Bacterial enrichment prior to third-generation metagenomic sequencing improves detection of BRD pathogens and genetic determinants of antimicrobial resistance in feedlot cattle.

Introduction: Bovine respiratory disease (BRD) is one of the most important animal health problems in the beef industry. While bacterial culture and antimicrobial susceptibility testing have been used for diagnostic testing, the common practice of examining one isolate per species does not fully reflect the bacterial population in the sample. In contrast, a recent study with metagenomic sequencing of nasal swabs from feedlot cattle is promising in terms of bacterial pathogen identification and detection of antimicrobial resistance genes (ARGs). However, the sensitivity of metagenomic sequencing was impeded by the high proportion of host biomass in the nasal swab samples. Methods: This pilot study employed a non-selective bacterial enrichment step before nucleic acid extraction to increase the relative proportion of bacterial DNA for sequencing. Results: Non-selective bacterial enrichment increased the proportion of bacteria relative to host sequence data, allowing increased detection of BRD pathogens compared with unenriched samples. This process also allowed for enhanced detection of ARGs with species-level resolution, including detection of ARGs for bacterial species of interest that were not targeted for culture and susceptibility testing. The long-read sequencing approach enabled ARG detection on individual bacterial reads without the need for assembly. Metagenomics following non-selective bacterial enrichment resulted in substantial agreement for four of six comparisons with culture for respiratory bacteria and substantial or better correlation with qPCR. Comparison between isolate susceptibility results and detection of ARGs was best for macrolide ARGs in Mannheimia haemolytica reads but was also substantial for sulfonamide ARGs within M. haemolytica and Pasteurella multocida reads and tetracycline ARGs in Histophilus somni reads. Discussion: By increasing the proportion of bacterial DNA relative to host DNA through non-selective enrichment, we demonstrated a corresponding increase in the proportion of sequencing data identifying BRD-associated pathogens and ARGs in deep nasopharyngeal swabs from feedlot cattle using long-read metagenomic sequencing. This method shows promise as a detection strategy for BRD pathogens and ARGs and strikes a balance between processing time, input costs, and generation of on-target data. This approach could serve as a valuable tool to inform antimicrobial management for BRD and support antimicrobial stewardship.

Improving the detection of integrative conjugative elements in bovine nasopharyngeal swabs using multiplex recombinase polymerase amplification.

Bovine respiratory disease (BRD) is an important health and economic burden to the cattle industry worldwide. Three bacterial pathogens frequently associated with BRD (Mannheimia haemolytica, Pasteurella multocida, and Histophilus somni) can possess integrative and conjugative elements (ICEs), a diverse group of mobile genetic elements that acquire antimicrobial resistance (AMR) genes (ARGs) and decrease the therapeutic efficacy of antimicrobial drugs. We developed a duplex recombinase polymerase amplification (RPA) assay to detect up to two variants of ICEs in these Pasteurellaceae. Whole genome sequence analysis of M. haemolytica, P. multocida, and H. somni isolates harbouring ICEs revealed the presence of tnpA or ebrB next to tet(H), a conserved ARG that is frequently detected in ICEs within BRD-associated bacteria. This real-time multiplex RPA assay targeted both ICE variants simultaneously, denoted as tetH_tnpA and tetH_ebrB, with a limit of detection (LOD) of 29 (95% CI [23, 46]) and 38 genome copies (95% CI [30, 59]), respectively. DNA was extracted from 100 deep nasopharyngeal swabs collected from feedlot cattle on arrival. Samples were tested for ICEs using a real-time multiplex RPA assay, and for M. haemolytica, P. multocida, H. somni, and Mycoplasma bovis using both culture methods and RPA. The assay provided sensitive and accurate identification of ICEs in extracted DNA, providing a useful molecular tool for timely detection of potential risk factors associated with the development of antimicrobial-resistant BRD in feedlot cattle.

Complete circular assembly of Histophilus somni PDS1537697-81-1 genome and phenotypic characterization of its antibiotic susceptibility.

A Histophilus somni isolate from a clinically healthy, fall-placed calf was obtained upon arrival to a commercial feedlot. Fall-placed calves are commonly viewed to be at high risk for the development of bovine respiratory disease. The isolate was phenotyped for antimicrobial susceptibility and sequenced to obtain a complete, circular, genome assembly.

The Canadian Cow-Calf Surveillance Network - productivity and health summary 2018 to 2022.

Cow-calf surveillance data provide critical information about changing herd demographics, productivity, health, and management as well as the opportunity to investigate the impact of differing management practices. A national cow-calf network was established to collect baseline information on herd health, production performance measures, and management. Questionnaires were used to collect information on herd attributes as well as data for the calving season, breeding, pregnancy testing, and weaning for herds from across Canada. From 2018 to 2022, a total of 565 calving record questionnaires, representing 110,658 calving female records from 171 herds were returned, along with 543 herd breeding to weaning questionnaires. Suggested benchmark values based on the 25th percentiles from Western and Eastern Canada were determined to be <5% for non-pregnancy, <2% for calf death from birth to 24 h, and < 2% for calf death from 24 h to weaning. Herds from Eastern Canada were more likely to report any assistance at calving (p < 0.001) than herds from Western Canada. Participating herds from the east had longer breeding (p < 0.001) and calving (p < 0.001) seasons than those from the west and were also more likely to use artificial insemination or embryo transfer (p < 0.001). Timing of calving season and use of large pastures for calving were not associated with mortality at birth. Herds that started calving before April were more likely to have calves die before 30 d than those that started calving later; however, this difference was not observed between 30 d and weaning. Herds that started to calve earlier were also more likely to report treating more calves for bovine respiratory disease, diarrhea, and navel or joint infections as well as to calf deaths from respiratory disease. Calves from herds in the east were more likely to be treated or die from diarrhea than from the west. Females from herds that started calving later were less likely to be pregnant. The unique longitudinal productivity and health data resulting from this network established a national baseline to address region-specific needs for knowledge translation and solutions to enhance productivity and support sustainability.

