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Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS)

ARCHIVED - 2009 - Preliminary Results

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Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS)
2009 - Preliminary Results

For more information please email cipars-picra@hc-sc.gc.ca

Preamble

The Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS) is pleased to present preliminary antimicrobial resistance (AMR) findings and bacterial recovery rates for the 2009 calendar year. This preliminary results document contains data from the following surveillance components:

  • Surveillance of Human Clinical Isolates
  • Farm Surveillance
  • Abattoir Surveillance
  • Retail Meat Surveillance
  • Surveillance of Animal Clinical Isolates

What’s New in 2009 CIPARS Surveillance

Changes to CIPARS Analyses and Reporting

  • New tables have been added to this report for each surveillance component (with the exception of data from E. coli), which show the number of isolates resistant to different antimicrobial classes and the number of antimicrobial classes in the resistance patterns.
  • Unlike previous years, antimicrobial resistance in S. Newport isolates is not highlighted in the human section of the preliminary report because most 2009 isolates were susceptible to all antimicrobials tested.

Changes in Methods

  • The Enterococcus CMV3AGPF plate replaced the CMV2AGPF plate. This new plate does not include flavomycin (Category IV) and the range of dilutions tested was increased for daptomycin, vancomycin, erythromycin, penicillin, quinupristin-dalfopristin and tetracycline. More details will be presented in the 2009 CIPARS Annual Report.
  • The new CLSI (M100-S20) resistance breakpoint for ceftriaxone was applied to the interpretation of 2009 Salmonella and Escherichia coli data. The breakpoint was 64 µg/mL and is now 4 µg/mL.

Important Notes

  • Antimicrobials were categorized on the basis of importance in human medicine (Veterinary Drugs Directorate, Health Canada;[1] categories revised in April 2009). Antimicrobials are generally listed first according to this classification and then alphabetically. The antimicrobial abbreviations are located in the appendix on page 55.
  • 2009 data for this report were extracted from the central data repository as of April 7th, 2010. Additional isolates may be included in the full 2009 report.

About CIPARS Surveillance Components

Surveillance of Human Clinical Isolates

The objectives of the Surveillance of Human Clinical Isolates component of CIPARS are to provide a representative and methodologically unified approach to monitor temporal trends in the development of AMR in Salmonella isolated from humans at the provincial level.

Hospital-based or private clinical laboratories usually culture human Salmonella isolates in Canada. Although reporting is mandatory through laboratory notification of reportable diseases to the National Notifiable Disease Reporting System, forwarding of Salmonella cultures to the Provincial Public Health Laboratories (PPHLs) laboratories is voluntary and passive. A high proportion (84% in 2001[2]) of Salmonella isolates is forwarded to the PPHLs but this proportion may vary among laboratories.

To ensure a statistically valid sampling plan, all human Salmonella isolates (outbreak-associated and non-outbreak-associated) received by PPHLs[3] in Saskatchewan, Manitoba, New Brunswick, Nova Scotia, Prince Edward Island, and Newfoundland and Labrador were forwarded to the National Microbiology Laboratory (NML). The PPHLs in more populated provinces (British Columbia, Alberta, Ontario, and Québec) forwarded only the isolates received from the 1st to the 15th of each month. However, all human isolates of S. Newport and S. Typhi were forwarded to the NML because of concerns regarding multidrug resistance and clinical importance respectively. The Territories did not forward any human Salmonella isolates to CIPARS, directly or through provincial public health laboratories. Currently, an agreement has not been set up between CIPARS and the Territories.

Farm Surveillance (pigs)

The objectives of the CIPARS Farm Surveillance component are to provide data on antimicrobial use and resistance, monitor temporal trends in the development of AMR, investigate associations between antimicrobial use and resistance in isolates from grower-finisher pigs, and provide data for human-health risk assessments.

This initiative is based on a sentinel farm framework that provides herd-level data on antimicrobial use and fecal samples for bacterial isolation and antimicrobial susceptibility testing. It is administered and coordinated by the Laboratory for Foodborne Zoonoses (LFZ). This surveillance component focuses on grower-finisher pigs.

