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Mário Nuno Ramos de Almeida Ramirez. Completed the Título de Agregado in Microbiologia in 2015/12/15 by Universidade de Lisboa Faculdade de Medicina and Doutoramento in Biologia in 1998 by Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia. Is Researcher in Instituto de Medicina Molecular João Lobo Antunes and Associate Professor in Universidade de Lisboa Faculdade de Medicina. Published 117 articles in journals. Supervised 8 PhD thesis(es) e co-supervised 3. Supervised 10 MSc dissertation(s) e co-supervised 6. Has received 1 awards and/or honors. Participates and/or participated as Principal investigator in 7 project(s) and Researcher in 10 project(s). Works in the area(s) of Medical and Health Sciences with emphasis on Health Sciences with emphasis on Infectious Diseases, Natural sciences with emphasis on Biological Sciences with emphasis on Microbiology and Exact Sciences with emphasis on Computer and Information Sciences with emphasis on Bioinformatics. In their professional activities interacted with 550 collaborator(s) co-authorship of scientific papers. In his curriculum Ciência Vitae the most frequent terms in the context of scientific, technological and artistic-cultural output are: Resistência aos antibióticos; Epidemiologia Molecular; Infecções respiratórias ; Streptococcus ; Genómica; Biologia de populações; Evolução; Virulência; Sequenciação de alto débito; Identificação bacteriana e rastreio; Doenças Infecciosas; Analise de Dados automatizada; Doença pneumocócica; Vacinas conjugadas pneumocócicas; Virulência e complemento genético; Genómica populacional; Infecção; Resistência a antimicrobianos; Medicina personalizada; Análise de DNA por microarrays (CGH); análise filogenética; algoritmos e estruturas de dados; NGS (Next Generation Sequencing); plataforma suportada na cloud; .
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Identification

Personal identification

Full name
Mário Nuno Ramos de Almeida Ramirez

Citation names

  • Ramirez, Mário

Author identifiers

Ciência ID
9C1C-F2A2-4226
ORCID iD
0000-0002-4084-6233
Google Scholar ID
EWHFzOAAAAAJ&h
Researcher Id
B-4993-2008
Scopus Author Id
7201568476

Addresses

  • Av. Prof. Egas Moniz, 1649-028, Lisboa, Lisboa, Portugal (Professional)

Websites

Knowledge fields

  • Natural sciences - Biological Sciences - Microbiology
  • Exact Sciences - Computer and Information Sciences - Bioinformatics
  • Medical and Health Sciences - Health Sciences - Infectious Diseases

Languages

Language Speaking Reading Writing Listening Peer-review
Portuguese (Mother tongue)
English Proficiency (C2) Proficiency (C2) Proficiency (C2) Proficiency (C2) Proficiency (C2)
Education
Degree Classification
2015/12/15
Concluded
 Microbiologia (Título de Agregado)
Universidade de Lisboa Faculdade de Medicina, Portugal
1998
Concluded
 Biologia (Doutoramento)
Major in Especialidade: Biologia Molecular
Universidade Nova de Lisboa Faculdade de Ciências e Tecnologia, Portugal
"Dna Exchange in Natural Populations of Streptococcus Pneumoniae" (THESIS/DISSERTATION)
Affiliation

Science

Category
Host institution 		Employer
2007/01/01 - Current Researcher (Research) Instituto de Medicina Molecular João Lobo Antunes, Portugal

Teaching in Higher Education

Category
Host institution 		Employer
2004/01/01 - Current Associate Professor (University Teacher) Universidade de Lisboa Faculdade de Medicina, Portugal
Projects

Grant

Designation Funders
2023/11/01 - 2025/06/30 Creating and refining whole-genome and core-genome typing schemas for pathogen surveillance - CENTAUR
ISIDORe
Principal investigator
Instituto de Medicina Molecular, Portugal
 União Europeia
Ongoing

Contract

Designation Funders
2018/10/01 - 2021/09/30 Ferramentas para análise filogenética em larga escala
PTDC/CCI-BIO/29676/2017
Researcher
Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal

Instituto de Medicina Molecular João Lobo Antunes, Portugal
Fundação para a Ciência e a Tecnologia
Ongoing
2017/01/01 - 2020/12/31 Plataforma Ómica para Prevenção e Controlo de infecções e de Resistência aos Antimicrobianos.
SAICTPAC/0015/2015
Researcher
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal

Fundação Calouste Gulbenkian, Portugal

Instituto de Medicina Molecular João Lobo Antunes, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2016/12/01 - 2019/11/30 BacGenTrack – Um sistema integrado para analise de genomas bacterianos usando metodos de sequenciação de alto débito: identificação de estirpes e visualização de resultados
TUBITAK/0004/2014
Researcher
Instituto de Medicina Molecular João Lobo Antunes, Portugal

Instituto de Engenharia de Sistemas e Computadores Investigação e Desenvolvimento em Lisboa, Portugal
Fundação para a Ciência e a Tecnologia
Concluded
2016/04/01 - 2019/09/30 As alterações dos pneumococos: adaptações à vacinação e a transição entre colonização e doença
PTDC/DTP-EPI/1555/2014
Researcher
Instituto de Medicina Molecular João Lobo Antunes, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2015 - 2016 Infections by group B streptococci in Portugal and Iceland: raising awareness and contributing to preventive strategies
147DT
Principal investigator
Instituto de Medicina Molecular João Lobo Antunes, Portugal
 EEA Grants
Concluded
2013/06/01 - 2015/05/31 A acção das vacinas conjugadas: alterações da população pneumocócica e as suas consequências genómicas
PTDC/DTP-EPI/1759/2012
Researcher
Instituto de Medicina Molecular João Lobo Antunes, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
2011/01 - 2014/06 In silico reconstruction of Streptococcus pneumoniae cellular networks and their impact on virulence
Provided by PTCRIS: 113824
113824
Researcher
Fundação para a Ciência e a Tecnologia, I.P.
2009/02 - 2012/12 Implications for therapy and disease presentation of the changes triggered by the use of the pneumococcal 7-valent conjugate vaccine
Provided by PTCRIS: 83065
83065
Principal investigator
Fundação para a Ciência e a Tecnologia, I.P.
2008/10 - 2012/05 Population and genomic consequences of vaccination against Streptococcus pneumoniae
64888
Provided by PTCRIS: 64888
Principal investigator
Fundação para a Ciência e a Tecnologia, I.P.
2008/08 - 2012/02 Streptococcus pyogenes invasive disease and antimicrobial resistance - two faces of a changing pathogen
72321
Provided by PTCRIS: 72321
Researcher
Fundação para a Ciência e a Tecnologia, I.P.
2008/10 - 2011/09 A computational biology approach using Streptococcus pneumoniae as a model towards an integrative view of bacteria/host interactions and evolution
71499
Provided by PTCRIS: 71499
Principal investigator
Fundação para a Ciência e a Tecnologia, I.P.
2009 - 2011 CAREPNEUMO - Combating antibiotic resistance pneumococci by novel strategies based on in vivo and in vitro host-pathogen interactions
FP7-HEALTH-2007-223111
Principal investigator
Instituto de Medicina Molecular João Lobo Antunes, Portugal
 União Europeia
Concluded
2007/01 - 2008/12 Molecular epidemiology of Streptococcus agalactiae infections in Portugal
82582
Provided by PTCRIS: 82582
Researcher
Fundação para a Ciência e a Tecnologia, I.P.
2005/05 - 2007/06 Molecular epidemiology of Streptococcus agalactiae infections in Portugal
57646
Provided by PTCRIS: 57646
Researcher
Fundação para a Ciência e a Tecnologia, I.P.
2006 - 2006 Population based identification of pneumococcal virulence and colonization factors
N/A
Principal investigator
Instituto de Medicina Molecular João Lobo Antunes, Portugal
 National Institute of Allergy and Infectious Diseases
Concluded
2004 - 2006 Pneumococcal Resistance Epidemicity and Virulence - an International Study: PREVIS
FP6-2002-CT-503413
Researcher
Instituto de Medicina Molecular João Lobo Antunes, Portugal
 União Europeia
Concluded
2001 - 2004 Caracterização do impacto de bacteriófagos em populações naturais de Streptococcus pneumoniae
POCTI/BME/34418/99-00
Principal investigator
Universidade Nova de Lisboa Instituto de Tecnologia Química e Biológica, Portugal
 Fundação para a Ciência e a Tecnologia
Concluded
Outputs

