Genomic Tools in Biological Invasions: Current State and Future Frontiers.

Human activities are accelerating rates of biological invasions and climate-driven range expansions globally, yet we understand little of how genomic processes facilitate the invasion process. Although most of the literature has focused on underlying phenotypic correlates of invasiveness, advances in genomic technologies are showing a strong link between genomic variation and invasion success. Here, we consider the ability of genomic tools and technologies to (i) inform mechanistic understanding of biological invasions and (ii) solve real-world issues in predicting and managing biological invasions. For both, we examine the current state of the field and discuss how genomics can be leveraged in the future. In addition, we make recommendations pertinent to broader research issues, such as data sovereignty, metadata standards, collaboration, and science communication best practices that will require concerted efforts from the global invasion genomics community.

Reply to Obegi, J.H. Distinguishing Prevention from Treatment in Suicide Prevention. Comment on "Turner et al. The Paradox of Suicide Prevention. Int. J. Environ. Res. Public Health 2022, 19, 14983".

One of the aims of our paper "The Paradox of Suicide Prevention" is to promote greater discourse on suicide prevention, with a particular focus on the mental health models used for the identification of, and interventions with, individuals who come into contact with tertiary mental health services [...].

Natural Language Processing in Electronic Health Records in relation to healthcare decision-making: A systematic review.

BACKGROUND: Natural Language Processing (NLP) is widely used to extract clinical insights from Electronic Health Records (EHRs). However, the lack of annotated data, automated tools, and other challenges hinder the full utilisation of NLP for EHRs. Various Machine Learning (ML), Deep Learning (DL) and NLP techniques are studied and compared to understand the limitations and opportunities in this space comprehensively. METHODOLOGY: After screening 261 articles from 11 databases, we included 127 papers for full-text review covering seven categories of articles: (1) medical note classification, (2) clinical entity recognition, (3) text summarisation, (4) deep learning (DL) and transfer learning architecture, (5) information extraction, (6) Medical language translation and (7) other NLP applications. This study follows the Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines. RESULT AND DISCUSSION: EHR was the most commonly used data type among the selected articles, and the datasets were primarily unstructured. Various ML and DL methods were used, with prediction or classification being the most common application of ML or DL. The most common use cases were: the International Classification of Diseases, Ninth Revision (ICD-9) classification, clinical note analysis, and named entity recognition (NER) for clinical descriptions and research on psychiatric disorders. CONCLUSION: We find that the adopted ML models were not adequately assessed. In addition, the data imbalance problem is quite important, yet we must find techniques to address this underlining problem. Future studies should address key limitations in studies, primarily identifying Lupus Nephritis, Suicide Attempts, perinatal self-harmed and ICD-9 classification.

The Paradox of Suicide Prevention.

The recognition that we cannot use risk stratification (high, medium, low) to predict suicide or to allocate resources has led to a paradigm shift in suicide prevention efforts. There are challenges in adapting to these new paradigms, including reluctance of clinicians and services to move away from traditional risk categorisations; and conversely, the risk of a pendulum swing in which the focus of care swings from one approach to determining service priority and focus (e.g., diagnosis, formulation, risk and clinical care) to a new focus (e.g., suicide specific and non-clinical care), potentially supplanting the previous approach. This paper argues that the Prevention Paradox provides a useful mental model to support a shift in paradigm, whilst maintaining a balanced approach that incorporates new paradigms within the effective aspects of existing ones. The Prevention Paradox highlights the seemingly paradoxical situation where the greatest burden of disease or death is caused by those at low to moderate risk due their larger numbers. Current planning frameworks and resources do not support successful or sustainable adoption of these new approaches, leading to missed opportunities to prevent suicidal behaviours in healthcare. Adopting systems approaches to suicide prevention, such as the Zero Suicide Framework, implemented in a large mental health service in Australia and presented in this paper as a case study, can support a balanced approach of population- and individual-based suicide prevention efforts. Results demonstrate significant reductions in re-presentations with suicide attempts for consumers receiving this model of care; however, the increasing numbers of placements compromise the capacity of clinical teams to complete all components of standardised pathway of care. This highlights the need for review of resource planning frameworks and ongoing evaluations of the critical aspects of the interventions.

