gcPathogen: a comprehensive genomic resource of human pathogens for public health.

Here, we present the manually curated Global Catalogue of Pathogens (gcPathogen), an extensive genomic resource designed to facilitate rapid and accurate pathogen analysis, epidemiological exploration and monitoring of antibiotic resistance features and virulence factors. The catalogue seamlessly integrates and analyzes genomic data and associated metadata for human pathogens isolated from infected patients, animal hosts, food and the environment. The pathogen list is supported by evidence from medical or government pathogenic lists and publications. The current version of gcPathogen boasts an impressive collection of 1 164 974 assemblies comprising 986 044 strains from 497 bacterial taxa, 4794 assemblies encompassing 4319 strains from 265 fungal taxa, 89 965 assemblies featuring 13 687 strains from 222 viral taxa, and 646 assemblies including 387 strains from 159 parasitic taxa. Through this database, researchers gain access to a comprehensive 'one-stop shop' that facilitates global, long-term public health surveillance while enabling in-depth analysis of genomes, sequence types, antibiotic resistance genes, virulence factors and mobile genetic elements across different countries, diseases and hosts. To access and explore the data and statistics, an interactive web interface has been developed, which can be accessed at https://nmdc.cn/gcpathogen/. This user-friendly platform allows seamless querying and exploration of the extensive information housed within the gcPathogen database.

Overview of game meat utilisation challenges and opportunities: A European perspective.

Re-wilding and similar initiatives have resulted in an increase in wildlife suitable for human consumption in Europe. However, game meat production and consumption present several challenges, including infectious diseases which pose risks to livestock, processers, and consumers. This review provides insights into the infectious diseases and toxic contaminants associated with game meat. The effect of killing method on the meat quality is also discussed and means of improving the meat quality of game meat is elucidated. The use of different food safety systems that could be applied to provide safe meat is reported. The importance of collaborative multi-sector approaches is emphasized, to generate and distribute knowledge and implement One Health strategies that ensure the safe, traceable, sustainable, and professional development of commercial game meat supply chains.

Frequency of intestinal protozoan infections diagnosed in patients from a clinical analysis laboratory

This study aimed to determine the frequency of infection by intestinal protozoa diagnosed in patients from a clinical analysis laboratory in Maceió, Alagoas, Brazil. This was a retrospective descriptive study, using a database of stool examination results from July to December 2015. The study population consisted of males and females of all ages, from the greater area of Alagoas. Data on epidemiological variables such as age and gender were obtained using a collection instrument. Protozoan species were identified from stool examinations. Results on the prevalence of intestinal parasites are described as simple and relative frequencies. We examined a total of 1277 stool samples, of which 12.69% were positive for one or more protozoa. 43.83% were from men and 56.17% were from women. Endolimax nana was the most prevalent (59.22%) protozoan species followed by Entamoeba coli (23.45%). Although non-pathogenic, they indicate fecal contamination of drinking water. The highest number (23.46%) of infected individuals was observed among children in the 0 to 11 years age group. A high prevalence (93.83%) of monoparasitism was noted. We concluded that there was a high frequency of infection and a high prevalence of E. nana. Infections were more common in women than in men. Our results emphasize the need for preventive measures to control intestinal parasitic infections.

Enteric pathogens induce tissue tolerance and prevent neuronal loss from subsequent infections.

The enteric nervous system (ENS) controls several intestinal functions including motility and nutrient handling, which can be disrupted by infection-induced neuropathies or neuronal cell death. We investigated possible tolerance mechanisms preventing neuronal loss and disruption in gut motility after pathogen exposure. We found that following enteric infections, muscularis macrophages (MMs) acquire a tissue-protective phenotype that prevents neuronal loss, dysmotility, and maintains energy balance during subsequent challenge with unrelated pathogens. Bacteria-induced neuroprotection relied on activation of gut-projecting sympathetic neurons and signaling via ß2-adrenergic receptors (ß2AR) on MMs. In contrast, helminth-mediated neuroprotection was dependent on T cells and systemic production of interleukin (IL)-4 and IL-13 by eosinophils, which induced arginase-expressing MMs that prevented neuronal loss from an unrelated infection located in a different intestinal region. Collectively, these data suggest that distinct enteric pathogens trigger a state of disease or tissue tolerance that preserves ENS number and functionality.

