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.

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).

Surveillance of antimicrobial resistance in Escherichia coli, Salmonella, and Campylobacter recovered from laying hens, their environment and products in Canada indicated a stable level of resistance to critically important antimicrobials, in varying time periods between 2007 and 2021.

The study objective was to determine the occurrence and antimicrobial resistance (AMR) attributes of select foodborne bacteria recovered from egg-producing (layer) chickens between 2007 and 2021 using different sample matrices (Study 1: liquid whole eggs, Study 2: spent hen cecal samples, Study 3: environmental sponge swabs and fecal samples from layer chicken barns, and Study 4: fecal samples from layer chicken barns). Samples from each study were submitted for the culture of Escherichia coli and Salmonella. In addition, samples from layer chicken barns were submitted for the culture of Campylobacter. Isolates were tested by microbroth dilution and interpreted using both clinical breakpoints and epidemiological cut-offs (ECOFFs). The ECOFFs were applied to detect non-wild type (NWT) strains. The proportion of resistant, NWT, and distribution of minimum inhibitory concentrations (MIC) were assessed. Ceftriaxone resistance was detected at a low-level in E. coli (< 2 %, all studies) and Salmonella (4.3 %, Study 2). Very low-level ciprofloxacin resistance was detected in E. coli (<1 %, Study 1) but a slightly elevated ciprofloxacin NWT E. coli (1 % to 6 %) observed. Only the farm fecal samples in Studies 2 and 3 were tested for Campylobacter as part of its study design, and moderate level ciprofloxacin resistance (<15 %) was observed. The MIC distribution patterns were similar across the organisms tested/studies and no substantial shifts in the distributions were detected. This analysis demonstrated that resistance to very important antimicrobials in bacteria from layers in Canada remains low, however, the detection of ciprofloxacin-resistant Campylobacter and the implications of this observation to the safety of egg products, and the role of laying flocks (i.e., as reservoir for resistant organisms) needs to be investigated.

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).

Assessing antimicrobial resistance in Campylobacter jejuni and Campylobacter coli and its association with antimicrobial use in Canadian turkey flocks.

Turkeys are important sources of antimicrobial-resistant Campylobacter. A total of 1063 isolates were obtained from 293 turkey flocks across Canada between 2016 and 2021 to evaluate their antimicrobial resistance (AMR) prevalence, patterns, distribution, and association with antimicrobial use (AMU). A high proportion of C. jejuni and C. coli isolates were resistant to tetracyclines and fluoroquinolones, despite the very low use of these drugs. C. jejuni isolates had a higher probability of being resistant to tetracyclines than C. coli isolates. The chance of C. jejuni isolates being resistant to fluoroquinolones, macrolides, and lincosamides was lower compared to C. coli. Isolates from the western region had a higher probability of being resistant to fluoroquinolones than isolates from Ontario. Isolates from Ontario had higher odds of being resistant to tetracyclines than isolates from Quebec. No associations were noted between the resistance and use of the same antimicrobial, but the use of certain antimicrobial classes may have played a role in the maintenance of resistance in Campylobacter (fluoroquinolone resistance - bacitracin and streptogramin use, tetracycline resistance - flavophospholipids and streptogramins use, macrolide resistance - flavophospholipid use). Low-level multidrug-resistant Campylobacter was observed indicating a stable AMR in turkeys. This study provided insights aiding future AMU and AMR surveillance.

Decrease in the prevalence of antimicrobial resistance in Escherichia coli isolates of Canadian turkey flocks driven by the implementation of an antimicrobial stewardship program.

