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Abstract Background The aim of this study was to detect the associations between bovine herpesvirus 1 (BHV-1) status of a herd and respiratory disease (BRD) occurrence and reproductive performance in pregnant heifers and cows. The association between management-related factors and higher BRD occurrence was also estimated. Methods Serum samples, collected from cows and youngstock from 103 dairy cattle herds, were analyzed for antibodies against BHV-1, bovine respiratory syncytial virus (BRSV), bovine viral diarrhoea virus (BVDV), and Mycoplasma bovis. A questionnaire was used to collect data concerning herd management factors and reproductive performance, as well as the occurrence of clinical signs of respiratory disease in the last two years, as evaluated by the veterinarian or farm manager. Multiple correspondence analysis (MCA) and logistic regression analysis were performed to identify and quantify the risk factors. Results A low to moderate prevalence (1-49%) of BRSV antibodies among youngstock was associated with a high occurrence of respiratory disease (OR = 6.2, p = 0.010) in cows and in-calf heifers. Employees of the farm may participate in the spread of such disease. Larger herd size, loose-housing of cows, housing youngstock separately from cows until pregnancy, and purchasing new animals were factors possibly related to a high occurrence of respiratory disease symptoms in pregnant heifers and cows. The highest risk of abortions (> 1.3%) and increased insemination index (number of inseminations per pregnancy) (> 1.9) occurred in herds with a moderate prevalence of BHV-1 antibodies (1-49%) in cows. Conclusions BHV-1 was not associated with acute respiratory disease in adult dairy cattle, however was significantly related to reproductive performance. BRSV possesses the main role in respiratory disease complex in adult dairy cattle.

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. This study aims to evaluate PRS and define most informative thresholds in relation to conventional clinical and physiological criteria of asthma using a multivariate statistical method. Clinical and genome-wide genotyping data were obtained from the Quebec City Case-Control Asthma Cohort (QCCCAC), which is an independent cohort from previous GWAS. PRS was derived using LDpred2 and integrated with other asthma phenotypes by means of Principal Component Analysis with Optimal Scaling (PCAOS). PRS was considered using 'ordinal level of scaling' to account for non-linear information. In two dimensional PCAOS space, the first component delineated individuals with and without asthma, whereas the severity of asthma was discerned on the second component. The positioning of high vs. low PRS in this space matched the presence and absence of airway hyperresponsiveness, showing that PRS delineated cases and controls at the same extent as a positive bronchial challenge test. The top 10% and the bottom 5% of the PRS were the most informative thresholds to define individuals at high and low genetic risk of asthma in this cohort. PRS used in a multivariate method offers a decision-making space similar to hyperresponsiveness in this cohort and highlights the most informative and asymmetrical thresholds to define high and low genetic risk of asthma., Competing Interests: Declarations. Ethical approval: The study protocol was approved by the Research Ethics Board of the Institut universitaire de cardiologie et de pneumologie de Québec – Université Laval (#20273). All participating subjects signed an informed consent approved by the REB. Subjects are de-identified using a code number for confidentiality. Access to data is protected using the data management structure approved by the REB. Consent for publication: Not applicable. Competing interests: The authors declare no competing interests., (© 2025. The Author(s).)

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 >1.1 million genetic variants was derived and validated in UK Biobank (n = 5419 lung cancer cases). The predictive ability and diagnostic discrimination performance of the PRS was tested in LORD/CARTaGENE and benchmarked against previous PRSs from the literature. Stratified analyses were performed by smoking status and genetic risk groups defined as low (<20th percentile), intermediate (20-80th percentile) and high (>80th percentile) PRS., Findings: The phenotypic variance explained and the effect size of the genome-wide PRS numerically outperformed previous PRSs. Individuals with high genetic risk had a 2-fold odds of lung cancer compared to low genetic risk. The PRS was an independent predictor of lung cancer beyond conventional clinical risk factors, but its diagnostic discrimination performance was incremental in an integrated risk model. Smoking increased the odds of lung cancer by 7.7-fold in low genetic risk and by 11.3-fold in high genetic risk. Smoking with high genetic risk was associated with a 17-fold increase in the odds of lung cancer compared to individuals who never smoked and with low genetic risk., Interpretation: Individuals at low genetic risk are not protected against the smoking-related risk of lung cancer. The joint multiplicative effect of PRS and smoking increases the odds of lung cancer by nearly 20-fold., Funding: This work was supported by the CQDM and the IUCPQ Foundation owing to a generous donation from Mr. Normand Lord., Competing Interests: Declaration of interests B. Arsenault received research grants from Silence Therapeutics, Pfizer and Eli Lilly; received consulting fees from Silence Therapeutics, Novartis, Eli Lilly and Editas Medicine. C. Labbé received consulting fees from Amgen, AstraZeneca, Bristol-Myers-Squibb, EMD Serono, Jazz Pharmaceuticals, LEO Pharma, Lilly, Merck, Pfizer, Roche and Sanofi Genzyme. S. Martel received research grants the Ministry of Health province of Quebec and Canadian Partnership Against Cancer. Y. Bossé has received research grants from the IUCPQ Foundation. The remaining authors declare no conflict of interest., (Copyright © 2024 The Authors. Published by Elsevier B.V. All rights reserved.)

