The reference laboratories of the Australian Meningococcal Surveillance Programme (AMSP) report data on the number of cases of invasive meningococcal disease (IMD) confirmed by laboratory testing using culture and molecular based techniques. Data contained in quarterly reports are restricted to a description of case numbers of IMD by jurisdiction and serogroup, where known. A full analysis of laboratory confirmations of IMD in each calendar year are contained in the AMSP annual reports.

This is the eighty-first epidemiological report for coronavirus disease 2019 (COVID-19), reported in Australia as at 23:59 Australian Eastern Daylight Time [AEST] 19 November 2023. It includes data on COVID-19 cases diagnosed in Australia.

The Australian National Neisseria Network (NNN) comprises reference laboratories in each state and territory that report data on antimicrobial susceptibility testing to an agreed group of antimicrobial agents for the Australian Gonococcal Surveillance Programme (AGSP). The AGSP data are presented quarterly in tabulated form, as well as in the AGSP annual report. This report presents national gonococcal antimicrobial resistance surveillance data from 1 April to 30 June 2023.

From 1 January to 31 December 2022, fifty-five institutions across Australia participated in the Australian Staphylococcus aureus Surveillance Outcome Program (ASSOP). The aim of ASSOP 2022 was to determine the proportion of Staphylococcus aureus bacteraemia (SAB) isolates in Australia that were antimicrobial resistant, with particular emphasis on susceptibility to methicillin and on characterisation of the molecular epidemiology of the methicillin-resistant isolates. A total of 3,214 SAB episodes were reported, of which 77.5% were community-onset. Overall, 15.0% of S. aureus were methicillin resistant. The 30-day all-cause mortality associated with methicillin-resistant SAB was 21.4%, which was significantly different to the 16.8% all-cause mortality associated with methicillin-susceptible SAB (p = 0.02). With the exception of the β-lactams and erythromycin, antimicrobial resistance in methicillin-susceptible S. aureus was rare. However, in addition to the β-lactams, approximately 31% of methicillin-resistant S. aureus (MRSA) were resistant to ciprofloxacin; 30% to erythromycin; 13% to tetracycline; 11% to gentamicin; and 2% to co-trimoxazole. One MRSA isolate, with a daptomycin MIC of 1.5 mg/L, harboured the A302V mprF and A23V cls2 mutations. When applying the European Committee on Antimicrobial Susceptibility Testing (EUCAST) breakpoints, teicoplanin resistance was detected in one MRSA isolate. Resistance to vancomycin or linezolid was not detected. Resistance to non-β-lactam antimicrobials was largely attributable to the healthcare-associated MRSA (HA-MRSA) clone ST22-IV [2B] (EMRSA-15), and to the community-associated MRSA (CA-MRSA) clone ST45-V [5C2&5] which has acquired resistance to multiple antimicrobials including ciprofloxacin, clindamycin, erythromycin, gentamicin, and tetracycline. The ST22-IV [2B] (EMRSA-15) clone is the predominant HA-MRSA clone in Australia. Nonetheless, 86% of methicillin-resistant SAB episodes were due to CA-MRSA clones. Although polyclonal, approximately 72% of CA-MRSA clones were characterised as ST93-IV [2B] (Queensland clone); ST5-IV [2B]; ST45-V [5C2&5]; ST1-IV [2B]; ST30-IV [2B]; ST97-IV [2B]; ST953-IV [2B]; and ST8-IV [2B]. As CA-MRSA is well established in the Australian community, it is important to monitor antimicrobial resistance patterns in community- and healthcare-associated SAB as this information will guide therapeutic practices in treating S. aureus bacteraemia.

The reference laboratories of the National Neisseria Network, Australia report data on invasive meningococcal disease (IMD) cases confirmed by culture and/or molecular techniques for the Australian Meningococcal Surveillance Programme (AMSP). Culture-positive cases and molecular-based diagnoses are defined as IMD by the Communicable Diseases Network Australia National Guidelines for Public Health Units.1 Data contained in the quarterly reports are restricted to a description of the number of cases by jurisdiction and serogroup, when known. Some minor corrections to data in Table 1 may be made in subsequent reports if additional data are received. IMD notifications in Australia in the first quarter of 2023 were greater than in the corresponding period in 2022 but still below the 36 IMD cases reported in quarter one of 2019 (prior to the SARS-CoV-2 pandemic).2 Notably, the predominance of N. meningitidis serogroup B (MenB) IMD continued in the first quarter of 2023 (21/23, 91.3% of notifications), showing an increase from 84% in the fourth quarter of 2022.3 In contrast, between 2019 and 2021, 50–62% of IMD was attributable to MenB.4 A full analysis of laboratory-confirmed cases of IMD in each calendar year is contained in the AMSP annual report published in Communicable Diseases Intelligence.

