The complete sequence of the mucosal pathogen Ureaplasma urealyticum

Ureaplasma infections: update on epidemiology, antimicrobial resistance, and pathogenesis

Human Ureaplasma species are being increasingly recognized as opportunistic pathogens in human genitourinary tract infections, infertility, adverse pregnancy, neonatal morbidities, and other adult invasive infections. Although some general reviews have focused on the detection and clinical manifestations of Ureaplasma spp., the molecular epidemiology, antimicrobial resistance, and pathogenesis of Ureaplasma spp. have not been adequately explained. The purpose of this review is to offer valuable insights into the current understanding and future research perspectives of the molecular epidemiology, antimicrobial resistance, and pathogenesis of human Ureaplasma infections. This review summarizes the conventional culture and detection methods and the latest molecular identification technologies for Ureaplasma spp. We also reviewed the global prevalence and mechanisms of antibiotic resistance for Ureaplasma spp. Aside from regular antibiotics, novel antibiotics with outstanding in vitro antimicrobial activity against Ureaplasma spp. are described. Furthermore, we discussed the pathogenic mechanisms of Ureaplasma spp., including adhesion, proinflammatory effects, cytotoxicity, and immune escape effects, from the perspectives of pathology, related molecules, and genetics.

Unraveling the adaptive strategies of Mycoplasma hominis through proteogenomic profiling of clinical isolates

Introduction

Mycoplasma hominis (M. hominis) belongs to the class Mollicutes, characterized by a very small genome size, reduction of metabolic pathways, including transcription factors, and the absence of a cell wall. Despite this, they adapt well not only to specific niches within the host organism but can also spread throughout the body, colonizing various organs and tissues. The adaptation mechanisms of M. hominis, as well as their regulatory pathways, are poorly understood. It is known that, when adapting to adverse conditions, Mycoplasmas can undergo phenotypic switches that may persist for several generations.

Methods

To investigate the adaptive properties of M. hominis related to survival in the host, we conducted a comparative phenotypic and proteogenomic analysis of eight clinical isolates of M. hominis obtained from patients with urogenital infections and the laboratory strain H-34.

Results

We have shown that clinical isolates differ in phenotypic features from the laboratory strain, form biofilms more effectively and show resistance to ofloxacin. The comparative proteogenomic analysis revealed that, unlike the laboratory strain, the clinical isolates possess several features related to stress survival: they switch carbon metabolism, activating the energetically least advantageous pathway of nucleoside utilization, which allows slowing down cellular processes and transitioning to a starvation state; they reconfigure the repertoire of membrane proteins; they have integrative conjugative elements in their genomes, which are key mediators of horizontal gene transfer. The upregulation of the methylating subunit of the restriction-modification (RM) system type I and the additional components of RM systems found in clinical isolates suggest that DNA methylation may play a role in regulating the adaptation mechanisms of M. hominis in the host organism. It has been shown that based on the proteogenomic profile, namely the genome sequence, protein content, composition of the RM systems and additional subunits HsdM, HsdS and HsdR, composition and number of transposable elements, as well as the sequence of the main variable antigen Vaa, we can divide clinical isolates into two phenotypes: typical colonies (TC), which have a high growth rate, and atypical (aTC) mini-colonies, which have a slow growth rate and exhibit properties similar to persisters.

Discussion

We believe that the key mechanism of adaptation of M. hominis in the host is phenotypic restructuring, leading to a slowing down cellular processes and the formation of small atypical colonies. This is due to a switch in carbon metabolism and activation the pathway of nucleoside utilization. We hypothesize that DNA methylation may play a role in regulating this switch.

Increase in the solubility of uvsY using a site saturation mutagenesis library for application in a lyophilized reagent for recombinase polymerase amplification

BACKGROUND

Recombinase uvsY from bacteriophage T4, along with uvsX, is a key enzyme for recombinase polymerase amplification (RPA), which is used to amplify a target DNA sequence at a constant temperature. uvsY, though essential, poses solubility challenges, complicating the lyophilization of RPA reagents. This study aimed to enhance uvsY solubility.

METHODS

Our hypothesis centered on the C-terminal region of uvsY influencing solubility. To test this, we generated a site-saturation mutagenesis library for amino acid residues Lys91-Glu134 of the N-terminal (His)6-tagged uvsY.

RESULTS

Screening 480 clones identified A116H as the variant with superior solubility. Lyophilized RPA reagents featuring the uvsY variant A116H demonstrated enhanced performance compared to those with wild-type uvsY.

CONCLUSIONS

The uvsY variant A116H emerges as an appealing choice for RPA applications, offering improved solubility and heightened lyophilization feasibility.

Structure, dynamics, and stability of the smallest and most complex 71 protein knot

Proteins can spontaneously tie a variety of intricate topological knots through twisting and threading of the polypeptide chains. Recently developed artificial intelligence algorithms have predicted several new classes of topological knotted proteins, but the predictions remain to be authenticated experimentally. Here, we showed by X-ray crystallography and solution-state NMR spectroscopy that Q9PR55, an 89-residue protein from Ureaplasma urealyticum, possesses a novel 71 knotted topology that is accurately predicted by AlphaFold 2, except for the flexible N terminus. Q9PR55 is monomeric in solution, making it the smallest and most complex knotted protein known to date. In addition to its exceptional chemical stability against urea-induced unfolding, Q9PR55 is remarkably robust to resist the mechanical unfolding-coupled proteolysis by a bacterial proteasome, ClpXP. Our results suggest that the mechanical resistance against pulling-induced unfolding is determined by the complexity of the knotted topology rather than the size of the molecule.

Antimicrobial Activity of N,N-Diethyldithiocarbamate against Ureaplasma parvum and Ureaplasma urealyticum

Ureaplasma species (Ureaplasma spp.) are commonly found as commensals in the human urogenital tracts, although their overgrowth can lead to infection in the urogenital tract and at distal sites. Furthermore, ureaplasmas lack a cell wall and do not synthesize folic acid, which causes all β-lactam and glycopeptide antibiotics, and sulfonamides and diaminopyrimidines, to be of no value. The antibiotics used in therapy belong to the fluoroquinolone, tetracycline, chloramphenicol and macrolide classes. However, the growing incidence of antibiotic-resistant Ureaplasma spp. in the population becomes a problem. Thus, there is a need to search for new drugs effective against these bacteria. Since 1951, the FDA-approved, well-tolerated, inexpensive, orally administered drug disulfiram (DSF) has been used in the treatment of chronic alcoholism, but recently, its antimicrobial effects have been demonstrated. The main biological metabolite of DSF, i.e., N,N-diethyldithiocarbamate (DDC), is generally believed to be responsible for most of the observed pharmacological effects of DSF. In the presented studies, the effect of DDC at concentrations of 2 µg/mL, 20 µg/mL and 200 µg/mL on the growth and survival of Ureaplasma urealyticum and Ureaplasma parvum was tested for the first time. The results indicated that all the used DDC concentrations showed both bacteriostatic and bactericidal activity against both tested strains.

Filamentous temperature sensitive mutant Z: a putative target to combat antibacterial resistance

In the pre-antibiotic era, common bacterial infections accounted for high mortality and morbidity. Moreover, the discovery of penicillin in 1928 marked the beginning of an antibiotic revolution, and this antibiotic era witnessed the discovery of many novel antibiotics, a golden era. However, the misuse or overuse of these antibiotics, natural resistance that existed even before the antibiotics were discovered, genetic variations in bacteria, natural selection, and acquisition of resistance from one species to another consistently increased the resistance to the existing antibacterial targets. Antibacterial resistance (ABR) is now becoming an ever-increasing concern jeopardizing global health. Henceforth, there is an urgent unmet need to discover novel compounds to combat ABR, which act through untapped pathways/mechanisms. Filamentous Temperature Sensitive mutant Z (FtsZ) is one such unique target, a tubulin homolog involved in developing a cytoskeletal framework for the cytokinetic ring. Additionally, its pivotal role in bacterial cell division and the lack of homologous structural protein in mammals makes it a potential antibacterial target for developing novel molecules. Approximately 2176 X-crystal structures of FtsZ were available, which initiated the research efforts to develop novel antibacterial agents. The literature has reported several natural, semisynthetic, peptides, and synthetic molecules as FtsZ inhibitors. This review provides valuable insights into the basic crystal structure of FtsZ, its inhibitors, and their inhibitory activities. This review also describes the available in vitro detection and quantification methods of FtsZ-drug complexes and the various approaches for determining drugs targeting FtsZ polymerization.

