Application of transmission electron microscopy to the clinical study of viral and bacterial infections: present and future

Call to action to properly utilize electron microscopy to measure organelles to monitor disease

This review provides an overview of the current methods for quantifying mitochondrial ultrastructure, including cristae morphology, mitochondrial contact sites, and recycling machinery and a guide to utilizing electron microscopy to effectively measure these organelles. Quantitative analysis of mitochondrial ultrastructure is essential for understanding mitochondrial biology and developing therapeutic strategies for mitochondrial-related diseases. Techniques such as transmission electron microscopy (TEM) and serial block face-scanning electron microscopy, as well as how they can be combined with other techniques including confocal microscopy, super-resolution microscopy, and correlative light and electron microscopy are discussed. Beyond their limitations and challenges, we also offer specific magnifications that may be best suited for TEM analysis of mitochondrial, endoplasmic reticulum, and recycling machinery. Finally, perspectives on future quantification methods are offered.

Real-time detection of virus antibody interaction by label-free common-path interferometry

Viruses have a profound influence on all forms of life, motivating the development of rapid and minimally invasive methods for virus detection. In this study, we present a novel methodology that enables quantitative measurement of the interaction between individual biotic nanoparticles and antibodies in solution. Our approach employs a label-free, full-field common-path interferometric technique to detect and track biotic nanoparticles and their interactions with antibodies. It is based on the interferometric detection of light scattered by viruses in aqueous samples for the detection of individual viruses. We employ single-particle tracking analysis to characterize the size and properties of the detected nanoparticles, and to monitor the changes in their diffusive mobility resulting from interactions. To validate the sensitivity of our detection approach, we distinguish between particles having identical diffusion coefficients but different scattering signals, using DNA-loaded and DNA-devoid capsids of the Escherichia coli T5 virus phage. In addition, we have been able to monitor, in real time, the interaction between the bacteriophage T5 and purified antibodies targeting its major capsid protein pb8, as well as between the phage SPP1 and nonpurified anti-SPP1 antibodies present in rabbit serum. Interestingly, these virus-antibody interactions are observed within minutes. Finally, by estimating the number of viral particles interacting with antibodies at different concentrations, we successfully quantify the dissociation constant K d of the virus-antibody reaction using single-particle tracking analysis.

Current Achievements and Future Prospects in Virus Elimination Technology for Functional Chrysanthemum

Chrysanthemum is an important functional plant that is used for food, medicine and tea. Functional chrysanthemums become infected with viruses all around the world, seriously lowering their quality and yield. Viral infection has become an important limiting factor in chrysanthemum production. Functional chrysanthemum is often propagated asexually by cutting during production, and viral infection of seedlings is becoming increasingly serious. Chrysanthemums can be infected by a variety of viruses causing different symptoms. With the development of biotechnology, virus detection and virus-free technologies for chrysanthemum seedlings are becoming increasingly effective. In this study, the common virus species, virus detection methods and virus-free technology of chrysanthemum infection are reviewed to provide a theoretical basis for virus prevention, treatment and elimination in functional chrysanthemum.

PS-Net: human perception-guided segmentation network for EM cell membrane

MOTIVATION

Cell membrane segmentation in electron microscopy (EM) images is a crucial step in EM image processing. However, while popular approaches have achieved performance comparable to that of humans on low-resolution EM datasets, they have shown limited success when applied to high-resolution EM datasets. The human visual system, on the other hand, displays consistently excellent performance on both low and high resolutions. To better understand this limitation, we conducted eye movement and perceptual consistency experiments. Our data showed that human observers are more sensitive to the structure of the membrane while tolerating misalignment, contrary to commonly used evaluation criteria. Additionally, our results indicated that the human visual system processes images in both global-local and coarse-to-fine manners.

RESULTS

Based on these observations, we propose a computational framework for membrane segmentation that incorporates these characteristics of human perception. This framework includes a novel evaluation metric, the perceptual Hausdorff distance (PHD), and an end-to-end network called the PHD-guided segmentation network (PS-Net) that is trained using adaptively tuned PHD loss functions and a multiscale architecture. Our subjective experiments showed that the PHD metric is more consistent with human perception than other criteria, and our proposed PS-Net outperformed state-of-the-art methods on both low- and high-resolution EM image datasets as well as other natural image datasets.

AVAILABILITY AND IMPLEMENTATION

The code and dataset can be found at https://github.com/EmmaSRH/PS-Net.

Monkeypox virus is nature's wake-up call: a bird's-eye view

Several infections have emerged in humans, domestic animals, wildlife, and plant populations, causing a severe problem for humanity. Since the discovery of the Monkeypox virus (Mpox) in 1958 in Copenhagen, Denmark, it has resurfaced several times, producing severe infections in humans and resulting in a significant fatality rate. Mpox is an Orthopoxvirus of the Poxviridae family. This family contains various medically important viruses. The natural reservoir of Mpox is unknown yet. Mpox might be carried by African rodents and nonhuman primates (such as monkeys). The role of monkeys has been confirmed by its various outbreaks. The infection may be transferred from unidentified wild animals to monkeys, who can then spread it to humans by crossing species barriers. In close contact, human-to-human transmission is also possible. Mpox outbreaks have been documented regularly in Central and Western Africa, but recently in 2022, it has spread to over one hundred-six countries. There is no specific treatment for it, although the smallpox vaccine, antivirals, and vaccinia immune globulin help in the effective management of Mpox. In conclusion: Monkeypox poses a severe threat to public health due to the lack of specific vaccinations and effective antivirals. Surveillance studies in affected regions can assist in the early diagnosis of disease and help to control significant outbreaks. The present review provides information on epidemiology, clinical symptoms, risk factors, diagnosis, and preventive measures of Mpox.

Magnetic biosensors for identification of SARS-CoV-2, Influenza, HIV, and Ebola viruses: a review

Infectious diseases such as novel coronavirus (SARS-CoV-2), Influenza, HIV, Ebola, etc kill many people around the world every year (SARS-CoV-2 in 2019, Ebola in 2013, HIV in 1980, Influenza in 1918). For example, SARS-CoV-2 has plagued higher than 317 000 000 people around the world from December 2019 to January 13, 2022. Some infectious diseases do not yet have not a proper vaccine, drug, therapeutic, and/or detection method, which makes rapid identification and definitive treatments the main challenges. Different device techniques have been used to detect infectious diseases. However, in recent years, magnetic materials have emerged as active sensors/biosensors for detecting viral, bacterial, and plasmids agents. In this review, the recent applications of magnetic materials in biosensors for infectious viruses detection have been discussed. Also, this work addresses the future trends and perspectives of magnetic biosensors.

