Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS): Antimicrobial Resistance

CIPARS collects, analyses, and communicates trends in antimicrobial use and in antimicrobial resistance for select bacteria from humans, animals, and retail meat across Canada.

  • Last updated: 2025-12-15

For AMR surveillance, the Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS) monitors and reports trends across Canada in AMR in select enteric and zoonotic bacteria from people, terrestrial animals, food and water sources. CIPARS is operationally linked with FoodNet Canada (FNC). FNC is the integrated sentinel site surveillance network for enteric disease in Canada. FNC provides AMR data for surface water, some retail food products and Campylobacter from people.

The interactive data visualizations are updated regularly and therefore may differ from published CIPARS reports. Diagnostic data of Salmonella isolates from sick animals are coming in 2026.

The COVID-19 pandemic resulted in several disruptions to CIPARS and FNC surveillance activities from 2020 to 2022. For more information, please refer to the important data details added below each figure.

Definitions and variable descriptions
Atlantic Atlantic region may include one or more of the following provinces: New Brunswick, Newfoundland and Labrador, Nova Scotia, and Prince Edward Island.
Prairies Prairie region may include one or more of the following provinces: Alberta, Manitoba, and Saskatchewan.
FNC sentinel sites FNC’s 4 sentinel sites are in Ontario (Middlesex-London Health Unit), British Columbia (Fraser Health), Alberta (Alberta Health Services: Calgary and Central Zones), Quebec (Région sociosanitaire de la Montérégie). The Quebec sentinel site was implemented in July 2019. In 2022, the boundaries of the Alberta site changed.
Farm Results shown for broiler chickens, layer chickens, turkeys, grower-finisher pigs, and feedlot cattle at farm were obtained from pooled fecal samples. Results shown for dairy cattle at farm were composite manure samples taken from pre-weaned calves, post-weaned heifers and lactating dairy cattle, and the manure pit. Samples were obtained from healthy animals at farm. The farm data presented are unadjusted for clustering of multiple isolates from the same farm.
Abattoir Results shown for abattoir were obtained from cecal samples. Samples were from healthy animals. Abattoir results are presented nationally, due to the sampling frame design, which is national in scope, based on Canadian slaughter volume. For cattle from the abattoir, testing for Salmonella was discontinued in 2003 due to low recovery.
Surface water Results shown for water were obtained from active FNC sampling across sentinel sites. Sampling may include irrigation, recreational or surface water from rivers. Sampling approaches vary from collecting water directly from the surface water with a pole, wading into the water, and collecting water from a raw water tap.

On this page

  • Antimicrobial resistance
  • Subtypes and recovery
  • Interpretive criteria
Antimicrobial resistance Download the data

CIPARS AMR interactive data visualizations include:

Figure 1. CIPARS-FNC: Frequency of antimicrobial resistance in isolates by host species or environment sample type.

Hover over the line graph to see more details. Click on a legend element to add or remove the corresponding lines from the graph. Red text in the hover over field highlights a small total isolate count (less than 20).

Important data details (details change based on filter selections)
  • Please note the change in the y-axis scale as different data series are selected.
  • For low isolate counts (red text in the hover over field), interpret proportions with caution.
  • Solid lines connecting the data points signify phenotypic testing and dashed lines connecting the data points signify predicted phenotypes from genotypic testing.
  • Some less common subtypes have breaks in the line graph for years where the subtype was not recovered.
  • Depending on the surveillance year, E. coli and Salmonella isolates were tested for susceptibility to 14, 15 or 16 antimicrobials and Campylobacter isolates were tested for susceptibility to 8 or 9 antimicrobials (details are available in the interpretive criteria tab).
  • Breakpoints used for interpretation of the minimum inhibitory concentration (MIC) results from antimicrobial susceptibility testing of bacterial isolates are available in the interpretive criteria tab. Pertaining to the “resistance to” filter, for all antimicrobials, isolates are classified as “resistant” when MICs correspond to resistant-level values. With the exception of ciprofloxacin for Salmonella and E. coli, where isolates are classified as “not susceptible” when MICs correspond to resistant-level or intermediate-level values to align with AMR prediction from whole genome sequencing data.

Table 1. CIPARS-FNC: Frequency of resistance in isolates in Canada (Resistant total / isolate total).

The asterisk (*) highlights a small total isolate count (less than 20).