Publications

Book chapter
  1. Silva-Costa, Catarina; Melo-Cristino, José; Ramirez, Mario. "Streptococcus pneumoniae". In Molecular Medical Microbiology, 1479-1490. Elsevier, 2024.
    10.1016/b978-0-12-818619-0.00095-2
Journal article
  1. Xie, Ouli; Morris, Jacqueline M.; Hayes, Andrew J.; Towers, Rebecca J.; Jespersen, Magnus G.; Lees, John A.; Ben Zakour, Nouri L.; et al. "Inter-species gene flow drives ongoing evolution of Streptococcus pyogenes and Streptococcus dysgalactiae subsp. equisimilis". Nature Communications 15 1 (2024): http://dx.doi.org/10.1038/s41467-024-46530-2.
    10.1038/s41467-024-46530-2
  2. Faria, Nuno Alexandre; Touret, Tiago; Simões, Alexandra S.; Palos, Carlos; Bispo, Soraia; Cristino, José Melo; Ramirez, Mário; et al. "Genomic Insights into the expansion of Carbapenem-Resistant Klebsiella pneumoniae within Portuguese Hospitals". Journal of Hospital Infection (2024): http://dx.doi.org/10.1016/j.jhin.2024.02.028.
    10.1016/j.jhin.2024.02.028
  3. Cezar Vinícius Würdig Riche; Mabel Kamweli Aworh; Renato Cassol; Diego Rodrigues Falci; Mario Ramirez; Cícero Armídio Gomes Dias. "Epidemiology and risk factors for mortality among methicillin-resistant Staphylococcus aureus bacteremic patients in Southern Brazil". PLOS ONE (2023): https://doi.org/10.1371/journal.pone.0283774.
    10.1371/journal.pone.0283774
  4. Silva-Costa, Catarina; Gomes-Silva, Joana; Santos, Andreia; Ramirez, Mario; Melo-Cristino, Jose. "Adult non-invasive pneumococcal pneumonia in Portugal is dominated by serotype 3 and non-PCV13 serotypes 3-years after near universal PCV13 use in children". Frontiers in Public Health (2023): https://publons.com/wos-op/publon/63701259/.
    10.3389/FPUBH.2023.1279656
  5. Xie, Ouli; Morris, Jacqueline M; Hayes, Andrew J.; Towers, Rebecca J; Jespersen, Magnus G.; Lees, John A.; Ben Zakour, Nouri L.; et al. "Inter-species gene flow drives ongoing evolution of Streptococcus pyogenes and Streptococcus dysgalactiae subsp. equisimilis". BioRxiv (2023): https://publons.com/wos-op/publon/64066903/.
    10.1101/2023.08.10.552873
  6. Catarina Inês Mendes; Pedro Vila-Cerqueira; Yair Motro; Jacob Moran-Gilad; João André Carriço; Mário Ramirez. "LMAS: evaluating metagenomic short de novo assembly methods through defined communities". GigaScience (2022): https://doi.org/10.1093/gigascience/giac122.
    10.1093/gigascience/giac122
  7. Catarina Silva-Costa; Joana Gomes-Silva; Marcos D. Pinho; Ana Friães; Mário Ramirez; José Melo-Cristino; Eleanor A. Powell; Laura Andrade de Oliveira. "Continued Vaccine Breakthrough Cases of Serotype 3 Complicated Pneumonia in Vaccinated Children, Portugal (2016–2019)". Microbiology Spectrum (2022): https://doi.org/10.1128/spectrum.01077-22.
    10.1128/spectrum.01077-22
  8. Elisabete R. Martins; Dulce Nascimento do Ó; Ana Luísa Marques Costa; José Melo-Cristino; Mário Ramirez; Jennifer M. Auchtung. "Characteristics of Streptococcus agalactiae Colonizing Nonpregnant Adults Support the Opportunistic Nature of Invasive Infections". Microbiology Spectrum (2022): https://doi.org/10.1128/spectrum.01082-22.
    10.1128/spectrum.01082-22
  9. A. Friães; R. Mamede; M. Ferreira; J. Melo-Cristino; M. Ramirez; Daniel J. Diekema. "Annotated Whole-Genome Multilocus Sequence Typing Schema for Scalable High-Resolution Typing of Streptococcus pyogenes". Journal of Clinical Microbiology (2022): https://doi.org/10.1128/jcm.00315-22.
    10.1128/jcm.00315-22
  10. Mukherjee, Debanjan; Chora, Angelo Ferreira; Lone, Jean-Christophe; Ramiro, Ricardo S.; Blankenhaus, Birte; Serre, Karine; Ramirez, Mario; et al. "Host lung microbiota promotes malaria-associated acute respiratory distress syndrome". Nature Communications (2022): https://publons.com/wos-op/publon/53681639/.
    10.1038/S41467-022-31301-8
  11. Birta Baeringsdottir; Helga Erlendsdottir; Erla Soffia Bjornsdottir; Elisabete R. Martins; Mário Ramirez; Asgeir Haraldsson; Thordur Thorkelsson. "Group B streptococcal infections in infants in Iceland: clinical and microbiological factors". Journal of Medical Microbiology (2021): https://doi.org/10.1099/jmm.0.001426.
    10.1099/jmm.0.001426
  12. Catarina Silva-Costa; Joana Gomes-Silva; Lúcia Prados; Mário Ramirez; José Melo-Cristino. "Pediatric Invasive Pneumococcal Disease Three Years after PCV13 Introduction in the National Immunization Plan—The Continued Importance of Serotype 3". Microorganisms (2021): https://doi.org/10.3390/microorganisms9071428.
    10.3390/microorganisms9071428
  13. Catarina Silva-Costa; Joana Gomes-Silva; Inês Teodoro; Mário Ramirez; José Melo-Cristino. "Invasive Pneumococcal Disease in Adults in Portugal: The Importance of Serotypes 8 and 3 (2015–2018)". Microorganisms (2021): https://doi.org/10.3390/microorganisms9051016.
    10.3390/microorganisms9051016
  14. Rafael Mamede; Pedro Vila-Cerqueira; Mickael Silva; João A Carriço; Mário Ramirez. "Chewie Nomenclature Server (chewie-NS): a deployable nomenclature server for easy sharing of core and whole genome MLST schemas". Nucleic Acids Research (2021): https://doi.org/10.1093/nar/gkaa889.
    10.1093/nar/gkaa889
  15. Ramirez, Mário. "Seroprevalence of anti-SARS-CoV-2 antibodies in COVID-19 patients and healthy volunteers up to 6 months post disease onset.". European journal of immunology (2020): https://europepmc.org/articles/PMC7756220.
    10.1002/eji.202048970
  16. Ramirez, Mário. "Two multi-fragment recombination events resulted in the ß-lactam-resistant serotype 11A-ST6521 related to Spain9V-ST156 pneumococcal clone spreading in south-western Europe, 2008 to 2016.". Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin (2020): https://europepmc.org/articles/PMC7189650.
    10.2807/1560-7917.es.2020.25.16.1900457
  17. Catarina I. Mendes; Erley Lizarazo; Miguel P. Machado; Diogo N. Silva; Adriana Tami; Mário Ramirez; Natacha Couto; John W. A. Rossen; João A. Carriço. "DEN-IM: dengue virus genotyping from amplicon and shotgun metagenomic sequencing". Microbial Genomics (2020): https://doi.org/10.1099/mgen.0.000328.
    10.1099/mgen.0.000328
  18. Catarina Silva-Costa; Maria J. Brito; Sandra I. Aguiar; Joana P. Lopes; Mário Ramirez; José Melo-Cristino. "Dominance of vaccine serotypes in pediatric invasive pneumococcal infections in Portugal (2012–2015)". Scientific Reports (2019): https://doi.org/10.1038/s41598-018-36799-x.
    10.1038/s41598-018-36799-x
  19. A. Friães; J. Melo-Cristino; M. Ramirez. "Changes in emm types and superantigen gene content of Streptococcus pyogenes causing invasive infections in Portugal". Scientific Reports (2019): https://doi.org/10.1038/s41598-019-54409-2.
    10.1038/s41598-019-54409-2
  20. Mark van der Linden; Rafael Mamede; Natascha Levina; Peter Helwig; Pedro Vila-Cerqueira; João André Carriço; José Melo-Cristino; Mário Ramirez; Elisabete R Martins. "Heterogeneity of penicillin-non-susceptible group B streptococci isolated from a single patient in Germany". Journal of Antimicrobial Chemotherapy (2019): https://doi.org/10.1093/jac/dkz465.
    10.1093/jac/dkz465
  21. Tiago F Jesus; Bruno Ribeiro-Gonçalves; Diogo N Silva; Valeria Bortolaia; Mário Ramirez; João A Carriço. "Plasmid ATLAS: plasmid visual analytics and identification in high-throughput sequencing data". Nucleic Acids Research (2019): https://doi.org/10.1093/nar/gky1073.
    10.1093/nar/gky1073
  22. Echaniz-Aviles, Gabriela; Guerreiro, Soraia, I; Silva-Costa, Catarina; Mendes, Catarina, I; Carrico, Joao Andre; Noemi Carnalla-Barajas, Maria; Soto-Nogueron, Araceli; et al. "Streptococcus pneumoniae Serotype 3 in Mexico (1994 to 2017): Decrease of the Unusual Clonal Complex 4909 Lineage following PCV13 Introduction". Journal of Clinical Microbiology (2019): https://publons.com/publon/2896153/.
    10.1128/JCM.01354-18
  23. Ramirez, Mário. "Group B Streptococcal Neonatal and Early Infancy Infections in Iceland, 1976-2015". Pediatric Infectious Disease Journal (2019): https://publons.com/publon/28258762/.
