Salmonella infections cost Australian society an estimated 140 million Australian Dollars (AUD) per year circa 2019. Salmonellosis is caused by Salmonella enterica, with over 2,500 serotypes of S. enterica identified. Knowledge of the epidemiology of Salmonella serotypes may facilitate traceback from strains detected in human cases to identify the cause of local and multijurisdictional outbreaks and to implement control measures. We analysed cases of human salmonellosis notified in the Northern Territory (NT), Australia, between 1 January 2005 and 31 December 2024. We calculated the incidence of salmonellosis for all locally acquired infections according to the NT location where the infection was most likely acquired. We mapped the geographical distribution of the 25 most frequently notified Salmonella serotypes to Statistical Areas Level 2. There were 8,706 salmonellosis cases acquired in the NT: Salmonella Saintpaul (1,047 notifications) was the most frequently notified serotype, followed by S. Virchow (948 notifications); S. Typhimurium (822 notifications); S. Ball (578 notifications); and S. Lansing (460 notifications). While S. Typhimurium was ubiquitous in the NT, S. Saintpaul, S. Virchow and S. Hvittingfoss showed distinct geographic patterns. Our atlas makes key epidemiological information about common NT Salmonella serotypes readily available, which may be useful for developing hypotheses during outbreak investigations; for facilitating traceback of suspected food vehicles; and for implementing control strategies more rapidly.

In 2017-2018, New South Wales (NSW), Australia, experienced a hepatitis A virus (HAV) outbreak predominantly affecting men who have sex with men (MSM). We aimed to estimate immunity and identify immunity gaps among MSM in NSW. We triangulated four data sources. We tested 409 residual sera collected from males undergoing syphilis testing between August and October 2017 for anti-HAV IgG. We surveyed all publicly funded sexual health clinics about HAV testing and vaccine provision for the preceding financial year. We conducted a convenience behavioural survey of 50 men at a sex-on-premises venue in October 2017, and we analysed community survey data from 2018 to 2019 (n = 5,924). Descriptive statistics and logistic regression ere used to examine associations with immunity and vaccination. Overall serological immunity was 62.8% (257/409) and increased with age, from 50.0% in those aged under 26 years to 79.0% in those over 45 years. Clinic immunity and community survey estimates were higher (74.5% and 76.8%). Immunity gaps were identified among bisexual men, those less connected to the gay community, and people born outside Australia. NSW Health implemented targeted vaccination and community engagement in response. Multisource assessment provided actionable evidence to guide targeted vaccination and outbreak response.

Identifying the sources of foodborne diseases is crucial for guiding national food safety strategies and supporting policies that promote safe and sustainable food production. Here we present global estimates of the proportions of burden of disease attributable to foodborne transmission, other major transmission pathways, and specific food categories for 29 viral, bacterial, parasitic, and chemical hazards, based on a structured expert judgement (SEJ) study commissioned by the World Health Organization (WHO) and supervised by the WHO Foodborne Disease Burden Epidemiology Reference Group (FERG) for 2021-2025. One-hundred forty-six experts provided 1463 assessments across 17 subregions within six WHO regions. The assessments were analyzed using Cooke's Classical Model and reviewed by FERG. Results showed that 13 of the 29 hazards were mainly (>50%) attributable to foodborne transmission, with non-typhoidal Salmonella (59-74%) and Campylobacter (45-71%) estimated to be predominantly foodborne in nearly all subregions. While plant-based foods were important sources of several pathogens, such as hepatitis A virus (63-74%) and Cryptosporidium (60-95%), foods of animal origin, including poultry, beef, eggs, seafood, and dairy products, remain critical intervention targets for several others, e.g., Campylobacter (86-97%), Salmonella (77-92%), Shiga toxin-producing E. coli (67-96%), and Listeria monocytogenes (50-85%). Regional differences in attributions highlight the influence of local epidemiological patterns, food systems, sanitation, and cultural practices. These estimates provide a global, uncertainty-quantified knowledge base to guide context-specific food safety interventions and future empirical data collection. Given persistent data gaps, SEJ remains a feasible approach to generate evidence supporting efforts to reduce the burden of foodborne diseases.

