Discussion
Pathogenomics: An updated European Research Agenda

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Abstract

The emerging genomic technologies and bioinformatics provide novel opportunities for studying life-threatening human pathogens and to develop new applications for the improvement of human and animal health and the prevention, treatment, and diagnosis of infections. Based on the ecology and population biology of pathogens and related organisms and their connection to epidemiology, more accurate typing technologies and approaches will lead to better means of disease control. The analysis of the genome plasticity and gene pools of pathogenic bacteria including antigenic diversity and antigenic variation results in more effective vaccines and vaccine implementation programs. The study of newly identified and uncultivated microorganisms enables the identification of new threats. The scrutiny of the metabolism of the pathogen in the host allows the identification of new targets for anti-infectives and therapeutic approaches. The development of modulators of host responses and mediators of host damage will be facilitated by the research on interactions of microbes and hosts, including mechanisms of host damage, acute and chronic relationships as well as commensalisms. The study of multiple pathogenic and non-pathogenic microbes interacting in the host will improve the management of multiple infections and will allow probiotic and prebiotic interventions. Needless to iterate, the application of the results of improved prevention and treatment of infections into clinical tests will have a positive impact on the management of human and animal disease.

The Pathogenomics Research Agenda draws on discussions with experts of the Network of Excellence “EuroPathoGenomics” at the management board meeting of the project held during 18–21 April 2007, in the Villa Vigoni, Menaggio, Italy. Based on a proposed European Research Agenda in the field of pathogenomics by the ERA-NET PathoGenoMics the meeting's participants updated the established list of topics as the research agenda for the future.

Introduction

Bacterial infections remain a major cause of disease and mortality in humans and animals throughout the world. Only the detailed understanding of their pathogenic processes will provide the innovative tools for their treatment, prevention and eradication. New concepts laid down in this Research Agenda contribute to a global policy of control of infections both in Europe and in the developing world. Several infections constitute novel and particularly onerous threats owing to the occurrence of new virulent strains and the development of antibiotic resistances. Innovations in diagnostic techniques and therapy, as well as the development of vaccines against pathogenic microorganisms, are expected to come out of the joint research activities recommended in the European Research Agenda in the field of pathogenomics.

Global approaches require technical platforms (i.e. genomics, microarrays, proteomics, imaging, structure, novel bioassays) that exceed the capacities of individual laboratories or institutions including the adaptation of international standards (i.e. MIAME (Gene expression), MIAPE (proteomics), MIARE (RNAi)). To that end, this proposed agenda will join together established European groups of the Network of Excellence “EuroPathoGenomics” as well as the ERA-NET PathoGenoMics to foster the development of new multidisciplinary paradigms in the study of infectious diseases.

Section snippets

The microbes

In order to enable the development of novel diagnostic tools, therapeutic agents and vaccine candidates it is necessary to characterize the molecular and cellular basis of infection caused by bacterial pathogens. Therefore, the following methods, techniques and research topics on microorganisms constitute the focus of the agenda.

Host–microbe interactions

The complex interaction between a microbial pathogen and a host (Fig. 4) is the underlying basis of the infectious disease. The understanding of the molecular and cellular details of these host–microbe interactions may lead to the identification of virulence-associated microbial genes and host-defence strategies. This information will be used for the design of a new generation of medical tools.

Development and improvement of tools for research and application

In order to identify novel targets for the eradication of and vaccination against pathogens new tools, methods and bioassays as well as novel diagnostic approaches and new in vitro screening techniques (e.g. small bioactive molecules) have to be developed and improved for research and application.

Outlook

The study of microbial pathogenesis, parasitism, symbiosis, and commensalism is a large field of research requiring extensive expertise in many different domains, including genomics, epidemiology, immunology, cellular biology, and imaging techniques. To cover this field it is necessary to federate European capacities of important research centers, laboratories and industry. Therefore, the EU-funded projects Network of Excellence “EuroPathoGenomics” (NoE EPG) and ERA-NET PathoGenoMics evolved

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