Recombinase polymerase amplification using novel thermostable strand-displacing DNA polymerases from Aeribacillus pallidus and Geobacillus zalihae

Recombinase polymerase amplification (RPA) is an isothermal DNA amplification reaction at around 41 °C using recombinase (Rec), single-stranded DNA-binding protein (SSB), and strand-displacing DNA polymerase (Pol). Component instability and the need to store commercial kits in a deep freezer until use are some limitations of RPA. In a previous study, Bacillus stearothermophilus Pol (Bst-Pol) was used as a thermostable strand-displacing DNA polymerase in RPA. Here, we attempted to optimize the lyophilization conditions for RPA with newly isolated thermostable DNA polymerases for storage at room temperature. We isolated novel two thermostable strand-displacing DNA polymerases, one from a thermophilic bacterium Aeribacillus pallidus (H1) and the other from Geobacillus zalihae (C1), and evaluated their performances in RPA reaction. Urease subunit β (UreB) DNA from Ureaplasma parvum serovar 3 was used as a model target for evaluation. The RPA reaction with H1-Pol or C1-Pol was performed at 41 °C with the in vitro synthesized standard UreB DNA. The minimal initial copy numbers of standard DNA from which the amplified products were observed were 600, 600, and 6000 copies for RPA with H1-Pol, C1-Pol, and Bst-Pol, respectively. Optimization was carried out using RPA components, showing that the lyophilized RPA reagents containing H1-Pol exhibited the same performance as the corresponding liquid RPA reagents. In addition, lyophilized RPA reagents with H1-Pol showed almost the same activity after two weeks of storage at room temperature as the freshly prepared liquid RPA reagents. These results suggest that lyophilized RPA reagents with H1-Pol are preferable to liquid RPA reagents for onsite use.

In vivo client proteins of the chaperonin GroEL-GroES provide insight into the role of chaperones in protein evolution

Protein folding is often hampered by intermolecular protein aggregation, which can be prevented by a variety of chaperones in the cell. Bacterial chaperonin GroEL is a ring-shaped chaperone that forms complexes with its cochaperonin GroES, creating central cavities to accommodate client proteins (also referred as substrate proteins) for folding. GroEL and GroES (GroE) are the only indispensable chaperones for bacterial viability, except for some species of Mollicutes such as Ureaplasma. To understand the role of chaperonins in the cell, one important goal of GroEL research is to identify a group of obligate GroEL/GroES clients. Recent advances revealed hundreds of in vivo GroE interactors and obligate chaperonin-dependent clients. This review summarizes the progress on the in vivo GroE client repertoire and its features, mainly for Escherichia coli GroE. Finally, we discuss the implications of the GroE clients for the chaperone-mediated buffering of protein folding and their influences on protein evolution.

Ureaplasma parvum infection induces inflammatory changes in vaginal epithelial cells independent of sialidase

BACKGROUND

Ureaplasma, a genus of the order Mycoplasmatales and commonly grouped with Mycoplasma as genital mycoplasma is one of the most common microbes isolated from women with infection/inflammation-associated preterm labor (PTL). Mycoplasma spp. produce sialidase that cleaves sialic acid from glycans of vaginal mucous membranes and facilitates adherence and invasion of the epithelium by pathobionts, and dysregulated immune response. However, whether Ureaplasma species can induce the production of sialidase is yet to be demonstrated. We examined U. parvum-infected vaginal epithelial cells (VECs) for the production of sialidase and pro-inflammatory cytokines.

METHODS

Immortalized VECs were cultured in appropriate media and treated with U. parvum in a concentration of 1 × 10⁵ DNA copies/ml. After 24 h of treatment, cells and media were harvested. To confirm infection and cell uptake, immunocytochemistry for multi-banded antigen (MBA) was performed. Pro-inflammatory cytokine production and protein analysis for sialidase confirmed pro-labor pathways.

RESULTS

Infection of VECs was confirmed by the presence of intracellular MBA. Western blot analysis showed no significant increase in sialidase expression from U. parvum-treated VECs compared to uninfected cells. However, U. parvum infection induced 2-3-fold increased production of GM-CSF (p = 0.03), IL-6 (p = 0.01), and IL-8 (p = 0.01) in VECs compared to controls.

CONCLUSION

U. parvum infection of VECs induced inflammatory imbalance associated with vaginal dysbiosis but did not alter sialidase expression at the cellular level. These data suggest that U. parvum's pathogenic effect could be propagated by locally produced pro-inflammatory cytokines and, unlike other genital mycoplasmas, may be independent of sialidase.

DnaJ, a promising vaccine candidate against Ureaplasma urealyticum infection

Abstract

Ureaplasma urealyticum (U. urealyticum, Uu) is a common sexually transmitted pathogen that is responsible for diseases such as non-gonococcal urethritis, chorioamnionitis, and neonatal respiratory diseases. The rapid emergence of multidrug-resistant bacteria threatens the effective treatment of Uu infections. Considering this, vaccination could be an efficacious medical intervention to prevent Uu infection and disease. As a highly conserved molecular chaperone, DnaJ is expressed and upregulated by pathogens soon after infection. Here, we assessed the vaccine potential of recombinant Uu-DnaJ in a mouse model and dendritic cells. Results showed that intramuscular administration of DnaJ induced robust humoral- and T helper (Th) 1 cell-mediated immune responses and protected against genital tract infection, inflammation, and the pathologic sequelae after Uu infection. Importantly, the DnaJ protein also induced the maturation of mouse bone marrow–derived dendritic cells (BMDCs), ultimately promoting naïve T cell differentiation toward the Th1 phenotype. In addition, adoptive immunization of DnaJ-pulsed BMDCs elicited antigen-specific Immunoglobulin G2 (IgG2) antibodies as well as a Th1-biased cellular response in mice. These results support DnaJ as a promising vaccine candidate to control Uu infections.

Key points

• A novel recombinant vaccine was constructed against U. urealyticum infection.

• Antigen-specific humoral and cellular immune responses after DnaJ vaccination.

• Dendritic cells are activated by Uu-DnaJ, which results in a Th1-biased immune response.

Supplementary Information

The online version contains supplementary material available at 10.1007/s00253-022-12230-4.

Cell-in-Cell Phenomena in Wall-Less Bacteria: Is It Possible?

This work describes curious structures formed by the mainly phytopathogenic mycoplasma Acholeplasma laidlawii, as well as the human pathogen Ureaplasma parvum cells which resemble cell-in-cell structures of higher eukaryotes and protists. The probable significance of such structures for the mycoplasma cell is discussed. The possibility of their formation in nature and their potential role in the transformation of genetic material, for example, by maintaining (on the one hand) the stability of the genome in the line of generations during asexual reproduction or (on the other hand) the genome plasticity, are substantiated. It should be especially noted that all the arguments presented are based only on morphological data. However, closer attention to unusual structures, the existence of which was shown by electron microscopy images in this case, may prompt researchers to analyze their data more carefully and find something rare and non-trivial among seemingly trivial things. If it is proven by additional methods that cell-in-cell structures can indeed be formed by prokaryotes without a cell wall, this phenomenon may acquire general biological significance.

Functional Characterization of the Cell Division Gene Cluster of the Wall-less Bacterium Mycoplasma genitalium

It is well-established that FtsZ drives peptidoglycan synthesis at the division site in walled bacteria. However, the function and conservation of FtsZ in wall-less prokaryotes such as mycoplasmas are less clear. In the genome-reduced bacterium Mycoplasma genitalium, the cell division gene cluster is limited to four genes: mraZ, mraW, MG_223, and ftsZ. In a previous study, we demonstrated that ftsZ was dispensable for growth of M. genitalium under laboratory culture conditions. Herein, we show that the entire cell division gene cluster of M. genitalium is non-essential for growth in vitro. Our analyses indicate that loss of the mraZ gene alone is more detrimental for growth of M. genitalium than deletion of ftsZ or the entire cell division gene cluster. Transcriptional analysis revealed a marked upregulation of ftsZ in the mraZ mutant. Stable isotope labeling by amino acids in cell culture (SILAC)-based proteomics confirmed the overexpression of FtsZ in MraZ-deprived cells. Of note, we found that ftsZ expression was upregulated in non-adherent cells of M. genitalium, which arise spontaneously at relatively high rates. Single cell analysis using fluorescent markers showed that FtsZ localization varied throughout the cell cycle of M. genitalium in a coordinated manner with the chromosome and the terminal organelle (TMO). In addition, our results indicate a possible role for the RNA methyltransferase MraW in the regulation of FtsZ expression at the post-transcriptional level. Altogether, this study provides an extensive characterization of the cell division gene cluster of M. genitalium and demonstrates the existence of regulatory elements controlling FtsZ expression at the temporal and spatial level in mycoplasmas.

