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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. We iteratively trained random forest classifiers removing important features and adding new positive labels each time. The initial model achieved 92.7% precision and 93.5% recall. Models maintained >90% precision and recall after nine iterations, revealing combinations of less obvious features influencing predictions. Applied to approximately 1.7 million patients, the final model identified 128,704 (7.7%) patients as potentially having injected drugs, beyond the 50,510 (2.9%) with known indicators of injecting drug use. This process produced explainable models that revealed otherwise hidden combinations of predictors, offering an adaptive approach to addressing the inherent challenge of inconsistently missing data in EMRs., Competing Interests: Competing interests: A.G.D. is a Deputy Editor of npj Digital Medicine. All other authors declare no competing interests., (© 2024. The Author(s).)

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., Methods: Four tools were selected: three rule-based (HMS Scrubber, MIT De-id, Philter) and one machine learning (MIST). 300 patient progress notes from three general practice clinics were manually annotated with personally identifying information. We conducted a pairwise comparison between the manual annotations and patient identifiers automatically detected by each tool, measuring recall (sensitivity), precision (positive predictive value), f1-score (harmonic mean of precision and recall), and f2-score (weighs recall 2x higher than precision). Error analysis was also conducted to better understand each tool's structure and performance., Results: Manual annotation detected 701 identifiers in seven categories. The rule-based tools detected identifiers in six categories and MIST in three. Philter achieved the highest aggregate recall (67%) and the highest recall for NAME (87%). HMS Scrubber achieved the highest recall for DATE (94%) and all tools performed poorly on LOCATION. MIST achieved the highest precision for NAME and DATE while also achieving similar recall to the rule-based tools for DATE and highest recall for LOCATION. Philter had the lowest aggregate precision (37%), however preliminary adjustments of its rules and dictionaries showed a substantial reduction in false positives., Conclusion: Existing off-the-shelf solutions for automated de-identification of clinical text are not immediately suitable for our context without modification. Philter is the most promising candidate due to its high recall and flexibility however will require extensive revising of its pattern matching rules and dictionaries., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2023 Elsevier B.V. All rights reserved.)

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. We examined HCV incidence among GBM to assess whether HCV incidence has changed since 2015., Methods: Data were drawn from the Australian Collaboration for Coordinated Enhanced Sentinel Surveillance. We included GBM who tested HCV antibody negative at their first test and had ≥1 subsequent test. Generalized linear modeling (Poisson distribution) was used to examine HCV incidence from 2009 to 2019 stratified by HIV status, and among HIV-negative GBM prescribed PrEP from 2016 to 2019., Results: Among 6744 GBM with HIV, HCV incidence was 1.03 per 100 person-years (PY). Incidence declined by 78% in 2019 compared to 2015 (incidence rate ratio [IRR], 0.22 [95% confidence interval {CI}: .09-.55]). Among 20 590 HIV-negative GBM, HCV incidence was 0.20/100 PY, with no significant change over time. Among 11 661 HIV-negative GBM prescribed PrEP, HCV incidence was 0.29/100 PY. Compared to 2016, incidence among GBM prescribed PrEP declined by 80% in 2019 (IRR, 0.20 [95% CI: .06-.64])., Conclusions: HCV incidence among GBM living with HIV declined following DAA availability. There was no observed change in HCV incidence among HIV-negative GBM overall. Among GBM prescribed PrEP, incidence declined since the early years of PrEP implementation in Australia. Australia is on track to eliminate HCV among GBM before global 2030 targets., (© The Author(s) 2021. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail: journals.permissions@oup.com.)

