WP nr 6 Birgitta Henriques Normark, Sweden Raquel Sa-Leao, Herminia de Lencastre, Portugal Regine Hakenbeck, Germany Chris Tang, UK Staffan Normark, Sweden

Progress Year 4 Serotyping, molecular typing (MLST) and antibiotic resistance among LRTI isolates, GRACE. Totally isolates. Clinical information needs to be correlated to the molecular characteristics of the strains. Performed microarray analysis on clinical pneumococcal isolates belonging to different serotypes, sequence types and of different invasive disease potential and we are studying the genetic relationsships between different clonal complexes as determined with the sequenced based molecular typing method MLST. Gene content variation among isolates of different eBURST groups may differ, potentially due to differences in transformability. Furthermore, our data show that assumptions of similarity in large clonal complexes should be done with caution. Pathogenicity islands studied in in vivo models. Correlation of disease to genomic content of the bacteria by molecular typing and sequencing of invasive and carriage isolates of the same serotype and clonal type Impact of two different patterns of antibiotic consumption on pneumococcal resistance in a country with widespread use of the seven-valent pneumococcal conjugate vaccine. Highly penicillin-resistant multidrug-resistant pneumococcus-like strains colonizing children: genomic characteristics and implications for surveillance. The stability of a multiple antibiotic and high penicillin-resistant clone Spain 23F-1 has been analyzed by comparing genome sequences of seven members of this clone Spain, South Africa, Hungary, Germany and France. A similar approach has been started using three genomes of the Hu19A-6 clone. Two distinct isolates have been sequenced which will be compared to the finished genome which is publicly available A model of the respiratory epithelial barrier has been developed to examine the traversal of the pneumococcus from the nasopharynx. Calu-3 cells are grown on semi-permeable membranes and become polarised, develop tight junctions, and are impermeable to flourescent tracer.

Progress Year 4

Deliverables Year 4 1. To create and maintain S. pneumoniae data base. 2. To collect pneumococcal isolates causing community-acquired LRTI in Europe. 3. To detect new and unusual antibiotic resistance profiles among S. pneumoniae causing community-acquired LRTI in Europe. 4. To determine the serotype distribution of antibiotic susceptible and non-susceptible pneumococci across Europe in community-acquired LRTI to inform vaccine design. 5. To monitor clonal spread of S. pneumoniae causing community-acquired LRTI in Europe important for intervention regimens. 6. To correlate antibiotic resistance, virulence characteristics and pneumococcal genotype to disease parameters such as severity of community-acquired LRTI aiming at optimise future treatment and intervention strategies. 7. To monitor pathogenicity islands and horizontally acquired DNA among pneumococcal isolates causing community-acquired LRTI by performing comparative genomics with microarray technology with the aim of finding genes important for virulence and for antibiotic resistance development. 8. To characterize in in vivo (mice) models the role of pathogenicity islands in pneumococcal disease.

Milestones Year 4 WP6 – DL9: Month 42 Strain collection, frequency of resistance and serotypes among pneumococcal isolates causing community-acquired LRTI during the surveillance period WP6 – DL10: Month 42 Molecular types of antibiotic susceptible and resistant pneumococcal isolates identified in DL1 and DL2 WP6 – DL11: Month 48 Strain collection, frequency of resistance and serotypes among pneumococcal isolates causing community-acquired LRTI during the surveillance period

Obstacles (if any) Less isolates than anticipated Several optochin resistant Clinical information about the isolates needed to perform correlations