A review on molecular detection techniques of white spot syndrome virus: Perspectives of problems and solutions in shrimp farming

This review aims to provide an update on the current scientific understanding of various aspects of White Spot Syndrome Virus (WSSV) formation, diagnostic procedures, transmission, ecological effects, pathophysiology and management strategies. In terms of production and financial benefits, the WSSV has been the most virulent in shrimp and several other crustacean sectors around the globe. It spreads vertically from diseased broodstock to post-larvae and horizontally by cannibalism, invertebrate vectors, freshwater and sediments. In the transfer of white spot disease (WSD) in newly stocked ponds, the survivability of WSSV in sediment is the most important variable. In typical cultural conditions, it is a highly infectious pathogen capable of inflicting total death within 3-10 days after an outbreak. Some of the current biosecurity strategies used to keep diseases out of shrimp ponds such as pond water disinfection, quarantine of new stocks before stocking and broader usage of specific pathogen-free shrimp. The sequencing and characterisation of various WSSV strains have provided details about pathogen biology, pathogenicity and disease. To develop successful control methods, knowledge of these characteristics is essential. In several shrimp-producing countries in Asia and the Americas, the infections produced by the WSSV have had disastrous socio-economic consequences. As a result of international trade or migration of diseased species, the World Animal Health Organization recognised several illnesses as posing a substantial hazard to farmed shrimp. WSD is receiving much scientific research due to the potential economic effects of the virus. Research is now being done to understand better the molecular biology and pathophysiology of WSSV, as well as how to treat and prevent the virus. However, further study should be conducted in countries with more resilient host species to understand their role in mitigating disease impacts since these revelations may aid in developing a WSD treatment.

Phenotypic and Genomic Characterization of Nine String-Positive Carbapenem-Resistant Acinetobacter baumannii Isolates from Israel

A positive "string test" indicates the ability of bacterial colonies grown on agar plates to form viscous strings of >5 mm when stretched. This phenotype is strongly associated with hypervirulence in Klebsiella pneumoniae but has never been described in carbapenem-resistant Acinetobacter baumannii (CRAB), an emerging human pathogen of high clinical significance. In this work, we screened 1,000 CRAB isolates, among which we identified and characterized 9 string-positive CRAB (stCRAB) isolates. Phenotypic and genotypic analyses revealed that the isolates were not phylogenetically related and possessed different antibiotic resistance and virulence profiles. Transmission electron microscopy (TEM) showed the presence of capsule in string-positive isolates. String-positive isolates were more motile but did not form more biofilm than non-string-positive isolates. They were less virulent in a murine thigh fitness model and a Galleria mellonella survival assay. In conclusion, here, we describe string-positive A. baumannii isolates and their phenotypic and molecular characteristics. We found that unlike K. pneumoniae, stCRAB isolates were not associated with increased virulence. IMPORTANCE Acinetobacter baumannii has been considered a major health care threat in recent years. Despite many efforts, the pathogenesis and molecular mechanism of A. baumannii virulence remain poorly understood. Moreover, the plasticity of its genome frequently gives rise to new and more virulent isolates. Our current study is of significant importance as it concerns a previously undescribed A. baumannii phenotype. The string-positive phenotype is strongly associated with increased fitness and virulence in other Gram-negative bacteria such as K. pneumoniae. Although no clear correlation with virulence or fitness was found in our 9 stCRAB isolates, this could have been due to the limited statistical power of our research. We suggest that this phenotype should be taken into consideration as due to its genome plasticity, the next change can give rise to string-positive and hypervirulent strains, as is known for K. pneumoniae. Additional future research is needed regarding its possible consequences.

How MALDI-TOF Mass Spectrometry Technology Contributes to Microbial Infection Control in Healthcare Settings

Healthcare settings have been utilizing matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS) since 2010. MALDI-TOF MS has various benefits over the conventional method of biochemical identification, including ease of use, speed, accuracy, and low cost. This approach can solve many of the obstacles to identifying bacteria, fungi and viruses. As technology advanced, more and more databases kept track of spectra, allowing species with similar morphological, genotypic, and biochemical traits to be identified. Using MALDI-TOF MS for identification has become more accurate and quicker due to advances in sample preparation and database enrichment. Rapid sample detection and colony identification using MALDI-TOF MS have produced promising results. A key application of MALDI-TOF MS is quickly identifying highly virulent and drug-resistant diseases. Here, we present a review of the scientific literature assessing the effectiveness of MALDI-TOF MS for locating clinically relevant pathogenic bacteria, fungi, and viruses. MALDI-TOF MS is a useful strategy for locating clinical pathogens, however, it also has some drawbacks. A small number of spectra in the database and inherent similarities among organisms can make it difficult to distinguish between different species, which can result in misidentifications. The majority of the time additional testing may correct these problems, which happen very seldom. In conclusion, infectious illness diagnosis and clinical care are being revolutionized by the use of MALDI-TOF MS in the clinical microbiology laboratory.

The OH system: A panorama view of the PPV-host interaction

Poxviruses are a family of specialized cytoplasm-parasitic DNA viruses that replicate and assembly in virus factory. In Parapoxvirus (PPV) genus, with the orf virus (ORFV) as a representative species of this genus, their behaviors are significantly different from that of Orthopoxvirus, and the plots of viral practical solutions for evading host immunity are intricate and fascinating, particularly to anti-host and host's antiviral mechanisms. In order to protect the virus factory from immune elimination caused by infection, PPVs attempt to interfere with multiple stress levels of host, mainly by modulating innate immunity response (IIR) and adaptive immunity response (AIR). Given that temporarily constructed by virus infection, ORFV-HOST (OH) system accompanied by viral strategies is carefully managed in the virus factory, thus directing many life-critical events once undergoing the IIR and AIR. Evolutionarily, to reduce the risk of system destruction, ORFV have evolved into a mild-looking mode to avoid overstimulation. Moreover, the current version of development also focus on recognizing and hijacking more than eight antiviral security mechanisms of host cells, such as the 2',5'-oligoadenylate synthetase (OAS)/RNase L and PKR systems, the ubiquitin protease system (UPS), and so on. In summary, this review assessed inescapable pathways as mentioned above, through which viruses compete with their hosts strategically. The OH system provides a panoramic view and a powerful platform for us to study the PPV-Host interaction, as well as the corresponding implications on a great application potential in anti-virus design.

Electron microscopy overview of SARS-COV2 and its clinical impact

Research centers around the world are competing to develop therapeutic and prophylactic agents to provide new intervention strategies that could halt or even help slow the progression of the COVID19 pandemic. This requires a deep understanding of the biology and cytopathology of the interaction of SARS-CoV-2 with the cell. This review highlights the importance of electron microscopy (EM) in better understanding the morphology, the subcellular morphogenesis, and pathogenesis of SARS-CoV-2, given its nanometric dimensions. The study also underscores the value of cryo-electron microscopy for analyzing the structure of viral protein complex at atomic resolution in its native state and the development of novel antibodies, vaccines, and therapies targeting the trimeric S spike proteins and the viral replication organelles. This review highlighted the emergence in a short period of time of several viral variants of concern with enhanced transmissibility and increased infectivity. This is due to the elevated affinity of the host receptor with acquired adaptive mutations in the spike protein gene of the virus.Subsequently, to the technical improvement of EM resolutions and the recent promising results with SARS-CoV2 variant structure determination, antibodies production, and vaccine development, it is necessary to maximize our investigations regarding the potential occurrence of immune pressure and viral adaptation secondary to repeated infection and vaccination.