Increasing Incidence of Invasive Group A Streptococcus Disease, Idaho, USA, 2008-2019.

We investigated invasive group A Streptococcus epidemiology in Idaho, USA, during 2008-2019 using surveillance data, medical record review, and emm (M protein gene) typing results. Incidence increased from 1.04 to 4.76 cases/100,000 persons during 2008-2019. emm 1, 12, 28, 11, and 4 were the most common types, and 2 outbreaks were identified. We examined changes in distribution of clinical syndrome, patient demographics, and risk factors by comparing 2008-2013 baseline with 2014-2019 data. Incidence was higher among all age groups during 2014-2019. Streptococcal toxic shock syndrome increased from 0% to 6.4% of cases (p = 0.02). We identified no differences in distribution of demographic or risk factors between periods. Results indicated that invasive group A Streptococcus is increasing among the general population of Idaho. Ongoing surveillance of state-level invasive group A Streptococcus cases could help identify outbreaks, track regional trends in incidence, and monitor circulating emm types.

Collaborative Approach to Supporting Staff in a Mental Healthcare Setting: "Always There" Peer Support Program.

This paper describes the development and implementation of a peer-support program Always There in a large public mental health service in Queensland, Australia. The program is modelled on Scott's three tier model of peer support, with trained responders providing emotional support to staff following a traumatic adverse event, or when experiencing acute or cumulative stress. Support is provided in complete confidentiality. Main lessons learned in the 2 years since the launch of the program are shared in this paper, outlining successes such as improvements in staff's perception of organisational culture, and challenges related to embedding the program to "business as usual".

Re-imagining crop domestication in the era of high throughput phenomics.

De novo domestication is an exciting option for increasing species diversity and ecosystem service functionality of agricultural landscapes. Genomic selection (GS), the application of genomic markers to predict phenotypic traits in a breeding population, offers the possibility of rapid genetic improvement, making GS especially attractive for modifying traits of long-lived species. However, for some wild species just entering the domestication pipeline, especially those with large and complex genomes, a lack of funding and/or prior genome characterization, GS is often out of reach. High throughput phenomics has the potential to augment traditional pedigree selection, reduce costs and amplify impacts of genomic selection, and even create new predictive selection approaches independent of sequencing or pedigrees.

Covid-19 Rates by Time since Vaccination during Delta Variant Predominance.

BACKGROUND: With the emergence of the delta variant, the United States experienced a rapid increase in Covid-19 cases in 2021. We estimated the risk of breakthrough infection and death by month of vaccination as a proxy for waning immunity during a period of delta variant predominance. METHODS: Covid-19 case and death data from 15 U.S. jurisdictions during January 3 to September 4, 2021 were used to estimate weekly hazard rates among fully vaccinated persons, stratified by age group and vaccine product. Case and death rates during August 1 to September 4, 2021 were presented across four cohorts defined by month of vaccination. Poisson models were used to estimate adjusted rate ratios comparing the earlier cohorts to July rates. RESULTS: During August 1 to September 4, 2021, case rates per 100,000 person-weeks among all vaccine recipients for the January to February, March to April, May to June, and July cohorts were 168.8 (95% confidence interval [CI], 167.5 to 170.1), 123.5 (95% CI, 122.8 to 124.1), 83.6 (95% CI, 82.9 to 84.3), and 63.1 (95% CI, 61.6 to 64.6), respectively. Similar trends were observed by age group for BNT162b2 (Pfizer-BioNTech) and mRNA-1273 (Moderna) vaccine recipients. Rates for the Ad26.COV2.S (Janssen-Johnson & Johnson) vaccine were higher; however, trends were inconsistent. BNT162b2 vaccine recipients 65 years of age or older had higher death rates among those vaccinated earlier in the year. Protection against death was sustained for the mRNA-1273 vaccine recipients. Across age groups and vaccine types, people who were vaccinated 6 months ago or longer (January-February) were 3.44 (3.36 to 3.53) times more likely to be infected and 1.70 (1.29 to 2.23) times more likely to die from COVID-19 than people vaccinated recently in July 2021. CONCLUSIONS: Our study suggests that protection from SARS-CoV-2 infection among all ages or death among older adults waned with increasing time since vaccination during a period of delta predominance. These results add to the evidence base that supports U.S. booster recommendations, especially for older adults vaccinated with BNT162b2 and recipients of the Ad26.COV2.S vaccine. (Funded by the Centers for Disease Control and Prevention.).

