pt en

Ramirez, Mário

Molecular Microbiology & Infection

Despite the successful use of antibiotics and vaccination, bacterial infections are still a major cause of morbidity and mortality worldwide. The changing demographics are shifting the attention to older adults where selective pressures may be radically different from those found in children. Several studies showed that bacterial populations are dominated by a few clones. The plasticity of bacterial genomes means that different isolates can carry a distinct array of antibiotic resistance and virulence genes. However, the relationship between carrying a certain gene complement and becoming a successful clone remains elusive. We have documented the bacterial population structure of several pathogens of the genus //Streptococcus// and found differences between bacteria that are asymptomatically carried and those causing distinct infections in the various age groups. In addition, we identified genes that are unevenly distributed in the bacterial population, potentially explaining the propensity of certain clones for particular hosts or infections. We have also studied the flow of genetic information between bacteria and the factors enhancing or limiting these exchanges and the role of mobile genetic elements in bacterial diversity. We are currently exploring the differences between bacterial populations at the whole-genome level. We are refining existing approaches to handle high throughput sequence (HTS) data and are developing tools for storing and mining this data in a unified platform, integrating information from existing databases. This is reflected in the development of novel bioinformatic tools with a focus on HTS. We hope to get a detailed view of the genetic differences between bacterial clones and to identify candidate genes to explain their different abundance. We are also looking at streptococci causing infections in humans and animals to identify key events allowing the adaptation to different host species and to evaluate the current potential for zoonotic acquisition. Understanding the dynamics and responses of a bacterial population to the multiple selective pressures imposed on it and the key genetic events allowing the differentiation of specific clones will allow us to better predict bacterial pathogen evolution. Our research also produces important epidemiological information allowing us to anticipate the potential benefits of vaccination or guiding the optimal empirical therapy for infections of suspected streptococcal etiology.

  • Research Areas

    • Population biology and genomics
    • Bioinformatics
    • Detection of antimalarial drug resistance
    • Molecular epidemiology
    • Diagnostic tools
    • Antibiotic resistance
    • Vaccines
  • Research Team

    • Ongoing Research Projects

      • 2009/2012 CAREPNEUMO – Combating antibiotic resistance pneumococci by novel strategies based on in vivo and in vitro host-pathogen interactions (FP7-HEALTH-2007-223111)
      • 2009/2012 Implications for therapy and disease presentation of the changes triggered by the use of the pneumococcal 7-valent conjugate vaccine (PIC/IC/83065/2007)
      • 2008/2011 Streptococcus pyogenes invasive disease and antimicrobial resistance - two faces of a changing pathogen (PTDC/SAU-ESA/72321/2006)
      • 2008/2011 Population and genomic consequences of vaccination against Streptococcus pneumoniae (PTDC/SAU-ESA/64888/2006)
      • 2008/2011 A computational biology approach using Streptococcus pneumoniae as a model towards an integrative view of bacteria/host interactions and evolution (PTDC/SAU-ESA/71499/2006)
      • 2007/2010 Caracterização microbiológica e molecular de Streptococcus spp. patogénicos e sua importância na profilaxia e terapêutica das infecções humanas em Portugal. Fundação Calouste Gulbenkian.
      • 2006/2009 Population based identification of pneumococcal virulence and colonization factors. National Institutes of Health – National Institute of Allergy and Infectious Diseases (NIH/NIAD). Pathogen Functional Genomics Resource Center (PFGRC) Program.
    • Prizes