Background: Monitoring trends in hepatitis C virus (HCV) incidence is critical for evaluating strategies aimed at eliminating HCV as a public health threat. We estimate HCV incidence and assess trends in incidence over time among primary care patients., Methods: Data were routinely extracted, linked electronic medical records from 12 primary care health services. Patients included were aged ≥16 years, tested HCV antibody negative on their first test recorded and had at least one subsequent HCV antibody or RNA test (January 2009-December 2020). HCV incident infections were defined as a positive HCV antibody or RNA test. A generalised linear model assessed the association between HCV incidence and calendar year., Results: In total, 6711 patients contributed 17,098 HCV test records, 210 incident HCV infections and 19,566 person-years; incidence was 1.1 per 100 person-years (95% confidence interval (CI): 0.9 to 1.2). Among 559 (8.2%) patients ever prescribed opioid-related pharmacotherapy (ORP) during the observation period, 135 infections occurred during 2,082 person-years (incidence rate of 6.5 per 100 person-years (95% CI: 5.4 to 7.7)). HCV incidence declined 2009-2020 overall (incidence rate ratio per calendar year 0.8 (95% CI: 0.8 to 0.9) and among patients ever prescribed ORT (incidence rate ratio per calendar year 0.9, 95% CI: 0.75 to 1.0)., Conclusion: HCV incidence declined among patients at primary care health services including among patients ever prescribed ORP and during the period following increased access to DAA therapy., Competing Interests: Declarations of Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 Elsevier B.V. All rights reserved.)

To achieve the elimination of the hepatitis C virus (HCV), sustained and sufficient levels of HCV testing is critical. The purpose of this study was to assess trends in testing and evaluate the effectiveness of strategies to diagnose people living with HCV. Data were from 12 primary care clinics in Victoria, Australia, that provide targeted services to people who inject drugs (PWID), alongside general health care. This ecological study spanned 2009-2019 and included analyses of trends in annual numbers of HCV antibody tests among individuals with no previous positive HCV antibody test recorded and annual test yield (positive HCV antibody tests/all HCV antibody tests). Generalised linear models estimated the association between count outcomes (HCV antibody tests and positive HCV antibody tests) and time, and χ2 test assessed the trend in test yield. A total of 44 889 HCV antibody tests were conducted 2009-2019; test numbers increased 6% annually on average [95% confidence interval (CI) 4-9]. Test yield declined from 2009 (21%) to 2019 (9%) (χ2P = <0.01). In more recent years (2013-2019) annual test yield remained relatively stable. Modest increases in HCV antibody testing and stable but high test yield within clinics delivering services to PWID highlights testing strategies are resulting in people are being diagnosed however further increases in the testing of people at risk of HCV or living with HCV may be needed to reach Australia's HCV elimination goals.

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. Individuals with HCV/HIV coinfection were prospectively enrolled from primary and tertiary care services. HCV viremic prevalence and HCV antibody/viremic incidence were measured using a statewide, linked, surveillance system., Results: Among 200 participants recruited, 186 initiated treatment during the study period. Sustained virological response in primary care (98% [95% confidence interval {CI}, 93%-100%]) was not different to tertiary care (98% [95% CI, 86%-100%]). From 2012 to 2019, between 2434 and 3476 GBM with HIV infection attended our primary care sites annually, providing 13 801 person-years of follow-up; 50%-60% received an HCV test annually, and 10%-14% were anti-HCV positive. Among those anti-HCV positive, viremic prevalence declined 83% during the study (54% in 2016 to 9% in 2019). HCV incidence decreased 25% annually from 1.7/100 person-years in 2012 to 0.5/100 person-years in 2019 (incidence rate ratio, 0.75 [95% CI, .68-.83]; P < .001)., Conclusions: High treatment effectiveness by nonspecialists demonstrates the feasibility of treatment scale-up in this population. Substantial declines in HCV incidence and prevalence among GBM provides proof-of-concept for HCV microelimination., Clinical Trials Registration: NCT02786758., (© The Author(s) 2020. Published by Oxford University Press for the Infectious Diseases Society of America. All rights reserved. For permissions, e-mail: journals.permissions@oup.com.)