Figure 1: Text description

Figure 2. CIPARS-FNC: Frequency of multidrug resistance measures (MDRM) in isolates.

Hover over the line graph to see more details. Click on a legend element to add or remove the corresponding lines from the graph. Red text in the hover over field highlights a small total isolate count (less than 20).

Important data details (details change based on filter selections)
  • Depending on the surveillance year, E. coli and Salmonella isolates were tested for susceptibility to antimicrobials in 6, 7 or 8 antimicrobial classes and Campylobacter isolates were tested for susceptibility to antimicrobials in 6 or 7 antimicrobial classes (details are available in the interpretive criteria tab).
  • Fully susceptible: CIPARS uses both phenotypic and genotypic testing of isolates. For phenotypic testing, “fully susceptible” means that resistance was not observed to any of the tested antimicrobials. For genotypic testing, “fully susceptible” means no known antimicrobial resistance genes or mutations validated for antimicrobial resistance prediction were detected.
  • Multidrug resistance measures (MDRM): For example – "resistant to 3 or more classes" means isolates were resistant to 3, 4, 5 and up to the maximum number of antimicrobial classes tested. The other MDRM except fully susceptible (definition above) follow the same pattern.
  • Please note the change in the y-axis scale as different data series are selected.
  • For low isolate counts (red text in the hover over field), interpret proportions with caution.
  • Solid lines connecting the data points signify phenotypic testing and dashed lines connecting the data points signify predicted phenotypes from genotypic testing.
  • Some less common subtypes have breaks in the line graph for years where the subtype was not recovered.

Table 2. CIPARS-FNC: Frequency of multidrug resistance measures (MDRM) in isolates in in Canada (MDRM total / isolate total).

The asterisk (*) highlights a small total isolate count (less than 20).

Figure 2: Text description
Subtypes and recovery Download the data

CIPARS subtypes and recovery interactive data visualizations include:

Figure 1. CIPARS-FNC: Frequency of Campylobacter and Salmonella subtypes.

Hover over the bar graph sections to see more details. Click on a legend element to add or remove the corresponding bar sections from the graph. Red text in the hover over field highlights a small total isolate count (less than 20).

Important data details (details change based on filter selections)
  • For low isolate counts (red text in the hover over field), interpret proportions with caution.

Table 1. CIPARS-FNC: Frequency of subtypes in in Canada (Subtype total / isolate total).

The asterisk (*) highlights a small total isolate count (less than 20).

Figure 1: Text description

Figure 2. CIPARS-FNC: Frequency of Campylobacter, Escherichia coli and non-typhoidal Salmonella recovery.

Hover over the line graph to see more details. Click on a legend element to add or remove the corresponding lines from the graph. Red text in the hover over field highlights a small number of samples tested (less than 20).

Important data details (details change based on filter selections)
  • Only surveillance components where samples are actively collected have recovery data.
  • Please note the change in the y-axis scale as different data series are selected.
  • For small numbers of samples (red text in the hover over field), interpret proportions with caution.
  • Salmonella isolates are non-typhoidal Salmonella (including S. Paratyphi B var. Java)

Table 2. CIPARS-FNC: Frequency of Campylobacter, Escherichia coli and non-typhoidal Salmonella recovery in in Canada (Isolates recovered / samples tested).

The asterisk (*) highlights a small number of samples tested (less than 20).

Figure 2: Text description
Interpretive criteria Download the data

Details of the antimicrobial resistance interpretive criteria used by CIPARS are available for:

Table 1. Antimicrobial susceptibility breakpoints for Salmonella and Escherichia coli.

