✎ pip:fct1555_2014 [Molecular Microbiology and Infection Unit]

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====== The changing pneumococci: adapting to vaccination and transitioning between colonization and disease ======

Acronym: TransPneumo

FCT reference: PTDC/DTP-EPI/1555/2014

Principal investigator: J. Melo-Cristino

Dates: 01-04-2016 to 31-03-2019

===== Summary =====


===== Publications =====

==== Papers ====
[[people:anacosta|Silva-Costa C]], Brito MJ, Aguiar SI, Lopes JP, [[people:ramirez|Ramirez M]], [[people:jmelocristino|Melo-Cristino J]], Portuguese Group for the Study of Streptococcal Infections, Portuguese Study Group of Invasive Pneumococcal Disease of the Pediatric Infectious Disease Society. 2019. <fc #0000FF>Dominance of vaccine serotypes in pediatric invasive pneumococcal infections in Portugal (2012-2015)</fc>. Sci Rep 9:6. [[https://doi.org/10.1038/s41598-018-36799-x|doi:10.1038/s41598-018-36799-x]] [[http://www.ncbi.nlm.nih.gov/pubmed/30626918|(PMID: 30626918)]]

Echániz-Aviles G, Guerreiro SI, [[people:anacosta|Silva-Costa C]], [[people:cmendes|Mendes CI]], [[people:jcarrico|Carriço JA]], Carnalla-Barajas MN, Soto-Noguerón A, Velazquez-Meza ME, [[people:jmelocristino|Melo-Cristino J]], Luévanos-Velazquez A, Martínez-Medina L, Vázquez-Larios MDR, [[people:ramirez|Ramirez M]]. 2019. <fc #0000FF>//Streptococcus pneumoniae// serotype 3 in Mexico (1994-2017): decrease of the unusual CC4909 lineage post-PCV13 introduction</fc>. J Clin Microbiol. 57 e01354-18 [[https://doi.org/10.1128/JCM.01354-18|doi:10.1128/JCM.01354-18]] [[http://www.ncbi.nlm.nih.gov/pubmed/30404945|(PMID: 30404945)]]

[[people:ahoracio|Horácio AN]], [[people:anacosta|Silva-Costa C]], Lopes E, [[people:ramirez|Ramirez M]], [[people:jmelocristino|Melo-Cristino J]], Portuguese Group for the Study of Streptococcal Infections. 2018. <fc #0000FF>Conjugate vaccine serotypes persist as major causes of non-invasive pneumococcal pneumonia in Portugal despite declines in serotypes 3 and 19A (2012-2015)</fc>. PLoS ONE 13:e0206912.[[https://doi.org/10.1371/journal.pone.0206912|doi:10.1371/journal.pone.0206912]] [[http://www.ncbi.nlm.nih.gov/pubmed/30388168|(PMID: 30388168)]]

[[people:anacosta|Silva-Costa C]], Brito MJ, [[people:mdpinho|Pinho MD]], [[people:afriaes|Friães A]], Aguiar SI, [[people:ramirez|Ramirez M]], [[people:jmelocristino|Melo-Cristino J]], Portuguese Group for the Study of Streptococcal Infections, Portuguese Study Group of Invasive Pneumococcal Disease of the Pediatric Infectious Disease Society. 2018. <fc #0000FF>Pediatric complicated pneumonia caused by //Streptococcus pneumoniae// serotype 3 in 13-valent pneumococcal conjugate vaccinees, Portugal, 2010-2015</fc>. Emerging Infect Dis 24: 1307–1314. [[http://www.ncbi.nlm.nih.gov/pubmed/29912700|(PMID: 29912700)]]

[[people:jmiranda|Diamantino-Miranda J]], [[people:siaguiar|Aguiar, SI]], [[people:jcarrico|Carriço JA]], [[people:jmelocristino|Melo-Cristino J]], [[people:ramirez|Ramirez M]]. 2017. <fc #0000FF>Clonal and serotype dynamics of serogroup 6 isolates causing invasive pneumococcal disease in Portugal: 1999-2012</fc>. PLoS ONE 12:e0170354. [[http://www.ncbi.nlm.nih.gov/pubmed/28152029|(PMID: 28152029)]]

[[people:ahoracio|Horácio AN]], [[people:anacosta|Silva-Costa C]], Lopes JP, [[people:ramirez|Ramirez M]], [[people:jmelocristino|Melo-Cristino J]], Portuguese Group for the Study of Streptococcal Infections. 2016. <fc #0000FF>Serotype 3 remains the leading cause of invasive pneumococcal disease in adults in Portugal (2012-2014) despite continued reductions in other 13-valent conjugate vaccine serotypes</fc>. Front Microbiol 7:1616. [[http://www.ncbi.nlm.nih.gov/pubmed/27790208|(PMID: 27790208)]]

