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We investigated whether gentamicin resistance (Gen(r)) in Escherichia coli isolates from human infections was related to Gen(r) 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 Gen(r) 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 Gen(r) 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 Gen(r) E. coli contained a bla(CTX-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 Gen(r) isolates; however, there were three small clusters of closely related isolates from human and chicken sources. Gen(r) and spectinomycin resistance (Spec(r)) 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 Gen(r) and Spec(r) 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, Gen(r) isolates and plasmids were mostly different in chickens and humans.

Extended-spectrum β-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 bla

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.

Antimicrobial resistance (AMR) in the aquatic environment represents an important means of introduction and dissemination of resistance genes, and presence of resistant pathogens in surface waters may pose a public health concern to recreational and drinking water users. The purpose of this study was to explore antimicrobial resistance patterns in water samples collected from the Grand River watershed (southwestern Ontario, Canada) to describe the composition, trends and potential risks of AMR in the aquatic environment. As part of FoodNet Canada and the Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS), stream water samples were collected bi-weekly from sampling sites within the Grand River watershed in the Waterloo, Ontario sentinel site and tested for the presence and antimicrobial susceptibility of Salmonella spp. (2005-2013) and generic Escherichia coli (2012-2013). Of all samples tested, 16% of Salmonella and 22% of E. coli isolates were resistant to at least one antimicrobial, including three Salmonella isolates and two E. coli isolates that were resistant to Category I antimicrobials, which are classified as very high importance for the treatment of serious bacterial infections in humans. The greatest proportion of resistant E. coli isolates were observed from the river site upstream of the drinking water intake, while the greatest proportion of resistant Salmonella isolates were from sites upstream in the watershed, and at one recreational water site. Salmonella resistance trends remained fairly stable between 2007 and 2013, with the exception of streptomycin and tetracycline which increased in 2010 and 2013. Continued surveillance of antimicrobial resistance patterns and exploration of risk factor data will allow for a better understanding of resistance transmission in the aquatic environment.

Antimicrobial resistance (AMR) threatens the health of humans and animals and has repeatedly been detected in wild animal species across the world. This cross-sectional study integrates whole-genome sequence data from Escherichia coli isolates with demonstrated phenotypic resistance that originated from a previous longitudinal wildlife study in southern Ontario, as well as phenotypically resistant E. coli water isolates previously collected as part of a public health surveillance program. The objective of this work was to assess for evidence of possible transmission of antimicrobial resistance determinants between wild meso-mammals, swine manure pits, and environmental sources on a broad scale in the Grand River watershed, and at a local scale—for the subset of samples collected on both swine farms and conservation areas in the previous wildlife study. Logistic regression models were used to assess potential associations between sampling source, location type (swine farm vs. conservation area), and the occurrence of select resistance genes and predicted plasmids. In total, 200 isolates from the following sources were included: water (n = 20), wildlife (n = 73), swine manure pit (n = 31), soil (n = 73), and dumpsters (n = 3). Several genes and plasmid incompatibility types were significantly more likely to be identified on swine farms compared to conservation areas. Conversely, internationally distributed sequence types (e.g., ST131), extended-spectrum beta-lactamase- and AmpC-producing E. coli were isolated in lower prevalences (

BackgroundAntimicrobial resistance (AMR) is a growing global crisis with long-term and unpredictable health, social and economic impacts, with which climate change is likely to interact. Understanding how to govern AMR amidst evolving climatic changes is critical. Scenario planning offers a suitable approach. By envisioning alternative futures, stakeholders more effectively can identify consequences, anticipate problems, and better determine how to intervene. This study explored future worlds and actions that may successfully address AMR in a changing climate in a high-income country, using Sweden as the case.MethodsWe conducted online scenario-building workshops and interviews with eight experts who explored: (1) how promising interventions (taxation of antimicrobials at point of sale, and infection prevention measures) could each combat AMR in 2050 in Sweden given our changing climate; and (2) actions to take starting in 2030 to ensure success in 2050. Transcripts were thematically analyzed to produce a narrative of participant validated alternative futures.ResultsRecognizing AMR to be a global problem requiring global solutions, participants looked beyond Sweden to construct three alternative futures: (1) “Tax Burn Out” revealed taxation of antimicrobials as a low-impact intervention that creates inequities and thus would fail to address AMR without other interventions, such as infection prevention measures. (2) “Addressing the Basics” identified infection prevention measures as highly impactful at containing AMR in 2050 because they would contribute to achieving the Sustainable Development Goals (SDGs), which would be essential to tackling inequities underpinning AMR and climate change, and help to stabilize climate-induced mass migration and conflicts; and (3) ”Siloed Nations” described a movement toward nationalism and protectionism that would derail the “Addressing the Basics” scenario, threatening health and wellbeing of all. Several urgent actions were identified to combat AMR long-term regardless which future un-folds, such as global collaboration, and a holistic approach where AMR and climate change are addressed as interlinked issues.ConclusionOur participatory scenario planning approach enabled participants from different sectors to create shared future visions and identify urgent actions to take that hinge on global collaboration, addressing AMR and climate change together, and achieving the SDGs to combat AMR under a changing climate.