Antimicrobial category1 Antimicrobial Antimicrobial Class Years Tested2 Range tested3 (μg/mL) Breakpoints4 (μg/mL)
S5 I6 R7
Ⅰ Amoxicillin-clavulanic acid Beta-lactams 2001-present 1.0/0.5–32/16 ≤ 8/4 16/8 ≥ 32/16
Ceftriaxone Beta-lactams 2001-present 0.25–64 ≤ 1 2 ≥ 4
Ceftiofur Beta-lactams 2001-2015 0.12-8 ≤ 2 4 ≥ 8
Ciprofloxacin Quinolones 2001-present 0.015–4 ≤ 0.06 0.12–0.5 ≥ 1
Colistin Polymixins 2020-present 0.25–8 N/A8 N/A N/A mcr9
Meropenem Beta-lactams 2016-present 0.06–4 ≤ 1 2 ≥ 4
Ⅱ Amikacin Aminoglycosides 2001-2010 0.5-64 ≤ 4 8 ≥ 16
Ampicillin Beta-lactams 2001-present 1–32 ≤ 8 16 ≥ 32
Azithromycin10 Macrolides 2011-present 0.25–64 ≤ 16 N/A ≥ 32
Cefoxitin Beta-lactams 2001-present 1–32 ≤ 8 16 ≥ 32
Cephalothin11 Beta-lactams 2001-2004 2-32 ≤ 8 16 ≥ 32
Gentamicin Aminoglycosides 2001-present 0.25–16 ≤ 2 4 ≥ 8
Kanamycin Aminoglycosides 2001-2013 8-64 ≤ 16 32 ≥ 64
Nalidixic acid Quinolones 2001-present 0.5–32 ≤ 16 N/A ≥ 32
Streptomycin12 Aminoglycosides 2014-2019 2-64 ≤ 16 N/A ≥ 32
Trimethoprim-sulfamethoxazole Folate pathway inhibitors 2001-present 0.12/2.38–4/76 ≤ 2/38 N/A ≥ 4/76
Ⅲ Chloramphenicol Phenicols 2001-present 2-32 ≤ 8 16 ≥ 32
Sulfamethoxazole13 Folate pathway inhibitors 2001-2004 16–512 ≤ 256 N/A ≥ 512
Sulfisoxazole Folate pathway inhibitors 2004-present 16–256 ≤ 256 N/A ≥ 512
Tetracycline Tetracyclines 2001-present 4–32 ≤ 4 8 ≥ 16
Footnotes
  • 1 Roman numerals I to IV indicate categories of importance to human medicine as outlined by Health Canada’s Veterinary Drugs Directorate. Health Canada’s categorization of antimicrobials of importance to human medicine and List A antimicrobials.
  • 2 NARMS susceptibility panels (Sensititre™) used by the Public Health Agency of Canada (PHAC) with year ranges: CMV6CNCD (2001), CMV7CNCD (2002-2004), CMV1AGNF (2005-2010), CMV2AGNF (2011-2013), CMV3AGNF (2014-2015), CMV4AGNF (2016-2019) and CMV5AGNF (2020 – present). Isolates tested external to PHAC may have different year ranges for susceptibility plates and antimicrobials tested.
  • 3 Range tested is for the most recent plate used for testing the antimicrobial.
  • 4 Breakpoints are from Clinical & Laboratory Standards Institute (CLSI) M100-33 unless otherwise noted.
  • 5 S = susceptible.
  • 6 I = intermediate susceptibility.
  • 7 R = resistant.
  • 8 N/A = not applicable.
  • 9 Resistance to colistin was defined as detecting an mcr gene from whole genome sequencing data (excluding mcr-9).
  • 10 No CLSI breakpoints for Enterobacterales were available for this antimicrobial. Breakpoints were based on those used by NARMS.
  • 11 Cephalothin AMR results are not presented in the CIPARS visualizations due to cephalothin only being tested for four years at the beginning of the program.
  • 12 Streptomycin AMR results are not presented prior to 2014 due to the range tested not being compatible with the current antimicrobial susceptibility breakpoint.
  • 13 Since sulfamethoxazole is similar to sulfisoxazole with the same testing range and breakpoints, the AMR results are combined and reported as sulfisoxazole.

Table 2. Antimicrobial susceptibility breakpoints for Campylobacter.