    10.1097/INF.0000000000002214
  24. Dias, Oscar; Saraiva, Joao; Faria, Cristiana; Ramirez, Mario; Pinto, Francisco; Rocha, Isabel. "iDS372, a Phenotypically Reconciled Model for the Metabolism of Streptococcus pneumoniae Strain R6". Frontiers in Microbiology (2019): https://publons.com/publon/20997934/.
    10.3389/FMICB.2019.01283
  25. Pinho, Marcos D.; Foster, Geoffrey; Pomba, Constanga; Machado, Miguel P.; Baily, Johanna L.; Kuiken, Thijs; Melo-Cristino, Jose; et al. "Streptococcus canis Are a Single Population Infecting Multiple Animal Hosts Despite the Diversity of the Universally Present M-Like Protein SCM". Frontiers in Microbiology (2019): https://publons.com/publon/28258761/.
    10.3389/FMICB.2019.00631
  26. Andreia N. Horácio; Daniela Flavia Hozbor; Catarina Silva-Costa; Elísia Lopes; Mário Ramirez; José Melo-Cristino. "Conjugate vaccine serotypes persist as major causes of non-invasive pneumococcal pneumonia in Portugal despite declines in serotypes 3 and 19A (2012-2015)". PLOS ONE (2018): https://doi.org/10.1371/journal.pone.0206912.
    10.1371/journal.pone.0206912
  27. Silva, Mickael; Machado, Miguel P.; Silva, Diogo N.; Rossi, Mirko; Moran-Gilad, Jacob; Santos, Sergio; Ramirez, Mario; Carrico, Joao Andre. "chewBBACA: A complete suite for gene-by-gene schema creation and strain identification". Microbial Genomics 4 3 (2018): http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000431156100010&KeyUID=WOS:000431156100010.
    10.1099/mgen.0.000166
  28. Carrico, J. A.; Rossi, M.; Moran-Gilad, J.; Van Domselaar, G.; Ramirez, M.. "A primer on microbial bioinformatics for nonbioinformaticians". Clinical Microbiology and Infection 24 4 (2018): 342-349. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000427826500005&KeyUID=WOS:000427826500005.
    10.1016/j.cmi.2017.12.015
  29. Silva-Costa, Catarina; Brito, Maria Joao; Pinho, Marcos D.; Friaes, Ana; Aguiar, Sandra I.; Ramirez, M.; Melo-Cristino, Jose; Portuguese Grp Study Streptococcal; Pediat Infect Dis Soc. "Pediatric Complicated Pneumonia Caused by Streptococcus pneumoniae Serotype 3 in 13-Valent Pneumococcal Conjugate Vaccinees, Portugal, 2010-2015". Emerging Infectious Diseases 24 7 (2018): 1307-1314. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000435635900017&KeyUID=WOS:000435635900017.
    10.3201/eid2407.180029
  30. Lopes, Elisia; Fernandes, Tania; Machado, Miguel P.; Carrico, Joao Andre; Mello-Cristino, Jose; Ramirez, Mario; Martins, Elisabete R.; Portuguese Grp Study Streptococcal. "Increasing macrolide resistance among Streptococcus agalactiae causing invasive disease in non-pregnant adults was driven by a single capsular-transformed lineage, Portugal, 2009 to 2015". Eurosurveillance 23 21 (2018): 14-23. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000433285600004&KeyUID=WOS:000433285600004.
    10.2807/1560-7917.ES.2018.23.21.1700473
  31. Natacha Couto; Leonard Schuele; Erwin C. Raangs; Miguel P. Machado; Catarina I. Mendes; Tiago F. Jesus; Monika Chlebowicz; et al. "Critical steps in clinical shotgun metagenomics for the concomitant detection and typing of microbial pathogens". Scientific Reports (2018): https://publons.com/publon/17448617/.
    10.1038/S41598-018-31873-W
  32. Catarina Pato; José Melo-Cristino; Mario Ramirez; Ana Friães. "Streptococcus pyogenes Causing Skin and Soft Tissue Infections Are Enriched in the Recently Emerged emm89 Clade 3 and Are Not Associated With Abrogation of CovRS". Frontiers in Microbiology (2018): https://publons.com/publon/17504803/.
    10.3389/FMICB.2018.02372
  33. Jorge Diamantino-Miranda; Herminia de Lencastre; Sandra Isabel Aguiar; João André Carriço; José Melo-Cristino; Mário Ramirez. "Clonal and serotype dynamics of serogroup 6 isolates causing invasive pneumococcal disease in Portugal: 1999-2012". PLOS ONE (2017):
    10.1371/journal.pone.0170354
  34. Martins, Elisabete R.; Pedroso-Roussado, Cristiano; Melo-Cristino, Jose; Ramirez, Mario; Portuguese Grp Study Streptococcal. "Streptococcus agalactiae Causing Neonatal Infections in Portugal (2005-2015): Diversification and Emergence of a CC17/PI-2b Multidrug Resistant Sublineage". Frontiers in Microbiology 8 (2017): http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000397612100001&KeyUID=WOS:000397612100001.
    10.3389/fmicb.2017.00499
  35. Nascimento, Marta; Sousa, Adriano; Ramirez, Mario; Francisco, Alexandre P.; Carrico, Joao A.; Vaz, Catia. "PHYLOViZ 2.0: providing scalable data integration and visualization for multiple phylogenetic inference methods". Bioinformatics 33 1 (2017): 128-129. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000397091600019&KeyUID=WOS:000397091600019.
    10.1093/bioinformatics/btw582
  36. Jamet, Anne; Touchon, Marie; Ribeiro-Goncalves, Bruno; Carrico, Joao Andre; Charbit, Alain; Nassif, Xavier; Ramirez, Mario; Rocha, Eduardo P. C.. "A widespread family of polymorphic toxins encoded by temperate phages". Bmc Biology 15 (2017): http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000408678700001&KeyUID=WOS:000408678700001.
    10.1186/s12915-017-0415-1
  37. Machado MP; Ribeiro-Gonçalves B; Silva M; Ramirez M; Carriço JA. "Epidemiological Surveillance and Typing Methods to Track Antibiotic Resistant Strains Using High Throughput Sequencing". Antibiotics: Methods and Protocols (2017): https://publons.com/publon/11299000/.
    10.1007/978-1-4939-6634-9_20
  38. Bruno Ribeiro-Gonçalves; Alexandre P. Francisco; Cátia Vaz; Mário Ramirez; João André Carriço. "PHYLOViZ Online: web-based tool for visualization, phylogenetic inference, analysis and sharing of minimum spanning trees". Nucleic Acids Research (2016):
    10.1093/nar/gkw359
  39. Pinho, Marcos D.; Erol, Erdal; Ribeiro-Goncalves, Bruno; Mendes, Catarina I.; Carrico, Joao A.; Matos, Sandra C.; Preziuso, Silvia; et al. "Beta-hemolytic Streptococcus dysgalactiae strains isolated from horses are a genetically distinct population within the Streptococcus dysgalactiae taxon". Scientific Reports 6 (2016): http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000381482100001&KeyUID=WOS:000381482100001.
    10.1038/srep31736
  40. Horacio, Andreia N.; Silva-Costa, Catarina; Lopes, Joana P.; Ramirez, Mario; Melo-Cristino, Jose; Portuguese Grp Study Streptococcal. "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". Frontiers in Microbiology 7 (2016): http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000388523200001&KeyUID=WOS:000388523200001.
    10.3389/fmicb.2016.01616
  41. Horacio, Andreia N.; Silva-Costa, Catarina; Diamantino-Miranda, Jorge; Lopes, Joana P.; Ramirez, Mario; Melo-Cristino, Jose; Portuguese Grp Study Streptococcal. "Population Structure of Streptococcus pneumoniae Causing Invasive Disease in Adults in Portugal before PCV13 Availability for Adults: 2008-2011". Plos One 11 5 (2016): http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000376587300078&KeyUID=WOS:000376587300078.
    10.1371/journal.pone.0153602
  42. Bjoernsdottir, E. S.; Martins, E. R.; Erlendsdottir, H.; Haraldsson, G.; Melo-Cristino, J.; Kristinsson, K. G.; Ramirez, M.. "Changing epidemiology of group B streptococcal infections among adults in Iceland: 1975-2014". Clinical Microbiology and Infection 22 4 (2016): http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000375399900015&KeyUID=WOS:000375399900015.
    10.1016/j.cmi.2015.11.020
  43. Barato, P.; Martins, E. R.; Vasquez, G. M.; Ramirez, M.; Melo-Cristino, J.; Martinez, N.; Iregui, C.. "Capsule impairs efficient adherence of Streptococcus agalactiae to intestinal epithelium in tilapias Oreochromis sp". Microbial Pathogenesis 100 (2016): 30-36. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000388548100004&KeyUID=WOS:000388548100004.
    10.1016/j.micpath.2016.08.040