Increased Capsule Thickness and Hypermotility Are Traits of Carbapenem-Resistant Acinetobacter baumannii ST3 Strains Causing Fulminant Infection

Background

Acinetobacter baumannii is a successful nosocomial pathogen, causing severe, life-threatening infections in hospitalized patients, including pneumonia and bloodstream infections. The spread of carbapenem-resistant Acinetobacter baumannii (CRAB) strains is a major health threat worldwide. The successful spread of CRAB is mostly due to its highly plastic genome. Although some virulence factors associated with CRAB have been uncovered, many mechanisms contributing to its success are not fully understood.

Methods

Here we describe strains of CRAB that were isolated from fulminant cases in 2 hospitals in Israel. These isolates show a rare hypermucoid (HM) phenotype and were investigated using phenotypic assays, comparative genomics, and an in vivo Galleria mellonella model.

Results

The 3 isolates belonged to the ST3 international clonal type and were closely related to each other, as shown by Fourier-transform infrared spectroscopy and phylogenetic analyses. These isolates possessed thickened capsules and a dense filamentous extracellular polysaccharides matrix as shown by transmission electron microscopy (TEM), and overexpressed the capsule polysaccharide synthesis pathway-related wzc gene.

Conclusions

The HM isolates possessed a unique combination of virulence genes involved in iron metabolism, protein secretion, adherence, and membrane glycosylation. HM strains were more virulent than control strains in 2 G. mellonella infection models. In conclusion, our findings demonstrated several virulence factors, all present in 3 CRAB isolates with rare hypermucoid phenotypes.

Ultrastructural and Immunohistochemical Diagnosis of a Neonatal Herpes Simplex Virus Infection Presenting as Fulminant Hepatitis: A Case Report

TORCH (Toxoplasmosis, Rubella, Cytomegalovirus, Herpes Simplex Virus and Syphilis) infections are a major cause of intrauterine and perinatal infections with associated morbidity and mortality. Neonatal Herpes Simplex Virus infection caused by an enveloped, double-stranded DNA virus of the Herpesviridae family is devastating and fatal. Herpes Viruses are not hepatotropic but may rarely cause hepatitis. Most cases of HSV hepatitis rapidly progress to fulminant hepatic failure and often fatal before the diagnosis or transplantation. Nowadays, despite the availability of antiviral treatment (acyclovir), the outcome remains poor because of late identification of hepatic Herpes Simplex Virus (HSV) infection. We report a male neonate suspected with a metabolic/mitochondrial disease and multi-organ involvement but who developed a fulminant hepatic failure and disseminated coagulopathy secondary to HSV type 1 (HSV-1) infection. The postmortem diagnosis was performed demonstrating HSV-1 in liver tissue by transmission electron microscopy and by retrospective detection of HSV specific antigens by immunohistochemistry.

Ultramicrotomy preparation of magnetic nanoparticles for transmission electron microscopy

Transmission electron microscopy (TEM) is one of the most important methods for the morphological characterization and structure analysis of nanomaterials. However, the characterization of magnetic materials has always been a challenge due to limitations arising from the design of electron microscopes. To tackle this problem, advanced sample preparation technology is needed, especially for magnetic materials. Here in this work ultrathin sectioning technology (ultramicrotomy) is used for the sample preparation of magnetic Fe₃O₄ nanoparticles embedded into a resin, where the loaded resin can be sliced into nanoscale sheets. By the optimization of the embedding method and the slicing process, nano-sheets with uniform thickness and exceptional flatness were prepared, where the nanoparticles exhibited uniform dispersion. It is shown that this technology also helps reducing the degree of pollution of the electron microscope by the magnetic nanoparticles under different electron beam irradiation intensities. Generally, the magnetic nanoparticles are more resistant to electron beam bombardment when embedded into a resin.

Revisiting staining of biological samples for electron microscopy: perspectives for recent research

This review revisits essential staining protocols for electron microscopy focussing on the visualization of active sites, i.e. enzymes, metabolites or proteins, in cells and tissues, which have been developed 50 to 60 years ago, however, never were established as standard protocols being used in electron microscopy in a routine fashion. These approaches offer numerous possibilities to expand the knowledge of cellular function and specifically address the localization of active compounds of these systems. It is our conviction, that many of these techniques are still useful, in particular when applied in conjunction with correlative light and electron microscopy. Revisiting specialized classical electron microscopy staining protocols for use in correlative microscopy is particularly promising, as some of these protocols were originally developed as staining methods for light microscopy. To account for this history, rather than summarizing the most recent achievements in literature, we instead first provide an overview of techniques that have been used in the past. While some of these techniques have been successfully implemented into modern microscopy techniques during recent years already, more possibilities are yet to be re-discovered and provide exciting new perspectives for their future use.

Emerging electron microscopy and 3D methodologies to interrogate Staphylococcus aureus osteomyelitis in murine models

Recent breakthroughs in our understanding of orthopaedic infections have come from advances in transmission electron microscopy (TEM) imaging of murine models of bone infection, most notably Staphylococcus aureus invasion and colonization of osteocyte-lacuno canalicular networks of live cortical bone during the establishment of chronic osteomyelitis. To further elucidate this microbial pathogenesis and evaluate the mechanism of action of novel interventions, additional advances in TEM imaging are needed. Here we present detailed protocols for fixation, decalcification, and epoxy embedment of bone tissue for standard TEM imaging studies, as well as the application of immunoelectron microscopy to confirm S. aureus occupation within sub-micron canaliculi. We also describe the first application of the novel Automated-Tape-UltraMicrotome system with three-dimensional reconstruction and volumetric analyses to quantify S. aureus occupation within the osteocyte-lacuno canalicular networks. Reconstruction of the three-dimensional volume broadened our perspective of S. aureus colonization of the canalicular network and, surprisingly, revealed adjacent noninfected canaliculi. This observation has led us to hypothesize that viable osteocytes of the osteocyte-lacuno canalicular networks respond and resist infection, opening future research directions to explain the paradox of adjacent uninfected canaliculi and life-long deep bone infection in patients with chronic osteomyelitis.

Virus identification in electron microscopy images by residual mixed attention network

BACKGROUND AND OBJECTIVE

Virus identification in electron microscopy (EM) images is considered as one of the front-line method in pathogen diagnosis and re-emerging infectious agents. However, the existing methods either focused on the detection of a single virus or required large amounts of manual labeling work to segment virus. In this work, we focus on the task of virus classification and propose an effective and simple method to identify different viruses.

METHODS

We put forward a residual mixed attention network (RMAN) for virus classification. The proposed network uses channel attention, bottom-up and top-down attention, and incorporates a residual architecture in an end-to-end training manner, which is suitable for dealing with EM virus images and reducing the burden of manual annotation.

