Background
Timely linkage of disease notifications to vaccination registries, hospitalisation records, and exposure event manifests underpins outbreak response, vaccine effectiveness (VE) estimation, and disease severity surveillance. Despite this need, few purpose-built tools exist for worldwide. We developed starling (v0.6.5), an open-source R package, to address this gap. The package supports linkage across multiple epidemiological contexts, including outbreak line-lists, flight manifest data, vaccination registries, and hospitalisation records, enabling a range of surveillance outputs from case ascertainment to real-time VE monitoring.

Methods
starling builds on the Fellegi-Sunter probabilistic record linkage framework — formalised in 1969 and validated extensively across epidemiological and administrative data applications over more than five decades — augmented with machine learning-enhanced blocking and similarity scoring. Core functions include clean_the_nest() for data standardisation, murmuration() for linkage, preening() for creating analysis-ready variables, molting()/homing() for de-identification, and plumage() for comorbidity coding (available at https://cran.r-project.org/web/packages/starling/index.html). Validation was performed by linking a measles outbreak dataset (n=99) arising from a Sunshine Coast outbreak between October and November 2025, to Australian Immunisation Register records, using manually verified vaccination records as the gold standard.

Results
starling achieved sensitivity of 97.3%, specificity of 91.7%, positive predictive value (PPV) of 97.3%, negative predictive value (NPV) of 91.7%, and overall accuracy of 96.0%. In 93.9% of cases, the number of vaccine doses identified exactly matched the manual record. In 3.0% of records, starling attributed more doses than were manually recorded — likely due to spurious linkage of a record from a different individual with similar identifying characteristics. In a further 3.0%, one or more genuine doses were not retrieved, reflecting insufficient overlap in identifying variables between datasets. Overall, two persons with confirmed vaccination records (2.0%) were misclassified as unvaccinated (false negatives), and two of 75 persons deemed vaccinated had no corresponding manual evidence (false positives, 2.7%).

Conclusions
starling demonstrates high accuracy for operational outbreak data linkage, with low rates of missed linkages and false attributions. Its flexible architecture supports broader public health surveillance applications including real-time VE monitoring, disease severity assessment, and flight manifest linkage for exposure investigations. The package is freely available on CRAN (https://cran.r-project.org/web/packages/starling/index.html).

RSV, COVID-19 and Influenza are key vaccine-preventable causes of acute respiratory infections in children, with young infants aged <6 months considered to be at high risk of adverse outcomes, including hospitalisation and ICU admission. This study aimed to compare the epidemiology and severity of RSV, COVID-19 and Influenza among Australian infants aged <6 months.

Using data from the PAEDS-FluCAN surveillance networks (1 January 2022 to 31 December 2025; all three viruses under surveillance 2024-2025), we identified hospitalised infants with laboratory-confirmed RSV, COVID-19 or Influenza across seven sentinel hospitals. Descriptive analyses examined time trends in case frequency, age distributions and severity, stratified by medical comorbidities and admission year. Logistic regression adjusted for age group and sex was used to assess the association of medical comorbidities with ICU admission.

PAEDS-FluCAN identified a total of 1,549, 596, and 2,344 cases of RSV, Influenza and COVID-19, respectively. RSV and Influenza showed strong winter-centric seasonality, whereas COVID-19 showed both winter activity and additional spring–summer waves. RSV accounted for the greatest hospitalisation burden in 2024 and 2025 (1,583 vs 367 Influenza and 705 COVID-19). RSV and COVID-19 admissions were concentrated in early infancy; infants <2 months accounted for 43% of admissions for each, compared to 33% for influenza. RSV had the highest ICU admission rate (10.1% vs. 7.6% Influenza vs. 4.5% COVID-19; p<0.0001). The presence of medical comorbidities was significantly associated with ICU admission across all conditions, with adjusted odds ratios of 2.38 (95% CI 1.54–3.60) for RSV, 8.85 (95% CI 4.34–18.5) for influenza, and 5.24 (95% CI 3.47–7.94) for COVID-19.

RSV was the leading cause of severe respiratory hospitalisation in infants aged <6 months, with strong seasonality and high ICU utilisation. Future actions should prioritise optimising maternal RSV vaccination and infant monoclonal antibody strategies and risk-stratified pathways for infants with comorbidities.

Background and Aim: People experiencing homelessness experience higher rates of communicable and vaccine-preventable diseases (VPDs) yet remain largely excluded from routine immunisation surveillance. Barriers to access, outreach, and documentation were highlighted during the COVID-19 pandemic and continue to limit understanding of vaccine coverage and disease burden in this population. This study aims to establish and apply a linked administrative data framework to quantify immunisation coverage and VPD burden among people experiencing homelessness in Western Australia, with an initial focus on influenza and COVID-19.

