycoplasma species at various anatomical sites of dogs from different types of kennels

This work aimed to detect Mycoplasma cynos, M. canis, M. edwardii, and M. molare in different types of kennels, in addition to evaluating their distribution in different colonization sites. The dogs belonged to different kennels from armed forces (n = 3), shelters (n = 3), and commercial purposes (n = 2). Samples of the oropharynx, genital mucosa, and ear canal were collected from each dog (n = 98), totaling 294 samples. Aliquots were submitted to isolation and the samples confirmed as Mycoplasma spp. were subjected to conventional PCR for M. canis and multiplex PCR for M. edwardii, M. molare, and M. cynos detection. Of the 98 dogs studied, 63.3% (62) were positive in at least one anatomical site evaluated for Mycoplasma spp. Among the 111 anatomical sites positive for Mycoplasma spp., M. canis, M. edwardii, and M. molare were detected in 29.7% (33/111), 40.5% (45/111), and 2.70% (3/111), respectively. No animal was positive for M. cynos.

Development of a long-read next generation sequencing workflow for improved characterization of fastidious respiratory mycoplasmas

Mycoplasma cynos and Mycoplasma felis are often associated with canine and feline infectious respiratory disease in dogs and cats, respectively. Mycoplasmas have a reduced genome and dearth of many biosynthetic pathways, making them dependent on rich medium for growth. Due to this fastidious nature, mycoplasmas have been historically underdiagnosed. The aim of this study was to develop a cost-effective and accurate sequencing workflow for genotypic characterization of clinical isolates of M. cynos and M. felis using a rapid long-read sequencing platform. We explored the following critical aspects of bacterial whole genome sequencing, including: (i) five solid and liquid-based culture approaches based on a specialized media formulation for Mycoplasma culture, (ii) three DNA extraction methods modified for long-read sequencing purposes, and (iii) two de novo assembly platforms, Flye and Canu, as key components of a bioinformatics pipeline. DNA extraction method 1, a solid-phase and column-based kit with enzymatic lysis, provided the best DNA quality and concentration followed by high coverage and sequencing contiguity. This was obtained with a culture volume of 45 ml in modified Hayflick's broth incubated for 48 h. DNA extracted directly from colonies on agar or from small broth volumes (6 ml) did not meet the criteria required for long-read sequencing. Overall, Flye generated more contiguous assemblies than the Canu assembler and was more time efficient. This 4-5 day sample-to-sequence workflow provides the scientific and clinical communities with a more comprehensive tool than laborious conventional methods for complete genomic characterization of M. cynos and M. felis clinical isolates.

Canine Parainfluenza Virus Infection in a Dog with Acute Respiratory Disease

Simple Summary

A one-day history of dry paroxysmal cough, associated with retching, induced by canine parainfluenza virus without the simultaneous presence of other pathogens, has been reported in a vaccinated household dog. The dog did not show nasal discharge or fever, but it was possible to evoke a dry cough through the palpation of the trachea. Radiographic findings of the thorax showed a diffuse unstructured interstitial pattern with the involvement of multiple lung lobes. Trachea-bronchoscopy and broncho-alveolar lavage were carried out. Edema without exudate and congested mucosa from the larynx to bronchi were observed. Cytological evaluation was negative for the presence of inflammatory or infectious processes. Nucleic acids were extracted from the collected specimens; biomolecular investigations tested positive only for canine parainfluenza virus and negative for all other pathogens associated with “kennel cough”. At first, the afebrile onset and the coughing fits suggested the presence of a foreign body, a common occurrence in Southern Italy during summer. The clinical signs and the absence of findings by cytology have directed the clinicians towards the correct diagnosis, with the support of biomolecular assays, which are fundamental to avoid underestimating the circulation of this virus, even in owned dogs.

