VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center

The Eukaryotic Pathogen, Vector and Host Informatics Resource (VEuPathDB, https://veupathdb.org) represents the 2019 merger of VectorBase with the EuPathDB projects. As a Bioinformatics Resource Center funded by the National Institutes of Health, with additional support from the Welllcome Trust, VEuPathDB supports >500 organisms comprising invertebrate vectors, eukaryotic pathogens (protists and fungi) and relevant free-living or non-pathogenic species or hosts. Designed to empower researchers with access to Omics data and bioinformatic analyses, VEuPathDB projects integrate >1700 pre-analysed datasets (and associated metadata) with advanced search capabilities, visualizations, and analysis tools in a graphic interface. Diverse data types are analysed with standardized workflows including an in-house OrthoMCL algorithm for predicting orthology. Comparisons are easily made across datasets, data types and organisms in this unique data mining platform. A new site-wide search facilitates access for both experienced and novice users. Upgraded infrastructure and workflows support numerous updates to the web interface, tools, searches and strategies, and Galaxy workspace where users can privately analyse their own data. Forthcoming upgrades include cloud-ready application architecture, expanded support for the Galaxy workspace, tools for interrogating host-pathogen interactions, and improved interactions with affiliated databases (ClinEpiDB, MicrobiomeDB) and other scientific resources, and increased interoperability with the Bacterial & Viral BRC.

Preserve a Voucher Specimen! The Critical Need for Integrating Natural History Collections in Infectious Disease Studies

Despite being nearly 10 months into the COVID-19 (coronavirus disease 2019) pandemic, the definitive animal host for SARS-CoV-2 (severe acute respiratory syndrome coronavirus 2), the causal agent of COVID-19, remains unknown. Unfortunately, similar problems exist for other betacoronaviruses, and no vouchered specimens exist to corroborate host species identification for most of these pathogens. This most basic information is critical to the full understanding and mitigation of emerging zoonotic diseases. To overcome this hurdle, we recommend that host-pathogen researchers adopt vouchering practices and collaborate with natural history collections to permanently archive microbiological samples and host specimens. Vouchered specimens and associated samples provide both repeatability and extension to host-pathogen studies, and using them mobilizes a large workforce (i.e., biodiversity scientists) to assist in pandemic preparedness. We review several well-known examples that successfully integrate host-pathogen research with natural history collections (e.g., yellow fever, hantaviruses, helminths). However, vouchering remains an underutilized practice in such studies. Using an online survey, we assessed vouchering practices used by microbiologists (e.g., bacteriologists, parasitologists, virologists) in host-pathogen research. A much greater number of respondents permanently archive microbiological samples than archive host specimens, and less than half of respondents voucher host specimens from which microbiological samples were lethally collected. To foster collaborations between microbiologists and natural history collections, we provide recommendations for integrating vouchering techniques and archiving of microbiological samples into host-pathogen studies. This integrative approach exemplifies the premise underlying One Health initiatives, providing critical infrastructure for addressing related issues ranging from public health to global climate change and the biodiversity crisis.

Advances in point-of-care nucleic acid extraction technologies for rapid diagnosis of human and plant diseases

Global health and food security constantly face the challenge of emerging human and plant diseases caused by bacteria, viruses, fungi, and other pathogens. Disease outbreaks such as SARS, MERS, Swine Flu, Ebola, and COVID-19 (on-going) have caused suffering, death, and economic losses worldwide. To prevent the spread of disease and protect human populations, rapid point-of-care (POC) molecular diagnosis of human and plant diseases play an increasingly crucial role. Nucleic acid-based molecular diagnosis reveals valuable information at the genomic level about the identity of the disease-causing pathogens and their pathogenesis, which help researchers, healthcare professionals, and patients to detect the presence of pathogens, track the spread of disease, and guide treatment more efficiently. A typical nucleic acid-based diagnostic test consists of three major steps: nucleic acid extraction, amplification, and amplicon detection. Among these steps, nucleic acid extraction is the first step of sample preparation, which remains one of the main challenges when converting laboratory molecular assays into POC tests. Sample preparation from human and plant specimens is a time-consuming and multi-step process, which requires well-equipped laboratories and skilled lab personnel. To perform rapid molecular diagnosis in resource-limited settings, simpler and instrument-free nucleic acid extraction techniques are required to improve the speed of field detection with minimal human intervention. This review summarizes the recent advances in POC nucleic acid extraction technologies. In particular, this review focuses on novel devices or methods that have demonstrated applicability and robustness for the isolation of high-quality nucleic acid from complex raw samples, such as human blood, saliva, sputum, nasal swabs, urine, and plant tissues. The integration of these rapid nucleic acid preparation methods with miniaturized assay and sensor technologies would pave the road for the "sample-in-result-out" diagnosis of human and plant diseases, especially in remote or resource-limited settings.

Infectious disease antibodies for biomedical applications: A mini review of immune antibody phage library repertoire

Antibody phage display is regarded as a critical tool for the development of monoclonal antibodies for infectious diseases. The different classes of antibody libraries are classified based on the source of repertoire used to generate the libraries. Immune antibody libraries are generated from disease infected host or immunization against an infectious agent. Antibodies derived from immune libraries are distinct from those derived from naïve libraries as the host's in vivo immune mechanisms shape the antibody repertoire to yield high affinity antibodies. As the immune system is constantly evolving in accordance to the health state of an individual, immune libraries can offer more than just infection-specific antibodies but also antibodies derived from the memory B-cells much like naïve libraries. The combinatorial nature of the gene cloning process would give rise to a combination of natural and un-natural antibody gene pairings in the immune library. These factors have a profound impact on the coverage of immune antibody libraries to target both disease-specific and non-disease specific antigens. This review looks at the diverse nature of antibody responses for immune library generation and discusses the extended potential of a disease-specified immune library in the context of phage display.

