ORCID Profile
0000-0001-6515-827X
Current Organisations
Monash University
,
Clemson University
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Nanomaterials | Biomaterials | Biomedical Engineering | Nanobiotechnology |
Expanding Knowledge in the Chemical Sciences | Expanding Knowledge in the Biological Sciences | Expanding Knowledge in Technology
Publisher: Elsevier BV
Date: 12-2021
Publisher: PeerJ
Date: 13-06-2017
DOI: 10.7287/PEERJ.PREPRINTS.3022V1
Abstract: Households are an important location for the transmission of communicable diseases. Social contact between household members is typically more frequent, of greater intensity, and is more likely to involve people of different age groups than contact occurring in the general community. Understanding household structure in different populations is therefore fundamental to explaining patterns of disease transmission in these populations. Indigenous populations in Australia tend to live in larger households than non Indigenous populations, but limited data is available on the structure of these households, and how they differ between remote and urban communities. We have developed a novel approach to the collection of household structure data, suitable for use in a variety of contexts, which provides a detailed view of age,gender, and room occupancy patterns in remote and urban Australian Indigenous households. Here we report analysis of data collected using this tool, which quantifies the extent of crowding in Indigenous households, particularly in remote areas. We use this data to generate matrices of age-specific contact rates, as used by mathematical models of infectious disease transmission. To demonstrate the impact of household structure, we use a mathematical model to simulate an influenza-like illness in different populations. Our simulations suggest that outbreaks in remote populations are likely to spread more rapidly and to a greater extent than outbreaks in non-Indigenous populations.
Publisher: Elsevier BV
Date: 03-2018
DOI: 10.1016/J.MBS.2018.08.007
Abstract: Infections with Sarcoptes scabiei, or scabies, remain common in many disadvantaged populations. Mass drug administration (MDA) has been used in such settings to achieve a rapid reduction in infection and transmission, with the goal of eliminating the public health burden of scabies. While prevalence has been observed to fall substantially following such an intervention, in some instances resurgence of infection to baseline levels has occurred over several years. To explore the biology underpinning this phenomenon, we have developed a theoretical model of scabies life-cycle and transmission dynamics in a homogeneously mixing population, and simulate the impact of mass drug treatment strategies acting on egg and mite life cycle stages (ovicidal) or mites alone (non-ovicidal). In order to investigate the dynamics of the system, we first define and calculate the optimal interval between treatment doses. We calculate the probability of eradication as a function of the number of optimally-timed successive treatment doses and the number of years over which a program is run. For the non-ovicidal intervention, we first show that at least two optimally-timed doses are required to achieve eradication. We then demonstrate that while more doses over a small number of years provides the highest chance of eradication, a similar outcome can be achieved with fewer doses delivered annually over a longer period of time. For the ovicidal intervention, we find that doses should be delivered as close together as possible. This work provides a platform for further research into optimal treatment strategies which may incorporate heterogeneity of transmission, and the interplay between MDA and enhancement of continuing scabies surveillance and treatment strategies.
Publisher: Cold Spring Harbor Laboratory
Date: 17-03-2023
DOI: 10.1101/2023.03.12.23287174
Abstract: Since the emergence of SARS-CoV-2 (COVID-19), there have been multiple waves of infection and multiple rounds of vaccination rollouts. Both prior infection and vaccination can prevent future infection and reduce severity of outcomes, combining to form hybrid immunity against COVID-19 at the in idual and population level. Here, we explore how different combinations of hybrid immunity affect the size and severity of near-future Omicron waves. To investigate the role of hybrid immunity, we use an agent-based model of COVID-19 transmission with waning immunity to simulate outbreaks in populations with varied past attack rates and past vaccine coverages, basing the demographics and past histories on the World Health Organization (WHO) Western Pacific Region (WPR). We find that if the past infection immunity is high but vaccination levels are low, then the secondary outbreak with the same variant can occur within a few months after the first outbreak meanwhile, high vaccination levels can suppress near-term outbreaks and delay the second wave. Additionally, hybrid immunity has limited impact on future COVID-19 waves with immune-escape variants. Enhanced understanding of the interplay between infection and vaccine exposure can aid anticipation of future epidemic activity due to current and emergent variants, including the likely impact of responsive vaccine interventions.