Abstract

The canine infectious respiratory disease complex (CIRDC) is an endemic respiratory syndrome caused by different bacterial and viral pathogens. This report describes a case of canine parainfluenza virus infection in a vaccinated household dog with an acute respiratory symptom (dry cough), who underwent clinical and endoscopic investigations for a suspected foreign body. Cytological investigations carried out on the broncho-alveolar lavage fluid (BALF) tested negative for the presence of inflammatory or infectious processes and could have been misleading the clinicians. By the molecular analyses (PCR) carried out on the BALF, canine parainfluenza virus was exclusively detected without the simultaneous presence of other respiratory pathogens associated to CIRDC. This case report emphasizes the role of molecular diagnostics in the differential diagnosis of respiratory diseases, in order to avoid underestimating the circulation of the parainfluenza virus in the canine population.

Characterization of a novel Mycoplasma cynos real-time PCR assay

Mycoplasma cynos is recognized as an emerging causative pathogen of canine infectious respiratory disease (CIRD) worldwide. We developed a new open-source real-time PCR (rtPCR) assay for M. cynos that performs well under standard rtPCR conditions. Primers and probes were designed to target the M. cynos tuf gene. Reaction efficiencies for the M. cynos tuf gene assay on 2 platforms were based on amplification of standard curves spanning 8 orders of magnitude: ABI 7500 platform, 94.3–97.9% (r² ≥ 0.9935); QuantStudio OpenArray platform, 119.1–122.5% (r² = 0.9784). The assay performed very well over a range of template input, from 10⁹ copies to the lower limit of quantification at 4 copies of the M. cynos genome on the ABI 7500 platform. Diagnostic performance was estimated by comparison with an in-house legacy assay on clinical specimens as well as testing isolates that were characterized previously by intergenic spacer region (ISR) sequencing. Exclusivity was established by testing 12 other Mycoplasma species. To substantiate the high specificity of the M. cynos tuf gene assay, sequence confirmation was performed on ISR PCR amplicons obtained from clinical specimens. One ISR amplicon sequence revealed M. mucosicanis rather than M. cynos. The complete protocol of the newly developed M. cynos tuf assay is provided to facilitate assay harmonization.

The detection and differentiation of canine respiratory pathogens using oligonucleotide microarrays

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Multiple canine respiratory pathogens were differentiated simultaneously.

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Wild type and vaccine strains of canine distemper virus were distinguished.

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Results were read with naked eye and no reader equipment was needed.

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High sensitivity, specificity and efficiency.

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Low money and time costs.

Canine respiratory diseases are commonly seen in dogs along with co-infections with multiple respiratory pathogens, including viruses and bacteria. Virus infections in even vaccinated dogs were also reported. The clinical signs caused by different respiratory etiological agents are similar, which makes differential diagnosis imperative. An oligonucleotide microarray system was developed in this study. The wild type and vaccine strains of canine distemper virus (CDV), influenza virus, canine herpesvirus (CHV), Bordetella bronchiseptica and Mycoplasma cynos were detected and differentiated simultaneously on a microarray chip. The detection limit is 10, 10, 100, 50 and 50 copy numbers for CDV, influenza virus, CHV, B. bronchiseptica and M. cynos, respectively. The clinical test results of nasal swab samples showed that the microarray had remarkably better efficacy than the multiplex PCR-agarose gel method. The positive detection rate of microarray and agarose gel was 59.0% (n = 33) and 41.1% (n = 23) among the 56 samples, respectively. CDV vaccine strain and pathogen co-infections were further demonstrated by the microarray but not by the multiplex PCR-agarose gel. The oligonucleotide microarray provides a highly efficient diagnosis alternative that could be applied to clinical usage, greatly assisting in disease therapy and control.

Molecular detection of nontuberculous mycobacteria: advantages and limits of a broad-range sequencing approach

The isolation of nontuberculous mycobacteria (NTM) from clinical specimens has become very common in recent years. Such organisms are typically environmental and occasionally pathogenic for humans and animals. Standard diagnosis of mycobacterial infections relies on direct examination and culture. However, molecular tools are now available which allow quicker and more accurate diagnosis. Detection of NTM can be performed directly from clinical samples, although identification is mostly carried out after isolation. Sequencing of genomic targets (such as 16S rRNA, ITS, rpoB or hsp65) allows accurate and rapid identification, but has some technical limitations. A brief summary of the molecular methods available for NTM identification and a discussion of the problems associated with the use of sequencing analysis together with a description of available algorithms for NTM identification are the major objectives of this review.