  44. Ana Friães; Miguel P. Machado; Catarina Pato; João Carriço; José Melo-Cristino; Mario Ramirez. "Emergence of the Same Successful Clade among Distinct Populations of emm89 Streptococcus pyogenes in Multiple Geographic Regions". mBio 6 6 (2015): https://doi.org/10.1128/mBio.01780-15.
    10.1128/mBio.01780-15
  45. Raquel Arinto-Garcia; Marcos Daniel Pinho; João André Carriço; José Melo-Cristino; Mário Ramirez; S. S. Richter. "Comparing Matrix-Assisted Laser Desorption Ionization–Time of Flight Mass Spectrometry and Phenotypic and Molecular Methods for Identification of Species within the Streptococcus anginosus Group". Journal of Clinical Microbiology 53 11 (2015): 3580-3588. http://dx.doi.org/10.1128/JCM.01892-15.
    10.1128/JCM.01892-15
  46. Silva-Costa, Catarina; Friaes, Ana; Ramirez, Mario; Melo-Cristino, Jose. "Macrolide-resistant Streptococcus pyogenes: prevalence and treatment strategies". Expert Review of Anti-Infective Therapy 13 5 (2015): 615-628. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000356442600009&KeyUID=WOS:000356442600009.
    10.1586/14787210.2015.1023292
  47. Coelho, Luis Pedro; Pato, Catarina; Friaes, Ana; Neumann, Ariane; von Koeckritz-Blickwede, Maren; Ramirez, Mario; Carrico, Joao Andre. "Automatic determination of NET (neutrophil extracellular traps) coverage in fluorescent microscopy images". Bioinformatics 31 14 (2015): 2364-2370. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000358173500017&KeyUID=WOS:000358173500017.
    10.1093/bioinformatics/btv156
  48. Teixeira, Andreia Sofia; Monteiro, Pedro T.; Carrico, Joao A.; Ramirez, Mario; Francisco, Alexandre P.. "Not Seeing the Forest for the Trees: Size of the Minimum Spanning Trees (MSTs) Forest and Branch Significance in MST-Based Phylogenetic Analysis". Plos One 10 3 (2015): http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000351987300036&KeyUID=WOS:000351987300036.
    10.1371/journal.pone.0119315
  49. Friaes, A.; Resina, C.; Manuel, V.; Lito, L.; Ramirez, M.; Melo-Cristino, J.. "Epidemiological survey of the first case of vancomycin-resistant Staphylococcus aureus infection in Europe". Epidemiology and Infection 143 4 (2015): 745-748. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000351058600011&KeyUID=WOS:000351058600011.
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  50. Rosini, Roberto; Campisi, Edmondo; De Chiara, Matteo; Tettelin, Herve; Rinaudo, Daniela; Toniolo, Chiara; Metruccio, Matteo; et al. "Genomic Analysis Reveals the Molecular Basis for Capsule Loss in the Group B Streptococcus Population". Plos One 10 5 (2015): http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000354049700099&KeyUID=WOS:000354049700099.
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  51. Ana Friães; Friães A; Catarina Pato; Pato C; José Melo-Cristino; Melo-Cristino J; Mario Ramirez; Ramirez M. "Consequences of the variability of the CovRS and RopB regulators among Streptococcus pyogenes causing human infections". Scientific Reports (2015): https://publons.com/publon/131527/.
    10.1038/SREP12057
  52. C. Silva-Costa; M. Ramirez; J. Melo-Cristino. "Declining macrolide resistance in Streptococcus pyogenes in Portugal (2007–13) was accompanied by continuous clonal changes". Journal of Antimicrobial Chemotherapy (2015): https://publons.com/publon/8833846/.
    10.1093/JAC/DKV182
  53. P Barato; E R Martins; J Melo-Cristino; C A Iregui; M Ramirez. "Persistence of a single clone of Streptococcus agalactiae causing disease in tilapia (Oreochromis sp.) cultured in Colombia over 8 years". Journal of Fish Diseases (2015): https://publons.com/publon/4141946/.
    10.1111/JFD.12337
  54. Cardoso, Liliana Sofia; Suissas, Claudia Elvas; Ramirez, Mario; Antunes, Marilia; Pinto, Francisco Rodrigues. "Comparison of alternative mixture model methods to analyze bacterial CGH experiments with multi-genome arrays.". BMC research notes 7 (2014): 148-148.
    10.1186/1756-0500-7-148
  55. Lopez, Elena; Domenech, Arnau; Ferrandiz, Maria-Jose; Frias, Maria Joao; Ardanuy, Carmen; Ramirez, Mario; Garcia, Ernesto; Linares, Josefina; de la Campa, Adela G.. "Induction of Prophages by Fluoroquinolones in Streptococcus pneumoniae: Implications for Emergence of Resistance in Genetically-Related Clones". Plos One 9 4 (2014):
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  56. Horacio, Andreia N; Lopes, Joana P; Ramirez, Mario; Melo-Cristino, Jose; Portuguese Group for the Study of Streptococcal Infections. "Non-invasive pneumococcal pneumonia in portugal-serotype distribution and antimicrobial resistance.". PloS one 9 7 (2014): e103092-e103092.
    10.1371/journal.pone.0103092
  57. Preziuso, S.; Pinho, M. D.; Attili, A. R.; Melo-Cristino, J.; Acke, E.; Midwinter, A. C.; Cuteri, V.; Ramirez, M.. "PCR based differentiation between Streptococcus dysgalactiae subsp equisimilis strains isolated from humans and horses". Comparative Immunology Microbiology and Infectious Diseases 37 3 (2014): 169-172.
    10.1016/j.cimid.2014.04.001
  58. Carrolo, Margarida; Pinto, Francisco Rodrigues; Melo-Cristino, Jose; Ramirez, Mario. "Pherotype Influences Biofilm Growth and Recombination in Streptococcus pneumoniae". Plos One 9 3 (2014):
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  59. Sanderson-Smith, Martina; De Oliveira, David M. P.; Guglielmini, Julien; McMillan, David J.; Vu, Therese; Holien, Jessica K.; Henningham, Anna; et al. "A Systematic and Functional Classification of Streptococcus pyogenes That Serves as a New Tool for Molecular Typing and Vaccine Development". Journal of Infectious Diseases 210 8 (2014): 1325-1338. http://gateway.webofknowledge.com/gateway/Gateway.cgi?GWVersion=2&SrcAuth=ORCID&SrcApp=OrcidOrg&DestLinkType=FullRecord&DestApp=WOS_CPL&KeyUT=WOS:000344609600019&KeyUID=WOS:000344609600019.
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  60. Olafsdottir, L. B.; Erlendsdottir, H.; Melo-Cristino, J.; Weinberger, D. M.; Ramirez, M.; Kristinsson, K. G.; Gottfredsson, M.. "Invasive infections due to Streptococcus pyogenes: seasonal variation of severity and clinical characteristics, Iceland, 1975 to 2012". Eurosurveillance (2014): https://publons.com/publon/8833851/.
    10.2807/1560-7917.ES2014.19.17.20784
  61. Aguiar, S. I.; Brito, M. J.; Horacio, A. N.; Lopes, J. P.; Ramirez, M.; Melo-Cristino, J.. "Decreasing incidence and changes in serotype distribution of invasive pneumococcal disease in persons aged under 18 years since introduction of 10-valent and 13-valent conjugate vaccines in Portugal, July 2008 to June 2012". Eurosurveillance (2014): https://publons.com/publon/1999095/.
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  62. Vaz, Catia; Francisco, Alexandre P.; Silva, Mickael; Jolley, Keith A.; Bray, James E.; Pouseele, Hannes; Rothganger, Joerg; Ramirez, Mario; Carrico, Joao A.. "TypOn: the microbial typing ontology". Journal of Biomedical Semantics (2014): https://publons.com/publon/1334377/.
    10.1186/2041-1480-5-43
  63. Horácio, A.N.; Diamantino-Miranda, J.; Aguiar, S.I.; Ramirez, M.; Melo-Cristino, J.. "The Majority of Adult Pneumococcal Invasive Infections in Portugal Are Still Potentially Vaccine Preventable in Spite of Significant Declines of Serotypes 1 and 5". PLoS ONE 8 9 (2013): http://www.scopus.com/inward/record.url?eid=2-s2.0-84884197325&partnerID=MN8TOARS.
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  64. Melo-Cristino, J.; Resina, C.; Manuel, V.; Lito, L.; Ramirez, M.. "First case of infection with vancomycin-resistant Staphylococcus aureus in Europe". The Lancet 382 9888 (2013): http://www.scopus.com/inward/record.url?eid=2-s2.0-84880510749&partnerID=MN8TOARS.
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  65. Mcmillan, D.J.; Drèze, P.-A.; Vu, T.; Bessen, D.E.; Guglielmini, J.; Steer, A.C.; Carapetis, J.R.; et al. "Updated model of group A Streptococcus M proteins based on a comprehensive worldwide study". Clinical Microbiology and Infection 19 5 (2013): http://www.scopus.com/inward/record.url?eid=2-s2.0-84876302878&partnerID=MN8TOARS.
