Publication Search Results

Now showing 1 - 7 of 7
  • (2008) Power, M; Marlon, J; Ortiz, N; Bartlein, P; Harrison, Simon; Mayle, F; Ballouche, A; Bradshaw, R; Carcaillet, C; Cordova, C; Mooney, Scott; Moreno, P; Prentice, I; Thonicke, K; Tinner, W; Whitlock, C; Zhang, Yanling; Zhao, Yong; Ali, Amna; Anderson, Richard; Beer, R; Behling, H; Briles, C; Brown, Katherine; Brunelle, A; Bush, M; Camill, P; Chu, G; Clark, J; Colombaroli, D; Connor, Stuart; Daniau, A; Daniels, M; Dodson, John; Doughty, E; Edwards, Meredith; Finsinger, W; Foster, Douglas; Frechette, J; Gaillard, M; Gavin, D; Gobet, E; Haberle, Simon; Hallett, D; Higuera, P; Hope, G; Horn, S; Inoue, J; Kaltenrieder, P; Kennedy, Liz; Kong, Z; Larsen, C; Long, C; Lynch, Jodi; Lynch, E; McGlone, M; Meeks, S; Mensing, S; Meyer, G; Minckley, T; Mohr, J; Nelson, D; New, J; Newnham, R; Noti, R; Oswald, W; Pierce, J; Richard, P; Rowe, C; Goni, M; Shuman, B; Takahara, H; Toney, J; Turney, C; Urrego-Sanchez, D; Umbanhowar, C; Vandergoes, M; Vanniere, B; Vescovi, E
    Journal Article
    Fire activity has varied globally and continuously since the last glacial maximum (LGM) in response to long-term changes in global climate and shorter-term regional changes in climate, vegetation, and human land use. We have synthesized sedimentary charcoal records of biomass burning since the LGM and present global maps showing changes in fire activity for time slices during the past 21,000 years (as differences in charcoal accumulation values compared to pre-industrial). There is strong broad-scale coherence in fire activity after the LGM, but spatial heterogeneity in the signals increases thereafter. In North America, Europe and southern South America, charcoal records indicate less-than-present fire activity during the deglacial period, from 21,000 to ∼11,000 cal yr BP. In contrast, the tropical latitudes of South America and Africa show greater-than-present fire activity from ∼19,000 to ∼17,000 cal yr BP and most sites from Indochina and Australia show greater-than-present fire activity from 16,000 to ∼13,000 cal yr BP. Many sites indicate greater-than-present or near-present activity during the Holocene with the exception of eastern North America and eastern Asia from 8,000 to ∼3,000 cal yr BP, Indonesia and Australia from 11,000 to 4,000 cal yr BP, and southern South America from 6,000 to 3,000 cal yr BP where fire activity was less than present. Regional coherence in the patterns of change in fire activity was evident throughout the post-glacial period. These complex patterns can largely be explained in terms of large-scale climate controls modulated by local changes in vegetation and fuel load.

  • (2009) Fiatarone-Singh, Maria; Singh, N; Hansen, R; Finnegan, T; Allen, Barry; Diamond, Terrence; Diwan, Ashish; Lloyd, Bradley; Williamson, Dawn; Smith, Elizabeth; Grady, J; Stavrinos, T; Thompson, M
    Journal Article
    Background. Age-related hip fractures are associated with poor functional outcomes, resulting in substantial personal and societal burden. There is a need to better identify reversible etiologic predictors of suboptimal functional recovery in this group. Methods. The Sarcopenia and Hip Fracture (SHIP) study was a 5-year prospective cohort study following community-dwelling older persons admitted to three Sydney hospitals for hip fracture. Information was collected at baseline, and 4 and 12 months, including health status, quality of life, nutritional status, body composition, muscle strength, range of motion, gait velocity, balance, walking endurance, disability, cognition, depression, fear of falling, self-efficacy, social support, physical activity level, vision, and fall-related data, with residential status, disability, and mortality reassessed at 5 years. Results. 193 participants enrolled (81 ± 8 years, 72% women). High levels of activities of daily living, disability and sedentariness were present prior to fracture. At admission, the cohort had high levels of chronic disease; 38% were depressed, 38% were cognitively impaired, and 26% had heart disease. Seventy-one percent of participants were sarcopenic, 58% undernourished, and 55% vitamin D deficient. Mobility, strength, and vision were severely impaired. There was little evidence that these comorbidities were either recognized or treated during hospitalization. Disability, sedentariness, malnutrition, and walking endurance predicted acute hospitalization length of stay. Conclusions. The complex comorbidity, pre-existing functional impairment, and sedentary behavior in patients with hip fracture suggest the need for thorough screening and targeting of potentially reversible impairments. Rehabilitation outcomes are likely to be highly dependent on amelioration of these highly prevalent accompaniments to hip fracture.