Background: Most studies assessing the HIV care cascade have typically been cross-sectional analyses, which do not capture the transition time to subsequent stages. We aimed to assess the longitudinal HIV cascade of care in Australia, and changes over time in transition times and associated factors., Methods: In this longitudinal cohort study, we included linked data for gay and bisexual men (GBM) with a new HIV diagnosis who attended clinics participating in the Australian Collaboration for Coordinated Enhanced Sentinel Surveillance in New South Wales and Victoria between Jan 1, 2012, and Dec 31, 2019. We assessed three cascade transition periods: diagnosis to linkage to care (stage 1 transition); linkage to care to antiretroviral therapy (ART) initiation (stage 2 transition); and ART initiation to virological suppression (viral load ≤200 copies per mL; stage 3 transition). We also calculated the probability of remaining virologically suppressed after the first recorded viral load of less than 200 copies per mL. We used the Kaplan-Meier method to estimate transition times and cumulative probability of stage transition., Findings: We included 2196 GBM newly diagnosed with HIV between 2012 and 2019 contributing 6747 person-years of follow-up in our analysis. Median time from HIV diagnosis to linkage to care (stage 1 transition) was 2 days (IQR 1-3). Median time from linkage to care to ART initiation (stage 2 transition) was 33 days (30-35). Median time from ART initiation to first recorded virological suppression (stage 3 transition) was 49 days (47-52). The cumulative probability of ART initiation within 90 days of linkage to care increased from 36·9% (95% CI 32·9-40·6) in the 2012-13 calendar period to 94·1% (91·2-96·0) in the 2018-19 calendar period and cumulative probability of virological suppression within 90 days of ART initiation increased from 54·3% (48·8-59·3) in the 2012-13 calendar period to 82·9% (78·4-86·4) in the 2018-19 calendar period. 91·6% (90·1-93·1) of GBM remained virologically supressed up to 2 years after their first recorded virological suppression event., Interpretation: In countries with high cross-sectional cascade estimates such as Australia, the impact of treatment as prevention is better estimated using longitudinal cascade analyses., Funding: National Health and Medical Research Council Australia., Competing Interests: Declaration of interests MWT has received honoraria for scientific meetings from Gilead Sciences. JHM and JFH have received grants via their institutions from Gilead Sciences, ViiV Health Care, and Merck Sharpe Dohme for the conduct of clinical trials and participation on advisory boards. MH has received funding for investigator-initiated research from Gilead Sciences and AbbVie, unrelated to this work. RG has received research support funding from Gilead Sciences. MS has received funding for investigator-initiated research from Gilead Sciences and AbbVie unrelated to this work; and consultancy fees from Gilead Sciences for activities unrelated to this work. All other authors declare no competing interests., (Copyright © 2021 Elsevier Ltd. All rights reserved.)

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. Those with heterosexual sexual contact as the only exposure were the focus of this study, with the other exposures included to better understand transmission networks. Additional reference sequences were extracted from the Los Alamos database. Maximum likelihood methods were used to infer the phylogeny and the robustness of the resulting tree was assessed using bootstrap analysis. Phylogenetic clusters were defined on the basis of bootstrap and genetic distance., Results: HIV pol sequences were available for 332 of 445 HIV notifications attributed to only heterosexual sexual contact in Victoria from 2005-2014. Forty-three phylogenetic clusters containing at least one heterosexual migrant were detected, 30 (70%) of which were pairs. The characteristics of these phylogenetic clusters varied considerably by cluster size. Pairs were more likely to be composed of people living with HIV from a single country of birth (p = 0.032). Larger clusters (n≥3) were more likely to contain people born in Australian/New Zealand (p = 0.002), migrants from more than one country of birth (p = 0.013) and viral subtype-B, the most common subtype in Australia (p = 0.006). Pairs were significantly more likely to contain females (p = 0.037) and less likely to include HIV diagnoses with male-to-male sexual contact reported as a possible exposure (p<0.001) compared to larger clusters (n≥3)., Conclusion: Migrants appear to be at elevated risk of HIV acquisition, in part due to intimate relationships between migrants from the same country of origin, and in part due to risks associated with the broader Australian HIV epidemic. However, there was no evidence of large transmission clusters driven by heterosexual transmission between migrants. A multipronged approach to prevention of HIV among migrants is warranted., Competing Interests: MH and MS has received investigator initiated funding from Gilead Sciences, AbbVie and Bristol Myers Squibb for research unrelated to this work. This does not alter our adherence to PLOS ONE policies on sharing data and materials.