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  66. Vaz, M.; Meirinhos-Soares, L.; Sousa, C.C.S.; Ramirez, M.; Melo-Cristino, J.; Lopes, J.A.. "Serotype discrimination of encapsulated Streptococcus pneumoniae strains by Fourier-transform infrared spectroscopy and chemometrics". Journal of Microbiological Methods 93 2 (2013): 102-107. http://www.scopus.com/inward/record.url?eid=2-s2.0-84875617863&partnerID=MN8TOARS.
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  67. Friães, A.; Lopes, J.P.; Melo-Cristino, J.; Ramirez, M.. "Changes in Streptococcus pyogenes causing invasive disease in Portugal: Evidence for superantigen gene loss and acquisition". International Journal of Medical Microbiology 303 8 (2013): 505-513. http://www.scopus.com/inward/record.url?eid=2-s2.0-84887607259&partnerID=MN8TOARS.
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  68. Costa, A.; Afonso, J.; Osório, C.; Gomes, A.L.; Caiado, F.; Valente, J.; Aguiar, S.I.; et al. "MiR-363-5p regulates endothelial cell properties and their communication with hematopoietic precursor cells". Journal of Hematology and Oncology 6 1 (2013): http://www.scopus.com/inward/record.url?eid=2-s2.0-84887928259&partnerID=MN8TOARS.
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  69. Silva-Costa, C.; Carriço, J.A.; Ramirez, M.; Melo-Cristino, J.. "Scarlet fever is caused by a limited number of streptococcus pyogenes lineages and is associated with the exotoxin genes ssa, speA and speC". Pediatric Infectious Disease Journal (2013): http://www.scopus.com/inward/record.url?eid=2-s2.0-84886424003&partnerID=MN8TOARS.
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  70. Martins, E.R.; Andreu, A.; Melo-Cristino, J.; Ramirez, M.. "Distribution of pilus islands in Streptococcus agalactiae that cause human infections: Insights into evolution and implication for vaccine development". Clinical and Vaccine Immunology 20 2 (2013): 313-316. http://www.scopus.com/inward/record.url?eid=2-s2.0-84874873141&partnerID=MN8TOARS.
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  71. Carriço, J.A.; Sabat, A.J.; Friedrich, A.W.; Ramirez, M.. "Bioinformatics in bacterial molecular epidemiology and public health: Databases, tools and the next-generation sequencing revolution". Eurosurveillance 18 4 (2013): http://www.scopus.com/inward/record.url?eid=2-s2.0-84873826425&partnerID=MN8TOARS.
  72. Frias, M.J.; Melo-Cristino, J.; Ramirez, M.. "Export of the pneumococcal phage SV1 lysin requires choline-containing teichoic acids and is holin-independent". Molecular Microbiology 87 2 (2013): 430-445. http://www.scopus.com/inward/record.url?eid=2-s2.0-84872374659&partnerID=MN8TOARS.
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  73. Friães, A.; Pinto, F.R.; Silva-Costa, C.; Ramirez, M.; Melo-Cristino, J.. "Superantigen gene complement of Streptococcus pyogenes - Relationship with other typing methods and short-term stability". European Journal of Clinical Microbiology and Infectious Diseases 32 1 (2013): 115-125. http://www.scopus.com/inward/record.url?eid=2-s2.0-84872539465&partnerID=MN8TOARS.
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  74. M D. Pinho; S C. Matos; L H. Wieler; M. D. Pinho; S. C. Matos; C Pomba; A Lubke-Becker; et al. "Multilocus Sequence Analysis of Streptococcus canis Confirms the Zoonotic Origin of Human Infections and Reveals Genetic Exchange with Streptococcus dysgalactiae subsp equisimilis". Journal of Clinical Microbiology (2013): https://publons.com/publon/200231/.
    10.1128/JCM.02912-12
  75. Almeida, J.; Tiple, J.; Ramirez, M.; Melo-Cristino, J.; Vaz, C.; P. Francisco, A.; Carriço, J.A.. "An ontology and a REST API for sequence based microbial typing data". Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics) 6620 LNBI (2012): 21-28. http://www.scopus.com/inward/record.url?eid=2-s2.0-84859317402&partnerID=MN8TOARS.
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  76. Martins, E.R.; Melo-Cristino, J.; Ramirez, M.; Lito, L.; Monteiro, L.; Martins, F.; Pessanha, M.A.; et al. "Dominance of serotype Ia among group B streptococci causing invasive infections in nonpregnant adults in Portugal". Journal of Clinical Microbiology 50 4 (2012): 1219-1227. http://www.scopus.com/inward/record.url?eid=2-s2.0-84858603460&partnerID=MN8TOARS.
    10.1128/JCM.05488-11
  77. Horácio, A.N.; Diamantino-Miranda, J.; Aguiar, S.I.; Ramirez, M.; Melo-Cristino, J.. "Serotype changes in adult invasive pneumococcal infections in Portugal did not reduce the high fraction of potentially vaccine preventable infections". Vaccine 30 2 (2012): 218-224. http://www.scopus.com/inward/record.url?eid=2-s2.0-84355161924&partnerID=MN8TOARS.
    10.1016/j.vaccine.2011.11.022
  78. Friães, A.; Pinto, F.R.; Silva-Costa, C.; Ramirez, M.; Melo-Cristino, J.. "Group A streptococci clones associated with invasive infections and pharyngitis in Portugal present differences in emm types, superantigen gene content and antimicrobial resistance". BMC Microbiology 12 (2012): http://www.scopus.com/inward/record.url?eid=2-s2.0-84872274958&partnerID=MN8TOARS.
    10.1186/1471-2180-12-280
  79. Silva-Costa, C.; Friães, A.; Ramirez, M.; Melo-Cristino, J.. "Differences between macrolide-resistant and -susceptible streptococcus pyogenes: Importance of clonal properties in addition to antibiotic consumption". Antimicrobial Agents and Chemotherapy 56 11 (2012): 5661-5666. http://www.scopus.com/inward/record.url?eid=2-s2.0-84868007828&partnerID=MN8TOARS.
    10.1128/AAC.01133-12
  80. Aguiar, S.I.; Melo-Cristino, J.; Ramirez, M.. "Use of the 13-valent conjugate vaccine has the potential to eliminate pilus carrying isolates as causes of invasive pneumococcal disease". Vaccine 30 37 (2012): 5487-5490. http://www.scopus.com/inward/record.url?eid=2-s2.0-84864321518&partnerID=MN8TOARS.
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  81. Francisco, A.P.; Vaz, C.; Monteiro, P.T.; Melo-Cristino, J.; Ramirez, M.; Carriço, J.A.. "PHYLOViZ: Phylogenetic inference and data visualization for sequence based typing methods". BMC Bioinformatics 13 1 (2012): http://www.scopus.com/inward/record.url?eid=2-s2.0-84865286374&partnerID=MN8TOARS.
    10.1186/1471-2105-13-87
  82. Martins, E.R.; Andreu, A.; Correia, P.; Juncosa, T.; Bosch, J.; Ramirez, M.; Melo-Cristino, J.. "Group B streptococci causing neonatal infections in barcelona are a stable clonal population: 18-Year surveillance". Journal of Clinical Microbiology 49 8 (2011): 2911-2918. http://www.scopus.com/inward/record.url?eid=2-s2.0-79960949392&partnerID=MN8TOARS.
    10.1128/JCM.00271-11
  83. Severiano, A.; Carriço, J.A.; Robinson, D.A.; Ramirez, M.; Pinto, F.R.. "Evaluation of Jackknife and Bootstrap for defining confidence intervals for pairwise agreement measures". PLoS ONE 6 5 (2011): http://www.scopus.com/inward/record.url?eid=2-s2.0-79956190902&partnerID=MN8TOARS.
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  84. Sá-Leao, R.; Pinto, F.; Aguiar, S.; Nunes, S.; Carriço, J.A.; Frazao, N.; Gonçalves-Sousa, N.; et al. "Analysis of invasiveness of pneumococcal serotypes and clones circulating in portugal before widespread use of conjugate vaccines reveals heterogeneous behavior of clones expressing the same serotype". Journal of Clinical Microbiology 49 4 (2011): 1369-1375. http://www.scopus.com/inward/record.url?eid=2-s2.0-79953881891&partnerID=MN8TOARS.
    10.1128/JCM.01763-10
  85. Severiano, A.; Pinto, F.R.; Ramirez, M.; Carriço, J.A.. "Adjusted Wallace coefficient as a measure of congruence between typing methods". Journal of Clinical Microbiology 49 11 (2011): 3997-4000. http://www.scopus.com/inward/record.url?eid=2-s2.0-80355145041&partnerID=MN8TOARS.
    10.1128/JCM.00624-11