RESULTS

We validate the proposed network through extensive experiments on a transmission electron microscopy virus image dataset. The top-1 error rate of our RMAN on 12 virus classes is 4.285%, which surpasses that of state-of-the-art networks and even human experts. In addition, the ablation study and the visualization of class activation mapping (CAM) further demonstrate the effectiveness of our method.

CONCLUSIONS

The proposed automated method contributes to the development of medical virology, which provides virologists with a high-accuracy approach to recognize viruses as well as assist in the diagnosis of viruses.

Rapid Scanning Electron Microscopy Detection and Sequencing of Severe Acute Respiratory Syndrome Coronavirus 2 and Other Respiratory Viruses

There is an urgent need for accurate and rapid testing methods to quickly identify infected patients as well as asymptomatic carriers, in order to prevent the spread of emerging viruses. Here, we developed a rapid testing strategy by scanning electron microscopy capable of detecting severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and other respiratory viruses directly from patients. We evaluated our results by comparing them to real-time reverse transcription-polymerase chain reaction (RT-PCR) and metagenomic sequencing results. We correlated the presence of the SARS-CoV-2 to the viral load, where samples with Ct values lower than 18 were all detected by scanning electron microscopy (SEM). The sensitivity deacresed progressively with higher Ct values. In addition, we found a correlation with metagenomic sequencing, where all samples detected by SEM were sequenced and viral sequences were easily recovered. Following this study, SEM proved its efficiency as a frontline method for directly detecting previously unknown microorganisms that cannot be targeted by molecular methods and can cause potential outbreaks.

Rapid identification of capsulated Acinetobacter baumannii using a density-dependent gradient test

Background

Gram-negative bacterial capsules are associated with production of carbohydrates, frequently resulting in a mucoid phenotype. Infections caused by capsulated or mucoid A. baumannii are associated with increased clinical severity. Therefore, it is clinically and epidemiologically important to identify capsulated A. baumannii. Here, we describe a density-dependent gradient test to distinguish between capsulated and thin/non-capsulated A. baumannii.

Results

Thirty-one of 57 A. baumannii isolates displayed a mucoid phenotype. The density-dependent gradient test was comprised of two phases, with silica concentrations of 30% (top phase) and 50% (bottom phase). Twenty-three isolates migrated to the bottom phase, indicating thin or non-capsulated strains, and 34 migrated to the top phase, suggesting strains suspected to be capsulated. There was agreement between the mucoid and the non-mucoid phenotypes and the density-dependent gradient test for all but three isolates. Total carbohydrates extracted from strains suspected to be capsulated were significantly higher. Transmission electron microscopy confirmed the presence of a capsule in the six representative strains suspected to be capsulated.

Conclusions

The density-dependent gradient test can be used to verify capsule presence in mucoid-appearing A. baumannii strains. Identifying capsulated strains can be useful for directing infection control measures to reduce the spread of hypervirulent strains.

Biosensors: frontiers in rapid detection of COVID-19

The rapid community-spread of novel human coronavirus 2019 (nCOVID19 or SARS-Cov2) and morbidity statistics has put forth an unprecedented urge for rapid diagnostics for quick and sensitive detection followed by contact tracing and containment strategies, especially when no vaccine or therapeutics are known. Currently, quantitative real-time polymerase chain reaction (qRT-PCR) is being used widely to detect COVID-19 from various types of biological specimens, which is time-consuming, labor-intensive and may not be rapidly deployable in remote or resource-limited settings. This might lead to hindrance in acquiring realistic data of infectivity and community spread of SARS-CoV-2 in the population. This review summarizes the existing status of current diagnostic methods, their possible limitations, and the advantages of biosensor-based diagnostics over the conventional ones for the detection of SARS-Cov-2. Novel biosensors used to detect RNA-viruses include CRISPR-Cas9 based paper strip, nucleic-acid based, aptamer-based, antigen-Au/Ag nanoparticles-based electrochemical biosensor, optical biosensor, and Surface Plasmon Resonance. These could be effective tools for rapid, authentic, portable, and more promising diagnosis in the current pandemic that has affected the world economies and humanity. Present challenges and future perspectives of developing robust biosensors devices for rapid, scalable, and sensitive detection and management of COVID-19 are presented in light of the test-test-test theme of the World Health Organization (WHO).

The Strengths of Scanning Electron Microscopy in Deciphering SARS-CoV-2 Infectious Cycle

Electron microscopy is a powerful tool in the field of microbiology. It has played a key role in the rapid diagnosis of viruses in patient samples and has contributed significantly to the clarification of virus structure and function, helping to guide the public health response to emerging viral infections. In the present study, we used scanning electron microscopy (SEM) to study the infectious cycle of SARS-CoV-2 in Vero E6 cells and we controlled some key findings by classical transmission electronic microscopy (TEM). The replication cycle of the virus was followed from 1 to 36 h post-infection. Our results revealed that SARS-CoV-2 infected the cells through membrane fusion. Particles are formed in the peri-nuclear region from a budding of the endoplasmic reticulum-Golgi apparatus complex into morphogenesis matrix vesicae. New SARS-CoV-2 particles were expelled from the cells, through cell lysis or by fusion of virus containing vacuoles with the cell plasma membrane. Overall, this cycle is highly comparable to that of SARS-CoV. By providing a detailed and complete SARS-CoV-2 infectious cycle, SEM proves to be a very rapid and efficient tool compared to classical TEM.

Combating the Coronavirus Pandemic: Early Detection, Medical Treatment, and a Concerted Effort by the Global Community

The World Health Organization (WHO) has declared the outbreak of 2019 novel coronavirus, known as 2019-nCoV, a pandemic, as the coronavirus has now infected over 2.6 million people globally and caused more than 185,000 fatalities as of April 23, 2020. Coronavirus disease 2019 (COVID-19) causes a respiratory illness with symptoms such as dry cough, fever, sudden loss of smell, and, in more severe cases, difficulty breathing. To date, there is no specific vaccine or treatment proven effective against this viral disease. Early and accurate diagnosis of COVID-19 is thus critical to curbing its spread and improving health outcomes. Reverse transcription-polymerase chain reaction (RT-PCR) is commonly used to detect the presence of COVID-19. Other techniques, such as recombinase polymerase amplification (RPA), loop-mediated isothermal amplification (LAMP), clustered regularly interspaced short palindromic repeats (CRISPR), and microfluidics, have allowed better disease diagnosis. Here, as part of the effort to expand screening capacity, we review advances and challenges in the rapid detection of COVID-19 by targeting nucleic acids, antigens, or antibodies. We also summarize potential treatments and vaccines against COVID-19 and discuss ongoing clinical trials of interventions to reduce viral progression.

