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8 Infectious Disease Incidence


Description | Specific Indicators | Corresponding OPHS Outcomes | Corresponding National Indicators | Data Sources |  Alternative Data Sources | ICD Codes | Analysis Check List | Method of Calculation |  Basic Categories | Indicator Comments | Cross-References to Other Sections | Cited References | Other References | Acknowledgements | Changes Made
  • The incidence rate is the total number of new cases of infectious diseases relative to the total population (per 100,000) in a specified time period.
  • Age-specific incidence rates are the annual number of new cases of infectious diseases in a given age group per 100,000 population in that age group in a specified time period.
  • Age-standardized incidence rate (SRATE): the number of new cases of infectious diseases that would occur in the population if it had the same age distribution as the 1991 Canadian population.
  • Standardized incidence ratio (SIR): the ratio of observed new cases of infectious diseases to the number expected if the population had the same age-specific incidence rates as Ontario.

Specific Indicators

 Vaccine Preventable Diseases (VPDs)
  • Incidence of Chickenpox (Varicella) 
  • Incidence of Diphtheria
  • Incidence of Haemophilus influenzae b disease, invasive
  • Incidence of Hepatitis B (acute)
  • Incidence of Influenza
  • Incidence of Measles
  • Incidence of Meningococcal disease, invasive
  • Incidence of Mumps
  • Incidence of Pertussis
  • Incidence of Poliomyelitis, acute (indigenous and imported)
  • Incidence of Rabies (human)
  • Incidence of Rubella
  • Incidence of Rubella, congenital syndrome
  • Incidence of Tetanus
 Sexually Transmitted Infections (STIs) and Blood-borne Infections
  • Incidence of Acquired Immunodeficiency syndrome  (AIDS) 
  • Incidence of Chlamydial infections 
  • Incidence of Gonorrhoea
  • Incidence of Hepatitis C
  • Incidence of human immunodeficiency virus (HIV) infection
  • Incidence of Syphilis (primary, secondary and congenital)
 Enteric Diseases
  • Incidence of Amebiasis 
  • Incidence of Botulism
  • Incidence of Campylobacter enteritis 
  • Incidence of Cholera 
  • Incidence of Cryptosporidiosis
  • Incidence of Cyclosporiasis
  • Incidence of Food Poisoning, All Causes
  • Incidence of Gastroenteritis, Institutional Outbreaks
  • Incidence of Giardiasis
  • Incidence of Hepatitis A
  • Incidence of Listeriosis  
  • Incidence of Paratyphoid Fever
  • Incidence of Salmonellosis
  • Incidence of Shigellosis
  • Incidence of Trichinosis
  • Incidence of Typhoid Fever
  • Incidence of Verotoxin-producing Escherichia coli (VTEC) infection
  • Incidence of Yersiniosis
  • Incidence of confirmed new active and re-treatment tuberculosis
  • Incidence of confirmed tuberculosis cases resistant to any one antibiotic
  • Incidence of confirmed cases of Multi-Drug Resistant (MDR) tuberculosis
  • Incidence of latent tuberculosis infections (LTBI)
 Vector Borne Diseases
  • Incidence of Lyme Disease
  • Incidence of malaria
  • Incidence of West Nile Virus (WNV) illness

Corresponding Outcomes from the Ontario Public Health Standards (OPHS)

  • Societal Outcome (Infectious Disease Prevention and Control): There is reduced incidence of infectious diseases of public health importance. 
  • Societal Outcome (Vaccine Preventable Diseases): There is reduced incidence of vaccine preventable diseases.
  • Societal Outcome (Sexual Health, Sexually Transmitted Infections, and Blood-borne Infections (including HIV)): There are reduced transmission and incidence rates of sexually transmitted infections and blood-borne infections.
  • Societal Outcome (Tuberculosis Prevention and Control): There is reduced transmission of TB.
  • Societal Outcome (Tuberculosis Prevention and Control): There is reduced progression of latent TB infection (LTBI) to active TB.  
  • Societal Outcome (Tuberculosis Prevention and Control): There is reduced incidence of drug-resistant TB.  
  • Societal Outcome (Food Safety): There is reduced incidence of food-borne illness.
  • Societal Outcome (Safe Water): There is reduced incidence of adverse events related to unsafe drinking water. 

