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

Description and prevalence of Mycoplasma ciconiae sp. nov. isolated from white stork nestlings (Ciconia ciconia)

The mycoplasma strain ST 57T was isolated from the trachea of a clinically healthy, free-ranging white stork nestling in Nielitz, Mecklenburg-Western Pomerania, Germany. Strain ST 57T grew in fried-egg-shaped colonies on mycoplasma (SP4) agar plates and was dependent on sterol for growth. The organism fermented glucose and did not hydrolyse arginine or urea. The optimal growth temperature was 37 °C, with a temperature range from 23 to 44 °C. Strain ST 57Tcould not be identified as a representative of any of the currently described mycoplasma species by alignment of the 16S rRNA gene sequence or 16S-23S intergenic transcribed spacer region, or by immunobinding assays. Thus, this organism appears to be a representative of a novel species, for which the name Mycoplasma ciconiae sp. nov. is proposed. The type strain is ST 57T (=ATCC BAA-2401T=DSM 25251T). Four further strains of this species are included in this description (ST 24=DSM 29908, ST 56 Clone 1=DSM 29054, ST 99=DSM 29909, ST 102=DSM 29010). The prevalence of this mycoplasma species in clinically healthy, white stork nestlings in northern Germany was determined. Our species-specific PCR detected 57.8 % (48/83) of the samples positive for M. ciconiae sp. nov. As this species appears to be widespread in the healthy free-ranging white stork population, we conclude that this species is either apathogenic or an opportunistic pathogen in white storks.

Validation of a mycoplasma molecular diagnostic test and distribution of mycoplasma species in bovine milk among New York State dairy farms

Mycoplasma mastitis is a contagious and costly disease of dairy cattle that significantly affects animal health and milk productivity. Mycoplasma bovis is the most prevalent and invasive agent of mycoplasma mastitis in dairy cattle, and early detection is critical. Other mycoplasma have been isolated from milk; however, the role and prevalence of these species as mastitis pathogens are poorly understood. Routine screening of milk for mycoplasma by bacteriological culture is an important component of a farm control strategy to minimize a herd mycoplasma outbreak, but phenotypic methods have limited ability to speciate mycoplasma, affecting how farms and practitioners can understand the role and effect of species other than M. bovis in herd health. Fastidious mycoplasma culture can be lengthy and inconclusive, resulting in delayed or false negative reports. We developed and validated a multitarget PCR assay that can in the same day confirm or reject a presumptive positive mycoplasma culture found upon bacteriological testing of clinical specimens, further discriminate between Acholeplasma and Mycoplasma, and identify M. bovis. Coupled with sequence analysis isolates can be further identified as bovine mycoplasma Mycoplasma arginini, Mycoplasma alkalescens, Mycoplasma canadense, Mycoplasma bovirhinis, Mycoplasma bovigenitalium, Mycoplasma californicum, Acholeplasma laidlawii, and Acholeplasma oculi. Assay validation included analysis of 845 mycoplasma representing these species and 30 additional bacterial species obtained from routine milk submissions to the Quality Milk Production Services from New York State farms and veterinary clinics between January 2012 and December 2015. Among 95 herds, we found 8 different Mycoplasma species and 3 different Acholeplasma species, with an overall prevalence of M. bovirhinis of 1%, A. oculi of 2%, M. arginini of 2%, M. californicum of 3%, M. canadense of 10%, M. bovigenitalium of 10%, A. laidlawii of 11%, M. alkalescens of 17%, and M. bovis of 78%. More than one mycoplasma was found in 14% of the herds tested, and both M. bovis and Acholeplasma were found in 6% of the farms. Incorporation of the validated molecular diagnostic assay into routine bacteriological screening as a supportive confirmation and identification tool will lead to an improved assessment of Mycoplasma and Acholeplasma prevalence data, which will facilitate increased knowledge about the role of these mycoplasma in mastitis.

