Evaluating the potential of third generation metagenomic sequencing for the detection of BRD pathogens and genetic determinants of antimicrobial resistance in chronically ill feedlot cattle.

BACKGROUND: Bovine respiratory disease (BRD) is an important cause of morbidity and mortality and is responsible for most of the injectable antimicrobial use in the feedlot industry. Traditional bacterial culture can be used to diagnose BRD by confirming the presence of causative pathogens and to support antimicrobial selection. However, given that bacterial culture takes up to a week and early intervention is critical for treatment success, culture has limited utility for informing rapid therapeutic decision-making. In contrast, metagenomic sequencing has the potential to quickly resolve all nucleic acid in a sample, including pathogen biomarkers and antimicrobial resistance genes. In particular, third-generation Oxford Nanopore Technology sequencing platforms provide long reads and access to raw sequencing data in real-time as it is produced, thereby reducing the time from sample collection to diagnostic answer. The purpose of this study was to compare the performance of nanopore metagenomic sequencing to traditional culture and sensitivity methods as applied to nasopharyngeal samples from segregated groups of chronically ill feedlot cattle, previously treated with antimicrobials for nonresponsive pneumonia or lameness. RESULTS: BRD pathogens were isolated from most samples and a variety of different resistance profiles were observed across isolates. The sequencing data indicated the samples were dominated by Moraxella bovoculi, Mannheimia haemolytica, Mycoplasma dispar, and Pasteurella multocida, and included a wide range of antimicrobial resistance genes (ARGs), encoding resistance for up to seven classes of antimicrobials. Genes conferring resistance to beta-lactams were the most commonly detected, while the tetH gene was detected in the most samples overall. Metagenomic sequencing detected the BRD pathogens of interest more often than did culture, but there was limited concordance between phenotypic resistance to antimicrobials and the presence of relevant ARGs. CONCLUSIONS: Metagenomic sequencing can reduce the time from sampling to results, detect pathogens missed by bacterial culture, and identify genetically encoded determinants of resistance. Increasing sequencing coverage of target organisms will be an essential component of improving the reliability of this technology, such that it can be better used for the surveillance of pathogens of interest, genetic determinants of resistance, and to inform diagnostic decisions.

Changes in the phenotypic susceptibility of Mannheimia haemolytica isolates to macrolide antimicrobials during the early feeding period following metaphylactic tulathromycin use in western Canadian feedlot calves.

Cattle at high-risk for bovine respiratory disease on entry to western Canadian feedlots are often treated metaphylactically with antimicrobials from the macrolide class. High levels of resistance to macrolides have been reported in Mannheimia haemolytica isolates from clinical samples, but it is less clear whether this trend extends to the broader feedlot population. The objective was to describe near-term [< 40 days on feed (DOF)] changes in the recovery and susceptibility of M. haemolytica isolates from healthy feedlot calves after metaphylactic exposure to tulathromycin. Eight cohorts of 100 calves (n = 800) were sampled via deep nasopharyngeal swab at entry processing (i.e., before metaphylaxis, at 1 DOF) and again at 13 DOF. Ten calves from each cohort (n = 80) were randomly sampled a third time at 36 DOF. Recovery of M. haemolytica isolates across all cohorts increased over the study period, from 33% (95% CI: 26.5 to 40.2%) at 1 DOF to 75% (95% CI: 71.4 to 78.3%) at 36 DOF. A significant shift in the minimum inhibitory concentration (MIC) distribution of tulathromycin from 1 DOF (MIC90 ≤ 8 µg/mL) to 13 DOF (MIC90 > 64 µg/mL) was observed. A subset of 36 isolates from 13 DOF screened for macrolide resistance genes via multiplex polymerase chain reaction all harbored the msrE and mphE genes. Recovery of M. haemolytica at 13 and 36 DOF did not decline in response to metaphylactic use of tulathromycin; conversely, we inferred the potential for rapid inter-pen spread of a macrolide-resistant clone by 13 DOF in 6 of 8 pens under selective pressure from antimicrobial use.