Antiprotozoal Activity against Entamoeba histolytica of Flavonoids Isolated from Lippia graveolens Kunth

Amebiasis caused by Entamoeba histolytica is nowadays a serious public health problem worldwide, especially in developing countries. Annually, up to 100,000 deaths occur across the world. Due to the resistance that pathogenic protozoa exhibit against commercial antiprotozoal drugs, a growing emphasis has been placed on plants used in traditional medicine to discover new antiparasitics. Previously, we reported the in vitro antiamoebic activity of a methanolic extract of Lippia graveolens Kunth (Mexican oregano). In this study, we outline the isolation and structure elucidation of antiamoebic compounds occurring in this plant. The subsequent work-up of this methanol extract by bioguided isolation using several chromatographic techniques yielded the flavonoids pinocembrin (1), sakuranetin (2), cirsimaritin (3), and naringenin (4). Structural elucidation of the isolated compounds was achieved by spectroscopic/spectrometric analyses and comparing literature data. These compounds revealed significant antiprotozoal activity against E. histolytica trophozoites using in vitro tests, showing a 50% inhibitory concentration (IC₅₀) ranging from 28 to 154 µg/mL. Amebicide activity of sakuranetin and cirsimaritin is reported for the first time in this study. These research data may help to corroborate the use of this plant in traditional Mexican medicine for the treatment of dyspepsia.

Report of the 23rd Meeting on Signal Transduction 2019-Trends in Cancer and Infection

The annual meeting "Signal Transduction-Receptors, Mediators and Genes" of the Signal Transduction Society (STS) is an interdisciplinary conference open to all scientists sharing the common interest in elucidating the signalling pathways underlying the physiological or pathological processes in health and disease of humans, animals, plants, fungi, prokaryotes and protists. The 23rd meeting on signal transduction was held from 4-6 November 2019 in Weimar, Germany, and focused on "Trends in Cancer and Infection". As usual, keynote presentations by invited scientists introduced the respective workshops and were followed by speakers chosen from the submitted abstracts. Ample time had been reserved for discussion of the presented data during the workshops. In this report, we provide a concise summary of the various workshops and further aspects of the scientific program.

Environmental and spatial determinants of enteric pathogen infection in rural Lao People's Democratic Republic: A cross-sectional study

TRIAL REGISTRATION

clinicaltrials.gov (NCT02342860).

Pathogen surveillance in the informal settlement, Kibera, Kenya, using a metagenomics approach

Background

Worldwide, the number of emerging and re-emerging infectious diseases is increasing, highlighting the importance of global disease pathogen surveillance. Traditional population-based methods may fail to capture important events, particularly in settings with limited access to health care, such as urban informal settlements. In such environments, a mixture of surface water runoff and human feces containing pathogenic microorganisms could be used as a surveillance surrogate.

Method

We conducted a temporal metagenomic analysis of urban sewage from Kibera, an urban informal settlement in Nairobi, Kenya, to detect and quantify bacterial and associated antimicrobial resistance (AMR) determinants, viral and parasitic pathogens. Data were examined in conjunction with data from ongoing clinical infectious disease surveillance.

Results

A large variation of read abundances related to bacteria, viruses, and parasites of medical importance, as well as bacterial associated antimicrobial resistance genes over time were detected. Significant increased abundances were observed for a number of bacterial pathogens coinciding with higher abundances of AMR genes. Vibrio cholerae as well as rotavirus A, among other virus peaked in several weeks during the study period whereas Cryptosporidium spp. and Giardia spp, varied more over time.

Conclusion

The metagenomic surveillance approach for monitoring circulating pathogens in sewage was able to detect putative pathogen and resistance loads in an urban informal settlement. Thus, valuable if generated in real time to serve as a comprehensive infectious disease agent surveillance system with the potential to guide disease prevention and treatment. The approach may lead to a paradigm shift in conducting real-time global genomics-based surveillance in settings with limited access to health care.

Helminthic Infections of the Central Nervous System

PURPOSE OF REVIEW

This article discusses select helminthic parasitic infections that may affect the central nervous system and reviews the epidemiology, neurologic presentation, recommended diagnostic testing, and treatment approach to these infections.

RECENT FINDINGS

Emigration from and travel to areas endemic for helminthic infections that affect the nervous system has led to increased incidence of parasitic neurologic disease in developed countries, necessitating that neurologists be familiar with the diagnostic and therapeutic approach to these diseases. Evidence is emerging on the optimal treatment for neurocysticercosis, which varies based on the form of the disease in the nervous system.

SUMMARY

Parenchymal neurocysticercosis is a leading cause of acquired epilepsy worldwide, and extraparenchymal neurocysticercosis is responsible for many cases of hydrocephalus. Recognition of the different stages and locations of neurocysticercosis is essential for proper management. Similarly, schistosomiasis constitutes a major cause of myelopathy in endemic areas and requires prompt diagnosis and treatment to avoid permanent deficits.

A highly multiplexed broad pathogen detection assay for infectious disease diagnostics

Rapid pathogen identification during an acute febrile illness is a critical first step for providing appropriate clinical care and patient isolation. Primary screening using sensitive and specific assays, such as real-time PCR and ELISAs, can rapidly test for known circulating infectious diseases. If the initial testing is negative, potentially due to a lack of developed diagnostic assays or an incomplete understanding of the pathogens circulating within a geographic region, additional testing would be required including highly multiplexed assays and metagenomic next generation sequencing. To bridge the gap between rapid point of care diagnostics and sequencing, we developed a highly multiplexed assay designed to detect 164 different viruses, bacteria, and parasites using the NanoString nCounter platform. Included in this assay were high consequence pathogens such as Ebola virus, highly endemic organisms including several Plasmodium species, and a large number of less prevalent pathogens to ensure a broad coverage of potential human pathogens. Evaluation of this panel resulted in positive detection of 113 (encompassing 98 different human pathogen types) of the 126 organisms available to us including the medically important Ebola virus, Lassa virus, dengue virus serotypes 1–4, Chikungunya virus, yellow fever virus, and Plasmodium falciparum. Overall, this assay could improve infectious disease diagnostics and biosurveillance efforts as a quick, highly multiplexed, and easy to use pathogen screening tool.