In 2006, the CIPARS Farm Surveillance component was implemented in swine herds across the 5 major pork-producing provinces in (Alberta, Saskatchewan, Manitoba, Ontario, and Québec). The swine industry was selected as the pilot commodity for development of the surveillance infrastructure because the Canadian Quality Assurance (CQA®) program had been extensively implemented by the industry, and there had not been a recent outbreak of foreign animal disease in pigs.

In 2009, the bacteria of interest in pigs were Salmonella, generic Escherichia coli, and Enterococcus recovered from composite fecal samples taken at the grower-finisher units. Nationally, 19 veterinarians and 91 sentinel grower-finisher sites were enrolled. In each of the participating provinces, the number of CIPARS sentinel sites was proportional to the national total of grower-finisher units, other than in Alberta where additional herds were enrolled with provincial support.

Abattoir Surveillance (beef cattle, chickens, and pigs)

The objective of the CIPARS Abattoir Surveillance component is to provide nationally representative, annual AMR data for bacteria isolated from animals entering the food chain, and to monitor temporal trends in the prevalence of AMR in these bacteria. Initially, this component targeted generic Escherichia coli and Salmonella from beef cattle, pigs, and broiler chickens. In 2003, the component was refined to discontinue Salmonella isolation from beef cattle because of the low prevalence of Salmonella in that population. An additional change was the inclusion of Campylobacter surveillance in beef cattle in late 2005.

In the Abattoir Surveillance component, the unit of concern (i.e. the subject of interest) is the bacterial isolate. The bacteria of interest were sampled from the caecal contents (not carcasses) of slaughtered food animals to avoid misinterpretation related to cross-contamination and to better reflect AMR in bacteria that originated on the farm.

Over 90% of all food-producing animals in Canada are slaughtered in federally inspected abattoirs annually. Forty-four federally inspected slaughter plants (6 beef cattle plants[4], 24 poultry plants, and 13 swine plants) from across Canada participated in 2009. The sampling method was designed with the goal that, across Canada, 150 isolates of each targeted bacterial would be recovered from each species over a 12-month period to avoid any potential seasonal bias in bacteria prevalence and antimicrobial susceptibility. The exception was Campylobacter isolated from beef cattle, for which it was estimated that 100 isolates would be recovered over the same period.

Retail Meat Surveillance (beef, chicken, and pork)

The objectives of the CIPARS Retail Meat Surveillance component are to provide data on antimicrobial AMR and to monitor temporal variations in select bacteria found in raw meat at the provincial level. Retail surveillance provides a measure of human exposure to antimicrobial-resistant bacteria through the consumption of undercooked meat. Retail food represents a logical sampling point for surveillance of AMR because it is the endpoint of food animal production and thus is indicative of human exposure. The scope of the surveillance framework can be modified (e.g. food commodities, bacteria, or regions) as necessary and functions as a research platform for investigation of specific questions regarding AMR in the agri-food sector.

As with Abattoir Surveillance, the unit of concern in Retail Meat Surveillance was the bacterial isolate cultured from one of the commodities of interest. In this situation, the commodities were raw meat products commonly consumed by Canadians, which originated from the 3 animal species sampled in the Abattoir Surveillance component. These raw meat products consisted of poultry (chicken legs or wings [skin on]), pork (chops), and beef (ground beef).

Bacteria of interest in chicken were Campylobacter, Salmonella, Enterococcus, and generic E. coli. In beef and pork, only E. coli was cultured and then tested for antimicrobial susceptibility given the low prevalence of Campylobacter and Salmonella in these commodities at the retail level as determined during the early phases of the program. Salmonella was isolated from pork but only to provide recovery estimates for this commodity for other Public Health Agency of Canada (PHAC) programs. These strains were submitted to antimicrobial susceptibility testing but results are not presented on an annual basis.