Globally, the utility of pathogen genomics for public health was highlighted by the COVID-19 pandemic. Approaches to enhance coordination and improve implementation of pathogen genomics for public health are needed. The Communicable Diseases Genomics Network (CDGN) was established in 2015 in Australia. The network, embedded at the public health laboratory interface and supported by the Australian Government, has facilitated a coordinated model in Australia for public health pathogen genomics. CDGN activities have facilitated pilot projects to demonstrate use cases, harmonisation of data sharing and governance arrangements, outbreak and pandemic response, translational research, policy development and workforce capacity building. The impact of CDGN has been enabling the significant progress towards public health genomics implementation in Australia, and providing a model that could be applied in other federated settings, aligned with international best practice.

BACKGROUND:Field Epidemiology Training Programs (FETPs) aim to develop a skilled public health workforce through applied competency-based learning. With 98 programs globally and over 20,000 graduates, these programs play a crucial role in disease preparedness and response activities around the world. Despite their importance, there have been few published evaluations. This paper presents the results of a consensus-building process to develop a preferred array of indicators for evaluating the outputs, outcomes, and impacts of FETPs. METHODS:We conducted a modified Delphi study to reach consensus on preferred evaluation indicators for FETPs. An initial list of evaluation indicators were identified from literature reviews and consultations with impact evaluation experts and FETP professionals. A modified Delphi process was subsequently employed, involving two rounds of surveys and a final expert review meeting, to reach consensus on indicators. The Delphi panel included 23 experts representing diverse global regions and FETP roles. RESULTS:Consensus was reached to include 134 evaluation indicators in the final impact evaluation framework. These indicators were grouped as output, outcome, and impact indicators. CONCLUSIONS:This study presents the first FETP impact evaluation framework with a comprehensive list of evaluation indicators for FETPs. This list of indicators is intended as a resource to promote and enhance the evaluation of FETPs and thus improve these important training programs which aim to strengthen national, regional and global health security.

ObjectivesUnderstanding the link between routine immunisation (RI) performance and vaccination during an epidemic can provide insights on health systems resilience and investments to strengthen health systems. We examined the relationship between RI performance and COVID-19 vaccination coverage in small island developing states (SIDS).MethodsWe analysed immunisation and health system performance data in 55 SIDS. Our primary outcome was COVID-19 vaccination coverage at four timepoints (June 2021, December 2021, June 2022 and December 2022). We examined associations with coverage of six childhood immunisations (5-year mean annual coverage for 2015-2019), pandemic-related disruptions to RI, new vaccine introductions, health system performance measures, and economic and demographic characteristics. We calculated Spearman correlation coefficients (r) with p-values (p < 0.05 considered significant) and 95% confidence intervals for continuous variables and mean COVID-19 vaccination coverage by categorical variables.FindingsCOVID-19 vaccination coverage was higher in countries that sustained pre-pandemic RI coverage during the pandemic, and where HPV, influenza and measles-containing (second dose) vaccines had been introduced. There were weak correlations (|r| < 0.4) between coverage of COVID-19 vaccination and RI, with a few exceptions of moderate correlations with the birth dose of hepatitis B vaccine (June 2022: r = 0.421, p = 0.007; December 2022: r = 0.438, p = 0.005) and first dose of measles vaccine (December 2021: r = 0.420, p = 0.002). COVID-19 vaccination coverage was strongly correlated with the density of physicians (June 2021: 0.897, p < 0.001; December 2021: 0.785, p < 0.001) and moderately correlated with that of nurses and midwives (June 2021: 0.630, p = 0.001; December 2021: 0.605, p = 0.002). COVID-19 vaccination coverage was lower in SIDS with lower country income and development status.ConclusionsCountries that achieved high COVID-19 vaccination coverage also sustained RI coverage during the pandemic, demonstrating health system resilience. Our findings highlight the importance of having sufficient skilled health professionals and experience in introducing new vaccines targeting different age groups into national programs, particularly in small island settings.

