Suppressing the Epidemic in New South Wales.
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ABSTRACT:
SUBMITTER: McAnulty JM
PROVIDER: S-EPMC7233304 | biostudies-literature | 2020 May
REPOSITORIES: biostudies-literature
Publications
Suppressing the Epidemic in New South Wales.
McAnulty Jeremy M JM Ward Kate K
The New England journal of medicine 20200508 21
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Project description:Changes over time in HIV-1 subtype diversity within a population reflect changes in factors influencing the development of local epidemics. Here we report on the genetic diversity of 2364 reverse transcriptase sequences from people living with HIV-1 in New South Wales (NSW) notified between 2004 and 2018. These data represent >70% of all new HIV-1 notifications in the state over this period. Phylogenetic analysis was performed to identify subtype-specific transmission clusters. Subtype B and non-B infections differed across all demographics analysed (p < 0.001). We found a strong positive association for infections among females, individuals not born in Australia or reporting heterosexual transmission being of non-B origin. Further, we found an overall increase in non-B infections among men who have sex with men from 50 to 79% in the last 10 years. However, we also found differences between non-B subtypes; heterosexual transmission was positively associated with subtype C only. In addition, the majority of subtype B infections were associated with clusters, while the majority of non-B infections were singletons. However, we found seven non-B clusters (?5 sequences) indicative of local ongoing transmission. In conclusion, we present how the HIV-1 epidemic has changed over time in NSW, becoming more heterogeneous with distinct subtype-specific demographic associations.
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Project description:This paper describes three datasets of seamless bathymetry and coastal topography for Sydney Harbour (Port Jackson), Botany and Bate Bays, and the Hawkesbury River. The datasets used to form these compilations were the most recent and highest quality available to the authors and were originally collated using the software ESRI ArcGIS. The original compilation of this data was undertaken to support tsunami modelling research by the authors of this paper. Before processing, all data were adjusted and/or reprojected to conform to the vertical datum Australian Height Datum (AHD) and horizontal projection WGS84 UTM zone 56. Data resolution and density was highly variable and grid resolutions of the final datasets were selected as the highest resolutions possible using the most sparse data in the compilation in question. For areas where no data were available, the ESRI ArcGIS interpolation tool, Topo to Raster, was used to provide a best estimate. These dastasets of three important Australian waterways provide a useful tool for coastal research and scientific interest.
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Project description:There is concern in Australia that droughts substantially increase the incidence of suicide in rural populations, particularly among male farmers and their families. We investigated this possibility for the state of New South Wales (NSW), Australia between 1970 and 2007, analyzing data on suicides with a previously established climatic drought index. Using a generalized additive model that controlled for season, region, and long-term suicide trends, we found an increased relative risk of suicide of 15% (95% confidence interval, 8%-22%) for rural males aged 30-49 y when the drought index rose from the first quartile to the third quartile. In contrast, the risk of suicide for rural females aged >30 y declined with increased values of the drought index. We also observed an increased risk of suicide in spring and early summer. In addition there was a smaller association during unusually warm months at any time of year. The spring suicide increase is well documented in nontropical locations, although its cause is unknown. The possible increased risk of suicide during drought in rural Australia warrants public health focus and concern, as does the annual, predictable increase seen each spring and early summer. Suicide is a complex phenomenon with many interacting social, environmental, and biological causal factors. The relationship between drought and suicide is best understood using a holistic framework. Climate change projections suggest increased frequency and severity of droughts in NSW, accompanied and exacerbated by rising temperatures. Elucidating the relationships between drought and mental health will help facilitate adaptation to climate change.
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Project description:BackgroundThe distribution of the duration that clinical cases of COVID-19 occupy hospital beds (the 'length of stay') is a key factor in determining how incident caseloads translate into health system burden. Robust estimation of length of stay in real-time requires the use of survival methods that can account for right-censoring induced by yet unobserved events in patient progression (e.g. discharge, death). In this study, we estimate in real-time the length of stay distributions of hospitalised COVID-19 cases in New South Wales, Australia, comparing estimates between a period where Delta was the dominant variant and a subsequent period where Omicron was dominant.MethodsUsing data on the hospital stays of 19,574 individuals who tested positive to COVID-19 prior to admission, we performed a competing-risk survival analysis of COVID-19 clinical progression.ResultsDuring the mixed Omicron-Delta epidemic, we found that the mean length of stay for individuals who were discharged directly from ward without an ICU stay was, for age groups 0-39, 40-69 and 70 +, respectively, 2.16 (95% CI: 2.12-2.21), 3.93 (95% CI: 3.78-4.07) and 7.61 days (95% CI: 7.31-8.01), compared to 3.60 (95% CI: 3.48-3.81), 5.78 (95% CI: 5.59-5.99) and 12.31 days (95% CI: 11.75-12.95) across the preceding Delta epidemic (1 July 2021-15 December 2021). We also considered data on the stays of individuals within the Hunter New England Local Health District, where it was reported that Omicron was the only circulating variant, and found mean ward-to-discharge length of stays of 2.05 (95% CI: 1.80-2.30), 2.92 (95% CI: 2.50-3.67) and 6.02 days (95% CI: 4.91-7.01) for the same age groups.ConclusionsHospital length of stay was substantially reduced across all clinical pathways during a mixed Omicron-Delta epidemic compared to a prior Delta epidemic, contributing to a lessened health system burden despite a greatly increased infection burden. Our results demonstrate the utility of survival analysis in producing real-time estimates of hospital length of stay for assisting in situational assessment and planning of the COVID-19 response.
