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.

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.

A One Health Genomic Investigation of Gentamicin Resistance in Escherichia coli from Human and Chicken Sources in Canada, 2014 to 2017.

We investigated whether gentamicin resistance (Genr) in Escherichia coli isolates from human infections was related to Genr E. coli in chicken and whether resistance may be due to coselection from use of lincomycin-spectinomycin in chickens on farms. Whole-genome sequencing was performed on 483 Genr E. coli isolates isolated between 2014 and 2017. These included 205 human-source isolates collected by the Canadian Ward (CANWARD) program and 278 chicken-source isolates: 167 from live/recently slaughtered chickens (animals) and 111 from retail chicken meat collected by the Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS). The predominant Genr gene was different in human and chicken sources; however, both sources carried aac(3)-IId, aac(3)-VIa, and aac(3)-IVa. Forty-one percent of human clinical isolates of Genr E. coli contained a blaCTX-M extended-spectrum beta-lactamase (ESBL) gene (84/205), and 53% of these were sequence type 131 (ST131). Phylogenomic analysis revealed a high diversity of Genr isolates; however, there were three small clusters of closely related isolates from human and chicken sources. Genr and spectinomycin resistance (Specr) genes were colocated in 148/167 (89%) chicken animal isolates, 94/111 (85%) chicken retail meat isolates, and 137/205 (67%) human-source isolates. Long-read sequencing of 23 isolates showed linkage of the Genr and Specr genes on the same plasmid in 14/15 (93%) isolates from chicken(s) and 6/8 (75%) isolates from humans. The use of lincomycin-spectinomycin on farms may be coselecting for gentamicin-resistant plasmids in E. coli in broiler chickens; however, Genr isolates and plasmids were mostly different in chickens and humans.

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.

One Health Genomic Analysis of Extended-Spectrum ß-Lactamase‒Producing Salmonella enterica, Canada, 2012‒2016.

Extended-spectrum ß-lactamases (ESBLs) confer resistance to extended-spectrum cephalosporins, a major class of clinical antimicrobial drugs. We used genomic analysis to investigate whether domestic food animals, retail meat, and pets were reservoirs of ESBL-producing Salmonella for human infection in Canada. Of 30,303 Salmonella isolates tested during 2012-2016, we detected 95 ESBL producers. ESBL serotypes and alleles were mostly different between humans (n = 54) and animals/meat (n = 41). Two exceptions were blaSHV-2 and blaCTX-M-1 IncI1 plasmids, which were found in both sources. A subclade of S. enterica serovar Heidelberg isolates carrying the same IncI1-blaSHV-2 plasmid differed by only 1-7 single nucleotide variants. The most common ESBL producer in humans was Salmonella Infantis carrying blaCTX-M-65, which has since emerged in poultry in other countries. There were few instances of similar isolates and plasmids, suggesting that domestic animals and retail meat might have been minor reservoirs of ESBL-producing Salmonella for human infection.

Antimicrobial use in lactating sows, piglets, nursery, and grower-finisher pigs on swine farms in Ontario, Canada during 2017 and 2018.

