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6B Congenital Infections

Description | Specific Indicators | Ontario Public Health Standards | Corresponding National Indicators | Data Sources |  Alternative Data Sources |  Analysis Check List | Method of Calculation |  Basic Categories | Indicator Comments | Definitions | Cross-References to Other IndicatorsCited References | Other References | Changes Made | Acknowledgements

Indicator Currently Under Revision

  • The proportion of new live born infants identified as being infected in utero or during delivery by any specific viral or bacterial agent known to have the potential to cause morbidity or mortality in a fetus or infant per 10,000 live births.
Specific Indicators
  • Incidence of rubella, congenital syndrome
  • Incidence of cytomegalovirus (CMV) infection, congenital
  • Incidence of herpes, neonatal
  • Incidence of Group B Streptococcal disease, neonatal
  • Incidence of ophthalmia neonatorum (gonorrhoea and chlamydia) 
  • Incidence of congenital gonorrhoea (other than conjunctivitis)
  • Incidence of congenital chlamydia (other than conjunctivitis)
  • Incidence of congenital syphilis
  • Incidence of congenital Human Immunodeficiency Virus (HIV) infection
  • Incidence of congenital Acquired Immunodeficiency Syndrome (AIDS) 
  • Incidence of congenital chicken pox (varicella)
  • Incidence of reportable congenital infections, total
Ontario Public Health Standards (OPHS)
The Ontario Public Health Standards (OPHS) establish requirements for the fundamental public health programs and services carried out by boards of health, which include assessment and surveillance, health promotion and policy development, disease and injury prevention, and health protection. The OPHS consist of one Foundational Standard and 13 Program Standards that articulate broad societal goals that result from the activities undertaken by boards of health and many others, including community partners, non-governmental organizations, and governmental bodies. These results have been expressed in terms of two levels of outcomes: societal outcomes and board of health outcomes. Societal outcomes entail changes in health status, organizations, systems, norms, policies, environments, and practices and result from the work of many sectors of society, including boards of health, for the improvement of the overall health of the population. Board of health outcomes are the results of endeavours by boards of health and often focus on changes in awareness, knowledge, attitudes, skills, practices, environments, and policies. Boards of health are accountable for these outcomes. The standards also outline the requirements that boards of health must implement to achieve the stated results.

Outcomes Related to this Indicator
  • Societal Outcome (Infectious Diseases Prevention and Control): There is reduced morbidity and mortality associated with infectious diseases of public health importance.
  • Societal Outcome (Sexual Health, Sexually Transmitted Infections, and Blood-borne Infections (including HIV)): There is reduced morbidity and mortality associated with sexually transmitted infections and blood-borne infections.
Assessment and Surveillance Requirements Related to this Indicator (Reproductive Health)
  • The board of health shall conduct epidemiological analysis of surveillance data... in the area of reproductive health outcomes.

Corresponding National Indicators

  • None

  • Data Sources (see Resources: Data Sources)


    Reportable Disease Data

    Original source: Integrated Public Health Information System (iPHIS), [Public Health Unit]
    Distributed by: Public Health Unit
    Suggested citation (see Data Citation Notes): iPHIS [years], Date Extracted: [date]


    Alternative Data Source 

  • Notifiable Diseases on-line, Health Canada, website (national and provincial level data only):

  • Denominator

    Note that 3 data sources are listed for use: 1) Vital statistics, 2) Hospitalization, 3) BORN. The choice of data source will depend upon data quality within a health unit as well as data access, and the specific analysis questions. For information related to the data sources, refer to the Data Source resources and the Reproductive Health Core Indicators Documentation Report.

    Alternative 1 
    Vital Statistics Live Birth Data
    Original source:
      ServiceOntario, Vital Statistics
    Distributed by:  Ontario Ministry of Health and Long-Term Care (MOHLTC): IntelliHEALTH ONTARIO (IntelliHEALTH)
    Suggested citation (see Data Citation Notes): Ontario Live Birth Data [years], Ontario Ministry of Health and Long-Term Care, IntelliHEALTH ONTARIO, Date Extracted: [date].

    Alternative 2 
    Hospitalization Data
    Original source:
      Discharge Abstract Database (DAD), Canadian Institute for Health Information (CIHI)
    Distributed by:  Ontario Ministry of Health and Long-Term Care (MOHLTC): IntelliHEALTH ONTARIO (IntelliHEALTH)
    Suggested citation (see Data Citation Notes): Inpatient Discharges [years], Ontario Ministry of Health and Long-Term Care, IntelliHEALTH ONTARIO, Date Extracted: [date].

    Alternative 3 
    BORN Information System
    Original source: The Newborn Screening dataset; The Niday Perinatal and NICU databases; The Ontario Midwifery Program database; The Fetal Alert Network database; The Multiple Marker Maternal Serum Screening dataset
    Distributed by: Better Outcomes Registry Network (BORN) Ontario
    Suggested citation (see Data Citation Notes): BORN Information System [years], Date Extracted: [date].