Identifying the causative agent in an acute febrile illness can be challenging diagnostically, especially when organisms in a particular region have overlapping clinical presentation or when that pathogen’s presence is unexpected. Ebola virus, for example, was not considered in an acute febrile illness differential diagnosis in West Africa until the explosive outbreak in 2013 presented the risk of infection. Besides the cost and time of screening a single patient sample for a large number of pathogens, limited sample volumes place further restrictions on what assays can be applied. Here, we developed a broad pathogen screening assay targeting 164 different human pathogens and show positive detection of over 100 of the organisms on the panel including Ebola virus, Plasmodium falciparum, and a large number of rare pathogens. The hands on time and sample volume requirement is minimal. The assay performed well in mock clinical and human clinical samples, demonstrating the clinical utility of this assay in cases where the initial diagnostic testing results in negative results. Our results provide a framework for further validation studies that would be required for formal clinical diagnostic applications.

Animal hoarding: The challenge for mental health, law enforcement, and animal welfare professionals

Animal hoarding has been considered a significant problem by animal welfare and law enforcement professionals for over a century. However, it has only been recognized as an indication of a mental disorder in the last decade. I review the different forms that animal hoarding can take and the current understanding of the prevalence, demographics and possible etiology of this disorder. Conventional animal cruelty laws have often been inadequate to respond to animal hoarding cases until they reach levels that may involve serious harm to animals and people. I document how prosecution of such cases can be difficult and often does not adequately consider the mental health issues underlying the problem or the high likelihood of recidivism. Attempts to solve these problems by enacting new laws specifically addressing animal hoarding have been controversial and ineffective. I explore new approaches that coordinate a variety of community resources in response to hoarding cases that offer the best opportunity to respond to both the human and animal problems associated with animal hoarding.

Evolutionary emergence of infectious diseases in heterogeneous host populations

The emergence and re-emergence of pathogens remains a major public health concern. Unfortunately, when and where pathogens will (re-)emerge is notoriously difficult to predict, as the erratic nature of those events is reinforced by the stochastic nature of pathogen evolution during the early phase of an epidemic. For instance, mutations allowing pathogens to escape host resistance may boost pathogen spread and promote emergence. Yet, the ecological factors that govern such evolutionary emergence remain elusive because of the lack of ecological realism of current theoretical frameworks and the difficulty of experimentally testing their predictions. Here, we develop a theoretical model to explore the effects of the heterogeneity of the host population on the probability of pathogen emergence, with or without pathogen evolution. We show that evolutionary emergence and the spread of escape mutations in the pathogen population is more likely to occur when the host population contains an intermediate proportion of resistant hosts. We also show that the probability of pathogen emergence rapidly declines with the diversity of resistance in the host population. Experimental tests using lytic bacteriophages infecting their bacterial hosts containing Clustered Regularly Interspaced Short Palindromic Repeat and CRISPR-associated (CRISPR-Cas) immune defenses confirm these theoretical predictions. These results suggest effective strategies for cross-species spillover and for the management of emerging infectious diseases.

The probability that an epidemic will break out is highly dependent on the ability of the pathogen to acquire new adaptive mutations and to induce evolutionary emergence. Forecasting pathogen emergence thus requires a good understanding of the interplay between the epidemiology and evolution taking place at the onset of an outbreak. Here, we provide a comprehensive theoretical framework to analyze the impact of host population heterogeneity on the probability of pathogen evolutionary emergence. We use this model to predict the impact of the fraction of susceptible hosts, the inoculum size of the pathogen, and the diversity of host resistance on pathogen emergence. Our experiments using lytic bacteriophages and CRISPR-resistant bacteria support our theoretical predictions and demonstrate that manipulating the diversity of resistance alleles in a host population may be an effective way to limit the emergence of new pathogens.

Application of Dendrimers for the Treatment of Infectious Diseases

Dendrimers are drug delivery systems that are characterized by a three-dimensional, star-shaped, branched macromolecular network. They possess ideal properties such as low polydispersity index, biocompatibility and good water solubility. They are made up of the interior and the exterior layers. The exterior layer consists of functional groups that are useful for conjugation of drugs and targeting moieties. The interior layer exhibits improved drug encapsulation efficiency, reduced drug toxicity, and controlled release mechanisms. These unique properties make them useful for drug delivery. Dendrimers have attracted considerable attention as drug delivery system for the treatment of infectious diseases. The treatment of infectious diseases is hampered severely by drug resistance. Several properties of dendrimers such as their ability to overcome drug resistance, toxicity and control the release mechanism of the encapsulated drugs make them ideal systems for the treatment of infectious disease. The aim of this review is to discuss the potentials of dendrimers for the treatment of viral and parasitic infections.

Navigating the jungles of tropical infectious gastrointestinal pathology: a pattern-based approach to the endoscopic biopsy

International travels and global human migration have had the unforeseen consequence of increasing the exposure of histopathologists in developed countries to the pathology of tropical infectious disease. The gastrointestinal tract (GIT) is often the primary site of infection due to the faecal-oral route of transmission and the high risk of exposure to contaminated water, food or soil when travelling to these regions. Whilst current microbiologic techniques are far more sensitive than histology in detecting infectious pathogens, the histopathologist nonetheless retains a pivotal role in diagnosing tropical GIT disease. This role entails evaluating endoscopic biopsies for any characteristic inflammatory pattern, identifying pathogens which may be present and excluding other look-alike pathologies. Recent advances in commercially available diagnostic modalities, including molecular techniques, have further broadened the scope of the histopathologist's armamentarium. This review outlines a practical pattern-based approach to diagnosing tropical GIT infections in endoscopic material, so as to assist pathologists less familiar with this spectrum of pathology.

