Phenotypic profile of priority multiresistant Аcinetobacter baumannii sequence types (ST 1167, ST 944, ST 208)

Introduction. About 1,000,000 cases of infections caused by Acinetobacter spp. per year are registered globally, making up 1.8% of all the cases of hospital-acquired infections. In compliance with long-term studies carried out in in this country and abroad, Acinetobacter baumannii is a clinically important representative of the Acinetobacter genus. Intraspecific typing of microorganisms is an integral part of a clinical microbiologist's contribution to scoring the outbreaks of purulent-septic infections within the sphere of HAI surveillance. Most of the practicing microbiological laboratories cannot use genotypic typing methods because of their high costs.Objective. Developing a test panel for intraspecific identification of A. baumannii sequence types (ST 1167, ST 944, ST 208) based on their phenotypic properties.Materials and methods. Intraspecific membership of 74 A. baumannii strains obtained from four multipurpose health settings of a large industrial centre was studied using a genetic method (multilocus sequence typing) and a suite of phenotypic methods (biochemical tests, biofilmogenous capacity, growth inhibition zones to antibacterial drugs, sensitivity to aniline dyes, disinfectants and Acinetobacter bacteriophage) was studied.Results. Phenotypic features of three predominant A. baumannii sequence types (ST 1167, 944, 208) were determined.Discussion. An efficacious economy set of differentiating tests allowing identification of intraspecific features of A. baumannii multiresistant strains was сreated.Conclusion. The test panel will enable the laboratories that cannot use sequencing methods to conduct intraspecific differentiation of common A. baumannii sequence types as part of microbiological monitoring.

Assessment of the microbial status of internal environment objects in second cleanliness class health care facilities

Objective. To assess internal environment objects ofsecond cleanliness class health care facilities according to microbiological standards.Materials and methods. The methods of swabbing, direct seeding, membrane filtration and instrumental aspiration were used for sampling. The microbial status was analyzed by cultural and biochemical methods on nutrient, differential and diagnostic media with species identification using the microbiological analyzer. The phenotypic features were studied in vitro by the standard biochemical and microbiological methods in accordance with the principles of good laboratory practice.Results. The microbiological testing of indoor air and internal environment objects of second cleanliness class health care facilities (dental offices) was done to determine the qualitative and quantitative composition of the microbiota. As a result of the taxonomic identification, it has been found that the most common representatives of the air microbiota are Staphylococcus, Micrococcus and Kocuria bacteria, which are true residents of the human dermis.Conclusion. The obtained data provide material for the study of the phenomenon of the modification of phenotypic properties and its use at the stages of hazard detection and profiling and for the minimization of uncertainty within the concept of microbial risk analysis.

Pseudodesulfovibrio sediminis sp. nov., a Mesophilic and Neutrophilic Sulfate-reducing Bacterium Isolated From Sediment of a Brackish Lake

A novel mesophilic and neutrophilic sulfate-reducing bacterium, strain SF6T, was isolated from sediment of a brackish lake in Japan. Cells of strain SF6T were motile and rod-shaped with length of 1.2–2.5 μm and width of 0.6–0.9 μm. Growth was observed at 10–37°C with an optimum growth temperature of 28°C. The pH range for growth was 5.8–8.2 with an optimum pH of 7.0. The most predominant fatty acid was anteiso-C15 : 0. Under sulfate-reducing conditions, strain SF6T utilized formate, lactate, ethanol and glucose as growth substrate. Chemolithoautotrophic growth on H2 was also observed. Fermentative growth occurred on pyruvate. As electron acceptor, sulfate, sulfite, thiosulfate and nitrate supported heterotrophic growth of the strain. The complete genome of strain SF6T is composed of a circular chromosome with length of 3.8 Mbp and G + C content of 54 mol%. Analyses of the 16S rRNA gene and whole genome sequence indicated that strain SF6T belongs to the genus Pseudodesulfovibrio but distinct form all existing species in the genus. On the basis of its genomic and phenotypic properties, strain SF6T (= DSM111931T = NBRC 114895T) is proposed as the type strain of a new species, with name of Pseudodesulfovibrio sediminis sp. nov.