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. We found that summary indices were highly correlated with the number of pesticides detected in the related matrix but not with which pesticides were present. Matrices collected from apple orchards generally contained a higher number of pesticides (7.6 pesticides per site) than matrices from sites collected from oilseed rape crops (3.5 pesticides), with fungicides being highly represented in apple crops. A greater number of pesticides were found in pollen-nectar stores/beebread and pollen matrices compared with nectar and bee body matrices. Our results show that for a complete assessment of pollinator pesticide exposure, it is necessary to consider several different exposure routes and multiple species of bees across different agricultural systems., Competing Interests: Declaration of competing interest The authors declare the following financial interests/personal relationships which may be considered as potential competing interests: Marie-Pierre CHAUZAT reports financial support was provided by European Commission. Marion LAURENT reports financial support was provided by European Commission. Matthias ALBRECHT reports financial support was provided by European Commission. Mark JF BROWN reports financial support was provided by European Commission. Joachim DE MIRANDA reports financial support was provided by European Commission. Reet KARISE reports financial support was provided by European Commission. Jessica KNAPP reports financial support was provided by European Commission. Jose SERRANO MARINO reports financial support was provided by European Commission. Simon G. POTTS reports financial support was provided by European Commission. Maj RUNDLOF reports financial support was provided by European Commission. Janine SCHWARZ reports financial support was provided by European Commission. Eleanor ATTRIDGE reports financial support was provided by European Commission. Irene BOTTERO reports financial support was provided by European Commission. Elena CINI reports financial support was provided by European Commission. Maria Pilar DE LA RUA reports financial support was provided by European Commission. Gennaro DI PRISCO reports financial support was provided by European Commission. Christophe DOMINIK reports financial support was provided by European Commission. Daniel DZUL reports financial support was provided by European Commission. Andres GARCIA REINA reports financial support was provided by European Commission. Simon HODGE reports financial support was provided by European Commission. Alexandra M KLEIN reports financial support was provided by European Commission. Anina KNAUER reports financial support was provided by European Commission. Marika MAND reports financial support was provided by European Commission. Vicente MARTINEZ LOPEZ reports financial support was provided by European Commission. Giorgia SERRA reports financial support was provided by European Commission. Helena PEREIRA-PEIXOTO reports financial support was provided by European Commission. Risto RAIMETS reports financial support was provided by European Commission. Oliver SCHWEIGER reports financial support was provided by European Commission. Deepa SENAPATHI reports financial support was provided by European Commission. Jane C. STOUT reports financial support was provided by European Commission. Giovanni TAMBURINI reports financial support was provided by European Commission. Cecilia COSTA reports financial support was provided by European Commission. Tomasz KILJANEK reports financial support was provided by European Commission. Anne-Claire MARTEL reports financial support was provided by European Commission. If there are other authors, they declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier B.V. All rights reserved.)

