Vaccine Preventable Diseases in Australia, 2005 to 2007

Vaccine preventable diseases data

Page last updated: 24 December 2010

Three main sources of routinely collected data were used for this surveillance report on vaccine preventable diseases in Australia. Disease notification data were obtained from the Office of Health Protection’s NNDSS; hospitalisation data were from the Australian Institute of Health and Welfare (AIHW) National Hospital Morbidity Database; and mortality data were from the AIHW National Mortality Database (unpublished data).

For a recent analysis of vaccine preventable diseases surveillance data and vaccination coverage focusing on Indigenous Australians, please refer to the report Vaccine preventable diseases and vaccination coverage in Aboriginal and Torres Strait Islander people, Australia, 2003 to 2006.1


The NNDSS was established in its current form in 1991, and includes de-identified information about cases of vaccine preventable diseases reported by state and territory authorities in Australia. Each of the eight jurisdictional health departments collect notifications of communicable diseases under their respective public health legislation. Prior to September 2007, there were no national legislative provisions for jurisdictions to report to NNDSS, although all jurisdictions voluntarily did so, with de-identified data electronically renewed daily or several times a week from jurisdictions as of 2007. In September 2007, the National Health Security Act 20072 received royal assent. This Act provides a legislative basis for and authorises the exchange of health information between jurisdictions and the Commonwealth, and includes the establishment of the National Notifiable Disease List.3 The National Health Security Agreement4 that followed, which was signed by Health Ministers in April 2008, established operational arrangements to formalise and enhance existing surveillance and reporting systems.5 Data quality of the NNDSS is continually monitored by the Office of Health Protection and the National Surveillance Committee (NSC), a jurisdictional committee comprised of surveillance and data managers. There is a continual process of reviewing the national consistency of communicable disease surveillance on a daily, fortnightly and quarterly basis.

Historically, state and territory notification criteria were based on the National Health and Medical Research Council (NHMRC) surveillance case definitions.6 However, application of these definitions differed among jurisdictions, with some using the 1994 NHMRC case definitions (e.g. South Australia and Western Australia) and others using their own modified definitions (e.g. New South Wales and Victoria). (See also Appendix 6.6 for case definitions in use prior to 2004.) In September 2003, a new set of national case definitions for notifiable diseases reported to NNDSS was endorsed by the Communicable Diseases Network Australia,7 with nearly all jurisdictions implementing the new definitions in January 2004 (New South Wales commenced in August 2004). Invasive pneumococcal disease and laboratory-confirmed influenza became notifiable to the NNDSS in 2001. Varicella and herpes zoster became nationally notifiable in 2006 in all Australian jurisdictions except New South Wales. However, data was not received from all notifying states until early 2008. Rotavirus infection is not notifiable to NNDSS, although it became notifiable in the Northern Territory in 1994, and laboratory notifiable in Queensland and Western Australia in 2005 and 2006, respectively.

The data collected by the NNDSS are frequently updated by jurisdictions. For this report, data extracted from the NNDSS as at 4 August 2008 were examined (except for pneumococcal disease for which data extracted on 5 December 2008 were analysed). Data were checked and cleaned where apparent errors were detected through consultation with appropriate surveillance staff in states and territories. There would be minor variations with NNDSS data referred to in the 2006 and 2007 Australia’s Notifiable Disease Status reports (the annual reports of the NNDSS) and the biennial AIHW publication Australia’s Health 2008,5,8,9 since different data versions were used for analysis. Disease notification data for cases with a date of diagnosis between 1 January 2006 and 31 December 2007 (2 years) are included in this report. Notifications with onset dates between 1 January 1993 and 31 December 2005 have been reported previously.10–13 It should be noted that historical notification data included in this report have been updated from previous reports.

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In this report, notification data are reported and presented by the ‘date of diagnosis’. Previous reports on data prior to 2005 analysed notification data by date of onset (if the date of onset from the clinical history was collected and was available), or the specimen collection date for laboratory-confirmed cases. As of mid 2005, a ‘date of diagnosis’ field was generated for every NNDSS record. For each notification record, a date of diagnosis is derived from the date of onset, or, where not supplied, the earliest date recorded among these fields: date of specimen, date of notification, or date when the notification was received (the only mandatory date field). This algorithm applies to all diseases collected by the NNDSS except for ‘hepatitis B, unspecified’ and ‘hepatitis C, unspecified’ (not included in this report), where the onset date would not contribute to assigning the date of diagnosis.

The variables extracted for analysis for every vaccine preventable disease in this report are: the disease, the date of diagnosis, age at onset, sex, and state or territory of residence. Comments on other fields, including their completeness, are made where relevant to a specific disease. These fields include whether the case met the definition of a confirmed case, the serogroup/serotype of the causal organism, the vaccination status (and its validation status) of the case, and whether mortality was reported.