[[people:ahoracio|Horácio AN]], [[people:anacosta|Silva-Costa C]], [[people:jmiranda|Diamantino-Miranda J]], Lopes JP, [[people:ramirez|Ramirez M]], [[people:jmelocristino|Melo-Cristino J]], Portuguese Group for the Study of Streptococcal Infections. 2016. <fc #0000FF>Population structure of //Streptococcus pneumoniae// causing invasive disease in adults in Portugal before PCV13 availability for adults: 2008-2011</fc>. PLoS ONE 11:e0153602. [[http://www.ncbi.nlm.nih.gov/pubmed/27168156|(PMID: 27168156)]]

==== Meeting presentations ====
**Silva-Costa C, Pinho M, Friães A, Gomes-Silva J, Guerreiro S, Brito M, Ramirez M, Melo-Cristino J.** 2019. Molecular diagnostics reveals persistence of serotype 3 as the main cause of pediatric complicated pneumonia in Portugal despite extensive PCV13 use (P263), 18–21 September, 12th International Meeting on Microbial Epidemiological Markers (IMMEM XII) Dubrovnik, Croatia.

**Gomes-Silva J, Silva-Costa C, Ramirez M, Melo-Cristino J**. 2019. Characterization of the genetic lineages responsible for pediatric invasive pneumococcal disease in Portugal (1999-2015) (P267), 18–21 September, 12th International Meeting on Microbial Epidemiological Markers (IMMEM XII) Dubrovnik, Croatia.

**C. Silva-Costa, J. Gomes-Silva, S. I. Guerreiro, L. Prados, M. J. Brito, M. Ramirez, J. Melo-Cristino, Portuguese Group for the Study of Streptococcal Infections, Portuguese Study Group of Invasive Pneumococcal Disease of the Paediatric Infectious Disease Society**. 2019. Serotypes 3, 8 and 10A dominate among pediatric invasive pneumococcal infections in Portugal (2015-2018) (Oral) 14th European Meeting on the Molecular Biology of the Pneumococcus, 11th – 14th June, Greifswald, Germany.

**C. Silva-Costa, M. D. Pinho, A. Friães, J. Gomes-Silva, S. I. Guerreiro, M.J. Brito, M. Ramirez, J. Melo-Cristino, Portuguese Group for the Study of Streptococcal Infections, Portuguese Study Group of Invasive Pneumococcal Disease of the Paediatric Infectious Disease Society**. 2019. Three years after PCV13 introduction in the National Immunization Plan serotype 3 is still the main cause of complicated pneumonia in Portugal (P46) 14th European Meeting on the Molecular Biology of the Pneumococcus, 11th – 14th June, Greifswald, Germany.

**Ramirez M**. 2019.  Maturing pneumococcal vaccination programs in children: implications for adult and at-risk group vaccination (Lecture). 4th Annual Dubai International Conference on Infectious Diseases and Vaccination, Dubai, UAE, 25-27th April.

**Silva-Costa C, Lopes JP, Ramirez M, Melo-Cristino J, The Portuguese Group for the Study of Streptococcal Infections**. 2018. Non-invasive pneumococcal pneumonia in adults in Portugal: continued decline of PCV13 serotypes (2015-2017) (P1452). IDWeek 2018. San Francisco, CA, USA, 3-7th October.

**Silva-Costa C, Lopes JP, Ramirez M, Melo-Cristino J, The Portuguese Group for the Study of Streptococcal Infections**. 2018. Serotypes 8 and 3 are the leading cause of invasive pneumococcal disease in adults in Portugal (2015-2017) (P1443). IDWeek 2018. San Francisco, CA, USA, 3-7th October.

**Silva-Costa C, Horácio A, Aguiar SI, Lopes JP, Brito MJ, Ramirez M, Melo-Cristino J, Portuguese Group for the Study of Streptococcal Infections, Portuguese Study Group of Invasive Pneumococcal Disease of the Pediatric Infectious Disease Society**. Persistence of PCV7 and PCV13 serotypes in pediatric invasive pneumococcal disease in Portugal after more than a decade of vaccine use (P278). 11th International Symposium on Pneumococci and Pneumococcal Diseases (ISPPD-11), Melbourne, Australia, 15-19 April 2018.

**Silva-Costa C, Brito MJ, Pinho MD, Friães A, Aguiar SI, Ramirez M, Melo-Cristino J, Portuguese Group for the Study of Streptococcal Infections, Portuguese Study Group of Invasive Pneumococcal Disease of the Pediatric Infectious Disease Society**. Serotype 3 is the leading cause of complicated pediatric pneumococcal pneumonia in Portugal even among PCV13 vaccinated children (2010-2015) (P279, oral). 11th International Symposium on Pneumococci and Pneumococcal Diseases (ISPPD-11), Melbourne, Australia, 15-19 April 2018.

**Mendes CI, Machado M, Melo-Cristino J, Carriço JA, Ramirez M**. Associations of serotype with characteristics of the spnD39III locus implicated in phase switching of pneumococci (P334). 11th International Symposium on Pneumococci and Pneumococcal Diseases (ISPPD-11), Melbourne, Australia, 15-19 April 2018.