The emergence of antimicrobial-resistant organisms at the human-animal-environment interface has raised global concern prompting governments and various stakeholders to take action. As a part of the stewardship initiative, Canadian turkey producers have implemented an antimicrobial use (AMU) strategy to manage antimicrobial resistance (AMR) in their sector. This study evaluated farm-level AMU and AMR data collected between 2016 and 2021 in major turkey-producing provinces/regions through the Canadian Integrated Program for Antimicrobial Resistance Surveillance to assess the progress of the strategy by characterizing the prevalence of homologous and multidrug resistance (MDR) in Escherichia coli isolated from turkeys. Multivariable mixed-effect logistic regression models assessed temporal and provincial/regional variations in AMR and MDR. Negative binomial regression models examined the temporal and regional variations in the total AMU. The total AMU (measured in mg/kg turkey biomass) significantly decreased in all provinces/regions in 2020 and 2021. Escherichia coli isolates from turkey flocks showed a significant decrease in resistance to gentamicin, sulfisoxazole, and tetracyclines during the six-year study period, consistent with the timing of the AMU reduction strategy. The prevalence of MDR isolates was significantly lower in 2020 and 2021 compared to 2016. Higher prevalence was observed in the Western region compared to Québec and Ontario. Two common AMR patterns were identified: ampicillin-streptomycin-tetracyclines and streptomycin-sulfisoxazole-tetracyclines. These AMR patterns indicate possible cross-resistances (same class), co-selection (unrelated classes) for resistance, or potential carryover of resistance determinants from previous production cycles. The decreasing prevalence of resistance to homologous antimicrobials, MDR, and AMU quantity are suggestive that the turkey sector's AMU strategy is achieving its desired impact. However, antimicrobials previously eliminated for preventive use in turkey flocks and the use of highly important antimicrobials in human medicine suggest that the AMU reduction strategy should be monitored and re-evaluated periodically to mitigate the emergence of MDR bacteria and safeguard animal and public health.

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.

Comparison of antimicrobial resistance among Salmonella enterica serovars isolated from Canadian turkey flocks, 2013 to 2021.

The emergence of antimicrobial resistance (AMR) in Salmonella from turkeys has raised a food safety concern in Canada as certain serovars have been implicated in human salmonellosis outbreaks in recent years. While several studies evaluated AMR in broiler chickens in Canada, there are limited studies that assess AMR in turkey flocks. This study analyzed data collected between 2013 and 2021 by the Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS) farm turkey surveillance program to determine the prevalence of AMR and differences in resistance patterns among Salmonella serovars recovered from turkey flocks. Salmonella isolates were tested for susceptibility to 14 antimicrobials using a microbroth dilution method. Hierarchical clustering dendrograms were constructed to compare the individual AMR status of Salmonella serovars. Differences in the probability of resistance between Salmonella serovars were determined using generalized estimating equation logistic regression models to account for farm-level clustering. Of the 1,367 Salmonella isolates detected, 55.3% were resistant to at least one antimicrobial and 25.3% were multidrug resistant (MDR) (resistant to ≥3 antimicrobial classes). The Salmonella isolates exhibited high resistance to tetracycline (43.3%), streptomycin (47.2%), and sulfisoxazole (29.1%). The 3 most frequently occurring serovars were S. Uganda (22.9%), S. Hadar (13.5%), and S. Reading (12.0%). Streptomycin-sulfisoxazole-tetracycline (n = 204) was the most frequent MDR pattern identified. Heatmaps showed that S. Reading exhibited coresistance to the quinolone class antimicrobials, ciprofloxacin, and nalidixic acid; S. Heidelberg to gentamicin and sulfisoxazole; and S. Agona to ampicillin and ceftriaxone. Salmonella Hadar isolates had higher odds of resistance to tetracycline (OR: 152.1, 95% CI: 70.6-327.4) while the probability of being resistant to gentamicin and ampicillin was significantly higher in S. Senftenberg than in all the other serovars. Moreover, S. Uganda had the highest odds of being MDR (OR: 4.7, 95% CI: 3.7-6.1). The high resistance observed warrants a reassessment of the drivers for AMR, including AMU strategies and other production factors. Differences in AMR patterns highlight the need to implement serovar-specific mitigation strategies.

Evaluating the effects of antimicrobial drug use on the ecology of antimicrobial resistance and microbial community structure in beef feedlot cattle.