An emerging mycoplasma associated with trichomoniasis, vaginal infection and disease

Humans are colonized by thousands of bacterial species, but it is difficult to assess the metabolic and pathogenic potential of the majority of these because they have yet to be cultured. Here, we characterize an uncultivated vaginal mycoplasma tightly associated with trichomoniasis that was previously known by its 16S rRNA sequence as "Mnola." In this study, the mycoplasma was found almost exclusively in women infected with the sexually transmitted pathogen Trichomonas vaginalis, but rarely observed in women with no diagnosed disease. The genomes of four strains of this species were reconstructed using metagenome sequencing and assembly of DNA from four discrete mid-vaginal samples, one of which was obtained from a pregnant woman with trichomoniasis who delivered prematurely. These bacteria harbor several putative virulence factors and display unique metabolic strategies. Genes encoding proteins with high similarity to potential virulence factors include two collagenases, a hemolysin, an O-sialoglycoprotein endopeptidase and a feoB-type ferrous iron transport system. We propose the name "Candidatus Mycoplasma girerdii" for this potential new pathogen.

Impact of next generation sequencing techniques in food microbiology

Understanding the Maxam-Gilbert and Sanger sequencing as the first generation, in recent years there has been an explosion of newly-developed sequencing strategies, which are usually referred to as next generation sequencing (NGS) techniques. NGS techniques have high-throughputs and produce thousands or even millions of sequences at the same time. These sequences allow for the accurate identification of microbial taxa, including uncultivable organisms and those present in small numbers. In specific applications, NGS provides a complete inventory of all microbial operons and genes present or being expressed under different study conditions. NGS techniques are revolutionizing the field of microbial ecology and have recently been used to examine several food ecosystems. After a short introduction to the most common NGS systems and platforms, this review addresses how NGS techniques have been employed in the study of food microbiota and food fermentations, and discusses their limits and perspectives. The most important findings are reviewed, including those made in the study of the microbiota of milk, fermented dairy products, and plant-, meat- and fish-derived fermented foods. The knowledge that can be gained on microbial diversity, population structure and population dynamics via the use of these technologies could be vital in improving the monitoring and manipulation of foods and fermented food products. They should also improve their safety.

Comparative genomics and phylogenomics of hemotrophic mycoplasmas

Hemotrophic mycoplasmas (hemoplasmas) are a group of animal pathogens of the Mollicutes class. Recently, the genomes of 8 hemoplasmas have been completely sequenced. The aim of this study was to gain a better understanding of their genomic features and relationship to other Mycoplasma species. The genome structure and dynamics of hemoplasmas were analyzed by evaluating gene synteny, adaptive evolution of paralogous gene families (PGF) and horizontal gene transfer (HGT). The Mollicutes class was then phylogenetically analyzed by constructing a distance matrix of the 16S rRNA genes and a phylogenetic tree with 32 conserved, concatenated proteins. Our results suggest that the hemoplasmas have dynamic genomes. The genome size variation (from 547 to 1,545 genes) indicates substantial gene gain/loss throughout evolution. Poorly conserved gene syntenies among hemoplasmas, positional shuffling of paralogous genes between strains, HGT, and codons under positive selection in PGFs were also observed. When compared to other Mollicutes species, the hemoplasmas experienced further metabolic reduction, and the 16S rRNA gene distance matrix of the available mollicutes suggests that these organisms presently constitute the most divergent clade within its class. Our phylogenetic tree of concatenated proteins showed some differences when compared to the 16S rRNA gene tree, but non-mycoplasma organisms, such as Ureaplasma spp. and Mesoplasma spp., continue to branch within Mycoplasma clades. In conclusion, while the hemoplasmas experienced further metabolic shrinkage through gene loss, PGFs with positively selected codons are likely beneficial to these species. Phylogeny of the mollicutes based on 16S rRNA genes or concatenated proteins do not obey the current taxonomy. The metabolism and genetic diversity of the mollicutes, the presence of HGT, and lack of standard for genus circumscription are likely to hinder attempts to classify these organisms based on phylogenetic analyses.

