E. Jane Parmley

Wild bird influenza survey, Canada, 2005.

Of 4,268 wild ducks sampled in Canada in 2005, real-time reverse transcriptase–PCR detected influenza A matrix protein (M1) gene sequence in 37% and H5 gene sequence in 5%. Mallards accounted for 61% of samples, 73% of M1-positive ducks, and 90% of H5-positive ducks. Ducks hatched in 2005 accounted for 80% of the sample.

Ciprofloxacin-Resistant Campylobacter spp. in Retail Chicken, Western Canada

During 2005–2010, the Canadian Integrated Program for Antimicrobial Resistance Surveillance identified increased prevalence of ciprofloxacin (a fluororquinolone) resistance among Campylobacter isolates from retail chicken in British Columbia (4%–17%) and Saskatchewan (6%–11%), Canada. Fluoroquinolones are critically important to human medicine and are not labeled for use in poultry in Canada.

Detection of low pathogenic avian influenza viruses in wild ducks from Canada: comparison of two sampling methods.

Surveillance for avian influenza viruses in wild birds was initiated in Canada in 2005. In 2006, in order to maximize detection of highly pathogenic avian influenza viruses, the sampling protocol used in Canadas Inter-agency Wild Bird Influenza Survey was changed. Instead of collecting a single cloacal swab, as previously done in 2005, cloacal and oropharyngeal swabs were combined in a single vial at collection. In order to compare the two sampling methods, duplicate samples were collected from 798 wild dabbling ducks (tribe Anatini) in Canada between 24 July and 7 September 2006. Low pathogenic avian influenza viruses were detected significantly more often (P<0.0001) in combined oropharyngeal and cloacal samples (261/798, 33%) than in cloacal swabs alone (205/798, 26%). Compared to traditional single cloacal samples, combined samples improved virus detection at minimal additional cost.

PREVALENCE AND CHARACTERISTICS OF ESCHERICHIA COLI AND SALMONELLA SPP. IN THE FECES OF WILD URBAN NORWAY AND BLACK RATS (RATTUS NORVEGICUS AND RATTUS RATTUS) FROM AN INNER-CITY NEIGHBORHOOD OF VANCOUVER, CANADA

Abstract Although rat feces are widely suspected to be a source of pathogenic bacteria, few investigators have studied fecal pathogens in rats. We investigated the prevalence and characteristics of Escherichia coli and Salmonella spp. in Norway and black rats (Rattus norvegicus and Rattus rattus, respectively) from an urban neighborhood of Vancouver, Canada, collected September 2011–August 2012. Colon content was cultured for E. coli and Salmonella spp. and screened for the seven most-common enteropathogenic Shiga toxin–producing E. coli (STEC) serotypes by PCR. Isolates were tested for antimicrobial resistance and Salmonella isolates were serotyped. We detected E. coli in 397/633 (62.7%) urban rats. Forty-one of 397 (6.5%) E. coli isolates were resistant to ≥1 antimicrobial while 17 (4.3%) were multidrug resistant (including two isolates demonstrating extended-spectrum &bgr;-lactamase resistance). Ten of 633 (1.6%) urban rats were carrying STEC serotypes including O145, O103, O26, and O45. Norway rats were more likely to be carrying E. coli compared to black rats, and there was geographic clustering of specific resistance patterns and STEC serotypes. Salmonella spp. were detected in 3/633 (0.5%) rats including serotypes Derby, Indiana, and Enteritidis. In contrast to zoonotic pathogens for which rats are the natural reservoir (e.g., Leptospira interrogans, Rickettsia typhi, Seoul virus), rats likely acquired E. coli and Salmonella spp. from their environment. The ability of rats to be a ‘sponge’ for environmental pathogens has received little consideration, and the ecology and public health significance of these organisms in rats requires further investigation.

Bait Trapping Linked to Higher Avian Influenza Virus Detection in Wild Ducks

In 2007, we assessed whether trapping method influenced apparent prevalence of low pathogenic avian influenza viruses (AIV) in wild ducks sampled during Canada’s Inter-agency Wild Bird Influenza Survey. Combined cloacal and oropharyngeal swabs were collected from 514 ducks captured by bait trapping (356) and netting from airboats (158), and tested by real-time reverse transcriptase polymerase chain reaction for influenza type A viruses. When controlling for species and capture site, ducks caught in bait traps were 2.6 times more likely to test positive for AIV compared with those netted from airboats (95% CI=1.2–6.0). If bait trapping increases AIV transmission among artificially aggregated ducks, this could have important implications for interpretation of disease surveillance results and waterfowl management programs.

The ecology of avian influenza viruses in wild dabbling ducks ( Anas spp.) in Canada

Avian influenza virus (AIV) occurrence and transmission remain important wildlife and human health issues in much of the world, including in North America. Through Canada’s Inter-Agency Wild Bird Influenza Survey, close to 20,000 apparently healthy, wild dabbling ducks (of seven species) were tested for AIV between 2005 and 2011. We used these data to identify and evaluate ecological and demographic correlates of infection with low pathogenic AIVs in wild dabbling ducks (Anas spp.) across Canada. Generalized linear mixed effects model analyses revealed that risk of AIV infection was higher in hatch-year birds compared to adults, and was positively associated with a high proportion of hatch-year birds in the population. Males were more likely to be infected than females in British Columbia and in Eastern Provinces of Canada, but more complex relationships among age and sex cohorts were found in the Prairie Provinces. A species effect was apparent in Eastern Canada and British Columbia, where teal (A. discors and/or A. carolinensis) were less likely to be infected than mallards (A. platyrhynchos). Risk of AIV infection increased with the density of the breeding population, in both Eastern Canada and the Prairie Provinces, and lower temperatures preceding sampling were associated with a higher probability of AIV infection in Eastern Canada. Our results provide new insights into the ecological and demographic factors associated with AIV infection in waterfowl.

Avian Pathogenicity Genes and Antibiotic Resistance in Escherichia coli Isolates from Wild Norway Rats (Rattus norvegicus) in British Columbia, Canada

Abstract 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.

A comparison of modelling options to assess annual variation in susceptibility of generic Escherichia coli isolates to ceftiofur, ampicillin and nalidixic acid from retail chicken meat in Canada

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.

Comparison of annual and regional variation in multidrug resistance using various classification metrics for generic Escherichia coli isolated from chicken abattoir surveillance samples in Canada

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.

Identifying non-traditional stakeholders with whom to engage, when mitigating antimicrobial resistance in foodborne pathogens (Canada)

ObjectiveAntimicrobial resistance (AMR) is a critical public health issue that involves interrelationships between people, animals, and the environment. Traditionally, interdisciplinary efforts to mitigate AMR in the food chain have involved public health, human and veterinary medicine, and agriculture stakeholders. Our objective was to identify a more diverse range of stakeholders, beyond those traditionally engaged in AMR mitigation efforts, via diagramming both proximal and distal factors impacting, or impacted by, use and resistance along the Canadian food chain.ResultsWe identified multiple stakeholders that are not traditionally engaged by public health when working to mitigate AMR in the food chain, including those working broadly in the area of food (e.g., nutrition, food security, international market economists) and health (e.g., health communication, program evaluation), as well as in domains as diverse as law, politics, demography, education, and social innovation. These findings can help researchers and policymakers who work on issues related to AMR in the food chain to move beyond engaging the ‘traditional’ agri-food stakeholders (e.g., veterinarians, farmers), to also engage those from the wider domains identified here, as potential stakeholders in their AMR mitigation efforts.