The sampling protocol was designed to evaluate AMR in the bacterial of interest and primarily involved continuous weekly submission of samples of retail meat from randomly selected geographic areas (i.e. census divisions defined by Statistics Canada), weighted by population, in each participating province. In 2009, retail meat samples were collected in British Columbia, Saskatchewan, Ontario, Québec, and in the Maritimes (New Brunswick, Nova Scotia and Prince Edward Island).

Prevalence estimates were used to determine the numbers of samples to be collected, which were based on an expected yield of 100 isolates per commodity per province per year plus 20% to account for lost or damaged samples. Because sampling was less frequent in British Columbia, Saskatchewan, and the Maritime provinces relative to Ontario and Québec, the target of 100 isolates per year may not have always been achieved in those provinces.

Surveillance of Animal Clinical Isolates (cattle, chickens, pigs, turkeys, and horses)

The objective of the Surveillance of Animal Clinical Isolates component is to detect new and/or emerging AMR patterns or new serovar/AMR pattern combinations in Salmonella. This component of CIPARS is based on submissions to veterinary diagnostic laboratories where the samples were collected by veterinarians and/or producers. Consequently, sample collection and submission, and Salmonella isolation varied among laboratories. Salmonella isolates were sent by provincial animal health laboratories from across the country to the Salmonella Typing Laboratory at the LFZ, Guelph, Ontario with the exception of Québec where isolates from animal health laboratories were sent to the Réseau des laboratoires de l'Institut national de santé animale, Saint-Hyacinthe for serotyping. Isolates and serotyping results from Québec are then forwarded to the LFZ to perform phagetyping and AMR testing on these isolates. However, unlike the Surveillance of Human Clinical Isolates component, all isolates received by provincial animal health laboratories were not necessarily forwarded to the LFZ, with the exception of the provinces of Ontario and Québec. Therefore, coverage may have varied considerably among provinces.

Salmonella isolates were sent by provincial animal health laboratories from across the country to the Salmonella Typing Laboratory at the LFZ, Guelph, Ontario with the exception of Québec where isolates from animal health laboratories were sent to the Réseau des laboratoires de l'Institut national de santé animale, Saint-Hyacinthe for serotyping. Isolates and serotyping results from Québec are then forwarded to the LFZ to perform phagetyping and AMR testing on these isolates.