Antimicrobial resistance (AMR) is a complex problem that is a threat to global public health. Consumption of turkey meat may be an important source of foodborne exposure to resistant bacteria; recent outbreaks of multi-drug-resistant Salmonella Reading in Canada and the USA have implicated raw turkey products. To better understand the epidemiology of AMR in farmed turkey production, a scoping review was conducted. The objectives were to identify (1) modifiable factors potentially associated with antimicrobial-resistant Campylobacter, Enterococcus, Escherichia coli and Salmonella enterica along the farm-to-fork pathway in turkeys, and (2) data gaps with respect to factors potentially associated with AMR and Canadian commercial turkey production. A comprehensive search of the peer-reviewed literature was conducted in 2019 and updated in 2021. Thirteen references were included, reporting 36 factors. Antimicrobial use factors and their potential associations with AMR were most frequently reported (n = 15 factors; 42%), followed by biosecurity (n = 11; 31%) and management practices (n = 10; 28%). This review revealed important data gaps; no factors pertaining to S. enterica or to stages other than the farm (e.g. abattoir, retail) were identified, and only one Canadian reference was identified. These findings will inform priorities for future research and surveillance regarding turkeys and AMR.

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 (Gen(r)) 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 Gen(r) 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 Gen(r) 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.

Summary Improving evidence for action is crucial to tackle antimicrobial resistance. The number of interventions for antimicrobial resistance is increasing but current research has major limitations in terms of efforts, methods, scope, quality, and reporting. Moving the agenda forwards requires an improved understanding of the diversity of interventions, their feasibility and cost–benefit, the implementation factors that shape and underpin their effectiveness, and the ways in which individual interventions might interact synergistically or antagonistically to influence actions against antimicrobial resistance in different contexts. Within the efforts to strengthen the global governance of antimicrobial resistance, we advocate for the creation of an international One Health platform for online learning. The platform will synthesise the evidence for actions on antimicrobial resistance into a fully accessible database; generate new scientific insights into the design, implementation, evaluation, and reporting of the broad range of interventions relevant to addressing antimicrobial resistance; and ultimately contribute to the goal of building societal resilience to this central challenge of the 21st century.

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, β-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.

