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Article ; Online: Developing a prediction model to estimate the true burden of respiratory syncytial virus (RSV) in hospitalised children in Western Australia

Amanuel Tesfay Gebremedhin / Alexandra B. Hogan / Christopher C. Blyth / Kathryn Glass / Hannah C. Moore

Scientific Reports, Vol 12, Iss 1, Pp 1-

2022 Volume 12

Abstract: Abstract Respiratory syncytial virus (RSV) is a leading cause of childhood morbidity, however there is no systematic testing in children hospitalised with respiratory symptoms. Therefore, current RSV incidence likely underestimates the true burden. We ... ...

Abstract	Abstract Respiratory syncytial virus (RSV) is a leading cause of childhood morbidity, however there is no systematic testing in children hospitalised with respiratory symptoms. Therefore, current RSV incidence likely underestimates the true burden. We used probabilistically linked perinatal, hospital, and laboratory records of 321,825 children born in Western Australia (WA), 2000–2012. We generated a predictive model for RSV positivity in hospitalised children aged < 5 years. We applied the model to all hospitalisations in our population-based cohort to determine the true RSV incidence, and under-ascertainment fraction. The model’s predictive performance was determined using cross-validated area under the receiver operating characteristic (AUROC) curve. From 321,825 hospitalisations, 37,784 were tested for RSV (22.8% positive). Predictors of RSV positivity included younger admission age, male sex, non-Aboriginal ethnicity, a diagnosis of bronchiolitis and longer hospital stay. Our model showed good predictive accuracy (AUROC: 0.87). The respective sensitivity, specificity, positive predictive value and negative predictive values were 58.4%, 92.2%, 68.6% and 88.3%. The predicted incidence rates of hospitalised RSV for children aged < 3 months was 43.7/1000 child-years (95% CI 42.1–45.4) compared with 31.7/1000 child-years (95% CI 30.3–33.1) from laboratory-confirmed RSV admissions. Findings from our study suggest that the true burden of RSV may be 30–57% higher than current estimates.
Keywords	Medicine ; R ; Science ; Q
Subject code	360
Language	English
Publishing date	2022-01-01T00:00:00Z
Publisher	Nature Portfolio
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Optimising the use of linked administrative data for infectious diseases research in Australia

Hannah C Moore / Christopher C Blyth

Public Health Research & Practice, Vol 28, Iss

2018 Volume 2

Abstract: Infectious diseases remain a major cause of morbidity in Australia. A wealth of data exists in administrative datasets, which are linked through established data-linkage infrastructure in most Australian states and territories. These linkages can support ...

Abstract	Infectious diseases remain a major cause of morbidity in Australia. A wealth of data exists in administrative datasets, which are linked through established data-linkage infrastructure in most Australian states and territories. These linkages can support robust studies to investigate the burden of disease, the relative contribution of various aetiological agents to disease, and the effectiveness of population-based prevention policies – research that is critical to the success of current and future vaccination programs. At a recent symposium in Perth, epidemiologists, clinicians and policy makers in the infectious diseases field discussed the various benefits of, and barriers to, data-linkage research, with a focus on respiratory infection research. A number of issues and recommendations emerged. The demand for data-linkage projects is starting to outweigh the capabilities of exisiting data-linkage infrastructure. There is a need to further streamline processes relating to data access, increase data sharing and conduct nationally collaborative projects. Concerns about data security and sharing across jurisdictional borders can be addressed through multiple safe data solutions. Researchers need to do more to ensure that the benefits of linking datasets to answer policy-relevant questions are being realised for the benefit of community groups, government authorities, funding bodies and policy makers. Increased collaboration and engagement across all sectors can optimise the use of linked data to help reduce the burden of infectious diseases.
Keywords	Public aspects of medicine ; RA1-1270
Language	English
Publishing date	2018-06-01T00:00:00Z
Publisher	Sax Institute
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Impact of Rotavirus Vaccines on Gastroenteritis Hospitalizations in Western Australia

Parveen Fathima / Mark A Jones / Hannah C Moore / Christopher C Blyth / Robyn A Gibbs / Thomas L Snelling

Journal of Epidemiology, Vol 31, Iss 8, Pp 480-

A Time-series Analysis

2021 Volume 486

Abstract: Background: Rotavirus vaccination was introduced into the Australian National Immunisation Program in mid-2007. We aimed to assess the impact of the rotavirus vaccination program on the burden of hospitalizations associated with all-cause acute ... ...