Complete genomes of two dipteran-associated spiroplasmas provided insights into the origin, dynamics, and impacts of viral invasion in spiroplasma

Spiroplasma is a genus of wall-less, low-GC, Gram-positive bacteria with helical morphology. As commensals or pathogens of plants, insects, ticks, or crustaceans, they are closely related with mycoplasmas and form a monophyletic group (Spiroplasma–Entomoplasmataceae–Mycoides) with Mycoplasma mycoides and its relatives. In this study, we report the complete genome sequences of Spiroplasma chrysopicola and S. syrphidicola from the Chrysopicola clade. These species form the sister group to the Citri clade, which includes several well-known pathogenic spiroplasmas. Surprisingly, these two newly available genomes from the Chrysopicola clade contain no plectroviral genes, which were found to be highly repetitive in the previously sequenced genomes from the Citri clade. Based on the genome alignment and patterns of GC-skew, these two Chrysopicola genomes appear to be relatively stable, rather than being highly rearranged as those from the Citri clade. Phylogenetic analyses suggest that the susceptibility to plectroviral invasion probably originated in the common ancestor of the Citri clade or one of its subclades. This susceptibility may be attributed to the absence of antiviral systems found in the Chrysopicola clade. Using the virus-free genomes of the Chrysopicola clade as references, we inferred the putative viral integration sites in the Citri genomes. Comparisons of syntenic regions suggest that the extensive viral invasion in the Citri clade promoted genome rearrangements and expansions. More importantly, the viral invasion may have facilitated horizontal gene transfers that contributed to adaptation in the Citri clade.

Prevalence and molecular analyses of hemotrophic Mycoplasma spp. (hemoplasmas) detected in sika deer (Cervus nippon yesoensis) in Japan

Hemotropic mycoplasmas (hemoplasmas) are cell-wall deficient, epierythrocytic bacteria that cause infectious anemia in several mammalian species. The prevalence of hemoplasma species was examined by screening and species-specific PCR using blood samples collected from 51 sika deer in Hokkaido, Japan. Molecular analyses were performed for the 16S rRNA, 23S rRNA and RNase P RNA (rnpB) gene sequences. A total of 23/51 (45%) deer DNA samples were positive for hemoplasmas in the screening PCR. Using species-specific PCR, 12 and 17 samples were positive for ‘Candidatus Mycoplasma haemocervae’ and ‘Candidatus M. erythrocervae’, respectively. Sequencing and phylogenetic trees of those three genes indicate that the ‘Candidatus M. haemocervae’ and ‘Candidatus M. erythrocervae’ detected in Japanese deer are potentially different species from the cervine hemoplasma found in deer from America and Brazil.

Collaborative study report: evaluation of the ATCC experimental mycoplasma reference strains panel prepared for comparison of NAT-based and conventional mycoplasma detection methods

The main goal of this collaborative study was to evaluate the experimental panel of cryopreserved mycoplasma reference strains recently prepared by the American Type Culture Collection (ATCC(®)) in order to assess the viability and dispersion of cells in the mycoplasma stocks by measuring the ratio between the number of genomic copies (GC) and the number of colony forming units (CFU) in the reference preparations. The employment of microbial reference cultures with low GC/CFU ratios is critical for unbiased and reliable comparison of mycoplasma testing methods based on different methodological approaches, i.e., Nucleic Acid Testing (NAT) and compendial culture-based techniques. The experimental panel included ten different mycoplasma species known to represent potential human and animal pathogens as well as common contaminants of mammalian and avian cell substrates used in research, development, and manufacture of biological products. Fifteen laboratories with expertise in field of mycoplasma titration and quantification of mycoplasmal genomic DNA participated in the study conducted from February to October of 2012. The results of this study demonstrated the feasibility of preparing highly viable and dispersed (possessing low GC/CFU ratios) frozen stocks of mycoplasma reference materials, required for reliable comparison of NAT-based and conventional mycoplasma detection methods.