Variation in Pen-Level Prevalence of BRD Bacterial Pathogens and Antimicrobial Resistance Following Feedlot Arrival in Beef Calves.

Antimicrobials are crucial for treating bovine respiratory disease (BRD) in beef feedlots. Evidence is needed to support antimicrobial use (AMU) decisions, particularly in the early part of the feeding period when BRD risk is highest. The study objective was to describe changes in prevalence and antimicrobial susceptibility of BRD bacterial pathogens at feedlot processing (1 day on feed (1DOF)), 12 days later (13DOF), and for a subset at 36DOF following metaphylactic antimicrobial treatment. Mixed-origin steer calves (n = 1599) from Western Canada were managed as 16 pens of 100 calves, receiving either tulathromycin (n = 1199) or oxytetracycline (n = 400) at arrival. Deep nasopharyngeal swabs collected at all time points underwent culture and antimicrobial susceptibility testing (AST). Variability in the pen-level prevalence of bacteria and antimicrobial susceptibility profiles were observed over time, between years, and metaphylaxis options. Susceptibility to most antimicrobials was high, but resistance increased from 1DOF to 13DOF, especially for tetracyclines and macrolides. Simulation results suggested that sampling 20 to 30 calves per pen of 200 reflected the relative pen-level prevalence of the culture and AST outcomes of interest. Pen-level assessment of antimicrobial resistance early in the feeding period can inform the evaluation of AMU protocols and surveillance efforts and support antimicrobial stewardship in animal agriculture.

Laboratory tools for the direct detection of bacterial respiratory infections and antimicrobial resistance: a scoping review.

Rapid laboratory tests are urgently required to inform antimicrobial use in food animals. Our objective was to synthesize knowledge on the direct application of long-read metagenomic sequencing to respiratory samples to detect bacterial pathogens and antimicrobial resistance genes (ARGs) compared to PCR, loop-mediated isothermal amplification, and recombinase polymerase amplification. Our scoping review protocol followed the Joanna Briggs Institute and PRISMA Scoping Review reporting guidelines. Included studies reported on the direct application of these methods to respiratory samples from animals or humans to detect bacterial pathogens ±ARGs and included turnaround time (TAT) and analytical sensitivity. We excluded studies not reporting these or that were focused exclusively on bioinformatics. We identified 5,636 unique articles from 5 databases. Two-reviewer screening excluded 3,964, 788, and 784 articles at 3 levels, leaving 100 articles (19 animal and 81 human), of which only 7 studied long-read sequencing (only 1 in animals). Thirty-two studies investigated ARGs (only one in animals). Reported TATs ranged from minutes to 2 d; steps did not always include sample collection to results, and analytical sensitivity varied by study. Our review reveals a knowledge gap in research for the direct detection of bacterial respiratory pathogens and ARGs in animals using long-read metagenomic sequencing. There is an opportunity to harness the rapid development in this space to detect multiple pathogens and ARGs on a single sequencing run. Long-read metagenomic sequencing tools show potential to address the urgent need for research into rapid tests to support antimicrobial stewardship in food animal production.

Comparison of virus-neutralizing and virus-specific ELISA antibody responses among bovine neonates differentially primed and boosted against bovine coronavirus.

Objective: This study addressed the current gap in knowledge of neonatal prime-boost immune responses for the control of bovine coronavirus (BCoV) respiratory disease in weaning-age beef cattle. Animals: Study 1 and Study 2 had 33 and 22 commercial cross neonatal beef calves, respectively. Procedures: Study 1 compared BCoV-neutralizing antibody concentrations of control calves with 3 groups of calves differentially vaccinated with mucosal and/or systemic BCoV modified live virus (MLV) vaccines. Study 2 compared specific and neutralizing antibody concentrations among mucosally BCoV primed groups of calves that were differentially systemically boosted. Results: In Study 1, calves that were mucosally primed and systemically boosted had higher BCoV-neutralizing antibody concentrations than the control group at weaning. In Study 2, boosting mucosally primed calves by injecting inactivated or MLV vaccine resulted in anamnestic BCoV-specific antibody responses at weaning. Conclusion: Neonatal mucosal priming and systemic boosting resulted in anamnestic BCoV antibody responses at weaning. Clinical relevance: Prime-boost vaccination should be considered for control of BCoV respiratory disease.

Comparaison des réponses en anticorps ELISA neutralisant le virus et spécifiques du virus chez des nouveau-nés bovins vaccinés par amorces-rappels différenciés contre le coronavirus bovin. Objectif: Cette étude a abordé le manque actuel de connaissances sur les réponses immunitaires néonatales de stimulation pour maitriser la maladie respiratoire à coronavirus bovin (BCoV) chez les bovins de boucherie en âge de sevrage. Animaux: Les études 1 et 2 portaient respectivement sur 33 et 22 veaux de boucherie néonatals croisés commerciaux. Procédures: L'étude 1 a comparé les concentrations d'anticorps neutralisant le BCoV de veaux témoins avec 3 groupes de veaux vaccinés de manière différentielle avec des vaccins à virus vivant modifié (MLV) contre le BCoV pour administration par voie mucosale et/ou systémique. L'étude 2 a comparé les concentrations d'anticorps spécifiques et neutralisants parmi des groupes de veaux sensibilisés au BCoV par voie mucosale et qui ont eu un rappel par voie systémique différentielle. Résultats: Dans l'étude 1, les veaux qui avaient reçu une amorce au niveau des muqueuses et un rappel systémique présentaient des concentrations d'anticorps neutralisant le BCoV plus élevées que le groupe témoin au sevrage. Dans l'étude 2, le rappel des veaux amorcés par voie mucosale par l'injection d'un vaccin inactivé ou MLV a entraîné une réponse anamnestique en anticorps spécifiques du BCoV au sevrage. Conclusion: En période néonatale, l'amorce par voie mucosale et le renforcement systémique ont entraîné des réponses anamnestiques en anticorps BCoV au sevrage. Pertinence clinique: La vaccination de rappel doit être envisagée pour maitriser la maladie respiratoire causée par le BCoV.(Traduit par Dr Serge Messier).