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Project description:BACKGROUND: Molecular epidemiology of Mycobacterium tuberculosis, its transmission dynamics and population structure have become important determinants of targeted tuberculosis control programs. Here we describe recent changes in the distribution of M. tuberculosis genotypes in New South Wales (NSW), Australia and compared strain types with drug resistance, site of disease and demographic data. METHODS: We evaluated all culture-confirmed newly identified tuberculosis cases in NSW, Australia, from 2010-2012. M. tuberculosis population structure and clustering rates were assessed using 24-loci Mycobacterial interspersed repetitive unit (MIRU) analysis and compared to MIRU data from 2006-2008. RESULTS: Of 1177 tuberculosis cases, 1128 (95.8%) were successfully typed. Beijing and East African Indian (EAI) lineage strains were most common (27.6% and 28.5%, respectively) with EAI strains increasing in relative abundance from 11.8% in 2006-2008 to 28.5% in 2010-2012. Few cases of multi-drug resistant tuberculosis were identified (18; 1.7%). Compared to 12-loci, 24-loci MIRU provided improved cluster resolution with 695 (61.6%) and 227 (20.1%) clustered cases identified, respectively. Detailed analysis of the largest cluster identified (an 11 member Beijing cluster) revealed wide geographic diversity in the absence of documented social contact. CONCLUSIONS: EAI strains of M. tuberculosis recently overtook Beijing family as a prevalent cause of tuberculosis in NSW, Australia. This lineage appeared to be less commonly related to multi-drug resistant tuberculosis as compared to Beijing strain lineage. The resolution provided by 24-loci MIRU typing was insufficient for reliable assessment of transmissions, especially of Beijing family strains.
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Project description:IntroductionPrescriber behaviour is important for understanding opioid use patterns. We described variations in practitioner-level opioid prescribing in New South Wales, Australia (2013-2018).MethodsWe quantified opioid prescribing patterns among medical practitioners using population-level dispensing claims data, and used partitioning around medoids to identify clusters of practitioners who prescribe opioids based on prescribing patterns and patient characteristics identified from linked dispensing claims, hospitalisations and mortality data.ResultsThe number of opioid prescribers ranged from 20,179 in 2013 to 23,408 in 2018. The top 1% of practitioners prescribed 15% of all oral morphine equivalent (OME) milligrams dispensed annually, with a median of 1382 OME grams (interquartile range [IQR], 1234-1654) per practitioner; the bottom 50% prescribed 1% of OMEs dispensed, with a median of 0.9 OME grams (IQR 0.2-2.6). Based on 63.6% of practitioners with ≥10 patients filling opioid prescriptions in 2018, we identified four distinct practitioner clusters. The largest cluster prescribed multiple analgesic medicines for older patients (23.7% of practitioners) accounted for 76.7% of all OMEs dispensed and comprised 93.0% of the top 1% of practitioners by opioid volume dispensed. The cluster prescribing analgesics for younger patients with high rates of surgery (18.7% of practitioners) prescribed only 1.6% of OMEs. The remaining two clusters comprised 21.2% of prescribers and 20.9% of OMEs dispensed.Discussion and conclusionWe observed substantial variation in opioid prescribing among practitioners, clustered around four general patterns. We did not assess appropriateness but some prescribing patterns are concerning. Our findings provide insights for targeted interventions to curb potentially harmful practices.
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Project description:BackgroundThere is uncertainty about factors associated with involuntary in-patient psychiatric care. Understanding these factors would help in reducing coercion in psychiatry.AimsTo explore variables associated with involuntary care in the largest database of involuntary admissions published.MethodWe identified 166 102 public mental health hospital admissions over 5 years in New South Wales, Australia. Demographic, clinical and episode-of-care variables were examined in an exploratory, multivariable logistic regression.ResultsA total of 54% of eligible admissions included involuntary care. The strongest associations with involuntary care were referral from the legal system (odds ratio 4.98, 95% CI 4.61-5.38), and psychosis (odds ratio 4.48, 95% CI 4.31-4.64) or organic mental disorder (odds ratio 4.40, 95% CI 3.85-5.03). There were moderately strong associations between involuntary treatment and substance use disorder (odds ratio 2.68, 95% CI 2.56-2.81) or affective disorder (odds ratio 2.06, 95% CI 1.99-2.14); comorbid cannabis and amphetamine use disorders (odds ratio 1.65, 95% CI 1.57-1.74); unmarried status (odds ratio 1.62, 95% CI 1.49-1.76) and being born in Asia (odds ratio 1.42, 95% CI 1.35-1.50), Africa or the Middle East (odds ratio 1.32, 95% CI 1.24-1.40). Involuntary care was less likely for people aged >75 years (odds ratio 0.68, 95% CI 0.62-0.74), with comorbid personality disorder (odds ratio 0.90, 95% CI 0.87-0.94) or with private health insurance (odds ratio 0.89, 95% CI 0.86-0.93).ConclusionsThis research strengthens the evidence linking diagnostic, socioeconomic and cultural factors to involuntary treatment. Targeted interventions are needed to reduce involuntary admissions in disadvantaged groups.
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