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. Domestic students were more likely than international students to have ever touched a partner's genitals (81% vs. 53%, p < 0.01), had oral sex (76% vs. 44%, p < 0.01), vaginal intercourse (67% vs. 41%, p < 0.01) and anal intercourse (31% vs. 6%, p < 0.01). Domestic students were younger when they first touched a partner's genitals (16 vs. 18 years, p < 0.01), had oral sex (17 vs. 18 years, p < 0.01) and vaginal intercourse (17 vs. 18 years, p < 0.01). Domestic students were less likely than Chinese international students to report only one lifetime partner for touching genitals (22% vs. 50%, p < 0.01), oral sex (25% vs. 55%, p < 0.01), vaginal intercourse (30% vs. 58%, p < 0.01) and anal intercourse (54% vs. 88%, p < 0.01). Domestic students were more likely than Chinese international students to use the oral contraceptive pill (48% vs. 16%, p < 0.01) and long-acting reversible contraceptives (19% vs. 1%, p < 0.01). Domestic students scored higher than international students on a contraception and chlamydia quiz (4/5 vs. 2/5, p < 0.01). Domestic and Chinese international students differed in sexual behaviours and knowledge highlighting the need for relevant sexual health promotion for both groups.

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. We explored hepatitis C testing within three-year periods immediately prior to (pre-DAA period) and following (post-DAA period) universal access to DAA treatments on 1st March 2016. Among ever RNA-positive individuals, we constructed two care cascades at the end of the pre-DAA and post-DAA periods., Results: The number of individuals HCV-tested was 13,784 (12.2% of those with a consultation) in the pre-DAA period and 14,507 (10.4% of those with a consultation) in the post-DAA period. The pre-DAA care cascade included 2,515 RNA-positive individuals; 1,977 (78.6%) were HCV viral load/genotype tested; 19 (0.8%) were prescribed treatment; and 12 had evidence of cure (0.5% of those RNA-positive and 63.6% of those eligible for cure). The post-DAA care cascade included 3,713 RNA-positive individuals; 3,276 (88.2%) were HCV viral load/genotype tested; 1,674 (45.1%) were prescribed treatment; and 863 had evidence of cure (23.2% of those RNA-positive and 94.9% of those eligible for cure)., Conclusion: Marked improvements in the cascade of hepatitis C care among patients attending primary care clinics were observed following the universal access of DAA treatments in Australia, although improvements in testing were less pronounced., Competing Interests: I have read the journal's policy and the authors of this manuscript have the following competing interests: JSD, DVS, MS, MH: Burnet Institute receives unrelated investigator-initiated research grants from Gilead Sciences, AbbVie, Merck/MSD, and Bristol Myers Squibb. MWT has received honoraria for speaking from Gilead Science. JSD: Honoraria for speaking from Gilead Sciences, Merck/MSD, and Abbvie; All other authors declare no conflicts of interest. This does not alter our adherence to PLOS ONE policies on sharing data and materials.

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., Objective: The aim of this study was to evaluate the use of GRHANITE software in ACCESS to extract and link deidentified data from participating clinics and laboratories. GRHANITE generates irreversible hashed linkage keys based on patient-identifying data captured in the patient electronic medical records (EMRs) at the site. The algorithms to produce the data linkage keys use probabilistic linkage principles to account for variability and completeness of the underlying patient identifiers, producing up to four linkage key types per EMR. Errors in the linkage process can arise from imperfect or missing identifiers, impacting the system's integrity. Therefore, it is important to evaluate the quality of the linkages created and evaluate the outcome of the linkage for ongoing public health surveillance., Methods: Although ACCESS data are deidentified, we created two gold-standard datasets where the true match status could be confirmed in order to compare against record linkage results arising from different approaches of the GRHANITE Linkage Tool. We reported sensitivity, specificity, and positive and negative predictive values where possible and estimated specificity by comparing a history of HIV and hepatitis C antibody results for linked EMRs., Results: Sensitivity ranged from 96% to 100%, and specificity was 100% when applying the GRHANITE Linkage Tool to a small gold-standard dataset of 3700 clinical medical records. Medical records in this dataset contained a very high level of data completeness by having the name, date of birth, post code, and Medicare number available for use in record linkage. In a larger gold-standard dataset containing 86,538 medical records across clinics and pathology services, with a lower level of data completeness, sensitivity ranged from 94% to 95% and estimated specificity ranged from 91% to 99% in 4 of the 6 different record linkage approaches., Conclusions: This study's findings suggest that the GRHANITE Linkage Tool can be used to link deidentified patient records accurately and can be confidently used for public health surveillance in systems such as ACCESS., (©Long Nguyen, Mark Stoové, Douglas Boyle, Denton Callander, Hamish McManus, Jason Asselin, Rebecca Guy, Basil Donovan, Margaret Hellard, Carol El-Hayek. Originally published in the Journal of Medical Internet Research (http://www.jmir.org), 24.06.2020.)