Revisão integrativa sobre doenças parasitárias em crianças de creches brasileiras / Integrative review on parasitic diseases in children in brazilian day care centers

As parasitoses intestinais constituem um importante problema de Saúde Pública, especialmente entre os pré-escolares, devido à imaturidade do sistema imune. Assim, este estudo objetivou realizar uma revisão integrativa dos estudos publicados entre os anos de 2010 a 2017 sobre parasitoses intestinais e os fatores associados ao desenvolvimento em crianças matriculadas em creches brasileiras. Foi realizada busca bibliográfica através das bases de dados Medline, Lilacs e SciELO, utilizando os descritores: infecção, parasitoses, diarreia e creches, e seus correspondentes em inglês: "infection", "parasitc diseases", "diarrhea" e "child day care centers". No caso das buscas no Medline o descritor Brazil também foi usado. Foram identificados 59 estudos, dos quais 11 foram incluídos no presente trabalho. Foi observado variação de 19,4% a 98,4% de parasitos e, a Giardia duodenalis foi o mais prevalente em crianças entre um e seis anos de idade, gênero masculino, com baixo peso, advindas de residências com alta densidade familiar e nível socioeconômico baixo. As análises mostraram a importância da compreensão dos fatores de risco para a incidência de parasitos, indicando a necessidade da promoção de estratégias efetivas para prevenção e controle das infecções parasitárias no país, visto que, tais infecções influenciam diretamente no desenvolvimento da criança, e em alguns casos, evoluindo a óbito.

Intestinal parasitosis is an important public health issue especially among pre-school children due to the immaturity of their immune system. Thus, this study aimed at carrying out an integrative review of studies published between 2010 and 2017 regarding intestinal parasites and associated factors in children registered in Brazilian day care centers. A bibliographic survey was performed through the Medline, Lilacs, and SciELO databases using the following descriptors: infection, parasitic diseases, diarrhea, and child day care centers, as well as their corresponding translations in Portuguese: "infecção", "parasitoses", "diarreia" and "creches". In the case of Medline searches, the descriptor Brazil was also used. Fifty-nine studies were identified, from which, 11 were included in this study. A variation of 19.4% to 98.4% of parasites could be observed, with Giardia duodenalis being the most prevalent in children between one and six years old, male, with low weight, coming from homes with high family density and low socioeconomic status. The analyzes showed the importance of understanding the risk factors for the incidence of parasites, showing the need to promote effective strategies for the prevention and control of parasitic infections in the country, since such infections have direct influence on the child's development, and in some cases, even evolving to death.

A Comprehensive Review on Crustaceans' Immune System With a Focus on Freshwater Crayfish in Relation to Crayfish Plague Disease.

Freshwater crayfish immunity has received great attention due to the need for urgent conservation. This concern has increased the understanding of the cellular and humoral defense systems, although the regulatory mechanisms involved in these processes need updating. There are, however, aspects of the immune response that require clarification and integration. The particular issues addressed in this review include an overall description of the oomycete Aphanomyces astaci, the causative agent of the pandemic plague disease, which affects freshwater crayfish, and an overview of crustaceans' immunity with a focus on freshwater crayfish. It includes a classification system of hemocyte sub-types, the molecular factors involved in hematopoiesis and the differential role of the hemocyte subpopulations in cell-mediated responses, including hemocyte infiltration, inflammation, encapsulation and the link with the extracellular trap cell death pathway (ETosis). In addition, other topics discussed include the identity and functions of hyaline cells, the generation of neoplasia, and the emerging topic of the role of sessile hemocytes in peripheral immunity. Finally, attention is paid to the molecular execution of the immune response, from recognition by the pattern recognition receptors (PRRs), the role of the signaling network in propagating and maintaining the immune signals, to the effector elements such as the putative function of the Down syndrome adhesion molecules (Dscam) in innate immune memory.

Pathogen disgust sensitivity protects against infection in a high pathogen environment.