Abstract	Background: Rotavirus vaccination was introduced into the Australian National Immunisation Program in mid-2007. We aimed to assess the impact of the rotavirus vaccination program on the burden of hospitalizations associated with all-cause acute gastroenteritis (including rotavirus gastroenteritis and non-rotavirus gastroenteritis) in the Aboriginal and non-Aboriginal population in Western Australia. Methods: We identified all hospital records, between July 2004 and June 2012, with a discharge diagnosis code for all-cause gastroenteritis. Age-specific hospitalization rates for rotavirus and non-rotavirus acute gastroenteritis before and after the introduction of the rotavirus vaccination program were compared. Interrupted time-series models were used to examine differences in the annual trends of all-cause gastroenteritis hospitalization between the two periods. Results: Between July 2004 and June 2012, there were a total of 106,974 all-cause gastroenteritis-coded hospitalizations (1,381 rotavirus-coded [15% among Aboriginal] and 105,593 non-rotavirus gastroenteritis-coded [7% among Aboriginal]). Following rotavirus vaccination introduction, significant reductions in rotavirus-coded hospitalization rates were observed in all children aged <5 years (up to 79% among non-Aboriginal and up to 66% among Aboriginal). Among adults aged ≥65 years, rotavirus-coded hospitalizations were 89% (95% confidence interval, 16–187%) higher in the rotavirus vaccination program period. The time-series analysis suggested reductions in all-cause gastroenteritis hospitalizations in the post-vaccination period among both vaccinated and unvaccinated (age-ineligible) children, with increases observed in adults aged ≥45 years. Conclusions: Rotavirus vaccination has been associated with a significant decline in gastroenteritis hospitalizations among children. The increase in the elderly requires further evaluation, including assessment of the cost-benefits of rotavirus vaccination in this population.
Keywords	rotavirus vaccine ; acute gastroenteritis ; vaccine impact ; hospitalizations ; time-series ; Medicine (General) ; R5-920
Subject code	333
Language	English
Publishing date	2021-08-01T00:00:00Z
Publisher	Japan Epidemiological Association
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Corrigendum to “Lower risk of multi-system Inflammatory Syndrome in Children (MIS-C) with the Omicron variant” [The Lancet Regional Health - Western Pacific 27 (2022) 100604]

Laura Lopez / David Burgner / Catherine Glover / Jeremy Carr / Julia Clark / Alison Boast / Nan Vasilunas / Brendan McMullan / Joshua R. Francis / Asha C. Bowen / Christopher C. Blyth / Kristine Macartney / Nigel W. Crawford / Emma Carey / Nicholas Wood / Philip N. Britton

The Lancet Regional Health. Western Pacific, Vol 35, Iss , Pp 100808- (2023)

2023

Keywords	Public aspects of medicine ; RA1-1270
Language	English
Publishing date	2023-06-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Using provider–parent strategies to improve influenza vaccination in children and adolescents with special risk medical conditions

Helen Marshall / Jennifer Couper / Christopher C Blyth / Nicholas Smith / Margaret Danchin / Andrew Kelly / Thomas R Sullivan / Mark Friswell / Andrew Tai / Jane Tuckerman / Kelly Harper / Jennifer Fereday / Richard Couper / Louise Flood

BMJ Open, Vol 12, Iss

a randomised controlled trial protocol

2022 Volume 2

Keywords	Medicine ; R
Language	English
Publishing date	2022-02-01T00:00:00Z
Publisher	BMJ Publishing Group
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Coronavax

Christopher C Blyth / Samantha Carlson / Lara McKenzie / Catherine Hughes / Paul Effler / Katie Attwell / Jordan Tchilingirian / Tauel Harper / Leah Roberts / Marco Rizzi / Darren Westphal / Valerie Swift

BMJ Open, Vol 11, Iss

preparing community and government for COVID-19 vaccination: a research protocol for a mixed methods social research project

2021 Volume 6

Abstract: Introduction Ahead of the implementation of a COVID-19 vaccination programme, the interdisciplinary Coronavax research team developed a multicomponent mixed methods project to support successful roll-out of the COVID-19 vaccine in Western Australia. This ...