One Health surveillance for antimicrobial resistance has been promoted by the scientific community and by international organizations for more than a decade. In this article, we highlight issues that need to be addressed to improve the understanding of the effectiveness of One Health surveillance for antimicrobial resistance. We also outline the evidence needed to support countries planning to increase the level of integration of their surveillance system. Based on experience in Canada and other countries, we argue that more effort is needed to understand and measure the added value of One Health for antimicrobial resistance surveillance and to identify the most effective integration strategies. To date, guidelines for the development of One Health surveillance have focused mainly on the types of data that should be integrated. However, it may be necessary to apply the concept of One Health to surveillance tasks beyond data integration to realize the full value of the approach. Integration can be enhanced across different surveillance activities (data collection, analysis, interpretation and dissemination), taking account of the different skills and perspectives of experts and stakeholders involved. More research is needed to investigate the mechanisms through which a One Health approach to surveillance can increase the performance of antimicrobial resistance surveillance and, ultimately, improve health outcomes.Cela fait plus de dix ans que la communauté scientifique et les organisations internationales préconisent l'application de l'approche «Un monde, une santé» à la surveillance de la résistance aux antimicrobiens. Cet article souligne les éléments à considérer pour mieux comprendre l'efficacité d'une surveillance fondée sur cette approche. Nous y évoquons également les données requises pour éclairer les pays dans la définition de leurs plans nationaux afin d'améliorer le niveau d'intégration de leur système de surveillance. À partir de l’expérience du Canada et d'autres pays, nous estimons que des efforts doivent encore être faits pour comprendre et mesurer la véritable valeur ajoutée de l'approche «Un monde, une santé» dans le cadre de la surveillance de la résistance aux antimicrobiens et afin d'identifier les stratégies d'intégration les plus efficaces. À ce jour, les lignes directrices pour l'établissement d'une surveillance fondée sur cette approche se sont principalement axées sur les types de données qui devraient être intégrées. Néanmoins, pour exploiter toute la valeur de cette approche, il pourrait être utile d'appliquer le concept «Un monde, une santé» aux activités de surveillance au-delà de la simple intégration des données. Une meilleure intégration peut être obtenue au niveau des différentes activités de surveillance (collecte, analyse, interprétation et diffusion des données) en tenant compte des différentes compétences et des différents points de vue des experts et des parties prenantes. De nouvelles recherches sont nécessaires pour comprendre les mécanismes par lesquels l'approche «Un monde, une santé» appliquée à la surveillance peut améliorer les performances de la surveillance de la résistance aux antimicrobiens et, en fin de compte, améliorer les résultats de santé.La comunidad científica y las organizaciones internacionales han promovido durante más de una década la vigilancia sanitaria de la resistencia a los antimicrobianos. En este artículo, destacamos las cuestiones que deben abordarse para mejorar la comprensión de la eficacia de la vigilancia de la resistencia a los antimicrobianos de One Health. También esbozamos las pruebas necesarias para apoyar a los países que planean aumentar el nivel de integración de su sistema de vigilancia. Basándonos en la experiencia de Canadá y de otros países, sostenemos que se necesitan más esfuerzos para comprender y medir el valor agregado de One Health para la vigilancia de la resistencia a los antimicrobianos y para identificar las estrategias de integración más eficaces. Hasta la fecha, las directrices para el desarrollo de vigilancia de One Health se han centrado principalmente en los tipos de datos que deben integrarse. Sin embargo, puede ser necesario aplicar el concepto de One Health a tareas de vigilancia que van más allá de la integración de datos para aprovechar todo el valor del enfoque. La integración puede mejorarse en las diferentes actividades de vigilancia (recopilación, análisis, interpretación y difusión de datos), teniendo en cuenta las diferentes competencias y perspectivas de los expertos y las partes interesadas. Se necesita más investigación para estudiar los mecanismos mediante los cuales un enfoque de vigilancia de One Health puede aumentar el rendimiento de la vigilancia de la resistencia a los antimicrobianos y, en última instancia, mejorar los resultados sanitarios.تم الترويج لمراقبة One Health لمكافحة مضادات الميكروبات بواسطة المجتمع العلمي ومنظمات دولية منذ ما يزيد عن عقد من الزمان. نسلط في هذا المقال الضوء على القضايا التي بحاجة للتناول لتحسين فهم فعالية مراقبة One Health لمكافحة مضادات الميكروبات. كما نوضح الأدلة اللازمة لدعم الدول التي تخطط لزيادة مستوى التكامل في نظام المراقبة الخاص بها. وبناءً على التجربة الكندية وتجارب بلدان أخرى، فإننا نزعم أننا بحاجة إلى بذل المزيد من الجهد لفهم وقياس القيمة المضافة لنظام One Health لمراقبة مكافحة مضادات الميكروبات، ولتحديد أكثر استراتيجيات التكامل من حيث الفعالية. وحتى الآن، ركزت إرشادات تطوير نظام One Health للمراقبة بشكل أساسي على أنواع البيانات التي ينبغي إحداث التكامل فيما بينها. ومع ذلك، قد يكون من الضروري تطبيق مفهوم One Health على مهام المراقبة التي تتجاوز تكامل البيانات، وذلك لإدراك القيمة الكاملة لهذا النهج. يمكن تعزيز التكامل عبر أنشطة المراقبة المختلفة (جمع البيانات وتحليلها وتفسيرها ونشرها)، مع الأخذ في الاعتبار المهارات المختلفة ووجهات نظر الخبراء وأصحاب المصلحة المعنيين. هناك حاجة إلى مزيد من الأبحاث للتحقيق في الآليات التي يمكن من خلالها لنهج One Health للمراقبة أن يزيد من أداء مراقبة مكافحة مضادات الميكروبات، مما يؤدي في النهاية إلى تحسين النتائج الصحية.十多年来，科学界和国际组织一直致力于对抗菌素耐药性进行“唯一健康”监测。在本文中，我们强调了需要解决的问题，旨在提高“唯一健康”监测对抗菌素耐药性有效性的认识。我们还对所需的证据进行了概述，以支持那些计划提高其监测系统整合水平的国家。根据加拿大及他国经验，我们认为需要付出更多努力来理解和衡量“唯一健康”监测对抗菌素耐药性的附加价值，并确定最有效的整合策略。迄今为止，制定“唯一健康”监测的指南主要侧重于应整合的数据类型。然而，可能有必要将“唯一健康”概念应用于数据整合之外的监测任务，以实现该方法的全部价值。可以通过不同的监测活动（数据收集、分析、解释和传播）加强整合，同时考虑到所涉专家和利益相关者的不同技能和观点。需进一步研究以调查提高抗菌素耐药性监测表现的“唯一健康”方法，并最终改善健康结果。.Система надзора за резистентностью к антимикробным препаратам One Health находит поддержку научного сообщества и международных организаций уже в течение более десяти лет. В этой статье освещаются проблемы, которые следует решить для улучшения понимания эффективности надзора за резистентностью к антимикробным препаратам One Health. Авторы также описывают характер подтверждений, необходимых для поддержки стран, планирующих повысить уровень интеграции своих надзорных систем. На основании опыта Канады и других стран оспаривается утверждение о том, что нужно больше усилий для понимания и измерения ценности системы надзора за резистентностью к антимикробным препаратам One Health и для выявления наиболее эффективных стратегий интеграции. На сегодня рекомендации по разработке системы надзора One Health в основном сосредотачивались на типах данных, которые следует интегрировать. Однако, чтобы оценить всю ценность подхода, может понадобиться применение концепции One Health к надзорным задачам, не ограничивающимся интеграцией данных. Интеграция может быть усилена между разного рода надзорной деятельностью (сбор данных, анализ, интерпретация и распространение) с учетом различия в навыках и точках зрения специалистов и партнеров, участвующих в работе системы. Требуются дополнительные исследования для изучения механизмов, посредством которых подход One Health к вопросам надзора может улучшить качество работы систем надзора за антимикробной резистентностью и, в конце концов, улучшить результаты работы системы здравоохранения.

