Phenotyping people with a history of injecting drug use within electronic medical records using an interactive machine learning approach.

People with a history of injecting drug use are a priority for eliminating blood-borne viruses and sexually transmissible infections. Identifying them for disease surveillance in electronic medical records (EMRs) is challenged by sparsity of predictors. This study introduced a novel approach to phenotype people who have injected drugs using structured EMR data and interactive human-in-the-loop methods.

An evaluation of existing text de-identification tools for use with patient progress notes from Australian general practice.

Introduction: Digitized patient progress notes from general practice represent a significant resource for clinical and public health research but cannot feasibly and ethically be used for these purposes without automated de-identification. Internationally, several open-source natural language processing tools have been developed, however, given wide variations in clinical documentation practices, these cannot be utilized without appropriate review. We evaluated the performance of four de-identification tools and assessed their suitability for customization to Australian general practice progress notes.

Undetected serovars: leptospirosis cases in the Cairns region during the 2021 wet season.

Background: Leptospirosis infection can lead to serious renal and cardiopulmonary complications and can be fatal. Following heavy rainfall and localised flooding in early 2021, Tropical Public Health Services in Cairns were alerted to an increase in leptospirosis cases in the region, with notifications almost three times higher than usual by mid-February. An epidemiological investigation was undertaken.

The Incidence of Hepatitis C Among Gay, Bisexual, and Other Men Who Have Sex With Men in Australia, 2009-2019.

Background: Hepatitis C virus (HCV) infection has been reported among gay, bisexual, and other men who have sex with men (GBM) globally including GBM with human immunodeficiency virus (HIV) and HIV-negative GBM, particularly those using HIV preexposure prophylaxis (PrEP). In Australia, HCV direct-acting antiviral treatment (DAA) was government-funded from 2016. Large implementation studies of PrEP also began in 2016.

Microelimination of Hepatitis C Among People With Human Immunodeficiency Virus Coinfection: Declining Incidence and Prevalence Accompanying a Multicenter Treatment Scale-up Trial.

Background: Gay and bisexual men (GBM) are a key population affected by human immunodeficiency virus (HIV) and hepatitis C virus (HCV) coinfection. We aimed to measure HCV treatment effectiveness and to determine the population impact of treatment scale-up on HCV prevalence and incidence longitudinally among GBM.

Methods: The co-EC Study (Enhancing Care and Treatment Among HCV/HIV Coinfected Individuals to Eliminate Hepatitis C Transmission) was an implementation trial providing HCV direct-acting antiviral treatment in Melbourne, Australia, during 2016-2018.

Phylogenetic clustering networks among heterosexual migrants with new HIV diagnoses post-migration in Australia.

Background: It is estimated that approximately half of new HIV diagnoses among heterosexual migrants in Victoria, Australia, were acquired post-migration. We investigated the characteristics of phylogenetic clusters in notified cases of HIV among heterosexual migrants.

Methods: Partial HIV pol sequences obtained from routine clinical genotype tests were linked to Victorian HIV notifications with the following exposures listed on the notification form: heterosexual sexual contact, injecting drug use, bisexual sexual contact, male-to male sexual contact or heterosexual sexual contact in combination with injecting drug use, unknown exposure.

The impact of universal access to direct-acting antiviral therapy on the hepatitis C cascade of care among individuals attending primary and community health services.

Background: Hepatitis C elimination will require widespread access to treatment and responses at the health-service level to increase testing among populations at risk. We explored changes in hepatitis C testing and the cascade of care before and after the introduction of direct-acting antiviral treatments in Victoria, Australia.

Methods: De-identified clinical data were retrospectively extracted from eighteen primary care clinics providing services targeted towards people who inject drugs.

Privacy-Preserving Record Linkage of Deidentified Records Within a Public Health Surveillance System: Evaluation Study.

Background: The Australian Collaboration for Coordinated Enhanced Sentinel Surveillance (ACCESS) was established to monitor national testing and test outcomes for blood-borne viruses (BBVs) and sexually transmissible infections (STIs) in key populations. ACCESS extracts deidentified data from sentinel health services that include general practice, sexual health, and infectious disease clinics, as well as public and private laboratories that conduct a large volume of BBV/STI testing. An important attribute of ACCESS is the ability to accurately link individual-level records within and between the participating sites, as this enables the system to produce reliable epidemiological measures.

Comparing sexual behaviours and knowledge between domestic students and Chinese international students in Australia: findings from two cross-sectional studies.

Few studies investigate sexual health among Chinese international students in Australia. We recruited domestic (n = 623) and Chinese international (n = 500) students for separate online surveys on sexual behaviours and knowledge. Samples were compared using Chi square, Fisher's exact and equality of medians tests.

Gaps in the HIV diagnosis and care cascade for migrants in Australia, 2013-2017: A cross-sectional study.

Background: Globally, few studies compare progress toward the Joint United Nations Program on HIV/AIDS (UNAIDS) Fast-Track targets among migrant populations. Fast-Track targets are aligned to the HIV diagnosis and care cascade and entail achieving 90-90-90 (90% of people living with HIV [PLHIV] diagnosed, 90% of those diagnosed on treatment, and 90% of those on treatment with viral suppression [VS]) by 2020 and 95-95-95 by 2030. We compared cascades between migrant and nonmigrant populations in Australia.