Plasmonic Biosensors for the Detection of Lung Cancer Biomarkers: A Review

Lung cancer is the most common and deadliest cancer type globally. Its early diagnosis can guarantee a five-year survival rate. Unfortunately, application of the available diagnosis methods such as computed tomography, chest radiograph, magnetic resonance imaging (MRI), ultrasound, low-dose CT scan, bone scans, positron emission tomography (PET), and biopsy is hindered due to one or more problems, such as phenotypic properties of tumours that prevent early detection, invasiveness, expensiveness, and time consumption. Detection of lung cancer biomarkers using a biosensor is reported to solve the problems. Among biosensors, optical biosensors attract greater attention due to being ultra-sensitive, free from electromagnetic interference, capable of wide dynamic range detection, free from the requirement of a reference electrode, free from electrical hazards, highly stable, capable of multiplexing detection, and having the potential for more information content than electrical transducers. Inspired by promising features of plasmonic sensors, including surface plasmon resonance (SPR), localised surface plasmon resonance (LSPR), and surface enhanced Raman scattering (SERS) such as ultra-sensitivity, single particle/molecular level detection capability, multiplexing capability, photostability, real-time measurement, label-free measurement, room temperature operation, naked-eye readability, and the ease of miniaturisation without sophisticated sensor chip fabrication and instrumentation, numerous plasmonic sensors for the detection of lung cancer biomarkers have been investigated. In this review, the principle plasmonic sensor is explained. In addition, novel strategies and modifications adopted for the detection of lung cancer biomarkers such as miRNA, carcinoembryonic antigen (CEA), cytokeratins, and volatile organic compounds (VOCs) using plasmonic sensors are also reported. Furthermore, the challenges and prospects of the plasmonic biosensors for the detection of lung cancer biomarkers are highlighted.

El Tor cholera at the contemporary stage of the seventh pandemia: pathogen evolution, clinical and epidemiological features, laboratory diagnostics

The phenotypic and molecular genetic properties of 133 strains of genetically modified (genovariant) Vibrio cholerae O1 El Tor biovar isolated from patients in Dagestan (1993, 1994, 1998), and compared with 246 strains of a typical toxigenic cholera vibrio El Tor biovar isolated in 1970–1990 at the Caucasus Region. It was found that 48.7% of the studied genetically modified strain variants had mixed phenotypic properties of the El Tor and classic biovars that evidences about a need to include the marker genes of the classical biovar (ctxBCl+, rtxC–) and the El Tor biovar (ctxBEl+, rtxC+) into the existing biotyping scheme. The genes of the El Tor biovar, isolated from patients in Dagestan, contain in addition to the El Tor ones, the genes of the classical biovar (ctxBCl and/or rstRCl), as well as the typical toxigenic cholera vibrios of El Tor, islands of persistence (EPI), pathogenicity (VPI-1 and VPI-2) and pandemicity (VSP-I and VSP-II). However, only the El Tor biovar genovariants were found to bear an integrative and conjugative SXT element with antibiotic polyresistance genes. Epidemic cholera outbreaks caused by the El Tor biovar genovariants that occurred in 1993–1998 at the Caucasus Region, correspond to classical (Asian) cholera based on disease severity. The epidemiological features of modern cholera were studied: the main way for transmission via fecal-oral route for typical El Tor cholera vibrio is waterborne, whereas for the El Tor gene variant — household. Primary infections upon water drinking and using domestic water from surface water bodies infected with typical El Tor vibrios occur outside the family hearth. In case of cholera caused by hybrid El Tor variants, infection is transmitted among family members via domestic factors under low sanitary level. The development of laboratory diagnostics and epidemiological surveillance of modern El Tor cholera is based on the development of PCR test systems taking into account the evolutionary genome transformations.