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., Methods and Findings: We conducted a serial cross-sectional survey for HIV diagnosis and care cascades using modelling estimates for proportions diagnosed combined with a clinical database for proportions on treatment and VS between 2013-2017. We estimated the number of PLHIV and number diagnosed using New South Wales (NSW) and Victorian (VIC) data from the Australian National HIV Registry. Cascades were stratified by migration status, sex, HIV exposure, and eligibility for subsidised healthcare in Australia (reciprocal healthcare agreement [RHCA]). We found that in 2017, 17,760 PLHIV were estimated in NSW and VIC, and 90% of them were males. In total, 90% of estimated PLHIV were diagnosed. Of the 9,391 who were diagnosed and retained in care, most (85%; n = 8,015) were males. We excluded 38% of PLHIV with missing data for country of birth, and 41% (n = 2,408) of eligible retained PLHIV were migrants. Most migrants were from Southeast Asia (SEA; 28%), northern Europe (12%), and eastern Asia (11%). Most of the migrants and nonmigrants were males (72% and 83%, respectively). We found that among those retained in care, 90% were on antiretroviral therapy (ART), and 95% of those on ART had VS (i.e., 90-90-95). Migrants had larger gaps in their HIV diagnosis and care cascade (85-85-93) compared with nonmigrants (94-90-96). Similarly, there were larger gaps among migrants reporting male-to-male HIV exposure (84-83-93) compared with nonmigrants reporting male-to-male HIV exposure (96-92-96). Large gaps were also found among migrants from SEA (72-87-93) and sub-Saharan Africa (SSA; 89-93-91). Migrants from countries ineligible for RHCA had lower cascade estimates (83-85-92) than RHCA-eligible migrants (96-86-95). Trends in the HIV diagnosis and care cascades improved over time (2013 and 2017). However, there was no significant increase in ART coverage among migrant females (incidence rate ratio [IRR]: 1.03; 95% CI 0.99-1.08; p = 0.154), nonmigrant females (IRR: 1.01; 95% CI 0.95-1.07; p = 0.71), and migrants from SEA (IRR: 1.03; 95% CI 0.99-1.07; p = 0.06) and SSA (IRR: 1.03; 95% CI 0.99-1.08; p = 0.11). Additionally, there was no significant increase in VS among migrants reporting male-to-male HIV exposure (IRR: 1.02; 95% CI 0.99-1.04; p = 0.08). The major limitation of our study was a high proportion of individuals missing data for country of birth, thereby limiting migrant status categorisation. Additionally, we used a cross-sectional instead of a longitudinal study design to develop the cascades and used the number retained as opposed to using all individuals diagnosed to calculate the proportions on ART., Conclusions: HIV diagnosis and care cascades improved overall between 2013 and 2017 in NSW and VIC. Cascades for migrants had larger gaps compared with nonmigrants, particularly among key migrant populations. Tracking subpopulation cascades enables gaps to be identified and addressed early to facilitate achievement of Fast-Track targets., Competing Interests: The authors have declared that no competing interests exist.

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., Results: There were 465 new diagnoses among women in Victoria between 1994 and 2016 and 613 women living with HIV in 2016. Women were diagnosed late, and frequently reported no HIV testing history, AIDS-defining illness or other symptoms of HIV at diagnosis. These indicators of delayed diagnosis were even greater for non-Australian-born women. Conclusions and implications for public health: For Victoria to reach the ambitious targets for diagnosis, treatment and viral suppression in 95% of people living with HIV, prevention programs and efforts to increase early diagnosis as well as support services must consider the epidemiology and diversity of women., (© 2019 The Authors.)

