Vaccine Preventable Diseases and Vaccination Coverage in Australia, 2003 to 2005

Vaccine preventable diseases data

Disclaimer: This is the fourth report on vaccine preventable disease and vaccination coverage in Australia, and is produced by the National Centre for Immunisation Research and Surveillance of Vaccine Preventable Diseases and the Australian Institute of Health and Welfare on behalf of the Australian Government Department of Health and Ageing published as a supplement to the Communicable Diseases Intelligence journal Volume 31, June 2007.

Page last updated: 20 July 2007

Three sources of routinely collected data were used for this report. Notification data were obtained from the National Notifiable Diseases Surveillance System (NNDSS), hospitalisation data from the Australian Institute of Health and Welfare (AIHW) National Hospital Morbidity Database, and mortality data from the AIHW Mortality Database (unpublished data).


The NNDSS database was established in its current form in 1991, and includes information about cases of vaccine preventable diseases reported by laboratories and health workers to state and territory authorities under their current public health legislation. State and territory notification criteria are based on the National Health and Medical Research Council (NHMRC) surveillance case definitions.10 However, historically, application of these definitions has differed between jurisdictions, with some using the 1994 NHMRC case definitions as written (e.g. South Australia and Western Australia) and others using their own definitions (e.g. New South Wales and Victoria) (see Appendix 6 for case definitions in use prior to 2004). In September 2003, new national case definitions for notifications reported to NNDSS were endorsed by the Communicable Diseases Network Australia,11 with nearly all jurisdictions implementing the new definitions in January 2004 (New South Wales commenced August 2004). In Queensland, most notifications are from laboratory-confirmed cases and the notification process is highly automated. There are some minor differences between the laboratory criteria for notification in Queensland and the national case definitions for some diseases (e.g. the criteria for laboratory notification of Hib, pertussis and Q fever). However, the public heath protocols for notification in Queensland require cases to meet the national case definitions for notification. In 2001, invasive pneumococcal disease and laboratory-confirmed influenza became notifiable to the NNDSS. Varicella and herpes zoster were made notifiable in all jurisdictions (except New South Wales) from 2006. Rotavirus infection is not notifiable to NNDSS.

Data extracted from the NNDSS as at 4 June 2006 were examined. Data were checked and cleaned where apparent errors were detected through consultation with appropriate surveillance staff in states and territories. Note that these data are later versions than those used for the 2003 and 2004 Australia’s Notifiable Disease Status reports and the AIHW publication Australia’s Health 2006.12–14 Disease notification data for cases with a date of diagnosis between 1 January 2003 and 31 December 2005 (three years) are included in this report. Notification data are presented and reported by date of diagnosis. Previous reports analysed notifications by date of onset where date of onset was collected from the clinical history where available, or the specimen collection date for laboratory-confirmed cases. As of mid 2005, a date of diagnosis field was generated for all NNDSS records. Date of diagnosis is completed using an algorithm whereby the earliest date in the fields date of onset, date of specimen, date of notification and date notification received (the only compulsory date field) is selected. This applies for all diseases except hepatitis B unspecified and hepatitis C unspecified (not included in this report) where onset date is not used in calculation of the date of diagnosis. Notifications with onset dates between 1 January 1993 and 31 December 2002 were reported previously.1–3 Historical notification data included within this report have been updated and are now presented by date of diagnosis. Q fever notifications are reported for the first time in this report.

The variables extracted for analysis for every disease were disease, date of diagnosis, age at onset, sex, and state or territory of residence. For the first time in this report, the fields for laboratory confirmation and vaccination status have been examined where relevant to that disease. This reflects the ongoing improvement in the completion rate of these fields. For a recent analysis of vaccine preventable diseases data by Indigenous status, please refer to the NCIRS report ‘Vaccine preventable diseases and vaccination coverage in Aboriginal and Torres Strait Islander people, Australia, 1999 to 2002’.15 Data from each state and territory were included when calculating rates only when that jurisdiction had been reporting for a complete year (see Appendix 2, Notifications by state or territory and year, for the years in which states and territories were reporting). Differences in surveillance systems between jurisdictions may have accounted for some of the differences in notification rates. Where there were known differences that were likely to differentially affect notification rates, these have been described under the disease chapter of interest.

