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

Antimicrobial resistance monitoring in the Danish swine production by phenotypic methods and metagenomics from 1999 to 2018

BackgroundIn Denmark, antimicrobial resistance (AMR) in pigs has been monitored since 1995 by phenotypic approaches using the same indicator bacteria. Emerging methodologies, such as metagenomics, may allow novel surveillance ways.AimThis study aimed to assess the relevance of indicator bacteria (Escherichia coli and Enterococcus faecalis) for AMR surveillance in pigs, and the utility of metagenomics.MethodsWe collated existing data on AMR and antimicrobial use (AMU) from the Danish surveillance programme and performed metagenomics sequencing on caecal samples that had been collected/stored through the programme during 1999-2004 and 2015-2018. We compared phenotypic and metagenomics results regarding AMR, and the correlation of both with AMU.ResultsVia the relative abundance of AMR genes, metagenomics allowed to rank these genes as well as the AMRs they contributed to, by their level of occurrence. Across the two study periods, resistance to aminoglycosides, macrolides, tetracycline, and beta-lactams appeared prominent, while resistance to fosfomycin and quinolones appeared low. In 2015-2018 sulfonamide resistance shifted from a low occurrence category to an intermediate one. Resistance to glycopeptides consistently decreased during the entire study period. Outcomes of both phenotypic and metagenomics approaches appeared to positively correlate with AMU. Metagenomics further allowed to identify multiple time-lagged correlations between AMU and AMR, the most evident being that increased macrolide use in sow/piglets or fatteners led to increased macrolide resistance with a lag of 3-6 months.ConclusionWe validated the long-term usefulness of indicator bacteria and showed that metagenomics is a promising approach for AMR surveillance.

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.

A scoping review of factors potentially linked with antimicrobial-resistant bacteria from turkeys (iAM.AMR Project)

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.

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

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

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

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.

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

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

Quantification and Trends of Antimicrobial Use in Commercial Broiler Chicken Production in Pakistan

Antimicrobial resistance (AMR) is a global health challenge and antimicrobial use (AMU) in the livestock sector has been considered as one of the contributing factors towards the development of AMR in bacteria. This study summarizes the results of a point prevalence survey conducted to monitor farm-level AMU in commercial broiler chicken farms in Punjab and Khyber Pakhtunkhwa (KPK) provinces of Pakistan. A cross-sectional study was conducted to quantify AMU and to check seasonal variations of AMU in 12 commercial broiler chicken farms (six from each province) during the summer and winter seasons of the year 2020–2021. AMU was recorded using three AMU metrics: kg, mg per population correction unit (mg/PCU), and mg/kg of final flock weight. A total of 22 antimicrobial drugs (348.59 kg) were used for therapeutic or prophylactic purposes in surveyed broiler chicken farms. The total combined AMU for all the broiler chicken farms was 462.57 mg/PCU. The use of most of the antimicrobials increased during winter flocks compared to summer. The top three antimicrobial drugs used during the summer were neomycin (111.39 mg/PCU), doxycycline (91.91 mg/PCU), and tilmicosin (77.22 mg/PCU), whereas doxycycline (196.81 mg/PCU), neomycin (136.74 mg/PCU), and amoxicillin (115.04 mg/PCU) during the winter. Overall, 60% of the antibiotics used in broiler chicken were critically important antimicrobial classes (CIA) for human medicine as characterized by the World Health Organization. Our findings showed high AMU in broiler chicken production and a call for urgent actions to regulate CIA use in food animals in Pakistan. This baseline survey is critical for the design and implementation of a subsequent national level AMU surveys that can include additional farming types, animals’ species, and geographical locations over a longer period of time.