Metal-Based Nanoparticles for the Treatment of Infectious Diseases

Infectious diseases can be transmitted and they cause a significant burden on public health globally. They are the greatest world killers and it is estimated that they are responsible for the demise of over 17 million people annually. The impact of these diseases is greater in the developing countries. People with compromised immune systems and children are the most affected. Infectious diseases may be caused by bacteria, viruses, and protozoa. The treatment of infectious diseases is hampered by simultaneous resistance to multiple drugs, indicating that there is a serious and pressing need to develop new therapeutics that can overcome drug resistance. This review will focus on the recent reports of metal-based nanoparticles that are potential therapeutics for the treatment of infectious diseases and their biological efficacy (in vitro and in vivo).

Reprint of "Neurocysticercosis-related mortality in Brazil, 2000-2011: Epidemiology of a neglected neurologic cause of death"

Neurocysticercosis (NCC) is an important cause of severe neurological disease mainly in low- and middle-income countries, but data on NCC mortality from endemic areas are scarce. Here we analysed the epidemiological patterns of NCC-related mortality in Brazil. We included all deaths recorded in Brazil between 2000 and 2011, in which NCC was mentioned on death certificates, either as underlying or as associated cause of death. NCC was identified in 1829/12,491,280 deaths (0.015%), 1130 (61.8%) as underlying cause, and 699 (38.2%) as associated cause. Overall age-adjusted mortality rate for the period was 0.97 deaths/1,000,000 inhabitants (95% confidence interval [CI]: 0.83-1.12). The highest NCC-related mortality rates were found in males, elderly, white race/colour and residents in endemic states/regions. Age-adjusted mortality rates at national level decreased significantly over time (annual percent change [APC]: -4.7; 95% CI: -6.0 to -3.3), with a decrease in the Southeast, South and Central-West regions, and a non-significant increasing trend in the North and Northeast regions. We identified spatial and spatiotemporal high-risk mortality clusters located mainly in NCC-endemic areas. Conditions related to the nervous system were the most commonly associated causes of death when NCC was mentioned as an underlying cause, and HIV/AIDS was the main underlying cause when NCC was an associated cause. NCC is a neglected and preventable cause of severe neurologic disease and death with high public health impact in Brazil. There is a clear need to strengthen nationwide epidemiological surveillance and control for the taeniasis/cysticercosis complex.

Amplicon-Based Pyrosequencing Reveals High Diversity of Protistan Parasites in Ships' Ballast Water: Implications for Biogeography and Infectious Diseases

Ships' ballast water (BW) commonly moves macroorganisms and microorganisms across the world's oceans and along coasts; however, the majority of these microbial transfers have gone undetected. We applied high-throughput sequencing methods to identify microbial eukaryotes, specifically emphasizing the protistan parasites, in ships' BW collected from vessels calling to the Chesapeake Bay (Virginia and Maryland, USA) from European and Eastern Canadian ports. We utilized tagged-amplicon 454 pyrosequencing with two general primer sets, amplifying either the V4 or V9 domain of the small subunit (SSU) of the ribosomal RNA (rRNA) gene complex, from total DNA extracted from water samples collected from the ballast tanks of bulk cargo vessels. We detected a diverse group of protistan taxa, with some known to contain important parasites in marine systems, including Apicomplexa (unidentified apicomplexans, unidentified gregarines, Cryptosporidium spp.), Dinophyta (Blastodinium spp., Euduboscquella sp., unidentified syndinids, Karlodinium spp., Syndinium spp.), Perkinsea (Parvilucifera sp.), Opisthokonta (Ichthyosporea sp., Pseudoperkinsidae, unidentified ichthyosporeans), and Stramenopiles (Labyrinthulomycetes). Further characterization of groups with parasitic taxa, consisting of phylogenetic analyses for four taxa (Cryptosporidium spp., Parvilucifera spp., Labyrinthulomycetes, and Ichthyosporea), revealed that sequences were obtained from both known and novel lineages. This study demonstrates that high-throughput sequencing is a viable and sensitive method for detecting parasitic protists when present and transported in the ballast water of ships. These data also underscore the potential importance of human-aided dispersal in the biogeography of these microbes and emerging diseases in the world's oceans.

Electrochemical magnetic microbeads-based biosensor for point-of-care serodiagnosis of infectious diseases

Access to appropriate diagnostic tools is an essential component in the evaluation and improvement of global health. Additionally, timely detection of infectious agents is critical in early diagnosis and treatment of infectious diseases. Conventional pathogen detection methods such as culturing, enzyme linked immunosorbent assay (ELISA) or polymerase chain reaction (PCR) require long assay times, and complex and expensive instruments making them not adaptable to point-of-care (PoC) needs at resource-constrained places and primary care settings. Therefore, there is an unmet need to develop portable, simple, rapid, and accurate methods for PoC detection of infections. Here, we present the development and validation of a portable, robust and inexpensive electrochemical magnetic microbeads-based biosensor (EMBIA) platform for PoC serodiagnosis of infectious diseases caused by different types of microorganisms (parasitic protozoa, bacteria and viruses). We demonstrate the potential use of the EMBIA platform for in situ diagnosis of human (Chagas disease and human brucellosis) and animal (bovine brucellosis and foot-and-mouth disease) infections clearly differentiating infected from non-infected individuals or animals. For Chagas disease, a more extensive validation of the test was performed showing that the EMBIA platform displayed an excellent diagnostic performance almost indistinguishable, in terms of specificity and sensitivity, from a fluorescent immunomagnetic assay and the conventional ELISA using the same combination of antigens. This platform technology could potentially be applicable to diagnose other infectious and non-infectious diseases as well as detection and/or quantification of biomarkers at the POC and primary care settings.