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The AIHW National Hospital Morbidity Database has received administrative, demographic and clinical information about patients admitted to public and private hospitals in Australia since 1993. Data are received by financial year of separation (discharge), and the three most recent years for which data are available (2002/2003, 2003/2004 and 2004/2005) were examined. Cases with separation dates between 1 July 1993 and 30 June 2002 (9 years) were reported previously.1–3 This report presents previously analysed historical data for years prior to and including 1997/1998 and updated data for all years from 1998/1999 onwards. Where hospitalisation data is analysed by month, reflecting seasonal trends, data are presented and reported by date of admission. Otherwise, as hospitalisation data for the most recent period (2002/2003–2004/2005) is defined by date of separation, analysis by other variables such as age and sex is grouped by year of separation. Data were extracted based on the International Statistical Classification of Diseases and Related Health Problems, 10th Revision, Australian Modification (ICD-10-AM). Eligible separations were those with the code of interest listed in the principal diagnosis (the diagnosis chiefly responsible for the admission of the patient to hospital) or in any other diagnoses. The proportion of separations for which the diseases were coded as the principal diagnosis is reported for each disease. For acute hepatitis B, only principal diagnoses were included. Where the ICD-10-AM code for a disease specifies a severe manifestation (e.g. measles encephalitis) the number and type of these were reported as complications. The variables extracted for analysis were date of admission, financial year of separation, age at admission, sex, state or territory of residence, length of stay (LOS), and diagnosis (principal and other diagnoses—up to 31 diagnoses were recorded for each admission) coded using ICD-10-AM in the relevant edition for the collection period. In addition, the mode of separation (whether the patient died in hospital) was analysed for hospitalisations due to meningococcal disease as, for this disease, this measure was felt to be of importance. Where state of residence was missing in hospitalisation data, this variable was replaced with state of hospitalisation, affecting 0.5% of records in 2002/2003, 2003/2004 and 2004/2005.

Appendix 3 presents hospitalisation data by disease, year and state or territory. All jurisdictions except New South Wales, Queensland and South Australia required data suppression for cells containing less than five hospitalisations. The figures less than five (but non-zero) in this table for the jurisdictions that requested suppression have been replaced with the symbol <5. Calculation of the suppressed figures (by subtraction from totals) has been prevented by the suppression of another figure with less than five in the same disease category but a different year and of another state's data where less than five (for the same row/year). Where there was not another figure in the same row or column that was less than five, a cell has been suppressed using the symbol n.p. (not published) to denote that the number was greater than five. In some cases, this has been achieved by suppressing the total for the disease/year or for the five year total by disease/state. The corresponding hospitalisation rates for suppressions are also designated with the symbol n.p.


Death data were obtained from the AIHW Mortality Database. These data are supplied annually to the AIHW from the Registrars of Births Deaths and Marriages in each state and territory via the Australian Bureau of Statistics (ABS). Deaths include those in Australian waters as well as on Australian soil, whereas ABS published data exclude deaths in Australian waters. Since 1997, the International Classification of Diseases, 10th Revision (1992) (ICD-10) has been used to identify the cause of death. Although multiple causes of death have been recorded since 1997, only those where the underlying cause of death was the disease of interest are used in this report. Deaths analysed in this report were those registered in 2003 to 2004 (two years). The variables extracted for each death were: underlying cause, age, year death was reported, sex, and state or territory in which death was recorded.


All rates were calculated using finalised ABS mid-year estimated resident populations as at June 2006. Rates are presented as annual rates or average annual rates per 100,000 total population or population in age, sex or geographical subgroups, as appropriate. Average annual rates were calculated by dividing the total number of cases for the period of investigation by the sum of each year’s population for the same period. For hospitalisation data, the mid-year population estimate for the first half of the financial year was used as the denominator—e.g. the 2002 mid-year population estimate was used to calculate rates for 2002/2003. For notification data, the denominator population for each year included only jurisdictions notifying cases for that entire year. Averages were calculated for rates of notifications and hospitalisations and for bed days per year. Medians and ranges, rather than averages, were used to describe the distribution of notifications and hospitalisations per month, and length of stay per admission, as these data were not normally distributed. Where there were small cell sizes for national hospitalisation data (three or less hospitalisations recorded per age/disease category), median length of stay estimates were not published (denoted by n.p.).

Report structure for individual diseases

For each disease, data are generally presented in the following format:
    • secular trends—the pattern of notifications and hospitalisations over time, with reference to seasonality and outbreaks;
    • severe morbidity and mortality—hospital bed days, length of stay, principal diagnosis, complications and mortality by age group in standard age categories;
    • age and sex distribution—data by age and sex groups as relevant for each particular disease;
    • geographical distribution—case numbers and rates by state or territory, as shown in Appendices 2 and 3. For hospitalisations, some jurisdictions required suppression of hospitalisation data for those cells where there were less than five cases;
    • vaccination status of notified cases and laboratory typing, as relevant;
  • comment—discussion of the data presented.

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