  86. Carrolo, M.; Frias, M.J.; Pinto, F.R.; Melo-Cristino, J.; Ramirez, M.. "Prophage spontaneous activation promotes DNA release enhancing biofilm formation in Streptococcus pneumoniae". PLoS ONE 5 12 (2010): http://www.scopus.com/inward/record.url?eid=2-s2.0-78650883397&partnerID=MN8TOARS.
    10.1371/journal.pone.0015678
  87. Pinho, M.D.; Melo-Cristino, J.; Ramirez, M.. "Fluoroquinolone resistance in Streptococcus dysgalactiae subsp. equisimilis and evidence for a shared global gene pool with Streptococcus pyogenes". Antimicrobial Agents and Chemotherapy 54 5 (2010): 1769-1777. http://www.scopus.com/inward/record.url?eid=2-s2.0-77951236835&partnerID=MN8TOARS.
    10.1128/AAC.01377-09
  88. Martins, E.R.; Melo-Cristino, J.; Ramirez, M.. "Evidence for rare capsular switching in Streptococcus agalactiae". Journal of Bacteriology 192 5 (2010): 1361-1369. http://www.scopus.com/inward/record.url?eid=2-s2.0-77749292150&partnerID=MN8TOARS.
    10.1128/JB.01130-09
  89. Aguiar, S.I.; Pinto, F.R.; Nunes, S.; Serrano, I.; Melo-Cristino, J.; Sá-Leão, R.; Ramirez, M.; De Lencastre, H.. "Denmark14-230 clone as an increasing cause of pneumococcal infection in Portugal within a background of diverse serotype 19A lineages". Journal of Clinical Microbiology 48 1 (2010): 101-108. http://www.scopus.com/inward/record.url?eid=2-s2.0-73949151881&partnerID=MN8TOARS.
    10.1128/JCM.00665-09
  90. Ramirez, M.; Melo-Cristino, J.. "Expanding the diagnosis of pediatric bacteremic pneumococcal pneumonia from blood cultures to molecular methods: Advantages and caveats". Clinical Infectious Diseases 51 9 (2010): 1050-1052. http://www.scopus.com/inward/record.url?eid=2-s2.0-77958570254&partnerID=MN8TOARS.
    10.1086/656580
  91. McMillan, D.J.; Bessen, D.E.; Pinho, M.; Ford, C.; Hall, G.S.; Melo-Cristino, J.; Ramirez, M.. "Population genetics of Streptococcus dysgalactiae subspecies equisimilisreveals widely dispersed clones and extensive recombination". PLoS ONE 5 7 (2010): http://www.scopus.com/inward/record.url?eid=2-s2.0-77955385273&partnerID=MN8TOARS.
    10.1371/journal.pone.0011741
  92. Melo-Cristino, J.; Santos, L.; Silva-Costa, C.; Friães, A.; Pinho, M.D.; Ramirez, M.. "The Viriato study: Update on antimicrobial resistance of microbial pathogens responsible for community-acquired respiratory tract infections in Portugal". Pediatric Drugs 12 SUPPL. 1 (2010): 11-17. http://www.scopus.com/inward/record.url?eid=2-s2.0-77954184517&partnerID=MN8TOARS.
  93. Aguiar, S.I.; Brito, M.J.; Gonçalo-Marques, J.; Melo-Cristino, J.; Ramirez, M.. "Serotypes 1, 7F and 19A became the leading causes of pediatric invasive pneumococcal infections in Portugal after 7 years of heptavalent conjugate vaccine use". Vaccine 28 32 (2010): 5167-5173. http://www.scopus.com/inward/record.url?eid=2-s2.0-77954953848&partnerID=MN8TOARS.
    10.1016/j.vaccine.2010.06.008
  94. Frias, M.J.; Melo-Cristino, J.; Ramirez, M.. "The autolysin LytA contributes to efficient bacteriophage progeny release in Streptococcus pneumoniae". Journal of Bacteriology 191 17 (2009): 5428-5440. http://www.scopus.com/inward/record.url?eid=2-s2.0-68949098479&partnerID=MN8TOARS.
    10.1128/JB.00477-09
  95. Francisco, A.P.; Bugalho, M.; Ramirez, M.; Carriço, J.A.. "Global optimal eBURST analysis of multilocus typing data using a graphic matroid approach". BMC Bioinformatics 10 (2009): http://www.scopus.com/inward/record.url?eid=2-s2.0-67650093575&partnerID=MN8TOARS.
    10.1186/1471-2105-10-152
  96. Carrolo, M.; Pinto, F.R.; Melo-Cristino, J.; Ramirez, M.. "Pherotypes are driving genetic differentiation within Streptococcus pneumoniae". BMC Microbiology 9 (2009): http://www.scopus.com/inward/record.url?eid=2-s2.0-70349656631&partnerID=MN8TOARS.
    10.1186/1471-2180-9-191
  97. Trigo, G.; Ferreira, P.; Ribeiro, N.; Dinis, M.; Andrade, E.B.; Melo-Cristino, J.; Ramirez, M.; Tavares, D.. "Identification of immunoreactive extracellular proteins of Streptococcus agalactiae in bovine mastitis". Canadian Journal of Microbiology 54 11 (2008): 899-905. http://www.scopus.com/inward/record.url?eid=2-s2.0-55849110023&partnerID=MN8TOARS.
    10.1139/W08-083
  98. Aguiar, S.I.; Serrano, I.; Pinto, F.R.; Melo-Cristino, J.; Ramirez, M.. "Changes in Streptococcus pneumoniae serotypes causing invasive disease with non-universal vaccination coverage of the seven-valent conjugate vaccine". Clinical Microbiology and Infection 14 9 (2008): 835-843. http://www.scopus.com/inward/record.url?eid=2-s2.0-50149095416&partnerID=MN8TOARS.
    10.1111/j.1469-0691.2008.02031.x
  99. Pinto, F.R.; Aguiar, S.I.; Melo-Cristino, J.; Ramirez, M.. "Optimal control and analysis of two-color genomotyping experiments using bacterial multistrain arrays". BMC Genomics 9 (2008): http://www.scopus.com/inward/record.url?eid=2-s2.0-44649164484&partnerID=MN8TOARS.
    10.1186/1471-2164-9-230
  100. Aguiar, S.I.; Serrano, I.; Pinto, F.R.; Melo-Cristino, J.; Ramirez, M.. "The presence of the pilus locus is a clonal property among pneumococcal invasive isolates". BMC Microbiology 8 (2008): http://www.scopus.com/inward/record.url?eid=2-s2.0-41149167131&partnerID=MN8TOARS.
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  101. Silva-Costa, C.; Pinto, F.R.; Ramirez, M.; Melo-Cristino, J.. "Decrease in macrolide resistance and clonal instability among Streptococcus pyogenes in Portugal". Clinical Microbiology and Infection 14 12 (2008): 1152-1159. http://www.scopus.com/inward/record.url?eid=2-s2.0-57749088762&partnerID=MN8TOARS.
    10.1111/j.1469-0691.2008.02104.x
  102. Pinto, F.R.; Melo-Cristino, J.; Ramirez, M.. "A confidence interval for the wallace coefficient of concordance and its application to microbial typing methods". PLoS ONE 3 11 (2008): http://www.scopus.com/inward/record.url?eid=2-s2.0-58149200162&partnerID=MN8TOARS.
    10.1371/journal.pone.0003696
  103. Faria, N.A.; Carrico, J.A.; Oliveira, D.C.; Ramirez, M.; De Lencastre, H.. "Analysis of typing methods for epidemiological surveillance of both methicillin-resistant and methicillin-susceptible Staphylococcus aureus strains". Journal of Clinical Microbiology 46 1 (2008): 136-144. http://www.scopus.com/inward/record.url?eid=2-s2.0-38149098343&partnerID=MN8TOARS.
    10.1128/JCM.01684-07
  104. Friães, A.; Ramirez, M.; Melo-Cristino, J.; Fonseca, A.; Coutinho, A.; Alves, A.F.; Albuquerque, L.; et al. "Nonoutbreak surveillance of group A streptococci causing invasive disease in Portugal identified internationally disseminated clones among members of a genetically heterogeneous population". Journal of Clinical Microbiology 45 6 (2007): 2044-2047. http://www.scopus.com/inward/record.url?eid=2-s2.0-34250615891&partnerID=MN8TOARS.
    10.1128/JCM.00496-07
  105. Pinto, F.R.; Carriço, J.A.; Ramirez, M.; Almeida, J.S.. "Ranked adjusted rand: Integrating distance and partition information in a measure of clustering agreement". BMC Bioinformatics 8 (2007): http://www.scopus.com/inward/record.url?eid=2-s2.0-33847331585&partnerID=MN8TOARS.
    10.1186/1471-2105-8-44
  106. Martins, E.R.; Florindo, C.; Martins, F.; Aldir, I.; Borrego, M.J.; Brum, L.; Ramirez, M.; Melo-Cristino, J.. "Streptococcus agalactiae serotype Ib as an agent of meningitis in two adult nonpregnant women". Journal of Clinical Microbiology 45 11 (2007): 3850-3852. http://www.scopus.com/inward/record.url?eid=2-s2.0-36349008805&partnerID=MN8TOARS.
    10.1128/JCM.01358-07
  107. Martins, E.R.; Melo-Cristino, J.; Ramirez, M.. "Reevaluating the serotype II capsular locus of Streptococcus agalactiae". Journal of Clinical Microbiology 45 10 (2007): 3384-3386. http://www.scopus.com/inward/record.url?eid=2-s2.0-35348876697&partnerID=MN8TOARS.
    10.1128/JCM.01296-07
