Identifying factors that influence the use of pathogen genomics in Australia and New Zealand: a protocol.

Pathogen genomics is rapidly becoming a cornerstone in the surveillance and response to infectious diseases. However, there is little evidence on how it shapes strategies for effective public health response and decision-making. This paper presents the evaluation protocol for the Australian Pathogen Genomics (AusPathoGen) program, which aims to assess the utility of whole genome sequencing in informing public health responses to infectious diseases in Australia. A mixed methods approach will be adopted to systematically explore the utility of whole genome sequencing in public health action and decision-making through a series of linked projects. Methods include situation assessment surveys of Australian public health laboratories, expert elicitation, and case study analysis. The situation assessment surveys will gather data on public health laboratories' processes, practices, and associated costs for whole genome sequencing. Expert elicitation will seek views on the prioritization of pathogens for whole genome sequencing. Case studies of specific pathogens and outbreaks will serve as the basis for both impact assessment and qualitative comparative analysis. Genomic and epidemiological data will shed light on the influence of whole genome sequencing on outbreak response. This comprehensive evaluation of pathogen whole genome sequencing in Australia will enhance our understanding of how this data can be applied in public health response and decision-making. The methods discussed can be adapted to different public health pathogen genomic surveillance systems globally. Undertaking evaluation of such systems is crucial for identifying areas of improvement and providing recommendations to optimize quality, efficiency and resource allocation of pathogen genomics to improve public health responses.

14 - Genetics and Genomics in Public Health

In recent years, public health genomics has been introduced in the scientific literature as a new endeavour, aiming at the translation of genome-based knowledge and technologies into health interventions and public policies for the benefit of public health (Brand and Brand 2006; Zimmern and Stewart 2006; Gwinn and Khoury 2006). In 2009, Public Health Genomics started to appear as an international journal and a new signpost of the emerging field; however, as the editors pointed out, the new journal builds on an earlier version which was already founded in 1998, published as Community Genetics (Knoppers and Brand 2009). Thus, as a new and emerging field, public health genomics does not only embody promises and expectations for the future. It is also rooted in a history of past attempts and achievements, constituting “community genetics” as a bridge between genetics and public health (ten Kate 2005). In this context the relationship between public health genomics and community genetics has become a matter of debate. As becomes clear from the establishment of the new Journal of Community Genetics, there is a continuing interest in community genetics, defined by aims independent from public health genomics. In an interesting sociological commentary in the first issue of this journal, it is indeed observed that we should not take for granted that “public health genetics and community genetics could be viewed as one and the same” (Raz 2010). In a farewell editorial, published in the final issue of the former journal Community Genetics, Leo ten Kate likewise emphasized that community genetics “is not just a name but a unique concept, which has its own place besides clinical genetics and public health genetics or genomics” (ten Kate 2008, see also Schmidtke and ten Kate 2010; and ten Kate et al. 2010). In this commentary, I will take a closer look at the uniqueness of the concept of community genetics, using the 11 volumes of the former journal Community Genetics as my primary source material.1 My aim is not a complete review of the contents of this journal, which would be an impossible task, but a discussion of some aspects and questions which I see as particularly interesting and significant for our understanding of the concept and agenda of community genetics. What can we learn from the history contained in this former journal about the particularities of community genetics and its relation with the emerging field of public health genomics? Most revealing in this history is the tension between a conception of community genetics as a professional and regulated endeavour and as a programme of individual empowerment. Although we can see this tension as a unique feature following from the concept and agenda of community genetics, it is also highly significant, as I will argue, for the future prospects of public health genomics.

BackgroundPathogen genomics is increasingly being translated from the research setting into the activities of public health professionals operating at different levels. This survey aims to appraise the literacy level and gather the opinions of public health experts and allied professionals working in the field of infectious diseases in Belgium concerning the implementation of next-generation sequencing (NGS) in public health practice.MethodsIn May 2019, Belgian public health and healthcare professionals were invited to complete an online survey containing eight main topics including background questions, general attitude towards pathogen genomics for public health practice and main concerns, genomic literacy, current and planned NGS activities, place of NGS in diagnostic microbiology pathways, data sharing obstacles, end-user requirements, and key drivers for the implementation of NGS. Descriptive statistics were used to report on the frequency distribution of multiple choice responses whereas thematic analysis was used to analyze free text responses. A multivariable logistic regression model was constructed to identify important predictors for a positive attitude towards the implementation of pathogen genomics in public health practice.Results146 out of the 753 invited public health professionals completed the survey. 63% of respondents indicated that public health agencies should be using genomics to understand and control infectious diseases. Having a high level of expertise in the field of pathogen genomics was the strongest predictor of a positive attitude (OR = 4.04, 95% CI = 1.11 – 17.23). A significantly higher proportion of data providers indicated to have followed training in the field of pathogen genomics compared to data end-users (p < 0.001). Overall, 79% of participants expressed interest in receiving further training. Main concerns were related to the cost of sequencing technologies, data sharing, data integration, interdisciplinary working, and bioinformatics expertise.ConclusionsBelgian health professionals expressed favorable views about implementation of pathogen genomics in their work activities related to infectious disease surveillance and control. They expressed the need for suitable training initiatives to strengthen their competences in the field. Their perception of the utility and feasibility of pathogen genomics for public health purposes will be a key driver for its further implementation.