Ureaplasma diversum clearance in lung mice infection is mediated by neutrophils

Pneumonia in cattle is one of the causes of morbidity rates and economic loss. The host response to lung infections caused by Ureaplasma diversum in bovines is virtually unknown. Here in the immune response was evaluated in a murine model for an experimental pulmonary infection by U. diversum. Therefore, AJ, BALB/C and C57BL/6 mice received intratracheal inoculation of U. diversum and were evaluated after 1, 2, 3, 7 and 14 days and the clinical specimens were collected. In bronchoalveolar lavages (BAL) an increase of inflammatory cells was observed. Neutrophils were the main cells recruited to the site of infection and the infiltration was coincided with the production of pro-inflammatory cytokines. We found a large amount of neutrophil in this initial period, followed by a decrease 7 and 14 days post infection, accompanied by bacterial clearance. Our results evidenced the presence of U. diversum within the neutrophil that suggests a phagocytic role of this cell in the elimination of the infection. The immune response features reported here are the initial evidence that healthy immune systems may control these microorganisms. This may be the first step to design new strategies immune based to control the infections in naturally infected hosts.

GTDB: an integrated resource for glycosyltransferase sequences and annotations

Glycosyltransferases (GTs), a large class of carbohydrate-active enzymes, adds glycosyl moieties to various substrates to generate multiple bioactive compounds, including natural products with pharmaceutical or agrochemical values. Here, we first collected comprehensive information on GTs, including amino acid sequences, coding region sequences, available tertiary structures, protein classification families, catalytic reactions and metabolic pathways. Then, we developed sequence search and molecular docking processes for GTs, resulting in a GTs database (GTDB). In the present study, 520 179 GTs from approximately 21 647 species that involved in 394 kinds of different reactions were deposited in GTDB. GTDB has the following useful features: (i) text search is provided for retrieving the complete details of a query by combining multiple identifiers and data sources; (ii) a convenient browser allows users to browse data by different classifications and download data in batches; (iii) BLAST is offered for searching against pre-defined sequences, which can facilitate the annotation of the biological functions of query GTs; and lastly, (iv) GTdock using AutoDock Vina performs docking simulations of several GTs with the same single acceptor and displays the results based on 3Dmol.js allowing easy view of models.

The Chaperonin GroESL Facilitates Caulobacter crescentus Cell Division by Supporting the Functions of the Z-Ring Regulators FtsA and FzlA

The highly conserved chaperonin GroESL performs a crucial role in protein folding; however, the essential cellular pathways that rely on this chaperone are underexplored. Loss of GroESL leads to severe septation defects in diverse bacteria, suggesting the folding function of GroESL may be integrated with the bacterial cell cycle at the point of cell division. Here, we describe new connections between GroESL and the bacterial cell cycle using the model organism Caulobacter crescentus. Using a proteomics approach, we identify candidate GroESL client proteins that become insoluble or are degraded specifically when GroESL folding is insufficient, revealing several essential proteins that participate in cell division and peptidoglycan biosynthesis. We demonstrate that other cell cycle events, such as DNA replication and chromosome segregation, are able to continue when GroESL folding is insufficient. We further find that deficiency of two FtsZ-interacting proteins, the bacterial actin homologue FtsA and the constriction regulator FzlA, mediate the GroESL-dependent block in cell division. Our data show that sufficient GroESL is required to maintain normal dynamics of the FtsZ scaffold and divisome functionality in C. crescentus. In addition to supporting divisome function, we show that GroESL is required to maintain the flow of peptidoglycan precursors into the growing cell wall. Linking a chaperone to cell division may be a conserved way to coordinate environmental and internal cues that signal when it is safe to divide.

Infection strategies of mycoplasmas: Unraveling the panoply of virulence factors

Mycoplasmas, the smallest bacteria lacking a cell wall, can cause various diseases in both humans and animals. Mycoplasmas harbor a variety of virulence factors that enable them to overcome numerous barriers of entry into the host; using accessory proteins, mycoplasma adhesins can bind to the receptors or extracellular matrix of the host cell. Although the host immune system can eradicate the invading mycoplasma in most cases, a few sagacious mycoplasmas employ a series of invasion and immune escape strategies to ensure their continued survival within their hosts. For instance, capsular polysaccharides are crucial for anti-phagocytosis and immunomodulation. Invasive enzymes degrade reactive oxygen species, neutrophil extracellular traps, and immunoglobulins. Biofilm formation is important for establishing a persistent infection. During proliferation, successfully surviving mycoplasmas generate numerous metabolites, including hydrogen peroxide, ammonia and hydrogen sulfide; or secrete various exotoxins, such as community-acquired respiratory distress syndrome toxin, and hemolysins; and express various pathogenic enzymes, all of which have potent toxic effects on host cells. Furthermore, some inherent components of mycoplasmas, such as lipids, membrane lipoproteins, and even mycoplasma-generated superantigens, can exert a significant pathogenic impact on the host cells or the immune system. In this review, we describe the proposed virulence factors in the toolkit of notorious mycoplasmas to better understand the pathogenic features of these bacteria, along with their pathogenic mechanisms.

Infection Prevalence and Antibiotic Resistance Levels in Ureaplasma urealyticum and Mycoplasma hominis in Gynecological Outpatients of a Tertiary Hospital in China from 2015 to 2018

The aim of this study was to estimate the Ureaplasma urealyticum and Mycoplasma hominis infection prevalence and antibiotic resistance levels in gynecological outpatients. Clinical characteristics and laboratory data of gynecological outpatients of the Fourth People's Hospital of Chongqing from 2015 to 2018 were retrospectively analyzed. Antibiotic resistance levels in U. urealyticum and M. hominis were defined by a commercial Mycoplasma kit for antibiotic susceptibility testing. Univariate analysis and multivariate logistic regression analysis were performed to evaluate risk factors associated with Mycoplasma isolation. Comparisons of yearly distributions and resistance rates were assessed by chi-square tests. Fifty-six percent of gynecological outpatients were positive for U. urealyticum, and 11.02% were positive for M. hominis. In the univariate analysis, women aged 30–39 years or with a history of pregnancy or gynecological diseases had an increased risk for Mycoplasma isolation, while women who were postmenopausal or had an education level of undergraduate degree or above had a decreased risk of Mycoplasma isolation. In the multivariate logistic regression model, an independent risk factor for Mycoplasma isolation was a history of gynecological diseases, while a bachelor's degree, master's degree, or above were protective factors against Mycoplasma isolation. There were distinctly gradual increases in the positivity rates of U. urealyticum and M. hominis from 2015 to 2018 and an overall increasing trend of resistance to ten antibiotics among U. urealyticum and M. hominis. The top three antibiotics associated with resistance were ofloxacin, sparfloxacin, and levofloxacin. Doxycycline, josamycin, and minocycline were preferred because they had the lowest levels of resistance. Increases in the prevalence of infection and antibiotic resistance in U. urealyticum and M. hominis were observed from 2015 to 2018, clearly confirming the necessity to monitor the standardized administration of antibiotics.

Antimicrobial activity of enacyloxin IIa and gladiolin against the urogenital pathogens Neisseria gonorrhoeae and Ureaplasma spp

AIMS

To determine the antimicrobial activity of enacyloxin IIa and gladiolin against Neisseria gonorrhoeae and Ureaplasma spp.

METHODS AND RESULTS

The Burkholderia polyketide antibiotics enacyloxin IIa and gladiolin were tested against 14 N. gonorrhoeae and 10 Ureaplasma spp. isolates including multidrug-resistant N. gonorrhoeae isolates WHO V, WHO X and WHO Z as well as macrolide, tetracycline and ciprofloxacin-resistant ureaplasmas. Susceptibility testing of N. gonorrhoeae was carried out by agar dilution, whereas broth micro-dilution and growth kinetic assays were used for Ureaplasma spp. The MIC range for enacyloxin IIa and gladiolin against N. gonorrhoeae was 0·015-0·06 mg l^-1 and 1-2 mg l^-1 respectively. The presence of resistance to front line antibiotics had no effect on MIC values. The MIC range for enacyloxin IIa against Ureaplasma spp. was 4-32 mg l^-1 with a clear dose-dependent effect when observed using a growth kinetic assay. Gladiolin had no antimicrobial activity on Ureaplasma spp. at 32 mg l^-1 and limited impact on growth kinetics.