Effect of water sulfate and dietary bismuth subsalicylate on feed and water intake, ruminal hydrogen sulfide concentration, and trace-mineral status of growing beef heifers.

In the Northern Great Plains, cattle may be exposed to water with an elevated sulfate concentration resulting in ruminal hydrogen sulfide (H2S) production and risk of copper deficiency. There are currently few strategies available to help mitigate effects arising from high-sulfate water (HS). The objective of this study was to evaluate the effects of feeding a moderate-forage diet with or without bismuth subsalicylate (BSS; 0.0% vs. 0.4% DM basis) when provided water with a low- (LS; 346 ±â€…13) or HS (4,778 ±â€…263 mg/L) concentration on feed and water intake, ruminal H2S concentration, and liver and serum trace-mineral concentrations. Twenty-four Limousin × Simmental cross beef heifers (221 ±â€…41 kg) were stratified based on initial liver Cu into a completely randomized block design with a 2 × 2 factorial treatment arrangement. Feed and water intake (measured weekly), ruminal H2S concentration (measured on days 42 and 91), liver (measured on days -13 and 91), and serum trace-mineral concentrations (measured on days 1, 28, 56, and 91) were evaluated. Initial liver trace-mineral concentrations were used as a covariate in the statistical model. Water intake tended to be reduced with the inclusion of BSS (P = 0.095) but was not affected by water sulfate (P = 0.40). Water sulfate and BSS did not affect dry matter intake (DMI; P ≥ 0.89). Heifers consuming HS had a ruminal H2S concentration that was 1.58 mg/L more (P < 0.001) than LS. The inclusion of BSS reduced (P = 0.035) ruminal H2S concentration by more than 44% (1.35 vs. 0.75 mg/L). Regardless of the water sulfate concentration, heifers fed BSS had lesser liver Cu concentration (average of 4.08 mg/kg) than heifers not provided BSS, and when not provided BSS, HS had lesser Cu than LS (42.2 vs. 58.3; sulfate × BSS, P = 0.019). The serum concentration of Cu did not differ over time for heifers not provided BSS; whereas, heifers provided BSS had lesser serum Cu concentration on day 91 than on days 28 and 55 (BSS × time, P < 0.001). The liver concentration of selenium was reduced (P < 0.001) with BSS inclusion but the selenium concentration in serum was not affected by sulfate, BSS, or time (P ≥ 0.16). BSS reduced ruminal H2S concentration, but depleted liver Cu and Se. Moreover, sulfate concentration in water did not appear to affect DMI, water intake, or growth, but increased ruminal H2S and reduced liver Cu concentration.

Water containing a high concentration of sulfate increases the risk of hydrogen sulfide production in the rumen and consequently of polioencephalomalacia. In addition, water with a high-sulfate concentration may induce copper deficiency indicated by depleted liver copper concentration. Bismuth subsalicylate (BSS) can bind to sulfides and may reduce the risk of hydrogen sulfide production and therefore may mitigate risks associated with high-sulfate water. In this study, the effects of water sulfate concentrations (346 ±â€…13 vs. 4,778 ±â€…263 mg/L) were tested along with 0.0% vs. 0.4% of dietary BSS. Water intake tended to be reduced with the inclusion of BSS but was not affected by water sulfate. Water sulfate concentration and BSS did not affect dry matter intake (DMI). Heifers consuming high-sulfate water (HS) had a ruminal H2S concentration that was 1.58 mg/L more than low-sulfate water (LS). The inclusion of BSS reduced ruminal H2S concentration by 44% (1.35 vs. 0.75 mg/L). Regardless of the water sulfate concentration, heifers fed BSS had lesser liver Cu concentration than heifers not provided BSS, and when not provided BSS, HS had lesser Cu than LS. BSS reduced ruminal hydrogen sulfide concentration but depleted liver Cu. Sulfate concentration in water did not affect DMI, water intake, or growth, but increased ruminal hydrogen sulfide concentration and reduced liver Cu concentration.

Antimicrobial resistance in generic E. coli isolated from western Canadian cow-calf herds.

