ARCHIVED - Canadian Integrated Surveillance Report: Salmonella, Campylobacter, verotoxigenic E. coli and Shigella, from 2000 to 2004

 

Appendix A: Data Sources

This section describes the data sources used to generate the integrated report. Data on human cases for this report were derived from:

  • National Notifiable Diseases Reporting System (NDRS) database
  • Enteric Diseases Program, National Microbiology Laboratory (NML) database
  • PulseNet Canada – PulseNet Canada Database
  • National Enteric Surveillance Program (NESP) database
  • Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS)
  • Hospital Morbidity Database (HMDB) from the Canadian Institute for Health Information (CIHI)
  • Death Database -Vital Statistics from Statistics Canada

Data on isolates from non-human sources were obtained from:

  • Laboratory for Foodborne Zoonoses (LFZ)
  • Includes non-human isolates from CIPARS (Abattoir and Retail Food Components)

Section 1

Data in the National Notifiable Disease Reporting System (NDRS) database includes data that are collected on a mandatory basis by the local public health units/authorities. These data were reported through the provincial/territorial Ministries of Health to the Infectious Disease and Emergency Preparedness Branch of the Public Health Agency of Canada (PHAC) for inclusion in the NDRS.

Data are submitted in case-level or aggregate form. Case-level data includes “confirmed” (laboratory identification of pathogen) and “closed” (investigation completed) reports. Eight provinces and territories provided case-level data, though completeness of data fields and values varied by region. However, disease, province and date were available for all. Date information varied from the date of diagnosis to the date the report was received. Other optional data included age, sex, and risk factor information such as travel and mode of transmission. Aggregate-level data are available from all provinces and territories in Canada. Information was aggregated by disease (e.g. Salmonellosis), age group, sex, year and month, and no case level information was included. Provincial/ territorial counts reflected the introduction of Nunavut in April of 1999. All data were verified at the provincial/territorial level. This involved summarizing monthly reports into an annual report that was sent back to the originating jurisdiction for verification. Once updated and approved, the data were returned to the PHAC. These data are then made available on the web at Notifiable Disease Online at http://dsol-smed.phac-aspc.gc.ca/dsol-smed/ndis/index_e.html.

Section 2

Data supplied by the Enteric Diseases Program, National Microbiology Laboratory (NML - formerly called the National Laboratory for Bacteriology and Enteric Pathogens) are primarily from the provincial public health and reference laboratories as well as from work performed at the NML. Local and regional laboratories forwarded some enteric pathogen isolates to provincial laboratories for confirmation and identification. Some isolates from the provincial laboratories were sent to the NML for reference services, such as confirmation and further strain characterizations. Provincial laboratories also sent aggregate information for all notifiable enteric agents observed each month to the NML. Both the aggregate and case level datasets included: organism, province, species, serovar/serotype, source (only human source data included in this report), isolate source (e.g. stool, urine), travel information, outbreak information when available, and age and gender. Additionally, both contained date information, but in the aggregate dataset this was the reporting date, and in the non-aggregate data set, the date of isolation was reported. Further details from these data are available from annual summaries [Laboratory Surveillance Data for Enteric Pathogens in Canada, 2000-2004 Annual Summaries (http://nml-lnm.gc.ca/english/NESP.htm)].

The National Enteric Surveillance Program (NESP) is a surveillance system that is jointly managed by the Centre for Food-borne, Environmental and Zoonotic Infectious Diseases (CFEZID) and the Enteric Diseases Program, National Microbiology Laboratory (NML) of the Public Health Agency of Canada, in co-operation with provincial public health and central reference laboratories (PHLs). The system receives weekly aggregate totals of new identifications on a select group of enteric organisms from the PHLs in order to provide weekly national analyses and reports. A broad range of bacterial, viral and parasitic diseases identified to the species or serovar level is tracked in this program. National coverage was established in April 1997 and 1998 marked the first full calendar year of data collection. Therefore, only data from 1998 onwards were used for this report. These data included counts by week and species or serovar for each province and territory. Additional information on antimicrobial resistance, outbreaks and case clusters, unusual isolation sites and travel were also reported, when available.

Section 3

Outbreaks and Case Clusters Data

The outbreak and case cluster data includes information collected through various surveillance systems, including the NML, NESP and PulseNet Canada, as well as from investigations in which the NML and CFEZID had provided assistance. The NESP defines case clusters as a group of cases that represent higher than expected incidence in time and/or space but with no or weak epidemiologic linkages established. An outbreak is defined as a group of cases that represent higher than expected incidence in time and/or space and for which an investigation is undertaken to determine source of the infections. There is currently no national outbreak reporting system and therefore outbreak data may not be representative of all of the outbreaks that have occurred in Canada during this period. As well, the case counts reported may not represent the final case distribution and may not reflect the total number of cases associated with the outbreaks. Although outbreak-related data for cases are captured in the NDRS, there is no unique identifier linking outbreak-related cases and, as with the NML/NESP, total outbreak-related case counts may not reflect actual final case counts.

