The Canadian VirusSeq Data Portal & Duotang: open resources for SARS-CoV-2 viral sequences and genomic epidemiology.

The COVID-19 pandemic led to a large global effort to sequence SARS-CoV-2 genomes from patient samples to track viral evolution and inform public health response. Millions of SARS-CoV-2 genome sequences have been deposited in global public repositories. The Canadian COVID-19 Genomics Network (CanCOGeN - VirusSeq), a consortium tasked with coordinating expanded sequencing of SARS-CoV-2 genomes across Canada early in the pandemic, created the Canadian VirusSeq Data Portal, with associated data pipelines and procedures, to support these efforts. The goal of VirusSeq was to allow open access to Canadian SARS-CoV-2 genomic sequences and enhanced, standardized contextual data that were unavailable in other repositories and that meet FAIR standards (Findable, Accessible, Interoperable and Reusable). The Portal data submission pipeline contains data quality checking procedures and appropriate acknowledgement of data generators that encourages collaboration. Here we also highlight Duotang, a web platform that presents genomic epidemiology and modeling analyses on circulating and emerging SARS-CoV-2 variants in Canada. Duotang presents dynamic changes in variant composition of SARS-CoV-2 in Canada and by province, estimates variant growth, and displays complementary interactive visualizations, with a text overview of the current situation. The VirusSeq Data Portal and Duotang resources, alongside additional analyses and resources computed from the Portal (COVID-MVP, CoVizu), are all open-source and freely available. Together, they provide an updated picture of SARS-CoV-2 evolution to spur scientific discussions, inform public discourse, and support communication with and within public health authorities. They also serve as a framework for other jurisdictions interested in open, collaborative sequence data sharing and analyses.

A comparison of brain retraction mechanisms using finite element analysis and the effects of regionally heterogeneous material properties.

Finite element (FE) simulations of the brain undergoing neurosurgical procedures present us with the great opportunity to better investigate, understand, and optimize surgical techniques and equipment. FE models provide access to data such as the stress levels within the brain that would otherwise be inaccessible with the current medical technology. Brain retraction is often a dangerous but necessary part of neurosurgery, and current research focuses on minimizing trauma during the procedure. In this work, we present a simulation-based comparison of different types of retraction mechanisms. We focus on traditional spatulas and tubular retractors. Our results show that tubular retractors result in lower average predicted stresses, especially in the subcortical structures and corpus callosum. Additionally, we show that changing the location of retraction can greatly affect the predicted stress results. As the model predictions highly depend on the material model and parameters used for simulations, we also investigate the importance of using region-specific hyperelastic and viscoelastic material parameters when modelling a three-dimensional human brain during retraction. Our investigations demonstrate how FE simulations in neurosurgical techniques can provide insight to surgeons and medical device manufacturers. They emphasize how further work into this direction could greatly improve the management and prevention of injury during surgery. Additionally, we show the importance of modelling the human brain with region-dependent parameters in order to provide useful predictions for neurosurgical procedures.

Putting everything in its place: using the INSDC compliant Pathogen Data Object Model to better structure genomic data submitted for public health applications.

Fast, efficient public health actions require well-organized and coordinated systems that can supply timely and accurate knowledge. Public databases of pathogen genomic data, such as the International Nucleotide Sequence Database Collaboration (INSDC), have become essential tools for efficient public health decisions. However, these international resources began primarily for academic purposes, rather than for surveillance or interventions. Now, queries need to access not only the whole genomes of multiple pathogens but also make connections using robust contextual metadata to identify issues of public health relevance. Databases that over time developed a patchwork of submission formats and requirements need to be consistently organized and coordinated internationally to allow effective searches.To help resolve these issues, we propose a common pathogen data structure called the Pathogen Data Object Model (DOM) that will formalize the minimum pieces of sequence data and contextual data necessary for general public health uses, while recognizing that submitters will likely withhold a wide range of non-public contextual data. Further, we propose contributors use the Pathogen DOM for all pathogen submissions (bacterial, viral, fungal, and parasites), which will simplify data submissions and provide a consistent and transparent data structure for downstream data analyses. We also highlight how improved submission tools can support the Pathogen DOM, offering users additional easy-to-use methods to ensure this structure is followed.

The DataHarmonizer: a tool for faster data harmonization, validation, aggregation and analysis of pathogen genomics contextual information.

Pathogen genomics is a critical tool for public health surveillance, infection control, outbreak investigations as well as research. In order to make use of pathogen genomics data, they must be interpreted using contextual data (metadata). Contextual data include sample metadata, laboratory methods, patient demographics, clinical outcomes and epidemiological information. However, the variability in how contextual information is captured by different authorities and how it is encoded in different databases poses challenges for data interpretation, integration and their use/re-use. The DataHarmonizer is a template-driven spreadsheet application for harmonizing, validating and transforming genomics contextual data into submission-ready formats for public or private repositories. The tool's web browser-based JavaScript environment enables validation and its offline functionality and local installation increases data security. The DataHarmonizer was developed to address the data sharing needs that arose during the COVID-19 pandemic, and was used by members of the Canadian COVID Genomics Network (CanCOGeN) to harmonize SARS-CoV-2 contextual data for national surveillance and for public repository submission. In order to support coordination of international surveillance efforts, we have partnered with the Public Health Alliance for Genomic Epidemiology to also provide a template conforming to its SARS-CoV-2 contextual data specification for use worldwide. Templates are also being developed for One Health and foodborne pathogens. Overall, the DataHarmonizer tool improves the effectiveness and fidelity of contextual data capture as well as its subsequent usability. Harmonization of contextual information across authorities, platforms and systems globally improves interoperability and reusability of data for concerted public health and research initiatives to fight the current pandemic and future public health emergencies. While initially developed for the COVID-19 pandemic, its expansion to other data management applications and pathogens is already underway.

A Schema for Digitized Surface Swab Site Metadata in Open-Source DNA Sequence Databases.

Large, open-source DNA sequence databases have been generated, in part, through the collection of microbial pathogens by swabbing surfaces in built environments. Analyzing these data in aggregate through public health surveillance requires digitization of the complex, domain-specific metadata that are associated with the swab site locations. However, the swab site location information is currently collected in a single, free-text, "isolation source", field-promoting generation of poorly detailed descriptions with various word order, granularity, and linguistic errors, making automation difficult and reducing machine-actionability. We assessed 1,498 free-text swab site descriptions that were generated during routine foodborne pathogen surveillance. The lexicon of free-text metadata was evaluated to determine the informational facets and the quantity of unique terms used by data collectors. Open Biological Ontologies (OBO) Foundry libraries were used to develop hierarchical vocabularies that are connected with logical relationships to describe swab site locations. 5 informational facets that were described by 338 unique terms were identified via content analysis. Term hierarchy facets were developed, as were statements (called axioms) about how the entities within these five domains are related. The schema developed through this study has been integrated into a publicly available pathogen metadata standard, facilitating ongoing surveillance and investigations. The One Health Enteric Package was available at NCBI BioSample, beginning in 2022. The collective use of metadata standards increases the interoperability of DNA sequence databases and enables large-scale approaches to data sharing and artificial intelligence as well as big-data solutions to food safety. IMPORTANCE The regular analysis of whole-genome sequence data in collections such as NCBI's Pathogen Detection Database is used by many public health organizations to detect outbreaks of infectious disease. However, isolate metadata in these databases are often incomplete and of poor quality. These complex, raw metadata must often be reorganized and manually formatted for use in aggregate analyses. These processes are inefficient and time-consuming, increasing the interpretative labor needed by public health groups to extract actionable information. The future use of open genomic epidemiology networks will be supported through the development of an internationally applicable vocabulary system with which swab site locations can be described.

Canadians' opinions towards COVID-19 data-sharing: a national cross-sectional survey.

OBJECTIVES: COVID-19 research has significantly contributed to pandemic response and the enhancement of public health capacity. COVID-19 data collected by provincial/territorial health authorities in Canada are valuable for research advancement yet not readily available to the public, including researchers. To inform developments in public health data-sharing in Canada, we explored Canadians' opinions of public health authorities sharing deidentified individual-level COVID-19 data publicly. DESIGN/SETTING/INTERVENTIONS/OUTCOMES: A national cross-sectional survey was administered in Canada in March 2022, assessing Canadians' opinions on publicly sharing COVID-19 datatypes. Market research firm Léger was employed for recruitment and data collection. PARTICIPANTS: Anyone greater than or equal to 18 years and currently living in Canada. RESULTS: 4981 participants completed the survey with a 92.3% response rate. 79.7% were supportive of provincial/territorial authorities publicly sharing deidentified COVID-19 data, while 20.3% were hesitant/averse/unsure. Datatypes most supported for being shared publicly were symptoms (83.0% in support), geographical region (82.6%) and COVID-19 vaccination status (81.7%). Datatypes with the most aversion were employment sector (27.4% averse), postal area (26.7%) and international travel history (19.7%). Generally supportive Canadians were characterised as being ≥50 years, with higher education, and being vaccinated against COVID-19 at least once. Vaccination status was the most influential predictor of data-sharing opinion, with respondents who were ever vaccinated being 4.20 times more likely (95% CI 3.21 to 5.48, p=0.000) to be generally supportive of data-sharing than those unvaccinated. CONCLUSIONS: These findings suggest that the Canadian public is generally favourable to deidentified data-sharing. Identifying factors that are likely to improve attitudes towards data-sharing are useful to stakeholders involved in data-sharing initiatives, such as public health agencies, in informing the development of public health communication and data-sharing policies. As Canada progresses through the COVID-19 pandemic, and with limited testing and reporting of COVID-19 data, it is essential to improve deidentified data-sharing given the public's general support for these efforts.

CARD 2023: expanded curation, support for machine learning, and resistome prediction at the Comprehensive Antibiotic Resistance Database.

The Comprehensive Antibiotic Resistance Database (CARD; card.mcmaster.ca) combines the Antibiotic Resistance Ontology (ARO) with curated AMR gene (ARG) sequences and resistance-conferring mutations to provide an informatics framework for annotation and interpretation of resistomes. As of version 3.2.4, CARD encompasses 6627 ontology terms, 5010 reference sequences, 1933 mutations, 3004 publications, and 5057 AMR detection models that can be used by the accompanying Resistance Gene Identifier (RGI) software to annotate genomic or metagenomic sequences. Focused curation enhancements since 2020 include expanded ß-lactamase curation, incorporation of likelihood-based AMR mutations for Mycobacterium tuberculosis, addition of disinfectants and antiseptics plus their associated ARGs, and systematic curation of resistance-modifying agents. This expanded curation includes 180 new AMR gene families, 15 new drug classes, 1 new resistance mechanism, and two new ontological relationships: evolutionary_variant_of and is_small_molecule_inhibitor. In silico prediction of resistomes and prevalence statistics of ARGs has been expanded to 377 pathogens, 21,079 chromosomes, 2,662 genomic islands, 41,828 plasmids and 155,606 whole-genome shotgun assemblies, resulting in collation of 322,710 unique ARG allele sequences. New features include the CARD:Live collection of community submitted isolate resistome data and the introduction of standardized 15 character CARD Short Names for ARGs to support machine learning efforts.

Early childhood development practices in a remote Aboriginal Community Controlled Health Services setting.

OBJECTIVE: Supporting Early Childhood Development (ECD) is an Australian national priority. Aboriginal children in Western Australia's Kimberley region have much higher rates of developmental concerns at school entry than non-Aboriginal children. We aimed to describe ECD practices in the participating service; document follow-up of identified developmental concerns; and identify barriers and enablers to incorporating ECD practices into clinic activity. DESIGN: Mixed-method design incorporating clinical audit and staff interviews. SETTING: An Aboriginal Community Controlled Health Service (ACCHS) in the Kimberley region. PARTICIPANTS: A total of 176 children receiving primary health care through the participating ACCHS; interviews with five ACCHS staff members. MAIN OUTCOME MEASURES: Frequency of developmental enquiry by age and domain; follow-up of identified developmental concerns; and barriers and enablers to ECD practices. RESULTS: Developmental enquiry was documented for 114 of 176 eligible children (65%), including in 80% of ACCHS child health assessments. Standardised ECD assessments were less common. Staff were aware of the importance of developmental enquiry, however, barriers to increasing ECD practices included a lack of resources and structured staff education, time pressures and a lack of role clarity between the ACCHS and government community health clinic. CONCLUSIONS: This study provides insight into ECD practices in an ACCHS setting, highlighting the potential of primary health care to have an enhanced role in ECD if appropriate systems, training and tools are provided. A lack of role clarity across services, combined with poor communication between services, creates a potential risk for missed opportunities to support ECD.

Future-proofing and maximizing the utility of metadata: The PHA4GE SARS-CoV-2 contextual data specification package.

BACKGROUND: The Public Health Alliance for Genomic Epidemiology (PHA4GE) (https://pha4ge.org) is a global coalition that is actively working to establish consensus standards, document and share best practices, improve the availability of critical bioinformatics tools and resources, and advocate for greater openness, interoperability, accessibility, and reproducibility in public health microbial bioinformatics. In the face of the current pandemic, PHA4GE has identified a need for a fit-for-purpose, open-source SARS-CoV-2 contextual data standard. RESULTS: As such, we have developed a SARS-CoV-2 contextual data specification package based on harmonizable, publicly available community standards. The specification can be implemented via a collection template, as well as an array of protocols and tools to support both the harmonization and submission of sequence data and contextual information to public biorepositories. CONCLUSIONS: Well-structured, rich contextual data add value, promote reuse, and enable aggregation and integration of disparate datasets. Adoption of the proposed standard and practices will better enable interoperability between datasets and systems, improve the consistency and utility of generated data, and ultimately facilitate novel insights and discoveries in SARS-CoV-2 and COVID-19. The package is now supported by the NCBI's BioSample database.

Real-world screening for diabetes in early pregnancy: Improved screening uptake using universal glycated haemoglobin.

AIMS: To improve perinatal outcomes, screening for hyperglycaemia using 75 g oral glucose tolerance test (OGTT) is recommended for all pregnant women at 24-28 weeks gestation (routine), and earlier if high-risk. Screening coverage for remote and Aboriginal Australian women is less than ideal. This study examined OGTT completion (early and routine) by women from rural and remote Western Australia compared with early glycated haemoglobin (HbA1c). METHODS: In 2015-2018, 27 primary health care sites recruited 600 (233 Aboriginal) women aged ≥16-years, without pre-existing diabetes, who delivered >30-weeks gestation. All women presenting <20-weeks gestation (541) were offered an early study HbA1c. Early OGTTs were requested at the discretion of the local clinician, with routine OGTT offered at 24-28 weeks. RESULTS: HbA1c uptake was high (85.7% Aboriginal, 86.4% non-Aboriginal); OGTT completion in Aboriginal women was low (early OGTT: 38.6% v 69.6% non-Aboriginal, P < 0.001; routine OGTT: 44.5% v 84.7% non-Aboriginal, P < 0.001). Aboriginal women with both early tests had HbA1c completed 3-weeks prior to OGTT (9.6 ± 3.5 v 12.5 ± 3.5 weeks gestation, P < 0.001). CONCLUSIONS: Universal early pregnancy HbA1c appears feasible as an early screening test for women at risk of hyperglycaemia in pregnancy and would expedite and increase screening in Aboriginal women compared to an early OGTT.

Equity in Access: A Mixed Methods Exploration of the National Disability Insurance Scheme Access Program for the Kimberley Region, Western Australia.

