The clinical value and most informative threshold of polygenic risk score in the Quebec City Case-Control Asthma Cohort.

Genome-wide association studies (GWAS) have identified genetic variants robustly associated with asthma. A potential near-term clinical application is to calculate polygenic risk score (PRS) to improve disease risk prediction. The value of PRS, as part of numerous multi-source variables used to define asthma, remains unclear.

Polygenic inheritance and its interplay with smoking history in predicting lung cancer diagnosis: a French-Canadian case-control cohort.

Background: The most near-term clinical application of genome-wide association studies in lung cancer is a polygenic risk score (PRS).

Methods: A case-control dataset was generated consisting of 4002 lung cancer cases from the LORD project and 20,010 ethnically matched controls from CARTaGENE. A genome-wide PRS including >1.

Novel indices reveal that pollinator exposure to pesticides varies across biological compartments and crop surroundings.

Declines in insect pollinators have been linked to a range of causative factors such as disease, loss of habitats, the quality and availability of food, and exposure to pesticides. Here, we analysed an extensive dataset generated from pesticide screening of foraging insects, pollen-nectar stores/beebread, pollen and ingested nectar across three species of bees collected at 128 European sites set in two types of crop. In this paper, we aimed to (i) derive a new index to summarise key aspects of complex pesticide exposure data and (ii) understand the links between pesticide exposures depicted by the different matrices, bee species and apple orchards versus oilseed rape crops.

Virulence genes, resistome and mobilome of strains isolated in France.

is a leading cause of infection in pigs, causing extensive economic losses. In addition, it can also infect wild fauna, and can be responsible for severe infections in humans. Increasing antimicrobial resistance (AMR) has been described in worldwide and most of the AMR genes are carried by mobile genetic elements (MGEs).

Distribution of infectious and parasitic agents among three sentinel bee species across European agricultural landscapes.

Infectious and parasitic agents (IPAs) and their associated diseases are major environmental stressors that jeopardize bee health, both alone and in interaction with other stressors. Their impact on pollinator communities can be assessed by studying multiple sentinel bee species. Here, we analysed the field exposure of three sentinel managed bee species (Apis mellifera, Bombus terrestris and Osmia bicornis) to 11 IPAs (six RNA viruses, two bacteria, three microsporidia).

MBPCA-OS: an exploratory multiblock method for variables of different measurement levels. Application to study the immune response to SARS-CoV-2 infection and vaccination.

Studying a large number of variables measured on the same observations and organized in blocks - denoted multiblock data - is becoming standard in several domains especially in biology. To explore the relationships between all these variables - at the block- and the variable-level - several exploratory multiblock methods were proposed. However, most of them are only designed for numeric variables.

Application of multiblock analysis to identify key areas and risk factors for dairy cow persistence.

The present study analysed the importance of individual variables and different thematic blocks of production areas, management, and herd infectious disease status on cow persistence, characterised by herd on-farm mortality rate (MR), culling rate (CR), and mean age of culled cows (MAofCC) applying multiblock partial least squares (mbPLS) analysis. This study included 120 free-stall dairy herds with ≥ 100 cows. Data on the previous year's predominant cow housing system and management practices were collected, and on-farm measurements and cow scoring were performed.

Infectious bursal disease virus: predicting viral pathotype using machine learning models focused on early changes in total blood cell counts.

Infectious bursal disease (IBD) is an avian viral disease caused in chickens by infectious bursal disease virus (IBDV). IBDV strains (Avibirnavirus genus, Birnaviridae family) exhibit different pathotypes, for which no molecular marker is available yet. The different pathotypes, ranging from sub-clinical to inducing immunosuppression and high mortality, are currently determined through a 10-day-long animal experiment designed to compare mortality and clinical score of the uncharacterized strain with references strains.

Monophasic Variant of Typhimurium Infection Affects the Serum Metabolome in Swine.

is the most relevant foodborne zoonotic agent found in swine, and its presence in French herds is significant. Its carriage is asymptomatic, which makes it difficult to detect during rearing, thus increasing the risk of its presence on pork meat. Studies have shown that enteric infection in animals could be associated with changes in the serum metabolome composition, through the immune response or changes in the digestive microbiota composition.

Antimicrobial resistance profiles of isolated from pigs, wild boars, and humans in France between 1994 and 2020.

an emerging zoonotic pathogen, causes invasive infections and substantial economic losses in the pig industry worldwide. Antimicrobial resistance against 22 antibiotics was studied for 200 . strains collected in different geographical regions of France.