Shigellosis is a leading cause of diarrheal mortality worldwide. Shigella boydii is one of four Shigella species that contributes to this burden, however studies on S. boydii are limited. Here we combined epidemiological and genomic data to better understand S. boydii circulating both in Australia and globally. Between 1991 and 2019, there were 294 cases of S. boydii infections notified to the National Notifiable Diseases Surveillance System by Australian states and territories, with an increasing trend in notifications observed from 2013. Of cases whose place of acquisition was known, 54% (111/206) were acquired overseas, mainly from South-East Asia (57%; 63/111). Our genomic analysis included 250 S. boydii isolates: 44 from Victoria, Australia spanning 22 years (2001-2022) and 206 international isolates spanning 91 years (1930-2020). Phylogenomic analyses identified five major S. boydii phylogenetic lineages circulating globally. The Australian isolates were distributed across all five lineages, but the highest proportion was in Lineage 3. Antimicrobial resistance was common in both international and Australian isolates with > 60% of isolates classified as multi-drug-resistant. Resistance to the main clinically relevant antimicrobials was rare in S. boydii. Ciprofloxacin resistance was detected in seven S. boydii, however reduced susceptibility to ciprofloxacin was detected in 56 isolates and found in both Australian and international data. Importantly, resistance mechanisms to third-generation cephalosporins and macrolides were also detected. This study is the largest genomic analysis of S. boydii to date, providing insights into the population structure, epidemiology and emerging AMR threats in this neglected Shigella species.

Background:Whole Genome Sequencing (WGS) is a powerful technology for monitoring and detecting outbreaks of infectious pathogens, including non-typhoidal Salmonella (NTS). Despite its higher cost than traditional typing methods, WGS offers numerous advantages, including higher resolution and potentially quicker turnaround time. However, evidence regarding its effectiveness in NTS surveillance has predominantly stemmed from micro-simulations or small-scale data. Notably, a recent systematic review identified a lack of real-world, large-scale evidence on the impact of WGS application in NTS surveillance. Our study fills this gap by estimating the effects of WGS on NTS surveillance in Australia using national notifiable disease datasets. Methods:The main dataset was the National Notifiable Diseases Surveillance System (NNDSS) for NTS from 2009 to 2024. The treatment variable was defined as a binary variable representing the period when WGS was implemented in each jurisdiction of Australia. To minimise the effects of unobserved confounders, we employed a two-stage difference-in-difference (2sDiD) approach. This method estimated the parameters of state and period fixed-effects and then adjusted the observed outcomes from those fixed-effects in the first stage. The average treatment effect was obtained in the second stage by regressing the adjusted outcome against the treatment in the second stage. We also conducted a sensitivity analysis using a multi-period DiD model with a double machine-learning estimator. Findings:Compared to the pre-WGS periods, the introduction of WGS was associated with an average of 11.6% reduction in NTS cases when a static specification was applied. Results of a dynamic specification were slightly higher, with a 12.7% reduction in NTS cases after WGS. The estimated effects increased to 17.5% when a multi-period DiD model with a double machine learning estimator was applied. Interpretation:Our study shows that WGS was associated with a significant reduction (11.6%-17.5%) of NTS cases in Australia. Using the cost and break-even point of NTS from previous Australian studies, our findings suggest that WGS is associated with 7200-10,900 cases of NTS averted, saving US$11.3 m-US$17.0 m per year. Funding:Australian National Health and Medical Research Council, Medical Research Futures Fund (FSPGN00049), and Investigator Grant (GNT1196103) to BPH.

In large public health jurisdictions, only a small proportion of people infected with Salmonella are interviewed due to resource constraints. As such, sources of illness are rarely found, and preventative action not implemented. We trialled alternative methods to contact notified salmonellosis cases to collect information on exposures and risks, focusing particularly on the feasibility of SMS (short message service)-based surveillance. Over five-years period we sequentially mailed letters, sent online surveys, and then text messages. The SMS approach was designed to assess the efficiency of a two-way personalized messaging model in gathering actionable public health data. The personalized SMS-follow-up model demonstrated the highest success: 56% of cases responded, enabling the identification and intervention of 10 distinct point-source outbreaks of Salmonella. SMS-based surveillance offers a novel, efficient, and acceptable method for collecting critical food exposure data in Salmonella cases. In settings where resources are constrained, SMS can complement traditional case follow-up methods, enhancing both the timeliness and effectiveness of outbreak detection. Integrating this follow-up with routine clinical care could further enhance the acceptance and success of this method. This study highlights the promise of SMS in streamlining surveillance efforts and warrants further exploration for application to other infectious diseases.