Disgust is hypothesized to be an evolved emotion that functions to regulate the avoidance of pathogen-related stimuli and behaviors. Individuals with higher pathogen disgust sensitivity (PDS) are predicted to be exposed to and thus infected by fewer pathogens, though no studies have tested this directly. Furthermore, PDS is hypothesized to be locally calibrated to the types of pathogens normally encountered and the fitness-related costs and benefits of infection and avoidance. Market integration (the degree of production for and consumption from market-based economies) influences the relative costs/benefits of pathogen exposure and avoidance through sanitation, hygiene, and lifestyle changes, and is thus predicted to affect PDS. Here, we examine the function of PDS in disease avoidance, its environmental calibration, and its socioecological variation by examining associations among PDS, market-related lifestyle factors, and measures of bacterial, viral, and macroparasitic infection at the individual, household, and community levels. Data were collected among 75 participants (ages 5 to 59 y) from 28 households in three Ecuadorian Shuar communities characterized by subsistence-based lifestyles and high pathogen burden, but experiencing rapid market integration. As predicted, we found strong negative associations between PDS and biomarkers of immune response to viral/bacterial infection, and weaker associations between PDS and measures of macroparasite infection, apparently mediated by market integration-related differences. We provide support for the previously untested hypothesis that PDS is negatively associated with infection, and document variation in PDS indicative of calibration to local socioeconomic conditions. More broadly, findings highlight the importance of evolved psychological mechanisms in human health outcomes.

The Effect of Olive Fruit Fly Bactrocera oleae (Rossi) Infestation on Certain Chemical Parameters of Produced Olive Oils.

Olives affected by active and damaging infestation (olive fruit fly Bactrocera oleae (Rossi)) were assayed for their chemical composition. Biophenols were determined by HPLC, sterols, triterpenic dialcohols, and fatty acids by gas chromatography analysis. The acquired data were statistically analyzed. Oils produced from "Istrska belica" fruit affected by active infestation compared to the oils made from fruit affected by damaging infestation showed higher amounts of total oleuropein biofenols (377.3 versus (vs.) 106.6 mg/kg), total biophenols (755 vs. 377 mg/kg), lignans (85.3 vs. 32.9 mg/kg), the dialdehydic form of decarboxymethyl oleuropein aglycone (DMO-Agl-dA) (148.3 vs. 49.0 mg/kg), its oxidized form (DMO-Agl-dA)ox (35.2 vs. 8.5 mg/kg), the dialdehydic form of oleuropein aglycone (O-Agl-dA) (61.1 vs. 8.0 mg/kg), the dialdehydic form of ligstroside aglycone (L-Agl-dA) (63.5 vs. 28.0 mg/kg), the aldehydic form of oleuropein aglycone (O-Agl-A) (40.6 vs. 8.4 mg/kg), and lower amounts of tyrosol (Tyr) (6.0 vs. 13. 9 mg/kg) and the aldehydic form of ligstroside aglycone (L-Agl-A) (13.8 vs. 40.3 mg/kg). Higher values of stigmasterol (2.99%) and lower values of campesterol (2.25%) were determined in oils affected by damaging infestation; an increase in triterpenic dialcohols was also observed (3.04% for damaging and 1.62% for active infestation). Oils affected by damaging infestation, compared to active infestation, showed lower amounts of oleic acid (73.89 vs. 75.15%) and higher amounts of myristic (0.013 vs. 0.011%), linoleic (7.27 vs. 6.48%), and linolenic (0.74 vs. 0.61%) acids.

How many human pathogens are there in Laos? An estimate of national human pathogen diversity and analysis of historical trends.

OBJECTIVE: The emergence of infectious diseases pose major global health threats. Estimates of total in-country human pathogen diversity, and insights as to how and when species were described through history, could be used to estimate the probability of new pathogen discoveries. Data from the Lao People's Democratic Republic (Laos) were used in this proof-of-concept study to estimate national human pathogen diversity and to examine historical discovery rate drivers. METHODS: A systematic survey of the French and English scientific and grey literature of pathogen description in Laos between 1874 and 2017 was conducted. The first descriptions of each known human pathogen in Laos were coded according to the diagnostic evidence available. Cumulative frequency of discovery across time informed the rate of discovery. Four distinct periods of health systems development in Laos were identified prospectively and juxtaposed to the unmodelled rate of discovery. A model with a time-varying rate of discovery was fitted to these data using a Markov-Chain- Monte-Carlo technique. RESULTS: From 6456 pathogen descriptions, 245 discoveries of known human pathogens in Laos, including repeat discoveries using different grades of evidence, were identified. The models estimate that the Laos human pathogen species diversity in 2017 is between 169 and 206. During the last decade, there has been a 33-fold increase in the discovery rate coinciding with the strengthening of medical research and microbiology. CONCLUSION: Discovery curves can be used to model and estimate country-level human pathogen diversity present in a territory. Combining this with historical assessment improves the understanding of the factors affecting local pathogen discovery. PROSPERO REGISTRATION NUMBER: A protocol of this work was registered on PROSPERO (ID:CRD42016046728).