Corresponding Health Indicator(s) from Statistics Canada and CIHI

  • None.

Corresponding Indicators from Other Sources

Comparable Health Indicators: Select "View" under latest issue and then "Data Tables")

  • Incidence rate for invasive meningococcal disease
  • Incidence rate for measles 
  • Incidence rate for Haemophilus influenza b (invasive) (Hib) disease
  • Incidence rate for chlamydia
  • Rate of newly reported HIV cases
  • Incidence rate for tuberculosis
  • Incidence rate for Verotoxogenic E. coli

Data Sources

Numerator: Reportable Disease Data

Original Source: Integrated Public Health Information System, [Public Health Unit] 
Distributed by: Public Health Unit
Suggested citation (see Data Citation Notes): iPHIS [years], Extracted: [date]
Denominator: Population Estimates
Original Source: Statistics Canada 
Distributed by: Ontario Ministry of Health and Long-Term Care: IntelliHEALTH ONTARIO
Suggested citation (see Data Citation Notes): Population Estimates [years]*, Ontario Ministry of Health and Long-Term Care, IntelliHEALTH ONTARIO, Date Extracted: [date].
* Note: To indicate which versions were used, include all the years of the estimates, including the most recent year, even if not all were used in the analysis. The years used in the analysis should be included in the report itself.


Alternative Data Sources

Analysis Check List
  • Consider aggregation of data values and/or cell suppression when dealing with small numbers to avoid risk of confidentiality breach. A new resource is currently under development to provide more detailed information on this issue.
  • For iPHIS:
    • To obtain an estimate of incidence, ensure that the "diagnosing health unit" is the health unit of interest.
    • To include only cases (and not case contacts or reports that were investigated and subsequently found not to be a case): Encounter (or Episode) Type = Case AND Diagnosis Status = Confirmed. For carriers, Encounter Type = Carrier AND Diagnosis Status = Carrier. For HIV cases, Encounter Type = Carrier. For LTBI Episode Type = LTBI.
    • Be aware that some diseases can occur more than once within the same person.

Method of Calculation

Total Incidence Rate:

total number of new cases in the specified time period

       x 100,000

total population in the specified time period

Age-Specific Incidence Rates:

total number of new cases in the specified time period in an age group

       x 100,000

total population in the specified time period in that age group

Age-standardized incidence rate or SRATE (See Resources: Standardization of Rates):

Sum of (age-specific rate of new cases in x 1991 Canadian population in that age group) 

       x 100,000 

Sum of 1991 Canadian population

Standardized incidence ratio or SIR (See Resources: Standardization of Rates):

Sum of new cases in the population

       x 100

Sum of (Ontario age-specific rate x population in that age group)

Basic Categories

  • Age groups for age-specific rates: <1, 1-4, 5-9, 10-19, 20-44, 45-64, 65-74, 75+, Total
  • Sex: male, female.
  • Geographic areas: public health unit
  • Immigrant status: Canadian born vs foreign born