Changements dans la sensibilité phénotypique des isolats de Mannheimia haemolytica aux a ntibiotiques de la classe des macrolides au début de la période d'alimentation après l'utilisation m étaphylactique de tulathromycine chez les veaux des parcs d'engraissement de l'Ouest canadien. Les bovins à risque élevé de maladies respiratoires bovines à leur entrée dans les parcs d'engraissement de l'Ouest canadien sont souvent traités métaphylactiquement avec des antimicrobiens de la classe des macrolides. Des taux élevés de résistance aux macrolides ont été signalés chez les isolats de Mannheimia haemolytica provenant d'échantillons cliniques, mais il est moins clair si cette tendance s'étend à la population plus large des parcs d'engraissement. L'objectif était de décrire les changements à court terme [< 40 jours d'alimentation (DOF)] dans la récupération et la sensibilité des isolats de M. haemolytica provenant de veaux sains en parc d'engraissement après une exposition métaphylactique à la tulathromycine. Huit cohortes de 100 veaux (n = 800) ont été échantillonnées via un prélèvement nasopharyngé profond lors du traitement d'entrée (i.e., avant la métaphylaxie, à 1 DOF) et à nouveau à 13 DOF. Dix veaux de chaque cohorte (n = 80) ont été échantillonnés au hasard une troisième fois à 36 DOF. La récupération des isolats de M. haemolytica dans toutes les cohortes a augmenté au cours de la période d'étude, passant de 33 % (IC 95 % : 26,5 à 40,2 %) à 1 DOF à 75 % (IC 95 % : 71,4 à 78,3 %) à 36 DOF. Un changement significatif dans la distribution de la concentration minimale inhibitrice (MIC) de la tulathromycine de 1 DOF (MIC90 ≤ 8 µg/mL) à 13 DOF (MIC90 > 64 µg/mL) a été observé. Un sous-ensemble de 36 isolats de 13 DOF criblés pour les gènes de résistance aux macrolides via une réaction d'amplification en chaîne par polymérase multiplex hébergeaient tous les gènes msrE et mphE. L'isolement de M. haemolytica à 13 et 36 DOF n'a pas diminué en réponse à l'utilisation métaphylactique de la tulathromycine; à l'inverse, nous avons suggéré le potentiel de propagation rapide entre les enclos d'un clone résistant aux macrolides par 13 DOF dans 6 des 8 enclos sous la pression sélective de l'utilisation d'antimicrobiens.(Traduit par Dr Serge Messier).

Household income, active travel, and their interacting impact on body mass index in a sample of urban Canadians: a Bayesian spatial analysis.

BACKGROUND: Active travel for utilitarian purposes contributes to total physical activity and may help counter the obesity epidemic. However, the evidence linking active travel and individual-level body weight is equivocal. Statistical modeling that accounts for spatial autocorrelation and unmeasured spatial predictors has not yet used to explore whether the health benefits of active travel are shared equally across socioeconomic groups. METHODS: Bayesian hierarchical models with spatial random effects were developed using travel survey data from Saskatoon, Canada (N = 4625). Differences in log-transformed body mass index (BMI) were estimated for levels of active travel use (vehicular travel only, mixed vehicular/active travel, and active travel only), household income, and neighbourhood deprivation after controlling for sociodemographic and physical activity variables. The modifying effect of household income on the association between active travel and BMI was also evaluated. RESULTS: Significant and meaningful decreases in BMI were observed for mixed (ß = - 0.02, CrI - 0.036 to - 0.004) and active only (ß = - 0.043, CrI - 0.06 to - 0.025) compared to vehicular only travelers. BMI was significantly associated with levels of household income and neighbourhood deprivation. Accounting for the interaction between travel mode and household income, decreases in BMI were observed for active only compared to vehicular only travellers in the highest income category (ß = - 0.061, CrI - 0.115 to - 0.007). CONCLUSION: Strategies to increase active travel use can support healthy weight loss and maintenance, but the opportunity to benefit from active travel use may be limited by low income. Considerations should be given to how interventions to increase active transportation might exacerbate social inequalities in BMI. Spatial statistical models are needed to account for unmeasured but spatially structured neighbourhood factors.