CONCLUSIONS

Enacyloxin IIa and gladiolin antibiotics have antimicrobial activity against a range of antibiotic susceptible and resistant N. gonorrhoeae and Ureaplasma isolates.

SIGNIFICANCE AND IMPACT OF THE STUDY

This study highlights the potential for a new class of antimicrobial against pathogens in which limited antibiotics are available. Development of these compounds warrants further investigation in the face of emerging extensively drug-resistant strains.

Codon usage pattern and evolutionary forces of mitochondrial ND genes among orders of class Amphibia

In this study, we used a bioinformatics approach to analyze the nucleotide composition and pattern of synonymous codon usage in mitochondrial ND genes in three amphibian groups, that is, orders Anura, Caudata, and Gymnophiona to identify the commonality and the differences of codon usage as no research work was reported yet. The high value of the effective number of codons revealed that the codon usage bias (CUB) was low in mitochondrial ND genes among the orders. Nucleotide composition analysis suggested that for each gene, the compositional features differed among Anura, Caudata, and Gymnophiona and the GC content was lower than AT content. Furthermore, a highly significant difference (p < .05) for GC content was found in each gene among the orders. The heat map showed contrasting patterns of codon usage among different ND genes. The regression of GC12 on GC3 suggested a narrow range of GC3 distribution and some points were located in the diagonal, indicating both mutation pressure and natural selection might influence the CUB. Moreover, the slope of the regression line was less than 0.5 in all ND genes among orders, indicating natural selection might have played the dominant role whereas mutation pressure had played a minor role in shaping CUB of ND genes across orders.

The complete mitochondrial genome of the lipid-producing yeast Rhodotorula toruloides

Mitochondria are semi-autonomous organelles with their own genome and crucial to cellular material and energy metabolism. Here, we report the complete mitochondrial genome of a lipid-producing basidiomycetous yeast Rhodotorula toruloides NP11. The mitochondrial genome of R. toruloides NP11 was assembled into a circular DNA molecule of 125937bp, encoding 15 proteins, 28 transfer RNAs, 2 ribosomal RNA subunits and 10 open reading frames with unknown function. The G + C content (41%) of the mitochondrial genome is substantially lower than that of the nuclear genome (62%) of R. toruloides NP11. Further reanalysis of the transcriptome data confirmed the transcription of four mitochondrial genes. The comparison of the mitochondrial genomes of R. toruloides NP11 and NBRC0880 revealed a significant genetic divergence. These data can complement our understanding of the genetic background of R. toruloides and provide fundamental information for further genetic engineering of this strain.

GrpE Immunization Protects Against Ureaplasma urealyticum Infection in BALB/C Mice

Nucleotide exchange factor (GrpE), a highly conserved antigen, is rapidly expressed and upregulated when Ureaplasma urealyticum infects a host, which could act as a candidative vaccine if it can induce an anti-U. urealyticum immune reaction. Here, we evaluated the vaccine potential of recombinant GrpE protein adjuvanted by Freund's adjuvant (FA), to protect against U. urealyticum genital tract infection in a mouse model. After booster immunization in mice with FA, the GrpE can induced both humoral and cellular immune response after intramuscular injection into BALB/c mice. A strong humoral immune response was detected in the GrpE-immunized mice characterized by production of high titers of antigen-specific serum IgG (IgG1, IgG2a, and IgG3) antibodies. At the same time, the GrpE also induced a Th1-biased cytokine spectrum with high levels of IFN-γ and TNF-α after re-stimulation with immunogen GrpE in vitro, suggesting that GrpE could trigger the Th1 response when used for vaccination in the presence of FA. Although GrpE vaccination in the presence of a Th1-type adjuvant-induced had readily detectable Th1 responses, there wasn't increase inflammation in response to the infection. More importantly, the robust immune responses in mice after immunization with GrpE showed a significantly reduced U. urealyticum burden in cervical tissues. Histopathological analysis confirmed that tissues of GrpE-immunized BALB/c mice were protected against the pathological effects of U. urealyticum infection. In conclusion, this study preliminarily reveals GrpE protein as a promising new candidate vaccine for preventing U. urealyticum reproductive tract infection.

Mycoplasma and Ureaplasma carriage in pregnant women: the prevalence of transmission from mother to newborn

Background

Mycoplasma and Ureaplasma have been extensively studied for their possible impact on pregnancy, and their involvement in newborn diseases. This work examined Mycoplasma and Ureaplasma carriage among gravidas women and newborns in Israel, as well as associations between carriage and demographic characteristics, risk factors, pregnancy outcomes, and newborn morbidity rates.

Methods

A total of 214 gravidas women were examined for vaginal pathogen carriage through standard culture and polymerase chain reaction assay. Pharyngeal swabs were collected from newborns of carrier mothers. Clinical and demographic data were collected and infected newborn mortality was monitored for 6 months.

Results

Nineteen mothers were carriers, with highest prevalence among younger women. Pathogen carriage rates were 2.32% for Mycoplasma genitalium (Mg), 4.19% for Ureaplasma parvum (Up) and 2.32% for Ureaplasma urealyticum (Uu). Arab ethnicity was a statistically significant risk factor (p = 0.002). A higher prevalence was seen among women residing in cities as compared to villages. Thirteen (68%) newborns born to carrier mothers were carriers as well, with a higher prevalence among newborns of women delivering for the first time, compared to women that had delivered before. Infection rates among newborns were 20% for Mg (p = 0.238), 100% for Up (p < 0.01), and 28.5% for Uu (p = 0.058), with more male than female newborns being infected. No association was found between maternal carriage and newborn morbidity.

Conclusions

Maternal Mycoplasma or Ureaplasma carriage may be associated with ethnicity and settlement type. Further studies will be needed to identify factors underlying these associations and their implications on delivery.

Intra-Amniotic Infection with Ureaplasma parvum Causes Preterm Birth and Neonatal Mortality That Are Prevented by Treatment with Clarithromycin

Preterm birth is the leading cause of neonatal morbidity and mortality worldwide. Multiple etiologies are associated with preterm birth; however, 25% of preterm infants are born to a mother with intra-amniotic infection, most commonly due to invasion of the amniotic cavity by Ureaplasma species. Much research has focused on establishing a link between Ureaplasma species and adverse pregnancy/neonatal outcomes; however, little is known about the taxonomy of and host response against Ureaplasma species. Here, we applied a multifaceted approach, including human samples, in vivo models, and in vitro manipulations, to study the maternal-fetal immunobiology of Ureaplasma infection during pregnancy. Furthermore, we investigated the use of clarithromycin as a treatment for this infection. Our research provides translational knowledge that bolsters scientific understanding of Ureaplasma species as a cause of adverse pregnancy/neonatal outcomes and gives strong evidence for the use of clarithromycin as the recommended treatment for women intra-amniotically infected with Ureaplasma species.

Intra-amniotic infection is strongly associated with adverse pregnancy and neonatal outcomes. Most intra-amniotic infections are due to Ureaplasma species; however, the pathogenic potency of these genital mycoplasmas to induce preterm birth is still controversial. Here, we first laid out a taxonomic characterization of Ureaplasma isolates from women with intra-amniotic infection, which revealed that Ureaplasma parvum is the most common bacterium found in this clinical condition. Next, using animal models, we provided a causal link between intra-amniotic inoculation with Ureaplasma species and preterm birth. Importantly, the intra-amniotic inoculation of Ureaplasma species induced high rates of mortality in both preterm and term neonates. The in vivo potency of U. parvum to induce preterm birth was not associated with known virulence factors. However, term-derived and preterm-derived U. parvum isolates were capable of inducing an intra-amniotic inflammatory response. Both U. parvum isolates invaded several fetal tissues, primarily the fetal lung, and caused fetal inflammatory response syndrome. This bacterium was also detected in the placenta, reproductive tissues, and most severely in the fetal membranes, inducing a local inflammatory response that was replicated in an in vitro model. Importantly, treatment with clarithromycin, a recently recommended yet not widely utilized antibiotic, prevented the adverse pregnancy and neonatal outcomes induced by U. parvum. These findings shed light on the maternal-fetal immunobiology of intra-amniotic infection.

