1. ERA-NET PathoGenoMics Meeting Bonn 7-8 April, 2005 Research topics of interest in the Area of Genomics of Bacterial and Fungal Pathogens of Humans Prof. Francisco García-del Portillo External Advisory Board. Spain.

2. March 16, 2005 Meeting at the Spanish Ministry Education and Science Attendees: Dr. Rosa Rodriguez Bernabé (Head of Life Science Department) Dr. José Antonio Salas (Life Science Department) 10 Representatives of groups working in Bacterial Pathogenesis Dr. F. García-del Portillo

3. March 16, 2005 Meeting at the Spanish Ministry Education and Science Topics discussed: Interest and opportunity of research in human bacterial and fungal pathogens Future areas of research in Genomics of pathogenic microbes Interactions between public and private Entities Search of common interests with other European conuntries

4. Major Areas of Interest How do highly pathogenic microbes emerge?  Microbial population, diversity and evolution of virulence How do microbes cause disease?  Molecular mechanisms underlying pathogenicity (bacteria-host interaction)  Mechanisms of antibiotic resistance Which pathogen functions can be used as targets for diagnosis, prevention and treatment?  Comparative and functional genomics

5. Genomics and Microbial populations (I) How representative of a bacterial species are the available microarrays? Best of the cases: contain non-redundant set of genes of 3-4 strains Scarce genome information on “epidemic” clones: Streptococcus pneumoniae multiresistant epidemic “international” clones: Spain23F-1, Spain6B-2 PFGE, MLEE, MST: limitation in resolving power for biodiversity studies

6. Genomics and Microbial populations (II) “Core” genome Genes specific to environmental clones Genes specific to epidemic clone 1 Genes specific to epidemic clone 2 Risk-indicator genes ? Epidemic strain 1 (2,3,4…) Annotation tasks Food Environment Epidemic clones 5,6,7.. Humans Animals Proposal of indicator genes (exclusive of all epidemic clones) Expression, functional analysis DNA-DNA hybridization Advantage: LIMITED SET OF GENES OF EPIDEMIC STRAIN 1 TO STUDY AT A FUNCTIONAL LEVEL

7. Our experience and infrastructures…  “Genome Sequencing Units” University of Valencia Scientific Park of Madrid. http://www.pcm.uam.es/ Scientific Park of Barcelona. http://www.pcb.ub.es/  Annotation, microarray design Listeria (EC-funded project) Brucella mellitensis “re-annotation” Endosymbionts ( Buchnera, Blochmannia ) Oligonucleotide-based Salmonella microarray  Infection models for functional analysis of candidate genes Extracellular and intracellular pathogens ( in vitro & in vivo models ): Salmonella, Listeria, Mycobacterium, Brucella, Staphylococci, Streptococci,..

8. Microbe-host interactions  Interest in promoting further studies in “model” pathogens and “infection models” (host cell type, tissue tropism)  Microarrays covering the entire genome of the strain/clone used in the study Test strain (virulent) ~ 8-10 % genome “non-represented” in the transcriptome (virulence genes?) In vivoIn vitro Correspondence of phenotypes observed in both systems Microarray “strain” 1 2

9. The “SALGENOMICS” Project Cell division Biofilm Dam methylation DNA-binding proteins Intracellular persistence model  Microarray representing 100% of the genome of the virulent reference strain used in all models

10. PATOGENOM “A Network funded by the Spanish Ministry of Education and Science to create new and foster existing collaborations among groups that apply genome wide-based technologies to study human pathogens” http://www.cnb.uam.es/redpatog/

11. PATOGENOM 17 groups : Candida albicans Salmonella spp. Escherichia coli (EHEC, EPEC) Brucella mellitensis Mycobacterium tuberculosis Listeria monocytogenes Streptococcus pneumoniae Staphylococcus aureus http://www.cnb.uam.es/redpatog/ Topics/interests : Bacteria-host cell interaction - Invasion, control of intracellular growth - Phagosome trafficking - Cell tropism Gene regulation Biofilm Persistent infections Antibiotic resistance Identification of new targets Diagnosis/treatment/vaccination

12. Research Areas of Interest Transcriptome analysis (Host & pathogen) Comparative genomics (epidemic strains, multiresistant clones, model pathogens) Proposal of new targets Functional post-genomics DIAGNOSIS PREVENTION TREATMENT Infection models Persistence, chronic infection Genome sequencing annotation PATOGENOM + Campylobacter spp. Helicobacter pylori * * * Some genes might not be expressed unless pathogen encounters the host !!