Determinants of self-perceived health for Canadians aged 40 and older and policy implications.

BACKGROUND: Perceived health status indicates people's overall perception of their health, including both physical and psychological dimensions. The aim of this study was to examine the determinants of self-perceived health for Canadians aged 40 and older using data from the Canadian Community Health Survey (2010). METHODS: Multiple logistic regression models were employed to identify factors associated with self-perceived health in two age groups: Adults aged 65+ and Adults aged 40-64. RESULTS: We found that higher income was significantly associated with better health status while chronic conditions and stress were associated with worse health status. In the 40-64 and 65+ age groups, individuals in the highest income bracket were 4.65 and 1.94 times, respectively, more likely to report better health than individuals in the lowest income bracket. The difference in the level of income associated health inequities between the two age groups point to the need for understanding the reasons behind lower inequities among seniors and how much the social protections provided by the Canadian government to seniors contribute to lowering inequities. CONCLUSIONS: Though Canada has a national public health insurance system providing coverage to all Canadians, health inequities associated with income persist providing further evidence of the importance of the social determinants of health. Examining the extent of these inequities and what factors influence them helps direct policy attention. In addition to documenting inequities, this paper discusses policy options for reducing the identified inequities.

Comparison of the levels of selected specific antibodies in the immunoglobulin G of colostrum versus milk and serum in dairy cows (Bos taurus).

Commercial products containing immunoglobulin G (IgG) sourced from colostrum, milk, and/or serum may be used to supplement or replace maternal colostrum in newborn dairy calves. To determine if antibody specificities in bovine milk and serum IgG differ from colostrum IgG, we sampled serum, colostrum (1 to 2 hours post-partum), and milk (day 5 post-partum) from 24 dairy heifers or cows. Specific antibodies [IgG class (H&L)] to 8 common pathogens were measured using enzyme-linked immunosorbent assays (ELISAs). Immunoglobin G1 and IgG2 subclass-specific ELISAs were performed for 3 of these pathogens. Colostrum-derived IgG contained more specific antibodies to rotavirus [IgG (H&L) and IgG1] and to IgG (H&L) of bovine respiratory syncytial virus (BRSV), bovine parainfluenza-3 virus (BPI3V), Staphylococcus aureus, Escherichia coli F5 (K99), and bovine coronavirus than milk IgG. Colostral IgG contained more antibodies to BRSV (IgG1), rotavirus (IgG1), and IgG (H&L) specific for BRSV, bovine herpesvirus-1 (BHV-1), BPI3V, E. coli F5 (K99), and Streptococcus uberis than serum IgG. Compared to serum, milk contained more IgG (H&L) antibody to BRSV, BHV-1, and BPI3V, IgG1-specific BRSV, and rotavirus. These data indicate that IgG derived from colostrum delivers more specific antibodies to these endemic pathogens of calves compared to IgG sourced from milk or serum. In addition, the IgG1 subclass predominates in milk and colostrum, and both deliver a similar spectrum of antibodies.