Objective: To examine antimicrobial resistance (AMR) in commensal fecal Escherichia coli (E. coli) from extensively managed beef calves and cows in western Canada and describe the differences among cows and calves in the spring and fall. Animal: Beef cattle, cow-calf. Procedure: Antimicrobial susceptibility testing was conducted on generic E. coli isolates collected from 388 calves and 387 cows from 39 herds following calving in 2021, 419 calves from 39 herds near weaning, and 357 cows from 36 herds at pregnancy testing. Minimum inhibitory concentrations were measured with the NARMS CMV5AGNF plate for Gram-negative bacteria and interpreted using Clinical and Laboratory Standards Institute standard breakpoints for humans. Results: Only 16% (242/1551) of all isolates from 97% (38/39) of herds were resistant to ≥ 1 antimicrobial. Generic E. coli isolates were most commonly resistant to sulfisoxazole (11%, 175/1551), followed by tetracycline (9.3%, 145/1551) and chloramphenicol (3.5%, 55/1551). Isolates from calves in the spring were more likely to be resistant to sulfisoxazole, tetracycline, and chloramphenicol than those from cows in the spring or calves in the fall. Multiclass-resistant isolates were identified in 5% (39/807) of calves. Only 2 isolates recovered from cows were resistant to antimicrobials of very high importance for human health. Conclusion and clinical relevance: Most generic E. coli isolates were pansusceptible. The observed resistance patterns were consistent with earlier studies of AMR from commensal E. coli in this region. Baseline AMR data for cow-calf herds are not currently collected as part of routine surveillance, but are essential to inform antimicrobial use policy and stewardship.

Résistance aux antimicrobiens chez E. coli générique isolé dans des troupeaux vache-veau de l'Ouest canadien. Objectif: Examiner la résistance aux antimicrobiens (RAM) chez Escherichia coli de la flore fécale commensale (E. coli) provenant de veaux et de vaches de boucherie en élevage extensif dans l'ouest du Canada et décrire les différences entre les vaches et les veaux au printemps et à l'automne. Animal: Bovins de boucherie, vache-veau. Procédure: Des tests de sensibilité aux antimicrobiens ont été effectués sur des isolats génériques d'E. coli collectés auprès de 388 veaux et 387 vaches de 39 troupeaux après le vêlage en 2021, de 419 veaux de 39 troupeaux à l'approche du sevrage et de 357 vaches de 36 troupeaux lors des tests de gestation. Les concentrations minimales inhibitrices ont été mesurées avec la plaque NARMS CMV5AGNF pour les bactéries à Gram négatif et interprétées à l'aide des seuils standard pour les humains du Clinical and Laboratory Standards Institute. Résultats: Seulement 16 % (242/1 551) de tous les isolats provenant de 97 % (38/39) des troupeaux étaient résistants à ≥ 1 antimicrobien. Les isolats génériques d'E. coli étaient le plus souvent résistants au sulfisoxazole (11 %, 175/1 551), suivi de la tétracycline (9,3 %, 145/1 551) et du chloramphénicol (3,5 %, 55/1 551). Les isolats provenant des veaux au printemps étaient plus susceptibles d'être résistants au sulfisoxazole, à la tétracycline et au chloramphénicol que ceux provenant des vaches au printemps ou des veaux à l'automne. Des isolats résistants à plusieurs classes ont été identifiés chez 5 % (39/807) des veaux. Seuls deux isolats récupérés chez des vaches étaient résistants à des antimicrobiens de très haute importance pour la santé humaine. Conclusion et pertinence clinique: La plupart des isolats génériques d'E. coli étaient sensibles à l'ensemble des antimicrobiens. Les profils de résistance observés concordaient avec les études antérieures sur la RAM provenant d'E. coli commensal dans cette région. Les données de base sur la RAM pour les troupeaux vache-veau ne sont pas actuellement recueillies dans le cadre de la surveillance de routine, mais elles sont essentielles pour éclairer la politique et la gestion de l'utilisation des antimicrobiens.(Traduit par Dr Serge Messier).

Antimicrobial resistance in Enterococcus isolated from western Canadian cow-calf herds.

BACKGROUND: Data on antimicrobial resistance (AMR) in cow-calf herds is limited and there have been no Canadian studies examining AMR in Enterococcus in cow-calf herds. Enterococcus is a ubiquitous Gram-positive indicator of AMR for enteric organisms that is also important in human health. The objective of this study was to describe AMR in specific Enterococcus species of interest from cow-calf herds; highlighting differences in AMR among isolates from cows and calves and samples collected in the spring and fall. Isolates (n = 1505) were examined from 349 calves and 385 cows from 39 herds in the spring of 2021 and 413 calves from 39 herds and 358 cows from 36 herds in the fall of 2021. Enterococcus species were identified using Matrix-Assisted Laser Desorption Ionization Time-Of-Flight mass spectrometry (MALDI-TOF MS) and antimicrobial susceptibility testing was completed based on a prioritization scheme for importance to human health and using the National Antimicrobial Resistance Monitoring System (NARMS) Gram positive Sensititre broth microdilution panel. RESULTS: Resistance was observed to at least one antimicrobial in 86% (630/734) of isolates from the spring and 84% (644/771) of isolates from the fall. The most common types of resistance across all species were: lincomycin, quinupristin/dalfopristin, daptomycin, ciprofloxacin, and tetracycline. However, the proportion of isolates with AMR varied substantially based on species. Multiclass resistance, defined as resistance to ≥3 antimicrobial classes after excluding intrinsic resistance, was highest in isolates from calves in the spring (6.9%) (24/349) and cows in the fall (6.7%) (24/357). Differences in resistance were seen between cows and calves in the spring and fall as well as across seasons, with no differences seen between cows and calves in the fall. CONCLUSIONS: While most Enterococcus isolates were resistant to at least one antimicrobial, questions remain regarding species differences in intrinsic resistance and the accuracy of certain antimicrobial breakpoints for specific Enterococcus spp. As a result, some species-specific AMR profiles should be interpreted with caution. Despite these constraints, Enterococcus species are important indicator organisms for AMR and resulting data can be used to inform stewardship initiatives.

Producer attitudes regarding antimicrobial use and resistance in Canadian cow-calf herds.