BACKGROUND: Data on antimicrobial use (AMU) in pig production are needed for the development of good antimicrobial stewardship practices to reduce the risk of antimicrobial resistance in bacteria that can cause illness in animals and humans. In Canada, there is a lack of quantitative data on AMU in the farrowing and nursery stages of pig production. This study aimed to determine which antimicrobial active ingredients are currently used in farrowing, nursery, and grower-finisher herds in the province of Ontario, Canada, and to quantify AMU using various metrics. We collected data on herd demographics, biosecurity, health status, and AMU during one production cycle from 25 farrowing and 25 nursery herds in Ontario, between May 2017 and April 2018, and obtained data from 23 Ontario grower-finisher herds during the same time frame from the Public Health Agency's Canadian Integrated Program for Antimicrobial Resistance Surveillance. We applied frequency measures, and weight-, and dose-based metrics to the data. RESULTS: In all pigs, the highest quantity of AMU was administered in-feed. By all routes of administration and compared to other production stages, nursery pigs used more antimicrobials in mg/kg biomass and the number of Canadian defined daily doses per 1000 pig-days (doseCA rate), while grower-finisher pigs used more antimicrobials in total kilograms and the number of Canadian defined daily doses per pig. In suckling pigs in some herds, there was routine disease prevention use of ceftiofur, an antimicrobial active ingredient categorized as very highly important in human medicine by Health Canada. The top antimicrobial used in each stage of pig production often varied by the metric used. There was producer-reported growth promotion use of antimicrobials in suckling and grower-finisher feed. CONCLUSIONS: The results of this study provide a current picture of AMU in pigs in Ontario and can be used as a basis for further research on AMU in farrowing and nursery herds in Canada. Our findings confirm that it would be useful to include farrowing and nursery herds in routine AMU surveillance in Canada. A future analysis using data from this project will examine factors that affect the quantity of AMU.

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.

Comprehensive Risk Pathway of the Qualitative Likelihood of Human Exposure to Severe Acute Respiratory Syndrome Coronavirus 2 from the Food Chain.

ABSTRACT: A group of experts from all Canadian federal food safety partners was formed to monitor the potential issues relating to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) food contamination, to gather and consider all of the relevant evidence and to determine the impact for Canadian food safety. A comprehensive risk pathway was generated to consider the likelihood of a SARS-CoV-2 contamination event at any of the relevant steps of the food processing and handling chain and the potential for exposure and transmission of the virus to the consumer. The scientific evidence was reviewed and assessed for each event in the pathway, taking into consideration relevant elements that could increase or mitigate the risk of contamination. The advantage of having an event-wise contextualization of the SARS-CoV-2 transmission pathway through the food chain is that it provides a systematic and consistent approach to evaluate any new data and communicate its importance and impact. The pathway also increases the objectivity and consistency of the assessment in a rapidly evolving and high-stakes situation. Based on our review and analysis, there is currently no comprehensive epidemiological evidence of confirmed cases of SARS-CoV-2, or its known variants, causing coronavirus disease 2019 from transmission through food or food packaging. Considering the remote possibility of exposure through food, the likelihood of exposure by ingestion or contact with mucosa is considered negligible to very low, and good hygiene practices during food preparation should continue to be followed.

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.

A One-Health Genomic Investigation of Gentamicin Resistance in Salmonella from Human and Chicken Sources in Canada, 2014 to 2017.

We investigated whether the increased prevalence of gentamicin resistance in Salmonella from human infections was related to a similar increased prevalence in isolates from broiler chickens and whether this increase may have been due to coselection from use of lincomycin-spectinomycin in chickens on farms. Whole-genome sequencing was performed on gentamicin-resistant (Genr) Salmonella isolates from human and chicken sources collected from 2014 to 2017 by the Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS). We determined the genomic relatedness of strains and characterized resistance genes and plasmids. From 2014 to 2017, 247 isolates of Genr Salmonella were identified by CIPARS: 188 were from humans, and 59 were from chicken sources (26 from live animals on farm and 33 from retail meat). The five most common Genr serovars were Salmonella enterica serovars Heidelberg (n = 93; 31.5%), 4,[5],12:i:- (n = 42; 14.2%), Kentucky (n = 37; 12.5%), Infantis (n = 33; 11.2%), and Typhimurium (n = 23; 7.8%). Phylogenomic analysis revealed that for S. Heidelberg and S. Infantis, there were closely related isolates from human and chicken sources. In both sources, resistance to gentamicin and spectinomycin was most frequently conferred by aac(3)-VIa and ant(3'')-Ia, respectively. Plasmid closure confirmed linkages of gentamicin and spectinomycin resistance genes and revealed instances of similar plasmids from both sources. Gentamicin and spectinomycin resistance genes were linked on the same plasmids, and some plasmids and isolates from humans and chickens were genetically similar, suggesting that the use of lincomycin-spectinomycin in chickens may be selecting for gentamicin-resistant Salmonella in broiler chickens and that these resistant strains may be acquired by humans.