Les produits commerciaux contenant de l'immunoglobuline G (IgG) provenant du colostrum, du lait et/ou du sérum peuvent être utilisés pour compléter ou remplacer le colostrum maternel chez les veaux laitiers nouveau-nés. Pour déterminer si les spécificités des anticorps dans le lait de vache et les IgG sériques diffèrent des IgG du colostrum, nous avons prélevé du sérum, du colostrum (1 à 2 heures après le vêlage) et du lait (5 jours après le vêlage) de 24 génisses ou vaches laitières. Des anticorps spécifiques [classe IgG (H&L)] dirigés contre huit agents pathogènes courants ont été mesurés par dosages immuno-enzymatiques (ELISA). Des tests ELISA spécifiques aux sous-classes d'IG1 et d'IgG2 ont été effectués pour trois de ces agents pathogènes. Les IgG dérivées du colostrum contenaient plus d'anticorps spécifiques contre le rotavirus [IgG (H&L) et IgG1] et des IgG (H&L) contre le virus respiratoire syncytial bovin (BRSV), le virus parainfluenza bovin 3 (BPI3V), Staphylococcus aureus, Escherichia coli F5 (K99) et le coronavirus bovin que les IgG du lait. Les IgG du colostrum contenaient plus d'anticorps dirigés contre le BRSV (IgG1), le rotavirus (IgG1) et des IgG (H&L) spécifiques contre BRSV, l'herpèsvirus bovin-1 (BHV-1), le BPI3V, E. coli F5 (K99) et Streptococcus uberis que les IgG du sérum. Comparé au sérum, le lait contenait plus d'anticorps IgG (H&L) contre le BRSV, le BHV-1 et le BPI3V, des IgG1 spécifiques au BRSV et au rotavirus. Ces données indiquent que les IgG dérivées du colostrum fournissent des anticorps plus spécifiques contre ces agents pathogènes endémiques des veaux que les IgG provenant du lait ou du sérum. De plus, la sous-classe IgG1 prédomine dans le lait et le colostrum, et les deux fournissent un spectre similaire d'anticorps.(Traduit par Docteur Serge Messier).

Protective and Risk Factors Associated With Youth Attitudes Toward Violence in Canada.

Adolescents and young adults are the main perpetrators and victims of violence in almost all parts of the world. Theories of human behavior predict that the intention to behave violently is formed in part by the individual's attitude toward violent behavior. The purpose of this study was thus to investigate factors which both promote and protect against violent youth attitudes in Toronto, Canada's largest urban center. Multinomial logit models were fit separately for males and females in Grades 7 to 9 using cross-sectional data from the 2006 International Youth Survey. Odds ratios were estimated for the associations between levels of attitude toward violence and select factors in each of the biological, familial, peer-related, school and community domains. A graded effect of school attachment on violent attitude was observed for both sexes; male and female students who do not like school at all are 9.89 (3.15-31.0) and 6.49 (2.19-19.2) times as likely as those who like school a lot to have the "most" versus "least" violent attitude, respectively. For every one-unit increase in (negative) perception of neighborhood score, male and female students are 1.15 (1.07-1.23) and 1.20 (1.12-1.28) times as likely to have the "most" versus "least" violent attitude. The number of victimization events was associated with attitude toward violence in males but not females, while the reverse was true for academic performance and exposure to prejudice. Our findings highlight the important relationships between connections to social environments and youth attitudes toward violence, and identify modifiable factors which may be amenable to intervention. Sex-specific differences in the predictors of violent youth attitudes warrant additional investigation and have implications for policy design.

The relationship between sociodemographic factors and reporting having terminated a pregnancy among Ghanaian women: a population-based study.

Background: Pregnancy termination is an illegal medical procedure in Ghana and 88% of induced abortions are performed in unsafe conditions, thus recipients face an elevated risk of abortion-related complications. This study aims to explore the associations between sociodemographic factors and reporting having terminated a pregnancy among Ghanaian women. Methods: Logistic regression models were estimated using data from the 2014 Ghana Demographic and Health Survey (n=9396). ORs were computed for the associations between reporting pregnancy termination and select demographic and socio-economic factors. Results: Education level, employment status, financial status and marital status of women are significantly associated with reporting having terminated a pregnancy. Conclusions: Women who are employed, cohabit with a partner and are considered middle class or wealthy are more likely than their counterparts to report having terminated a pregnancy. Ghanaian women with intermediate levels of education are more likely than both their more- and less-educated counterparts to report having terminated a pregnancy. These findings highlight the need for the development of policies aimed at reducing unsafe abortions associated with unintended pregnancies. Specific recommendations include providing family planning education and outreach to high-risk groups to reduce unintended pregnancies and improving working conditions for expectant mothers, including provisions for paid maternity leave and job protection.