Proteomic analysis of the antimicrobial effects of sublethal concentrations of thymol on Salmonella enterica serovar Typhimurium

Salmonella enterica serovar Typhimurium is an important foodborne pathogen that causes serious and extensive food contamination as well as disease and death worldwide. Considering the increasing severity of antibiotic resistance, antibiotic alternatives are urgently needed. As a natural biocide and a component of some essential oils from herbs, thymol is capable of killing various bacteria through a potentially unique mechanism, although the targets of thymol have not been completely elucidated. In this study, the variation in the whole proteome of Salmonella after thymol stress was evaluated using the SWATH multiplex technique. The strain Salmonella Typhimurium CVCC541 was treated with a sublethal concentration (75 μg/mL) of thymol, which rapidly increased the permeability of bacterial membranes at the tested concentration. Thymol destroyed the integrity of the bacterial membrane, as observed by transmission electron microscopy. The proteomes of the treated and untreated cells were characterized after an 8-h treatment. The proteomic analysis of thymol-treated cells indicated that 144 proteins exhibited upregulation or downregulation compared with the control cells, particularly those involved in cellular structure and metabolism. The results of this study showed that thymol may play an antimicrobial role in altering the membrane permeability, virulence change, and antioxidant response of Salmonella Typhimurium. The results of the present study provide an improved understanding of the proteomic response of Salmonella Typhimurium to thymol stress, including the identification of promising targets for the future exploration of innovative approaches to control Salmonella Typhimurium.

Viral infections alter antennal epithelium ultrastructure in honey bees

Varroa destructor and its associated viruses, in particular deformed wing virus (DWV), have been identified as probable causes of honey bee (Apis mellif era L.) colony losses. Evidence suggests that elevated DWV titres in bees could compromise sensory and communication abilities resulting in negative consequences for hygienic behaviour. As antennae play a central role in this behaviour, we compared antennal ultrastructure in DWV-symptomatic and asymptomatic bees. The results show that virus capsids accumulate in the basal regions of the antennal epithelium, close to the haemolymph. No virus particles were detected at the level of sensory sensilla, such as pore plates, nor within the sensory cell dendrites associated with these sensilla. However, membranous structures appeared to be more prevalent in supporting cells surrounding the dendrites of DWV-symptomatic bees. Para-crystalline arrays containing large numbers of virus particles were detected in the antennae of DWV-symptomatic bees but not in asymptomatic bees.

Estimating Bacterial Concentrations in Fibrous Substrates Through a Combination of Scanning Electron Microscopy and ImageJ

Conventional signal-based microanalytical techniques for estimating bacterial concentrations are often susceptible to false signals. A visual quantification, therefore, may compliment such techniques by providing additional information and support better management decisions in the event of outbreaks. Herein, we explore a method that combines electron microscopy (EM) and image-analysis techniques and allows both visualization and quantification of pathogenic bacteria adherent even to complex nonuniform substrates. Both the estimation and imaging parameters were optimized to reduce the estimation error ( E, %) to close to ±5%. The method was validated against conventional microbiological techniques such as the use of optical density, flow cytometry, and quantitative real-time PCR (qPCR). It could easily be tailored to estimate different species of pathogens, such as Escherichia coli O157, Listeria innocua, Staphylococcus aureus, Enterococcus faecalis, and Bacillus anthracis, on samples similar to those in real-time contamination scenarios. The present method is sensitive enough to detect ∼100 bacterial CFU/mL but has the potential to estimate even lower concentrations with increased imaging and computation times. Overall, this imaging-based method may greatly complement any signal-based pathogen-detection technique, especially in negating false signals, and therefore may significantly contribute to the field of analytical microbiology and biochemistry.

Transmission Electron Microscopy Improves the Diagnostic Sensitivity in Nonbacterial Etiology of Severe Pneumonia: A Retrospective Study

Background

Severe pneumonia is responsible for great mortality and morbidity worldwide, and early-applied effective anti-infective therapy can improve the prognosis of patients. However, identification of infectious agents in severe pneumonia remains a major challenge so far. In this study, the potential utility of transmission electron microscopy (TEM) in detecting nonbacterial pathogens in patients with severe pneumonia was retrospectively evaluated.

Materials and Methods

A total of 106 patients diagnosed with severe pneumonia at our hospital from September 2015 to December 2017 were included, and their baseline clinical characteristics were collected. Nonbacterial infectious agents detected by TEM in bronchoalveolar lavage fluid (BALF) and serological tests were summarized. The detection rates were further compared between TEM and serological tests.

Results

BALF examination under the transmission electron microscope revealed 24 viruses, 16 mycoplasmas, 18 chlamydia, 2 fungi and 74 bacteria in 99 samples, among which 61 samples were mixed infections. The combined use of serological tests and TEM significantly improved the detection rate of nonbacterial infectious agents in patients with severe pneumonia.

Conclusions

Our data support that implementation of TEM could improve the sensitivity for detecting viruses, atypical pathogens and mixed infections in BALF from patient of severe pneumonia. Therefore, TEM may be used as an auxiliary diagnostic method of other microbiological tests in severe pneumonia.

Virus detection by transmission electron microscopy: Still useful for diagnosis and a plus for biosafety

Transmission electron microscopy (TEM) is the only imaging technique allowing the direct visualization of viruses, due to its nanometer‐scale resolution. Between the 1960s and 1990s, TEM contributed to the discovery of many types of viruses and served as a diagnostic tool for identifying viruses directly in biological samples, either in suspension or in sections of tissues or mammalian cells grown in vitro in contact with clinical samples. The diagnosis of viral infections improved considerably during the 1990s, with the advent of highly sensitive techniques, such as enzyme‐linked immunosorbent assay (ELISA) and PCR, rendering TEM obsolete for this purpose. However, the last 20 years have demonstrated the utility of this technique in particular situations, due to its “catch‐all” nature, making diagnosis possible through visualization of the virus, without the need of prior assumptions about the infectious agent sought. Thus, in several major outbreaks in which molecular techniques failed to identify the infectious agent, TEM provided the answer. TEM is also still occasionally used in routine diagnosis to characterize infections not diagnosed by molecular assays. It is also used to check the microbiological safety of biological products. Many biopharmaceuticals are produced in animal cells that might contain little‐known, difficult‐to‐detect viruses. In this context, the “catch‐all” properties of TEM make it possible to document the presence of viruses or virus‐like particles in these products.

Fowl adenovirus serotype 4: Epidemiology, pathogenesis, diagnostic detection, and vaccine strategies

Fowl adenovirus (FAdV) serotype-4 is highly pathogenic for chickens, especially for broilers aged 3 to 5 wk, and it has emerged as one of the foremost causes of economic losses to the poultry industry in the last 30 years. The liver is a major target organ of FAdV-4 infections, and virus-infected chickens usually show symptoms of hydropericardium syndrome. The virus is very contagious, and it is spread both vertically and horizontally. It can be isolated from infected liver homogenates and detected by several laboratory diagnostic methods (including an agar gel immunodiffusion test, indirect immunofluorescence assays, counterimmunoelectrophoresis, enzyme-linked immunosorbent assays, restriction endonuclease analyses, polymerase chain reaction (PCR), real-time PCR, and high-resolution melting-curve analyses). Although inactivated vaccines have been deployed widely to control the disease, attenuated live vaccines and subunit vaccines also have been developed, and they are more attractive vaccine candidates. This article provides a comprehensive review of FAdV-4, including its epidemiology, pathogenesis, diagnostic detection, and vaccine strategies.