New insights on the biology of swine respiratory tract mycoplasmas from a comparative genome analysis

BACKGROUND

Mycoplasma hyopneumoniae, Mycoplasma flocculare and Mycoplasma hyorhinis live in swine respiratory tracts. M. flocculare, a commensal bacterium, is genetically closely related to M. hyopneumoniae, the causative agent of enzootic porcine pneumonia. M. hyorhinis is also pathogenic, causing polyserositis and arthritis. In this work, we present the genome sequences of M. flocculare and M. hyopneumoniae strain 7422, and we compare these genomes with the genomes of other M. hyoponeumoniae strain and to the a M. hyorhinis genome. These analyses were performed to identify possible characteristics that may help to explain the different behaviors of these species in swine respiratory tracts.

RESULTS

The overall genome organization of three species was analyzed, revealing that the ORF clusters (OCs) differ considerably and that inversions and rearrangements are common. Although M. flocculare and M. hyopneumoniae display a high degree of similarity with respect to the gene content, only some genomic regions display considerable synteny. Genes encoding proteins that may be involved in host-cell adhesion in M. hyopneumoniae and M. flocculare display differences in genomic structure and organization. Some genes encoding adhesins of the P97 family are absent in M. flocculare and some contain sequence differences or lack of domains that are considered to be important for adhesion to host cells. The phylogenetic relationship of the three species was confirmed by a phylogenomic approach. The set of genes involved in metabolism, especially in the uptake of precursors for nucleic acids synthesis and nucleotide metabolism, display some differences in copy number and the presence/absence in the three species.

CONCLUSIONS

The comparative analyses of three mycoplasma species that inhabit the swine respiratory tract facilitated the identification of some characteristics that may be related to their different behaviors. M. hyopneumoniae and M. flocculare display many differences that may help to explain why one species is pathogenic and the other is considered to be commensal. However, it was not possible to identify specific virulence determinant factors that could explain the differences in the pathogenicity of the analyzed species. The M. hyorhinis genome contains differences in some components involved in metabolism and evasion of the host's immune system that may contribute to its growth aggressiveness. Several horizontal gene transfer events were identified. The phylogenomic analysis places M. hyopneumoniae, M. flocculare and M. hyorhinis in the hyopneumoniae clade.

Hemotropic mycoplasma infection in wild black bears (Ursus thibetanus japonicus)

This is the first report on Mycoplasma infection in wild bears. We report a novel hemotropic Mycoplasma (also called hemoplasma) detected in a free-ranging black bear (Ursus thibetanus japonicus) in Japan. We then used real-time PCR to look for hemoplasma DNA in blood samples collected from 15 bears and found that eight (53%) were positive. Among these eight PCR samples, seven showed a melting temperature of around 85.5°C, while the remaining one showed a single peak at 82.26°C. Almost the entire region of the 16S rRNA gene as well as the 16S-23S rRNA intergenic transcribed spacer (ITS) region from the sample that showed a melting temperature of 82.26°C was successfully amplified by means of end-point PCR. The nucleotide sequences of the 16S rRNA gene and the ITS region were then determined and compared with those of authentic Mycoplasma species. Our examinations revealed the presence of a novel hemoplasma in Japanese black bears.

Two clusters among Mycoplasma haemomuris strains, defined by the 16S-23S rRNA intergenic transcribed spacer sequences

Mycoplasma haemomuris is a causative organism of infectious anemia or splenomegaly in rodents. Here, we report two distinct genetic groups among M. haemomuris strains detected from rats and mice, respectively, by examining the nucleotide sequences of the 16S-23S rRNA intergenic transcribed spacer region that has been shown to be a stable genetic marker for mycoplasma species. Our results may reveal host-tropism of each cluster of M. haemomuris strains, and suggest an idea to distinguish M. haemomuris into two different genetic clusters.