Evaluation of selective media in antimicrobial surveillance programs capturing broad-spectrum ß-lactamase producing Escherichia coli from chickens at slaughter.

Antimicrobial resistance surveillance targeting agricultural animals is practiced in many countries but does not often include media selective for cephalosporin resistance. Here, we compared the frequency of recovery of resistant Escherichia coli using selective and non-selective media from the cecal contents of 116 chickens collected by the Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS). Third generation cephalosporin resistance was detected in 24 samples including 12, 10, and 2 on selective, non-selective, and both media, respectively. Isolates producing the CTX-M-1 ESBL were grown from 11 samples, 10 on selective medium only. Our results suggest that current surveillance approaches underestimate the true prevalence of resistance to critically important antimicrobials.

Évaluation de milieux sélectifs dans des programmes de surveillance antimicrobienne isolant Escherichia coli produisant des ß-lactamases à large spectre provenant de poulets à l'abattage. La surveillance de la résistance aux antimicrobiens ciblant les animaux d'élevage est pratiquée dans de nombreux pays mais n'inclut pas souvent les milieux sélectifs pour la résistance aux céphalosporines. Ici, nous avons comparé la fréquence d'isolement d'Escherichia coli résistants à l'aide de milieux sélectifs et non sélectifs à partir du contenu caecal de 116 poulets collectés dans le cadre du Programme intégré canadien de surveillance de la résistance aux antimicrobiens (PICRA). Une résistance aux céphalosporines de troisième génération a été détectée dans 24 échantillons dont 12, 10 et 2 sur des milieux sélectifs, non sélectifs et les deux, respectivement. Les isolats produisant les BLSE CTX-M-1 ont été cultivés à partir de 11 échantillons, 10 sur un milieu sélectif uniquement. Nos résultats suggèrent que les approches de surveillance actuelles sous-estiment la prévalence réelle de la résistance aux antimicrobiens d'importance critique.(Traduit par Dr Serge Messier).

Choosing which metrics to use when reporting antimicrobial use information to veterinarians in the Canadian swine industry.

The objective of this study was to evaluate preferences for various metrics and denominators among Canadian swine veterinarians, in order to improve reporting of antimicrobial use (AMU) information to these stakeholders and to facilitate enhanced stewardship decisions. An online survey was made available to swine veterinarians across Canada; 12 responses (estimated response rate 17.6%) were submitted and analyzed. Responses represented veterinarians from every major pig-producing province and from a range of year of graduation from veterinary college. Participants self-evaluated their understanding of dose-based metrics as higher than weight- and frequency-based metrics and interpreted most results of AMU analyses correctly. Participants preferred dose-based metrics over others, and had various objectives for AMU information, including improving AMU on their clients' farms and enabling comparisons with other farms. The results are useful to those making decisions about which AMU metrics to use in reports targeted to swine veterinarians.

Choix des paramètres à utiliser lors de la communication d'informations sur l'utilisation des antimicrobiens aux vétérinaires de l'industrie porcine canadienne. L'objectif de la présente étude était d'évaluer les préférences pour divers paramètres et dénominateurs chez les vétérinaires porcins canadiens, afin d'améliorer la déclaration de l'information sur l'utilisation d'antimicrobiens (UMA) à ces intervenants et de faciliter des décisions de gérance améliorées. Un sondage en ligne a été mis à la disposition des vétérinaires porcins partout au Canada; 12 réponses (taux de réponse estimé à 17,6 %) ont été soumises et analysées. Les réponses représentaient des vétérinaires de toutes les grandes provinces productrices de porcs et d'une gamme d'années d'obtention du diplôme d'un collège vétérinaire. Les participants ont auto-évalué leur compréhension des mesures basées sur la dose comme étant supérieure aux mesures basées sur le poids et la fréquence et ont interprété correctement la plupart des résultats des analyses UMA. Les participants préféraient les mesures basées sur la dose aux autres, et avaient divers objectifs pour l'information sur l'UMA, notamment l'amélioration de l'UMA dans les fermes de leurs clients et la possibilité de comparer avec d'autres fermes. Les résultats sont utiles à ceux qui prennent des décisions sur les paramètres d'UMA à utiliser dans les rapports destinés aux vétérinaires porcins.(Traduit par Dr Serge Messier).