Statistical modelling of antimicrobial resistance (AMR) data is an important aspect of AMR surveillance programs; however, minimum inhibitory concentration (MIC) data can be challenging to model. The conventional approach is to dichotomize data using established breakpoints, then use logistic regression modelling for analysis. A disadvantage of this approach is a loss of information created by dichotomizing the data. The objectives of the study were to compare the performance and results of different regression models for the analysis of annual variation in susceptibility of generic Escherichia coli (E. coli) isolates to ceftiofur, ampicillin and nalidixic acid from retail chicken meat surveillance samples. E. coli susceptibility data for the three antimicrobials from retail chicken samples from 2007 to 2014 were obtained from the Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS). Annual variation in susceptibility for each antimicrobial was evaluated using multivariable linear, tobit, logistic, multinomial, ordinal and complementary log-log regression models (clog-log). MIC (log2), censored MIC (log2), resistant/susceptible, and categorized MIC (3 or 4 categories) data were used as outcome variables for the appropriate statistical models. Year and region were modelled as categorical predictor variables. Random intercepts were included in the ceftiofur and ampicillin models to account for clustering by retail establishment. The model assumptions evaluated for the mixed models included homoscedasticity and normality of residuals (linear and tobit), homoscedasticity and normality of best linear unbiased predictions (all models), proportional odds (ordinal), and proportional hazards (clog-log). Fixed effects models were used for the nalidixic acid models. The model assumptions evaluated for the fixed effects models included homoscedasticity and normality of residuals (linear and tobit), goodness-of-fit test (logistic and multinomial), proportional odds (ordinal), and proportional hazards (clog-log).Only logistic and multinomial models met model assumptions. Significant annual variation in susceptibility to all three antimicrobials was identified by the multinomial regression models, whereas the logistic regression models only identified significant annual variation in susceptibility to ceftiofur. The multinomial regression model consistently identified additional significant annual variation in susceptibility compared to the logistic regression model. The multinomial modelling approach was able to identify differences between MIC categories within susceptible MIC values, which were below the breakpoint (R) detection level. Given the convention of dichotomizing susceptibility data, the logistic regression approach is likely to remain the standard method of analysis for AMR surveillance data; however, the results of this study demonstrate that multinomial regression should be considered for the analysis of AMR surveillance data.