Exposure Setting Description (NESP and NML data)

Community outbreaks included unrelated cases (i.e. no common household or institutional event) with similar illness that can be epidemiologicallylinked (i.e. associated by time and/or place and/or exposure). For events and private functions, cases of infection are related to groups of individuals with common exposure to specific events (e.g. banquets, weddings, parties). Food service outbreaks are related to food establishments (e.g. restaurant, cafeteria, bakery) and/or the commercial distribution of prepared meals. Household clusters generally involve small numbers of immediate family members and friends and may include cases of secondary transmission or may be related to larger community or other events. A residential institution is a place where individuals reside under the care of staff for short or long periods of time (e.g. nursing home, hospital). Non-residential institutional settings include daycare centres, schools, colleges/ universities, etc. Travel-related outbreaks occurring within Canada are included here, but clusters of cases related to foreign travel are not.

Section 4

The Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS), initiated in 2002, is a national program dedicated to the collection, integration, analysis and communication of trends in antimicrobial use and the development of resistance in selected bacterial organisms from human, animal and food sources across Canada. The program is based on several representative and methodologically unified surveillance components that can be linked to examine the relationship between antimicrobials used in food-animals and humans and the associated health impacts. From 2002 to 2004, CIPARS activities included the operation of: two active surveillance components, including: 1) abattoir surveillance involving the collection and analysis of isolates of generic E. coli and Salmonella from the intestinal contents of healthy animals at slaughter across Canada; and 2) retail surveillance involving the collection and analysis of isolates of generic E. coli, Salmonella, and Campylobacter from retail meat in Ontario and Québec. The program also collected passive surveillance data on antimicrobial resistance (AMR) in Salmonella isolates from human and diseased animal specimens collected from laboratories across Canada. For this report, only human and nonhuman Salmonella isolates collected between 2002 and 2004 were included.

The Surveillance of Human Clinical Isolate component of CIPARS is designed to provide representative data on Salmonella isolates at the provincial level. All human Salmonella isolates received by the provincial public health laboratories in New Brunswick, Newfoundland, Nova Scotia, Manitoba, Prince Edward Island, and Saskatchewan are forwarded to the National Microbiology Laboratory of the Public Health Agency of Canada in Winnipeg, Manitoba. More populated provinces (Alberta, British Columbia, Ontario, and Québec) forward isolates received from the first to the 15th of each month. In addition, all human isolates of S. Newport and S. Typhi are forwarded to the National Microbiology Laboratory because of concerns of emerging multidrug resistance and clinical importance, respectively.

Section 5

The Laboratory for Foodborne Zoonoses (LFZ) data included Salmonella isolates from non-human sources that were submitted to their facility for testing. This laboratory serves as a national centre for serotyping Salmonella from non-human sources. For this report, isolates from research projects and quality assurance programs were excluded. Included in the report were data from environmental assessment or food quality programs (e.g. supply flocks, exportation, quality monitoring), veterinary diagnostic submissions, as well as from the abattoir and retail components of the Canadian Integrated Program for Antimicrobial Resistance Surveillance (CIPARS) (See CIPARS description above). Isolates were received from provincial veterinary laboratories, other federal laboratories, university laboratories, private laboratories as well as agencies investigating outbreaks. There were inconsistency in the submission of isolates during the time period covered by this report as the types of samples and regional distribution varied from year to year. Routine data collected for each record included isolate source, type of sample, species or product, submitting laboratory, specimen number, date of collection, province, county or municipality, establishment, program, priority, serovar, phagetype, and biochemical characteristics. Further details from these data are available from annual summaries [Laboratory Surveillance Data for Enteric Pathogens in Canada, 2000 to 2004 Annual Summaries (http://nml-lnm.gc.ca/english/NESP.htm)].

Section 6

The Hospital Morbidity Database (HMDB) from CIHI captures administrative, clinical and demographic information on hospital inpatients from acute care facilities and some chronic care and rehabilitation facilities across Canada. For this report, records were selected in which the following enteric pathogens were indicated in the first three diagnostic codes from the International Statistical Classification of Diseases and Related Health Problems, Ninth Revision and Tenth Revision (ICD-9 and ICD-10): Cholera (001.0- 001.9 and A000, A001 and A009), Typhoid/ Paratyphoid (002.0-002.9 and A010-A014), Salmonella (003.0-003.9 and A020-A029), Shigella (004.0-004.9 and A030-A039), Other Food Poisoning (005.0-005.9 and A050-A059), Amebiasis (006.0-006.9 and A060-A069), Other Protozoal Intestinal Diseases (007.0-007.9 and A071-A079), pathogenic E. coli (008.0 and A040- A044) Other Organisms (008.1-008.8 and A046- A049), Gastrointestinal Anthrax (022.2 and A222), Listeriosis (027.0 and A32), and Viral Hepatitis A (007.0-007.1 and A080-A085). Only the first four numbers of the ICD-9 were available and therefore the data were not specific enough for the analysis of Campylobacter infections. In ICD-10, Campylobacter is coded as A045, therefore only the ICD-10 counts are presented in the report. Records from CIHI are given by fiscal year but the data were analysed by calendar year. Key variables included diagnostic codes, age, sex, province/ territory, and exit code (e.g. discharged or death).


Page details

Date modified: