The need for ethical reflection on the use of molecular microbial characterisation in outbreak management

Rump, Babette; Cornelis, Candice; Woonink, Frits; Verweij, Marcel

doi:10.2807/ese.18.04.20384-en

Cited by 9 publications

(18 citation statements)

References 12 publications

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“…Significant investment in establishing standards, databases and communication tools will be required to maximize the opportunities provided by WGS in epidemiology. There may also be organizational and ethical issues with data ownership and access [52].…”

Section: Conclusion and Future Perspectivesmentioning

confidence: 99%

Genomics and outbreak investigation: from sequence to consequence

2013

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Outbreaks of infection can be devastating for individuals and societies. In this review, we examine the applications of new high-throughput sequencing approaches to the identification and characterization of outbreaks, focusing on the application of whole-genome sequencing (WGS) to outbreaks of bacterial infection. We describe traditional epidemiological analysis and show how WGS can be informative at multiple steps in outbreak investigation, as evidenced by many recent studies. We conclude that high-throughput sequencing approaches can make a significant contribution to the investigation of outbreaks of bacterial infection and that the integration of WGS with epidemiological investigation, diagnostic assays and antimicrobial susceptibility testing will precipitate radical changes in clinical microbiology and infectious disease epidemiology in the near future. However, several challenges remain before WGS can be routinely used in outbreak investigation and clinical practice.

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Section: Conclusion and Future Perspectivesmentioning

confidence: 99%

Genomics and outbreak investigation: from sequence to consequence

2013

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“…At the intersection of genomics and infectious diseases, there has been some discussion of the ELSIs of using pathogen genomics for source and contact tracing [29][30][31], but little attention has been paid to the ELSI issues regarding testing for and using host genetic information in infectious disease prevention and control. As shown in Figure 1, the introduction of genomic information to infectious disease management may complicate or exacerbate existing ELSI issues, or create variations on existing challenges for clinical practice, public health and policy making.…”

Section: Relevant Ethics Scholarship: What We Know and What Might Be mentioning

confidence: 99%

“…The ELSI issues associated with at least one application of genomics to infectious disease management have received some attention. The ability to identify a human source of infection or a 'super-spreader' creates potential questions of blame or legal liability, stigmatization, and risks to privacy [29,30]. Similar issues could arise from the ability to identify people at a higher risk for contracting or spreading a disease using human genetic markers.…”

Section: Elsi Challenges In Genomics and Infectious Diseasementioning

confidence: 99%

Genomics and infectious disease: a call to identify the ethical, legal and social implications for public health and clinical practice

et al. 2014

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Advances in genomics are contributing to the development of more effective, personalized approaches to the prevention and treatment of infectious diseases. Genetic sequencing technologies are furthering our understanding of how human and pathogen genomic factors - and their interactions - contribute to individual differences in immunologic responses to vaccines, infections and drug therapies. Such understanding will influence future policies and procedures for infectious disease management. With the potential for tailored interventions for particular individuals, populations or subpopulations, ethical, legal and social implications (ELSIs) may arise for public health and clinical practice. Potential considerations include balancing health-related benefits and harms between individuals and the larger community, minimizing threats to individual privacy and autonomy, and ensuring just distribution of scarce resources. In this Opinion, we consider the potential application of pathogen and host genomic information to particular viral infections that have large-scale public health consequences but differ in ELSI-relevant characteristics such as ease of transmission, chronicity, severity, preventability and treatability. We argue for the importance of anticipating these ELSI issues in advance of new scientific discoveries, and call for the development of strategies for identifying and exploring ethical questions that should be considered as clinical, public health and policy decisions are made.

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“…Nevertheless, expanding surveillance activities by adding molecular typing data to the reporting of the food-borne pathogens, strengthens the connection between human disease and the potential source/vehicle. Molecular typing can also strengthen the legal basis for recall of contaminated food by reducing the uncertainty when linking the specific food to human disease (Rump et al, 2013). Agreement is required to ensure that isolates collected for a specific purpose (e.g.…”

Section: Data Requirements For Integrated Cross-sectoral Surveillancementioning

confidence: 99%

Scientific Opinion on the evaluation of molecular typing methods for major food-borne microbiological hazards and their use for attribution modelling, outbreak investigation and scanning surveillance: Part 2 (surveillance and data management activities)

Publication¹

2014

EFSA Journal

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Surveillance programmes based on active and harmonised sampling are considered the most suitable for foodborne outbreak investigations, hypothesis generation, early detection of emerging pathogen subtypes, attribution modelling and genetic studies of bacterial populations. Currently, prototype molecular databases are not widely linked and contain limited epidemiological data, therefore development of linkage mechanisms is a priority. A key technical requirement is determination of an agreed threshold value for the level of genetic variation amongst isolates that can still be regarded as epidemiologically-related. Molecular typing data should be coupled with a minimum required set of epidemiological data and datasets should be comparable to facilitate joint analyses in conjunction with human case data. Rules for assembling strain collections and associated provenance data should be agreed and introduced as EU standards. The data collection process and the characteristics of the data repository should ensure reproducibility and maximise compatibility and interoperability between different datasets. Molecular bacterial characterisation developments, particularly Whole Genome Sequencing (WGS), should be harmonised with those used for surveillance in the human population and food industry. Reference methods and materials, including sequence data, should be adopted for typing of food-borne pathogens. Upload of molecular data should only be allowed for approved laboratories and should be subject to External Quality Assessment. Ongoing international oversight is required to ensure a consensual ‗one-health' approach. The establishment of a joint EFSA-ECDC-EU-RLs committee for the support of cross-sectoral molecular surveillance, with a balance of public health and veterinary expertise and including both epidemiologists and microbiologists is strongly recommended. Revision of the legal basis of programmes for pathogen reduction based on historic organism nomenclature may be necessary following the increased use of WGS and the subsequent identification of more biologically relevant groupings of organisms. Following that request, the BIOHAZ Panel adopted, on 5 December 2013, a Scientific Opinion addressing the evaluation of molecular typing methods and their suitability for the different applications that were considered (EFSA, 2013a). Important conclusions of that Opinion were that data from strain characterisation should be linked with epidemiological data, that the selection of isolates must be unbiased and statistically representative of the population to be assessed and that international harmonisation of molecular characterisation outputs by means of standardisation or appropriate quality control procedures is essential. Important recommendations were that cross-sector (humans, food, food animals and related environments) and international coordination of method validation is required as a priority, and that development and improvement of international initiatives with regard to harmonised platforms for sharin...

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The need for ethical reflection on the use of molecular microbial characterisation in outbreak management

Cited by 9 publications

References 12 publications

Genomics and outbreak investigation: from sequence to consequence

Genomics and outbreak investigation: from sequence to consequence

Genomics and infectious disease: a call to identify the ethical, legal and social implications for public health and clinical practice

Scientific Opinion on the evaluation of molecular typing methods for major food-borne microbiological hazards and their use for attribution modelling, outbreak investigation and scanning surveillance: Part 2 (surveillance and data management activities)

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