Abstract	Introduction Ahead of the implementation of a COVID-19 vaccination programme, the interdisciplinary Coronavax research team developed a multicomponent mixed methods project to support successful roll-out of the COVID-19 vaccine in Western Australia. This project seeks to analyse community attitudes about COVID-19 vaccination, vaccine access and information needs. We also study how government incorporates research findings into the vaccination programme.Methods and analysis The Coronavax protocol employs an analytical social media study, and a qualitative study using in-depth interviews with purposively selected community groups. Participant groups currently include healthcare workers, aged care workers, first responders, adults aged 65+ years, adults aged 30–64 years, young adults aged 18–29 years, education workers, parents/guardians of infants and young children (<5 years), parents/guardians of children aged 5–18 years with comorbidities and parents/guardians who are hesitant about routine childhood vaccines. The project also includes two studies that track how Australian state and Commonwealth (federal) governments use the study findings. These are functional dialogues (translation and discussion exercises that are recorded and analysed) and evidence mapping of networks within government (which track how study findings are used).Ethics and dissemination Ethics approval has been granted by the Child and Adolescent Health Service Human Research Ethics Committee (HREC) and the University of Western Australia HREC. Study findings will be disseminated by a series of journal articles, reports to funders and stakeholders, and invited and peer-reviewed presentations.
Keywords	Medicine ; R
Subject code	306
Language	English
Publishing date	2021-06-01T00:00:00Z
Publisher	BMJ Publishing Group
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Levels of pneumococcal conjugate vaccine coverage and indirect protection against invasive pneumococcal disease and pneumonia hospitalisations in Australia

Jocelyn Chan / Heather F Gidding / Christopher C Blyth / Parveen Fathima / Sanjay Jayasinghe / Peter B McIntyre / Hannah C Moore / Kim Mulholland / Cattram D Nguyen / Ross Andrews / Fiona M Russell

PLoS Medicine, Vol 18, Iss 8, p e

An observational study.

2021 Volume 1003733

Abstract: Background There is limited empiric evidence on the coverage of pneumococcal conjugate vaccines (PCVs) required to generate substantial indirect protection. We investigate the association between population PCV coverage and indirect protection against ... ...

Abstract	Background There is limited empiric evidence on the coverage of pneumococcal conjugate vaccines (PCVs) required to generate substantial indirect protection. We investigate the association between population PCV coverage and indirect protection against invasive pneumococcal disease (IPD) and pneumonia hospitalisations among undervaccinated Australian children. Methods and findings Birth and vaccination records, IPD notifications, and hospitalisations were individually linked for children aged <5 years, born between 2001 and 2012 in 2 Australian states (New South Wales and Western Australia; 1.37 million children). Using Poisson regression models, we examined the association between PCV coverage, in small geographical units, and the incidence of (1) 7-valent PCV (PCV7)-type IPD; (2) all-cause pneumonia; and (3) pneumococcal and lobar pneumonia hospitalisation in undervaccinated children. Undervaccinated children received <2 doses of PCV at <12 months of age and no doses at ≥12 months of age. Potential confounding variables were selected for adjustment a priori with the assistance of a directed acyclic graph. There were strong inverse associations between PCV coverage and the incidence of PCV7-type IPD (adjusted incidence rate ratio [aIRR] 0.967, 95% confidence interval [CI] 0.958 to 0.975, p-value < 0.001), and pneumonia hospitalisations (all-cause pneumonia: aIRR 0.991 95% CI 0.990 to 0.994, p-value < 0.001) among undervaccinated children. Subgroup analyses for children <4 months old, urban, rural, and Indigenous populations showed similar trends, although effects were smaller for rural and Indigenous populations. Approximately 50% coverage of PCV7 among children <5 years of age was estimated to prevent up to 72.5% (95% CI 51.6 to 84.4) of PCV7-type IPD among undervaccinated children, while 90% coverage was estimated to prevent 95.2% (95% CI 89.4 to 97.8). The main limitations of this study include the potential for differential loss to follow-up, geographical misclassification of children ...
Keywords	Medicine ; R
Subject code	360
Language	English
Publishing date	2021-08-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Urinary tract infections in children

Jessica A. Ramsay / Steven Mascaro / Anita J. Campbell / David A. Foley / Ariel O. Mace / Paul Ingram / Meredith L. Borland / Christopher C. Blyth / Nicholas G. Larkins / Tim Robertson / Phoebe C. M. Williams / Thomas L. Snelling / Yue Wu

BMC Medical Research Methodology, Vol 22, Iss 1, Pp 1-

building a causal model-based decision support tool for diagnosis with domain knowledge and prospective data

2022 Volume 17

Abstract: Abstract Background Diagnosing urinary tract infections (UTIs) in children in the emergency department (ED) is challenging due to the variable clinical presentations and difficulties in obtaining a urine sample free from contamination. Clinicians need to ...