Cell division protein FtsZ: from structure and mechanism to antibiotic target

Antimicrobial resistance to virtually all clinically applied antibiotic classes severely limits the available options to treat bacterial infections. Hence, there is an urgent need to develop and evaluate new antibiotics and targets with resistance-breaking properties. Bacterial cell division has emerged as a new antibiotic target pathway to counteract multidrug-resistant pathogens. New approaches in antibiotic discovery and bacterial cell biology helped to identify compounds that either directly interact with the major cell division protein FtsZ, thereby perturbing the function and dynamics of the cell division machinery, or affect the structural integrity of FtsZ by inducing its degradation. The impressive antimicrobial activities and resistance-breaking properties of certain compounds validate the inhibition of bacterial cell division as a promising strategy for antibiotic intervention.

Ureaplasma species and preterm birth: current perspectives

Preterm birth is the leading cause of neonatal morbidity and mortality worldwide, and the human Ureaplasma species are most frequently isolated from the amniotic fluid and placenta in these cases. Ureaplasma colonisation is associated with infertility, stillbirth, histologic chorioamnionitis, and neonatal morbidities, including congenital pneumonia, bronchopulmonary dysplasia, meningitis and perinatal death. The human Ureaplasma spp. are separated into Ureaplasma urealyticum and Ureaplasma parvum with 14 known serotypes. The small genome has several genes, which code for surface proteins; most significantly the Multiple Banded Antigen (MBA) where an antigenic C-terminal domain elicits a host antibody response. Other genes code for various virulence factors such as IgA protease and urease. Ureaplasma spp. infection is diagnosed by culture and polymerase chain reaction (PCR) and commercial assays are available to improve turnaround time. Microbroth dilution assays are routinely used to test antimicrobial susceptibility of clinical Ureaplasma spp. especially against doxycycline, azithromycin, ofloxacin and josamycin. Resistance to macrolides, fluoroquinolones and tetracyclines has been reported. A concise review of Ureaplasma spp. and their role in pregnancy outcomes, especially preterm birth, offers insight into the early diagnosis and appropriate antibiotic therapy to prevent long-term complications of Ureaplasma spp. infections.

Comparative genomics of three clinical Ureaplasma species: analysis of their core genomes and multiple-banded antigen locus

Aim: To compare the genome sequences among clinical and American-Type Culture Collection Ureaplasma strains and to reveal the potential molecular mechanisms of multiple banded antigen (MBA) variation. Materials & methods: Two strains of Ureaplasma urealyticum 132 and 315 and one strain of Ureaplasma parvum 106 isolated from infertile males were sequenced using Illumina and Nanopore technologies. Comparative genomic analysis was performed of the three strains and two American-Type Culture Collection strains. Results & conclusion: The Ureaplasma species shared a core genome. Strains 132 and 315 shared a distant relationship with previously sequenced Ureaplasma spp. The MBA locus is more informative for studying MBA mutations than is the mba gene alone. The mechanisms of MBA variation are more flexible and complex than previously reported. The variation in MBA is not limited to the mba gene but occurs in other genes within the MBA locus.

Genomic Characterization of a Novel Gut Symbiont From the Hadal Snailfish

Hadal trenches are characterized by not only high hydrostatic pressure but also scarcity of nutrients and high diversity of viruses. Snailfishes, as the dominant vertebrates, play an important role in hadal ecology. Although studies have suggested possible reasons for the tolerance of hadal snailfish to high hydrostatic pressure, little is known about the strategies employed by hadal snailfish to cope with low-nutrient and virus-rich conditions. In this study, the gut microbiota of hadal snailfish was investigated. A novel bacterium named "Candidatus Mycoplasma liparidae" was dominant in the guts of three snailfish individuals from both the Mariana and Yap trenches. A draft genome of "Ca. Mycoplasma liparidae" was successfully assembled with 97.8% completeness by hybrid sequencing. A set of genes encoding riboflavin biosynthesis proteins and a clustered regularly interspaced short palindromic repeats (CRISPR) system was present in the genome of "Ca. Mycoplasma liparidae," which was unusual for Mycoplasma. The functional repertoire of the "Ca. Mycoplasma liparidae" genome is likely set to help the host in riboflavin supplementation and to provide protection against viruses via a super CRISPR system. Remarkably, genes encoding common virulence factors usually exist in Tenericutes pathogens but were lacking in the genome of "Ca. Mycoplasma liparidae." All of these characteristics supported an essential role of "Ca. Mycoplasma liparidae" in snailfish living in the hadal zone. Our findings provide further insights into symbiotic associations in the hadal biosphere.

Differential cytokine and metabolite production by cervicovaginal epithelial cells infected with Lactobacillus crispatus and Ureaplasma urealyticum

INTRODUCTION

We sought to quantify targeted metabolites (d-lactate, pyruvate, urea, ammonia) and the cytokine IL-8 produced by human cervicovaginal epithelial cells co-cultured with Ureaplasma urealyticum (a preterm birth-associated bacterium) or Lactobacillus crispatus (a healthy vaginal commensal associated with term birth).

METHODS

Concentrations of d-lactate, pyruvate, urea and ammonia measured by enzyme-based spectrophotometry and IL-8 by ELISA were determined and compared between monolayer-cultured HeLa cells (ATCC 35241) infected with strains of U. urealyticum (ATCC 27618, 0.5 mL = 3640 CFU/mL, U. urealyticum) or L. crispatus (ATCC 33820, MOI = 10,000, 1000 and 100, L. crispatus) and incubated in 5% CO₂ at 37 °C for 24 h. Uninfected HeLa cells (Hc) were used as controls and cytotoxicity was determined by the amount (optical density) of lactate dehydrogenase (LDH) released by the dead HeLa cells.

RESULTS

The amount of LDH released by untreated Hc (P = 0.002) and U. urealyticum-infected cells (P < 0.0001) was higher than those of L. crispatus-infected cells, with U. urealyticum-infected cells recording the highest % cytotoxicity and L. crispatus-infected cells MOI 10,000 (Lc10,000) the least (P < 0.0001). Though there was no significant difference in the concentration of urea between the samples, U. urealyticum-infected cells showed higher ammonia compared to other samples (p = 0.03). In contrast, all L. crispatus samples had higher d-lactate than untreated Hc (p = 0.01) and U. urealyticum-infected cells (P = 0.01). Also, Lc10,000 had the highest d-lactate (p = 0.001) and lowest pyruvate (P = 0.04, excluding UU) compared to other samples. Furthermore, U. urealyticum-infected cells produced the highest IL-8 (P = 0.01) compared to other samples, with Lc10,000 producing undetectable levels.

CONCLUSION

Infection of cervicovaginal epithelial cells by U. urealyticum stimulates production of ammonia from urea and induces elevated IL-8 production possibly leading to significantly higher cytotoxicity. In contrast, L. crispatus appeared protective against HeLa cell inflammation and death, producing more d-lactate and less IL-8, consistent with a role for L. crispatus in promoting vaginal floral health and reducing infection/inflammation-associated preterm birth.

Comparative genomic analyses of Mycoplasma synoviae vaccine strain MS-H and its wild-type parent strain 86079/7NS: implications for the identification of virulence factors and applications in diagnosis of M. synoviae

Mycoplasma synoviae is an economically important avian pathogen worldwide, causing respiratory disease, infectious synovitis, airsacculitis and eggshell apex abnormalities in commercial chickens. Despite the widespread use of MS-H as a live attenuated vaccine over the past two decades, the precise molecular basis for loss of virulence in this vaccine is not yet fully understood. To address this, the whole genome sequence of the vaccine parent strain, 86079/7NS, was obtained and compared to that of the MS-H vaccine. Except for the vlhA expressed region, both genomes were nearly identical. Thirty-two single nucleotide polymorphisms (SNPs) were identified in MS-H, including 11 non-synonymous mutations that were predicted, by bioinformatics analysis, to have changed the secondary structure of the deduced proteins. One of these mutations caused truncation of the oppF-1 gene, which encodes the ATP-binding protein of an oligopeptide permease transporter. Overall, the attenuation of MS-H strain may be caused by the cumulative and complex effects of several mutations. The SNPs identified in MS-H were further analyzed by comparing the MS-H and 86079/7NS sequences with the strains WVU-1853 and MS53. In the genomic regions conserved between all strains, 30 SNPs were found to be unique to MS-H lineage. These results have provided a foundation for developing novel biomarkers for the detection of virulence in M. synoviae and also for designing new genotyping assays for discrimination of MS-H from field strains.