Australia's goal of eliminating hepatitis C by 2030 requires increases in uptake of and access to testing and treatment. As hepatitis C is a notifiable condition, health departments have access to information about people exposed to the hepatitis C virus (HCV), including the details of notifying clinicians who ordered their diagnostic pathology tests. Hepatitis C RNA testing confirms active infection that requires treatment, whereas a positive antibody test result only indicates prior exposure to the virus. We undertook a pilot project in Queensland to follow up hepatitis C notifications with clinicians, aiming to increase HCV-RNA testing and treatment uptake. For all individuals with a first-time hepatitis C notification in Queensland between 3 November 2020 and 28 May 2021, we sought information regarding hepatitis C RNA testing from laboratories, excluding those cases diagnosed in prisons. Cases who did not have RNA testing identified as part of or after their initial diagnostic tests were followed up via their notifying clinician. Interviews with selected clinicians were undertaken to improve our understanding of the follow-up process. There were 769 new hepatitis C notifications during our study period: 244 had no subsequent RNA test identified and were followed up for this study. Of these, 134 cases were lost to follow-up; 26 were already being effectively case managed; 22 reported previous treatment and no further risk; and 62 were eligible for HCV-RNA testing. Twenty-six cases subsequently started hepatitis C treatment. Thirty-four percent of notifications that required follow-up resulted from testing initially requested in hospital settings. Following up hepatitis C notifications can result in increased treatment rates; however, the process was resource-intensive and often failed to result in further contact between clinicians and patients. Our findings also highlight the importance of supporting better continuity of care between hospitals and community settings.

For 30 years the Australian Paediatric Surveillance Unit (APSU) has conducted national surveillance of rare communicable diseases and rare complications of communicable diseases. In this report, we describe the results of thirteen such studies surveyed by the APSU in 2022, including reported case numbers and incidence estimates, demographics, clinical features, management and short-term outcomes. Conditions described are: acute flaccid paralysis (AFP); congenital cytomegalovirus (cCMV); neonatal and infant herpes simplex virus (HSV) infection; perinatal exposure to human immunodeficiency virus (HIV) and paediatric HIV infection; severe complications of influenza; juvenile-onset recurrent respiratory papillomatosis (JoRRP); congenital rubella infection/syndrome; congenital varicella syndrome (CVS) and neonatal varicella infection (NVI); and the new conditions dengue; Q fever; and severe acute hepatitis. In 2022, cases of severe complications of influenza were reported to the APSU for the first time since 2019. This likely reflects the easing of government-mandated restrictions imposed in 2020-2021 to curb the transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) and the re-emergence of a range of infectious diseases. As previously, AFP surveillance by the APSU contributed to Australia achieving a minimum target incidence of one AFP case per 105 children aged less than 15 years. Cases of JoRRP and NVI were reported in 2022. This indicates potential gaps in human papillomavirus (HPV) and varicella vaccination coverage respectively, especially in high-risk groups such as young migrant and refugee women of childbearing age from countries without universal vaccination programs. Paediatric HIV case numbers resulting from mother-to-child-transmission (MTCT) of HIV remain low in Australia due to use of effective intervention strategies. However, there has been an increase in the number of imported cases of HIV in children (mainly perinatally-acquired) from countries with a high HIV prevalence. Without effective vaccines, there has been no decline in the incidence of congenital CMV and neonatal HSV, indicating the importance of early identification and management to reduce morbidity and mortality. The first cases of dengue, Q fever and severe acute hepatitis were received by APSU in 2022, including two cases of acute hepatitis in which aetiology has not been confirmed to date. The APSU has an important ongoing role in monitoring rare childhood infections.

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FluTracking provided evidence for an early, long, but moderate influenza season in the Australian community compared to prior years. Influenza-like illness (ILI) activity in 2019 peaked earlier (week ending 16 June) than any season on record in FluTracking data. ILI attack rates were above average early in the 2019 season (peak of 2.2%), and the duration of peak activity was longer than most prior years. However, ILI attack rates were lower than the five-year average in the latter half of the season. FluTracking participants reported higher vaccination coverage in 2019 (73.3%) compared with 2018 (65.7%), with the most notable increase in children aged less than five years (69.3% in 2019, compared to 55.6% in 2018). The total 2019 count of laboratory notifications (312,945) was higher than prior years (2007 onwards), and the peak weekly count of 18,429 notifications in 2019 was also higher than all prior years, except 2017. FluTracking makes a comparison to another surveillance system each year. The peak weekly percentage of calls to HealthDirect that were influenza-related was higher in 2019 (12.8%) than for 2014-2018 (range of 8.2-11.4% for peak week of activity each year). FluTracking participants reported a 2.5 times increase in influenza testing from 2018 to 2019 and a 1.5 times increase from 2017. Although 2019 was of higher activity and severity than 2018, Flutracking data indicates that 2019 was a lower activity and severity season than 2017, and notifications and influenza-related calls were heightened by increased community concern and testing.

The Licence does not cover, and there is no permission given for, use of any of the following material found in this publication (if any): • the Commonwealth Coat of Arms (by way of information, the terms under which the Coat of Arms may be used can be found at www.itsanhonour.gov.au); • any logos (including the Department of Health and Aged Care's logo) and trademarks; • any photographs and images; • any signatures; and • any material belonging to third parties.