Objective: To describe producer attitudes toward antimicrobial use (AMU) and antimicrobial resistance (AMR), identify factors associated with attitudes, and inform stewardship initiatives. Animal: Beef cattle, cow-calf. Procedure: Cow-calf producers from the Canadian Cow-Calf Surveillance Network (C3SN) completed a survey (n = 146) on producers' attitudes toward AMU, AMR, and impacts of recent regulatory changes requiring a prescription for the purchase of medically important antimicrobials (MIA). Results: Most producers (78%, 114/146) reported being aware of initiatives to improve antimicrobial stewardship within the beef industry and 67% (97/146) indicated that AMR was a highly important issue to the industry and producers personally. Almost half of producers reported concerns that AMR development has impacted AMU decisions on their operations. Overall, veterinarians were producers' primary source of information regarding AMU, including treatment protocols, stewardship programs, and regulatory changes. Following introduction of the 2018 prescription-only regulations, 95% (138/146) of producers reported no change in AMU on their operations. Similarly, 77% (112/146) of producers reported no change in antimicrobial product access, whereas 63% (91/146) reported no change in cost. Conclusion: Most producers reported little change in access to antimicrobials and in AMU following the introduction of regulations requiring a prescription for MIA. Clinical relevance: Producers rely on veterinarians as their primary source of information regarding antimicrobial regulations and AMU. It is therefore important for veterinarians to understand their role as educators for beef cow-calf producers. Ultimately, veterinarians and producers need to work together to ensure that the health and welfare of animals are protected while using antimicrobials in a responsible manner.

Attitudes des producteurs à l'égard de l'utilisation des antimicrobiens et de la résistance dans les troupeaux vache-veau canadiens. Objectif: Décrire les attitudes des producteurs à l'égard de l'utilisation des antimicrobiens (AMU) et de la résistance aux antimicrobiens (RAM), identifier les facteurs associés à ces attitudes et les informations sur les initiatives de gouvernance. Animal: Bovins de boucherie, vache-veau. Procédure: Les producteurs naisseurs du Réseau canadien de surveillance vache-veau (C3SN) ont répondu à une enquête (n = 146) sur les attitudes des producteurs à l'égard de l'AMU, de la RAM et des impacts des récents changements réglementaires exigeant une ordonnance pour l'achat d'antimicrobiens médicalement importants (MIA). Résultats: La plupart des producteurs (78 %, 114/146) ont déclaré être au courant des initiatives visant à améliorer la gouvernance des antimicrobiens au sein de l'industrie du bœuf et 67 % (97/146) ont indiqué que la RAM était un problème très important pour l'industrie et les producteurs personnellement. Près de la moitié des producteurs ont fait part de leurs inquiétudes quant au fait que le développement de la RAM ait un impact sur les décisions d'AMU sur leurs opérations. Dans l'ensemble, les médecins vétérinaires étaient la principale source d'information des producteurs concernant l'AMU, y compris les protocoles de traitement, les programmes de gouvernance et les changements réglementaires. À la suite de l'introduction de la réglementation sur prescription uniquement en 2018, 95 % (138/146) des producteurs n'ont signalé aucun changement dans l'AMU de leurs opérations. De même, 77 % (112/146) des producteurs n'ont signalé aucun changement dans l'accès aux produits antimicrobiens, tandis que 63 % (91/146) n'ont signalé aucun changement dans le coût. Conclusion: La plupart des producteurs ont signalé peu de changements dans l'accès aux antimicrobiens et dans l'AMU par suite de l'introduction de réglementations exigeant une prescription pour le MIA. Pertinence clinique: Les producteurs comptent sur les médecins vétérinaires comme principale source d'information concernant la réglementation antimicrobienne et l'AMU. Il est donc important que les médecins vétérinaires comprennent leur rôle d'éducateurs auprès des producteurs de vaches-veaux de boucherie. En fin de compte, les médecins vétérinaires et les producteurs doivent travailler ensemble pour garantir la protection de la santé et du bien-être des animaux tout en utilisant les antimicrobiens de manière responsable.(Traduit par Dr Serge Messier).

Complete genome sequence of Mannheimia bovis isolated from a healthy feedlot calf in Saskatchewan, Canada.

A lack of whole genome sequences for Mannheimia spp. other than Mannheimia haemolytica complicates their identification. Here, we present the genome sequence of Mannheimia bovis 39324.S-11, isolated from a healthy calf on a feedlot in Saskatchewan, Canada, and compare it to ZY190616T, which is currently the only other isolate of M. bovis for which sequence is publicly available.

Vaccine use in Canadian cow-calf herds and opportunities for improvement.

Vaccinations are one of the most impactful tools available to cow-calf producers to control within herd disease and later, in feedlots. While vaccine use has been studied across Canada, inconsistent and variable regional data makes analysis and interpretation difficult. The objective of this study was to describe vaccination protocols and factors associated with vaccine use in Canadian cow-calf herds and define associations between vaccine use and productivity outcomes. Surveys describing vaccine use in 2020 were collected from 131 cow-calf herds (40 eastern, 91 western), recruited through a national beef cattle surveillance program. Ninety-two percent of cows and replacement heifers, and 72% of bulls were vaccinated with Infectious Bovine Rhinotracheitis (IBR), Bovine Viral Diarrhea Virus (BVDV), Parainfluenza3 Virus (PI3), and Bovine Respiratory Syncytial Virus (BRSV). At least half of cows and bulls were vaccinated for clostridial pathogens and cows and heifers for viral calf scours. Clostridial vaccines were significantly more likely to be used in western Canada compared to eastern Canada. While 92% of producers vaccinated suckling calves against IBR/BRSV/PI3, only 47% provided a second vaccine prior to weaning; 78% of calves were also vaccinated at least once for BVDV before weaning. Producers who vaccinated calves against IBR/BRSV/PI3 before 3 months of age provided a second dose prior to weaning more often than producers who administer the first IBR/BRSV/PI3 vaccine later. Vaccine use has increased across Canada, particularly in calves, prior to weaning. Relative to label recommendations for annual vaccination, clostridial vaccines were generally underutilized in cows and bulls, and by producers in eastern Canada as compared to western Canada. Opportunities also exist to improve adherence to label recommendations for the booster dose of scours vaccine when used in bred replacement heifers. Protocols including product choices, the timing and boosting of respiratory vaccines in nursing calves vary widely across herds. Use of intranasal vaccines in neonatal calves less than 2 weeks old has increased in western Canada compared to previous reports. There is a need to better understand how timing of vaccination in nursing calves contributes to effectiveness, for respiratory disease in nursing and weaned calves.