Introduction: Use of antimicrobial drugs (AMDs) in food producing animals has received increasing scrutiny because of concerns about antimicrobial resistance (AMR) that might affect consumers. Previously, investigations regarding AMR have focused largely on phenotypes of selected pathogens and indicator bacteria, such as Salmonella enterica or Escherichia coli. However, genes conferring AMR are known to be distributed and shared throughout microbial communities. The objectives of this study were to employ target-enriched metagenomic sequencing and 16S rRNA gene amplicon sequencing to investigate the effects of AMD use, in the context of other management and environmental factors, on the resistome and microbiome in beef feedlot cattle. Methods: This study leveraged samples collected during a previous longitudinal study of cattle at beef feedlots in Canada. This included fecal samples collected from randomly selected individual cattle, as well as composite-fecal samples from randomly selected pens of cattle. All AMD use was recorded and characterized across different drug classes using animal defined daily dose (ADD) metrics. Results: Overall, fecal resistome composition was dominated by genes conferring resistance to tetracycline and macrolide-lincosamide-streptogramin (MLS) drug classes. The diversity of bacterial phyla was greater early in the feeding period and decreased over time in the feedlot. This decrease in diversity occurred concurrently as the microbiome represented in different individuals and different pens shifted toward a similar composition dominated by Proteobacteria and Firmicutes. Some antimicrobial drug exposures in individuals and groups were associated with explaining a statistically significant proportion of the variance in the resistome, but the amount of variance explained by these important factors was very small (<0.6% variance each), and smaller than associations with other factors measured in this study such as time and feedlot ID. Time in the feedlot was associated with greater changes in the resistome for both individual animals and composite pen-floor samples, although the proportion of the variance associated with this factor was small (2.4% and 1.2%, respectively). Discussion: Results of this study are consistent with other investigations showing that, compared to other factors, AMD exposures did not have strong effects on antimicrobial resistance or the fecal microbial ecology of beef cattle.

Associations between antimicrobial resistance in fecal Escherichia coli isolates and antimicrobial use in Canadian turkey flocks.

Antimicrobial resistance (AMR) in enteric bacteria continues to be detected in turkey flocks and retail products worldwide, including in Canada. However, studies assessing linkages between on-farm antimicrobial use (AMU) and the development of AMR are lacking. This study aims to identify AMU characteristics that impact the development of AMR in the indicator bacteria Escherichia coli in turkey flocks, building on the Canadian Integrated Program for Antimicrobial Resistance Surveillance methodology for farm-level AMU and AMR data integration. Two analytic approaches were used: (1) multivariable mixed-effects logistic regression models examined associations between AMU (any route, route-specific, and route-disease-specific indication) summarized as the number of defined daily doses in animals using Canadian standards ([nDDDvetCA]/1,000 kg-animal-days at risk) and AMR and (2) multivariable mixed-effects Poisson regression models studied the linkages between AMU and the number of classes to which an E. coli isolate was resistant (nCR E. coli ). A total of 1,317 E. coli isolates from a network of 16 veterinarians and 334 turkey producers across the five major turkey-producing provinces in Canada between 2016 and 2019 were used. Analysis indicated that AMR emerged with the use of related antimicrobials (e.g., tetracycline use-tetracycline resistance), however, the use of unrelated antimicrobial classes was also impacting AMR (e.g., aminoglycosides/streptogramins use-tetracycline resistance). As for studying AMU-nCR E. coli linkages, the most robust association was between the parenteral aminoglycosides use and nCR E. coli , though in-feed uses of four unrelated classes (bacitracin, folate pathway inhibitors, streptogramins, and tetracyclines) appear to be important, indicating that ongoing uses of these classes may slow down the succession from multidrug-resistant to a more susceptible E. coli populations. The analysis of AMU (route and disease-specific)-AMR linkages complemented the above findings, suggesting that treatment of certain diseases (enteric, late-stage septicemic conditions, and colibacillosis) are influential in the development of resistance to certain antimicrobial classes. The highest variances were at the flock level indicating that stewardship actions should focus on flock-level infection prevention practices. This study added new insights to our understanding of AMU-AMR linkages in turkeys and is useful in informing AMU stewardship in the turkey sector. Enhanced surveillance using sequencing technologies are warranted to explain molecular-level determinants of AMR.