Risk of Subsequent HIV Infection Following Sexually Transmissible Infections Among Men Who Have Sex With Men.

Background: HIV and bacterial sexually transmissible infection (STI) notifications among men who have sex with men (MSM) have increased in Australia and many other countries. The relationship between HIV infection and other STIs has been demonstrated previously. However, the relationship between the cumulative history of STIs and subsequent HIV infection remains largely unexplored and limits our understanding of the mechanisms underpinning the elevated HIV risk.

Pathology Laboratory Surveillance in the Australian Collaboration for Coordinated Enhanced Sentinel Surveillance of Sexually Transmitted Infections and Blood-Borne Viruses: Protocol for a Cohort Study.

Background: Passive surveillance is the principal method of sexually transmitted infection (STI) and blood-borne virus (BBV) surveillance in Australia whereby positive cases of select STIs and BBVs are notified to the state and territory health departments. A major limitation of passive surveillance is that it only collects information on positive cases and notifications are heavily dependent on testing patterns. Denominator testing data are important in the interpretation of notifications.

Two decades of surveillance data show late presentation among a diverse group of women diagnosed with HIV in Victoria, Australia.

Objective: To develop an HIV response suited to women and to inform appropriate services, we describe the characteristics of women diagnosed and living with HIV using 22 years of high-quality surveillance data.

Methods: Data on women newly diagnosed with HIV between 1994 and 2016 and women living with diagnosed HIV in Victoria at 31 December 2016 were extracted from the Victorian Public Health Surveillance System. Descriptive analysis by place of birth was performed and Poisson regression used to assess trends over time.

Estimating the syphilis epidemic among gay, bisexual and other men who have sex with men in Australia following changes in HIV care and prevention.

Unlabelled: Background Syphilis control remains a challenge in many high-income countries, including Australia, where diagnoses are concentrated among gay, bisexual men and other men who have sex with men (GBM). The aim of this study is to project the syphilis epidemic among GBM under a range of scenarios.

Methods: A dynamic coinfection model of HIV and syphilis transmission among GBM in Victoria, Australia, was parametrised to test data from clinics in Melbourne and syphilis case notifications in Victoria.

Association of HIV Preexposure Prophylaxis With Incidence of Sexually Transmitted Infections Among Individuals at High Risk of HIV Infection.

Importance: Emerging evidence suggests that risk of bacterial sexually transmitted infections (STIs) increases among gay and bisexual men following initiation of HIV preexposure prophylaxis (PrEP).

Objective: To describe STI incidence and behavioral risk factors among a cohort of predominantly gay and bisexual men who use PrEP, and to explore changes in STI incidence following PrEP commencement.

Design, Setting, And Participants: The Pre-exposure Prophylaxis Expanded (PrEPX) Study, a multisite, open-label intervention study, was nested within the Australian Collaboration for Coordinated Enhanced Sentinel Surveillance (ACCESS) clinic network.

Monitoring the Control of Sexually Transmissible Infections and Blood-Borne Viruses: Protocol for the Australian Collaboration for Coordinated Enhanced Sentinel Surveillance (ACCESS).

Background: New biomedical prevention interventions make the control or elimination of some blood-borne viruses (BBVs) and sexually transmissible infections (STIs) increasingly feasible. In response, the World Health Organization and governments around the world have established elimination targets and associated timelines. To monitor progress toward such targets, enhanced systems of data collection are required.

Aiming for 90-90-90 - the importance of understanding the risk factors for HIV exposure and advanced HIV infection in migrant populations and other groups who do not report male-to-male sex.

Unlabelled: Background In Australia, new HIV diagnoses increasingly occur among people who do not report male-to-male sex. Among migrants, it is not clear what proportion acquired infection before migration. Similarly, among Australian-born people, it is not clear what proportion acquired infection in-country.

Eliminating hepatitis C virus as a public health threat among HIV-positive men who have sex with men: a multi-modelling approach to understand differences in sexual risk behaviour.

Introduction: Outbreaks of hepatitis C virus (HCV) infections among HIV-positive men who have sex with men (MSM) have been observed globally. Using a multi-modelling approach we estimate the time and number of direct-acting antiviral treatment courses required to achieve an 80% reduction in HCV prevalence among HIV-positive MSM in the state of Victoria, Australia.

Methods: Three models of HCV transmission, testing and treatment among MSM were compared: a dynamic compartmental model; an agent-based model (ABM) parametrized to local surveillance and behavioural data ("ABM1"); and an ABM with a more heterogeneous population ("ABM2") to determine the influence of extreme variations in sexual risk behaviour.

Utility of risk-based chlamydia testing in primary care: analysis of retrospective surveillance data among women in Melbourne, Australia.

Unlabelled: Background Chlamydia (Chlamydia trachomatis) continues to be a public health challenge in Australia, with some contention as to the best screening approach. In the present study we examined chlamydia testing, positivity and sexual behaviour among women with the aim of informing targeted testing among women aged ≥30 years.

Methods: A longitudinal analysis was conducted on retrospective surveillance data collected among women attending general practice, family planning and sexual health clinics participating in sentinel surveillance in Melbourne, Australia.