To better understand the contribution of wildlife to the dissemination of Salmonella and antimicrobial resistance in Salmonella and Escherichia coli, we examined whole-genome sequence data from Salmonella and E. coli isolates collected from raccoons (Procyon lotor) and environmental sources on farms in southern Ontario. All Salmonella and phenotypically resistant E. coli collected from raccoons, soil, and manure pits on five swine farms as part of a previous study were included. We assessed for evidence of potential transmission of these organisms between different sources and farms utilizing a combination of population structure assessments (using core-genome multi-locus sequence typing), direct comparisons of multi-drug resistant isolates, and epidemiological modeling of antimicrobial resistance (AMR) genes and plasmid incompatibility (Inc) types. Univariable logistic regression models were fit to assess the impact of source type, farm location, and sampling year on the occurrence of select resistance genes and Inc types. A total of 159 Salmonella and 96 resistant E. coli isolates were included. A diversity of Salmonella serovars and sequence types were identified, and, in some cases, we found similar or identical Salmonella isolates and resistance genes between raccoons, soil, and swine manure pits. Certain Inc types and resistance genes associated with source type were consistently more likely to be identified in isolates from raccoons than swine manure pits, suggesting that manure pits are not likely a primary source of those particular resistance determinants for raccoons. Overall, our data suggest that transmission of Salmonella and AMR determinants between raccoons and swine manure pits is uncommon, but soil-raccoon transmission appears to be occurring frequently. More comprehensive sampling of farms, and assessment of farms with other livestock species, as well as additional environmental sources (e.g., rivers) may help to further elucidate the movement of resistance genes between these various sources.

We report avian pathogenic and antibiotic resistant Escherichia coli in wild Norway rats ( Rattus norvegicus ) trapped at a commercial chicken hatchery in British Columbia, Canada, and provide evidence that rats can become colonized with, and possibly act as a source of, poultry pathogens present in their environment.

Antimicrobial resistance is a complex issue with a large volume of published literature, and there is a need for synthesis of primary studies for an integrated understanding of this topic. Our research team aimed to have a more complete understanding of antimicrobial resistance in Canada (IAM.AMR Project) using multiple methods including the literature reviews and quantitative modelling. To accomplish this goal, qualitative features of publications (e.g., geographical location, study population) describing potential relationships between the occurrence of antimicrobial resistance and factors (e.g., antimicrobial use; management system) were of particular interest. The objectives of this review were to (a) describe the available peer-reviewed literature reporting potential relationships between factors and antimicrobial resistance; and (b) to highlight data gaps. A comprehensive literature search and screening were performed to identify studies investigating factors potentially linked with antimicrobial resistance in Campylobacter species, Escherichia coli and Salmonella enterica along the farm-to-fork pathway (farm, abattoir (slaughter houses) and retail meats) for the major Canadian livestock species (beef cattle, broiler chicken and pigs). The literature search returned 14,966 potentially relevant titles and abstracts. Following screening of titles, abstracts and full-text articles, the qualitative features of retained studies (n = 28) were extracted. The most common factors identified were antimicrobial use (n = 13 studies) and type of farm management system (e.g., antibiotic-free, organic; n = 8). Most studies were conducted outside of Canada and involved investigations at the farm level. Identified data gaps included the effect of vaccination, industry-specific factors (e.g., livestock density) and factors at sites other than farm along the agri-food chain. Further investigation of these factors and other relevant industry activities are needed for the development of quantitative models that aim to identify effective interventions to mitigate the occurrence of antimicrobial resistance along the agri-food chain.