Impact of climate change on human infectious diseases: Empirical evidence and human adaptation

Climate change refers to long-term shifts in weather conditions and patterns of extreme weather events. It may lead to changes in health threat to human beings, multiplying existing health problems. This review examines the scientific evidences on the impact of climate change on human infectious diseases. It identifies research progress and gaps on how human society may respond to, adapt to, and prepare for the related changes. Based on a survey of related publications between 1990 and 2015, the terms used for literature selection reflect three aspects--the components of infectious diseases, climate variables, and selected infectious diseases. Humans' vulnerability to the potential health impacts by climate change is evident in literature. As an active agent, human beings may control the related health effects that may be effectively controlled through adopting proactive measures, including better understanding of the climate change patterns and of the compound disease-specific health effects, and effective allocation of technologies and resources to promote healthy lifestyles and public awareness. The following adaptation measures are recommended: 1) to go beyond empirical observations of the association between climate change and infectious diseases and develop more scientific explanations, 2) to improve the prediction of spatial-temporal process of climate change and the associated shifts in infectious diseases at various spatial and temporal scales, and 3) to establish locally effective early warning systems for the health effects of predicated climate change.

[THE CONDITION AND TENDENCIES OF DEVELOPMENT OF CLINICAL AND SANITARY MICROBIOLOGY IN THE RUSSIAN FEDERATION AND PROBLEM OF IMPORT SUBSTITUTION]

The import substitution becomes one of the strategic tasks of national economy as a result of prolongation of economic sanctions concerning the Russian Federation of part of the USA, EU countries, Japan and number of other countries. It is not proper to be limited in import substitution only by goods because in conditions ofsanctions when access toforeign technologies is complicated Russia is needed to substitute foreign technologies by national designs in faster manner One of directions of effective import substitution is localization of production of laboratory equipment and consumables for clinical and sanitary microbiology on the territory ofthe Russian Federation and countries of Customs union. In Russia, in the field ofdiagnostic of dangerous and socially significant infections, all components for import substitution to implement gene diagnostic, immune diagnostic. bio-sensory and biochip approaches, isolation and storage of live microbial cultures, implementation of high-tech methods of diagnostic are available. At the same time, national diagnostic instrument-making industry for microbiology is factually absent. The few devices of national production more than on 50% consist of import components. The microbiological laboratories are to be equipped only with import devices of open type for applying national components. The most perspective national designs to be implemented are multiplex polimerase chain reaction test-systems and biochips on the basis of national plotters and readers. The modern development of diagnostic equipment and diagnostic instruments requires supplement of national collections of bacterial and viral pathogens and working-through of organizational schemes of supplying collections with strains. The presented data concerning justification of nomenclature of laboratory equipment and consumables permits to satisfy in fill scope the needs of clinical and sanitary microbiology in devices, growth mediums, consumables of national production and to refuse import deliveries without decreasing quality of microbiological analysis. This approach will ensure appropriate response to occurring challenges and new biological dangers and maintenance of biosecurity of the Russian Federation at proper level.

Global and local health burden trade-off through the hybridisation of quantitative microbial risk assessment and life cycle assessment to aid water management

Life cycle assessment (LCA) and quantitative risk assessment (QRA) are commonly used to evaluate potential human health impacts associated with proposed or existing infrastructure and products. Each approach has a distinct objective and, consequently, their conclusions may be inconsistent or contradictory. It is proposed that the integration of elements of QRA and LCA may provide a more holistic approach to health impact assessment. Here we examine the possibility of merging LCA assessed human health impacts with quantitative microbial risk assessment (QMRA) for waterborne pathogen impacts, expressed with the common health metric, disability adjusted life years (DALYs). The example of a recent large-scale water recycling project in Sydney, Australia was used to identify and demonstrate the potential advantages and current limitations of this approach. A comparative analysis of two scenarios - with and without the development of this project - was undertaken for this purpose. LCA and QMRA were carried out independently for the two scenarios to compare human health impacts, as measured by DALYs lost per year. LCA results suggested that construction of the project would lead to an increased number of DALYs lost per year, while estimated disease burden resulting from microbial exposures indicated that it would result in the loss of fewer DALYs per year than the alternative scenario. By merging the results of the LCA and QMRA, we demonstrate the advantages in providing a more comprehensive assessment of human disease burden for the two scenarios, in particular, the importance of considering the results of both LCA and QRA in a comparative assessment of decision alternatives to avoid problem shifting. The application of DALYs as a common measure between the two approaches was found to be useful for this purpose.

The Spectrum of Infectious Diseases in Kidney Transplantation: A Review of the Classification, Pathogens and Clinical Manifestations

Kidney transplantation is the treatment-of-choice for a significant number of patients with end-stage renal disease. Renal transplant recipients (RTRs) benefit from a longer life expectancy, with a better quality of life. Despite, recent accomplishments in the field of kidney transplantation, both short- and long-term, surgical and medical complications still exist. Among these complications, cardiovascular disease, carcinogenesis and infections are the most important. Infectious diseases constitute the most common complications after renal transplantation and the second most common cause of death among RTRs with a functioning graft. Theoretically, all infectious pathogens could cause disease in immunocompromised RTRs, yet among these, one could identify more important ones, such as the Enterobacteriaceae, causing urinary tract infections; pneumonia due to Pneumocystis jirovecii; Candida species which cause invasive fungal infections; herpes viruses; hepatitis viruses and parasites. Early diagnosis and effective treatment are key elements in salvaging both the allograft and the patient. However, clinical manifestations and diagnosis of such infectious diseases are not easily identified due to the altered state of immune response of the RTR. Thus, apart from possessing a deep knowledge of the etiology and the treatment options in each case, transplant physicians should also always remain alert when dealing with RTRs.