Does swab type matter? Comparing methods for Mannheimia haemolytica recovery and upper respiratory microbiome characterization in feedlot cattle.

BACKGROUND: Bovine respiratory disease (BRD) is caused by interactions among host, environment, and pathogens. One standard method for antemortem pathogen identification in cattle with BRD is deep-guarded nasopharyngeal swabbing, which is challenging, costly, and waste generating. The objective was to compare the ability to recover Mannheimia haemolytica and compare microbial community structure using 29.5 inch (74.9 cm) deep-guarded nasopharyngeal swabs, 16 inch (40.6 cm) unguarded proctology swabs, or 6 inch (15.2 cm) unguarded nasal swabs when characterized using culture, real time-qPCR, and 16S rRNA gene sequencing. Samples for aerobic culture, qPCR, and 16S rRNA gene sequencing were collected from the upper respiratory tract of cattle 2 weeks after feedlot arrival. RESULTS: There was high concordance of culture and qPCR results for all swab types (results for 77% and 81% of sampled animals completely across all 3 swab types for culture and qPCR respectively). Microbial communities were highly similar among samples collected with different swab types, and differences identified relative to treatment for BRD were also similar. Positive qPCR results for M. haemolytica were highly concordant (81% agreed completely), but samples collected by deep-guarded swabbing had lower amounts of Mh DNA identified (Kruskal-Wallis analysis of variance on ranks, P < 0.05; Dunn-test for pairwise comparison with Benjamini-Hochberg correction, P < 0.05) and lower frequency of positive compared to nasal and proctology swabs (McNemar's Chi-square test, P < 0.05). CONCLUSIONS: Though differences existed among different types of swabs collected from individual cattle, nasal swabs and proctology swabs offer comparable results to deep-guarded nasopharyngeal swabs when identifying and characterizing M. haemolytica by culture, 16S rRNA gene sequencing, and qPCR.

Canadian Collaboration to Identify a Minimum Dataset for Antimicrobial Use Surveillance for Policy and Intervention Development across Food Animal Sectors.

Surveillance of antimicrobial use (AMU) and antimicrobial resistance (AMR) is a core component of the 2017 Pan-Canadian Framework for Action. There are existing AMU and AMR surveillance systems in Canada, but some stakeholders are interested in developing their own AMU monitoring/surveillance systems. It was recognized that the establishment of core (minimum) AMU data elements, as is necessary for policy or intervention development, would inform the development of practical and sustainable AMU surveillance capacity across food animal sectors in Canada. The Canadian Animal Health Surveillance System (CAHSS) AMU Network was established as a multisectoral working group to explore the possibility of harmonizing data inputs and outputs. There was a consensus that a minimum AMU dataset for AMU surveillance (MDS-AMU-surv) should be developed to guide interested parties in initiating AMU data collection. This multisectoral collaboration is an example of how consultative consensus building across relevant sectors can contribute to the development of harmonized approaches to AMU data collection and reporting and ultimately improve AMU stewardship. The MDS-AMU-surv could be used as a starting point for the progressive development or strengthening of AMU surveillance programs, and the collaborative work could serve as a model for addressing AMR and other shared threats at the human-animal-environment interface.

Informing Stewardship Measures in Canadian Food Animal Species through Integrated Reporting of Antimicrobial Use and Antimicrobial Resistance Surveillance Data-Part II, Application.

Using the methodology developed for integrated analysis and reporting of antimicrobial use (AMU) and antimicrobial resistance (AMR) data, farm-level surveillance data were synthesized and integrated to assess trends and explore potential AMU and AMR associations. Data from broiler chicken flocks (n = 656), grower-finisher pig herds (n = 462) and turkey flocks (n = 339) surveyed by the Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS) at the farm-level (2015-2019) were used. The analyses showed a reduction in mean flock/herd level number of defined daily doses using Canadian standards (nDDDvetCA) adjusted for kg animal biomass that coincided with the decline in % resistance in the three species. This was noted in most AMU-AMR pairs studied except for ciprofloxacin resistant Campylobacter where resistance continued to be detected (moderate to high levels) despite limited fluoroquinolone use. Noteworthy was the significantly negative association between the nDDDvetCA/kg animal biomass and susceptible Escherichia coli (multispecies data), an early indication that AMU stewardship actions are having an impact. However, an increase in the reporting of diseases in recent years was observed. This study highlighted the value of collecting high-resolution AMU surveillance data with animal health context at the farm-level to understand AMR trends, enable data integration and measure the impact of AMU stewardship actions.