Antimicrobial category1 Antimicrobial Antimicrobial Class Years Tested2 Range tested3 (μg/mL) Breakpoints4 (μg/mL)
S5 I6 R7
Ⅰ Ciprofloxacin Quinolones 2003-present 0.015–64 ≤ 1 2 ≥ 4
Meropenem8 Beta-lactams 2020-present 0.004–16 ≤ 1 2 ≥ 4
Telithromycin Ketolides 2006-2019 0.015-8 ≤ 4 N/A9 ≥ 8
Ⅱ Azithromycin8 Macrolides 2003-present 0.015–64 ≤ 2 4 ≥ 8
Clindamycin8 Lincosamides 2003-present 0.03–16 ≤ 2 4 ≥ 8
Erythromycin Macrolides 2003-present 0.03–64 ≤ 8 16 ≥ 32
Gentamicin8 Aminoglycosides 2003-present 0.12–32 ≤ 2 4 ≥ 8
Nalidixic acid8 Quinolones 2003-present 4–64 ≤ 16 32 ≥ 64
Ⅲ Chloramphenicol10 Phenicols 2003-2005 0.016-256 ≤ 16 N/A ≥ 32
Florfenicol8 Phenicols 2006-present 0.12–64 ≤ 4 N/A ≥ 8
Tetracycline Tetracyclines 2003-present 0.12–64 ≤ 4 8 ≥ 16
Footnotes
  • 1 Roman numerals I to IV indicate categories of importance to human medicine as outlined by Health Canada’s Veterinary Drugs. Health Canada’s categorization of antimicrobials of importance to human medicine and List A antimicrobials.
  • 2 Antimicrobial susceptibility testing methodology used by PHAC with year ranges: ETest® (2003-05), and NARMS susceptibility panels (Sensititre™) CAMPY (2006-19) and CMVCAMPY (2020-present). Isolates tested external to PHAC may have different year ranges for susceptibility plates and antimicrobials tested.
  • 3 Range tested is for the most recent plate used for testing the antimicrobial.
  • 4 Breakpoints are from CLSI M45-ED-3 unless otherwise noted.
  • 5 S = susceptible.
  • 6 I = intermediate susceptibility.
  • 7 R = resistant
  • 8 No CLSI breakpoints available. The breakpoints used by CIPARS are based on NARMS breakpoints.
  • 9 N/A = not applicable.
  • 10 Chloramphenicol AMR results are not presented in the CIPARS visualizations due to chloramphenicol only being tested for three years at the beginning of the program.

Antimicrobial resistance prediction from whole genome sequencing data

The prediction of antimicrobial resistance (AMR) from whole genome sequencing (WGS) data is performed using PHAC’s Staramr program1 (available at https://github.com/phac-nml/staramr). Staramr incorporates the Centre for Genomic Epidemiology’s databases for ResFinder (resistance genes), PointFinder (resistance mutations), PlasmidFinder, and PubMLST and the gene-drug key developed by the United States Centers for Disease Control (US CDC) for prediction of AMR profiles. It also checks quality metrics for the genome assembly.

  • Validation tests performed by PHAC’s National Microbiology Laboratory found that the prediction of AMR from WGS data for Salmonella is accurate and reliable1. Staramr was validated for prediction of resistance to the antimicrobials on the CMV4AGNF and CMV5AGNF National Antimicrobial Resistance Monitoring System (NARMS) susceptibility panels (15 antimicrobials).

The Staramr program is periodically updated. Staramr versions 0.7.0 or 0.7.1, which were based on the same gene/mutation-drug key, were used for WGS data from 2017 to 2021. Staramr versions 0.8.0 or 0.9.1, which were based on the same gene/mutation-drug key, were used for WGS data from 2022 to 2024.

Comparison of the two gene/mutation-drug keys outlined above was performed to identify relevant differences and where possible interpretations were updated to align with the current Staramr version (0.9.1). When new genes/mutations are added to new versions of the gene/mutation-drug key, interpretations are unable to be applied retrospectively, as the new gene/mutation was not screened for in the previous version. For genes of higher interest (ESBL, mcr, carbapenemases), if sequences are identified that are not perfect matches to the gene/mutation in the database, an alignment is performed to identify if it is a new resistance variant or mutation, which minimizes missing newly identified genes and mutations.

Footnotes

Additional information

Please contact CIPARS with any questions about our data or if you require additional data. For more information, please visit the Public Health Agency of Canada’s (PHAC) Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS), Veterinary antimicrobial sales reporting, PHAC’s FoodNet Canada (FNC) and FNC’s interactive data visualizations.

Acknowledgments

PHAC acknowledges the significant efforts by all CIPARS collaborators who help to make this program a continued success.

Suggested citation

Public Health Agency of Canada. (YYYY (last updated)) CIPARS: Antimicrobial Resistance. Government of Canada. Available from: https://health-infobase.canada.ca/cipars/antimicrobial-resistance.html. Accessed MM/DD/YYYY.

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