Indicator Comments

  • Each health unit utilizes the centralized provincial reporting system, the Integrated Public Health Information System (iPHIS) which is used to collect reportable disease data. Provincial summaries are compiled by the Ontario Ministry of Health and Long Term Care's Infectious Diseases Branch, which allows for comparisons with Ontario rates. Comparisons with other health units can be problematic however, because of inconsistencies across health units.1 Some cases may also be double-counted among people who move or cross various health unit boundaries.There were some issues around data integrity when RDIS first began operation in 1990. In some cases, case definitions have changed over time. Refer to Case Definition Comparison Document ( username and password required).
  • iPHIS was implemented in every Ontario health unit in 2005.
  • There were some issues around data integrity when the previous reporting system, the Reportable Disease Information System (RDIS) was first implemented in 1990. For some diseases, case definitions have changed over time. These data quality issues remain relevant, as RDIS cases were migrated into iPHIS. Refer to Case Definition Comparison Document ( username and password required).
  • There may be considerable under-reporting of actual cases for some diseases. For instance, when an infected person has mild clinical symptoms they may not seek medical care and/or laboratory testing may not be performed.
  • To best understand mortality or disease trends in a population, it is important to determine crude rates, age-specific rates and age-standardized rates (SRATES) or ratios (SMRs, SIRs). The crude death (or disease) rate is the number of deaths (or disease cases) divided by the number of people in the population. This rate depicts the “true” picture of death /disease in a community although it is greatly influenced by the age structure of the population. An older population would likely have a higher crude death rate whereas a younger population may have a higher crude birth rate. Age-specific rates can best describe the “true” death /disease pattern of a community and allow comparison of populations that have different age structures.
  • Since many age-specific rates are cumbersome to present, age standardized rates have the advantage of providing a single summary number that allows different populations to be compared; however, they present an “artificial” picture of the death /disease pattern in a community. It is important to examine the data carefully before standardizing. In general, the SMR or SIR is used to compare an area (e.g., health unit) with one other area (e.g., Ontario). This indirect form of standardization requires a comparator that has a large population and stable age-specific rates. SRATEs, on the other hand, are generally used to compare a number of rates at the same time, e.g., health units across a region or rates over time. This direct form of standardization requires all comparators to have relatively stable age-specific rates. For more information about standardization, refer to the Resources section: Standardization of Rates.

Vaccine Preventable Diseases

  • The diseases listed in this indicator are all preventable through adequate immunization.
  • Chickenpox data are not collected in the same manner as other vaccine preventable diseases. Chickenpox data are collected at an aggregate, rather than an individual, level. Discuss this issue with immunization staff prior to analysis.
Sexually Transmitted and Blood-borne Infections
  • Syphilis has several stages: congenital, primary, secondary and latent. The rate of congenital syphilis is one indicator while the rate of combined primary and secondary syphilis is a second indicator. Latent syphilis is not used in the calculation of rates since such persons are usually not infectious and represent previous infections.
Enteric Diseases
  • The incidence of enteric diseases is typically highest among children under the age of 4.
  • An increased proportion of tuberculosis cases are due to immigration from endemic areas and increased prevalence of HIV infections.
  • Multi-drug resistance (MDR) is an increasing concern globally and needs to be monitored in Canada. Rates of resistance to any one of the antibiotics (particularly Isoniazid or Rifampin) is important for program planning.

Cross-References to Other Sections

  • None

Cited References

  1. Dawson K. Data Quality in RDIS: Issues related to Combining Data Sets. Central East Health Information Partnership, October 2000.