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.

Antimicrobial Resistance Profiles of Escherichia coli and Salmonella Isolates in Canadian Broiler Chickens and Their Products.

Antimicrobial resistance (AMR) is a global public health threat. The main purpose of this study was to evaluate AMR in generic Escherichia coli and Salmonella recovered from broiler chickens in Canada. To do this, an analysis of the antimicrobial susceptibility results was performed on a sample of generic E. coli and Salmonella isolates from the 2012 to 2013 national microbiological baseline study in broiler chicken. Of the 1135 generic E. coli isolates tested, 940 (82.8%) were resistant to at least one antimicrobial, with a large number of unique AMR profiles observed. Of the 1495 Salmonella isolates tested, 879 (58.8%) were resistant to at least one antimicrobial. Resistance was most common to aminoglycosides, ß-lactams, and tetracyclines and, for generic E. coli isolates only, folate inhibitors. Differences in AMR patterns were observed across regions for both E. coli and Salmonella. For Salmonella, the levels of resistance were similar across the different sectors sampled along the food chain (e.g., slaughterhouse and retail) and the types of product sampled. There were also considerable differences in the levels and patterns of resistance among different Salmonella serovars, with most Salmonella Enteritidis isolates being susceptible to all antimicrobials tested.

Antimicrobial Resistance of Campylobacter in Broiler Chicken Along the Food Chain in Canada.

Antimicrobial resistance (AMR) is a major public health threat worldwide. The main objective of this study was to compare AMR in Campylobacter from broiler chickens raised on Canadian farms and their products in different geographical regions of Canada. To do this, antimicrobial susceptibility results from isolates of Campylobacter recovered from a national microbiological baseline study conducted in federally registered establishments and in the retail marketplace were analyzed. Among 1460 isolates tested, 774 (53%) were resistant to at least one antimicrobial, with a predominance of three profiles: tetracycline (39%), quinolone-tetracycline (6.6%), and quinolones only (3.5%). The results showed no significant difference in the frequency of resistant profiles (p ≥ 0.05) among the isolates originating from different points in the food processing chain at slaughterhouses and in retail establishments. This suggests that AMR observed in Campylobacter isolates from raw chicken at retail originated further upstream in the system. A difference in the frequency of certain resistance profiles was observed between the regions of Canada. For instance, in British Columbia, there was more resistance to quinolones, while in Ontario and Quebec, Campylobacter isolates were more resistant to tetracyclines, macrolides, ketolides, and lincosamides. Comparison of AMR data from this study with those from the Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS) did not show any significant difference and provides evidence that CIPARS produces nationally representative resistance results.

Extended-Spectrum ß-Lactamase and AmpC ß-Lactamase-Producing Escherichia coli Isolates from Chickens Raised in Small Flocks in Ontario, Canada.

Food-producing animals are recognized to play a role in the epidemiology of antimicrobial resistance in Canada. However, the presence of resistant organisms in particular groups of animals, such as chickens raised in small-holder flocks, has not been studied. The purpose of this study was, therefore, to identify and characterize Escherichia coli possessing broad-spectrum ß-lactamase genes among a collection of third-generation cephalosporin-resistant isolates recovered from 205 small flocks in southern Ontario. Extended-spectrum ß-lactamase (ESBL; CTX-M-1) positive strains were isolated from 26 out of 205 flocks (12.7%), whereas 39 strains possessing AmpC (CMY-2) were grown from 31 out of 205 flocks (15.1%). Pulsed-field gel electrophoresis (PFGE) revealed that the isolates were genetically heterogeneous. Further testing by multi-locus sequence typing confirmed that none of the PFGE-defined clusters belonged to ST131. Our results suggest that the dissemination of this resistance in bacteria isolated from chickens in small-holder flocks may be associated with the spread of plasmids rather than particular E. coli clones and that these isolates do not possess the ESBL types most commonly associated with human infections (CTX-M-15).

Antimicrobial Use and Antimicrobial Resistance Indicators-Integration of Farm-Level Surveillance Data From Broiler Chickens and Turkeys in British Columbia, Canada.

Using data from the Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS), we aimed to describe trends in antimicrobial use (AMU) in broiler chickens and turkeys, to compare AMU across species, to compare with trends in antimicrobial resistance (AMR), and to assess the effects of various AMU/AMR units of measurement (metrics and indicators) on data integration. Data on AMU and AMR in enteric bacteria, collected from 2013 to 2017 from broiler chickens (n = 143 flocks) and turkeys (n = 145) were used. In broiler chickens, the total AMU in milligrams/population correction unit (mg/PCUBr) decreased by 6%, the number (n) of defined daily doses for animals using Canadian standards (nDDDvetCA) per 1,000 broiler chicken-days decreased by 12%, and nDDDvetCA/PCU decreased by 6%. In turkeys, the mg/PCUTk decreased by 1%, whereas the nDDDvetCA/1,000 turkey-days and the nDDDvetCA/PCU increased by 1 and 5%, respectively. The types of antimicrobial classes used in both species were similar. Using the frequency of flocks reporting use (i.e., number of flocks reporting use/number of flocks participating) as a measurement, the use of certain antimicrobials changed over time (e.g., Broilers, decreased cephalosporin use, virginiamycin use, emerging use of lincomycin-spectinomycin, and avilamycin; Turkeys: increased trimethoprim-sulfonamides and macrolide use). The trends in resistance to specific antimicrobials paralleled the frequency and quantity of use (e.g., ceftriaxone use decreased-ceftriaxone resistance decreased, and gentamicin use increased-gentamicin resistance increased) in some situations, but not others (decreased fluoroquinolone use-increased ciprofloxacin resistance). AMR data were summarized using the AMR indicator index (AMR Ix). The most notable AMR Ix trend was the decrease in ceftriaxone AMR Ix among Escherichia coli (0.19 to 0.07); indicative of the success of the poultry industry action to eliminate the preventive use of third generation cephalosporins. Other trends observed were the increase in ciprofloxacin AMR Ix among Campylobacter from 0.23 to 0.41 and gentamicin AMR Ix among E. coli from 0.11 to 0.22, suggestive of the persistence/emergence of resistance related to previous and current AMU not captured in our surveillance timeframe. These data highlight the necessity of multiple AMU and AMR indicators for monitoring the impact of stewardship activities and interventions.

Diversity of CTX-M-positive Escherichia coli recovered from animals in Canada.

Historically, extended-spectrum cephalosporin resistance in bacteria from animals in Canada has been attributed to the SHV and CMY ß-lactamase families. This pattern is beginning to change with the emergence of the blaCTX-M gene family among Escherichia coli recovered from various animal species. Here we analyze and compare whole genome sequences of blaCTX-M-positive E. coli isolates (n = 173) from dogs, chicken, swine, horses and beef cattle in Canada. Ten blaCTX-M variants were identified with blaCTX-M-1,-14, -15, -27 and blaCTX-M-55 being identified in most animal species. These variants occurred across many sequence types, suggesting that mobile genetic elements mediate the spread of blaCTX-M. The variants blaCTX-M-14, -15, -27 and blaCTX-M-55 are associated with the global spread of blaCTX-M in human clinical isolates and their presence could be indicative of transfer between humans and animals. These variants were also the principal variants identified among sequence type 131 isolates, which were not associated with any other species than dogs. These isolates carried the same blaCTX-M variants as E. coli isolates found in humans. Close contact may promote the transmission of these isolates between humans and companion animals.