A Scoping Review of Antimicrobial Usage and Antimicrobial Resistance in Beef Cow-Calf Herds in the United States and Canada.

BACKGROUND: The magnitude and knowledge gaps regarding antimicrobial use (AMU) and antimicrobial resistance (AMR) have not been summarized for the North American cow-calf production sector, although estimates of AMU and AMR are essential to AMR risk analysis. The objectives of this scoping review were to map AMU and AMR in the beef cow-calf sector in Canada and the United States, summarize published AMU/AMR predictors, and identify research gaps. METHODS: An electronic search was conducted of four bibliographic databases and Google Scholar, augmented by a hand-search of captured studies. RESULTS: Twenty-three of three-hundred and forty-three publications screened advanced to data extraction. Of these, 10 were conducted in the USA and 13 in Canada. Thirteen studied AMR and twelve studied AMU, with two reporting both. Of twelve captured AMU studies, nine presented counts of herd AMU by antimicrobial class or specific antimicrobial. Antimicrobial resistance in Escherichia coli (E. coli) was reported in nine studies. Risk factors for AMU include herd size, vaccine use, and start date of calving season. CONCLUSIONS: Overall, a small number of AMR studies were available for synthesis in primarily one population (cows) reporting E. coli AMR. Additional studies targeting reasons for AMU in calves, the impact of management procedures on AMU, potential environmental AMR sources, and AMR in respiratory pathogens and enteric organisms other than E. coli for pre-weaning calves are required to inform AMR risk mitigation strategies.

Update on copper and selenium in Canadian cow-calf herds: regional differences and estimation of serum reference values.

Trace mineral supplementation of beef cattle is essential for efficient reproduction and herd health. Understanding regional differences in cow trace mineral status could inform decisions about risks of deficiencies and supplementation management. Cow-calf surveillance projects provided three opportunities to evaluate the trace mineral status of Canadian beef cow herds. Blood samples were collected at pregnancy testing in 2014 from 102 cow-calf herds and in 2016 from 86 cow-calf herds in Western Canada. In 2019, blood samples were collected at pregnancy testing from cows in 163 cow-calf herds from Eastern and Western Canada. Serum samples were analyzed for copper, selenium, and molybdenum concentrations using a plasma mass spectrometer. The prevalence of copper deficient cows sampled from the Western provinces ranged from 24% to 43% across the three periods, and was 20% from Eastern Canada in 2019. The prevalence of selenium deficient cows ranged from 0.2% to 0.4% across the three projects in Western Canada, but was higher in Eastern Canada at 4.6% in 2019. High serum molybdenum was identified in 9.4% to 14% of cows across the three periods in Western Canada and in 15% of cows sampled in Eastern Canada in 2019. Serum copper, selenium, and molybdenum concentrations varied by cow age and month of sample collection. Serum selenium and molybdenum concentrations, but not copper, varied by soil type associated with the location of the farm. A subsample of samples from cows from Western Canadian herds provided body condition score (BCS) data, pregnancy status, and calf survival data and were used to estimate updated serum reference values for adequate concentrations. Age-specific values were required for selenium and molybdenum. Reference intervals (80%) were estimated from 2,406 pregnant beef cows from 99 herds with each cow having a BCS ≥ 2.5/5 and a live calf at 3 wk with no retained placenta: copper for all cows (0.379 to 0.717 ppm), selenium for cows <4 yr (0.052 to 0.152 ppm), and selenium for cows ≥4 yr (0.064 to 0.184 ppm). Upper 90% reference limits were also estimated for serum molybdenum for cows <4 yr (>0.104 ppm) and cows ≥4 yr (>0.110 ppm). The lower limits for the reference intervals for adequate copper and selenium are below those previously reported; nevertheless, they represent a large sample that was specifically applicable to extensively managed beef animals in western Canada.

Factors associated with antimicrobial resistant enterococci in Canadian beef cattle: A scoping review.