Abstract	Abstract Background Diagnosing urinary tract infections (UTIs) in children in the emergency department (ED) is challenging due to the variable clinical presentations and difficulties in obtaining a urine sample free from contamination. Clinicians need to weigh a range of observations to make timely diagnostic and management decisions, a difficult task to achieve without support due to the complex interactions among relevant factors. Directed acyclic graphs (DAG) and causal Bayesian networks (BN) offer a way to explicitly outline the underlying disease, contamination and diagnostic processes, and to further make quantitative inference on the event of interest thus serving as a tool for decision support. Methods We prospectively collected data on children present to ED with suspected UTIs. Through knowledge elicitation workshops and one-on-one meetings, a DAG was co-developed with clinical domain experts (the Expert DAG) to describe the causal relationships among variables relevant to paediatric UTIs. The Expert DAG was combined with prospective data and further domain knowledge to inform the development of an application-oriented BN (the Applied BN), designed to support the diagnosis of UTI. We assessed the performance of the Applied BN using quantitative and qualitative methods. Results We summarised patient background, clinical and laboratory characteristics of 431 episodes of suspected UTIs enrolled from May 2019 to November 2020. The Expert DAG was presented with a narrative description, elucidating how infection, specimen contamination and management pathways causally interact to form the complex picture of paediatric UTIs. Parameterised using prospective data and expert-elicited parameters, the Applied BN achieved an excellent and stable performance in predicting Escherichia coli culture results, with a mean area under the receiver operating characteristic curve of 0.86 and a mean log loss of 0.48 based on 10-fold cross-validation. The BN predictions were reviewed via a validation workshop, and we ...
Keywords	DAG ; Causal model ; Bayesian network ; Clinical decision support ; Urinary tract infection ; Medicine (General) ; R5-920
Subject code	650 ; 310
Language	English
Publishing date	2022-08-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Predicting the causative pathogen among children with pneumonia using a causal Bayesian network.

Yue Wu / Steven Mascaro / Mejbah Bhuiyan / Parveen Fathima / Ariel O Mace / Mark P Nicol / Peter C Richmond / Lea-Ann Kirkham / Michael Dymock / David A Foley / Charlie McLeod / Meredith L Borland / Andrew Martin / Phoebe C M Williams / Julie A Marsh / Thomas L Snelling / Christopher C Blyth

PLoS Computational Biology, Vol 19, Iss 3, p e

2023 Volume 1010967

Abstract: Background Pneumonia remains a leading cause of hospitalization and death among young children worldwide, and the diagnostic challenge of differentiating bacterial from non-bacterial pneumonia is the main driver of antibiotic use for treating pneumonia ... ...

Abstract	Background Pneumonia remains a leading cause of hospitalization and death among young children worldwide, and the diagnostic challenge of differentiating bacterial from non-bacterial pneumonia is the main driver of antibiotic use for treating pneumonia in children. Causal Bayesian networks (BNs) serve as powerful tools for this problem as they provide clear maps of probabilistic relationships between variables and produce results in an explainable way by incorporating both domain expert knowledge and numerical data. Methods We used domain expert knowledge and data in combination and iteratively, to construct, parameterise and validate a causal BN to predict causative pathogens for childhood pneumonia. Expert knowledge elicitation occurred through a series of group workshops, surveys and one-on-one meetings involving 6-8 experts from diverse domain areas. The model performance was evaluated based on both quantitative metrics and qualitative expert validation. Sensitivity analyses were conducted to investigate how the target output is influenced by varying key assumptions of a particularly high degree of uncertainty around data or domain expert knowledge. Results Designed to apply to a cohort of children with X-ray confirmed pneumonia who presented to a tertiary paediatric hospital in Australia, the resulting BN offers explainable and quantitative predictions on a range of variables of interest, including the diagnosis of bacterial pneumonia, detection of respiratory pathogens in the nasopharynx, and the clinical phenotype of a pneumonia episode. Satisfactory numeric performance has been achieved including an area under the receiver operating characteristic curve of 0.8 in predicting clinically-confirmed bacterial pneumonia with sensitivity 88% and specificity 66% given certain input scenarios (i.e., information that is available and entered into the model) and trade-off preferences (i.e., relative weightings of the consequences of false positive versus false negative predictions). We specifically highlight that a ...
Keywords	Biology (General) ; QH301-705.5
Subject code	006
Language	English
Publishing date	2023-03-01T00:00:00Z
Publisher	Public Library of Science (PLoS)
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Correction to

Jane Oliver / Elise Thielemans / Alissa McMinn / Ciara Baker / Philip N. Britton / Julia E. Clark / Helen S. Marshall / Christopher C. Blyth / Joshua Francis / Jim Buttery / Andrew C. Steer / Nigel W. Crawford / on behalf of the PAEDS investigators

BMC Public Health, Vol 21, Iss 1, Pp 1-

Invasive group A Streptococcus disease in Australian children: 2016 to 2018 – a descriptive cohort study

2021 Volume 1

Abstract: An amendment to this paper has been published and can be accessed via the original article. ...

Abstract	An amendment to this paper has been published and can be accessed via the original article.
Keywords	Public aspects of medicine ; RA1-1270
Language	English
Publishing date	2021-05-01T00:00:00Z
Publisher	BMC
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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