  • (2023) Zillur Rahman, Kazi Mohammad
    Current healthcare infection surveillance rarely monitors the distribution of antimicrobial resistance (AMR) in bacteria beyond clinical settings in Australia and overseas. This results in a significant gap in our ability to fully understand and manage the spread of AMR in the general community. This thesis explores whether wastewater-based monitoring could reveal geospatial-temporal and demographic trends of antibiotic-resistant bacteria in the urban area of Greater Sydney, Australia. Untreated wastewater from 25 wastewater treatment plants sampled between 2017 and 2019 consistently contained extended-spectrum β-lactamases-producing Enterobacteriaceae (ESBL-E) isolates, suggesting its endemicity in the community. Carbapenem-resistant Enterobacteriaceae (CRE), vancomycin-resistant enterococci (VRE), and methicillin-resistant Staphylococcus aureus (MRSA) isolates were occasionally detected. Demographic and healthcare infection-related factors correlated with the ESBL-E load, and demographic variables influenced the VRE load. In contrast, the healthcare infection-related factor mainly drove the CRE load. These findings demonstrate the potential of wastewater-based surveillance to understand the factors driving AMR distribution in the community. The subsequent thesis work covers the genomic characterisation of selected ESBL-E and CRE wastewater isolates to reveal their nature, origin, and underlying resistance mechanisms. Phylogenetic analysis showed that Escherichia coli isolates were related to high-risk human-associated pandemic clones and non-human-associated clones. The Klebsiella pneumoniae and K. variicola isolates were related to globally disseminated and emerging human-associated clones, and some were detected for the first time in Australia. Genomic analysis also indicated novel resistance mechanisms against nitrofurantoin in E. coli, and against piperacillin/tazobactam and ticarcillin/clavulanic acid in Klebsiella isolates. The virulence gene content indicated that some E. coli and Klebsiella isolates were likely associated with infections, while the asymptomatic carriage was suggested for other isolates. These results demonstrate a clear potential for wastewater-based surveillance to monitor the emergence and dissemination of resistance in non-clinical isolates, and in particular, isolates from the community and non-human sources. The findings of this study can complement healthcare infection surveillance to inform management strategies to mitigate the emergence and dissemination of AMR and important human pathogens in the general community.

  • (2020) Khan, Mahjabeen
    Pseudomonas aeruginosa causes both contact lens and non-contact lens-related keratitis (corneal infection). This opportunistic bacterium naturally has the ability to resist the mechanism of action of many antibiotics which are used for treatment. P. aeruginosa resistance patterns and the mechanism of resistance in isolates from keratitis are not well understood. This thesis described the phenotypic and genotypic patterns of antimicrobial resistance and compared these between ocular isolates of P. aeruginosa from Australia (contact lens) and India (non-contact lens). Changes in the antimicrobial susceptibility between isolates over time were also analysed. Susceptibility to antibiotics, multipurpose disinfecting solutions and disinfectants was analysed for twenty-seven Australian isolates from contact lens-related keratitis and forty non-contact lens-related isolated from India. The whole genomes of fourteen Australian (historical and recent) and twelve Indian isolates were sequenced using Illumina® MiSeq®. Computational analysis of the genomes was performed to analyse their core and pan genomes and these were examined for the presence of acquired resistance genes, virulence genes, gene mutations, and these compared to their phenotypic resistance to antibiotics. Indian isolates possessed large pan genomes with more acquired resistance (30) genes and larger numbers of genetic variations. The Indian isolates contained clones of three sequence types ST308, ST316 and ST491, whereas Australian isolates contained only one sequence type ST233. Isolates with larger gene variations had mutations in the DNA mismatch repair system. Most multi-drug resistant Indian (non-contact lens) isolates were exoU +. Indian isolates had large accessory genes compared to Australian isolates and this increased the pan genome size of the Indian isolates. The number of core genome mutations were larger in the Indian isolates a median of 50006 (IQR=26967-50600) compared to Australian isolates a median of 26317 (IQR=25681-33780). There were differences between isolates from Australia and India with respect to their antibiotic resistance and associated genes. Indian strains had more genetic diversity and were multi-drug resistant. However, there was no evidence of substantial genetic or phenotypic changes within isolates from their respective countries.

