Agent-based modelling of Mycobacterium tuberculosis transmission: a systematic review.

Background: Traditional epidemiological models tend to oversimplify the transmission dynamics of Mycobacterium tuberculosis (M.tb) to replicate observed tuberculosis (TB) epidemic patterns. This has led to growing interest in advanced methodologies like agent-based modelling (ABM), which can more accurately represent the complex heterogeneity of TB transmission.

The role of economic evaluation in modelling public health and social measures for pandemic policy: a systematic review.

Background: Dynamic transmission models are often used to provide epidemiological guidance for pandemic policy decisions. However, how economic evaluation is typically incorporated into this technique to generate cost-effectiveness estimates of pandemic policy responses has not previously been reviewed.

Methods: We systematically searched the Embase, PubMed and Scopus databases for dynamic epidemiological modelling studies that incorporated economic evaluation of public health and social measures (PHSMs), with no date restrictions, on 7 July 2024.

A data science pipeline applied to Australia's 2022 COVID-19 Omicron waves.

The field of software engineering is advancing at astonishing speed, with packages now available to support many stages of data science pipelines. These packages can support infectious disease modelling to be more robust, efficient and transparent, which has been particularly important during the COVID-19 pandemic. We developed a package for the construction of infectious disease models, integrated it with several open-source libraries and applied this composite pipeline to multiple data sources that provided insights into Australia's 2022 COVID-19 epidemic.

The prevalence of tuberculosis infection among foreign-born Canadians: a modelling study.

Background: The prevalence of tuberculosis infection is critical to the design of tuberculosis prevention strategies, yet is unknown in Canada. We estimated the prevalence of tuberculosis infection among Canadian residents born abroad.

Methods: We estimated the prevalence of tuberculosis infection by age and year of migration to Canada for people from each of 168 countries by constructing country-specific and calendar year-specific trends for annual risk of infection using a previously developed model.

Finding and treating both tuberculosis disease and latent infection during population-wide active case finding for tuberculosis elimination.

In recognition of the high rates of undetected tuberculosis in the community, the World Health Organization (WHO) encourages targeted active case finding (ACF) among "high-risk" populations. While this strategy has led to increased case detection in these populations, the epidemic impact of these interventions has not been demonstrated. Historical data suggest that population-wide (untargeted) ACF can interrupt transmission in high-incidence settings, but implementation remains lacking, despite recent advances in screening tools.

Replicating superspreader dynamics with compartmental models.

Infectious disease outbreaks often exhibit superspreader dynamics, where most infected people generate no, or few secondary cases, and only a small fraction of individuals are responsible for a large proportion of transmission. Although capturing this heterogeneity is critical for estimating outbreak risk and the effectiveness of group-specific interventions, it is typically neglected in compartmental models of infectious disease transmission-which constitute the most common transmission dynamic modeling framework. In this study we propose different classes of compartmental epidemic models that incorporate transmission heterogeneity, fit them to a number of real outbreak datasets, and benchmark their performance against the canonical superspreader model (i.

Estimating Australian Hospitalization Ratios and Costs for Wildtype SARS-CoV-2 in 2020.

Utilizing a retrospective cohort study of SARS-CoV-2 wildtype (Wuhan) strain, we aimed to 1) utilize the unique Australian experience of temporarily eliminating SARS-CoV-2 to document and estimate the hospitalization demand; and 2) estimate the inpatient hospital costs associated with treatment. Case data was based on Victoria Australia from March 29 to December 31, 2020. Outcomes measures included hospitalization demand and case fatality ratio and inpatient hospitalization costs.

Mental health and wellbeing of health and aged care workers in Australia, May 2021 - June 2022: a longitudinal cohort study.

Objectives: To assess the mental health and wellbeing of health and aged care workers in Australia during the second and third years of the coronavirus disease 2019 (COVID-19) pandemic, overall and by occupation group.

Design, Setting, Participants: Longitudinal cohort study of health and aged care workers (ambulance, hospitals, primary care, residential aged care) in Victoria: May-July 2021 (survey 1), October-December 2021 (survey 2), and May-June 2022 (survey 3).