Informing Stewardship Measures in Canadian Food Animal Species through Integrated Reporting of Antimicrobial Use and Antimicrobial Resistance Surveillance Data-Part I, Methodology Development.

This study explores methodologies for the data integration of antimicrobial use (AMU) and antimicrobial resistance (AMR) results within and across three food animal species, surveyed at the farm-level by the Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS). The approach builds upon existing CIPARS methodology and principles from other AMU and AMR surveillance systems. Species level data integration involved: (1) standard CIPARS descriptive and temporal analysis of AMU/AMR, (2) synthesis of results, (3) selection of AMU and AMR outcomes for integration, (4) selection of candidate AMU indicators to enable comparisons of AMU levels between species and simultaneous assessment of AMU and AMR trends, (5) exploration of analytic options for studying associations between AMU and AMR, and (6) interpretation and visualization. The multi-species integration was also completed using the above approach. In addition, summarized reporting of internationally-recognized indicators of AMR (i.e., AMR adjusted for animal biomass) and AMU (mg/population correction unit, mg/kg animal biomass) is explored. It is envisaged that this approach for species and multi-species AMU-AMR data integration will be applied to the annual CIPARS farm-level data and progressively developed over time to inform AMU-AMR integrated surveillance best practices for further enhancement of AMU stewardship actions.

Reduction in Antimicrobial Use and Resistance to Salmonella, Campylobacter, and Escherichia coli in Broiler Chickens, Canada, 2013-2019.

Antimicrobial use contributes to the global rise of antimicrobial resistance (AMR). In 2014, the poultry industry in Canada initiated its Antimicrobial Use Reduction Strategy to mitigate AMR in the poultry sector. We monitored trends in antimicrobial use and AMR of foodborne bacteria (Salmonella, Escherichia coli, and Campylobacter) in broiler chickens during 2013 and 2019. We quantified the effect of antimicrobial use and management factors on AMR by using LASSO regression and generalized mixed-effect models. AMR in broiler chickens declined by 6%-38% after the decrease in prophylactic antimicrobial use. However, the withdrawal of individual compounds, such as cephalosporins and fluoroquinolones, prompted an increase in use of and resistance levels for other drug classes, such as aminoglycosides. Canada's experience with antimicrobial use reduction illustrates the potential for progressive transitions from conventional antimicrobial-dependent broiler production to more sustainable production with respect to antimicrobial use.

Antimicrobial resistance and recovery of Salmonella, Campylobacter, and Escherichia coli from chicken egg layer flocks in Canadian sentinel surveillance sites using 2 types of sample matrices.

Eggs are important to the diet of Canadians. This product is one of the supply-managed commodities in Canada, but unlike other commodities, where food safety risks are extensively explored and reported, information on the prevalence of enteric organisms (e.g., Salmonella, Campylobacter) and antimicrobial resistance (AMR) in layers in Canada are limited. This study was conducted to determine the prevalence of select bacteria and the associated AMR patterns in layer flocks using 2 sample matrices. Farms were located within FoodNet Canada and the Canadian Integrated Program for Antimicrobial Resistance Surveillance sentinel sites (SS). Fecal samples (Ontario: ONSS1a, ONSS1b) and environmental sponge swabs (British Columbia: BCSS2a) were collected. Salmonella prevalence was 29% and 8% in ONSS1a and ONSS1b, respectively, and 7% in BCSS2a. S. Kentucky and S. Livingstone were the most frequently isolated serovars and no S. Enteritidis was detected. Campylobacter was not detected in the BC sponge swabs but was isolated from 89% and 53% of Ontario fecal samples (ONSS1a and ONSS1b, respectively). Seven C. jejuni from Ontario were ciprofloxacin-resistant. Escherichia coli prevalence was high in both sample types (98%). Overall, tetracycline resistance among E. coli ranged from 26% to 69%. Resistance to ceftiofur (n = 2 isolates) and gentamicin (n = 2) was relatively low. There were diverse resistance patterns (excludes susceptible isolates) observed among E. coli in Ontario (10 patterns) and British Columbia (14 patterns). This study revealed that fecal samples are more informative for farm-level monitoring of pathogen and AMR prevalence. Without further validation, sponge swabs are limited in their utility for Campylobacter detection and thus, for public health surveillance.