    • Selected Publications

      • Jamet A, Touchon M, Ribeiro-Gonçalves B, Carriço JA, Charbit A, Nassif X, Ramirez M, Rocha EPC. 2017. A widespread family of polymorphic toxins encoded by temperate phages. BMC Biol 15:75
      • Martins ER, Pedroso-Roussado C, Melo-Cristino J, Ramirez M, Portuguese Group for the Study of Streptococcal Infections. 2017. Streptococcus agalactiae causing neonatal infections in Portugal (2005-2015): diversification and emergence of a CC17/PI-2b multidrug resistant sublineage. Front Microbiol 8:499.
      • Visser BJ, de Vries SG, Vingerling R, Gritter M, Kroon D, Aguilar LC, Kraan RBJ, Wieten RW, Danion F, Sjouke B, Adegnika AA, Agnandji ST, Kremsner PG, Hänscheid T, Mens PF, van Vugt M, Grobusch MP. 2017. Serum lipids and lipoproteins during uncomplicated malaria: A cohort study in Lambaréné, Gabon. Am J Trop Med Hyg 96:1205–1214
      • Horácio AN, Silva-Costa C, Lopes JP, Ramirez M, Melo-Cristino J, Portuguese Group for the Study of Streptococcal Infections. 2016. 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. Front Microbiol 7:1616
      • Ribeiro-Gonçalves B, Francisco AP, Vaz C, Ramirez M, Carriço JA. 2016. PHYLOViZ Online: web-based tool for visualization, phylogenetic inference, analysis and sharing of minimum spanning trees. Nucleic Acids Res. 44:W246-251
      • Barato P, Martins ER, Vasquez GM, Ramirez M, Melo-Cristino J, Martínez N, Iregui C. 2016. Capsule impairs efficient adherence of Streptococcus agalactiae to intestinal epithelium in tilapias Oreochromis sp. Microb Pathog. 100:30–36.
      • Pinho MD, Erol E, Ribeiro-Gonçalves B, Mendes CI, Carriço JA, Matos SC, Preziuso S, Luebke-Becker A, Wieler LH, Melo-Cristino J, Ramirez M. 2016. Beta-hemolytic Streptococcus dysgalactiae strains isolated from horses are a genetically distinct population within the Streptococcus dysgalactiae taxon. Sci Rep 6:31736
      • Rebelo M, Grenho R, Orban A, Hänscheid T. 2016. Transdermal diagnosis of malaria using vapor nanobubbles. Emerging Infect Dis 22:343–344
      • Friães A, Machado MP, Pato C, Carriço JA, Melo-Cristino J, Ramirez M. 2015. Emergence of the same successful clade among distinct populations of emm89 Streptococcus pyogenes in multiple geographic regions. MBio 6. pii: e01780-15.
      • Silva-Costa C, Ramirez M, Melo-Cristino J, Portuguese Group for the Study of Streptococcal Infections. 2015. Declining macrolide resistance in Streptococcus pyogenes in Portugal (2007-13) was accompanied by continuous clonal changes. J Antimicrob Chemother. 70:2729–2733.
      • Aguiar, S.I., M. Brito, Horácio, A. N., J. Lopes, M. Ramirez, J. Melo-Cristino, and Portuguese Group for the Study of Streptococcal Infections and the Portuguese Study Group of Invasive Pneumococcal Disease of the Paediatric Infectious Disease Society. 2014. 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. Euro Surveill. 19:pii: 20750.
      • Silva-Costa, C. , J. A. Carriço, M. Ramirez, and J. Melo-Cristino. 2014. Scarlet fever is caused by a limited number of Streptococcus pyogenes lineages and is associated with the exotoxin genes ssa, speA and speC. Pediatr Infect Dis J. 33(3):306-10.
      • Melo-Cristino J., C. Resina, V. Manuel, L. Lito, M. Ramirez. 2013. First case of infection with vancomycin-resistant Staphylococcus aureus in Europe. The Lancet. 382:205
      • Rebelo, M., C. Sousa, H. M. Shapiro, M. M. Mota, M. P. Grobusch, and T. Hänscheid. 2013. A novel flow cytometric hemozoin detection assay for real-time sensitivity testing of Plasmodium falciparum. PLoS ONE 8:e61606.
      • Carriço J. A., Sabat A., Friederich A., Ramirez M., on behalf of the ESCMID Study Group for Epidemiological Markers (ESGEM). 2013. Bioinformatics in bacterial molecular epidemiology and public health: databases, tools and the next-generation sequencing revolution. Euro Surveill. 2013. 18:pii=20382.

    This site uses cookies. Some of the cookies we use are essential for parts of the site to operate and have already been set.
    You may delete and block all cookies from this site, but parts of the site will not work.