**Mendes CI, Machado MP, Melo-Cristino J, Ramirez M, Carriço JA.** 2018. A mapping methodology for the characterization of modular genes (OP S2). Bioinformatics Open Days, Braga, Portugal, 15-16 March.

**Silva-Costa C, Horácio A, Aguiar SI, Lopes JP, Brito MJ, Ramirez M, Melo-Cristino J, Portuguese Group for the Study of Streptococcal Infections, Portuguese Study Group of Invasive Pneumococcal Disease of the Pediatric Infectious Disease Society.** 2017. Pediatric invasive pneumococcal disease in Portugal: changing epidemiology (2012-2016) (P172). MicroBioTec'17, Porto, Portugal, 7-9 December.

**Mendes CI, Machado MP, Melo-Cristino J, Ramirez M, Carriço JA.** 2017. Phase-variable type I restriction-modification systems: A new characterization methodology for high throughput sequencing data (P156). MicroBioTec'17, Porto, Portugal, 7-9 December.

**Horácio AN, Silva-Costa C, Lopes JP, Ramirez M, Melo-Cristino J, Portuguese Group for the Study of Streptococcal Infections.** 2017. Importance of vaccine serotypes and emergence of non-vaccine serotypes causing non-invasive pneumococcal pneumonia in adults in Portugal (2012-2015) (OS6-4). International Congress of Chemotherapy and Infection (ICC 2017). Taipei, Taiwan, 24-27th November.

**Silva-Costa C, Horácio A, Aguiar SI, Lopes JP, Brito MJ, Ramirez M, Melo-Cristino J, Portuguese Group for the Study of Streptococcal Infections, Portuguese Study Group of Invasive Pneumococcal Disease of the Pediatric Infectious Disease Society.** 2017. PCV13 serotypes are still important causes of pediatric invasive pneumococcal disease in Portugal after more than a decade of conjugate vaccine (PS532). International Congress of Chemotherapy and Infection (ICC 2017). Taipei, Taiwan, 24-27th November.

**Ramirez M.** 2017. Global burden of pneumococcal diseases (Invited lecture SP18-1). International Congress of Chemotherapy and Infection (ICC 2017). Taipei, Taiwan, 24-27th November.

**Silva-Costa C, Aguiar SI, Pinho MD, Friães A, Ramirez M, Melo-Cristino J, The Portuguese Group for the Study of Streptococcal Infections, The Portuguese Study Group of Invasive Pneumococcal Disease of the Paediatric Infectious Disease Society.** 2017. Serotype distribution among //Streptococcus pneumoniae// isolates causing complicated pneumonia in children in Portugal (2010-2015) (P0059). 27th European Congress of Clinical Microbiology and Infectious Diseases, Vienna, Austria, 22-25 April.


**Silva-Costa C, Aguiar S, Pinho M, Friães A, Ramirez M, Melo-Cristino J, The Portuguese Group for the Study of Streptococcal Infections, The Portuguese Study Group of Invasive Pneumococcal Disease of the Pediatric Infectious Disease Society**. 2016. High prevalence of serotype 3 in pneumococcal isolates causing complicated pneumonia and empyema in Portugal (2010-2015) (20.169). International Meeting on Emerging Diseases and Surveillance (IMED 2016). Viena, Austria, 4th–7rd November.

**Ramirez M**. 2016. Novos serotipos: implicações na prática clínica. 13º encontro de Infecciologia Pediátrica - Novas ou velhas doenças? (Invited oral presentation), Coimbra, Portugal, 7th October.

**Horácio AN, Silva-Costa C, Lopes JP, Ramirez M, Melo-Cristino J, The Portuguese Group for the Study of Streptococcal Infections and The  Portuguese Study Group of Invasive Pneumococcal Disease of the Paediatric Infectious Disease Society**. 2016. Serotypes and antimicrobial resistance of isolates causing invasive pneumococcal disease in adult patients in Portugal after the 13-valent conjugate vaccine received an adult indication - 2012-2014 (P789). IDWeek 2016. New Orleans, LA, USA, 26-30th October.

**Silva-Costa C, Horácio AN, Lopes JP, Ramirez M, Melo-Cristino J, The Portuguese Group for the Study of Streptococcal Infections and The  Portuguese Study Group of Invasive Pneumococcal Disease of the Paediatric Infectious Disease Society**. 2016. Isolates expressing PCV13 serotypes are still the leading cause of pediatric invasive pneumococcal disease in Portugal (P169). 10th International Symposium on Pneumococci and Pneumococcal Diseases – ISPPD10, Glasgow, Scotland, 26-30th June.

**Horácio AN, Silva-Costa C, Lopes JP, Ramirez M, Melo-Cristino J, Portuguese Group for the Study of Streptococcal Infections.** 2016. Serotype and antimicrobial resistance of isolates causing invasive pneumococcal disease in adults in Portugal (2012-2014) (P630). 10th International Symposium on Pneumococci and Pneumococcal Diseases – ISPPD10, Glasgow, Scotland, 26-30th June.