Introduction: Antimicrobial resistance (AMR) is a global health concern, occurring when bacteria evolve to render antimicrobials no longer effective. Antimicrobials have important roles in beef production; however, the potential to introduce AMR to people through beef products is a concern. This scoping review identifies factors associated with changes in the prevalence of antimicrobial-resistant Enterococcus spp. applicable to the Canadian farm-to-fork beef continuum. Methods: Five databases (MEDLINE, BIOSIS, Web of Science, Embase, and CAB Abstracts) were searched for articles published from January 1984 to March 2022, using a priori inclusion criteria. Peer-reviewed articles were included if they met all the following criteria: written in English, applicable to the Canadian beef production context, primary research, in vivo research, describing an intervention or exposure, and specific to Enterococcus spp. Results: Out of 804 screened articles, 26 were selected for inclusion. The included articles discussed 37 factors potentially associated with AMR in enterococci, with multiple articles discussing at least two of the same factors. Factors discussed included antimicrobial administration (n = 16), raised without antimicrobials (n = 6), metal supplementation (n = 4), probiotics supplementation (n = 3), pen environment (n = 2), essential oil supplementation (n = 1), grass feeding (n = 1), therapeutic versus subtherapeutic antimicrobial use (n = 1), feeding wet distiller grains with solubles (n = 1), nutritional supplementation (n = 1) and processing plant type (n = 1). Results were included irrespective of their quality of evidence. Discussion: Comparability issues arising throughout the review process were related to data aggregation, hierarchical structures, study design, and inconsistent data reporting. Findings from articles were often temporally specific in that resistance was associated with AMR outcomes at sampling times closer to exposure compared to studies that sampled at longer intervals after exposure. Resistance was often nuanced to unique gene and phenotypic resistance patterns that varied with species of enterococci. Intrinsic resistance and interpretation of minimum inhibitory concentration varied greatly among enterococcal species, highlighting the importance of caution when comparing articles and generalizing findings. Systematic Review Registration: [http://hdl.handle.net/1880/113592].

Antimicrobial Use in Canadian Cow-Calf Herds.

Despite growing concern surrounding antimicrobial use (AMU) and the importance of cow-calf herds to the Canadian livestock industry, surveillance of AMU in cow-calf herds to inform antimicrobial stewardship programs has been sporadic. Producers from the Canadian Cow-Calf Surveillance Network (87%, 146/168) provided data and almost all reported AMU in at least one animal (99%, 145/146 herds) in 2019-2020. The most common reasons for AMU were treatment of respiratory disease in nursing calves in 78% of herds and neonatal diarrhea in 67% of herds, as well as for lameness in cows in 83% of herds. However, most herds treated <5% of animals for these reasons. Less than 2.5% of herds treated more than 30% of calves for either bovine respiratory disease or neonatal diarrhea and no herds treated more than 30% of cows for lameness. The most frequently reported antimicrobial was oxytetracycline in 81% of herds, followed by florfenicol in 73% of herds. Antimicrobials with very high importance to human health, such as ceftiofur, were used at least once by 20% of herds but were only used in >30% of nursing calves from one herd. Similarly, while 56% of herds used macrolides at least once, within-herd use was the highest in nursing calves where <4% of herds reported use in >30% of animals. Herds using artificial insemination and calving in the winter were more likely (p = 0.05) to treat >5% of nursing calves for respiratory disease, suggesting the importance of vaccination programs for herds at risk. Overall, AMU was similar to previous Canadian studies; however, the percentage of herds using macrolides had increased from a comparable study in 2014.

Comparative efficacy of modified-live and inactivated vaccines in boosting disease-sparing responses to bovine viral diarrhea virus challenge in neonatally mucosally primed weanling beef calves.

Objective: This study compares immune and clinical responses of bovine viral diarrhea virus (BVDV)-maternal antibody (MatAb)-positive beef calves primed with intranasal modified-live virus vaccine (MLV) and differentially boosted with a systemic MLV or an inactivated vaccine (KV). Animal: Eighteen commercial Black Angus steers. Procedure: Calves were mucosally primed at ~24 h of age with an MLV and boosted by injection of a MLV (IN-MLV) or inactivated vaccine (IN-KV) at an average age of 54 d. Challenge occurred at weaning with a virulent non-cytopathic BVDV-2 strain, 24515. Results: Clinically, the IN-KV group had a longer duration of fever, leukopenia, and viremia, whereas the IN-MLV group had greater BVDV Types-1 and -2 heterospecific antibody responses. Conclusion: Altogether, these data indicated that systemic MLV boosting resulted in a more robust protection to BVDV Type-2 challenge at weaning. Clinical relevance: Mucosal prime-boosting of neonatal calves provided protection against BVDV Type-2 challenge at weaning.

Efficacité comparative des vaccins vivants modifiés et inactivés pour stimuler les réponses épargnant la maladie à la provocation par le virus de la diarrhée virale bovine chez des veaux de boucherie sevrés sensibilisés par voie mucosale en période néo-natale. Objectif: Cette étude compare les réponses immunitaires et cliniques des veaux de boucherie positifs au virus de la diarrhée virale bovine (BVDV) dus aux anticorps maternels (MatAb), sensibilisés avec un vaccin intranasal à virus vivant modifié (MLV) et différentiellement stimulés avec un vaccin MLV systémique ou un vaccin inactivé (KV). Animal: Dix-huit bouvillons commerciaux Black Angus. Procédure: Les veaux ont été sensibilisés par voie mucosale à environ 24 h d'âge avec un MLV et ont reçu un rappel par injection d'un MLV (IN-MLV) ou d'un vaccin inactivé (IN-KV) à un âge moyen de 54 jours. L'épreuve a eu lieu au sevrage avec une souche virulente non cytopathique de BVDV-2, 24515. Résultats: Cliniquement, le groupe IN-KV présentait une durée plus longue de fièvre, de leucopénie et de virémie, tandis que le groupe IN-MLV présentait des réponses en anticorps hétérospécifiques BVDV de types 1 et 2 plus importantes. Conclusion: Dans l'ensemble, ces données ont indiqué que le renforcement par le vaccin MLV systémique entraînait une protection plus robuste contre la provocation par le BVDV de type 2 au sevrage. Pertinence clinique: La stimulation mucosale des veaux nouveau-nés a fourni une protection contre la provocation par le BVDV de type 2 au sevrage.(Traduit par Dr Serge Messier).