Consumer and Carer Perspectives of a Zero Suicide Prevention Program: A Qualitative Study.

This study explored the experiences of healthcare consumers who had recently attempted suicide, and their carers, following placement on a Suicide Prevention Pathway based on the Zero Suicide framework. Qualitative interviews were conducted with 10 consumers and 5 carers using a semi-structured interview schedule. Interviews were transcribed and thematic analysis was applied to identify prominent themes and sub-themes. Three interrelated themes were identified. The first theme was 'Feeling safe and valued' with the associated sub-theme pertaining to perceived stigmatizing treatment and self-stigma. The second was 'Intersection of consumer and staff/organizational needs' with a related sub-theme of time pressure and reduced self-disclosure. The final theme was 'Importance of the 'whole picture', highlighting the relevance of assessing and addressing psychosocial factors when planning for consumer recovery. Overall, consumers and their carers reported a favorable experience of the Suicide Prevention Pathway; however, there were several areas identified for improvement. These included reconciling the time-pressures of a busy health service system, ensuring consumers and carers feel their psychosocial concerns are addressed, and ensuring that adequate rapport is developed. Key to this is ensuring consumers feel cared for and reducing perceptions of stigma.

A lived experience co-designed study protocol for a randomised control trial: the Attempted Suicide Short Intervention Program (ASSIP) or Brief Cognitive Behavioural Therapy as additional interventions after a suicide attempt compared to a standard Suicide Prevention Pathway (SPP).

BACKGROUND: Despite being preventable, suicide is a leading cause of death and a major global public health problem. For every death by suicide, many more suicide attempts are undertaken, and this presents as a critical risk factor for suicide. Currently, there are limited treatment options with limited underpinning research for those who present to emergency departments with suicidal behaviour. The aim of this study is to assess if adding one of two structured suicide-specific psychological interventions (Attempted Suicide Short Intervention Program [ASSIP] or Brief Cognitive Behavioural Therapy [CBT] for Suicide Prevention) to a standardised clinical care approach (Suicide Prevention Pathway [SPP]) improves the outcomes for consumers presenting to a Mental Health Service with a suicide attempt. METHODS: This is a randomised controlled trial with blinding of those assessing the outcomes. People who attempt suicide or experience suicidality after a suicide attempt, present to the Gold Coast Mental Health and Specialist Services, are placed on the Suicide Prevention Pathway (SPP), and meet the eligibility criteria, are offered the opportunity to participate. A total of 411 participants will be recruited for the study, with 137 allocated to each cohort (participants are randomised to SPP, ASSIP + SPP, or CBT + SPP). The primary outcomes of this study are re-presentation to hospitals with suicide attempts. Presentations with suicidal ideation will also be examined (in a descriptive analysis) to ascertain whether a rise in suicidal ideation is commensurate with a fall in suicide attempts (which might indicate an increase in help-seeking behaviours). Death by suicide rates will also be examined to ensure that representations with a suicide attempt are not due to participants dying, but due to a potential improvement in mental health. For participants without a subsequent suicide attempt, the total number of days from enrolment to the last assessment (24 months) will be calculated. Self-reported levels of suicidality, depression, anxiety, stress, resilience, problem-solving skills, and self- and therapist-reported level of therapeutic engagement are also being examined. Psychometric data are collected at baseline, end of interventions, and 6,12, and 24 months. DISCUSSION: This project will move both ASSIP and Brief CBT from efficacy to effectiveness research, with clear aims of assessing the addition of two structured psychological interventions to treatment as usual, providing a cost-benefit analysis of the interventions, thus delivering outcomes providing a clear pathway for rapid translation of successful interventions. TRIALS REGISTRATION: ClinicalTrials.gov NCT04072666 . Registered on 28 August 2019.

A cluster of Achromobacter xylosoxidans led to identification of Pseudomonas aeruginosa and Serratia marcescens contamination at a long-term-care facility.