Methods and Analysis: We have constructed a large, longitudinal cohort using linked primary care, hospital, emergency department, and mortality data from the Home2Health program. Probabilistic linkage methods have been used to link these administrative datasets for the period 2010 - 2026. Existing data support preliminary analyses of influenza and COVID-19 vaccination coverage delivered in primary care and notifiable vaccine preventable disease data from pathology results. The dataset is being strengthened through linkage to the Australian Immunisation Register (AIR) and the WA Notifiable Infectious Disease Database (WANIDD) to enable comprehensive assessment of historic vaccinations and notifiable VPDs. Planned analyses include descriptive coverage estimates, temporal trends, predictors of uptake, missed opportunities for vaccination, disease incidence, hospitalisation, and vaccine effectiveness where feasible.

Outcomes: Primary outcomes to be presented include cohort size and characteristics, linkage methods, success and data completeness, and preliminary estimates of influenza and COVID-19 vaccination coverage. Secondary outcomes include burden of disease estimation (infection and hospitalisation) and vaccine effectiveness analyses.

Conclusion and Future actions: This study explores the feasibility of using linked administrative data to support immunisation and disease surveillance in a structurally excluded population. Ongoing analyses incorporating AIR and WANIDD data will inform equitable vaccine policy, service delivery strategies, and future linkage-based research in vulnerable populations.

Paediatric inflammatory multi-system syndrome temporally associated with SARS-CoV-2 (PIMS-TS) is a rare but severe complication of SARS-CoV-2 infection in children. PIMS-TS epidemiology has evolved since its first description in 2020, including reduced severity and declining incidence, or in some locations, apparent disappearance of the syndrome. We analysed national surveillance data to describe the epidemiology of PIMS-TS in Australia.

Paediatric Active Enhanced Disease Surveillance (PAEDS) network surveillance nurses identified PIMS-TS cases from eight sentinel hospitals across six Australian states and territories from March 2020 to December 2025. SARS-CoV-2 infections were assigned to variant periods based on the dominant strain 28 days before case symptom onset. Clinical characteristics, severity, and treatments were compared across variants and between age groups (<5 and ≥5years), excluding cases with missing data. Sex‑adjusted logistic regression was used to estimate the association of Kawasaki disease (KD)‑like disease features with age.

PAEDS identified a total of 213 PIMS-TS cases in Australia, with frequency peaking at 109 cases during the early Omicron variant period (December 2021 to April 2022) and declining subsequently (70 cases May 2022 to December 2025). PIMS‑TS presented after a median lag of 27.5 days(IQR:20–36.75) from SARS-CoV-2 test detection. Male predominance was observed (60%); median age of cases was 7.8 years (IQR:4.7–10.8). Rash, conjunctival injection, abdominal pain, and vomiting were the most frequently reported clinical features (72%,68%,67%,67%). Children <5 years had higher odds of KD–like features compared with older children (aOR 2.5;95%CI 1.4–4.8; p=0.004). 29% of PIMS TS cases required ICU admission; there were no deaths. Clinical features and severity were not significantly different across variant periods.

PIMS-TS cases continued to be identified in Australia in 2025 but were considerably less frequent than in prior years. Severity and clinical features have remained stable across variant periods. PAEDS has maintained high-quality surveillance across the pandemic. There is an ongoing need for awareness, timely recognition, and management of this uncommon but severe complication of COVID-19 in children.

Background and Aim
Over the past 25 years, the Northern Territory (NT) has experienced an epidemiological transition toward chronic and ageing-associated conditions, while communicable diseases such as pneumonia, influenza, and skin infections continue to contribute substantially to hospital morbidity. Hospital separations provide critical surveillance data to monitor disease burden and guide prevention strategies. This study examines long-term trends in communicable disease morbidity using NT public hospital data from 1999-2024, highlighting both progress and remaining opportunities to strengthen health equity.
Methods and Analysis
A retrospective analysis of NT public hospital separation data from 1999–2024 was undertaken. Principal diagnoses were classified using ICD-10-AM and analysed by age, sex, and Indigenous status. Age-standardised hospitalisation rates were calculated using Australian Bureau of Statistics population estimates. Communicable disease categories examined included respiratory infections, skin and soft tissue infections, gastrointestinal infections, and influenza-related admissions.
Outcomes
Communicable diseases remained among the ten leading causes of hospitalisation across all age groups. Pneumonia was the leading cause in 1999 (ASR 7.1 per 1,000) and, despite a decline over time, continued to contribute substantially to hospital morbidity in 2024, together with influenza and other acute respiratory infections. Skin infections such as cellulitis increased markedly over the period, becoming the second leading cause of hospitalisation by 2024 (ASR 5.7 per 1,000). Infectious gastroenteritis and viral respiratory infections remained major causes of paediatric admissions. Aboriginal Territorians experienced substantially higher communicable disease hospitalisation rates, with pneumonia rates exceeding 11 per 1,000 in 2024 compared with significantly lower rates among non-Aboriginal residents. These patterns suggest ongoing transmission risks, environmental exposures, and barriers to preventive care.
Conclusion and Future actions
The gains achieved in declining communicable disease morbidity reflect strengths in preventive public health action and immunisation. Continued efforts in vaccination coverage, early detection, and culturally appropriate, community-led prevention strategies are essential to sustain improvements and close remaining gaps.