Dissemination at meetings INVITED ORAL TALKS AT CONFERENCES (SELECTED) Sá-Leão, R O ecossistema da nasofaringe (“The nasopharyngeal ecosystem”). Congresso Nacional de Pediatria (“National Pediatrics Congress”). Tróia, Portugal. October 15-17, 2009 Henriques Normark, The Epidemiology of pneumococcus, Semmering, Austria, April 23-26,2009 Henriques Normark, Key note lecturer, ECCMID Helsinki, May 19,2009 Henriques Normark, Nobelsymposium Stockholm, June 11-13, 2009 Henriques Normark, Umeå Bacterial cellbiology and pathogenesis Invited speaker, Umeå, June 14-18, 2009 ABSTRACTS SELECTED FOR ORAL PRESENTATIONS IN INTERNATIONAL AND NATIONAL MEETINGS (SELECTED) Frazão, N., R. Sá-Leão, and H. de Lencastre Effect of a single dose of the 7-valent pneumococcal conjugate vaccine (PCV7) on the composition of the nasopharyngeal flora. Abstr. D-O5, p. 59. In Programme and Abstract Book of the 9 th European Meeting on the Molecular Biology of the Pneumococcus. Bern, Switzerland. June 4 - 7, Valente C., S. Nunes, R. Sá-Leão, and H. de Lencastre Dynamics of serogroup 6 of Streptococcus pneumoniae during the last decade in Portugal, including the recently described serotype 6C. Abstr. p. 29. In Programme and Abstract Book of the 9 th European Meeting on the Molecular Biology of the Pneumococcus-Europneumo Bern, Switzerland, June Simões A. S., R. Sá-Leão, S. Nunes, N. Frazão, A. Tavares, H. de Lencastre. Penicillin resistance caused by dissemination of serotype 14 - clone Spain 9V ST156 - in the vaccine era. Abstr. O494, p. 74. In Programme and Abstract Book of the 19 th European Congress of Clinical Microbiology and Infectious Diseases (ECCMID). Finland. May , th European Congress of Clinical Microbiology and Infectious Diseases (ECCMID) Nunes, S., R. Sá-Leão, A.S. Simões, N. Frazão, A. Brito-Avô, and H. de Lencastre Colonization of Streptococcus pneumoniae in the era of seven-valent conjugate pneumococcal vaccine. Abstr. ID 153. In Microbiotec’09 Oral Session S5: Health and Pharmaceutical Biotechnology. Vilamoura, Portugal. November 28-30, Sá-Leão, R., S. Nunes, N. Frazão, A.S. Simões, A. Brito-Avô 3, and H. de Lencastre “Impacto da vacina pneumocócica conjugada sete-valente (PCV7) em colonização” Abstr. p. 7. In Programme and Abstract Book of the “XI Jornadas Nacionais de Infecciologia Pediátrica – I Jornadas Lusófonas de Infecciologia Pediátrica”. Aveiro, Portugal. May 7 - 9, SEVERAL POSTERS ON NATIONAL AND INTERNATIONAL CONFERENCES

Publication plan PUBLISHED ORIGINAL ARTICLES IN SCIENTIFIC PEER-REVIEWED JOURNALS Blomberg et al. Pattern of accessory regions and invasive disease potential in Streptococcus pneumoniae. J Infect Dis Apr 1;199(7): Simões, A.S. †, R. Sá-Leão †, M.J. Eleveld, D.A. Tavares, J. Carriço, H.J. Bootsma, and P.W.M. Hermans Highly penicillin-resistant multidrug-resistant pneumococcus-like strains colonizing children: genomic characteristics and implications for surveillance. J. Clin. Microbiol. 48: Rodrigues, F. †, S. Nunes †, R. Sá-Leão, G. Gonçalves, L. Lemos, and H. de Lencastre. Streptococcus pneumoniae nasopharyngeal carriage in children attending day care centers in the central region of Portugal, in the era of 7- valent pneumococcal conjugate vaccine. Microb. Drug Resist. Microb. Drug Resist. 15: Sá-Leão, R., S. Nunes, A. Brito-Avô, N. Frazão, A. Simões, M.I. Crisóstomo, A.C.S. Paulo, J. Saldanha, I. Santos- Sanches, and H. de Lencastre Changes in pneumococcal serotypes and antibiotypes carried by vaccinated and unvaccinated day-care center attendees in Portugal, a country with widespread use of the seven-valent pneumococcal conjugate vaccine. Clin. Microbiol. Infect. 15: Nunes, S. †, C. Valente †, R. Sá-Leão, and H. De Lencastre Secular trends and molecular epidemiology of the recently described serotype 6C of Streptococcus pneumoniae. J. Clin. Microbiol. 47: SUBMITTED MANUSCRIPTS Blomberg C, Dagerhamn J, Browall S, Normark S, Henriques-Normark B. Gene content variation within clonal complexes of Streptococcus pneumoniae Submitted PLANNED -LRTI PNEUMOCOCCAL ISOLATES (GRACE COLLECTION), CHARACTERISTICS CORRELATED TO CLINICAL INFORMATION -GENOMIC COMPARISON AND CORRELATION TO CARRIAGE AND DISEASE