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., Methods: Data from HIV-negative MSM who attended high-HIV caseload primary care clinics in Melbourne, Australia, from 2007 to 2014 with 2 or more HIV and STI tests were included. Controlling for sexual behaviors self-reported at clinic visits, discrete time survival analyses using generalized linear modeling estimated the effect of an STI at the prior test event and the cumulative history of STIs (none, 1, 2, or more [repeated]) on risk of HIV infection., Results: A total of 8941 MSM met the study criteria; 227 (2.5%) were diagnosed with HIV over the follow-up period. Adjusting for sexual behaviors, a cumulative history of repeated rectal gonorrhea infections (adjusted hazard ratio [aHR], 6.27; 95% confidence interval [CI], 2.68-14.50) and a single rectal gonorrhea infection (aHR, 2.09; 95% CI, 1.15-3.79) were associated with increased HIV infection risk., Conclusions: Repeated and single rectal gonorrhea infections were independently associated with increased HIV infection risk. These findings suggest that MSM with any history of rectal gonorrhea, particularly repeat rectal gonorrhea, represent a group for whom preventive interventions for HIV should be emphasized., (© The Author(s) 2019. Published by Oxford University Press on behalf of Infectious Diseases Society of America.)

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., Objective: The aim of this study is to establish a national pathology laboratory surveillance system, part of a larger national sentinel surveillance system called ACCESS (the Australian Collaboration for Coordinated Enhanced Sentinel Surveillance). ACCESS is designed to utilize denominator testing data to understand trends in case reporting and monitor the uptake and outcomes of testing for STIs and BBVs., Methods: ACCESS involves a range of clinical sites and pathology laboratories, each with a separate method of recruitment, data extraction, and data processing. This paper includes pathology laboratory sites only. First established in 2007 for chlamydia only, ACCESS expanded in 2012 to capture all diagnostic and clinical monitoring tests for STIs and BBVs, initially from pathology laboratories in New South Wales and Victoria, Australia, to at least one public and one private pathology laboratory in all Australian states and territories in 2016. The pathology laboratory sentinel surveillance system incorporates a longitudinal cohort design whereby all diagnostic and clinical monitoring tests for STIs and BBVs are collated from participating pathology laboratories in a line-listed format. An anonymous, unique identifier will be created to link patient data within and between participating pathology laboratory databases and to clinical services databases. Using electronically extracted, line-listed data, several indicators for each STI and BBV can be calculated, including the number of tests, unique number of individuals tested and retested, test yield, positivity, and incidence., Results: To date, over 20 million STI and BBV laboratory test records have been extracted for analysis for surveillance monitoring nationally. Recruitment of laboratories is ongoing to ensure appropriate coverage for each state and territory; reporting of indicators will occur in 2019 with publication to follow., Conclusions: The ACCESS pathology laboratory sentinel surveillance network is a unique surveillance system that collects data on diagnostic testing, management, and care for and of STIs and BBVs. It complements the ACCESS clinical network and enhances Australia's capacity to respond to STIs and BBVs., International Registered Report Identifier (irrid): DERR1-10.2196/13625., (©Caroline van Gemert, Rebecca Guy, Mark Stoove, Wayne Dimech, Carol El-Hayek, Jason Asselin, Clarissa Moreira, Long Nguyen, Denton Callander, Douglas Boyle, Basil Donovan, Margaret Hellard. Originally published in JMIR Research Protocols (http://www.researchprotocols.org), 08.08.2019.)

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. Projected outcomes were new syphilis infections between 2018 and 2025 under seven testing and behaviour change scenarios., Results: Among HIV-negative GBM, the model estimated that increasing syphilis testing coverage (69% - 75%) and frequency (~8-monthly - 6-monthly) could prevent 5% and 13% of syphilis cases respectively between 2018 and 2025 compared to the status quo. Among HIV-positive GBM, less syphilis testing due to changes in HIV care increased syphilis cases by 29% between 2018 and 2025 compared to the status quo. Under a scenario of 20% HIV pre-exposure prophylaxis (PrEP) coverage among HIV-negative GBM (and associated increased serodiscordant sex, reduced condom use and increased syphilis testing), syphilis cases were estimated to decrease by 6% among HIV-negative GBM and by 3% among HIV-positive GBM compared to the status quo, driven by increased testing among PrEP users., Conclusion: The present study findings support syphilis control policies focusing on increased testing among GBM. Current Australian PrEP guidelines of quarterly syphilis testing are likely to negate any increases in syphilis due to risk compensation occurring with PrEP scale-up.