    Analysis Check List

    • Rates and proportions based on counts less than 5 may be suppressed, at the discretion of the health unit. iPHIS data are not subject to provincial suppression rules because it is the health unit that collects the information. A health unit may want to report, for example, that it had only one case of congenital syphilis over the past 5 years.
    • Small numbers of reported events may require the suppression of information, collapsing several years of data, or the use of smoothing techniques to eliminate large variations in reported rates.
    • For iPHIS:
      • Cases are classified in iPHIS according to the Ministry of Health and Long Term Care case definitions(1).
      • Rubella, congenital syndrome; cytomegalovirus infection, congenital; herpes, neonatal; Group B Streptococcal disease, neonatal; and ophthalmia neonatorum are all specific disease codes within iPHIS and can be selected based on Diagnosis. 
      • For congenital syphilis, select cases with a case classification of "Early Congenital Syphilis".
      • Ensure that the "diagnosing health unit" is the health unit of interest.

    Birth Data General 

    • Exclude stillbirths 
    • The IntelliHEALTH licensing agreement does not require suppression of small cells, but caution should be used when reporting at a level that could identify individuals, (e.g. reporting at the postal code level by age and sex). Please note that privacy policies may vary by organization. Prior to releasing data, ensure adherence to the privacy policy of your organization.
    • Aggregation (e.g. combining years, age groups, categories) should also be considered when small numbers result in unstable rates.
    • Exclude births to mothers that reside out-of-province. Births to Ontario mothers that occur out-of-province are not included in the data.
    • Include all births, not just those for mothers aged 15-49 years.
    • Include live births with birth weight <500g. For more information, refer to the Reproductive Health Core Indicators Documentation Report.
    • HELPS Data: Historically, PHUs obtained data for live births, stillbirths, therapeutic abortions, congenital anomalies, and deaths from the Ministry of Health through HELPS (the HEalthPlanning System). Although these data are no longer commonly used, some PHUs may still be accessing these data files. Information about the data can be found in the HELPS Data Source resource.

    Vital Statistics

    • In IntelliHEALTH under Standard Reports, folder "01 Vital Stats", open " Birth Summary V2". This report summarizes information on births by age group and mother's residence (Ontario, PHU and LHIN). IntelliHEALTH also provides population data (total population, female population aged 15-49 years) for the calculation of rates. Refer to the Notes tab for information. Open tab "1.2 Births x PHU x Type x Age" to obtain public health unit data and tab "1.1 ON Births x Type x Age" to obtain Ontario data. The report can be modified, renamed and saved under your own folder or can be exported into Excel.
    • The predefined report provides live birth and population data for the calendar years from 2000 to the most recent available. Table options can be edited to change the number of years of data presented. For years that are not displayed modify the calendar year filter to include the required years.
    • The data contained in the Birth Summary V2 report includes birth to Ontario mothers in Ontario only.
    • The notes section of the report provides important data caveats and background information on data sources and should be consulted.


    • Under the Inpatient Discharge Main Table data source from the ‘05 Inpatient Discharges' folder, use the "Hospital Births" predefined report. This report can be modified, renamed and saved under your own folder.
    • The report provides hospital birth counts (Admit Entry Type = N for Newborn or S for Stillbirth) for Ontario and by PHU, including only Ontario residents (Patient Province equal to ON).
    • The calendar year for date of admission is used (Admit CYear) rather than date of discharge since the date of admission will be the same as the birthdate for newborns.
    • Select the appropriate calendar years, PHU, and "Newborn - Born Alive in Reporting Institution" (i.e., exclude stillborn infants) as prompted from the pre-defined filters.
    • Even though counts are grouped by calendar year of admission, it is the actual number of discharges that are counted.

    BORN Information System

    • The number of live births can be obtained through BORN Ontario.
    • Refer to the BORN Data Source for more information about the data. 

    Method of Calculation

    Rate of Congenital Infection

    total number of live births reported as infected by specific infectious agent/s (or any of the agents for total)

        x 10,000

    total number of live births for area & period 


    Basic Categories
    • Geographic areas: public health unit
    • Specific infection