Building composite indices in the age of big data - Application to honey bee exposure to infectious and parasitic agents.

Pollinator insects play a crucial role in maintaining biodiversity and agricultural production worldwide. Yet they are subject to various infectious and parasitic agents (IPAs). To better assess their exposure to IPAs, discriminative and quantitative molecular methods have been developed.

Avian metapneumovirus: A five-plex digital droplet RT-PCR method for identification of subgroups A, B, C, and D.

End-point and real-time avian metapneumovirus (AMPV) RT-PCRs have been developed to detect one or two of the four recognized subgroups (A,B,C, and D) simultaneously or for broad range AMPV detection. Current subgroup specific tests target variable areas of the genome which makes these PCRs sensitive to specificity defects as recently documented. In the current study, a single five-plex digital droplet RT-PCR targeting the conserved viral polymerase gene of AMPV, which is less prone to genetic drift, has been designed.

High antigenic diversity of serotype 1 infectious bursal disease virus revealed by antigenic cartography.

The antigenic characterization of IBDV, a virus that causes an immunosuppressive disease in young chickens, has been historically addressed using cross virus neutralization (VN) assay and antigen-capture enzyme-linked immunosorbent (AC-ELISA). However, VN assay has been usually carried out either in specific antibody negative embryonated eggs, for non-cell culture adapted strains, which is tedious, or on chicken embryo fibroblasts (CEF), which requires virus adaptation to cell culture. AC-ELISA has provided crucial information about IBDV antigenicity, but this information is limited to the epitopes included in the tested panel with a lack of information of overall antigenic view.

Efficacy of passive immunization in broiler chicks via an inactivated autogenous vaccine administered to broiler breeder hens.

Avian pathogenic (APEC) cause extra-intestinal infections called colibacillosis, which is the dominant bacterial disease in broilers. To date, given the diversity of APEC strains and the need for an acceptable level of protection in day-old chicks, no satisfactory commercial vaccine is available. As part of a French nationwide project, we selected three representative strains among several hundred APEC that cause colibacillosis disease.

Blood B Cell Depletion Reflects Immunosuppression Induced by Live-Attenuated Infectious Bursal Disease Vaccines.

Immunosuppression in poultry production is a recurrent problem worldwide, and one of the major viral immunosuppressive agents is Infectious Bursal Disease Virus (IBDV). IBDV infections are mostly controlled by using live-attenuated vaccines. Live-attenuated Infectious Bursal Disease (IBD) vaccine candidates are classified as "mild," "intermediate," "intermediate-plus" or "hot" based on their residual immunosuppressive properties.

Genome Evolution of Two Genetically Homogeneous Infectious Bursal Disease Virus Strains During Passages and in the Presence of a Mutagenic Nucleoside Analog.

The infectious bursal disease virus (IBDV) is responsible for a highly contagious and sometimes lethal disease of chickens (). IBDV genetic variation is well-described for both field and live-attenuated vaccine strains, however, the dynamics and selection pressures behind this genetic evolution remain poorly documented. Here, genetically homogeneous virus stocks were generated using reverse genetics for a very virulent strain, rvv, and a vaccine-related strain, rCu-1.

Spatiotemporal clustering and Random Forest models to identify risk factors of African swine fever outbreak in Romania in 2018-2019.

African swine fever (ASF) has affected Romania since July 2017, with considerable economic and social consequences, despite the implementation of control measures mainly based on stamping out of infected pig populations. On the basis of the 2973 cumulative recorded cases up to September 2019 among wild boars and domestic pigs, analysis of the epidemiological characteristics could help to identify the factors favoring the persistence and spread of ASF. A statistical framework, based on a random forest methodology, was therefore developed to assess the spatiotemporal features of the epidemics and their relationships with environmental, human, and agricultural factors.

Investigation on eggshell apex abnormality (EAA) syndrome in France: isolation of Mycoplasma synoviae is frequently associated with Mycoplasma pullorum.

Background: Mycoplasma synoviae (MS) is known to cause Eggshell Apex Abnormality (EAA) syndrome characterized by an altered shell surface with increased translucency on the apex. However, no large-scale studies have been conducted to obtain prevalence data of EAA and MS isolates associated to this syndrome. This manuscript reports the results of two field studies performed in the French poultry industry (2015-2017): focusing mainly on investigation of presence and prevalence of EAA in different types of laying hen flocks (phase 1), and isolation of MS strains from EAA-infected flocks (phase 2).