Electron Microscopic Study Using Formalin-fixed, Paraffin-embedded Material, with Special Reference to Observation of Microbial Organisms and Endocrine Granules

In the diagnostic pathology practice, specimens for electron microscopy (EM) are not necessarily handled and fixed under the ideal condition. In the present article, the author describes ultrastructural study using formalin-fixed and/or paraffin-embedded material. The fine morphologic preservation is often acceptable, particularly when small cubes are dug out of paraffin blocks. Particulate structures such as neuroendocrine granules and microbes are consistently observed even using paraffin sections. Paraffin sections signalized with silver particles in Grimelius and Grocott stains or diaminobenzidine products in immunostaining and in situ hybridization are applicable to EM evaluation by using a pre-embedding sequence. The practical merit includes the targeted approach: highly accurate sampling from focal lesions can be achieved for EM analysis, after observing hematoxylin and eosin-stained or specific-signalized paraffin-sections. This allows us pathologists a convenient and practical way for identifying focally infected pathogens, as well as a retrospective ultrastructural analysis of rare lesions long kept as a form of paraffin blocks.

Rapid Viral Diagnosis of Orthopoxviruses by Electron Microscopy: Optional or a Must?

Diagnostic electron microscopy (DEM) was an essential component of viral diagnosis until the development of highly sensitive nucleic acid amplification techniques (NAT). The simple negative staining technique of DEM was applied widely to smallpox diagnosis until the world-wide eradication of the human-specific pathogen in 1980. Since then, the threat of smallpox re-emerging through laboratory escape, molecular manipulation, synthetic biology or bioterrorism has not totally disappeared and would be a major problem in an unvaccinated population. Other animal poxviruses may also emerge as human pathogens. With its rapid results (only a few minutes after arrival of the specimen), no requirement for specific reagents and its "open view", DEM remains an important component of virus diagnosis, particularly because it can easily and reliably distinguish smallpox virus or any other member of the orthopoxvirus (OPV) genus from parapoxviruses (PPV) and the far more common and less serious herpesviruses (herpes simplex and varicella zoster). Preparation, enrichment, examination, internal standards and suitable organisations are discussed to make clear its continuing value as a diagnostic technique.

Utilization of Capsules for Negative Staining of Viral Samples within Biocontainment

Transmission electron microscopy (TEM) is used to observe the ultrastructure of viruses and other microbial pathogens with nanometer resolution. Most biological materials do not contain dense elements capable of scattering electrons to create an image; therefore, a negative stain, which places dense heavy metal salts around the sample, is required. In order to visualize viruses in suspension under the TEM they must be applied to small grids coated with a transparent surface only nanometers thick. Due to their small size and fragility, these grids are difficult to handle and easily moved by air currents. The thin surface is easily damaged, leaving the sample difficult or impossible to image. Infectious viruses must be handled in a biosafety cabinet (BSC) and some require a biocontainment laboratory environment. Staining viruses in biosafety levels (BSL)-3 and -4 is especially challenging because these environments are more turbulent and technicians are required to wear personal protective equipment (PPE), which decreases dexterity. In this study, we evaluated a new device to assist in negative staining viruses in biocontainment. The device is a capsule that works as a specialized pipette tip. Once grids are loaded into the capsule, the user simply aspirates reagents into the capsule to deliver the virus and stains to the encapsulated grid, thus eliminating user handling of grids. Although this technique was designed specifically for use in BSL-3 or -4 biocontainment, it can ease sample preparation in any lab environment by enabling easy negative staining of virus. This same method can also be applied to prepare negative stained TEM specimens of nanoparticles, macromolecules and similar specimens.

Structure and organization of paramyxovirus particles

The paramyxovirus family comprises major human and animal pathogens such as measles virus (MeV), mumps virus (MuV), the parainfluenzaviruses, Newcastle disease virus (NDV), and the highly pathogenic zoonotic hendra (HeV) and nipah (NiV) viruses. Paramyxovirus particles are pleomorphic, with a lipid envelope, nonsegmented RNA genomes of negative polarity, and densely packed glycoproteins on the virion surface. A number of crystal structures of different paramyxovirus proteins and protein fragments were solved, but the available information concerning overall virion organization remains limited. However, recent studies have reported cryo-electron tomography-based reconstructions of Sendai virus (SeV), MeV, NDV, and human parainfluenza virus type 3 (HPIV3) particles and a surface assessment of NiV-derived virus-like particles (VLPs), which have yielded innovative hypotheses concerning paramyxovirus particle assembly, budding, and organization. Following a summary of the current insight into paramyxovirus virion morphology, this review will focus on discussing the implications of these particle reconstructions on the present models of paramyxovirus assembly and infection.

Pathology of infectious diseases: what does the future hold?

The demand for expertise in pathology for the diagnosis of infectious diseases (ID) is continually growing, due to an increase in ID in immunocompromised patients and in the (re)-emergence of common and uncommon diseases, including tropical infections and infections with newly identified microbes. The microbiology laboratory plays a crucial role in diagnosing infections, identifying the responsible infectious agents and establishing sensitivity of pathogens to drug therapy. Pathology, however, is the only way to correlate the presence of an infectious agent with the reaction it evokes at cell and tissue level. For pathologists working in the field of ID pathology, it is essential to dispose of competence in cell and tissue pathology as well as in microbiology. Expertise in ID includes understanding of taxonomy and classification of pathogens as well as morphological criteria supporting their identification. Moreover, ID pathologists must master the methods used to detect pathogens in fixed cell and tissue samples, notably immunohistochemistry, in situ hybridization and the polymerase chain reaction. Paradoxically, the increasing frequency of lesions caused by pathogens and diagnosed in a pathology laboratory appears to be paralleled by a gradual loss of expertise of pathologists in the field of infectious and tropical diseases. We contend that this may be due at least in part to the continuously increasing number of samples of tumor tissue pathologists deal with and the rapidly expanding number of tissue based biomarkers with predictive value for new anti-cancer therapies. In this review, we highlight current and future issues pertaining to ID pathology, in order to increase awareness of its importance for surgical and molecular pathology. The intention is to contribute to the development of best practice in ID pathology.