Background and Aim: Group A Streptococcus is a pathogen responsible for a wide spectrum of diseases, including life-threatening invasive conditions (iGAS). Globally, iGAS is recognised as one of the top 10 infectious causes of mortality. We aimed to describe the epidemiology and outcomes of iGAS in Northern Queensland, Australia.
Methods and Analysis: Age and sex-standardized incidence rates, potential risk factors for the disease and outcomes, spatial distribution, and disease burden were analysed using a linked hospital data spanning for 21 years.
Outcomes: 933 iGAS events were identified among 870 individuals. The mean age was 45 years (SD = 24.3). Incidence increased over time, and the highest burden was in infants and older adults. Males had a 31% higher incidence than females (IRR = 1.31, 95% CI: 1.13–1.52), and Indigenous individuals had a 9.3-fold higher incidence than non-Indigenous individuals (IRR = 9.33, 95% CI: 8.17–10.7). Sepsis was the most common diagnosis (60.5%). Streptococcal toxic shock syndrome (1.07%) and necrotising fasciitis (3.11%) were more frequent among non-Indigenous individuals. Spatial analysis demonstrated significant geographical clustering (Moran’s I = 0.19, z = 3.45, p = 0.0003).
There were 45 deaths (case fatality rate, 4.8%) and 219 (23%) intensive care unit admissions. Most deaths were attributed to sepsis (80%) with necrotising fasciitis (18%) and septic shock (13.3%) also contributing. Competing Risks Regression showed higher mortality among individuals with renal failure (SHR = 3.3; 95% CI: 1.54-7.08), and non-Indigenous individuals (SHR = 2.5; 95% CI: 1.3–4.9). The total disability-adjusted life years attributable to iGAS was 1,375 years.
Conclusion and Future actions: iGAS incidence is rising in Northern Queensland, particularly among Indigenous populations, while mortality is higher among non-Indigenous individuals. These findings highlight the need for further investigation and targeted public health strategies.

Background and Aim: A major challenge in caring for children with community-acquired pneumonia (CAP) complicated by pleural empyema is that traditional culture-based methods fail to identify the causative organism in >75% of cases, preventing optimal targeted antibiotic therapy for individual patients and limiting our understanding of aetiology and vaccine impact. We developed a molecular assay targeting the most common bacterial causes of paediatric empyema which outperforms culture 3.8-fold overall and 8.3-fold for pneumococcus. We describe the aetiology of paediatric empyema in Victoria, Australia, and assess the early impact on serotypes of a 13-valent pneumococcal conjugate vaccine (PCV13) schedule change from 3+0 to 2+1.
Methods and Analysis: Pleural fluid and upper respiratory tract swabs were collected from 142 children with CAP and pleural empyema at The Royal Children’s Hospital (May 2019–September 2025, “2+1 era”). Samples underwent DNA extraction and qPCR to identify bacteria and viruses. Pneumococcal-positive samples were serotyped by TaqMan Array. The schedule change was evaluated by comparing serotypes in the 2+1 era with previously published data (“3+0 era”).
Outcomes: The median age was 3.9 years (IQR 2.2-6.0) with most children (92.3%) fully PCV13 vaccinated. A pathogen was identified in 89.4% of children, most commonly pneumococcus (68.3%), followed by Streptococcus pyogenes (21.8%). Bacterial co-detection occurred in 11 children (7.7%). The most common pneumococcal serotypes were 3 (75.0%) and 19F (12.5%). The most common viruses detected from swabs (n=75) were rhinovirus (21.3%), RSV (10.7%), and influenza A (5.3%). From the 3+0 to the 2+1 era, serotype 3 prevalence remained similar, whereas serotype 19F increased (1.9% vs 12.5%, p=0.001).
Conclusions and Future actions: Empyema was primarily caused by pneumococcal serotype 3, with 19F increasing despite high PCV13 uptake. Routine molecular testing could improve clinical care and understanding of vaccine impact. The study remains ongoing, with future evaluation planned to assess PCV20’s impact following its introduction to the National Immunisation Program in September 2025.