Table of Contents

List of Figures

  • Figure 1. Temporal variation in resistance to selected antimicrobials in human isolates of Salmonella serovars Enteritidis, Heidelberg, and Paratyphi A and B; Surveillance of Human Clinical Isolates, 2003–2009.
  • Figure 2. Temporal variation in resistance to selected antimicrobials in human isolates of Salmonella serovars Typhi, Typhimurium, and “Other Serovars”; Surveillance of Human Clinical Isolates, 2003–2009.
  • Figure 3. Resistance to antimicrobials in Salmonella isolates from cattle; Surveillance of Animal Clinical Isolates, 2009.
  • Figure 4. Resistance to antimicrobials in Escherichia coli isolates from beef cattle; Abattoir Surveillance, 2009.
  • Figure 5. Temporal variation in resistance to selected antimicrobials in Escherichia coli isolates from beef cattle; Abattoir Surveillance, 2003–2009.
  • Figure 6. Resistance to antimicrobials in Escherichia coli isolates from beef; Retail Meat Surveillance, 2009.
  • Figure 7. Temporal variation in resistance to selected antimicrobials in Escherichia coli isolates from beef; Retail Meat Surveillance, 2003–2009.
  • Figure 8. Resistance to antimicrobials in Campylobacter isolates from beef cattle; Abattoir Surveillance, 2009.
  • Figure 9. Temporal variation in resistance to selected antimicrobials in Campylobacter isolates from beef cattle; Abattoir Surveillance, 2006–2009.
  • Figure 10. Resistance to antimicrobials in Salmonella isolates from chickens; Abattoir Surveillance, 2009.
  • Figure 11. Temporal variation in resistance to selected antimicrobials in Salmonella isolates from chickens; Abattoir Surveillance, 2003–2009.
  • Figure 12. Resistance to antimicrobials in Salmonella isolates from chicken; Retail Meat Surveillance, 2009.
  • Figure 13. Temporal variation in resistance to selected antimicrobials in Salmonella isolates from chicken; Retail Meat Surveillance, 2003–2009.
  • Figure 14. Resistance to antimicrobials in Salmonella isolates from chickens; Surveillance of Animal Clinical Isolates, 2009.
  • Figure 15. Resistance to antimicrobials in Escherichia coli isolates from chickens; Abattoir Surveillance, 2009.
  • Figure 16. Temporal variation in resistance to selected antimicrobials in Escherichia coli isolates from chickens; Abattoir Surveillance, 2003–2009.
  • Figure 17. Resistance to antimicrobials in Escherichia coli isolates from chicken; Retail Meat Surveillance, 2009.
  • Figure 18. Temporal variation in resistance to selected antimicrobials in Escherichia coli isolates from chicken; Retail Meat Surveillance, 2003–2009.
  • Figure 19. Resistance to antimicrobials in Campylobacter isolates from chicken; Retail Meat Surveillance, 2009.
  • Figure 20. Resistance to antimicrobials in Campylobacter isolates (n = 325) from chicken, by Campylobacter species; Retail Meat Surveillance, 2009.
  • Figure 21. Temporal variation in resistance to selected antimicrobials in Campylobacter isolates from chicken; Retail Meat Surveillance, 2003–2009.
  • Figure 22. Resistance to antimicrobials in Enterococcus isolates from chicken, by province; Retail Meat Surveillance, 2009.
  • Figure 23. Resistance to antimicrobials in Enterococcus isolates from chicken, by Enterococcus species; Retail Meat Surveillance, 2009.
  • Figure 24. Temporal variation in resistance to selected antimicrobials in Enterococcus isolates from chicken; Retail Meat Surveillance, 2003–2009.
  • Figure 25. Resistance to antimicrobials in Salmonella isolates from pigs; Farm Surveillance, 2009.
  • Figure 26. Temporal variation in resistance to selected antimicrobials in Salmonella isolates from pigs; Farm Surveillance, 2006–2009.
  • Figure 27. Resistance to antimicrobials in Salmonella isolates from pigs; Abattoir Surveillance, 2009.
  • Figure 28. Temporal variation in resistance to selected antimicrobials in Salmonella isolates from pigs; Abattoir Surveillance, 2003–2009.
  • Figure 29. Resistance to antimicrobials in Salmonella isolates from pigs; Surveillance of Animal Clinical Isolates, 2009.
  • Figure 30. Resistance to antimicrobials in Escherichia coli isolates from pigs; Farm Surveillance, 2009.
  • Figure 31. Temporal variation in resistance to selected antimicrobials in Escherichia coli isolates from pigs; Farm Surveillance, 2006–2009.
  • Figure 32. Resistance to antimicrobials in Escherichia coli isolates from pigs; Abattoir Surveillance, 2009.
  • Figure 33. Temporal variation in resistance to selected antimicrobials in Escherichia coli isolates from pigs; Abattoir Surveillance, 2003–2009.
  • Figure 34. Resistance to antimicrobials in Escherichia coli isolates from pork, by province; Retail Meat Surveillance, 2009.
  • Figure 35. Temporal variation in resistance to selected antimicrobials in Escherichia coli isolates from pork; Retail Meat Surveillance, 2003–2009.
  • Figure 36. Resistance to antimicrobials in Enterococcus isolates from pigs; Farm Surveillance, 2009.
  • Figure 37. Temporal variation in resistance to selected antimicrobials in Enterococcus isolates from pigs; Farm Surveillance, 2006–2009.
  • Figure 38. Resistance to antimicrobials in Salmonella isolates from turkeys; Surveillance of Animal Clinical Isolates, 2009.
  • Figure 39. Resistance to antimicrobials in Salmonella isolates from horses; Surveillance of Animal Clinical Isolates, 2009.