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 (the process by which an admitted patient completes an episode of care by being discharged, dying, transferring to another hospital, or changing type of care).14 The two most recent (financial) years for which hospitalisation data are available (1 July 2005 to 30 June 2007) are included in this report. Cases with hospital separation dates between 1 July 1993 and 30 June 2005 (12 years) have been reported previously.10–13 For trend analysis, this report presents some of these previously analysed historical data for years prior to and including 2004/2005 together with updated data for the 2 years 2005/2006 and 2006/2007.

As hospitalisation data for the reporting periods are defined by the date of separation of a hospitalisation episode, analyses by most variables such as age and sex are grouped by the financial year within which the hospital separation occurred. The exception is with analysis of seasonal trends by month (secular trend), when available data (based on hospital separation dates within the reporting period) are presented and reported by the month of hospital admission (as distinct from hospital separation).

Data for each reported disease are extracted based on the International Statistical Classification of Diseases and Related Health Problems, 10th Revision, Australian Modification (ICD-10-AM). Eligible records of hospital separations include those with the code(s) of interest listed as the principal diagnosis (the diagnosis established after study to be chiefly responsible for occasioning an episode of admitted patient care, an episode of residential care or attendance at a health care establishment) or as any other diagnosis for that episode of hospitalisation. The proportion of hospital separations where the disease of interest has been coded as the principal diagnosis is reported for each disease. For hepatitis B disease, only hospitalisations with acute hepatitis B coded as the principal diagnosis are included, consistent with the approach taken in previous reports. Where the ICD-10-AM code for a disease specifies a severe manifestation of the disease (e.g. measles encephalitis), the number and type of these episodes with these diagnoses are reported as complications of the disease.

The variables extracted for analysis include: date of admission, financial year of separation, age on admission, sex, state or territory of residence, length of stay (LOS), and diagnosis (principal and other diagnoses – up to 31 diagnoses could be recorded for each admission) coded using the relevant edition of ICD-10-AM for the collection period. In addition, the mode of separation (whether death was the outcome of that hospitalisation episode) has been specifically analysed for hospitalisations due to meningococcal disease, as this measure is considered to be an important indicator of this disease. Hospitalisation episodes with fatal outcome are also reported as supplementary information for a few other diseases (e.g. invasive pneumococcal disease). For hospitalisation records where data on the jurisdiction of residence are missing, the jurisdiction in which the hospitalisation occurred is used to replace the jurisdiction of residence datum. This substitution was required in 0.6% (214/35,859) of all the records of hospitalisation in 2005/2006 and 2006/2007 analysed for this report.

Appendix 6.3 summarises the hospitalisation data by disease, year and jurisdiction. Regarding hospitalisation data in this publication, all Australian jurisdictions except New South Wales, Queensland and South Australia have required suppression for all cells with counts of less than five (but non-zero). In these tables, the exact count in each of these cells has been replaced by the symbol ‘<5’ for these jurisdictions. Data in additional selected cells have to be suppressed (denoted ‘n.p.’) to prevent back calculation (by subtraction from row or column totals) of the suppressed counts of data from the five jurisdictions.

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Death data were obtained from the AIHW National 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 death data published by the ABS 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, this report only analyses records in which the disease of interest is recorded as the underlying cause of death, consistent with previous reports. Deaths analysed in this report are the deaths registered in the two calendar years of 2005 and 2006 (not necessarily the year in which the death occurred). The variables extracted for each death record are: underlying cause of death, age, year death was reported, sex, and state or territory in which the death was recorded.

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All rates are calculated using the mid-year estimated resident populations, released by the Australian Bureau of Statistics in December 2007, as population denominator. 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. The reported rate estimates for the populations not stratified by age groups (i.e. all ages together) are crude rates that have not been age-standardised.

For hospitalisation data, the mid-year population estimate for the first half of the financial year is used as the denominator; for example, the 2005 mid-year population estimate is used to calculate rates for 2005/2006. (This is consistent with previous reports in this series.) For notification and death data, the mid-year population estimates for the corresponding calendar year are used as the denominator population. Averages are calculated for rates of notifications and hospitalisations and for bed-days of hospitalisation episodes per year. The median (rather than average) and range are used to describe the distribution of notifications and hospitalisations per month, and the length of stay per hospitalisation episode, as these data are not normally distributed. Where there are ≤3 hospitalisation episodes recorded per age/disease category in the national hospitalisation data, the median length of stay data are not published (denoted by ‘n.p.’).

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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 – hospitalisation bed days; length of stay of hospitalisation; proportion of hospitalisations with disease attributed as the principal diagnosis over any one of the diagnoses; complications; mortality; by age categories standardised across different reported diseases, as in previous reports
  • age and sex distribution – by age groups and sex as relevant for each particular disease
  • geographical distribution – by state or territory by year, as shown in Appendices 6.2 and 6.3; for hospitalisation data, some jurisdictions required suppression of hospitalisation data for those cells where there were fewer than 5 cases
  • vaccination status of notified cases and laboratory serogroup/serotype information, as relevant
  • comments – commentary and discussion on the presented data

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