The Role of Ureaplasma spp. in the Development of Nongonococcal Urethritis and Infertility among Men

Ureaplasma spp. are a genus of bacteria for which two human-associated species exist: Ureaplasma urealyticum and Ureaplasma parvum Their definition as a pathogen in the context of nongonococcal urethritis (NGU) and infertility among males remains highly controversial, largely due to historically high rates of isolation of these bacteria from the urethra of seemingly healthy men. This review summarizes the emerging evidence suggesting a true pathogenic role of these bacteria under specific conditions, which we term risk factors. We examine the historical, clinical, and experimental studies which support a causal role for Ureaplasma spp. in the development of NGU as well as some of the proposed mechanisms behind the association of Ureaplasma spp. and the development of infertility. Finally, we discuss the potential for developing a case-by-case risk-based approach toward the management of men who present with seemingly idiopathic NGU but who are positive for Ureaplasma spp.

Emerging role for Ureaplasma parvum serovar 3: Active infection in women with silent high-risk human papillomavirus and in women with idiopathic infertility

Recently, there are controversial opinions on the presence of Mycoplasmas/Ureaplasmas as colonizers or pathogens, and on the use of a targeted therapy. This study aimed to characterize Mycoplasmas/Ureaplasmas infections in reproductive age women, including the acquisition of sexually transmitted (ST) pathogens and poor birth outcomes. A total of 646 healthy Italian women fulfilled the inclusion criteria including 521 infertile women, 65 pregnant women, and 60 fertile women with identified risk factors and symptomatic for vaginitis/cervicitis. Multiplex and quantitative molecular techniques and direct automatic DNA sequencing were performed to assess the genome structure of Mycoplasma/Ureaplasma species and ST infected pathogens. Ureaplasma parvum serovar 3 represented the predominant colonizer of the urogenital tract of this series and the unique species significantly associated with ST pathogens coinfection (p < 0.01). U. parvum load >10⁴ bacteria/ml, suggestive of active infection, has been measured only in asymptomatic high-risk human papillomavirus infected women (24.3%) and in 40% of women with idiopathic infertility. To note, 16% of the follicular fluid from these idiopathic women resulted infected with U. parvum. In conclusion, the present study focused the attention on U. parvum serovar 3 as emerging microorganism in sexually active women that may have the benefit of targeted therapy.

Genomic Signatures Among Acanthamoeba polyphaga Entoorganisms Unveil Evidence of Coevolution

The definition of a genomic signature (GS) is "the total net response to selective pressure". Recent isolation and sequencing of naturally occurring organisms, hereby named entoorganisms, within Acanthamoeba polyphaga, raised the hypothesis of a common genomic signature despite their diverse and unrelated evolutionary origin. Widely accepted and implemented tests for GS detection are oligonucleotide relative frequencies (OnRF) and relative codon usage (RCU) surveys. A common pattern and strong correlations were unveiled from OnRFs among A. polyphaga's Mimivirus and virophage Sputnik. RCU showed a common A-T bias at third codon position. We expanded tests to the amoebal mitochondrial genome and amoeba-resistant bacteria, achieving strikingly coherent results to the aforementioned viral analyses. The GSs in these entoorganisms of diverse evolutionary origin are coevolutionarily conserved within an intracellular environment that provides sanctuary for species of ecological and biomedical relevance.

Type II restriction modification system in Ureaplasma parvum OMC-P162 strain

Ureaplasma parvum serovar 3 strain, OMC-P162, was isolated from the human placenta of a preterm delivery at 26 weeks’ gestation. In this study, we sequenced the complete genome of OMC-P162 and compared it with other serovar 3 strains isolated from patients with different clinical conditions. Ten unique genes in OMC-P162, five of which encoded for hypothetical proteins, were identified. Of these, genes UPV_229 and UPV_230 formed an operon whose open reading frames were predicted to code for a DNA methyltransferase and a hypothetical protein, respectively. DNA modification analysis of the OMC-P162 genome identified N4-methylcytosine (m4C) and N6-methyladenine (m6A), but not 5-methylocytosine (m5C). UPV230 recombinant protein displayed endonuclease activity and recognized the CATG sequence, resulting in a blunt cut between A and T. This restriction enzyme activity was identical to that of the cultivated OMC-P162 strain, suggesting that this restriction enzyme was naturally expressed in OMC-P162. We designated this enzyme as UpaP162. Treatment of pT7Blue plasmid with recombinant protein UPV229 completely blocked UpaP162 restriction enzyme activity. These results suggest that the UPV_229 and UPV_230 genes act as a type II restriction-modification system in Ureaplasma OMC-P162.

Comparative Analyses of the Digestive Tract Microbiota of New Guinean Passerine Birds

The digestive tract microbiota (DTM) plays a plethora of functions that enable hosts to exploit novel niches. However, our understanding of the DTM of birds, particularly passerines, and the turnover of microbial communities along the digestive tract are limited. To better understand how passerine DTMs are assembled, and how the composition changes along the digestive tract, we investigated the DTM of seven different compartments along the digestive tract of nine New Guinean passerine bird species using Illumina MiSeq sequencing of the V4 region of the 16S rRNA. Overall, passerine DTMs were dominated by the phyla Firmicutes and Proteobacteria. We found bird species-specific DTM assemblages and the DTM of different compartments from the same species tended to cluster together. We also found a notable relationship between gut community similarity and feeding guilds (insectivores vs. omnivores). The dominant bacterial genera tended to differ between insectivores and omnivores, with insectivores mainly having lactic acid bacteria that may contribute to the breakdown of carbohydrates. Omnivorous DTMs were more diverse than insectivores and dominated by the bacterial phyla Proteobacteria and Tenericutes. These bacteria may contribute to nitrogen metabolism, and the diverse omnivorous DTMs may allow for more flexibility with varying food availability as these species have wider feeding niches. In well-sampled omnivorous species, the dominant bacterial genera changed along the digestive tracts, which was less prominent for insectivores. In conclusion, the DTMs of New Guinean passerines seem to be species specific and, at least in part, be shaped by bird diet. The sampling of DTM along the digestive tract improved capturing of a more complete set of members, with implications for our understanding of the interactions between symbiont and gut compartment functions.

Infection-induced thrombin production: a potential novel mechanism for preterm premature rupture of membranes (PPROM)

BACKGROUND

Preterm premature rupture of membranes is a leading contributor to maternal and neonatal morbidity and death. Epidemiologic and experimental studies have demonstrated that thrombin causes fetal membrane weakening and subsequently preterm premature rupture of membranes. Although blood is suspected to be the likely source of thrombin in fetal membranes and amniotic fluid of patients with preterm premature rupture of membranes, this has not been proved. Ureaplasma parvum is emerging as a pathogen involved in prematurity, which includes preterm premature rupture of membranes; however, until now, prothrombin production that has been induced directly by bacteria in fetal membranes has not been described.

OBJECTIVE

This study was designed to investigate whether Ureaplasma parvum exposure can induce prothrombin production in fetal membranes cells.

STUDY DESIGN

Primary fetal membrane cells (amnion epithelial, chorion trophoblast, and decidua stromal) or full-thickness fetal membrane tissue explants from elective, term, uncomplicated cesarean deliveries were harvested. Cells or tissue explants were infected with live Ureaplasma parvum (1×10⁵, 1×10⁶ or 1×10⁷ colony-forming units per milliliter) or lipopolysaccharide (Escherichia coli J5, L-5014; Sigma Chemical Company, St. Louis, MO; 100 ng/mL or 1000 ng/mL) for 24 hours. Tissue explants were fixed for immunohistochemistry staining of thrombin/prothrombin. Fetal membrane cells were fixed for confocal immunofluorescent staining of the biomarkers of fetal membrane cell types and thrombin/prothrombin. Protein and messenger RNA were harvested from the cells and tissue explants for Western blot or quantitative reverse transcription polymerase chain reaction to quantify thrombin/prothrombin protein or messenger RNA production, respectively. Data are presented as mean values ± standard errors of mean. Data were analyzed using 1-way analysis of variance with post hoc Dunnett's test.