This study explored the process and early outcomes of work undertaken by a program to increase Aboriginal people's awareness of, and access to, the National Disability Insurance Scheme (NDIS). This 'Access Program' was implemented through the Aboriginal Community Controlled Sector in the remote Kimberley region of Western Australia. Access Program staff were interviewed to explore the strengths, challenges, and future directions of the program. The demographics, primary disability types, and NDIS access outcomes for clients who engaged with the program in the first 12 months of its implementation have been described. The Access Program engaged with 373 clients during the study period and assisted 118 of these to achieve access to the NDIS. The program was reported as successful by staff in its aim of connecting eligible people with the NDIS. Vital to this success was program implementation by the Aboriginal Community Controlled Sector. Staff in these organisations held community trust, provided culturally appropriate services, and utilised strengths-based approaches to overcome barriers that have historically hindered Aboriginal people's engagement with disability services. Our results demonstrate the Access Program is a successful start in increasing awareness of, and access to, the NDIS for Aboriginal people in the Kimberley region. Much work remains to assist the large number of Aboriginal people in the Kimberley region believed to be eligible for NDIS support who are yet to achieve access.

Prediabetes and pregnancy: Early pregnancy HbA1c identifies Australian Aboriginal women with high-risk of gestational diabetes mellitus and adverse perinatal outcomes.

AIMS: To assess whether early pregnancy HbA1c can predict gestational diabetes mellitus (GDM) and adverse birth outcomes in Australian women. METHODS: Prospective study of 466 women without diabetes, aged ≥16-years at first antenatal presentation. Recruitment was from 27 primary healthcare sites in rural and remote Australia from 9-January 2015 to 31-May 2018. HbA1c was measured with first antenatal investigations (<20-weeks gestation). Primary outcome measure was predictive value of HbA1c for GDM, by routine 75 g oral glucose tolerance test (OGTT; ≥24-weeks gestation), and for large-for-gestational-age (LGA) newborn. RESULTS: Of 396 (129 Aboriginal) women with routine OGTT, 28.8% had GDM (24.0% Aboriginal). HbA1c ≥5.6% (≥38 mmol/mol) was highly predictive (71.4%, 95% CI; 47.8-88.7%) for GDM in Aboriginal women, and in the total cohort increased risk for LGA newborn (RR 2.04, 95% CI; 1.03-4.01, P = 0.040). There were clear differences between Aboriginal and non-Aboriginal women: 16.3% v 5.2% (P < 0.001) had elevated HbA1c whereas 12.4% v 29.6% (P < 0.001) developed hyperglycemia during pregnancy. CONCLUSIONS: Early pregnancy HbA1c ≥5.6% (≥38 mmol/mol) identifies Aboriginal women with apparent prediabetes and elevated risk of having an LGA newborn. Universal HbA1c at first antenatal presentation could facilitate earlier management of hyperglycemia and improved perinatal outcome in this high-risk population.

Addressing Privacy Concerns in Sharing Viral Sequences and Minimum Contextual Data in a Public Repository During the COVID-19 Pandemic.

COVID-19 was declared to be a pandemic in March 2020 by the World Health Organization. Timely sharing of viral genomic sequencing data accompanied by a minimal set of contextual data is essential for informing regional, national, and international public health responses. Such contextual data is also necessary for developing, and improving clinical therapies and vaccines, and enhancing the scientific community's understanding of the SARS-CoV-2 virus. The Canadian COVID-19 Genomics Network (CanCOGeN) was launched in April 2020 to coordinate and upscale existing genomics-based COVID-19 research and surveillance efforts. CanCOGeN is performing large-scale sequencing of both the genomes of SARS-CoV-2 virus samples (VirusSeq) and affected Canadians (HostSeq). This paper addresses the privacy concerns associated with sharing the viral sequence data with a pre-defined set of contextual data describing the sample source and case attribute of the sequence data in the Canadian context. Currently, the viral genome sequences are shared by provincial public health laboratories and their healthcare and academic partners, with the Canadian National Microbiology Laboratory and with publicly accessible databases. However, data sharing delays and the provision of incomplete contextual data often occur because publicly releasing such data triggers privacy and data governance concerns. The CanCOGeN Ethics and Governance Expert Working Group thus has investigated several privacy issues cited by CanCOGeN data providers/stewards. This paper addresses these privacy concerns and offers insights primarily in the Canadian context, although similar privacy considerations also exist in other jurisdictions. We maintain that sharing viral sequencing data and its limited associated contextual data in the public domain generally does not pose insurmountable privacy challenges. However, privacy risks associated with reidentification should be actively monitored due to advancements in reidentification methods and the evolving pandemic landscape. We also argue that during a global health emergency such as COVID-19, privacy should not be used as a blanket measure to prevent such genomic data sharing due to the significant benefits it provides towards public health responses and ongoing research activities.