List of Tables

  • Table 1. Resistance to antimicrobials in Salmonella Enteritidis isolates from humans, by province; Surveillance of Human Clinical Isolates, 2009.
  • Table 2. Resistance to antimicrobials in Salmonella Heidelberg isolates from humans, by province; Surveillance of Human Clinical Isolates, 2009.
  • Table 3. Resistance to antimicrobials in Salmonella Paratyphi A and Paratyphi B isolates from humans by province; Surveillance of Human Clinical Isolates, 2009.
  • Table 4. Resistance to antimicrobials in Salmonella Typhi isolates from humans by province; Surveillance of Human Clinical Isolates, 2009.
  • Table 5. Resistance to antimicrobials in Salmonella Typhimurium isolates from humans by province; Surveillance of Human Clinical Isolates, 2009.
  • Table 6. Resistance to antimicrobials in Salmonella “Other Serovars” isolates from humans by province; Surveillance of Human Clinical Isolates, 2009.
  • Table 7. Number of antimicrobial classes in resistance patterns of Salmonella isolates from humans, by province and serovar; Surveillance of Human Clinical Isolates, 2009.
  • Table 8. Number of antimicrobial classes in resistance patterns of Salmonella isolates from cattle, by serovar; Surveillance of Animal Clinical Isolates, 2009.
  • Table 9. Number of antimicrobial classes in resistance patterns of Campylobacter isolates from beef cattle, by Campylobacter species; Abattoir Surveillance, 2009.
  • Table 10. Number of antimicrobial classes in resistance patterns of Salmonella isolates from chickens, by serovar; Abattoir Surveillance, 2009.
  • Table 11. Number of antimicrobial classes in resistance patterns of Salmonella isolates from chicken, by serovar; Retail Meat Surveillance, 2009.
  • Table 12. Number of antimicrobial classes in resistance patterns of Salmonella isolates from chickens, by serovar; Surveillance of Animal Clinical Isolates, 2009.
  • Table 13. Number of antimicrobial classes in resistance pattern of Campylobacter isolates from chicken, by species; Retail Meat Surveillance, 2009.
  • Table 14. Number of antimicrobial classes in resistance pattern of Enterococcus isolates from chicken, by species; Retail Meat Surveillance, 2009.
  • Table 15. Number of antimicrobial classes in resistance pattern in Salmonella isolates from pigs, by serovar; Farm Surveillance, 2009.
  • Table 16. Number of antimicrobial classes in resistance patterns of Salmonella isolates from pigs, by serovar; Abattoir Surveillance, 2009.
  • Table 17. Number of antimicrobial classes in resistance patterns of Salmonella isolates from pigs, by serovar; Surveillance of Animal Clinical Isolates, 2009.
  • Table 18. Number of antimicrobial classes in resistance patterns of Enterococcus isolates from pigs, by species; Farm Surveillance, 2009.
  • Table 19. Number of antimicrobial classes in resistance patterns of Salmonella isolates from turkeys, by serovar; Surveillance of Animal Clinical Isolates, 2009.
  • Table 20. Number of antimicrobial classes in resistance patterns of Salmonella isolates from horses, by serovar; Surveillance of Animal Clinical Isolates, 2009.
  • Table A.1. Recovery rates and number of isolates submitted for antimicrobial susceptibility testing across the bacterial species, the active surveillance components and the animal species; CIPARS, 2002–2009.

1 Categorization of Antimicrobial Drugs Based on Importance in Human MedicineThis link will take you to another Web site (external site)

2 Report of the 2001 Canadian Laboratory Study, National Studies on Acute Gastrointestinal Illness, Division of Enteric, Foodborne and Waterborne Diseases, 2002.

3 The Yukon, Northwest Territories, and Nunavut, which do not have a PPHL counterpart, also forward isolates to one of the PPHLs.

4 May include a very small number of samples from dairy cattle, as a small number of plants slaughter both commodities, however veal is excluded.