  • (2023) Paul, Kishor Kumar
    The transmission of dengue fever is already being impacted by the changing climate. This phenomenon poses a considerable public health challenge for countries like Bangladesh, where regular seasonal outbreaks of dengue fever are already prevalent. This thesis aims to investigate how changing climate will impact long-term dengue epidemiology in Bangladesh as a whole and more specifically in Dhaka, the capital city of the country over the 21st Century. Several statistical models have been developed to estimate the short-term risk of dengue outbreaks as a function of climate variables but the underlying causal relationships that contribute to dengue transmission and the observed patterns of dengue epidemiology are not accounted for in these models. Initially, we determined the suitability of using climate projections for 21st Century from Global Climate Models (GCM) to assess the impact of changing climate on future dengue risk in Bangladesh setting. We then used the GCM output to assess the impact of changing climate on one aspect of dengue transmission by calculating the change in vectorial capacity (VC) of Aedes aegypti mosquitoes at a seasonal level for all regions in Bangladesh under two future climate change scenarios. The analysis indicates that the annual VC in all divisions of Bangladesh is expected to consistently exceed the threshold for dengue transmission throughout the 21st Century, regardless of the climate change scenarios considered. However, during the latter half of the century, there is a projected decline in the annual VC compared to the period between 1986 and 2005. Despite this, monthly VC variations reveal that the winter/dry season could see an increase in VC, potentially leading to a longer dengue season with outbreaks occurring year-round. The application of the VC calculation is limited by the fact that it only accounts for temperature and does not consider the impact of other climate variables such as rainfall and humidity, as well as the role of host immunity. To incorporate these factors, we then developed a mechanistic dengue transmission model that considers the influence of temperature, rainfall, and humidity on the transmission of two different dengue serotypes among human hosts and mosquito vectors. We calibrated and validated the model against observed dengue epidemiology data from Dhaka for 1995-2014 using observed climate data as input. We then used GCM output for two future climate change scenarios to simulate the model for two future periods (2030-2049 and 2080-2099) to assess the potential changes in dengue epidemiology in Dhaka. When utilizing observed climate data and climate projections from GCMs specific to Dhaka, our mechanistic model reasonably reproduced the observed dengue epidemiology in Dhaka between 1995 and 2014 in terms of the recurring annual dengue outbreaks, the seasonal pattern of transmission, and the increase in seroprevalence. Simulations for 2030-2049 indicate that dengue transmission is likely to increase regardless of the combination of initial seroprevalence, GCM, and climate change scenario, when compared to the baseline period of 1995-2014. However, for the period 2080-2099, the projected changes in dengue transmission vary, with some combinations of initial seroprevalence, GCM, and climate change scenario predicting a slight increase and others indicating a decrease. The simulations also suggest the seasonal pattern of dengue infections is likely to change in future, with more pronounced change projected for the 2080-2099 period, resulting in a lengthening of the dengue season. The primary contribution of this thesis is to present a modelling framework that considers the anticipated changes in the future climate and immunological factors to project the long-term risk of dengue epidemics. The model is flexible enough to be adapted to other settings and other pathogens transmitted by the same mosquito vector.