    Indicator Comments

    • Each health unit utilizes the centralized provincial reporting system, the Integrated Public Health Information System (iPHIS) that is used to collect reportable disease data. Provincial summaries are compiled by the Ministry of Health and Long Term Care's Public Health Protection and Prevention branch, which allows for comparisons with Ontario rates. iPHIS case definitions have also changed over time. Refer to Resources: Canadian and Ontario Case Definitions for Infectious Diseases.
    • Congenital infections may be under-reported in either the newborn or the mother because of under-diagnosis, especially in less severe cases, or under-reporting by physicians.
    • Health units investigate reportable diseases and determine whether a case is pregnant with the specific intention to prevent congenital infections.
    • Health units may have incomplete case information in iPHIS for chicken pox and would not be able to determine congenital infections from this disease. 
    • Specific disease comments are available in the definition section.
    • Acquired immunodeficiency syndrome (AIDS) - late clinical stage of infection with the human immunodeficiency virus (HIV). The virus can be transmitted from mother to infant during pregnancy, delivery, or breastfeeding. Women who are infected with HIV can be treated during pregnancy to reduce the rate of transmission to their unborn child (2).
    • Chickenpox - a highly contagious viral disease caused by the varicella zoster virus. Infants of mothers who contract chickenpox during early pregnancy have a higher likelihood of being born with congenital varicella syndrome. Babies born to women who develop chickenpox within five days before delivery or two days after delivery are at risk of developing a severe form of the disease (2). Many health units may not enter sufficient information into iPHIS to determine congenital infections from chicken pox.
    • Chlamydia trachomatis - the most commonly reported sexually transmitted disease in Ontario (3). Complications in adult females include pelvic inflammatory disease, ectopic pregnancy, and chronic pelvic pain. Infection during pregnancy can lead to conjunctival (ophthalmia neonatorum) and pneumonic infection of the newborn (2).
    • Congenital cytomegalovirus - caused by the cytomegalovirus (CMV). CMV can cause serious illness in immunosuppressed people and newborns. It is acquired in utero from an infected mother and can result in spontaneous abortion, serious or fatal neonatal illness or anomaly, or birth of a normal infant, depending on the timing of the infection, the strain, and whether the mother's infection was primary or recurrent (2). 
    • Congenital rubella syndrome (CRS) - caused by the rubella (German measles) virus. Fetuses infected  early in pregnancy are at the greatest risk of intrauterine death, spontaneous abortion or congenital malformations of major organ systems. CRS occurs in up to 90% of women with confirmed rubella infection during the first 20 weeks of pregnancy (2). 
    • Congenital syphilis - a form of syphilis acquired in utero that can lead to spontaneous abortion, stillbirth, premature birth, morbidity, long-term disability (e.g. blindness), or death if untreated. Signs and symptoms of infection may be detected in the neonatal period or remain undetected until puberty (2).
    • Gonorrhea (Neisseria gonorrhea) - a common sexually transmitted disease that can lead to pelvic inflammatory disease, ectopic pregnancy, infertility, and generalized infection in adults. It is a common cause of ophthalmia neonatorum in infants (2).  
    • HIV or Human Immunodeficiency Virus - destroys the body's ability to fight off infection, resulting in the development of AIDS (acquired immunodeficiency syndrome). The virus can be transmitted from mother to infant during pregnancy, delivery, or breastfeeding (2).
    • Live birth - the complete expulsion or extraction from its mother of a product of conception, irrespective of the duration of the pregnancy, which, after such separation, breathes or shows any other evidence of life such as heartbeat, umbilical cord pulsation, or definite movement of voluntary muscles, whether the umbilical cord has been cut or the placenta is attached. A live birth is not necessarily a viable birth. See early neonatal death.
    • Neonatal group B streptococcus (GBS) - produces invasive disease in newborns, including generalized infection (sepsis), pneumonia and meningitis. About 4% of infants with GBS die and those that survive may have long-term disabilities (2).
    • Neonatal herpes - the infection of a newborn with the herpes simplex virus. Among neonates, the virus is transmitted most commonly during birth. Infections can be divided into three clinical presentations and two of these, those involving the liver and the brain are often lethal. The third involves infections limited to skin, eyes or mouth (2).
    • Ophthalmia neonatorum - an eye infection of the newborn that is caused by chlamydia trachomatis and/or Neisseria gonorrhea. The bacteria are transmitted during birth and can lead to blindness, if untreated. Newborns are routinely treated with antibiotics to prevent ophthalmia neonatorum. Also called neonatal conjunctivitis (2).
    Cross-References to Other Indicators
    Cited References
    1. Ontario Ministry of Health & Long-Term Care. Ontario Public Health Standards: Infectious Diseases Protocol, 2009, Appendix B. Toronto, ON: Queen's Printer for Ontario; 2009. Available from:
    2. Heymann DL. Control of Communicable Diseases Manual. American Public Health Association, 2008.
    3. Ontario Ministry of Health & Long-Term Care. Ontario Public Health Standards: Infectious Diseases Protocol, 2009, Appendix A. Toronto, ON: Queen's Printer for Ontario; 2009. Available  from:

    Other References

    • None

    Changes Made 


    Type of Review - Formal or Ad Hoc

    Changes Made By


    October 2010


    Infectious Disease Sub-Group

    • Added list of diseases as specific indicators. 
    • Updated indicator to reflect new case definition.
    • Replaced Mandatory Health Programs section with updated Ontario Public Health Standards outcomes.
    • Changed data source from RDIS to iPHIS.
    • Updated references.

    March 29, 2012


    Reproductive Health Sub-Group

    • Three data sources are cited for the total number of births.
    • All births included - no longer exclude births with birthweight less than 500g.
    June 22, 2012Ad HocSherri Deamond
    • Updated specific indicator names to reflect names in Infectious Diseases Protocol, 2009, Appendix B 
    • Updated iPHIS section in analysis checklist



    Lead Authors

    • Vidya Sunil

    Contributing Authors

    • Infectious Disease Sub-Group, Reproductive Health Sub-Group



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