Antimicrobials Used for the Therapy of Necrotic Enteritis and Coccidiosis in Broiler Chickens and Turkeys in Canada, Farm Surveillance Results (2013-2017).

Since 2013, the Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS) has collected antimicrobial use (AMU) and antimicrobial resistance data from sentinel broiler chicken flocks (Br, five provinces) and sentinel turkey flocks (Tk, one province 2013-2015, three provinces 2016-2017). The objectives of this paper were to describe various preventive strategies aimed at controlling necrotic enteritis (NE) and coccidiosis in the broiler chicken and turkey flocks participating in CIPARS and FoodNet Canada Farm Surveillance Program between 2013 and 2017, to quantify and identify trends in antimicrobials used in feed, and to describe temporal changes in the diagnoses of bacterial and protozoal diseases in relation to antimicrobial use in feed. Comprehensive data were collected (by questionnaire) enabling AMU assessment by various count-based metrics (i.e., frequency and number of medicated rations), weight-based metrics (i.e., inclusion rate in feed and kilograms consumed), and technical indicators (i.e., milligrams per population correction unit [mg/PCU]). Qualitative information such as reasons for use and frequency of diagnosed diseases provided context to the trends in AMU. Between 2013 and 2017, 646 broiler flocks (14.9 million kg biomass) and 234 turkey flocks (12.4 million kg biomass) were surveyed. Overall, antimicrobials used for the prevention of Clostridium perfringens infections (NE) contributed to 85% (109/128 mg/PCUBr) and 95% (59/62 mg/PCUTk) of the quantity of antimicrobials administered via feed in broiler chickens and turkeys, respectively. Three NE programs were used: either 1, 2, or ≥3 antimicrobials administered throughout the production cycle. The treatment protocol in which a single antimicrobial was used throughout the cycle was the most frequent NE preventive program for broiler chickens (58%) and turkeys (76%). Bacitracin and virginiamycin were the top two most frequently used antimicrobials in both species for NE. For coccidiosis control, ionophores and chemical coccidiostats contributed to 66% (3091 kg) and 68% (1561 kg) of the total feed antimicrobial exposures in broiler chickens and turkeys, respectively. Documented coccidiosis programs included continuous or straight (1 drug/cycle), shuttle or dual control (≥2 drugs/cycle), and vaccination. Variations in coccidiosis programs between species were noted: broiler chickens frequently used a shuttle or dual-control program (68%), whereas turkey flocks used primarily a continuous or straight program (74%). Flocks raised without antibiotics and organic farms (10.3% of broiler chickens and 9.8% turkey flocks) used vaccines to prevent coccidiosis. A small number of broiler flocks (n = 6) used a combination of a vaccination and a coccidiostat during the cycle. During the surveillance timeframe used for this paper, the total feed AMU decreased over time in broiler chickens from 136 to 120 mg/PCUBr and in turkeys from 85 to 62 mg/ PCUTk, with no remarkable changes in the frequency of flocks diagnosed with bacterial and protozoal diseases. Surveillance findings such as these will be used as valid reference points in light of the upcoming changes in Canadian federal AMU regulations and industry-led initiatives aimed at reducing AMU.