Preconception Care in a Remote Aboriginal Community Context: What, When and by Whom?

Preconception care (PCC) is acknowledged as a vital preventive health measure aiming to promote health today and for subsequent generations. We aimed to describe the content and context of PCC delivery in a very remote Australian Aboriginal Community Controlled Health Service setting. A retrospective audit was undertaken to identify what PCC was delivered between 2011 and 2018 to 127 Aboriginal women who had at least one pregnancy during this period. Of 177 confirmed pregnancies, 121 had received PCC prior to the pregnancy. Sexually transmissible infection screening (71%) was the most common care delivered, followed by folic acid prescription (57%) and smoking cessation support (43%). Younger women received PCC less often, particularly screening for modifiable pregnancy risk factors. Rates of prediabetes/diabetes, albuminuria, overweight/obesity and smoking were high amongst those screened (48-60%). PCC was usually patient-initiated and increased significantly over the audit period. Presentation for antenatal care in the first trimester of pregnancy was high at 73%. Opportunities to increase PCC delivery include integration with routine health checks, pregnancy tests and chronic disease programs. PCC programs codesigned with young people are also recommended. All primary care providers should be supported and assisted to provide opportunistic PCC and health promotion.

CARD 2020: antibiotic resistome surveillance with the comprehensive antibiotic resistance database.

The Comprehensive Antibiotic Resistance Database (CARD; https://card.mcmaster.ca) is a curated resource providing reference DNA and protein sequences, detection models and bioinformatics tools on the molecular basis of bacterial antimicrobial resistance (AMR). CARD focuses on providing high-quality reference data and molecular sequences within a controlled vocabulary, the Antibiotic Resistance Ontology (ARO), designed by the CARD biocuration team to integrate with software development efforts for resistome analysis and prediction, such as CARD's Resistance Gene Identifier (RGI) software. Since 2017, CARD has expanded through extensive curation of reference sequences, revision of the ontological structure, curation of over 500 new AMR detection models, development of a new classification paradigm and expansion of analytical tools. Most notably, a new Resistomes & Variants module provides analysis and statistical summary of in silico predicted resistance variants from 82 pathogens and over 100 000 genomes. By adding these resistance variants to CARD, we are able to summarize predicted resistance using the information included in CARD, identify trends in AMR mobility and determine previously undescribed and novel resistance variants. Here, we describe updates and recent expansions to CARD and its biocuration process, including new resources for community biocuration of AMR molecular reference data.

Eleven High-Quality Reference Genome Sequences and 360 Draft Assemblies of Shiga Toxin-Producing Escherichia coli Isolates from Human, Food, Animal, and Environmental Sources in Canada.

We report high-quality closed reference genomes for 1 bovine strain and 10 human Shiga toxin (Stx)-producing Escherichia coli (STEC) strains from serogroups O26, O45, O91, O103, O104, O111, O113, O121, O145, and O157. We also report draft assemblies, with standardized metadata, for 360 STEC strains isolated from watersheds, animals, farms, food, and human infections.