Other References

  • Evans AS, Brachman PS. Bacterial Infections in Humans: Epidemiology and Control. Springer, 1998.
  • Evans AS, Kaslow RA. Viral Infections of Humans: Epidemiology and Control. Springer, 1997.
  • Heymann DL. Control of Communicable Diseases Manual. American Public Health Association, 2004.
Vaccine Preventable Diseases
 Sexually Transmitted and Blood-borne Infections
  • Alexander D. Epidemiology of AIDS/TB coinfection in Ontario – 1990-1995. PHERO, Volume 8(4), April 25, 1997;94-98.
  • Kerbel C. Epidemiology of Tuberculosis in Ontario 1995. PHERO, Volume 8(4), April 25, 1997; 81-93.
  • Tuberculosis Prevention and Control, Public Health Agency of Canada, and the Canadian Lung Association/Canadian Thoracic Society. Canadian Tuberculosis Standards, 6th Edition. Ottawa, ON: Public Health Agency of Canada, 2007. Available at:
Enteric Diseases
  • P. Michel, JB Wilson, SW Martin, RC Clarke, SA McEwen, CL Gyles. A Descriptive Study of Verotoxigenic Escherichia coli (VTEC) Cases Reported in Ontario, 1990-1994. Canadian Journal of Public Health, Volume 89(4), July/August 1998;253-257.
  • JD Greig, P Michel, JB Wilson, AM Lammerding, SE Majowicz, J Stratton, JJ Aramini, RK Meyers, D Middleton, SA McEwen. A Descriptive Analysis of Giardiasis Cases Reported in Ontario, 1990-1998. Canadian Journal of Public Health. Volume 92(5), September/October 2001;361-365.
  • SE Majowicz, P Michel, JJ Aramini, SE McEwen, JB Wilson. Descriptive Analysis of Endemic Cryptosporidiosis Cases Reported in Ontario, 1996-1997. Canadian Journal of Public Health. Volume 92(1),January/February 2001;62-66.
  • Middleton D. Descriptive Epidemiology of Enteric Disease due to Microbial Causes in Ontario: 1998. PHERO, Volume 11(5), May 26, 2000;76-85.
  • Michel P, Wilson JB, Martin SW, Clarker RC, McEwen SA, Gyles CL. Temporal and Geographical Distributions of Reported Cases of Escherichia coli O157:H7 Infection in Ontario. PHERO, Volume 11(7), July and August 2000;164-171. Reprinted from Epidemiology and Infection, Vol 122, No. 2 (April 1999).
  • Michel P, Wilson JB, Martin W, Clarke RC, McEwen SA, Gyles CL. Estimation of the under-reporting rates for the surveillance of Escherichia coli O157:H7 cases in Ontario, Canada. PHERO, Volume 12(2), February 25, 2001;54-61. Reprinted from Epidemiology and Infection (2000), 125, 35-45.
  • Dawson K. Data Quality in RDIS: Issues related to Combining Data Sets. Central East Health Information Partnership, October 2000. 
  • Rajda Z, Middleton D. Descriptive epidemiology of enteric illness for selected reportable diseases in Ontario, 2003. Canadian Communicable Disease Report 2006;32(23):275-85. Available at:
  • Rajda Z, Middleton D. Descriptive epidemiology of enteric diseases in Ontario, 2002. Public Health Epidemiology Report Ontario 2004;15(4).
  • Majowicz SE, Edge VL, Fazil A, McNab WB, Doré KA, Sockett PN, Flint JA, Middleton D, McEwen SA, Wilson JB. Estimating the under-reporting rate for infectious gastrointestinal illness in Ontario.Can J Public Health. 2005;96(3):178-81.
  • Liu et al. Descriptive epidemiology of verotoxin-producing E. coli reported in Ontario, 1996-2005. CCDR. 1 April 2007, Vol 33, Num 7. Available at:
  • Government of Canada. National Integrated Enteric Pathogen Surveillance Program
    (C-EnterNet) 2005-2006. Guelph, ON: Public Health Agency of Canada, 2006. Available at:



Lead Author(s)

Anne Arthur, Toronto Public Health
Popy Dimoulas-Graham, formerly Region of Waterloo Public Health

Contributing Author(s)

Core Indicators Infectious Disease Subgroup

CIWG Reviewers

Core Indicators Infectious Disease Subgroup

External Reviewers

Camille Achonu, Toronto Public Health
Effie Gournis, Toronto Public Health
Elizabeth Rea, Toronto Public Health
Rachel Savage, Ontario Agency for Health Protection and Promotion
Rebecca Stuart, Toronto Public Health


Changes Made


Type of Review

(Formal or Adhoc)

Changes made by


Dec. 9, 2008


Infectious Disease subgroup

  • Combined all incidence indicators, previously were separated into Vaccine-Preventable Disease Incidence, Sexually Transmitted Infection Incidence, Tuberculosis Incidence, and Enteric Diseases Incidence. Expanded STIs to include blood-borne infections and added vector borne diseases.
  • Added incidence of chicken pox, human rabies and meningococcal disease as specific indicators.
Nov. 29, 2010 Ad hocSherri Deamond on behalf of CIWG
  • Added links to Case Definition Comparison Document and (Canadian and Ontario) Case Definition Comparison Table
June 13, 2011 Ad hocSherri Deamond on behalf of CIWG
  •  Added acknowledgements section


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