RESULTS

Prothrombin production and localization were confirmed by Western blot and immunostainings in all primary fetal membrane cells and tissue explants. Immunofluorescence observations revealed a perinuclear localization of prothrombin in amnion epithelial cells. Localization of prothrombin in chorion and decidua cells was perinuclear and cytoplasmic. Prothrombin messenger RNA and protein expression in fetal membranes were increased significantly by Ureaplasma parvum, but not lipopolysaccharide, treatments in a dose-dependent manner. Specifically, Ureaplasma parvum at a dose of 1×10⁷ colony-forming units/mL significantly increased both prothrombin messenger RNA (fold changes in amnion: 4.1±1.9; chorion: 5.7±4.2; decidua: 10.0±5.4; fetal membrane: 9.2±3.0) and protein expression (fold changes in amnion: 138.0±44.0; chorion: 139.6±15.1; decidua: 56.9±29.1; fetal membrane: 133.1±40.0) compared with untreated control subjects. Ureaplasma parvum at a dose of 1×10⁶ colony-forming units/mL significantly up-regulated prothrombin protein expression in chorion cells (fold change: 54.9±5.3) and prothrombin messenger RNA expression in decidua cells (fold change: 4.4±1.9).

CONCLUSION

Our results demonstrate that prothrombin can be produced directly by fetal membrane amnion, chorion, and decidua cells. Further, prothrombin production can be stimulated by Ureaplasma parvum exposure in fetal membranes. These findings represent a potential novel underlying mechanism of Ureaplasma parvum-induced rupture of fetal membranes.

Biochanin A partially restores the activity of ofloxacin and ciprofloxacin against topoisomerase IV mutation-associated fluoroquinolone-resistant Ureaplasma species

PURPOSE

This study aims to investigate the synergistic antimicrobial activity of four phytoalexins in combination with fluoroquinolones against Ureaplasma spp., a genus of cell wall-free bacteria that are intrinsically resistant to many available antibiotics, making treatment inherently difficult.

METHODOLOGY

A total of 22 958 urogenital tract specimens were assessed for Ureaplasma spp. identification and antimicrobial susceptibility. From these, 31 epidemiologically unrelated strains were randomly selected for antimicrobial susceptibility testing to determine the minimum inhibitory concentration (MIC) of four fluoroquinolones and the corresponding quinolone resistance-determining regions (QRDRs). Synergistic effects between fluoroquinolones and four phytoalexins (reserpine, piperine, carvacrol and biochanin A) were evaluated by fractional inhibitory concentration indices (FICIs).

RESULTS

Analysis of the QRDRs suggested a vital role for the mutation of Ser-83→Leu in ParC in fluoroquinolone-resistant strains, and the occurrence of mutations in QRDRs showed significant associations with the breakpoint of levofloxacin. Moreover, diverse synergistic effects of the four phytoalexins with ofloxacin or ciprofloxacin were observed and biochanin A was able to enhance the antimicrobial activity of fluoroquinolones significantly.

CONCLUSION

This is the first report of the antimicrobial activity of biochanin A in combination with fluoroquinolones against a pathogenic mycoplasma, and opens up the possibility of using components of biochanin A as a promising therapeutic option for treating antibiotic-resistant Ureaplasma spp. infections.

Cytological Features Associated with Ureaplasma Urealyticum in Pap Cervical Smear

Purpose: Ureaplasma urealyticum is associated with several obstetric complications and increases the importance of risk management in pregnant women. Furthermore, U. urealyticum has been identified as a cofactor that interacts with human papillomavirus infection in cervical cancer onset. The aim of this study was to assess specific cytological features of U. urealyticum infection in Pap smears to determine whether additional microbiological testing should be performed for pregnant women with a high possibility of U. urealyticum infection. Methods: Liquid-based cytology specimens (LBC) from cervical swabs of a total of 55 women, including 33 pregnant women who were negative for intraepithelial lesion or malignancy (NILM) on Pap testing and with U. urealyticum diagnosed without any other infectious microbes and 22 U. urealyticum-negative controls, were used in this study. We evaluated the localization of U. urealyticum by immunofluorescence, cytological features of secondary changes in squamous cells caused by inflammation, and the specimen background in Pap smears. Results: Based on analysis of Pap smears, a significant relationship was observed between U. urealyticum infection and cannonballs (p < 0.05) as well as predominance of coccoid bacteria (p < 0.05). A large number of U. urealyticum were detected in cannonballs by immunofluorescence. Conclusion: In the present study, cytological features in Pap smears of U. urealyticum infected samples, which have hardly been understood thus far, were assessed. The cytological features included cannonballs and predominance of coccoid bacteria. Our results might help in determining whether additional microbiological testing should be performed for pregnant women with a high possibility of U. urealyticum infection.

Limitations of a metabolic network-based reverse ecology method for inferring host-pathogen interactions

Background

Host–pathogen interactions are important in a wide range of research fields. Given the importance of metabolic crosstalk between hosts and pathogens, a metabolic network-based reverse ecology method was proposed to infer these interactions. However, the validity of this method remains unclear because of the various explanations presented and the influence of potentially confounding factors that have thus far been neglected.

Results

We re-evaluated the importance of the reverse ecology method for evaluating host–pathogen interactions while statistically controlling for confounding effects using oxygen requirement, genome, metabolic network, and phylogeny data. Our data analyses showed that host–pathogen interactions were more strongly influenced by genome size, primary network parameters (e.g., number of edges), oxygen requirement, and phylogeny than the reserve ecology-based measures.

Conclusion

These results indicate the limitations of the reverse ecology method; however, they do not discount the importance of adopting reverse ecology approaches altogether. Rather, we highlight the need for developing more suitable methods for inferring host–pathogen interactions and conducting more careful examinations of the relationships between metabolic networks and host–pathogen interactions.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-017-1696-7) contains supplementary material, which is available to authorized users.

Coupling de novo protein folding with subunit exchange into pre-formed oligomeric protein complexes: the 'heritable template' hypothesis

Despite remarkable advances in synthetic biology, the fact remains that it takes a living cell to make a new living cell. The information encoded in the genome is necessary to direct assembly of all cellular components, but it may not be sufficient. Some components (e.g. mitochondria) cannot be synthesized de novo, and instead require pre-existing templates, creating a fundamental continuity of life: if the template information is ever lost, the genomic code cannot suffice to ensure proper biogenesis. One type of information only incompletely encoded in the genome is the structures of macromolecular assemblies, which emerge from the conformations of the constituent molecules coupled with the ways in which these molecules interact. For many, if not most proteins, gene sequence is not the sole determinant of native conformation, particularly in the crowded cellular milieu. A partial solution to this problem lies in the functions of molecular chaperones, encoded by nearly all cellular genomes. Chaperones effectively restrict the ensemble of conformations sampled by polypeptides, promoting the acquisition of native, functional forms, but multiple proteins have evolved ways to achieve chaperone independence, perhaps by coupling folding with higher-order assembly. Here, I propose the existence of another solution: a novel mechanism of de novo folding in which the folding of specific proteins is templated by pre-folded molecules of a partner protein whose own folding also required similar templating. This hypothesis challenges prevailing paradigms by predicting that, in order to achieve a functional fold, some non-prion proteins require a seed passed down through generations.

The Human Ureaplasma Species as Causative Agents of Chorioamnionitis

The human Ureaplasma species are the most frequently isolated microorganisms from the amniotic fluid and placentae of women who deliver preterm and are also associated with spontaneous abortions or miscarriages, neonatal respiratory diseases, and chorioamnionitis. Despite the fact that these microorganisms have been habitually found within placentae of pregnancies with chorioamnionitis, the role of Ureaplasma species as a causative agent has not been satisfactorily explained. There is also controversy surrounding their role in disease, particularly as not all women infected with Ureaplasma spp. develop chorioamnionitis. In this review, we provide evidence that Ureaplasma spp. are associated with diseases of pregnancy and discuss recent findings which demonstrate that Ureaplasma spp. are associated with chorioamnionitis, regardless of gestational age at the time of delivery. Here, we also discuss the proposed major virulence factors of Ureaplasma spp., with a focus on the multiple-banded antigen (MBA), which may facilitate modulation/alteration of the host immune response and potentially explain why only subpopulations of infected women experience adverse pregnancy outcomes. The information presented within this review confirms that Ureaplasma spp. are not simply "innocent bystanders" in disease and highlights that these microorganisms are an often underestimated pathogen of pregnancy.