  108. Martins, E.R.; Pessanha, M.A.; Ramirez, M.; Melo-Cristino, J.; Lopes, P.; Calheiros, I.; Felício, L.; et al. "Analysis of group B streptococcal isolates from infants and pregnant women in Portugal revealing two lineages with enhanced invasiveness". Journal of Clinical Microbiology 45 10 (2007): 3224-3229. http://www.scopus.com/inward/record.url?eid=2-s2.0-35348859651&partnerID=MN8TOARS.
    10.1128/JCM.01182-07
  109. Melo-Cristino, J.; Santos, L.; Ramirez, M.; Lozano, S.; Fonseca, A.; Coutinho, A.; Alves, A.F.; et al. "The Viriato Study: Update of antimicrobial susceptibility data of bacterial pathogens from community-acquired respiratory tract infections in Portugal in 2003 and 2004 | Estudo Viriato: Actualização de dados de susceptibilidade aos antimicrobianos de bactérias responsáveis por infecções adquiridas na comunidade em Portugal em 2003 e 2004". Revista Portuguesa de Pneumologia 12 1 (2006): 9-10. http://www.scopus.com/inward/record.url?eid=2-s2.0-33645635124&partnerID=MN8TOARS.
  110. Serrano, I.; Melo-Cristino, J.; Ramirez, M.. "Heterogeneity of pneumococcal phase variants in invasive human infections". BMC Microbiology 6 (2006): http://www.scopus.com/inward/record.url?eid=2-s2.0-33748052378&partnerID=MN8TOARS.
    10.1186/1471-2180-6-67
  111. Carriço, J.A.; Silva-Costa, C.; Melo-Cristino, J.; Pinto, F.R.; De Lencastre, H.; Almeida, J.S.; Ramirez, M.. "Illustration of a common framework for relating multiple typing methods by application to macrolide-resistant Streptococcus pyogenes". Journal of Clinical Microbiology 44 7 (2006): 2524-2532. http://www.scopus.com/inward/record.url?eid=2-s2.0-33746255226&partnerID=MN8TOARS.
    10.1128/JCM.02536-05
  112. Silva-Costa, C.; Ramirez, M.; Melo-Cristino, J.. "Identification of macrolide-resistant clones of Streptoccus pyogenes in Portugal". Clinical Microbiology and Infection 12 6 (2006): 513-518. http://www.scopus.com/inward/record.url?eid=2-s2.0-33646675065&partnerID=MN8TOARS.
    10.1111/j.1469-0691.2006.01408.x
  113. Pinho, M.D.; Melo-Cristino, J.; Ramirez, M.. "Clonal relationships between invasive and noninvasive Lancefield group C and G Streptococci and emm-specific differences in invasiveness". Journal of Clinical Microbiology 44 3 (2006): 841-846. http://www.scopus.com/inward/record.url?eid=2-s2.0-33644889954&partnerID=MN8TOARS.
    10.1128/JCM.44.3.841-846.2006
  114. Aguiar, S.I.; Frias, M.J.; Santos, L.; Melo-Cristino, J.; Ramirez, M.; Lozano, S.; Fonseca, A.; et al. "Emergence of optochin resistance among Streptococcus pneumoniae in Portugal". Microbial Drug Resistance 12 4 (2006): 239-245. http://www.scopus.com/inward/record.url?eid=2-s2.0-33846251546&partnerID=MN8TOARS.
    10.1089/mdr.2006.12.239
  115. Figueiredo, T.A.; Aguiar, S.I.; Melo-Cristino, J.; Ramirez, M.. "DNA methylase activity as a marker for the presence of a family of phage-like elements conferring efflux-mediated macrolide resistance in streptococci". Antimicrobial Agents and Chemotherapy 50 11 (2006): 3689-3694. http://www.scopus.com/inward/record.url?eid=2-s2.0-33750587170&partnerID=MN8TOARS.
    10.1128/AAC.00782-06
  116. Silva-Costa, C.; Ramirez, M.; Melo-Cristino, J.. "Rapid inversion of the prevalences of macrolide resistance phenotypes paralleled by a diversification of T and emm types among Streptococcus pyogenes in Portugal". Antimicrobial Agents and Chemotherapy 49 5 (2005): 2109-2111. http://www.scopus.com/inward/record.url?eid=2-s2.0-18244394279&partnerID=MN8TOARS.
    10.1128/AAC.49.5.2109-2111.2005
  117. Serrano, I.; Melo-Cristino, J.; Carriço, J.A.; Ramirez, M.. "Characterization of the genetic lineages responsible for pneumococcal invasive disease in Portugal". Journal of Clinical Microbiology 43 4 (2005): 1706-1715. http://www.scopus.com/inward/record.url?eid=2-s2.0-16844377427&partnerID=MN8TOARS.
    10.1128/JCM.43.4.1706-1715.2005
  118. Figueira-Coelho, J.; Ramirez, M.; Salgado, M.J.; Melo-Cristino, J.. "Streptococcus agalactiae in a Large Portuguese Teaching Hospital: Antimicrobial Susceptibility, Serotype Distribution, and Clonal Analysis of Macrolide-Resistant Isolates". Microbial Drug Resistance 10 1 (2004): 31-36. http://www.scopus.com/inward/record.url?eid=2-s2.0-1942434649&partnerID=MN8TOARS.
    10.1089/107662904323047772
  119. Serrano, I.; Ramirez, M.; Melo-Cristino, J.. "Invasive Streptococcus pneumoniae from Portugal: Implications for vaccination and antimicrobial therapy". Clinical Microbiology and Infection 10 7 (2004): 652-656. http://www.scopus.com/inward/record.url?eid=2-s2.0-4043097641&partnerID=MN8TOARS.
    10.1111/j.1469-0691.2004.00869.x
  120. Brito, D.A.; Ramirez, M.; De Lencastre, H.. "Serotyping Streptococcus pneumoniae by multiplex PCR". Journal of Clinical Microbiology 41 6 (2003): 2378-2384. http://www.scopus.com/inward/record.url?eid=2-s2.0-0037505612&partnerID=MN8TOARS.
  121. Melo-Cristino, J.; Lopes, P.; Magalhães, C.; Sobral, L.; Vaz, T.; Girão, M.; Afonso, T.; et al. "Macrolide resistance in Streptococcus pneumoniae isolated from patients with community-acquired lower respiratory tract infections in Portugal: Results of a 3-year (1999-2001) multicenter surveillance study". Microbial Drug Resistance 9 1 (2003): 73-80. http://www.scopus.com/inward/record.url?eid=2-s2.0-0037357088&partnerID=MN8TOARS.
  122. Alou, L.; Ramirez, M.; García-Rey, C.; Prieto, J.; De Lencastre, H.. "Streptococcus pneumoniae isolates with reduced susceptibility to ciprofloxacin in Spain: Clonal diversity and appearance of ciprofloxacin-resistant epidemic clones". Antimicrobial Agents and Chemotherapy 45 10 (2001): 2955-2957. http://www.scopus.com/inward/record.url?eid=2-s2.0-0034806776&partnerID=MN8TOARS.
    10.1128/AAC.45.10.2955-2957.2001
  123. Ramirez, M.; Tomasz, A.. "Acquisition of new capsular genes among clinical isolates of antibiotic- resistant Streptococcus pneumoniae". Microbial Drug Resistance 5 4 (1999): 241-246. http://www.scopus.com/inward/record.url?eid=2-s2.0-0033387366&partnerID=MN8TOARS.
  124. Severina, E.; Ramirez, M.; Tomasz, A.. "Prophage carriage as a molecular epidemiological marker in Streptococcus pneumoniae". Journal of Clinical Microbiology 37 10 (1999): 3308-3315. http://www.scopus.com/inward/record.url?eid=2-s2.0-0032849749&partnerID=MN8TOARS.
  125. Ramirez, M.; Severina, E.; Tomasz, A.. "A high incidence of prophage carriage among natural isolates of Streptococcus pneumoniae". Journal of Bacteriology 181 12 (1999): 3618-3625. http://www.scopus.com/inward/record.url?eid=2-s2.0-0033055030&partnerID=MN8TOARS.
  126. Marchese, A.; Ramirez, M.; Schito, G.C.; Tomasz, A.. "Molecular epidemiology of penicillin-resistant Streptococcus pneumoniae isolates recovered in Italy from 1993 to 1996". Journal of Clinical Microbiology 36 10 (1998): 2944-2949. http://www.scopus.com/inward/record.url?eid=2-s2.0-0031682158&partnerID=MN8TOARS.
  127. Nesin, M.; Ramirez, M.; Tomasz, A.. "Capsular transformation of a multidrug-resistant Streptococcus pneumoniae in vivo". Journal of Infectious Diseases 177 3 (1998): 707-713. http://www.scopus.com/inward/record.url?eid=2-s2.0-0031887641&partnerID=MN8TOARS.
  128. Ramirez, M.; Tomasz, A.. "Molecular characterization of the complete 23F capsular polysaccharide locus of Streptococcus pneumoniae". Journal of Bacteriology 180 19 (1998): 5273-5278. http://www.scopus.com/inward/record.url?eid=2-s2.0-0031683056&partnerID=MN8TOARS.
  129. Ramirez, M.; Morrison, D.A.; Tomasz, A.. "Ubiquitous distribution of the competence related genes comA and comC among isolates of Streptococcus pneumoniae". Microbial Drug Resistance 3 1 (1997): 39-52. http://www.scopus.com/inward/record.url?eid=2-s2.0-0030987056&partnerID=MN8TOARS.
  130. Sanches, I.S.; Ramirez, M.; Troni, H.; Abecassis, M.; Padua, M.; Tomasz, A.; De Lencastre, H.. "Evidence for the geographic spread of a methicillin-resistant Staphylococcus aureus clone between Portugal and Spain". Journal of Clinical Microbiology 33 5 (1995): 1243-1246. http://www.scopus.com/inward/record.url?eid=2-s2.0-0028958767&partnerID=MN8TOARS.