In vivo experimental drug resistance study in Trypanosoma vivax isolates from tsetse infested and non-tsetse infested areas of Northwest Ethiopia

Ethiopia, particularly in the Northwest region, is affected by both tsetse fly and non-tsetse fly transmitted trypanosomosis with a significant impact on livestock productivity. The control of trypanosomosis in Ethiopia relies on either curative or prophylactic treatment of animals with diminazene aceturate (DA) or isometamidium chloride (ISM), respectively. However, since these two trypanocides have been on the market for more than 40 years, this may have resulted in drug-resistance. Therefore, in vivo drug resistance tests on two Ethiopian isolates of Trypanosoma vivax were completed, one from an area where tsetse flies are present and one from an area where tsetse flies are not present. Twenty four cattle (Bos indicus) aged between 6 and 12 months, purchased from a trypanosome-free area (Debre Brehan: Northcentral Ethiopia) and confirmed to be trypanosome-negative, were randomly assigned into four groups of six animals, which were infected with T. vivax isolated from a tsetse-infested or non-tsetse infested area, and in each case treated with curative doses of DA or ISM. Each animal were inoculated intravenously 3×10(6) trypanosomes from donor animals. Parasitaemia became patent earlier in infections with non-tsetse T. vivax (∼7 days post-infection) than tsetse (∼14 days post-infection). Both groups were treated at the highest peak parasitaemia with DA or ISM and nine cattle, four with non-tsetse T. vivax (two ISM- and two DA-treated) and five with tsetse T. vivax (three ISM- and two DA-treated) showed relapses of parasitaemia. Moreover, treatment did not improve diagnostic host markers of trypanosome infections in these animals. In conclusion, in vivo drug tests indicated the presence of resistant parasites (>20% of treated animals in each group relapsed) against recommended doses of both available trypanocidal drugs.

Surveillance for antimicrobial drug resistance in under-resourced countries

TOC summary: New programs can be improved by drawing on lessons from previous successful efforts.

Antimicrobial drug resistance is usually not monitored in under-resourced countries because they lack surveillance networks, laboratory capacity, and appropriate diagnostics. This accelerating problem accounts for substantial number of excess deaths, especially among infants. Infections particularly affected by antimicrobial drug resistance include tuberculosis, malaria, severe acute respiratory infections, and sepsis caused by gram-negative bacteria. Nonetheless, mapping antimicrobial drug resistance is feasible in under-resourced countries, and lessons can be learned from previous successful efforts. Specimen shipping conditions, data standardization, absence of contamination, and adequate diagnostics must be ensured. As a first step toward solving this problem, we propose that a road map be created at the international level to strengthen antimicrobial resistance surveillance in under-resourced countries. This effort should include a research agenda; a map of existing networks and recommendations to unite them; and a communication plan for national, regional, and international organizations and funding agencies.

Standardized metadata for human pathogen/vector genomic sequences

High throughput sequencing has accelerated the determination of genome sequences for thousands of human infectious disease pathogens and dozens of their vectors. The scale and scope of these data are enabling genotype-phenotype association studies to identify genetic determinants of pathogen virulence and drug/insecticide resistance, and phylogenetic studies to track the origin and spread of disease outbreaks. To maximize the utility of genomic sequences for these purposes, it is essential that metadata about the pathogen/vector isolate characteristics be collected and made available in organized, clear, and consistent formats. Here we report the development of the GSCID/BRC Project and Sample Application Standard, developed by representatives of the Genome Sequencing Centers for Infectious Diseases (GSCIDs), the Bioinformatics Resource Centers (BRCs) for Infectious Diseases, and the U.S. National Institute of Allergy and Infectious Diseases (NIAID), part of the National Institutes of Health (NIH), informed by interactions with numerous collaborating scientists. It includes mapping to terms from other data standards initiatives, including the Genomic Standards Consortium's minimal information (MIxS) and NCBI's BioSample/BioProjects checklists and the Ontology for Biomedical Investigations (OBI). The standard includes data fields about characteristics of the organism or environmental source of the specimen, spatial-temporal information about the specimen isolation event, phenotypic characteristics of the pathogen/vector isolated, and project leadership and support. By modeling metadata fields into an ontology-based semantic framework and reusing existing ontologies and minimum information checklists, the application standard can be extended to support additional project-specific data fields and integrated with other data represented with comparable standards. The use of this metadata standard by all ongoing and future GSCID sequencing projects will provide a consistent representation of these data in the BRC resources and other repositories that leverage these data, allowing investigators to identify relevant genomic sequences and perform comparative genomics analyses that are both statistically meaningful and biologically relevant.

Timing of pathogen adaptation to a multicomponent treatment

The sustainable use of multicomponent treatments such as combination therapies, combination vaccines/chemicals, and plants carrying multigenic resistance requires an understanding of how their population-wide deployment affects the speed of the pathogen adaptation. Here, we develop a stochastic model describing the emergence of a mutant pathogen and its dynamics in a heterogeneous host population split into various types by the management strategy. Based on a multi-type Markov birth and death process, the model can be used to provide a basic understanding of how the life-cycle parameters of the pathogen population, and the controllable parameters of a management strategy affect the speed at which a pathogen adapts to a multicomponent treatment. Our results reveal the importance of coupling stochastic mutation and migration processes, and illustrate how their stochasticity can alter our view of the principles of managing pathogen adaptive dynamics at the population level. In particular, we identify the growth and migration rates that allow pathogens to adapt to a multicomponent treatment even if it is deployed on only small proportions of the host. In contrast to the accepted view, our model suggests that treatment durability should not systematically be identified with mutation cost. We show also that associating a multicomponent treatment with defeated monocomponent treatments can be more durable than associating it with intermediate treatments including only some of the components. We conclude that the explicit modelling of stochastic processes underlying evolutionary dynamics could help to elucidate the principles of the sustainable use of multicomponent treatments in population-wide management strategies intended to impede the evolution of harmful populations.

Humanized mice for the study of infectious diseases

Many of the pathogens that cause human infectious diseases do not infect rodents or other mammalian species. Small animal models that allow studies of the pathogenesis of these agents and evaluation of drug efficacy are critical for identifying ways to prevent and treat human infectious diseases. Immunodeficient mice engrafted with functional human cells and tissues, termed 'humanized' mice, represent a critical pre-clinical bridge for in vivo studies of human pathogens. Recent advances in the development of humanized mice have allowed in vivo studies of multiple human infectious agents providing novel insights into their pathogenesis that was otherwise not possible.