Main Outcome Measures: Proportions of respondents (adjusted for age, gender, socio-economic status) reporting moderate to severe symptoms of depression (Patient Health Questionnaire-9, PHQ-9), anxiety (Generalized Anxiety Disorder scale, GAD-7), or post-traumatic stress (Impact of Event Scale-6, IES-6), burnout (abbreviated Maslach Burnout Inventory, aMBI), or high optimism (10-point visual analogue scale); mean scores (adjusted for age, gender, socio-economic status) for wellbeing (Personal Wellbeing Index-Adult, PWI-A) and resilience (Connor Davidson Resilience Scale 2, CD-RISC-2).

Transmission of SARS-CoV-2 in a primary school setting with and without public health measures using real-world contact data: A modelling study.

Background: Stringent public health measures have been shown to influence the transmission of SARS-CoV-2 within school environments. We investigated the potential transmission of SARS-CoV-2 in a primary school setting with and without public health measures, using fine-grained physical positioning traces captured before the COVID-19 pandemic.

Methods: Approximately 172.

Detecting Mycobacterium tuberculosis Infection in Children Migrating to Australia.

In 2015, Australia updated premigration screening for tuberculosis (TB) disease in children 2-10 years of age to include testing for infection with Mycobacterium tuberculosis and enable detection of latent TB infection (LTBI). We analyzed TB screening results in children <15 years of age during November 2015-June 2017. We found 45,060 child applicants were tested with interferon-gamma release assay (IGRA) (57.

Mental Health Outcomes in Australian Healthcare and Aged-Care Workers during the Second Year of the COVID-19 Pandemic.

Objective: the COVID-19 pandemic has incurred psychological risks for healthcare workers (HCWs). We established a Victorian HCW cohort (the Coronavirus in Victorian Healthcare and Aged-Care Workers (COVIC-HA) cohort study) to examine COVID-19 impacts on HCWs and assess organisational responses over time.

Methods: mixed-methods cohort study, with baseline data collected via an online survey (7 May-18 July 2021) across four healthcare settings: ambulance, hospitals, primary care, and residential aged-care.

Population-wide active case finding and prevention for tuberculosis and leprosy elimination in Kiribati: the PEARL study protocol.

Introduction: Population-wide interventions offer a pathway to tuberculosis (TB) and leprosy elimination, but 'real-world' implementation in a high-burden setting using a combined approach has not been demonstrated. This implementation study aims to demonstrate the feasibility and evaluate the effect of population-wide screening, treatment and prevention on TB and leprosy incidence rates, as well as TB transmission.

Methods And Analysis: A non-randomised 'screen-and-treat' intervention conducted in the Pacific atoll of South Tarawa, Kiribati.

Estimating the long-term effects of mass screening for latent and active tuberculosis in the Marshall Islands.

Background: Ambitious population-based screening programmes for latent and active tuberculosis (TB) were implemented in the Republic of the Marshall Islands in 2017 and 2018.

Methods: We used a transmission dynamic model of TB informed by local data to capture the Marshall Islands epidemic's historical dynamics. We then used the model to project the future epidemic trajectory following the active screening interventions, as well as considering a counterfactual scenario with no intervention.

A multistate model of health transitions in older people: a secondary analysis of ASPREE clinical trial data.

Background: Understanding the nature of transitions from a healthy state to chronic diseases and death is important for planning health-care system requirements and interventions. We aimed to quantify the trajectories of disease and disability in a population of healthy older people.

Methods: We conducted a secondary analysis of data from the ASPREE trial, which was done in 50 sites in Australia and the USA and recruited community-dwelling, healthy individuals who were aged 70 years or older (≥65 years for Black and Hispanic people in the USA) between March 10, 2010, and Dec 24, 2014.

Estimating tuberculosis drug resistance amplification rates in high-burden settings.

Background: Antimicrobial resistance develops following the accrual of mutations in the bacterial genome, and may variably impact organism fitness and hence, transmission risk. Classical representation of tuberculosis (TB) dynamics using a single or two strain (DS/MDR-TB) model typically does not capture elements of this important aspect of TB epidemiology. To understand and estimate the likelihood of resistance spreading in high drug-resistant TB incidence settings, we used epidemiological data to develop a mathematical model of Mycobacterium tuberculosis (Mtb) transmission.

Sustaining effective COVID-19 control in Malaysia through large-scale vaccination.

Introduction: As of 3rd June 2021, Malaysia is experiencing a resurgence of COVID-19 cases. In response, the federal government has implemented various non-pharmaceutical interventions (NPIs) under a series of Movement Control Orders and, more recently, a vaccination campaign to regain epidemic control. In this study, we assessed the potential for the vaccination campaign to control the epidemic in Malaysia and four high-burden regions of interest, under various public health response scenarios.