Identification of Trueperella bernardiae isolated from peking ducks (Anas platyrhynchos domesticus) by phenotypical and genotypical investigations and by a newly developed loop-mediated isothermal amplification (LAMP) assay

Trueperella (T.) bernardiae is a well-known bacterial pathogen in infections of humans, rarely in animals. In the present study, five T. bernardiae isolates, isolated from five Peking ducks of four different farms, were identified by phenotypic properties, by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) analysis, and genotypically by sequencing the 16S ribosomal RNA (rRNA) gene, the superoxide dismutase A encoding gene sodA, and the glyceraldehyde-3-phosphate dehydrogenase encoding gene gap. In addition, the T. bernardiae isolates could be identified with a newly developed loop-mediated isothermal amplification (LAMP) assay based on the gyrase encoding housekeeping gene gyrA. All these tests clearly identified the T. bernardiae isolates to the species level. However, the detection of the specific gene gyrA with the newly designed LAMP assay appeared with a high sensitivity and specificity, and could help to identify this bacterial species in human and animal infections in future. The importance of the T. bernardiae isolates for the clinical condition of the ducks and for the problems at farm level remains unclear.

3D Hepatic Organoid-Based Advancements in LIVER Tissue Engineering

Liver-associated diseases and tissue engineering approaches based on in vitro culture of functional Primary human hepatocytes (PHH) had been restricted by the rapid de-differentiation in 2D culture conditions which restricted their usability. It was proven that cells growing in 3D format can better mimic the in vivo microenvironment, and thus help in maintaining metabolic activity, phenotypic properties, and longevity of the in vitro cultures. Again, the culture method and type of cell population are also recognized as important parameters for functional maintenance of primary hepatocytes. Hepatic organoids formed by self-assembly of hepatic cells are microtissues, and were able to show long-term in vitro maintenance of hepato-specific characteristics. Thus, hepatic organoids were recognized as an effective tool for screening potential cures and modeling liver diseases effectively. The current review summarizes the importance of 3D hepatic organoid culture over other conventional 2D and 3D culture models and its applicability in Liver tissue engineering.

Cellular and transcriptional diversity over the course of human lactation

Human breast milk is a dynamic fluid that contains millions of cells, but their identities and phenotypic properties are poorly understood. We used single-cell RNA-seq (scRNA-seq) to characterize the transcriptomes of cells from human breast milk (hBM) across lactational time from 3 to 632 days postpartum in 15 donors. We find that the majority of cells in human breast milk are lactocytes, a specialized epithelial subset, and cell type frequencies shift over the course of lactation yielding greater epithelial diversity at later points. Analysis of lactocytes reveals a continuum of cell states characterized by transcriptional changes in hormone, growth factor, and milk production related pathways. Generalized additive models suggest that one sub-cluster, LALBAlow epithelial cells, increase as a function of time postpartum, daycare attendance, and the use of hormonal birth control. We identify several sub-clusters of macrophages in hBM that are enriched for tolerogenic functions, possibly playing a role in protecting the mammary gland during lactation. Our description of the cellular components of breast milk, their association with maternal-infant dyad metadata and quantification of alterations at the gene and pathways levels provides the first detailed longitudinal picture of human breast milk cells across lactational time. This work paves the way for future investigations of how a potential division of cellular labor and differential hormone regulation might be leveraged therapeutically to support healthy lactation and potentially aid in milk production.