A cluster of Achromobacter xylosoxidans, an emerging multidrug-resistant aquaphilic bacterium, was identified in 3 long-term-care facility residents. As Pseudomonas aeruginosa and Serratia marcescens were also present in clinical specimens, we conducted an investigation of all 3 water-associated species and identified P. aerguniosa and S. marcescens contamination at the facility. Sequencing analysis linked P. aeruginosa to a clinical isolate. Findings highlight the need for precautionary measures to prevent transmission of water-associated multidrug-resistant bacteria in long-term-care facilities.

Investigation and public health response to a COVID-19 outbreak in a rural resort community-Blaine County, Idaho, 2020.

Blaine County, Idaho, a rural area with a renowned resort, experienced a COVID-19 outbreak early in the pandemic. We undertook an epidemiologic investigation to describe the outbreak and guide public health action. Confirmed cases of COVID-19 were identified from reports of SARS-CoV-2-positive laboratory test results to South Central Public Health District. Information on symptoms, hospitalization, recent travel, healthcare worker status, and close contacts was obtained by medical record review and patient interviews. Viral sequence analysis was conducted on a subset of available specimens. During March 13-April 10, 2020, a total of 451 COVID-19 cases among Blaine County residents (1,959 cases per 100,000 population) were reported, with earliest illness onset March 1. The median patient age was 51 years (interquartile range [IQR]: 37-63), 52 (11.5%) were hospitalized, and 5 (1.1%) died. The median duration between specimen collection and a positive laboratory result was 9 days (IQR: 4-10). Forty-four (9.8%) patients reported recent travel and an additional 37 cases occurred in out-of-state residents. Healthcare workers comprised 56 (12.4%) cases; 33 of whom worked at the only hospital in the county, leading to a 15-day disruption of hospital services. Among 562 close contacts monitored by public health authorities, laboratory-confirmed COVID-19 or compatible symptoms were identified in 51 (9.1%). Sequencing results from 34 specimens supported epidemiologic findings indicating travel as a source of SARS-CoV-2, and identified multiple lineages among hospital workers. Community mitigation strategies included school and resort closure, stay-at-home orders, and restrictions on incoming travelers. COVID-19 outbreaks in rural communities can disrupt health services. Lack of local laboratory capacity led to long turnaround times for COVID-19 test results. Rural communities frequented by tourists face unique challenges during the COVID-19 pandemic. Implementing restrictions on incoming travelers and other mitigation strategies helped reduce COVID-19 transmission early in the pandemic.

The impact of viral epidemics and pandemics on acute mental health service use: an integrative review.

The aim of this integrative review was to examine the impact of past viral epidemics on mental health, with a specific focus on changes in numbers of acute mental health presentations and mental health service recommendations in response to this, in the context of the COVID-19 pandemic. Following PRISMA methodology, databases were searched for relevant publications. A total of 83 articles with a range of methodologies were included to ensure broad coverage of this rapidly emerging research area. The literature supports an initial increase in mental health concerns which generally do not reach the threshold for diagnosis with a mental illness, but present to frontline telephone services. There is a potential delay before community and hospital-based mental health services see an increase in new or relapsing mental illness presentations. However vulnerable populations, such as people with pre-existing mental illness, are at increased risk of mental health issues during such public health crises. Many of the general recommendations distilled from the literature are closely aligned with existing strategic frameworks for mental health service provision. However, in review of these frameworks, gaps in the literature become more apparent, such as a failure to include people with lived experience, peer workers, and First Nations People in the COVID-19 mental health response.

Suicide prevention during COVID-19: identification of groups with reduced presentations to emergency departments.

OBJECTIVE: Reductions in suicidal and self-harm presentations to emergency departments (EDs) since COVID-19 indicate changes in help-seeking behaviours, but it is unknown if hospital avoidance equally affects all population groups. METHOD: Socio-demographic and clinical information relating to suicidal and self-harm presentations to EDs in Queensland, Australia, were compared for the period before (March-August 2019) and since the COVID-19 outbreak (March-August 2020). RESULTS: Since COVID, Indigenous Australians and persons with less severe suicidal and self-harm presentations had significantly reduced presentations, while persons younger than 18 years had more presentations. Less suicidal presentations resulted in an admission to inpatient care. CONCLUSIONS: Patterns of reduced attendance to ED in some groups suggest the need for innovative and community-based models of care to help prevent suicides during the pandemic.