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. A total of 4275 participants were enrolled (July 26, 2016-April 1, 2018) in Victoria, Australia. Of these, 2981 enrolled at 5 ACCESS clinics (3 primary care, 1 sexual health, and 1 community-based HIV rapid testing service), had at least 1 follow-up visit, and were monitored until April 30, 2018., Exposures: Upon enrollment, participants received daily oral tenofovir disoproxil fumurate and emtricitabine for HIV PrEP, quarterly HIV and STI testing, and clinical monitoring., Main Outcomes and Measures: The primary outcome was incidence of chlamydia, gonorrhea, or syphilis. Incidence rates and hazard ratios describing behavioral risk factors of STI diagnosis were calculated. Incidence rate ratios (IRRs), adjusted for change in testing frequency, described changes in STI incidence from 1-year preenrollment to study follow-up among participants with preenrollment testing data (n = 1378)., Results: Among the 2981 individuals (median age, 34 years [interquartile range, 28-42]), 98.5% identified as gay or bisexual males, 29% used PrEP prior to enrollment, 89 (3%) withdrew and were censored at date of withdrawal, leaving 2892 (97.0%) enrolled at final follow-up. During a mean follow-up of 1.1 years (3185.0 person-years), 2928 STIs were diagnosed among 1427 (48%) participants (1434 chlamydia, 1242 gonorrhea, 252 syphilis). STI incidence was 91.9 per 100 person-years, with 736 participants (25%) accounting for 2237 (76%) of all STIs. Among 2058 participants with complete data for multivariable analysis, younger age, greater partner number, and group sex were associated with greater STI risk, but condom use was not. Among 1378 participants with preenrollment testing data, STI incidence increased from 69.5 per 100 person-years prior to enrollment to 98.4 per 100 person-years during follow-up (IRR, 1.41 [95% CI, 1.29-1.56]). After adjusting for testing frequency, the increase in incidence from 1 year preenrollment to follow-up was significant for any STI (adjusted IRR, 1.12 [95% CI, 1.02-1.23]) and for chlamydia (adjusted IRR, 1.17 [95% CI, 1.04-1.33])., Conclusions and Relevance: Among gay and bisexual men using PrEP, STIs were highly concentrated among a subset, and receipt of PrEP after study enrollment was associated with an increased incidence of STIs compared with preenrollment. These findings highlight the importance of frequent STI testing among gay and bisexual men using PrEP.

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. This paper describes the Australian Collaboration for Coordinated Enhanced Sentinel Surveillance (ACCESS)., Objective: This study aims to establish a national surveillance network designed to monitor public health outcomes and evaluate the impact of strategies aimed at controlling BBVs and STIs., Methods: ACCESS is a sentinel surveillance system comprising health services (sexual health clinics, general practice clinics, drug and alcohol services, community-led testing services, and hospital outpatient clinics) and pathology laboratories in each of Australia's 8 states and territories. Scoping was undertaken in each jurisdiction to identify sites that provide a significant volume of testing or management of BBVs or STIs or to see populations with particular risks for these infections ("priority populations"). Nationally, we identified 115 health services and 24 pathology laboratories as relevant to BBVs or STIs; purposive sampling was undertaken. As of March 2018, we had recruited 92.0% (104/113) of health services and 71% (17/24) of laboratories among those identified as relevant to ACCESS. ACCESS is based on the regular and automated extraction of deidentified patient data using specialized software called GRHANITE, which creates an anonymous unique identifier from patient details. This identifier allows anonymous linkage between and within participating sites, creating a national cohort to facilitate epidemiological monitoring and the evaluation of clinical and public health interventions., Results: Between 2009 and 2017, 1,171,658 individual patients attended a health service participating in ACCESS network comprising 7,992,241 consultations. Regarding those with unique BBV and STI-related health needs, ACCESS captured data on 366,441 young heterosexuals, 96,985 gay and bisexual men, and 21,598 people living with HIV., Conclusions: ACCESS is a unique system with the ability to track efforts to control STIs and BBVs-including through the calculation of powerful epidemiological indicators-by identifying response gaps and facilitating the evaluation of programs and interventions. By anonymously linking patients between and within services and over time, ACCESS has exciting potential as a research and evaluation platform. Establishing a national health surveillance system requires close partnerships across the research, government, community, health, and technology sectors., International Registered Report Identifier (irrid): DERR1-10.2196/11028., (©Denton Callander, Clarissa Moreira, Carol El-Hayek, Jason Asselin, Caroline van Gemert, Lucy Watchirs Smith, Long Nguyen, Wayne Dimech, Douglas IR Boyle, Basil Donovan, Mark Stoové, Margaret Hellard, Rebecca Guy. Originally published in JMIR Research Protocols (http://www.researchprotocols.org), 20.11.2018.)

