Chapter 1. Design and Methods

Text Equivalent - Summary of CIPARS Samples and Data Flow

Summary of CIPARS Samples and Data Flow

This image summarises all of the CIPARS surveillance components and data sources that are pulled together for analysis and reporting purposes.

The top half of the figure includes all of the antimicrobial resistance (AMR) components of CIPARS. The antimicrobial use (AMU) components of CIPARS are along the bottom of the figure. Additional data sources as well as data integration, analysis and reporting are in the middle.


Active surveillance components

In the AMR section, the 3 active surveillance components (farm, abattoir and retail) are depicted:

  • The farm component started in 2006 and now includes samples collected from grower-finisher pigs and broiler chicken on farms. Generic Escherichia coli and Salmonella are isolated from both pig and chicken samples and Campylobacter is also isolated from chicken samples.
  • The abattoir component was initiated in 2002 and currently includes samples collected from beef cattle, chickens and pigs at slaughter. All samples are tested for presence of generic E. coli and Campylobacter and Salmonella are also isolated from chicken and pig samples.
  • The retail component started in 2003 and currently involves collection of beef, chicken, pork and turkey retail meat samples. Generic E. coli are isolated from each sample type, Salmonella are isolated from chicken, pork and turkey samples, and Campylobacter are isolated from chicken and turkey samples.

Passive surveillance components

In addition to the active AMR surveillance components, there are 3 passive surveillance components of CIPARS:

  • monitoring (feeds)
  • diagnostic animal
  • diagnostic human

The monitoring component covers several different feed sample types and the diagnostic animal component can include many animal species. All passive AMR components only include Salmonella isolates.

Additionally, AMR research projects can involve multiple commodities and animal species, bacteria, methodologies (sampling, lab, molecular, data analysis). These projects are time limited and complement the data captured through routine AMR surveillance.

Lastly, all the human AMR data are entered into the Labware data management system at the National Microbiology Laboratory and all of the data from agri-food AMR surveillance components are entered into Labware at the Laboratory for Foodborne Zoonoses (LFZ). The research project AMR data are also entered into Labware at LFZ. All data are then put into a central data repository and accessed by CIPARS analysts.


In the AMU section, the 3 surveillance components (farm, the Canadian Animal Health Institute, and human) are depicted:

  • The farm AMU data are collected about grower-finisher pigs and broiler chickens and are entered into a custom internal database and report generator.
  • The Canadian Animal Health Institute (CAHI) data summarise the quantity of antimicrobials distributed for sale for use in animals; these data are provided directly to CIPARS from CAHI.
  • The human AMU data come from 3 separate databases: pharmacy, physician and hospital. All human AMU data are provided by IMS Health Canada Inc.

The data from AMU surveillance components are complemented by AMU research projects. These projects are time limited, involve varying collection methods and may include qualitative and/or quantitative data collection methods.

Demographic data are required to interpret the AMU data that are collected. For humans, the demographic data accessed consist of population estimates; for food animals, the demographic data consists of the number of farms and animals and the per-capita feed consumption.

All animal AMU data are pulled together by CIPARS analysts and the human AMU data are analysed by a different group of CIPARS analysts. All of CIPARS analysis (AMR and AMU) as well as AMU research projects feed into data integration, reporting and other types of communication.

CIPARS surveillance component leads:

  1. Farm pigs: David Léger ( and Sheryl Gow (; farm chicken: Agnes Agunos (;
  2. Abattoir: Anne Deckert (;
  3. Retail meat: Brent Avery (;
  4. Monitoring feeds: Jane Parmley (;
  5. human: Rita Finley (;
  6. human: Michael Mulvey (;
  7. CAHI: Carolee Carson (

CIPARS Coordinators:

  • Rebecca Irwin (;
  • Michael Mulvey (;
  • Rita Finley (
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