Publisher: Wiley
Date: 11-2022
DOI: 10.1111/TPJ.15952
Abstract: Breeding has increasingly altered the genetics of crop plants since the domestication of their wild progenitors. It is postulated that the genetic ersity of elite wheat breeding pools is too narrow to cope with future challenges. In contrast, plant genetic resources (PGRs) of wheat stored in genebanks are valuable sources of unexploited genetic ersity. Therefore, to ensure breeding progress in the future, it is of prime importance to identify the useful allelic ersity available in PGRs and to transfer it into elite breeding pools. Here, a erse collection consisting of modern winter wheat cultivars and genebank accessions was investigated based on reduced‐representation genomic sequencing and an iSelect single nucleotide polymorphism (SNP) chip array. Analyses of these datasets provided detailed insights into population structure, levels of genetic ersity, sources of new allelic ersity, and genomic regions affected by breeding activities. We identified 57 regions representing genomic signatures of selection and 827 regions representing private alleles associated exclusively with genebank accessions. The presence of known functional wheat genes, quantitative trait loci, and large chromosomal modifications, i.e., introgressions from wheat wild relatives, provided initial evidence for putative traits associated within these identified regions. These findings were supported by the results of ontology enrichment analyses. The results reported here will stimulate further research and promote breeding in the future by allowing for the targeted introduction of novel allelic ersity into elite wheat breeding pools.
Publisher: Cambridge University Press (CUP)
Date: 08-05-2018
DOI: 10.1017/S0950268818001061
Abstract: Prevalence of skin sores and scabies in remote Australian Aboriginal communities remains unacceptably high, with Group A Streptococcus (GAS) the dominant pathogen. We aim to better understand the drivers of GAS transmission using mathematical models. To estimate the force of infection, we quantified the age of first skin sores and scabies infection by pooling historical data from three studies conducted across five remote Aboriginal communities for children born between 2001 and 2005. We estimated the age of the first infection using the Kaplan–Meier estimator parametric exponential mixture model and Cox proportional hazards. For skin sores, the mean age of the first infection was approximately 10 months and the median was 7 months, with some heterogeneity in median observed by the community. For scabies, the mean age of the first infection was approximately 9 months and the median was 8 months, with significant heterogeneity by the community and an enhanced risk for children born between October and December. The young age of the first infection with skin sores and scabies reflects the high disease burden in these communities.
Publisher: Wiley
Date: 30-04-2019
Publisher: Springer Science and Business Media LLC
Date: 13-05-2022
DOI: 10.1186/S13756-022-01109-8
Abstract: Healthcare associated infections are of significant burden in Australia and globally. Previous estimates in Australia have relied on single-site studies, or combinations thereof, which have suggested the burden of these infections is high in Australia. Here, we estimate the burden of five healthcare associated infections (HAIs) in Australian public hospitals using a standard international framework, and compare these estimates to those observed in Europe. We used data from an Australian point prevalence survey to estimate the burden of HAIs amongst adults in Australian public hospitals using an incidence-based approach, introduced by the ECDC Burden of Communicable Diseases in Europe. We estimate that 170,574 HAIs occur in adults admitted to public hospitals in Australia annually, resulting in 7583 deaths. Hospital acquired pneumonia is the most frequent HAI, followed by surgical site infections, and urinary tract infections. We find that blood stream infections contribute a small percentage of HAIs, but contribute the highest number of deaths (3207), more than twice that of the second largest, while pneumonia has the higher impact on years lived with disability. This study is the first time the national burden of HAIs has been estimated for Australia from point prevalence data collected using validated surveillance definitions. Per-capita, estimates are similar to that observed in Europe, but with significantly higher occurrences of bloodstream infections and healthcare-associated pneumonia, primarily amongst women. Overall, the estimated burden is high and highlights the need for continued investment in HAI prevention.
Publisher: American Association for the Advancement of Science (AAAS)
Date: 08-04-2022
Abstract: In controlling transmission of coronavirus disease 2019 (COVID-19), the effectiveness of border quarantine strategies is a key concern for jurisdictions in which the local prevalence of disease and immunity is low. In settings like this such as China, Australia, and New Zealand, rare outbreak events can lead to escalating epidemics and trigger the imposition of large-scale lockdown policies. Here, we develop and apply an in idual-based model of COVID-19 to simulate case importation from managed quarantine under various vaccination scenarios. We then use the output of the in idual-based model as input to a branching process model to assess community transmission risk. For parameters corresponding to the Delta variant, our results demonstrate that vaccination effectively counteracts the pathogen’s increased infectiousness. To prevent outbreaks, heightened vaccination in border quarantine systems must be combined with mass vaccination. The ultimate success of these programs will depend sensitively on the efficacy of vaccines against viral transmission.