Les oeufs sont importants pour l'alimentation des Canadiens. Ce produit est l'un des produits soumis à la gestion de l'offre au Canada, mais contrairement à d'autres produits, où les risques pour la salubrité des aliments sont largement étudiés et signalés, des informations sur la prévalence des organismes entériques (p. ex. Salmonella, Campylobacter) et la résistance aux antimicrobiens (RAM) chez les pondeuses au Canada sont limitées. Cette étude a été menée pour déterminer la prévalence de certaines bactéries et les patrons de résistance aux antimicrobiens associés dans les troupeaux de pondeuses en utilisant deux matrices d'échantillons. Les fermes étaient situées au sein de FoodNet Canada et des sites sentinelles (SS) du Programme intégré canadien de surveillance de la résistance aux antimicrobiens. Des échantillons de matières fécales (Ontario : ONSS1a, ONSS1b) et des éponges environnementales (Colombie-Britannique : BCSS2a) ont été prélevés. La prévalence de Salmonella était de 29 % et 8 % pour ONSS1a et ONSS1b, respectivement, et de 7 % pour BCSS2a. Salmonella Kentucky et S. Livingstone étaient les sérotypes les plus fréquemment isolés et aucun S. Enteritidis n'a été détecté. Campylobacter n'a pas été détecté dans les éponges de la Colombie-Britannique, mais a été isolé de 89 % et 53 % des échantillons de matières fécales de l'Ontario (ONSS1a et ONSS1b, respectivement). Sept C. jejuni de l'Ontario étaient résistants à la ciprofloxacine. La prévalence d'Escherichia coli était élevée dans les deux types d'échantillons (98 %). Dans l'ensemble, la résistance à la tétracycline chez E. coli variait de 26 % à 69 %. La résistance au ceftiofur (n = 2 isolats) et à la gentamicine (n = 2) était relativement faible. Divers profils de résistance (à l'exclusion des isolats sensibles) ont été observés chez E. coli en Ontario (10 profils) et en Colombie-Britannique (14 profils). Cette étude a révélé que les échantillons fécaux sont plus informatifs pour la surveillance au niveau de la ferme de la prévalence des agents pathogènes et de la résistance aux antimicrobiens. Sans validation supplémentaire, les éponge sont limitées dans leur utilité pour la détection de Campylobacter et donc pour la surveillance en santé publique.(Traduit par Docteur Serge Messier).

Feedlot Cattle Antimicrobial Use Surveillance Network: A Canadian Journey.

Antimicrobial drugs are important tools for maintaining human and animal health. Globally, antimicrobial use (AMU) in food-producing animals is under increasing scrutiny due to its potential to promote antimicrobial resistance (AMR). Historically, comprehensive Canadian data related to the types of antimicrobial drugs used, extent of use, common indicators of use and the demographics of the cattle populations receiving antimicrobial drugs have been limited, in part due to segmentation in the cattle industry and fragmentation of the drug distribution system. Appropriate AMU estimates are required to understand AMU practices, to interpret AMR levels and patterns, to meaningfully assess associated public health risks, and to inform stewardship activities. The Canadian beef cattle industry has a long history of collaboration in AMU and AMR research. Prior research projects identified both opportunities and challenges in the collection of AMU data. Cornerstone projects provided insight into the complexity of collecting AMU data in Canada's feedlot sector. This paper will discuss how the lessons learned from past work have contributed to the formation of a Canadian fed-cattle antimicrobial surveillance program that was initiated in 2019. This important surveillance program will allow feedlot cattle AMU to improve management decisions and support AMU best practices in the evolving Canadian AMR landscape.