  • (2024) Koon, William
    Coastal areas including beaches, rock platforms, tidal bodies such as bays and harbours, and the open ocean itself, hold significant economic, social, and cultural value for many communities. While often associated with recreation, the coast also poses risks due to environmental hazards such as waves and dangerous currents. The interplay of these physical hazards with human and social factors creates a complex, ever-changing risk profile. In many communities, the majority of drowning deaths occur in coastal areas, resulting in thousands of lives lost each year. In Australia, approximately 40% of all drowning deaths occur at coastal sites, 2,303 between 2002 and 2022, and the prevention of these events has long been a social and civic priority. This thesis uses a mixed-methods, multi-disciplinary approach to expand the evidence base for the prevention of coastal drowning by presenting a series of studies that identify and subsequently address gaps in coastal drowning prevention science by advancing methods, thinking, and understanding of the issue to inform prevention efforts and ultimately, help keep people safe. In Chapter 1, I present an overview of drowning, coastal safety, the complex nature of risk in the coastal environment, and the structure and aims of the thesis guided by the Public Health Approach to Injury Prevention. Chapter 2 is a comprehensive scoping review of coastal drowning literature characterising the field by mapping 146 studies dating back to 1963. Chapter 2 serves as the foundation for the thesis as it identifies several gaps in the literature that subsequent chapters aimed to address, broadly grouped into a collection of epidemiology studies and prevention program focused studies. Chapter 3 is an epidemiological review of coastal drowning in Australia which, for the first time, comprehensively incorporates revised risk measurements based on exposure and a trend analysis on a national scale, showing drowning rates have not changed in 17 years. In Chapter 4, I present a comprehensive epidemiological analysis of all drowning deaths from my home state of California. This research guided a nascent multisectoral drowning prevention coalition and underpinned the recently released California Water Safety Strategy, the first such state-level strategy in the United States. This work represents one of the major impacts from my time as a PhD student as I was able to participate in and learn from the well-developed drowning prevention and coastal safety sectors in Australia and transfer some of that learning to a Californian context. Chapter 5 evaluates the relationship between tidal variables and risk of drowning on surf beaches. This study shows lower tidal water levels and time periods closer to low tide were associated with increased likelihood of fatal drowning, while tidal phase (rising vs falling), tide range, and the rate of change of falling or rising water levels were not – contrary to prevailing understanding by lifeguards. Chapter 6 examines pre-COVID-19 coastal fatalities of international visitors, establishing a risk profile distinct from residents. This study explores the tourism industry’s role in coastal safety, which is particularly important as tourism evolves and grows in the post COVID-19 era. In Chapter 7, I describe the co-design process of a high school beach safety program with ocean lifeguards and high school (year 7) students, challenging traditional educational approaches to beach safety education programs. Chapter 8 is a three-part, mixed-methods evaluation of a novel program that teaches surfers basic ocean rescue techniques and cardiopulmonary resuscitation (CPR). We found these programs improve skills and knowledge around safe rescue and further endorse the role surfers play as bystander rescuers, often in locations without lifeguards. Chapter 9 synthesizes the findings and recommendations from the thesis. This closing chapter includes a reflection on my personal learning from the thesis process and discusses implications of for the coastal safety field and future research.

  • (2024) Rayamajhee, Binod
    Acanthamoeba, a free-living heterotrophic protist, typically resides in a variety of aquatic environments. It is known to pose a risk to humans, causing various diseases, including eye infections (keratitis), often transmitted through contact lenses. The primary risk factor for Acanthamoeba keratitis (AK) in developed countries is engaging in recreational water activities while wearing contact lenses. Late and misdiagnosis of AK are commonly observed, often leading to worse clinical outcomes. Treatment of Acanthamoeba infections is challenging due to the absence of drugs that can effectively eradicate both trophozoites and resilient cysts. In a remarkable dual role, Acanthamoeba behaves as a phagocytic predator, consuming other microbes, but also as an environmental host for diverse bacteria which can resist the intracellular killing mechanism of the amoebal host. Among AK patients, coinfections with various bacteria and fungi have been reported in recent years, presenting as a complex polymicrobial keratitis. The research in this thesis investigates the incidence of Acanthamoeba in Sydney's largest domestic water reservoir and determines the associations between Acanthamoeba and physicochemical as well as microbiological parameters of the water. In addition, the research evaluated the incidence of Acanthamoeba spp. within coastal lagoons on the eastern coast of Australia using a metagenomic approach and investigate their associations with aquatic bacteria. The research also examined the genotypes of Acanthamoeba species recovered from AK patients in Hyderabad, India and Sydney, Australia, along with the types of intracellular bacteria they harbor, using microbiome