Publisher: PeerJ
Date: 26-10-2017
DOI: 10.7717/PEERJ.3958
Abstract: Households are an important location for the transmission of communicable diseases. Social contact between household members is typically more frequent, of greater intensity, and is more likely to involve people of different age groups than contact occurring in the general community. Understanding household structure in different populations is therefore fundamental to explaining patterns of disease transmission in these populations. Indigenous populations in Australia tend to live in larger households than non-Indigenous populations, but limited data are available on the structure of these households, and how they differ between remote and urban communities. We have developed a novel approach to the collection of household structure data, suitable for use in a variety of contexts, which provides a detailed view of age, gender, and room occupancy patterns in remote and urban Australian Indigenous households. Here we report analysis of data collected using this tool, which quantifies the extent of crowding in Indigenous households, particularly in remote areas. We use these data to generate matrices of age-specific contact rates, as used by mathematical models of infectious disease transmission. To demonstrate the impact of household structure, we use a mathematical model to simulate an influenza-like illness in different populations. Our simulations suggest that outbreaks in remote populations are likely to spread more rapidly and to a greater extent than outbreaks in non-Indigenous populations.
Publisher: Springer Science and Business Media LLC
Date: 11-2021
DOI: 10.1038/S41467-021-26558-4
Abstract: During 2020, Victoria was the Australian state hardest hit by COVID-19, but was successful in controlling its second wave through aggressive policy interventions. We calibrated a detailed compartmental model of Victoria’s second wave to multiple geographically-structured epidemic time-series indicators. We achieved a good fit overall and for in idual health services through a combination of time-varying processes, including case detection, population mobility, school closures, physical distancing and face covering usage. Estimates of the risk of death in those aged ≥75 and of hospitalisation were higher than international estimates, reflecting concentration of cases in high-risk settings. We estimated significant effects for each of the calibrated time-varying processes, with estimates for the in idual-level effect of physical distancing of 37.4% (95%CrI 7.2−56.4%) and of face coverings of 45.9% (95%CrI 32.9−55.6%). That the multi-faceted interventions led to the dramatic reversal in the epidemic trajectory is supported by our results, with face coverings likely particularly important.
Publisher: Cambridge University Press (CUP)
Date: 16-10-2019
Publisher: Oxford University Press (OUP)
Date: 17-12-2021
DOI: 10.1093/JAC/DKAA506
Abstract: The urgent need to develop effective therapeutics and disseminate information from clinical studies has led to data from clinical trials being made available by alternate methods prior to peer-reviewed publication, including press releases, social media and pre-print papers. While this allows clinicians more open access to these data, a trust has to be placed with the investigators releasing these data without the availability of scientifically rigorous peer review. The ex les of results from trials studying dexamethasone and hydroxychloroquine for treatment of COVID-19 have had contrasting outcomes, including the potential for significant numbers of lives saved with the early release of results from the RECOVERY trial studying dexamethasone contrasting with unsubstantiated data being presented from trials studying hydroxychloroquine. Clinicians and researchers must maintain a healthy scepticism when reviewing results prior to peer-reviewed publication, but also consider when these opportunities may allow for early implementation of potentially lifesaving interventions for people infected with COVID-19.
Publisher: The Royal Society
Date: 2021
Abstract: COVID-19 is highly transmissible and containing outbreaks requires a rapid and effective response. Because infection may be spread by people who are pre-symptomatic or asymptomatic, substantial undetected transmission is likely to occur before clinical cases are diagnosed. Thus, when outbreaks occur there is a need to anticipate which populations and locations are at heightened risk of exposure. In this work, we evaluate the utility of aggregate human mobility data for estimating the geographical distribution of transmission risk. We present a simple procedure for producing spatial transmission risk assessments from near-real-time population mobility data. We validate our estimates against three well-documented COVID-19 outbreaks in Australia. Two of these were well-defined transmission clusters and one was a community transmission scenario. Our results indicate that mobility data can be a good predictor of geographical patterns of exposure risk from transmission centres, particularly in outbreaks involving workplaces or other environments associated with habitual travel patterns. For community transmission scenarios, our results demonstrate that mobility data add the most value to risk predictions when case counts are low and spatially clustered. Our method could assist health systems in the allocation of testing resources, and potentially guide the implementation of geographically targeted restrictions on movement and social interaction.
Publisher: Cold Spring Harbor Laboratory
Date: 07-10-2021
DOI: 10.1101/2021.10.05.21264587
Abstract: Healthcare associated infections (HAIs) are associated with increased morbidity and mortality, but there are few data that quantify the burden of infection nationally in Australia. We used data from an Australian national point prevalence survey to estimate the burden of HAIs amongst adults in Australian public hospitals. The incidence based appropach, introduced by the ECDC Burden of Comunicable Diseases in Europe was used. We estimate that 170,574 HAIs occur in adults admitted to public hospitals in Australia annually, resulting in 7583 deaths. Hospital acquired pneumonia is the most frequent HAI, followed by surgical site infections, and urinary tract infections. We find that blood stream infections contribute a small percentage of HAIs, but contribute the highest number of deaths (3512), more than twice that of the second largest, while pneumonia has the highert impact on years lived with disability. This study is the first time the national burden of HAIs has been estimated for Australia from point prevalence data. The estimated burden is high, and highlights the need for continued investment in HAI prevention.