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. There is a need to better understand the epidemiology of HIV in people who do not report male-to-male sex., Methods: Victorian public health surveillance data were used to classify migrants as having likely acquired HIV before or after arrival to Australia using a CD4 cell count decline method to estimate date of infection. Place of exposure for Australian-born people was estimated based on self-report. Factors associated with place of HIV acquisition, advanced infection and newly acquired infection were explored among migrants and among Australian-born people., Results: Between July 1996 and June 2014, there were 821 new non-MSM HIV diagnoses. Most (58%) were migrants, and of these, half (54%) were estimated to have acquired HIV before migration. Among Australian-born people, 27% reported exposure likely occurring abroad; the majority of these were men who reported exposure in South-East Asia. Advanced infection was common in migrants (45%) and Australian-born people (35%). Among migrants, birth in South-East Asia was associated with increased odds of advanced infection., Conclusion: These results highlight the potential vulnerability of migrants after arrival in Australia, especially those from South-East Asia and Sub-Saharan Africa, and that of Australian-born men travelling to these regions. Public health practice must be strengthened to meet prevention needs of these populations in line with Australian policy.

Background: Pre-exposure prophylaxis (PrEP) is the use of HIV anti-retroviral therapy to prevent HIV transmission in people at high risk of HIV acquisition. PrEP is highly efficacious when taken either daily, or in an on-demand schedule. In Australia co-formulated tenofovir-emtricitabine is registered for daily use for PrEP, however, this co-formulation is not listed yet on the national subsidized medicines list. We describe a study protocol that aims to demonstrate if the provision of PrEP to up to 3800 individuals at risk of HIV in Victoria, Australia reduces HIV incidence locally by 25% generally and 30% among GBM. Methods: PrEPX is a population level intervention study in Victoria, Australia in which generic PrEP will be delivered to 3800 individuals for up to 36 months. Study eligibility is consistent with the recently updated 2017 Australian PrEP guidelines. Participants will attend study clinics, shared care clinics, or outreach clinics for quarterly HIV/STI screening, biannual renal function tests and other clinical care as required. Study visits and STI diagnoses will be recorded electronically through the ACCESS surveillance system. At each study visit participants will be invited to complete behavioral surveys that collect demographics and sexual risk data. Diagnosis and behavioral data will be compared between PrEPX participants and other individuals testing within the ACCESS surveillance system. A subset of participants will complete in depth surveys and interviews to collect attitudes, beliefs and acceptability data. Participating clinics will provide clinic level data on implementation and management of PrEPX participants. The population level impact on HIV incidence will be assessed using Victorian HIV notification data. Discussion: This study will collect evidence on the real world impact of delivery of PrEP to 3800 individuals at risk of acquiring HIV in Victoria. This study will provide important information for the broader implementation of PrEP planning upon listing of the tenofovir-emtricitabine on the national subsidized list of medicines. The study is registered on the Australian New Zealand Clinical Trials Registry (ACTRN12616001215415).