The invaluable lessons learned from the application of pathogen genomics during the HIV and COVID-19 pandemics hold significant implications for pandemic preparedness. These insights can shape our strategies to tackle...

The capacity for pathogen genomics in public health expanded rapidly during the coronavirus disease 2019 (COVID-19) pandemic, but many public health laboratories did not have the infrastructure in place to handle the vast amount of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequence data generated. The California Department of Public Health, in partnership with Theiagen Genomics, was an early adopter of cloud-based resources for bioinformatics and genomic epidemiology, resulting in the creation of a SARS-CoV-2 genomic surveillance system that combined the efforts of more than 40 sequencing laboratories across government, academia and industry to form California COVIDNet, California's SARS-CoV-2 Whole-Genome Sequencing Initiative. Open-source bioinformatics workflows, ongoing training sessions for the public health workforce, and automated data transfer to visualization tools all contributed to the success of California COVIDNet. While challenges remain for public health genomic surveillance worldwide, California COVIDNet serves as a framework for a scaled and successful bioinformatics infrastructure that has expanded beyond SARS-CoV-2 to other pathogens of public health importance.

Dear Sirs, The Public Health Genomics European Network (PHGEN) is a mapping exercise for the responsible and effective integration of genome-based knowledge and technologies into public policy and health services for the benefit of population health. In 2005, the European Commission called for a “networking exercise…to lead to an inventory report on genetic determinants relevant for public health”[1], this lead to the funding of a PHGEN three year project (EC project 2005313).This project started in early 2006 with a kick-off meeting in Bielefeld / Germany.The project work is comprised of, according to the public health trias, three one year periods of assessment, policy development and assurance.At the end of the assessment phase a network meeting was held in Rome from January, 31st to February 2nd 2007 with over 90 network members and network observers in attendance. The participants represented different organisations throughout the European Union with expertise in areas such as human genetics and other medical disciplines,epidemiology,public health, law, ethics, political and social sciences. The aim of the meeting was to wrap up the last year’s assessment period and to herald the policy development phase.The assessment period of PHGEN was characterised by several activities: - Contact and cooperation with other European and internationally funded networks and projects on public health genomics or related issues (e.g. EuroGenetest, EUnetHTA, Orphanet, IPTS, PHOEBE, GRaPHInt, P3G) - Identification of key experts in public health genomics in the European members states, applicant countries and EFTA/EEA countries from different disciplines (e.g. human genetics and other medical disciplines, public health, law, philosophy, epidemiology, political and social sciences) - Building up national task forces on public health genomics in the above mentioned countries - Establishing and work in three working groups: public health genomics definitions, genetic exceptionalism and public health genomics issues and priorities - Participation in the development process on OECD and European Council documents on genetic testing - Dissemination of results in journals, on websites and in conferences.

SummaryRapid advances in DNA sequencing technology (“next-generation sequencing”) have inspired optimism about the potential of human genomics for “precision medicine.” Meanwhile, pathogen genomics is already delivering “precision public health” through more effective investigations of outbreaks of foodborne illnesses, better-targeted tuberculosis control, and more timely and granular influenza surveillance to inform the selection of vaccine strains. In this article, we describe how public health agencies have been adopting pathogen genomics to improve their effectiveness in almost all domains of infectious disease. This momentum is likely to continue, given the ongoing development in sequencing and sequencing-related technologies.

The completion of the Human Genome Project triggered a whole new field of genomic research which is likely to lead to new opportunities for the promotion of population health. As a result, the distinction between genetic and environmental diseases has faded. Presently, genomics and knowledge deriving from systems biology, epigenomics, integrative genomics or genome-environmental interactions give a better insight on the pathophysiology of common diseases. However, it is barely used in the prevention and management of diseases. Together with the boost in the amount of genetic association studies, this demands for appropriate public health actions. The field of Public Health Genomics analyses how genome-based knowledge and technologies can responsibly and effectively be integrated into health services and public policy for the benefit of population health. Environmental exposures interact with the genome to produce health information which may help explain inter-individual differences in health, or disease risk. However today, prospects for concrete applications remain distant. In addition, this information has not been translated into health practice yet. Therefore, evidence-based recommendations are few. The lack of population-based research hampers the evaluation of the impact of genomic applications. Public Health Genomics also evaluates the benefits and risks on a larger scale, including normative, legal, economic and social issues. These new developments are likely to affect all domains of public health and require rethinking the role of genomics in every condition of public health interest. This article aims at providing an introduction to the field of and the ideas behind Public Health Genomics.