BACKGROUND:Addressing the barriers to outbreak reporting is critical to prevent future outbreaks from becoming epidemics or pandemics. As most emerging infectious diseases are zoonotic in origin, this requires understanding the barriers affecting both the human and animal health sectors. However, previous reviews of outbreak reporting barriers have only looked at barriers with respect to humans or animals independently. Therefore, we undertook a One Health approach to holistically understand the impact of outbreak reporting barriers across the human health, animal health, and environmental sectors. METHODS:We conducted a scoping review of the peer-reviewed and grey literature to identify barriers and facilitators for outbreak reporting affecting human health, animal health, and the environment. We selected studies that identified discrete barriers or facilitators at the subnational, national, and international levels using quantitative research, qualitative research, mixed methods, or reviews. We extracted information on publication information, barriers, and facilitators, and we thematically summarised our findings. RESULTS:Among 5,177 records examined, we selected 151 matched parameters for data abstraction and analysis. The most employed methodology was qualitative (56 studies), and the East Asia and Pacific (43 studies) and Sub-Saharan Africa (40 studies) regions were the most studied. Only 45 studies evaluated outbreak reporting with respect to a specific disease. Identified outbreak reporting barriers and facilitators fell under three major themes: technical; economic, political, and bureaucratic; and behavioural and social. We found substantial evidence for technical barriers to outbreak reporting across all regions and sectors and resistance to reporting among agricultural producers. However, evidence for additional barriers, particularly barriers to environmental reporting, is more limited. CONCLUSIONS:This study affirms the importance of building countries' technical capacity to report outbreaks. However, it also indicates the need to sensitize reporters and government officials on the importance of outbreak reporting. A comprehensive understanding of the full breadth of outbreak reporting barriers and facilitators across human health, animal health, and the environment otherwise remains incomplete, with critical implications for ongoing and future outbreaks. Future studies should endeavour to fill these gaps in the evidence base as part of an integrated One Health strategy to improve the outbreak reporting process.

Background:Pathogen genomics has transformed infectious disease response, yet prioritisation frameworks for genome sequencing remain underdeveloped. This study establishes evidence-based criteria for prioritising pathogens for genome sequencing to maximise public health impact in Australia. Methods:We conducted a modified Delphi study with experts in public health, infection prevention, and pathogen genomics to examine both prioritisation mechanisms, selection criteria and specific pathogen rankings across surveillance contexts. Initially, 38 experts evaluated 89 statements on a 5-point Likert scale with accompanying feedback. In round two, participants reassessed 48 statements, including 28 that were revised based on first-round input. Quantitative data was analysed using STATA-18 and qualitative data using Atlas.ti. Findings:Consensus was achieved on 53 statements across both rounds across three domains: decision-making processes, prioritisation criteria, and high-priority surveillance scenarios to prioritise specific pathogens for genome sequencing. Experts agreed that a national priority pathogen list for genome sequencing should be developed collaboratively with public health laboratories and complemented by state level lists, with biennial reviews and flexibility for situation-based adjustments. Consensus was achieved on prioritising pathogens associated with antimicrobial resistance, novel and emerging potential, virulence, institutional transmission risk, and disproportionate impact on Aboriginal and Torres Strait Islander communities. For routine surveillance, Mycobacterium tuberculosis received highest consensus for sequencing, followed by multidrug-resistant Staphylococcus aureus. Eleven pathogens were prioritised for sequencing in outbreak investigation, including Carbapenemase producing Enterobacterales, pathogenic Escherichia coli subtypes, and Salmonella species. Three pathogens, Shigella, Neisseria gonorrhoeae, and invasive Group A Streptococcus, were prioritised for periodic surveillance sequencing. Our qualitative analysis showed experts emphasised public health significance and actionability while advocating for balanced national-local governance and cross jurisdictional collaboration to maximise resources. Interpretation:This study establishes foundational evidence for developing a comprehensive framework for prioritising pathogens for genomic sequencing in Australian public health surveillance and response. Funding:Australian National Health and Medical Research Council, Medical Research Futures Fund (FSPGN00049).