Preparation of viral samples within biocontainment for ultrastructural analysis: Utilization of an innovative processing capsule for negative staining

Transmission electron microscopy can be used to observe the ultrastructure of viruses and other microbial pathogens with nanometer resolution. In a transmission electron microscope (TEM), the image is created by passing an electron beam through a specimen with contrast generated by electron scattering from dense elements in the specimen. Viruses do not normally contain dense elements, so a negative stain that places dense heavy metal salts around the sample is added to create a dark border. To prepare a virus sample for a negative stain transmission electron microscopy, a virus suspension is applied to a TEM grid specimen support, which is a 3mm diameter fragile specimen screen coated with a few nanometers of plastic film. Then, deionized (dI) water rinses and a negative stain solution are applied to the grid. All infectious viruses must be handled in a biosafety cabinet (BSC) and many require a biocontainment laboratory environment. Staining viruses in biosafety levels (BSL) 3 and 4 is especially challenging because the support grids are small, fragile, and easily moved by air currents. In this study we evaluated a new device for negative staining viruses called mPrep/g capsule. It is a capsule that holds up to two TEM grids during all processing steps and for storage after staining is complete. This study reports that the mPrep/g capsule method is valid and effective to negative stain virus specimens, especially in high containment laboratory environments.

Viral Infection at High Magnification: 3D Electron Microscopy Methods to Analyze the Architecture of Infected Cells

As obligate intracellular parasites, viruses need to hijack their cellular hosts and reprogram their machineries in order to replicate their genomes and produce new virions. For the direct visualization of the different steps of a viral life cycle (attachment, entry, replication, assembly and egress) electron microscopy (EM) methods are extremely helpful. While conventional EM has given important information about virus-host cell interactions, the development of three-dimensional EM (3D-EM) approaches provides unprecedented insights into how viruses remodel the intracellular architecture of the host cell. During the last years several 3D-EM methods have been developed. Here we will provide a description of the main approaches and examples of innovative applications.

Visualizing viral protein structures in cells using genetic probes for correlated light and electron microscopy

Structural studies of viral proteins most often use high-resolution techniques such as X-ray crystallography, nuclear magnetic resonance, single particle negative stain, or cryo-electron microscopy (EM) to reveal atomic interactions of soluble, homogeneous viral proteins or viral protein complexes. Once viral proteins or complexes are separated from their host's cellular environment, their natural in situ structure and details of how they interact with other cellular components may be lost. EM has been an invaluable tool in virology since its introduction in the late 1940's and subsequent application to cells in the 1950's. EM studies have expanded our knowledge of viral entry, viral replication, alteration of cellular components, and viral lysis. Most of these early studies were focused on conspicuous morphological cellular changes, because classic EM metal stains were designed to highlight classes of cellular structures rather than specific molecular structures. Much later, to identify viral proteins inducing specific structural configurations at the cellular level, immunostaining with a primary antibody followed by colloidal gold secondary antibody was employed to mark the location of specific viral proteins. This technique can suffer from artifacts in cellular ultrastructure due to compromises required to provide access to the immuno-reagents. Immunolocalization methods also require the generation of highly specific antibodies, which may not be available for every viral protein. Here we discuss new methods to visualize viral proteins and structures at high resolutions in situ using correlated light and electron microscopy (CLEM). We discuss the use of genetically encoded protein fusions that oxidize diaminobenzidine (DAB) into an osmiophilic polymer that can be visualized by EM. Detailed protocols for applying the genetically encoded photo-oxidizing protein MiniSOG to a viral protein, photo-oxidation of the fusion protein to yield DAB polymer staining, and preparation of photo-oxidized samples for TEM and serial block-face scanning EM (SBEM) for large-scale volume EM data acquisition are also presented. As an example, we discuss the recent multi-scale analysis of Adenoviral protein E4-ORF3 that reveals a new type of multi-functional polymer that disrupts multiple cellular proteins. This new capability to visualize unambiguously specific viral protein structures at high resolutions in the native cellular environment is revealing new insights into how they usurp host proteins and functions to drive pathological viral replication.

The rebirth of culture in microbiology through the example of culturomics to study human gut microbiota

Bacterial culture was the first method used to describe the human microbiota, but this method is considered outdated by many researchers. Metagenomics studies have since been applied to clinical microbiology; however, a "dark matter" of prokaryotes, which corresponds to a hole in our knowledge and includes minority bacterial populations, is not elucidated by these studies. By replicating the natural environment, environmental microbiologists were the first to reduce the "great plate count anomaly," which corresponds to the difference between microscopic and culture counts. The revolution in bacterial identification also allowed rapid progress. 16S rRNA bacterial identification allowed the accurate identification of new species. Mass spectrometry allowed the high-throughput identification of rare species and the detection of new species. By using these methods and by increasing the number of culture conditions, culturomics allowed the extension of the known human gut repertoire to levels equivalent to those of pyrosequencing. Finally, taxonogenomics strategies became an emerging method for describing new species, associating the genome sequence of the bacteria systematically. We provide a comprehensive review on these topics, demonstrating that both empirical and hypothesis-driven approaches will enable a rapid increase in the identification of the human prokaryote repertoire.

Creating standards for absolute quantification of Coxiella burnetii in real-time PCR--a comparative study based on transmission electron microscopy

Quantitative standards are a prerequisite for quality control and quantification of pathogens. In this study the creation of quantitative standards for use in qPCR is described using the pathogen Coxiella burnetii. Quantification of Coxiella burnetii particles by transmission electron microscopy (TEM) was used as primary standard and compared with data obtained by light microscopy as well as genome equivalents (GE) and plasmid units (recombinant plasmid). Based on pathogen quantification using TEM and light microscopy, pathogen detection limits of 6 and 2 C. burnetii particles could be determined per com1 qPCR reaction, respectively. In comparison, the detection limits were 17 and 13 pathogen units using GE and plasmid units, respectively. The standard generated by TEM can be used as gold standard for universal application due to high accuracy, quantitative control of the producing process and supplying intact pathogen particles.

[What place and what future for the pathology of infectious and tropical diseases in France?]

The management of tissues and cellular samples by the pathologists in the infectious and tropical diseases pathology field in 2014 needs a strong knowledge of both morphological and molecular domains which includes the good control: (i) of the taxonomy of infectious and tropical diseases pathology leading to the pathogens identification and (ii) of the ancillary methods which can be used in fixed samples in order to detect or better identify these pathogens. There is a recent paradox in France concerning the frequency of infectious diseases to be diagnosed in pathology laboratories and the progressive loss of pathologist's expertise in this domain. Different reasons could explain this statement including the omnipresence of the tumour lesions to be managed in a pathology laboratory as well as the recent constraints associated with the different biomarkers that are mandatory to be detected by immunohistochemistry and/or by molecular biology. Even if the microbiologists play a pivotal role for identifying the different pathogens as well as for the assessment of their sensitivity to the anti-microbial drugs, a large number of infectious diseases can be diagnosed only on fixed tissue and/or cells by the pathologists. The purpose of this review is to describe the current and future issues of infectious and tropical diseases diagnoses in pathology laboratories, in particular in France.