Mechanisms Involved in Type II Macrophage Activation and Effector Functions

<p>Autoimmunities are extremely difficult to treat and involved in their pathogenesis are pro-inflammatory immune responses redirected against one's own tissues. Studies in our lab have shown macrophages that are induced to become type II macrophages protect against an animal model of MS, experimental autoimmune encephalomyelitis (EAE), with protection due to immune deviation. Another way to deviate immune responses away from inflammation is by infection with the parasitic helminth Schistosoma mansoni, which also protects against EAE. The contribution of type II macrophages in this protection is unknown, as are the mechanisms involved in promoting the phenotype induced by type II activation. This project investigates key mechanisms involved in type II activation, while also elucidating the possible effect of schistosome exposure on the induction of this activation state. Using a validated model of type II activation in vitro, we compared the effects of schistosome immune complexes on various macrophage properties such as cytokine, surface marker and enzymatic profiles. This thesis identified that exposure to schistosome complexes induces a macrophage state with characteristics of two distinct activation states (type II and alternative activation), as well as completely novel characteristics. This activation state shows many phenotypic properties associated with immune regulation, and may have important consequences for understanding mechanisms involved in protection against inflammatory illnesses. We also investigated key mechanisms involved in the anti-inflammatory responses induced by type II activation. Cytokine, chemokine and surface marker profiles of macrophages were assessed in response to type II activation in vitro, with the main emphasis on determining the effects of IL-10 and CD40 on the type II activation phenotype and function. This investigation found that type II activated macrophages depend on low levels of CD40/CD40L signalling to polarise Th2 development, as the expression of receptors for Th2-inducing cytokines are significantly impaired in the absence of this interaction. This suggests an important role for the low but maintained levels of CD40 on type II activated macrophages, in aiding the deviation of immune responses, while maintaining Th2 polarization. We also suggest a suppressive role of CD40/CD40L in IL-10 production, which is a novel find. The requirement of new treatments for MS is escalating as more people are affected each year. The impact of MS on the quality of life is severe and long lasting. Having a greater understanding of the mechanisms involved in deviating pro-inflammatory or anti-inflammatory responses will enable the development of much more effective treatments and therapies in the future.</p>

Mechanisms Involved in Type II Macrophage Activation and Effector Functions

<p>Autoimmunities are extremely difficult to treat and involved in their pathogenesis are pro-inflammatory immune responses redirected against one's own tissues. Studies in our lab have shown macrophages that are induced to become type II macrophages protect against an animal model of MS, experimental autoimmune encephalomyelitis (EAE), with protection due to immune deviation. Another way to deviate immune responses away from inflammation is by infection with the parasitic helminth Schistosoma mansoni, which also protects against EAE. The contribution of type II macrophages in this protection is unknown, as are the mechanisms involved in promoting the phenotype induced by type II activation. This project investigates key mechanisms involved in type II activation, while also elucidating the possible effect of schistosome exposure on the induction of this activation state. Using a validated model of type II activation in vitro, we compared the effects of schistosome immune complexes on various macrophage properties such as cytokine, surface marker and enzymatic profiles. This thesis identified that exposure to schistosome complexes induces a macrophage state with characteristics of two distinct activation states (type II and alternative activation), as well as completely novel characteristics. This activation state shows many phenotypic properties associated with immune regulation, and may have important consequences for understanding mechanisms involved in protection against inflammatory illnesses. We also investigated key mechanisms involved in the anti-inflammatory responses induced by type II activation. Cytokine, chemokine and surface marker profiles of macrophages were assessed in response to type II activation in vitro, with the main emphasis on determining the effects of IL-10 and CD40 on the type II activation phenotype and function. This investigation found that type II activated macrophages depend on low levels of CD40/CD40L signalling to polarise Th2 development, as the expression of receptors for Th2-inducing cytokines are significantly impaired in the absence of this interaction. This suggests an important role for the low but maintained levels of CD40 on type II activated macrophages, in aiding the deviation of immune responses, while maintaining Th2 polarization. We also suggest a suppressive role of CD40/CD40L in IL-10 production, which is a novel find. The requirement of new treatments for MS is escalating as more people are affected each year. The impact of MS on the quality of life is severe and long lasting. Having a greater understanding of the mechanisms involved in deviating pro-inflammatory or anti-inflammatory responses will enable the development of much more effective treatments and therapies in the future.</p>