A morphological analysis of fresh and brine-cured olives attacked by Bactrocera oleae using light microscopy and ESEM-EDS.

The present study investigated the morphology of fresh and brine-cured table olives (TOs) as well as the changes that occur when drupes are attacked by the fruit fly Bactrocera oleae. Morphological analyses were performed using light microscopy (LM) and environmental scanning electron microscopy coupled with energy dispersive spectroscopy (ESEM-EDS). The LM analysis was carried out with visible light to evaluate sections stained with either PAS or Azan mixtures as well as unstained sections observed at fluorescence microscopy. The results of the analyses showed that: i) Azan and PAS staining played a useful complementary role, increasing the information provided by the histological analysis. Indeed, in both fresh and brine-cured TOs, epidermal layers and mesocarpal cells were clearly revealed, including sclereid cells. The histological analysis allowed also to identifying the presence of secoiridoid-biophenols (seco-BPs) in both cell walls and vacuoles, as well as in the drupe regions that had been attacked by fruit flies, where they were found at higher concentrations; ii) in fresh and brine-cured olives, the excitation at 480 nm revealed the distribution of the fluorophores, among which the seco-BP are enclosed; iii) the ESEM-EDS analysis revealed the natural morphology of fresh olives, including the dimensions of their cell layers and the size and depth of the mechanical barriers of suberized or necrotic cells around the larva holes. In addition, the elemental composition of regions of interest of the drupe was determined in fresh and brine-cured TOs. The results highlighted the effectiveness of combined use of LM and ESEM-EDS in order to obtain a picture, as complete as possible, of the structural morphology of TOs. Such analytical combined approach can be used to support multidisciplinary studies aimed at the selection of new cultivars more resistant to fly attack.

Infección por helicobacter pylori en consulta provincial de Gastroenterología del Hospital "Faustino Pérez", de Matanzas / Infection for helicobacter pylori in provincial consultation de gastroenterología of the Hospital "Faustino Pérez", de Matanzas

RESUMEN Introducción: la infección por Helicobacter pylori es una de las más prevalentes en el planeta. Supone una carga significativa para los sistemas sanitarios, debido a la elevada resistencia a antibióticos que presenta para su erradicación. Objetivo: determinar las características clínico epidemiológicas de infección por Helicobacter pylori de pacientes atendidos en Consulta Provincial de Gastroenterología. Materiales y métodos: se realizó un estudio observacional descriptivo. El universo estuvo conformado por los 167 pacientes con determinación de Helicobacter pylori positivo, por test de ureasa. Las variables a considerar fueron: la edad, el sexo, diagnóstico histológico, síntomas clínicos y la evolución clínica posterior al tratamiento específico para Helicobacter pylori. Se utilizó la técnica estadística de análisis de distribución de frecuencias. Resultados: un 59,6 % de los pacientes resultó con Helicobacter pylori positivo con predominio del sexo masculino. Fue la gastritis crónica la alteración gástrica que más se asoció a la infección. La epigastralgia y distensión abdominal resultaron los síntomas más frecuentes. Evolucionaron de forma satisfactoria el 49 % de los casos y solo un 17 % presentaron una mala respuesta al tratamiento. Conclusiones: se obtuvo un alto porcentaje de infección por Helicobacter pylori y una buena respuesta al tratamiento utilizado (AU).