Molecular identification of Mycoplasma cynos from laboratory beagle dogs with respiratory disease

In this study, we examined a colony of 20 beagle dogs in a laboratory animal facility. Mycoplasma was detected by consensus PCR assay in 1 dog with respiratory and constitutional symptoms. None of the other dogs were affected. The dog was euthanized and necropsied. In postmortem examinations, gray or plum-colored gross lesions were found on the lung, most commonly in the apical and cardiac lobes. Some lesions showed clear demarcation and consolidation. Microscopic examination showed peribronchiolar lymphoid hyperplasia and interstitial thickening, lesions pathognomonic for mycoplasma pneumonia. To identify canine Mycoplasma species, we used species-specific PCR reactions for M. arginini, M. canis, M. cynos, M. edwardii, M. felis, M. gateae, M. maculosum, M. molare, M. opalescens, M. spumans, Mycoplasma sp. HRC 689, and M. collis. As the result, we identified Mycoplasma cynos by amplification of DNA extracted from lung tissue of the laboratory beagle dog with respiratory disease.

RNA polymerase beta subunit (rpoB) gene and the 16S-23S rRNA intergenic transcribed spacer region (ITS) as complementary molecular markers in addition to the 16S rRNA gene for phylogenetic analysis and identification of the species of the family Mycoplasmataceae

Conventional classification of the species in the family Mycoplasmataceae is mainly based on phenotypic criteria, which are complicated, can be difficult to measure, and have the potential to be hampered by phenotypic deviations among the isolates. The number of biochemical reactions suitable for phenotypic characterization of the Mycoplasmataceae is also very limited and therefore the strategy for the final identification of the Mycoplasmataceae species is based on comparative serological results. However, serological testing of the Mycoplasmataceae species requires a performance panel of hyperimmune sera which contains anti-serum to each known species of the family, a high level of technical expertise, and can only be properly performed by mycoplasma-reference laboratories. In addition, the existence of uncultivated and fastidious Mycoplasmataceae species/isolates in clinical materials significantly complicates, or even makes impossible, the application of conventional bacteriological tests. The analysis of available genetic markers is an additional approach for the primary identification and phylogenetic classification of cultivable species and uncultivable or fastidious organisms in standard microbiological laboratories. The partial nucleotide sequences of the RNA polymerase β-subunit gene (rpoB) and the 16S-23S rRNA intergenic transcribed spacer (ITS) were determined for all known type strains and the available non-type strains of the Mycoplasmataceae species. In addition to the available 16S rRNA gene data, the ITS and rpoB sequences were used to infer phylogenetic relationships among these species and to enable identification of the Mycoplasmataceae isolates to the species level. The comparison of the ITS and rpoB phylogenetic trees with the 16S rRNA reference phylogenetic tree revealed a similar clustering patterns for the Mycoplasmataceae species, with minor discrepancies for a few species that demonstrated higher divergence of their ITS and rpoB in comparison to their neighbor species. Overall, our results demonstrated that the ITS and rpoB gene could be useful complementary phylogenetic markers to infer phylogenetic relationships among the Mycoplasmataceae species and provide useful background information for the choice of appropriate metabolic and serological tests for the final classification of isolates. In summary, three-target sequence analysis, which includes the ITS, rpoB, and 16S rRNA genes, was demonstrated to be a reliable and useful taxonomic tool for the species differentiation within the family Mycoplasmataceae based on their phylogenetic relatedness and pairwise sequence similarities. We believe that this approach might also become a valuable tool for routine analysis and primary identification of new isolates in medical and veterinary microbiological laboratories.