Understanding how Victoria, Australia gained control of its second COVID-19 wave.

During 2020, Victoria was the Australian state hardest hit by COVID-19, but was successful in controlling its second wave through aggressive policy interventions. We calibrated a detailed compartmental model of Victoria's second wave to multiple geographically-structured epidemic time-series indicators. We achieved a good fit overall and for individual health services through a combination of time-varying processes, including case detection, population mobility, school closures, physical distancing and face covering usage.

Modelling direct and herd protection effects of vaccination against the SARS-CoV-2 Delta variant in Australia.

Objectives: To analyse the outcomes of COVID-19 vaccination by vaccine type, age group eligibility, vaccination strategy, and population coverage.

Design: Epidemiologic modelling to assess the final size of a COVID-19 epidemic in Australia, with vaccination program (Pfizer, AstraZeneca, mixed), vaccination strategy (vulnerable first, transmitters first, untargeted), age group eligibility threshold (5 or 15 years), population coverage, and pre-vaccination effective reproduction number ( ) for the SARS-CoV-2 Delta variant as factors.

Main Outcome Measures: Numbers of SARS-CoV-2 infections; cumulative hospitalisations, deaths, and years of life lost.

Vaccines and variants: Modelling insights into emerging issues in COVID-19 epidemiology.

Mathematical modelling has played a pivotal role in understanding the epidemiology of and guiding public health responses to the ongoing coronavirus disease of 2019 (COVID-19) pandemic. Here, we review the role of epidemiological models in understanding evolving epidemic characteristics, including the effects of vaccination and Variants of Concern (VoC). We highlight ways in which models continue to provide important insights, including (1) calculating the herd immunity threshold and evaluating its limitations; (2) verifying that nascent vaccines can prevent severe disease, infection, and transmission but may be less efficacious against VoC; (3) determining optimal vaccine allocation strategies under efficacy and supply constraints; and (4) determining that VoC are more transmissible and lethal than previously circulating strains, and that immune escape may jeopardize vaccine-induced herd immunity.

Tuberculosis in the Western Pacific Region: Estimating the burden of disease and return on investment 2020-2030 in four countries.

Background: We aimed to estimate the disease burden of Tuberculosis (TB) and return on investment of TB care in selected high-burden countries of the Western Pacific Region (WPR) until 2030.

Methods: We projected the TB epidemic in Viet Nam and Lao People's Democratic Republic (PDR) 2020-2030 using a mathematical model under various scenarios: counterfactual (no TB care); baseline (TB care continues at current levels); and 12 different diagnosis and treatment interventions. We retrieved previous modeling results for China and the Philippines.

Tuberculosis in migrants to Australia: Outcomes of a national screening program.

Background: Few low-incidence countries are on track to achieve the ambitious target of reaching TB pre-elimination by 2035. Australia is a high-income country with a low burden of TB, which is particularly concentrated in migrant populations. As part of Australia's migration program, permanent, provisional and humanitarian visa applicants are screened for TB, along with some applicants for temporary visas.

Understanding COVID-19 dynamics and the effects of interventions in the Philippines: A mathematical modelling study.

Background: COVID-19 initially caused less severe outbreaks in many low- and middle-income countries (LMIC) compared with many high-income countries, possibly because of differing demographics, socioeconomics, surveillance, and policy responses. Here, we investigate the role of multiple factors on COVID-19 dynamics in the Philippines, a LMIC that has had a relatively severe COVID-19 outbreak.

Methods: We applied an age-structured compartmental model that incorporated time-varying mobility, testing, and personal protective behaviors (through a "Minimum Health Standards" policy, MHS) to represent the first wave of the Philippines COVID-19 epidemic nationally and for three highly affected regions (Calabarzon, Central Visayas, and the National Capital Region).

Ethics of selective restriction of liberty in a pandemic.

Liberty-restricting measures have been implemented for centuries to limit the spread of infectious diseases. This article considers if and when it may be ethically acceptable to impose selective liberty-restricting measures in order to reduce the negative impacts of a pandemic by preventing particularly vulnerable groups of the community from contracting the disease. We argue that the commonly accepted explanation-that liberty restrictions may be justified to prevent harm to others when this is the least restrictive option-fails to adequately accommodate the complexity of the issue or the difficult choices that must be made, as illustrated by the COVID-19 pandemic.