Morphological changes in vero cells postinfection with dengue virus type-2

Although no specific antiviral tablets or injections that can kill the dengue virus are currently available, adequate care and treatment could control its morbidity. Interaction of dengue virus to target cells could be an important feature for virus propagation. Ultrastructural analysis of this interaction was studied with vero cells. Vero cells were treated with Dengue virus type-2 at different time intervals at multiplicity of infection (m.o.i) < 10, m.o.i > 10, and m.o.i = 100. It was found that m.o.i < 10 is best to study morphological changes. At an m.o.i > 10 apoptosis occurs and at m.o.i. = 100, cell necrosis occurs. While studying morphological changes, it was found that at 30 min postinfection cells have morphology very similar to that of the control cells although some have irregular outline and show cytoplasmic projections and intense cytoplasmic vacuolization. After 1-12 hours postinfection (h.p.i), the nuclei ran from normal looking to diffuse. Nuclear membrane begins to disintegrate. Some nucleoli are difficult to be seen. The cytoplasm appears as a mottled, lumps diffuse mass distributed throughout the cytosol, with dense lysosomes and myelin figures, also in the mitochondria. In later hours (24 h.p.i), the intranuclear euchromatin is dispersed and heterochromatin forms peripheral clumps. The cytoplasmic processes are short and few in numbers. A proportion of damaged mitochondria with disrupted cristae appear, suggesting that dengue virus may induce mitochondrial dysfunction and nucleus and mitochondria may be the primary organelles helping in dissemination of virus.

A simple procedure to analyze positions of interest in infectious cell cultures by correlative light and electron microscopy

Plastic cell culture dishes that contain a thin bottom of highest optical quality including an imprinted finder grid (μ-Dish Grid-500) are optimally suited for routine correlative light and electron microscopy using chemical fixation. Such dishes allow high-resolution fluorescence and bright-field imaging using fixed and living cells and are compatible with standard protocols for scanning and transmission electron microscopy. Ease of use during cell culture and imaging, as well as a tight cover render the dishes particularly suitable for working with infectious organisms up to the highest biosafety level. Detailed protocols are provided and demonstrated by showing two examples: monitoring the production of virus-like particles of the Human Endogenous Retrovirus HERV-K(HML-2) by HeLa cells and investigation of Rab11-positive membrane-compartments of HeLa cells after infection with Chlamydia trachomatis.

Comparative advantages and limitations of the basic metrology methods applied to the characterization of nanomaterials

Fabrication of modern nanomaterials and nanostructures with specific functional properties is both scientifically promising and commercially profitable. The preparation and use of nanomaterials require adequate methods for the control and characterization of their size, shape, chemical composition, crystalline structure, energy levels, pathways and dynamics of physical and chemical processes during their fabrication and further use. In this review, we discuss different instrumental methods for the analysis and metrology of materials and evaluate their advantages and limitations at the nanolevel.

Molecular studies neglect apparently gram-negative populations in the human gut microbiota

Studying the relationships between gut microbiota, human health, and diseases is a major challenge that generates contradictory results. Most studies draw conclusions about the gut repertoire using a single biased metagenomics approach. We analyzed 16 different stool samples collected from healthy subjects who were from different areas, had metabolic disorders, were immunocompromised, or were treated with antibiotics at the time of the stool collection. The analyses performed included Gram staining, flow cytometry, transmission electron microscopy (TEM), quantitative real-time PCR (qPCR) of the Bacteroidetes and Firmicutes phyla, and pyrosequencing of the 16S rRNA gene amplicons targeting the V6 region. We quantified 10(10) prokaryotes per gram of feces, which is less than was previously described. The Mann-Whitney test revealed that Gram-negative proportions of the prokaryotes obtained by Gram staining, TEM, and pyrosequencing differed according to the analysis used, with Gram-negative prokaryotes yielding median percentages of 70.6%, 31.0%, and 16.4%, respectively. A comparison of TEM and pyrosequencing analyses highlighted a difference of 14.6% in the identification of Gram-negative prokaryotes, and a Spearman test showed a tendency toward correlation, albeit not significant, in the Gram-negative/Gram-positive prokaryote ratio (ρ = 0.3282, P = 0.2146). In contrast, when comparing the qPCR and pyrosequencing results, a significant correlation was found for the Bacteroidetes/Firmicutes ratio (ρ = 0.6057, P = 0.0130). Our study showed that the entire diversity of the human gut microbiota remains unknown because different techniques generate extremely different results. We found that to assess the overall composition of bacterial communities, multiple techniques must be combined. The biases that exist for each technique may be useful in exploring the major discrepancies in molecular studies.

Rapid and reliable detection of bacterial endospores in environmental samples by diagnostic electron microscopy combined with X-ray microanalysis

Diagnostic negative staining electron microscopy is a front-line method for the rapid investigation of environmental and clinical samples in emergency situations caused by bioterrorism or outbreaks of an infectious disease. Spores of anthrax are one of the diagnostic targets in case of bioterrorism, because they have been used as a bio-weapon in the past and their production and transmission are rather simple. With negative staining electron microscopy bacterial spores can be identified based on their morphology at the single cell level. However, because of their particular density, no internal structures are visible which sometimes makes it difficult to distinguish spores from particles with a similar size and shape that are frequently present in environmental samples. Spores contain a high concentration of calcium ions besides other elements, which may allow a proper discrimination of spores from other suspicious particles. To investigate this hypothesis, negative staining electron microscopy, using either transmission or scanning electron microscopes, was combined with energy dispersive X-ray microanalysis, which reveals the element content of individual nanoparticles. A peak pattern consisting of calcium, sulphur and phosphorus was found as a typical signature within the X-ray spectrum of spores in various Clostridium and Bacillus species, including all strains of anthrax (Bacillus anthracis) tested. Moreover, spores could be reliably identified by this combined approach in environmental samples, like household products, soil or various presumed bioterrorist samples. In summary, the use of X-ray spectroscopy, either directly in the transmission electron microscope, or in a correlative approach by using scanning electron microscopy, improves the emergency diagnostics of suspicious environmental samples.

Prevalence of parvoviruses in commercial turkey flocks

Turkey parvovirus belongs to the family Parvoviridae, subfamily Parvovirinae, Genus parvovirus. Since the initial report on turkey parvovirus in the United States appeared in 1983, there had been no further reports of parvovirus in turkeys until 2008. The aims of our study were to determine the prevalence of parvovirus in commercial turkey flocks using PCR; to determine their genetic relationship to previous strains identified in North America and Europe; and to test samples for enteric viruses by transmission electron microscopy (TEM). A total of 169 fecal samples collected from 42 turkey farms in four different states within the United States between 2000 and 2010 were examined. We found that the most frequently detected viruses by TEM were small round viruses, accounting for 52% of the examined samples; however, the PCR detected parvoviruses in 71% of the samples. The phylogenetic analysis of partial nonstructural gene sequences showed a certain degree of variability among the turkey samples tested in the study. Moreover, there was a clear dichotomy in the phylogenetic tree between chicken and turkey samples, with the exception of one turkey isolate from 2000, which clustered together with the chicken group.