sequencing. Finally, the research examined whether naturally acquired intracellular bacteria in Acanthamoeba led to more severe ocular infections in an animal model. In this thesis, two review papers (chapters 1B and 1C) summarised the growing importance of Acanthamoeba as a potential human pathogen, elucidating its role as an environmental predator. An invited narrative review (chapter 1B) highlighted how Acanthamoeba predation in environmental habitats can be a key factor shaping the structure and composition of microbial populations. This review comprehensively examined and listed Acanthamoeba-resisting bacteria, along with in vitro interactions and adaptations between Acanthamoeba and bacteria. A systematic review in this thesis (chapter 1C) examined the diversity of microbial species identified in environmental and clinical isolates of Acanthamoeba spp. The comprehensive systematic review also outlined the knowledge gap of whether Acanthamoeba minimicrobiome contains phylogenetically distinct bacteria. In the past, approximately 20% of AK patients in the Sydney metropolitan reported swimming in seawater or freshwater while wearing their contact lenses before they became infected. The current research identified that 34.5% of water samples from Warragamba dam, the largest water reservoir in Sydney contained viable Acanthamoeba spp. (chapter 2), and the incidence of Acanthamoeba spp. in the dam was positively correlated with a higher concentration of algal biovolume. Additionally, 38% of water samples from four lagoons on the NSW, Central Coast were positive for Acanthamoeba, with significantly higher numbers observed in summer compared to other seasons (chapter 3). Water from a highly urbanised area were more commonly infested with Acanthamoeba than non-urbanised areas. Most strains belonged to the pathogenic genotype T4 clade. Water turbidity, temperature, intl1 gene concentration (a proxy measure of anthropogenic pollution), and dissolved oxygen were significantly associated with Acanthamoeba numbers. This study (chapter 3) found a positive correlation between the abundance of Acanthamoeba in coastal waterways and the levels of cyanobacteria, Pseudomonas spp., Candidatus Planktoluna, Curvibacter sp., Polynucleobacter cosmopolitanus, Mycobacterium spp., Vibrio pacinii, and marine bacteria of the Bacteroidota phylum. Overall, the presence of Acanthamoeba spp. had a significant influence on the composition of bacterial communities in lagoons (chapter 3). Subsequent studies in this thesis investigated the genotypes of Acanthamoeba recovered from ocular infections in Hyderabad (chapter 4A) and Sydney (chapter 4B). Most Indian (92.3%) and all Australian corneal isolates belonged to genotype T4. Among Indian isolates, nine strains harboured intracellular bacteria and one contained the fungus Malassezia restricta. The presence of intracellular microbes was associated with a higher proportion of stromal infiltrates, epithelial defect and hypopyon compared to AK cases without intracellular microbes. Ocular trauma was the major reported risk factor among AK patients in Hyderabad, India where 46.2% required surgical intervention, and one case underwent evisceration. This study also analysed domestic tap water of nine AK patients in Sydney, and Acanthamoeba was detected in four of them. Notably, one isolate was found to harbor viable Pseudomonas aeruginosa (chapter 4B). Chapter 5 of this thesis assessed the intracellular microbiome composition of 51 Acanthamoeba species isolated in Australia and India, 41% harboured intracellular bacteria which were clustered into four major phyla: Pseudomonadota, Bacteroidota, Actinomycetota, and Bacillota. Distinct microbial abundance patterns were observed among the samples; Pseudomonas species were abundant in Australian corneal isolates, Enterobacteriales in Indian ocular isolates, and Bacteroidota was abundant in Australian water isolates. More diverse intracellular bacteria were identified in water isolates as compared to clinical isolates. The beta diversity measure of bacterial communities in corneal isolates of Acanthamoeba exhibited significant difference based on the country of origin, while alpha diversity did not vary significantly as per the source of isolation or country of origin. Chapter 6 of this thesis examined the impact of naturally acquired viable intracellular P. aeruginosa in the development of AK in rats cornea. The findings from this study (chapter 6) demonstrated that AK infection in rat's corneas, using an Acanthamoeba strain containing intracellular P. aeruginosa, resulted in acute keratitis with a high neutrophil response, whereas Acanthamoeba alone induced only very mild infections. During the infection in rat corneas, intracellular P. aeruginosa cells were expelled, as no intracellular bacteria were observed in Acanthamoeba trophozoites reisolated from the rats' corneas. No severe keratitis developed when Acanthamoeba and intracellular P. aeruginosa were separately inoculated in distinct groups of rat corneas, unlike their combined inoculation. These findings suggest that the concurrent infection of Acanthamoeba, coupled with the release of intracellular bacteria onto a compromised cornea, can contribute to the development of complex microbial keratitis. In summary, this thesis observed a relatively high prevalence of pathogenic Acanthamoeba in both the water reservoir and coastal waterways of Sydney. It also identified potential contributors in water habitats that could promote the proliferation of Acanthamoeba strains, determined circulating genotypes of Acanthamoeba among AK patients in Hyderabad and Sydney, comprehensively characterised the microbiome that can inhabit Acanthamoeba spp., and assessed the impact of a member of this microbiome on corneal infection in rats.