Hyperglycaemic presentations in type 2 diabetes

BACKGROUND: Hyperosmolar hyperglycaemic state (HHS) is a syndrome that occurs in patients with type 2 diabetes mellitus (T2DM) and is comparable to diabetic ketoacidosis (DKA) seen in patients with type 1 diabetes. For a general practitioner working in a rural emergency department, recognition of HHS in a patient presenting with the triad of severe dehydration, hyperglycaemia and hyperosmolality is important to guide management and plan for disposition. OBJECTIVES: This article reviews the hyperglycaemic states that can occur in patients with T2DM. The reasons for the biochemical derangements in both HHS and DKA are outlined, with a focus on the recognition and management of HHS. DISCUSSION: Knowledge of the pathophysiology that influences HHS helps understand of its clinical presentation and treatment. HHS has a high mortality rate (5­20%), and having access to clinical guidelines from a referring hospital is useful to guide early management strategies.

Pregnancy intentions in a group of remote-dwelling Australian Aboriginal women: a qualitative exploration of formation, expression and implications for clinical practice.

BACKGROUND: Unintended pregnancies are associated with poorer obstetric outcomes and are sometimes measured at a population level as a surrogate marker for reproductive autonomy and access to health services, including contraception. Aboriginal Australians face many disparities in health outcomes, including in reproductive health and antenatal care. We aimed to explore the formation and expression of pregnancy intentions in an Aboriginal population to inform health service improvements. METHODS: Semi-structured interviews were conducted with 27 remote-dwelling Aboriginal women, aged 18-49 years. Content analysis was conducted; key themes were discussed with groups of women from participating communities to refine interpretation. RESULTS: Most (19/27) participants expressed pregnancy intentions congruent with reported contraceptive behaviour while eight expressed ambivalent or uncertain intentions. Intentions were shaped by traditional kinship practices, reproductive autonomy and desired family formation. Younger women tended to aspire to smaller family sizes than older women and support was expressed for the postponement of first pregnancy to achieve other life goals. Women in these communities hold strong traditional beliefs, including regarding conception, but did not use traditional methods of contraception in place of modern methods. Reproductive coercion, in the form of pressure to fall pregnant, was recognised as an important issue by women in the community. CONCLUSION: Consultation strategies that promote rapport, allow space for uncertainty and are inclusive of important personal and cultural contexts are likely to improve shared understanding of pregnancy intention. Universal screening for reproductive coercion and broad counselling on contraceptive options (including discrete methods) may reduce unmet need for contraception. Community approaches supporting reproductive autonomy that is inclusive of men, and enhanced educational and occupational opportunities for young women are needed.

Acute kidney injury in Indigenous Australians in the Kimberley: age distribution and associated diagnoses.

OBJECTIVE: To describe the frequencies of acute kidney injury (AKI) and of associated diagnoses in Indigenous people in a remote Western Australian region. DESIGN: Retrospective population-based study of AKI events confirmed by changes in serum creatinine levels. SETTING, PARTICIPANTS: Aboriginal and Torres Strait Islander residents of the Kimberley region of Western Australia, aged 15 years or more and without end-stage kidney disease, for whom AKI between 1 June 2009 and 30 May 2016 was confirmed by an acute rise in serum creatinine levels. MAIN OUTCOME MEASURES: Age-specific AKI rates; principal and other diagnoses. RESULTS: 324 AKI events in 260 individuals were recorded; the median age of patients was 51.8 years (IQR, 43.9-61.0 years), and 176 events (54%) were in men. The overall AKI rate was 323 events (95% CI, 281-367) per 100 000 population; 92 events (28%) were in people aged 15-44 years. 52% of principal diagnoses were infectious in nature, including pneumonia (12% of events), infections of the skin and subcutaneous tissue (10%), and urinary tract infections (7.7%). 80 events (34%) were detected on or before the date of admission; fewer than one-third of discharge summaries (61 events, 28%) listed AKI as a primary or other diagnosis. CONCLUSION: The age distribution of AKI events among Indigenous Australians in the Kimberley was skewed to younger groups than in the national data on AKI. Infectious conditions were common in patients, underscoring the significance of environmental determinants of health. Primary care services can play an important role in preventing community-acquired AKI; applying pathology-based criteria could improve the detection of AKI.