ABSTRACT Introduction: the infection for Helicobacter pylori is one of the more prevalent in the world; it supposes a significant burden for the sanitary systems, due to the high resistance to antibiotics that it presents for its eradication. Objective: to determine the clinical epidemiological characteristics of the infection due to Helicobacter pylori in patients treated in the provincial consultation of Gastroenterología. Materials and methods: an observational, descriptive study was carried out in a universe formed by 167 patients with positive Helicobacter pylori determined by urease test. The variables to consider were age, sex, histologic diagnosis, clinical symptoms and clinical evolution after the specific treatment for Helicobacter pylori. The statistical technique of analysis of frequencies distribution was used. Results: 59, 6% of the patients was Helicobacter pylori positive with prevalence of the male sex; chronic gastritis was the gastric alteration more associated to the infection. Epigastralgia and abdominal distension were the most frequent symptoms. 49% of the cases evolved in a satisfactory way and only 17% answered bad to the treatment. Conclusions: a high percent of infection by Helicobacter pylori was found and also a good answer to the used treatment (AU).

An overview of in silico vaccine design against different pathogens and cancer.

INTRODUCTION: Due to overcome the hardness of the vaccine design, computational vaccinology is emerging widely. Prediction of T cell and B cell epitopes, antigen processing analysis, antigenicity analysis, population coverage, conservancy analysis, allergenicity assessment, toxicity prediction, and protein-peptide docking are important steps in the process of designing and developing potent vaccines against various viruses and cancers. In order to perform all of the analyses, several bioinformatics tools and online web servers have been developed. Scientists must take the decision to apply more suitable and precise servers for each part based on their accuracy. AREAS COVERED: In this review, a wide-range list of different bioinformatics tools and online web servers has been provided. Moreover, some studies were proposed to show the importance of various bioinformatics tools for predicting and developing efficient vaccines against different pathogens including viruses, bacteria, parasites, and fungi as well as cancer. EXPERT OPINION: Immunoinformatics is the best way to find potential vaccine candidates against different pathogens. Thus, the selection of the most accurate tools is necessary to predict and develop potent preventive and therapeutic vaccines. To further evaluation of the computational and in silico vaccine design, in vitro/in vivo analyses are required to develop vaccine candidates.

Transcriptomic analysis of Dubas bug (Ommatissus lybicus Bergevin) infestation to Date Palm.

Date palm (Phoenix dactylifera L.) and its fruit possess sociocultural, health and economic importance in Middle East. The date palm plantations are prone to Dubas bug (DB; Ommatissus lybicus DeBergevin; Homoptera: Tropiduchidae) attacks that severely damages the tree's growth and reduces fruit production. However, the transcriptome related datasets are not known to understand how DB activates physiological and gene regulatory mechanisms during infestation. Hence, we performed RNA-Seq of leaf infected with or without DB to understand the molecular responses of date palm seedlings. Before doing that, we noticed that DB infestation significantly increase superoxide anion and malondialdehyde production to two-folds as compared to healthy control. Stress-responsive genes such as proline transporter 2, NADP-dependent glyceraldehyde and superoxide dismutase were found significantly upregulated in infected seedlings. The infection repercussions were also revealed by significantly higher contents of endogenous phytohormonal signaling of jasmonic acid (JA) and salicylic acid (SA) compared with control. These findings persuaded to dig out intrinsic mechanisms and gene regulatory networks behind DB infestation to date palm by RNA-Seq analysis. Transcriptome analysis revealed upregulation of 6,919 genes and down-regulation of 2,695 genes in leaf during the infection process. The differentially expressed genes were mostly belongs to cellular functions (calcium and MAPK), phytohormones (auxin, gibberellins, abscisic acid, JA and SA), and secondary metabolites (especially coumarinates and gossypol). The data showed that defense responses were aggravated by gene networks involved in hypersensitive responses (PAR1, RIN4, PBS1 etc.). In conclusion, the results revealed that date palm's leaf up-regulates both cellular and phytohormonal determinants, followed by intrinsic hypersensitive responses to counter infestation process by Dubas bug.

The 2015-2016 El Niño increased infection parameters of copepods on Eastern Tropical Pacific dolphinfish populations.