Streptococcus suis 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 S. suis worldwide and most of the AMR genes are carried by mobile genetic elements (MGEs). This contributes to their dissemination by horizontal gene transfer. A collection of 102 strains isolated from humans, pigs and wild boars in France was subjected to whole genome sequencing in order to: (i) study their genetic diversity, (ii) evaluate their content in virulence-associated genes, (iii) decipher the mechanisms responsible for their AMR and their association with MGEs, and (iv) study their ability to acquire extracellular DNA by natural transformation. Analysis by hierarchical clustering on principal components identified a few virulence-associated factors that distinguish invasive CC1 strains from the other strains. A plethora of AMR genes ( n =217) was found in the genomes. Apart from the frequently reported erm (B) and tet (O) genes, more recently described AMR genes were identified [ vga (F)/ sprA , vat (D)]. Modifications in PBPs/MraY and GyrA/ParC were detected in the penicillin- and fluoroquinolone-resistant isolates respectively. New AMR gene-MGE associations were detected. The majority of the strains have the full set of genes required for competence, i.e for the acquisition of extracellular DNA (that could carry AMR genes) by natural transformation. Hence the risk of dissemination of these AMR genes should not be neglected.

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). The sentinel bees were deployed at 128 sites in eight European countries adjacent to either oilseed rape fields or apple orchards during crop bloom. Adult bees of each species were sampled before their placement and after crop bloom. The IPAs were detected and quantified using a harmonised, high-throughput and semi-automatized qPCR workflow. We describe differences among bee species in IPA profiles (richness, diversity, detection frequencies, loads and their change upon field exposure, and exposure risk), with no clear patterns related to the country or focal crop. Our results suggest that the most frequent IPAs in adult bees are more appropriate for assessing the bees' IPA exposure risk. We also report positive correlations of IPA loads supporting the potential IPA transmission among sentinels, suggesting careful consideration should be taken when introducing managed pollinators in ecologically sensitive environments., (© 2024. The Author(s).)

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. Bulk tank milk (BTM) and heifer blood samples (10 samples per herd) were collected and analysed for antibodies against the selected pathogens. In total, 172 variables were aggregated into 14 thematic blocks. The annual CR, MR, and MAofCC values were calculated for each herd. Thematic blocks with significant impact on cow persistence (included herd MR, CR and MAofCC) were 'infectious diseases' (block importance index out of all blocks = 13.6%, 95% CI 10.3; 20.5), 'fertility management' (16.3%, 95% CI 6.8; 26.9), 'lactating cow management' (11.5%, 95% CI 6.4; 17.8), 'milking' (11.3%, 95% CI 3.2; 17.1), 'herd characteristics' (10.1%, 95% CI 6.3; 14.2), 'close-up period management' (9.7%, 95% CI 2.7; 15.7), 'calving management' (7.9%, 95% CI 3.1; 11.4) and 'disease management' (7.3%, 95% CI 0.2; 12.0). Variable categories with the highest importance in explaining composite outcome including herd MR, CR and MAofCC were rear-end and udder lesions in ≥ 20% of the cows, BTM and heifers seropositive to bovine respiratory syncytial virus, vaccination against bovine herpesvirus 1, twice daily milking and herd location in Northwest region. Larger herd size, higher levels of milk yield, and rearing predominantly Holstein breed cattle were herd factors associated with poorer cow persistency. Grazing cows and having semi-insulated barns were associated with lower CR and MR, respectively. Heat detection and farm pregnancy testing strategies were significant factors in the fertility block. Using disposable dry papers for teat cleaning and not using any wet teat-cleaning tools were risk factors for high MR. A robotic milking system was protective for increased herd MR and CR. A high pre-calving body condition score and poor rear body cleanliness of ≥ 30% of cows were associated with inferior herd persistency outcomes. Calving in group pens with deep litter bedding was associated with a lower CR. Multiblock PLS model is innovative tool that helped to identify most influential farming areas but also single risk factors associated with cow persistency described by multiple parameters., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 The Authors. Published by Elsevier B.V. All rights reserved.)

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. In reality, some data sets contain variables of different measurement levels (i.e., numeric, nominal, ordinal). In this article, we focus on exploratory multiblock methods that handle variables at their appropriate measurement level. Multi-Block Principal Component Analysis with Optimal Scaling (MBPCA-OS) is proposed and applied to multiblock data from the CURIE-O-SA French cohort. In this study, variables are of different measurement levels and organized in four blocks. The objective is to study the immune responses according to the SARS-CoV-2 infection and vaccination statuses, the symptoms and the participant's characteristics., (© 2023 Walter de Gruyter GmbH, Berlin/Boston.)