Chapter 21 - Public Health Genomics

Background Pathogen genomics has increasingly been integrated into infectious disease surveillance, outbreak detection, and response globally. However, formal evaluation of pathogen genomic surveillance systems has been a major gap. Where evaluation has been undertaken, this has largely focused on economics, rather than assessing system attributes that contribute to the usefulness and acceptability of pathogen genomic surveillance systems. In Australia, the AusTrakka platform was established and deployed nationally to address barriers to genomic data sharing across jurisdictions, enhance interoperability and usability, and improve governance of public health genomic data. Here we present our evaluation of AusTrakka and examine how its utilisation and impact shifted throughout the COVID-19 pandemic. Methods We utilised the United States’ Centers for Disease Control (CDC) Updated Guidelines for Evaluating Public Health Surveillance Systems to guide assessment of the AusTrakka platform. The evaluation used a mixed-methods approach consisting of a quantitative analysis of AusTrakka utilisation data throughout the COVID-19 pandemic and a qualitative component comprised of key informant interviews and analysis of investigation reports produced by the AusTrakka National Analysis Team. Semi-structured individual and group interviews were held with key informants (n=63) representing all jurisdictions across Australia and New Zealand. These included individuals representing public health laboratories and health departments, infectious disease physicians, genomic epidemiologists and bioinformaticians. Results End users reported that AusTrakka had a very high degree of usefulness as a centralised platform to enable sharing sequence data across jurisdictions, facilitate multijurisdictional outbreak investigations and clarifying transmission chains. Acceptability was a key system that contributed to the usefulness of the platform, enhanced through collective design of data governance frameworks. Integration of epidemiological data with the pathogen genomic data was an ongoing challenge in data completeness. Conclusions Robust evaluation of pathogen genomics surveillance systems is critical to identify contextual and system elements that impact the capacity of these systems to accomplish their objectives. Our findings demonstrate the importance of strong stakeholder engagement in developing data governance mechanisms for pathogen genomics in ultimately ensuring the capacity of surveillance systems to detect outbreaks and support public health utility, and reinforce the value of a nationally developed, purpose-built approach in Australia.

Chapter 23 - Public and Population Health Genomics

COVID-19 Highlights Critical Need for Public Health Data Modernization to Remain a Priority.

The emerging field of public health ethics

Description: Among the two leading causes of death in the United States, each responsible for one in every four deaths, heart disease costs Americans $300 billion, while cancer costs Americans $216 billion per year. They also rank among the top three causes of death in Europe and Asia. In 2012 the University of Michigan Center for Public Health and Community Genomics and Genetic Alliance, with the support of the Centers for Disease Control and Prevention Office of Public Health Genomics, hosted a conference in Atlanta, Georgia to consider related action strategies based on public health genomics. The aim of the conference was consensus building on recommendations to implement genetic screening for three major heritable contributors to these mortality and cost figures: hereditary breast and ovarian cancer (HBOC), familial hypercholesterolemia (FH), and Lynch syndrome (LS). Genetic applications for these three conditions are labeled with a “Tier 1” designation by the U.S. Centers for Disease Control and Prevention because they have been fully validated and clinical practice guidelines based on systematic review support them. Methodology: The conference followed a deliberative sequence starting with nationally recognized clinical and public health presenters for each condition, followed by a Patient and Community Perspectives Panel, working group sessions for each of the conditions, and a final plenary session. The 74 conference participants represented disease research and advocacy, public health, medicine and nursing, genetics, governmental health agencies, and industry. Participants drew on a public health framework interconnecting policy, clinical intervention, surveillance, and educational functions for their deliberations. Results: Participants emphasized the importance of collaboration between clinical, public health, and advocacy groups in implementing Tier 1 genetic screening. Advocacy groups could help with individual and institutional buy-in of Tier 1 programs. Groups differed on funding strategies, with alternative options such as large-scale federal funding and smaller scale, incremental funding solutions proposed. Piggybacking on existing federal breast and colorectal cancer control programs was suggested. Public health departments need to assess what information is now being collected by their state cancer registries. The groups advised that information on cascade screening of relatives be included in toolkits for use by states. Participants stressed incorporation of family history into health department breast cancer screening programs, and clinical HBOC data into state surveillance systems. The carrying out of universal LS screening of tumors in those with colorectal cancer was reviewed. Expansion of universal screening to include endometrial tumors was discussed, as was the application of guidelines recommending cholesterol screening of children 9–11 years old. States more advanced in terms of Tier 1 testing could serve as models and partners with other states launching screening and surveillance programs. A multidisciplinary team of screening program champions was suggested as a means of raising awareness among the consumer and health care communities. Participants offered multiple recommendations regarding use of electronic health records, including flagging of at-risk family members and utilization of state-level health information exchanges. The paper contains an update of policy developments and happenings for all three Tier 1 conditions, as well as identified gaps. Conclusions: Implementation of cascade screening of family members for HBOC and FH, and universal screening for LS in CRC tumors has reached a point of readiness within the U.S., with creative solutions at hand. Facilitating factors such as screening coverage through the Patient Protection and Affordable Care Act, and state health information exchanges can be tapped. Collaboration is needed between public health departments, health care systems, disease advocacy groups, and industry to fully realize Tier 1 genetic screening. State health department and disease networks currently engaged in Tier 1 screening can serve as models for the launch of new initiatives.