Identification and characterization of novel Mycoplasma spp. belonging to the hominis group from griffon vultures

Mycoplasmas are commensals and pathogens of various avian species, and are also regularly found in birds of prey, although their significance to birds' health remains unclear. Here we describe two novel Mycoplasma isolated from the upper respiratory tract of four Eurasian griffon vultures (Gyps fulvus) housed in a wildlife recovery centre in Sardinia (Italy). By sequencing the 16S rRNA gene and the entire 16S/23S intergenic spacer region, the new strains were classified within the Mycoplasma taxonomy at the group and cluster levels, showing that the two isolates fall into the Mycoplasma synoviae and Mycoplasma hominis clusters of the hominis group, respectively. We combined molecular tools and immunoblotting methods in order to further characterize these isolates, and antigenic analyses overall confirmed the molecular findings. Different levels of pathogenicity and prevalence of these strains might have different implications for the conservation and reintroduction of vultures.

Identification and differentiation of canine Mycoplasma isolates by 16S–23S rDNA PCR-RFLP

Conventional serological methods for the identification of canine mycoplasma isolates depend on the availability of a panel of species-specific diagnostic antisera and are not always reliable in terms of specificity. To enable simultaneous identification of field isolates, PCR-RFLP analysis of the 16S-23S rRNA intergenic spacer region was used to characterize the type strains of the 12 currently described canine mycoplasmas of the Genus Mycoplasma which represent the "classic" non-hemotropic species. The use of 16S-23S rDNA PCR in the first step of this analysis revealed specific size differences of amplicons which allowed to classify these 12 canine Mycoplasma species into three groups. Depending on the length of the amplicon, subsequent RFLP analysis of PCR products using two restriction endonucleases in a single digest (ApoI/DdeI or TaqI/VspI) generated unique banding patterns. For further evaluation of the 16S-23S rDNA PCR-RFLP assay system as identification and differentiation tool, a total of 262 field isolates collected from the canine genital tract were tested. PCR-RFLP results for 251 field isolates correlated with traditional serological test results. The remaining 11 isolates had an RFLP pattern distinct from the type strains included in this study and were identified by 16S rDNA sequencing as closely related to M. sp. HRC689. The PCR-RFLP assay established in this study enabled a rapid, accurate and easily performed identification and differentiation of all 12 currently described non-hemotropic canine Mycoplasma species.

Revised minimal standards for description of new species of the class Mollicutes (division Tenericutes)

Minimal standards for novel species of the class Mollicutes (trivial term, mollicutes), last published in 1995, require revision. The International Committee on Systematics of Prokaryotes Subcommittee on the Taxonomy of Mollicutes proposes herein revised standards that reflect recent advances in molecular systematics and the species concept for prokaryotes. The mandatory requirements are: (i) deposition of the type strain into two recognized culture collections, preferably located in different countries; (ii) deposition of the 16S rRNA gene sequence into a public database, and a phylogenetic analysis of the relationships among the 16S rRNA gene sequences of the novel species and its neighbours; (iii) deposition of antiserum against the type strain into a recognized collection; (iv) demonstration, by using the combination of 16S rRNA gene sequence analyses, serological analyses and supplementary phenotypic data, that the type strain differs significantly from all previously named species; and (v) assignment to an order, a family and a genus in the class, with an appropriate specific epithet. The 16S rRNA gene sequence provides the primary basis for assignment to hierarchical rank, and may also constitute evidence of species novelty, but serological and supplementary phenotypic data must be presented to substantiate this. Serological methods have been documented to be congruent with DNA-DNA hybridization data and with 16S rRNA gene placements. The novel species must be tested serologically to the greatest extent that the investigators deem feasible against all neighbouring species whose 16S rRNA gene sequences show >0.94 similarity. The investigator is responsible for justifying which characters are most meaningful for assignment to the part of the mollicute phylogenetic tree in which a novel species is located, and for providing the means by which novel species can be identified by other investigators. The publication of the description should appear in a journal having wide circulation. If the journal is not the International Journal of Systematic and Evolutionary Microbiology, copies of the publication must be submitted to that journal so that the name may be considered for inclusion in a Validation List as required by the International Code of Bacteriological Nomenclature (the Bacteriological Code). Updated informal descriptions of the class Mollicutes and some of its constituent higher taxa are available as supplementary material in IJSEM Online.