There are an estimated 4.7 million cases of foodborne illness in Australia each year, but the contaminated food items that are the source of these illnesses are rarely identified. Current knowledge relies largely on the few foodborne outbreaks where the implicated food commodity was identified. To better understand which foods cause outbreaks, we analyzed 18 years of foodborne outbreak data collected in New South Wales (NSW) and classified the food dishes responsible for the outbreaks into standardized categories based on type of dish and preparation method. A total of 869 outbreaks were reported in NSW from 2000 to 2017. Outbreaks with a suspected contaminated food or dish reported (57.1%) underwent dish reclassification that assigned the implicated food into two groupings that characterized the food consumed into commonly understood dish types (e.g., sandwich, stew, etc.) and how it was prepared (e.g., sliced, heated, etc.). The dish type associated with the most outbreaks was sandwiches (18.8%) followed by desserts (13.1%) and then stir fries (9.1%). The dishes associated with more serious outbreak outcomes (higher numbers of cases, hospitalizations, and deaths per outbreak) were those associated with ready to eat fresh produce. Dish preparations that did not involve a cooking step also resulted in more serious outcomes. While identifying contaminated food is crucial for food safety reasons, people rarely consider these risks when eating. Food carries the combined risks posed by the ingredients and preparation method followed. Education of food business operators and consumers needs to promote a view of food safety risk that goes beyond unsafe commodities, encouraging a holistic perspective that considers ingredients and preparation methods.

Field epidemiology training programs (FETPs) are designed to equip public health professionals with the skills necessary to investigate, monitor, and respond to disease outbreaks and other public health emergencies. Since the 1950s, when the first FETP started in the United States, the training model has been adopted by numerous countries around the world. Today, there are 98 FETPs in operation, and over 20,000 graduates. This review assesses published studies that report on the evaluation of FETPs. A literature search yielded 402 records, with 16 publications meeting inclusion criteria after duplicate removal and eligibility screening. The 16 FETP evaluations encompassed 37 national and four regional assessments across 26 countries. Most of the evaluations were descriptive reviews using quantitative methods focusing on outputs and short- or medium-term outcomes. Only four published evaluations focused on longer term impacts of an FETP. The evaluations describe and quantify numerous outputs and outcomes, providing evidence of trainees and graduates applying skills to strengthen core health system functions. Several challenges were also identified, including poor utilisation of FETP graduates by senior management stemming from a limited understanding of what field epidemiologists can contribute to the health system. While these evaluations indicate that FETPs are successful training programs, there are relatively few published impact evaluations providing the level of evidence increasingly expected by funders and stakeholders. There is a need and opportunity to develop tools and resources to support FETP evaluators in the implementation of impact evaluations.

Despite the growth and diversification of Field Epidemiology Training Programs (FETPs) globally, there are few published evaluations. Those that have been published largely focus on program processes and outputs, with some including short–medium-term outcomes and very few focusing on sustained impact. This paper describes the process of developing an FETP impact evaluation framework and FETP impact evaluation planning tool to facilitate FETP impact evaluations. The impact framework was developed to be simple, flexible and efficient. A theory of change process for an FETP in Papua New Guinea formed the basis of the impact evaluation framework. With support from independent impact evaluation experts, the framework was developed using an iterative approach. A review of the literature and technical input from FETP representatives underpinned its development. A simple planning tool was developed to help operationalise the impact framework. The final FETP impact evaluation framework consists of a high-level summary framework and a detailed operational framework. The high-level framework follows the flow of outputs, outcomes and impacts for trainees, graduates, the public health systems, and communities. The detailed FETP Impact Evaluation Framework includes activities, enablers and barriers, and output, outcome and impact indicators. The FETP Impact Evaluation Planning Tool consists of five steps using a theory-based approach. The long history and global growth of the FETP model suggest success and imply impact, yet few published papers provide necessary backing evidence. There is growing interest across the FETP community and funders to understand the longer-term changes that FETPs contribute to. We developed an impact framework and planning tool specifically designed to support FETP impact evaluation. The framework and tool are intended to be used by FETP staff with no prior evaluation experience. The evaluation approach is intentionally flexible, allowing contextual application and integration with established quantitative and qualitative evaluation methods.