Montpellier Infectious Diseases (MID), 2nd annual meeting (2012)

For the second consecutive year, teams of the network "Montpellier Infectious Diseases" held their annual meeting. Whereas the 2011 meeting was focused on host-pathogen interaction and pathophysiology, the 2012 meeting was focused on the cooperation between medical and chemical sciences interdisciplinary approaches to fight against virus, bacteria and parasites. Several approaches aimed at designing new bioactive compounds were described during this meeting.

The role of remote sensing and GIS for spatial prediction of vector-borne diseases transmission: a systematic review

There have been several attempts made to the appreciation of remote sensing and GIS for the study of vectors, biodiversity, vector presence, vector abundance and the vector-borne diseases with respect to space and time. This study was made for reviewing and appraising the potential use of remote sensing and GIS applications for spatial prediction of vector-borne diseases transmission. The nature of the presence and the abundance of vectors and vector-borne diseases, disease infection and the disease transmission are not ubiquitous and are confined with geographical, environmental and climatic factors, and are localized. The presence of vectors and vector-borne diseases is most complex in nature, however, it is confined and fueled by the geographical, climatic and environmental factors including man-made factors. The usefulness of the present day availability of the information derived from the satellite data including vegetation indices of canopy cover and its density, soil types, soil moisture, soil texture, soil depth, etc. is integrating the information in the expert GIS engine for the spatial analysis of other geoclimatic and geoenvironmental variables. The present study gives the detailed information on the classical studies of the past and present, and the future role of remote sensing and GIS for the vector-borne diseases control. The ecological modeling directly gives us the relevant information to understand the spatial variation of the vector biodiversity, vector presence, vector abundance and the vector-borne diseases in association with geoclimatic and the environmental variables. The probability map of the geographical distribution and seasonal variations of horizontal and vertical distribution of vector abundance and its association with vector -borne diseases can be obtained with low cost remote sensing and GIS tool with reliable data and speed.

Tropical diseases: definition, geographic distribution, transmission, and classification

The term tropical diseases encompasses all diseases that occur principally in the tropics. This term covers all communicable and noncommunicable diseases, genetic disorders, and disease caused by nutritional deficiencies or environmental conditions (such as heat, humidity, and altitude) that are encountered in areas that lie between, and alongside, the Tropic of Cancer and Tropic of Capricorn belts. In tropical countries, apart from noncommunicable diseases, a severe burden of disease is caused by an array of different microorganisms, parasites, land and sea animals, and arthropods.

Evolutionary determinants of genetic variation in susceptibility to infectious diseases in humans

Although genetic variation among humans in their susceptibility to infectious diseases has long been appreciated, little focus has been devoted to identifying patterns in levels of variation in susceptibility to different diseases. Levels of genetic variation in susceptibility associated with 40 human infectious diseases were assessed by a survey of studies on both pedigree-based quantitative variation, as well as studies on different classes of marker alleles. These estimates were correlated with pathogen traits, epidemiological characteristics, and effectiveness of the human immune response. The strongest predictors of levels of genetic variation in susceptibility were disease characteristics negatively associated with immune effectiveness. High levels of genetic variation were associated with diseases with long infectious periods and for which vaccine development attempts have been unsuccessful. These findings are consistent with predictions based on theoretical models incorporating fitness costs associated with the different types of resistance mechanisms. An appreciation of these observed patterns will be a valuable tool in directing future research given that genetic variation in disease susceptibility has large implications for vaccine development and epidemiology.

Of mice and microflora: considerations for genetically engineered mice

The phenotype of genetically engineered mice is a combination of both genetic and environmental factors that include the microflora of the mouse. The impact a particular microbe has on a mouse reflects the host-microbe interaction within the context of the mouse genotype and environment. Although often considered a confounding variable, many host-microbe interactions have resulted in the generation of novel model systems and characterization of new microbial agents. Microbes associated with overt disease in mice have been the historical focus of the laboratory animal medical and pathology community and literature. The advent of genetic engineering and the complex of mouse models have revealed previously unknown or disregarded agents that now oblige the attention of the biomedical research community. The purpose of this article is to describe and illustrate how phenotypes can be affected by microflora by focusing on the infectious diseases present in genetically engineered mouse (GEM) colonies of our collective institutions and by reviewing important agents that are rarely seen in most research facilities today. The goal is to introduce the concept of the role of microflora on phenotypes and in translational research using GEM models.

Behavioural defences in animals against pathogens and parasites: parallels with the pillars of medicine in humans

No other theme in animal biology seems to be more central than the concept of employing strategies to survive and successfully reproduce. In nature, controlling or avoiding pathogens and parasites is an essential fitness strategy because of the ever-present disease-causing organisms. The disease-control strategies discussed here are: physical avoidance and removal of pathogens and parasites; quarantine or peripheralization of conspecifics that could be carrying potential pathogens; herbal medicine, animal style, to prevent or treat an infection; potentiation of the immune system; and care of sick or injured group members. These strategies are seen as also encompassing the pillars of human medicine: (i) quarantine; (ii) immune-boosting vaccinations; (iii) use of medicinal products; and (iv) caring or nursing. In contrast to animals, in humans, the disease-control strategies have been consolidated into a consistent and extensive medical system. A hypothesis that explains some of this difference between animals and humans is that humans are sick more often than animals. This increase in sickness in humans leading to an extensive, cognitively driven medical system is attributed to an evolutionary dietary transition from mostly natural vegetation to a meat-based diet, with an increase in health-eroding free radicals and a dietary reduction of free-radical-scavenging antioxidants.