The oceanographic conditions of the Pacific Ocean are largely modified by El Niño (EN), affecting several ecological processes. Parasites and other marine organisms respond to environmental variation, but the influence of the EN cycle on the seasonal variation of parasitic copepods has not been yet evaluated. We analysed the relation between infection parameters (prevalence and mean intensity) of the widespread parasitic copepods Caligus bonito and Charopinopsis quaternia in the dolphinfish Coryphaena hippurus and oceanography during the strong 2015-16 EN. Fish were collected from capture fisheries on the Ecuadorian coast (Tropical Eastern Pacific) over a 2-year period. Variations of sea surface temperature (SST), salinity, chlorophyll a (Chl-a), Oceanic Niño Index (ONI), total host length (TL) and monthly infection parameters of both copepod species were analysed using time series and cross-correlations. We used the generalised additive models for determine the relationship between environmental variables and infection parameters. The total body length of the ovigerous females and the length of the eggs of C. bonito were measured in both periods. Infection parameters of both C. bonito and Ch. quaternia showed seasonal and annual patterns associated with the variation of environmental variables examined (SST, salinity, Chl-a and ONI 1+2). Infection parameters of both copepod species were significantly correlated with ONI 1+2, SST, TL and Chl-a throughout the GAMLSS model, and the explained deviance contribution ranged from 16%-36%. Our results suggest than an anomaly higher than +0.5°C triggers a risen in infection parameters of both parasitic copepods. This risen could be related to increases in egg length, female numbers and the total length of the ovigerous females in EN period. This study provides the first evidence showing that tropical parasitic copepods are sensitive to the influence of EN event, especially from SST variations. The observed behaviour of parasitic copepods likely affects the host populations and structure of the marine ecosystem at different scales.

The ABC of Major Histocompatibility Complexes and T Cell Receptors in Health and Disease.

A seminal discovery of major histocompatibility complex (MHC) restriction in T cell recognition by Peter Doherty and Rolf Zinkernagel has led to 45 years of exciting research on the mechanisms governing peptide MHC (pMHC) recognition by T cell receptors (TCRs) and their importance in health and disease. T cells provide a significant level of protection against viral, bacterial, and parasitic infections, as well as tumors, hence, the generation of protective T cell responses is a primary goal for cell-mediated vaccines and immunotherapies. Understanding the mechanisms underlying generation of optimal high-avidity effector T cell responses, memory development, maintenance, and recall is of major importance for the rational design of preventative and therapeutic vaccines/immunotherapies. In this review, we summarize the lessons learned over the last four decades and outline our current understanding of the basis and consequences of pMHC/TCR interactions on T cell development and function, and TCR diversity and composition, driving better clinical outcomes and prevention of viral escape. We also discuss the current models of T cell memory formation and determinants of immunodominant T cell responses in animal models and humans. As TCR composition and diversity can affect both the protective capacity of T cells and protection against viral escape, defining the spectrum of TCR selection has implications for improving the functional efficacy of effector T cell responsiveness and memory formation.

Galectins in Host Defense Against Microbial Infections.

Galectins are differentially expressed in a variety of cell types, including immune cells, and characterized by the affinity for ß-galactoside-containing glycans. There are fifteen galectin members in mammals. Galectins are primarily located intracellularly, but can be secreted outside the cells. They exhibit pivotal roles during microbial infection, such as pathogen recognition and innate and adaptive immunity, and this review aims to discuss the functions of endogenous galectins during infection by four main types of microbes (bacteria, fungi, viruses, and parasites). Extracellular galectins are known to exert a bacteriostatic effect on some bacteria via association with bacterial glycans, whereas cytosolic galectins are recognized to control antibacterial autophagy by binding to luminal host glycans of ruptured endo-lysosomes. With regard to fungal infections, most studies deal with galectin-3. Galectin-3 modulates fungal burdens, the adaptive immune responses, and mortality in fungi-infected mice, which has been shown to be associated with its ability to manipulate fungicidal functions in neutrophils and cytokine expression in dendritic cells. Some viral infections, such as human immunodeficiency virus (HIV) and influenza virus infections, can be regulated by galectin-1 and -3, and they affect various aspects of viral infections, including viral binding, replication, budding, transmission, and infection-associated inflammation. Functions of galectins during a number of different parasitic infections have been identified in studies using galectin-knockout mice. Different parasitic infections have consistently demonstrated a role of galectins in tuning T helper immune responses in infected hosts.