Investigating effective testing strategies for the control of Johne's disease in western Canadian cow-calf herds using an agent-based simulation model.

Johne's disease is an insidious infectious disease of ruminants caused by Mycobacterium avium subspecies paratuberculosis (MAP). Johne's disease can have important implications for animal welfare and risks causing economic losses in affected herds due to reduced productivity, premature culling and replacement, and veterinary costs. Despite the limited accuracy of diagnostic tools, testing and culling is the primary option for controlling Johne's disease in beef herds. However, evidence to inform specific test and cull strategies is lacking. In this study, a stochastic, continuous-time agent-based model was developed to investigate Johne's disease and potential control options in a typical western Canadian cow-calf herd. The objective of this study was to compare different testing and culling scenarios that included varying the testing method and frequency as well as the number and risk profile of animals targeted for testing using the model. The relative effectiveness of each testing scenario was determined by the simulated prevalence of cattle shedding MAP after a 10-year testing period. A second objective was to compare the direct testing costs of each scenario to identify least-cost options that are the most effective at reducing within-herd disease prevalence. Whole herd testing with individual PCR at frequencies of 6 or 12 months were the most effective options for reducing disease prevalence. Scenarios that were also effective at reducing prevalence but with the lowest total testing costs included testing the whole herd with individual PCR every 24 months and testing the whole herd with pooled PCR every 12 months. The most effective method with the lowest annual testing cost per unit of prevalence reduction was individual PCR on the whole herd every 24 months. Individual PCR testing only cows that had not already been tested 4 times also ranked well when considering both final estimated prevalence at 10 years and cost per unit of gain. A more in-depth economic analysis is needed to compare the cost of testing to the cost of disease, taking into account costs of culling, replacements and impacts on calf crops, and to determine if testing is an economically attractive option for commercial cow-calf operations.

Seroprevalence of Mycobacterium avium spp. paratuberculosis in cow-calf herds located in the prairie provinces of Canada.

Objective: To determine the prevalence of Mycobacterium avium spp. paratuberculosis (MAP) in cow-calf herds located in the prairie provinces of Alberta, Saskatchewan, and Manitoba using a serum ELISA test. Animals: Study herds were recruited from the Western Canadian Cow-calf Surveillance Network (WC3SN) designed to monitor factors related to the health and productivity of cow-calf herds. Overall, 1791 cows from 92 herds were included in the study. Procedure: Blood samples were collected from 20 cows per herd in a systematic random fashion by private veterinarians in the fall of 2014. A serum ELISA (IDEXX, Westbrook, Maine, USA) test was used for the detection of MAP antibodies in the blood samples. Results: The cow level seroprevalence across all 3 provinces was 1.5%. Alberta had the lowest cow seroprevalence (1.3%) followed by Saskatchewan (1.7%), and Manitoba (2.1%). Herd level data showed that 24% of herds had at least 1 positive animal and 5% had at least 2 positive animals. Seroprevalence estimates varied between geographical regions within each province and with herd size. Conclusions: The apparent prevalence of MAP in prairie cow-calf herds remains low and similar to past estimates for the region. However, controlling the spread of Johne's disease in the western Canadian cow-calf herd should be considered an important discussion point in the beef industry. Clinical relevance: Ongoing surveillance of Johne's disease in western Canadian beef herds is necessary for mitigating disease spread before it becomes a disease of major concern within the industry.

Séroprévalence de Mycobacterium avium spp. paratuberculosis dans les troupeaux de vaches-veaux situés dans les provinces des Prairies du Canada. Objectif: Pour déterminer la prévalence de Mycobacterium avium spp. paratuberculosis (MAP) dans des troupeaux de vachesveaux situés dans les provinces des Prairies de l'Alberta, de la Saskatchewan et du Manitoba à l'aide d'un test ELISA sérique. Animaux: Les troupeaux à l'étude ont été recrutés à partir du Réseau de surveillance des vaches-veaux de l'Ouest canadien (WC3SN) conçu pour surveiller les facteurs liés à la santé et à la productivité des troupeaux de vaches-veaux. Au total, 1791 vaches de 92 troupeaux ont été incluses dans l'étude. Procédure: Des échantillons de sang ont été prélevés de 20 vaches par troupeau de façon aléatoire systématique par des vétérinaires en pratique privée à l'automne 2014. Un test ELISA sérique (IDEXX, Westbrook, Maine, États-Unis) a été utilisé pour la détection des anticorps MAP dans les échantillons de sang. Résultats: La séroprévalence chez les vaches dans les trois provinces était de 1,5 %. L'Alberta avait la plus faible séroprévalence chez les vaches (1,3 %), suivie de la Saskatchewan (1,7 %) et du Manitoba (2,1 %). Les données au niveau du troupeau ont montré que 24 % des troupeaux avaient au moins un animal positif et 5 % avaient au moins deux animaux positifs. Les estimations de la séroprévalence variaient entre les régions géographiques de chaque province et selon la taille du troupeau. Conclusions: La prévalence apparente de la MAP dans les troupeaux de vaches-veaux des Prairies demeure faible et semblable aux estimations antérieures pour la région. Cependant, la maitrise de la propagation de la maladie de Johne dans le troupeau vache-veau de l'Ouest canadien devrait être considérée comme un point de discussion important dans l'industrie bovine. Pertinence clinique: La surveillance continue de la maladie de Johne dans les troupeaux de bovins de boucherie de l'Ouest canadien est nécessaire pour atténuer la propagation de la maladie avant qu'elle ne devienne une maladie préoccupante au sein de l'industrie.(Traduit par Dr Serge Messier).