Genetic analysis of housekeeping genes of members of the genus Acholeplasma: Phylogeny and complementary molecular markers to the 16S rRNA gene

The partial nucleotide sequences of the rpoB and gyrB genes as well as the complete sequence of the 16S-23S rRNA intergenic transcribed spacer (ITS) were determined for all known Acholeplasma species. The same genes of Mesoplasma and Entomoplasma species were also sequenced and used to infer phylogenetic relationships among the species within the orders Entomoplasmatales and Acholeplasmatales. The comparison of the ITS, rpoB, and gyrB phylogenetic trees with the 16S rRNA phylogenetic tree revealed a similar branch topology suggesting that the ITS, rpoB, and gyrB could be useful complementary phylogenetic markers for investigation of evolutionary relationships among Acholeplasma species. Thus, the multilocus phylogenetic analysis of Acholeplasma multilocale sequence data (ATCC 49900 (T) = PN525 (NCTC 11723)) strongly indicated that this organism is most closely related to the genera Mesoplasma and Entomoplasma (family Entomoplasmataceae) and form the branch with Mesoplasma seiffertii, Mesoplasma syrphidae, and Mesoplasma photuris. The closest genetic relatedness of this species to the order Entomoplasmatales was additionally supported by the finding that A. multilocale uses UGA as the tryptophan codon in its gyrB and gyrA sequences. Use of the UGA codon for encoding tryptophan was previously reported as a unique genetic feature of Entomoplasmatales and Mycoplasmatales but not of Acholeplasmatales. These data, as well as previously published data on metabolic features of A. multilocale, leads to the proposal to reclassify A. multilocale as a member of the family Entomoplasmataceae.

16S rDNA PCR and denaturing gradient gel electrophoresis; a single generic test for detecting and differentiating Mycoplasma species

Diagnosis of Mycoplasma infection is normally based on culture and serological tests, which can be time-consuming and laborious. A number of specific PCRs have been developed but to date there has not been a single generic test capable of detecting and differentiating mycoplasmas to a species level. This report describes the development of a new diagnostic test based on PCR of the 16S rRNA gene with Mycoplasma-specific primers and separation of the PCR product according to primary sequence using denaturing gradient gel electrophoresis (DGGE). DGGE enabled the differentiation of 67 Mycoplasma species of human and veterinary origin and represents a significant improvement on current tests as diagnosis of Mycoplasma infection can be made directly from clinical samples in less than 24 h.

Canine mycoplasmas

This review aims to summarise our current understanding of the role of mycoplasmas in domestic dogs. Canine mycoplasmology is a small field, with less than 50 publications in the past 40 years. In this time we have gained knowledge about the number of species and have made associations with infections in dogs. However much evidence is still lacking. The importance of all canine mycoplasmas remains unknown, yet certain species are associated with canine anaemia (Mycoplasma haemocanis), respiratory disease (Mycoplasma cynos) and urogenital tract infections (Mycoplasma canis). Mycoplasmas can be isolated in pure culture from canine clinical specimens and it is hoped that this review will stimulate veterinarians to consider mycoplasmas as a potential cause of disease in dogs, especially when antibiotic therapy is failing.

Development of a polymerase chain reaction for the detection of Mycoplasma felis in domestic cats

Mycoplasma felis is associated with conjunctivitis and respiratory disease in domestic cats. Currently no rapid diagnostic test is available for the detection of M. felis in clinical samples that does not rely on prior cultivation of the organism. The objective of this study was to determine whether a polymerase chain reaction (PCR) based upon the 16S/23S rRNA intergenic spacer sequence is suitable for the identification of M. felis directly in feline clinical samples. The high conservation between the 16S/23S rRNA intergenic spacers (IGS) of differing isolates of M. felis was established by sequence analysis and a PCR was developed to this region by comparison to IGS of other mycoplasmas. The PCR was found to be highly specific for M. felis and further PCR analysis on clinical samples showed the PCR to be highly sensitive and more rapid than the other methods of identification currently available.