Antimicrobianos utilizados para el tratamiento de la enteritis necrótica y coccidiosis en pollos de engorde y pavos en Canadá, resultados de la vigilancia en granjas (2013-2017). Desde el año 2013, el Programa Integrado Canadiense para Vigilancia de la Resistencia a los Antimicrobianos (con las siglas en inglés CIPARS) ha recopilado datos sobre el uso de antimicrobianos (UMA) y sobre la resistencia a los antimicrobianos en parvadas de pollos de pollos de engorde centinelas (Br, cinco provincias) y de parvadas de pavos centinelas (Tk, una provincia entre 2013-2015 y tres provincias entre 2016-2017). Los objetivos de artículo fueron describir varias estrategias preventivas dirigidas a controlar la enteritis necrótica (NE) y la coccidiosis en las parvadas de pollos de pollos de engorde y pavos que participan en el programa CIPARS y en el Programa de Vigilancia Agrícola de FoodNet en Canadá entre los años 2013 y 2017, para cuantificar e identificar las tendencias en los antimicrobianos utilizados en los alimentos y describir cambios temporales en el diagnóstico de enfermedades bacterianas y protozoarias con relación con el uso de estos antimicrobianos en el alimento. Se recopiló información completa (por cuestionario) que permitió la evaluación del uso de antimicrobianos mediante diversos parámetros basados en conteos (por ejemplo, frecuencia y número de raciones medicadas), parámetros basados en peso (por ejemplo, tasa de inclusión en alimentos y kilogramos consumidos) e indicadores técnicos (por ejemplo, miligramos por unidad de corrección de la población [mg/PCU]). La información cualitativa, como las razones para el uso y la frecuencia de enfermedades diagnosticadas, proporcionó un contexto a las tendencias en el uso de antimicrobianos. Entre los años 2013 y 2017, se analizaron 646 parvadas de pollos de engorde (14.9 millones de kg de biomasa) y 234 parvadas de pavos (12.4 millones de kg de biomasa). En general, los antimicrobianos utilizados para la prevención de infecciones por Clostridium perfringens (NE) contribuyeron al 85% (109/128 mg/PCUBr) y al 95% (59/62 mg/PCUTk) de la cantidad de antimicrobianos administrados en el alimento en pollos de engorde y pavos, respectivamente. Se utilizaron tres programas para enteritis necrótica: ya sea uno, dos o tres o más antimicrobianos administrados a lo largo del ciclo de producción. El protocolo de tratamiento en el que se utilizó un solo antimicrobiano durante todo el ciclo fue el programa preventivo para enteritis necrótica más frecuente para pollos de engorde (58%) y pavos (76%). La bacitracina y la virginiamicina fueron los dos principales antimicrobianos utilizados con mayor frecuencia en ambas especies contra la enteritis necrótica. Para el control de la coccidiosis, los ionóforos y los coccidiostáticos químicos contribuyeron al 66% (3091 kg) y el 68% (1561 kg) de la exposición total a antimicrobianos en los pollos de engorde y pavos, respectivamente. Los programas de coccidiosis documentados incluyeron el control continuo o directo (un fármaco por ciclo), o programas combinados o dobles (dos o más fármacos por ciclo) y la vacunación. Se observaron variaciones en los programas de coccidiosis entre las especies: en pollo de engorde se usaron con frecuencia programas combinados/duales (68%), mientras que en las parvadas de pavos se usaron principalmente programas continuos/directos (74%). Las parvadas criadas sin antibióticos y granjas orgánicas (10.3% de las parvadas de pollos de engorde y 9.8% de las parvadas de pavo) utilizaron vacunas para prevenir la coccidiosis. Un pequeño número de parvadas de pollos de engorde (n = 6) usaron una combinación de una vacuna y un coccidiostato durante el ciclo. Durante el período de tiempo de la vigilancia incluido en este artículo, el uso total de antimicrobianos en el alimento disminuyó con el tiempo en pollos de engorde de 136 a 120 mg/PCUBr y en pavos de 85 a 62 mg/PCUTk, sin cambios importantes en la frecuencia de parvadas con diagnóstico de bacterias y enfermedades protozoarias. Los hallazgos de la vigilancia como estos se utilizarán como puntos de referencia válidos ante los próximos cambios en las regulaciones federales canadienses relacionados con el uso de antimicrobianos y las iniciativas lideradas por la industria dirigidas a reducir el uso de antimicrobianos.