Antimicrobial Use Indices-The Value of Reporting Antimicrobial Use in Multiple Ways Using Data From Canadian Broiler Chicken and Turkey Farms.

We have previously described the importance of using multiple indicators for reporting national farm-level antimicrobial use (AMU) information, but the distribution of flock-level AMU and how these indicators relate to each other has not yet been fully explored. Using farm-level surveillance data (2013-2019), for broiler chickens (n = 947 flocks) and turkeys (n = 427), this study aims to (1) characterize flock-level AMU and identify high users, (2) identify appropriate AMU indicators and biomass denominator [population correction unit (PCU) vs. kg weight at pre-slaughter], and (3) make recommendations on the application to veterinarian-producer and national-level reporting. Diverse AMU patterns were identified in broiler chickens (156 patterns) and turkeys (68 patterns); of these, bacitracin, reported by 25% of broiler chicken and 19% of turkey producers, was the most frequently occurring pattern. Depending on the indicator chosen, variations in reported quantity of use, temporal trends and relative ranking of the antimicrobials changed. Quantitative AMU analysis yielded the following results for broiler chickens: mean 134 mg/PCU; 507 number (n) of Canadian (CA) defined daily doses (DDDvet) per 1,000 chicken-days and 18 nDDDvetCA/PCU. Analysis in turkey flocks yielded the following: mean 64 mg/PCU, 99 nDDDvetCA/1,000 turkey-days at risk and 9 nDDDvetCA/PCU. Flocks were categorized based on the percentiles of the mg/PCU distribution: "medium" to "low" users (≤75th percentile) and "high" users (>75th percentile). The odds of being a high user in both broiler chickens and turkeys were significantly increased: if water medications were used, and if trimethoprim-sulfonamides, bacitracins, and tetracyclines were used. Pairwise correlation analysis showed moderate correlation between mg/PCU and the nDDDvetCA/1,000 animal days at risk and between mg/PCU and nDDDvetCA/PCU. Significantly high correlation between nDDDvetCA/1,000 animal days at risk and nDDDvetCA/PCU was observed, suggestive that either of these could be used for routine monitoring of trends in AMU. One source of discrepancy between the indicators was the antimicrobial. Understanding the choice of parameter input and effects on reporting trends in AMU will inform surveillance reporting best practices to help industry understand the impacts of their AMU reduction strategies and to best communicate the information to veterinarians, their producers, and other stakeholders.

Presence and Diversity of Extended-Spectrum Cephalosporin Resistance Among Escherichia coli from Urban Wastewater and Feedlot Cattle in Alberta, Canada.

A recent preliminary study from our group found that extended-spectrum cephalosporin-resistance determinants can be detected in the majority of composite fecal samples collected from Alberta feedlot cattle. Most notably, blaCTX-M genes were detected in 46.5% of samples. Further isolate characterization identified blaCTX-M-15 and blaCTX-M-27, which are widespread in bacteria from humans. We hypothesized that Escherichia coli of human and beef cattle origins share the same pool of blaCTX-M genes. In this study, we aimed to assess and compare the genomic profiles of a larger collection of blaCTX-M-positive E. coli recovered from fecal composite samples from Canadian beef feedlot cattle and human wastewater through whole-genome sequencing. The variants blaCTX-M-55, blaCTX-M-32, blaCTX-M-27, blaCTX-M-15, and blaCTX-M-14 were found in both urban wastewater and cattle fecal isolates. Core genome multilocus sequence typing showed little similarity between the fecal and wastewater isolates. Thus, if the dissemination of genes between urban wastewater and feedlot cattle occurs, it does not appear to be related to the expansion of specific clonal lineages. Further investigations are warranted to assemble and compare plasmids carrying these genes to better understand the modalities and directionality of transfer.