Antimicrobial resistance (AMR) and related multidrug resistance (MDR) are important global public health issues. The Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS) conducts surveillance of AMR in enteric bacteria and monitors MDR. However, the analysis of MDR is complicated by the lack of consensus for MDR definitions. The objectives were to describe the most common resistance patterns in generic E. coli isolates from chicken cecal samples and determine the impact of using different MDR metrics for analysis of annual and regional variation in MDR. From 2006 to 2015, 1598 E. coli isolates were collected from chickens at slaughter for CIPARS. Three MDR classification metrics were used: MDR-drug (MDR if the isolate was resistant (R) to ≥3 of the 13 antimicrobials); MDR-cat (MDR if R to ≥3 of the 9 antimicrobials categories); and MDR-class (MDR if R to ≥3 of the 6 antimicrobial classes). The most frequent resistance patterns overall, and by year and region were extracted along with patterns that included resistance to quinolones , and third generation cephalosporins and/or β-lactams with β-lactamase inhibitors . For each MDR metric, mixed logistic regression models, which included random intercepts for abattoir, were fitted to analyze the association between prevalence of MDR, and year and region. Interaction effects between year and region were evaluated. Overall, and in all years and regions, non-resistant was the most common resistance pattern (24.9%, 95% CI 22.8–27.1%). Resistance patterns that included third generation cephalosporins and β-lactams with β-lactamase inhibitors were common. The prevalence of MDR was variable: MDR-class 38.5% (95% CI 36.1–41.0%); MDR-cat 49.4% (95% CI 46.9–51.9%); and MDR-drug 53.3% (95% CI 50.8–55.8%). Based on models fitted with individual fixed effects, significant annual variation in the prevalence of MDR was identified with MDR-drug and MDR-class models. Significant regional variation was identified for all three MDR metric models. Significant interaction effects between year and region were identified with the MDR-drug and MDR-cat multivariable mixed logistic regression models. The interpretation of the association between the prevalence of MDR, and year and region differed depending on the MDR metric used. These results are supportive of the previous concerns that caution must be taken when comparing MDR results between studies. Global consensus is needed for the optimal MDR classification metric for foodborne enteric bacteria AMR surveillance.

This study characterized cefoxitin-resistant and -susceptible Salmonella enterica serovar Heidelberg strains from humans, abattoir poultry, and retail poultry to assess the molecular relationships of isolates from these sources in Québec in 2012. Isolates were collected as part of the Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS). All isolates were subjected to antimicrobial susceptibility testing, PCR for CMY-2, pulsed-field gel electrophoresis (PFGE), and whole-genome sequencing (WGS). A total of 113 S . Heidelberg isolates from humans ( n = 51), abattoir poultry ( n = 18), and retail poultry ( n = 44) were studied. All cefoxitin-resistant isolates ( n = 65) were also resistant to amoxicillin-clavulanic acid, ampicillin, ceftiofur, and ceftriaxone, and all contained the CMY-2 gene. PFGE analysis showed that 111/113 (98.2%) isolates clustered together with ≥90% similarity. Core genome analysis using WGS identified 13 small clusters of isolates with 0 to 4 single nucleotide variations (SNVs), consisting of cefoxitin-resistant and -susceptible human, abattoir poultry, and retail poultry isolates. CMY-2 plasmids from cefoxitin-resistant isolates all belonged to incompatibility group I1. Analysis of IncI1 plasmid sequences revealed high identity (95 to 99%) to a previously described plasmid (pCVM29188_101) found in Salmonella Kentucky. When compared to pCVM29188_101, all sequenced cefoxitin-resistant isolates were found to carry 1 of 10 possible variant plasmids. Transmission of S . Heidelberg may be occurring between human, abattoir poultry, and retail poultry sources, and transmission of a common CMY-2 plasmid may be occurring among S . Heidelberg strains with variable genetic backgrounds.

Human campylobacteriosis, a notifiable disease in Canada, is the most common cause of bacterial enteric infections among persons in Canada; in 2005, the incidence rate of campylobacteriosis was 30.9 cases per 100,000 population(1). In chickens, Campylobacter spp. are not clinically relevant; however, the presence of these bacteria in poultry represents a potential threat to public health (2). Ciprofloxacin, a fluoroquinolone antimicrobial drug, is indicated for the treatment of respiratory, urinary, skin, and bone/joint infections and gastroenteritis in adults (3). In 2008 in Canada, fluoroquinolones were the fourth most frequently dispensed class of antimicrobial drug (dispensed for oral use by retail pharmacists; www.phac-aspc.gc.ca/cipars-picra/2008/4-eng.php#Hum0). A study investigating antimicrobial drug use and resistance in 2 health units in Ontario found that ciprofloxacin was the antimicrobial drug most frequently used to treat human campylobacteriosis (4). Fluoroquinolones are considered “critically” or “very” important to human medicine by the World Health Organization (5) and the Veterinary Drugs Directorate (VDD), Health Canada (6). The veterinary fluoroquinolones enrofloxacin and danofloxacin are VDD Category I antimicrobial drugs labeled for use in companion animals and beef cattle, but they are not labeled for use in poultry. The VDD has established a policy recommending against the extra-label use of Category I antimicrobial drugs in food-producing animals (7); however, Canada does not have legislation restricting this extra-label use.