Responding to the Pandemic: Challenges With Public Health Surveillance Systems and Development of a COVID-19 National Surveillance Case Definition to Support Case-Based Morbidity Surveillance During the Early Response.

Responding to introductions of diseases and conditions of unknown etiology is a critical public health function. In late December 2019, investigation of a cluster of pneumonia cases of unknown origin in Wuhan, China, resulted in the identification of a novel coronavirus, severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Multiple public health surveillance actions were rapidly implemented to detect introduction of the virus into the United States and track its spread including establishment of a national surveillance case definition and addition of the disease, coronavirus disease 2019, to the list of nationally notifiable conditions. Challenges in conducting effective case-based surveillance and the public health data supply chain and infrastructure are discussed.

Efficacy of the Zero Suicide framework in reducing recurrent suicide attempts: cross-sectional and time-to-recurrent-event analyses.

BACKGROUND: The Zero Suicide framework is a system-wide approach to prevent suicides in health services. It has been implemented worldwide but has a poor evidence-base of effectiveness. AIMS: To evaluate the effectiveness of the Zero Suicide framework, implemented in a clinical suicide prevention pathway (SPP) by a large public mental health service in Australia, in reducing repeated suicide attempts after an index attempt. METHOD: A total of 604 persons with 737 suicide attempt presentations were identified between 1 July and 31 December 2017. Relative risk for a subsequent suicide attempt within various time periods was calculated using cross-sectional analysis. Subsequently, a 10-year suicide attempt history (2009-2018) for the cohort was used in time-to-recurrent-event analyses. RESULTS: Placement on the SPP reduced risk for a repeated suicide attempt within 7 days (RR = 0.29; 95% CI 0.11-0.75), 14 days (RR = 0.38; 95% CI 0.18-0.78), 30 days (RR = 0.55; 95% CI 0.33-0.94) and 90 days (RR = 0.62; 95% CI 0.41-0.95). Time-to-recurrent event analysis showed that SPP placement extended time to re-presentation (HR = 0.65; 95% CI 0.57-0.67). A diagnosis of personality disorder (HR = 2.70; 95% CI 2.03-3.58), previous suicide attempt (HR = 1.78; 95% CI 1.46-2.17) and Indigenous status (HR = 1.46; 95% CI 0.98-2.25) increased the hazard for re-presentation, whereas older age decreased it (HR = 0.92; 95% CI 0.86-0.98). The effect of the SPP was similar across all groups, reducing the risk of re-presentation to about 65% of that seen in those not placed on the SPP. CONCLUSIONS: This paper demonstrates a reduction in repeated suicide attempts after an index attempt and a longer time to a subsequent attempt for those receiving multilevel care based on the Zero Suicide framework.

Implementing a systems approach to suicide prevention in a mental health service using the Zero Suicide Framework.

OBJECTIVE: The Zero Suicide Framework, a systems approach to suicide prevention within a health service, is being implemented across a number of states in Australia, and internationally, although there is limited published evidence for its effectiveness. This paper aims to provide a description of the implementation process within a large health service in Australia and describes some of the outcomes to date and learnings from this process. METHOD: Gold Coast Mental Health and Specialist Services has undertaken an implementation of the Zero Suicide Framework commencing in late 2015, aiming for high fidelity to the seven key elements. This paper describes the practical steps undertaken by the service, the new practices embedded, emphasis on supporting staff following the principles of restorative just culture and the development of an evaluation framework to support a continuous quality improvement approach. RESULTS: Improvements have been demonstrated in terms of processes implementation, enhanced staff skills and confidence, positive cultural change and innovations in areas such as the use of machine learning for identification of suicide presentations. A change to 'business as usual' has benefited thousands of consumers since the implementation of a Suicide Prevention Pathway in late 2016 and achieved reductions in rates of repeated suicide attempts and deaths by suicide in Gold Coast Mental Health and Specialist Services consumers. CONCLUSION: An all-of-service, systems approach to suicide prevention with a strong focus on cultural shifts and aspirational goals can be successfully implemented within a mental health service with only modest additional resources when supported by engaged leadership across the organisation. A continuous quality improvement approach is vital in the relentless pursuit of zero suicides in healthcare.