Ureaplasma diversum Genome Provides New Insights about the Interaction of the Surface Molecules of This Bacterium with the Host

Whole genome sequencing and analyses of Ureaplasma diversum ATCC 49782 was undertaken as a step towards understanding U. diversum biology and pathogenicity. The complete genome showed 973,501 bp in a single circular chromosome, with 28.2% of G+C content. A total of 782 coding DNA sequences (CDSs), and 6 rRNA and 32 tRNA genes were predicted and annotated. The metabolic pathways are identical to other human ureaplasmas, including the production of ATP via hydrolysis of the urea. Genes related to pathogenicity, such as urease, phospholipase, hemolysin, and a Mycoplasma Ig binding protein (MIB)-Mycoplasma Ig protease (MIP) system were identified. More interestingly, a large number of genes (n = 40) encoding surface molecules were annotated in the genome (lipoproteins, multiple-banded antigen like protein, membrane nuclease lipoprotein and variable surface antigens lipoprotein). In addition, a gene encoding glycosyltransferase was also found. This enzyme has been associated with the production of capsule in mycoplasmas and ureaplasma. We then sought to detect the presence of a capsule in this organism. A polysaccharide capsule from 11 to 17 nm of U. diversum was observed trough electron microscopy and using specific dyes. This structure contained arabinose, xylose, mannose, galactose and glucose. In order to understand the inflammatory response against these surface molecules, we evaluated the response of murine macrophages J774 against viable and non-viable U. diversum. As with viable bacteria, non-viable bacteria were capable of promoting a significant inflammatory response by activation of Toll like receptor 2 (TLR2), indicating that surface molecules are important for the activation of inflammatory response. Furthermore, a cascade of genes related to the inflammasome pathway of macrophages was also up-regulated during infection with viable organisms when compared to non-infected cells. In conclusion, U. diversum has a typical ureaplasma genome and metabolism, and its surface molecules, including the identified capsular material, represent major components of the organism immunopathogenesis.

Mollicutes/HIV Coinfection and the Development of AIDS: Still Far from a Definitive Response

Background. Mycoplasmas are known to cause various infections in humans, mainly in the respiratory and urogenital tracts. The different species are usually host-specific and cause diseases in well-defined sites. New species have been isolated, including those from HIV-infected persons. Summary. Its in vitro properties, combined with clinical findings, have led to the hypothesis that these microorganisms may act as cofactors of HIV in AIDS development. Even today this point of view is quite polemic among infectious disease specialists and many aspects remain to be clarified, in contrast to what happens, for instance, with HIV/Mycobacterium tuberculosis coinfection. Dozens of papers have been published covering aspects of Mollicutes/HIV coinfection, but they add little to no information about the putative contribution of Mollicutes to the evolution of AIDS. Very few researchers have devoted their efforts to trying to answer this question, which remains open. In this review, we discuss the evidences that may support this statement in the light of current knowledge in the field of mycoplasmology.

Molecular biology of mycoplasmas: from the minimum cell concept to the artificial cell

ABSTRACT Mycoplasmas are a large group of bacteria, sorted into different genera in the Mollicutes class, whose main characteristic in common, besides the small genome, is the absence of cell wall. They are considered cellular and molecular biology study models. We present an updated review of the molecular biology of these model microorganisms and the development of replicative vectors for the transformation of mycoplasmas. Synthetic biology studies inspired by these pioneering works became possible and won the attention of the mainstream media. For the first time, an artificial genome was synthesized (a minimal genome produced from consensus sequences obtained from mycoplasmas). For the first time, a functional artificial cell has been constructed by introducing a genome completely synthesized within a cell envelope of a mycoplasma obtained by transformation techniques. Therefore, this article offers an updated insight to the state of the art of these peculiar organisms' molecular biology.

Performance of the Sysmex UF-1000i urine analyser in the rapid diagnosis of urinary tract infections in hospitalized patients

BACKGROUND

Urinary tract infections (UTIs) are the second most frequently encountered nosocomial infectious diseases, and they greatly increase the cost of medical care and prolong the duration of hospital stays.

AIM

We aimed to evaluate the performance of the Sysmex UF-1000i analyser for the rapid prediction of UTIs in hospitalized patients with or without indwelling catheters at a comprehensive teaching hospital that encounters complex disease types.

METHODS

Urine specimens (n = 1016) were cultured and examined for WBC, RBC, bacteria (BACT) and yeast-like cell (YLC) count using the Sysmex UF-1000i. The results were compared with the urine culture results. Receiver operating characteristic curve analysis was applied to determine BACT and YLC cutoff values for bacterial and fungal UTIs independently. The diagnostic ability of the UF-1000i was also compared for patients with and without indwelling catheters.

FINDINGS

A cutoff value of 38.7/μL was acceptable for ruling out bacterial UTIs. In this setting, we achieved a sensitivity of 90%, a negative predictive value of 94.5%, a false negative rate of 2.85% (29 cases), and avoided culturing in 52% of the samples. The BACT count presented a larger area under the curve for patients with indwelling catheters than for those without (0.939 vs. 0.861); however, no significant difference in the diagnostic ability of the two curves was found.

CONCLUSION

The Sysmex UF-1000i analyser could be a reliable method for excluding bacterial UTIs in hospitalized patients with or without urinary catheters and could help clinicians determine whether antibiotic therapy is necessary.

Intra-uterine experimental infection by Ureaplasma diversum induces TNF-α mediated womb inflammation in mice

Ureaplasma diversum is an opportunistic pathogen associated with uterine inflammation, impaired embryo implantation, infertility, abortions, premature birth of calves and neonatal pneumonia in cattle. It has been suggested that the intra-uterine infection by Ureaplasma diversum can cause vascular changes that hinder the success of pregnancy. Thus, the aim of this study was to evaluate the changes of intrauterine site of A/J mice in estrus or proestrus phase inoculated with Ureaplasma diversum. The infection was monitored at 24, 48 and 72 hours by the PCR methodology to detect the Ureaplasma in the inoculation site and the profile of circulating blood cells. Morphological changes, intensity of inflammation and the production of cytokines were compared. The infected mice showed local inflammation through the production of IFN-γ and TNF-α. Ureaplasma diversum infections in the reproductive tract of studied mice seemed to be associated with the production of pro-inflammatory cytokines in uterine parenchyma. The levels of TNF-α of infected mice were dependent on the bacterial load of inoculated Ureaplasma. Uterine experimental infections by Ureaplasma diversum have not been mentioned yet and herein we presented the first report of an intrauterine infection model in mice.

Ureaplasma: current perspectives

Ureaplasma species are the most prevalent genital Mycoplasma isolated from the urogenital tract of both men and women. Ureaplasma has 14 known serotypes and is divided into two biovars- Ureaplasma parvum and Ureaplasma urealyticum. The organism has several genes coding for surface proteins, the most important being the gene encoding the Multiple Banded Antigen (MBA). The C-terminal domain of MBA is antigenic and elicits a host antibody response. Other virulence factors include phospholipases A and C, IgA protease and urease. Besides genital tract infections and infertility, Ureaplasma is also associated with adverse pregnancy outcomes and diseases in the newborn (chronic lung disease and retinopathy of prematurity). Infection produces cytokines in the amniotic fluid which initiates preterm labour. They have also been reported from renal stone and suppurative arthritis. Genital infections have also been reported with an increasing frequency in HIV-infected patients. Ureaplasma may be a candidate 'co factor' in the pathogenesis of AIDS. Culture and polymerase chain reaction (PCR) are the mainstay of diagnosis. Commercial assays are available with improved turnaround time. Micro broth dilution is routinely used to test antimicrobial susceptibility of isolates. The organisms are tested against azithromycin, josamycin, ofloxacin and doxycycline. Resistance to macrolides, tetracyclines and fluoroquinolones have been reported. The susceptibility pattern also varies among the biovars with biovar 2 maintaining higher sensitivity rates. Prompt diagnosis and initiation of appropriate antibiotic therapy is essential to prevent long term complications of Ureaplasma infections. After surveying PubMed literature using the terms 'Ureaplasma', 'Ureaplasma urealyticum' and 'Ureaplasma parvum', relevant literature were selected to provide a concise review on the recent developments.