Other

Other output
  1. Molecular Epidemiology of Streptococcus pneumoniae. 2015. Mário Ramirez; Joáo A. Carriço; Mark van der Linden; José Melo-Cristino. http://dx.doi.org/10.1016/b978-0-12-410530-0.00001-6.
    10.1016/b978-0-12-410530-0.00001-6
  2. Streptococcus pneumoniae. 2015. Mario Ramirez. http://dx.doi.org/10.1016/b978-0-12-397169-2.00086-x.
    10.1016/b978-0-12-397169-2.00086-x
  3. Analysis of Typing Results. 2014. João André Carriço; Mário Ramirez. http://dx.doi.org/10.1002/9781118278666.ch5.
    10.1002/9781118278666.ch5
Activities

Supervision

Thesis Title
Role 		Degree Subject (Type)
Institution / Organization
2021/01/01 - Current Inter-laboratory reproducibility and expansion of the gene-by-gene typing approach in an era of whole genome sequencing
Supervisor
Universidade de Lisboa Faculdade de Medicina, Portugal
2014/03/01 - Current New tools for visualization and analysis of draft genomes for microbial molecular epidemiology
Co-supervisor
 Ciências da Saúde (PhD)
Universidade de Lisboa Faculdade de Medicina, Portugal
2018/01/01 - 2023/04/17 Towards accreditation in metagenomics for clinical microbiology
Co-supervisor
 Programa Doutoral do Centro Académico de Medicina de Lisboa (ramo de Medicina; ramo de Ciências Biomédicas; ramo de Ciências e Tecnologias da Saúde) (PhD)
Universidade de Lisboa Faculdade de Medicina, Portugal
2020/09/01 - 2022/02/09 The Shewanella genus – understanding an emerging human pathogen
Co-supervisor
 Microbiologia Clínica e Doenças Infeciosas Emergentes (Master)
Universidade de Lisboa Faculdade de Medicina, Portugal
2019/09 - 2020/10/13 Peptidoglycan hydrolases: Sub-cellular localization of pneumococcal LytA and LytB
Co-supervisor
 Microbiologia Clínica e Doenças Infeciosas Emergentes (Master)
Universidade de Lisboa Faculdade de Medicina, Portugal
2012 - 2019 Understanding pherotype specificity and its influence on the genetic structure of Streptococcus pneumoniae
Supervisor
 Ciências e Tecnologias da Saúde
Universidade de Lisboa Faculdade de Medicina, Portugal
2012 - 2018 Naturally ocurring mutations in regulatory proteins among Streptococcus pyogenes isolates from distinct human infections
Supervisor
 Ciências e Tecnologias da Saúde (PhD)
Universidade de Lisboa Faculdade de Medicina, Portugal
2014 - 2015 Streptococcus agalactiae in neonatal infections – a changing population?
Supervisor
 Microbiologia
Universidade de Lisboa Faculdade de Medicina, Portugal
2013 - 2014 Streptococcus anginosus como agentes de infeção em humanos: um estudo epidemiológico numa taxonomia em mudança
Supervisor
 Microbiologia Médica (Master)
Universidade Nova de Lisboa, Portugal
2011 - 2014 Characterization of Streptococcus pyogenes associated with tonsillo-pharyngitis in Portugal with particular emphasis on macrolide resistance
Co-supervisor
 Ciências e Tecnologias da Saúde (PhD)
Universidade de Lisboa Faculdade de Medicina, Portugal
2007 - 2014 Lancefield group C and G streptococci in human infection: Molecular typing, virulence and antimicrobial susceptibility
Supervisor
 Ciências e Tecnologias da Saúde (PhD)
Universidade de Lisboa Faculdade de Medicina, Portugal
2012 - 2013 Distribuição e diversidade de elementos genéticos associados à virulência em Streptococcus pneumoniae
Supervisor
 Microbiologia Aplicada (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2011 - 2013 Exotoxin profile of Lancefield group C and G streptococci from animal and human infections
Supervisor
 Ciências Biofarmacêuticas (Master)
Universidade de Lisboa Faculdade de Farmácia, Portugal
2010 - 2013 Molecular Characterization of Streptococus Pyogenes isolates associated with invasive infections and pharyngitis in Portugal: Evaluation of typing methods and relatioship with invasive ability
Co-supervisor
 Ciências e Tecnologias da Saúde (PhD)
Universidade de Lisboa Faculdade de Medicina, Portugal
2010 - 2011 Streptococcus pyogenes como agente de infecção da pele e tecidos moles
Supervisor
 Microbiologia Aplicada (Master)
Universidade de Lisboa Faculdade de Ciências, Portugal
2008 - 2011 Lysis strategy of streptococcus pneumoniae bacteriophages: mechanisms and host implications.
Supervisor
 Ciências e Tecnologias da Saúde (PhD)
Universidade de Lisboa Faculdade de Medicina, Portugal
2008 - 2011 New insights into the sociomicrobiology of Streptococcus pneumoniae: exploring biofilm formation
Supervisor
 Ciências e Tecnologias da Saúde (PhD)
Universidade de Lisboa Faculdade de Medicina, Portugal
2007 - 2011 Caracterização fenotípica e genotípica de Streptococcus pneumoniae responsável por infecção em crianças de idade pré-escolar
Supervisor
 Ciências e Tecnologias da Saúde (PhD)
Universidade de Lisboa Faculdade de Medicina, Portugal
2007 - 2011 Streptococcus agalactiae causing human infections: genetic diversity and capsular switching.
Supervisor
 Ciências e Tecnologias da Saúde (PhD)
Universidade de Lisboa Faculdade de Medicina, Portugal
2008 - 2009 Staphylococcus aureus adquirido na comunidade, em idade pediátrica: resistência aos antimicrobianos, importância da leucocidina de Panton-Valentine, caracterização molecular e correlação com a clínica
Supervisor
 Microbiologia Clínica (Master)
Universidade de Lisboa Faculdade de Medicina, Portugal
2007 - 2008 Aplicação de Espectroscopia de FT-IR para a Serotipagem e Avaliação da Susceptibilidade à Penicilina em Streptococcus Peneumoniae
Co-supervisor
 Microbiologia Clínica (Master)
Universidade de Lisboa Faculdade de Medicina, Portugal
2007 - 2008 Estudo Genético e Fenótipico do Operão fsr e gelE-sprE em Diferentes Espécies de Enterococcus
Co-supervisor
 Microbiologia Clínica
Universidade de Lisboa Faculdade de Medicina, Portugal
2007 - 2008 Transformações capsulares em Streptococcus agalactiae
Supervisor
 Microbiologia Clínica (Master)
Universidade de Lisboa Faculdade de Medicina, Portugal
2006 - 2008 Avaliação de estruturas mosaico em estirpes clínicas de Chlamydia trachomatis
Co-supervisor
 Microbiologia Clínica
Universidade de Lisboa Faculdade de Medicina, Portugal
2006 - 2008 Pesquisa de serogrupos e genes virulentos de Escherichia coli produtora de shiga-toxina em alimentos e em fezes de bovinos
Co-supervisor
 Microbiologia Clínica (Master)
Universidade de Lisboa Faculdade de Medicina, Portugal
2003 - 2008 Contribuição para a Caracterização da População de Streptococcus Pneumoniae Causadora de Infecções Graves
Supervisor
 Ciências e Tecnologias da Saúde (PhD)
Universidade de Lisboa Faculdade de Medicina, Portugal
2006 - 2007 A Partícula de Reconhecimento de Sinal do Streptococcus Pneumoniae é Essencial para a sua Viabilidade
Co-supervisor
 Microbiologia Clínica (Master)
Universidade de Lisboa Faculdade de Medicina, Portugal
2006 - 2007 Estudo da contribuição de proteínas fágicas e da autolisina bacteriana na lise de Streptococcus pneumoniae
Supervisor
 Microbiologia Clínica (Master)
Universidade de Lisboa Faculdade de Medicina, Portugal
2005 - 2007 Caracterização dos mecanismos moleculares de resistência às fluoroquinolonas em estirpes clínicas de Escherichia coli de origem animal
Co-supervisor
 Microbiologia Clínica (Master)
Universidade de Lisboa Faculdade de Medicina, Portugal
2005 - 2006 Caracterização fenotípica e genotípica de Streptococcus pneumoniae responsáveis por infecção em crianças de idade pré-escolar
Supervisor
 Microbiologia Clínica (Master)
Universidade de Lisboa Faculdade de Medicina, Portugal
2005 - 2006 Diversidade clonal e contribuição do gene emm para a virulência de Streptococcus spp. dos grupos C e G de Lancefield isolados de infecção no Homem
Co-supervisor
 Microbiologia Clínica (Master)
Universidade de Lisboa Faculdade de Medicina, Portugal
2004 - 2005 Caracterização de Bacteriófagos em Populações Naturais de Streptococcus Pneumoniae
Supervisor
 Mestrado em Microbiologia Clínica (Master)
Universidade de Lisboa Faculdade de Medicina, Portugal
2001 - 2002 Epidemiologia molecular de estirpes de Streptococcus pneumoniae isoladas em Portugal
Supervisor
 Mestrado em Microbiologia Molecular (Master)
Universidade de Aveiro, Portugal

Committee member

Activity description
Role 		Institution / Organization
2023/01/01 - Current Treasurer of the ESCMID Study Group for Genomic and Molecular Diagnostics - ESGMD
Other
 European Society of Clinical Microbiology and Infectious Diseases, Switzerland
2020/04/01 - Current Program Committee member of the European Congress of Clinical Microbiology and Infectious Diseases
Advisor / Consultant
 European Society of Clinical Microbiology and Infectious Diseases, Switzerland
2011/01/01 - Current Founder and treasurer of the Immunisations and Vaccines Working Group of the International Society of Antimicrobial Chemotherapy (ISAC)
Other
 The International Society of Antimicrobial Chemotherapy, United Kingdom
Distinctions

Award

2016 Prémios Científicos Universidade de Lisboa. 2016. Menção honrosa
Universidade de Lisboa Reitoria, Portugal