Publisher: Public Library of Science (PLoS)
Date: 05-10-2020
Publisher: Cold Spring Harbor Laboratory
Date: 11-01-2023
DOI: 10.1101/2023.01.10.23284209
Abstract: We report on an analysis of Australian COVID-19 case data to estimate the impact of TTIQ systems on SARS-CoV-2 transmission in 2020–21. We estimate that in a low prevalence period in the state of New South Wales (tens of cases per day), TTIQ contributed to a 54% reduction in transmission. In a higher prevalence period in the state of Victoria (hundreds of cases per day), TTIQ contributed to a 42% reduction in transmission. Our results also suggest that case-initiated contact tracing can support timely quarantine in times of system stress. Contact tracing systems for COVID-19 in Australia were highly effective and adaptable in supporting the national suppression strategy through 2020 and 2021.
Publisher: Elsevier BV
Date: 04-2019
Abstract: To quantify the childhood infectious disease burden and antibiotic use in the Northern Territory's East Arnhem region through synthesis and analysis of historical data resources. We combined primary health clinic data originally reported in three separate publications stemming from the East Arnhem Healthy Skin Project (Jan-01 to Sep-07). Common statistical techniques were used to explore the prevalence of infectious conditions and the seasonality of infections, and to measure rates of antibiotic use. There was a high monthly prevalence of respiratory (mean: 32% [95% confidence interval (CI): 20%, 34%]) and skin (mean: 20% [95%CI: 19%, 22%]) infectious syndromes, with upper respiratory tract infections (mean: 29% [95%CI: 27%, 31%]) and skin sores (mean: 15% [95%CI: 14%, 17%]) the most common conditions. Antibiotics were frequently prescribed with 95% (95%CI: 91%, 97%) of children having received at least one antibiotic prescription by their first birthday, and 47% having received six antibiotic prescriptions skin sores being a key driver. Early life infections drive high antibiotic prescribing rates in remote Aboriginal communities. Implications for public health: Eliminating skin disease could reduce antibiotic use by almost 20% in children under five years of age in this population.
Publisher: Cold Spring Harbor Laboratory
Date: 06-12-2022
DOI: 10.1101/2022.12.04.22282996
Abstract: Since the emergence of SARS-CoV-2 in 2019 through to mid-2021, much of the Australian population lived in a COVID-19 free environment. This followed the broadly successful implementation of a strong suppression strategy, including international border closures. With the availability of COVID-19 vaccines in early 2021, the national government sought to transition from a state of minimal incidence and strong suppression activities to one of high vaccine coverage and reduced restrictions but with still-manageable transmission. This transition is articulated in the national “re-opening” plan released in July 2021. Here we report on the dynamic modelling study that directly informed policies within the national re-opening plan including the identification of priority age groups for vaccination, target vaccine coverage thresholds and the anticipated requirements for continued public health measures — assuming circulation of the Delta SARS-CoV-2 variant. Our findings demonstrated that adult vaccine coverage needed to be at least 70% to minimise public health and clinical impacts following the establishment of community transmission. They also supported the need for continued application of test-trace-isolate-quarantine and social measures during the vaccine roll-out phase and beyond.
Publisher: Springer Science and Business Media LLC
Date: 02-2016
DOI: 10.1007/S11538-016-0144-6
Abstract: Recently, pandemic response has involved the use of antivirals. These antivirals are often allocated to households dynamically throughout the pandemic with the aim being to retard the spread of infection. A drawback of this is that there is a delay until infection is confirmed and antivirals are delivered. Here an alternative allocation scheme is considered, where antivirals are instead preallocated to households at the start of a pandemic, thus reducing this delay. To compare these two schemes, a deterministic approximation to a novel stochastic household model is derived, which allows efficient computation of key quantities such as the expected epidemic final size, expected early growth rate, expected peak size and expected peak time of the epidemic. It is found that the theoretical best choice of allocation scheme depends on strain transmissibility, the delay in delivering antivirals under a dynamic allocation scheme and the stockpile size. A broad summary is that for realistic stockpile sizes, a dynamic allocation scheme is superior with the important exception of the epidemic final size under a severe pandemic scenario. Our results, viewed in conjunction with the practical considerations of implementing a preallocation scheme, support a focus on attempting to reduce the delay in delivering antivirals under a dynamic allocation scheme during a future pandemic.
Start Date: 2018
End Date: 12-2021
Amount: $604,543.00
Funder: Australian Research Council
View Funded Activity