QMRAspot: a tool for Quantitative Microbial Risk Assessment from surface water to potable water

In the Netherlands, a health based target for microbially safe drinking water is set at less than one infection per 10,000 persons per year. For the assessment of the microbial safety of drinking water, Dutch drinking water suppliers must conduct a Quantitative Microbial Risk Assessment (QMRA) at least every three years for the so-called index pathogens enterovirus, Campylobacter, Cryptosporidium and Giardia. In order to collect raw data in the proper format and to automate the process of QMRA, an interactive user-friendly computational tool, QMRAspot, was developed to analyze and conduct QMRA for drinking water produced from surface water. This paper gives a description of the raw data requirements for QMRA as well as a functional description of the tool. No extensive prior knowledge about QMRA modeling is required by the user, because QMRAspot provides guidance to the user on the quantity, type and format of raw data and performs a complete analysis of the raw data to yield a risk outcome for drinking water consumption that can be compared with other production locations, a legislative standard or an acceptable health based target. The uniform approach promotes proper collection and usage of raw data and, warrants quality of the risk assessment as well as enhances efficiency, i.e., less time is required. QMRAspot may facilitate QMRA for drinking water suppliers worldwide. The tool aids policy makers and other involved parties in formulating mitigation strategies, and prioritization and evaluation of effective preventive measures as integral part of water safety plans.

Tracing personalized health curves during infections

By concentrating on the relationship between health and microbe number over the course of infections, most pathogenic and mutualistic infections can be summarized by a small alphabet of curves, which has implications not only for basic research but for how we might treat patients.

It is difficult to describe host–microbe interactions in a manner that deals well with both pathogens and mutualists. Perhaps a way can be found using an ecological definition of tolerance, where tolerance is defined as the dose response curve of health versus parasite load. To plot tolerance, individual infections are summarized by reporting the maximum parasite load and the minimum health for a population of infected individuals and the slope of the resulting curve defines the tolerance of the population. We can borrow this method of plotting health versus microbe load in a population and make it apply to individuals; instead of plotting just one point that summarizes an infection in an individual, we can plot the values at many time points over the course of an infection for one individual. This produces curves that trace the course of an infection through phase space rather than over a more typical timeline. These curves highlight relationships like recovery and point out bifurcations that are difficult to visualize with standard plotting techniques. Only nine archetypical curves are needed to describe most pathogenic and mutualistic host–microbe interactions. The technique holds promise as both a qualitative and quantitative approach to dissect host–microbe interactions of all kinds.

A review of infectious gill disease in marine salmonid fish

Infectious gill diseases of marine salmonid fish present a significant challenge in salmon-farming regions. Infectious syndromes or disease conditions affecting marine-farmed salmonids include amoebic gill disease (AGD), proliferative gill inflammation (PGI) and tenacibaculosis. Pathogens involved include parasites, such as Neoparamoeba perurans, bacteria, such as Piscichlamydia salmonis and Tenacibaculum maritimum, and viruses, such as the Atlantic salmon paramyxovirus (ASPV). The present level of understanding of these is reviewed with regard to risk factors, potential impacting factors, methods of best practice to mitigate infectious gill disease, as well as knowledge gaps and avenues for future research.

Parasite prevalence and the worldwide distribution of cognitive ability

In this study, we hypothesize that the worldwide distribution of cognitive ability is determined in part by variation in the intensity of infectious diseases. From an energetics standpoint, a developing human will have difficulty building a brain and fighting off infectious diseases at the same time, as both are very metabolically costly tasks. Using three measures of average national intelligence quotient (IQ), we found that the zero-order correlation between average IQ and parasite stress ranges from r=-0.76 to r=-0.82 (p<0.0001). These correlations are robust worldwide, as well as within five of six world regions. Infectious disease remains the most powerful predictor of average national IQ when temperature, distance from Africa, gross domestic product per capita and several measures of education are controlled for. These findings suggest that the Flynn effect may be caused in part by the decrease in the intensity of infectious diseases as nations develop.

Detection of blood-transmissible agents: can screening be miniaturized?

Transfusion safety relating to blood-transmissible agents is a major public health concern, particularly when faced with the continuing emergence of new infectious agents. These include new viruses appearing alongside other known reemerging viruses (West Nile virus, Chikungunya) as well as new strains of bacteria and parasites (Plasmodium falciparum, Trypanosoma cruzi) and finally pathologic prion protein (variant Creutzfeldt-Jakob disease). Genomic mutations of known viruses (hepatitis B virus, hepatitis C virus, human immunodeficiency virus) can also be at the origin of variants susceptible to escaping detection by diagnostic tests. New technologies that would allow the simultaneous detection of several blood-transmissible agents are now needed for the development and improvement of screening strategies. DNA microarrays have been developed for use in immunohematology laboratories for blood group genotyping. Their application in the detection of infectious agents, however, has been hindered by additional technological hurdles. For instance, the variability among and within genomes of interest complicate target amplification and multiplex analysis. Advances in biosensor technologies based on alternative detection strategies have offered new perspectives on pathogen detection; however, whether they are adaptable to diagnostic applications testing biologic fluids is under debate. Elsewhere, current nanotechnologies now offer new tools to improve the sample preparation, target capture, and detection steps. Second-generation devices combining micro- and nanotechnologies have brought us one step closer to the potential development of innovative and multiplexed approaches applicable to the screening of blood for transmissible agents.

Infectious hepatopathies in dogs and cats

This article serves to review the various infectious diseases that affect the liver primarily or as a part of systemic infection. Although bacterial infections are probably the most common cause of infectious hepatitis, the clinician should be aware of other potential organisms and other commonly involved systems. Therefore, this article includes a description of common bacterial, mycobacterial, viral, fungal, protozoal, parasitic, and rickettsial diseases in dogs and cats.

Species decline and extinction: synergy of infectious disease and Allee effect?

Host-parasite models with density-dependent (mass action) incidence and a critical Allee effect in host growth can explain both species decline and disappearance (extinction). The behaviour of the model is consistent with both the novel pathogen hypothesis and the endemic pathogen hypothesis for chytridiomycosis. Mathematically, the transition from decline to disappearance is mediated by a Hopf bifurcation and is marked by the occurrence of a heteroclinic orbit. The Hopf bifurcation is supercritical if intra-specific host competition increases with host density at a large power and subcritical if the power is small. In the supercritical case, host-parasite coexistence can be at equilibrium or periodic; in the subcritical case it is only at equilibrium.