Molecular Microbiology and Infection Unit

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The main objective of the Molecular Microbiology and Infection Unit is to understand the dynamics of populations of bacterial pathogens and how they respond to selective forces. Current work focuses on characterizing the effect of antimicrobial use and human vaccination on the bacterial population. Investigations are also exploring the relationships between commensal and disease causing populations of the same bacterial pathogen with the aim of identifying particularly successful clones at causing disease as well as successful colonizers for further characterization. A strong bioinformatics effort in the area of data warehousing, the development of user interfaces, data analysis and visualization tools is ongoing. The development of novel laboratory methodologies for the diagnosis of infectious diseases is also an active area of research.

Population biology and epidemiology
Bacteriophage genomics
Antimicrobial resistance mechanisms
Novel diagnostic tools
Bioinformatics

The investigations on this field have benefited from a close contact with clinical practice and have focused on issues directly relevant to the clinician. Special attention has been given to the epidemiology of antimicrobial resistance at a national level. These data are essential for the preparation of guidelines for empirical therapy as well as for an understanding of the evolution and dissemination of antimicrobial resistance. The evaluation of the in vitro activity of new antimicrobial agents against clinical isolates and the investigation on the possibility of using bacteriophages as alternative prophylactic or therapeutic agents both stem from our interest in new therapeutic approaches.
The use of molecular technologies provides further detail to these analyses by allowing the molecular identification of bacterial clones and their association to known resistance determinants. This affords new insights into the 1) clonality of clinical isolates; 2) the distribution of antimicrobial resistance determinants and 3) the dispersal of clones. The later information will be particularly useful at the health-care center level were outbreak detection can be the basis for the implementation of containment measures. A more fundamental development will be the identification of clones with high epidemicity or particularly virulent for future analyses including our ongoing efforts at characterizing the genetic complement of characterized populations using microarray technologies.
The lab currently works with the following streptococcal species: S. pneumoniae, S. pyogenes, S. agalactiae and streptococci of the Lancefield groups C and G .

The immediate developments in this line of research will follow the recent realization that flow cytometric principles allow the detection of malaria pigment. This finding will be further explored with the development of this application to the diagnosis of malaria and the development of a novel sensitivity test. This method will also be investigated for it’s usefulness as markers of disease severity. Furthermore, this research will be used to address questions on the interactions of hemozoin and its effect on the immune system. Finally, the results of this research may be useful for the understanding and development of novel antimalarial drugs, because hemozoin seems to be the target of several of the most effective antimalarials available today.

Lack of knowledge on the dynamics of pathogenic bacteria population structure and the forces shaping it motivates our research in this area. We are interested in the role of chromosome plasticity in bacterial adaptation, with a special emphasis in gene exchange and mobile genetic elements. Current efforts in the characterization of the bacteriophage (phage) population of Streptococcus pneumoniae addresses the role of phages as bacterial “predators” and their potential influence in the bacterial population structure and bacterial “social” interactions. Simultaneously, their role in bacterial pathogenesis is investigated by testing for the presence of virulence enhancing traits in phage genomes. Another project is focusing on the response of the population of disease causing bacteria to another major selective pressure, i.e., the introduction of a vaccine. Underlying these questions is the fundamental issue of the relationship between colonizing isolates and the ones causing disease. Taking advantage of the detailed information available on colonization isolates in Portugal we are addressing this question by characterizing contemporary disease causing isolates and exploring the relationships between these two populations. The availability of novel genomic technologies allows the survey the gene complement of these two populations and the relative distribution of mobile genetic elements among them. We expect that the use of these technologies will also open new lines of research on the bacterial adaptation to the expression of acquired genes, of particular interest is the change in virulence caused by gene acquisition.

The large amounts of data collected for clinically relevant strains require a concerted effort of data management and data analysis techniques. We are addressing these topics by the development of databases of strains for several species as well as developing online databases for novel typing methodologies based on DNA sequences. We are also focusing in the in silico simulation of bacterial populations using known evolutionary models and developing new data analysis techniques to interpret and visualize the effect of mutation and recombination as evolutionary driving forces. The analyses of population genomics using “comparative genomic hybridization” also lead to the development of new methodologies to analyze this kind of data. Finally, a systems biology approach is driving the development of models integrating the bacterial pathogens and its human hosts in an ecological and evolutionary perspective.

Hänscheid, T., Egan, T.J., Grobusch, M.P. 2007. Haemozoin: from melatonin pigment to drug target, diagnostic tool, and immune modulator. Lancet Infect. Dis. 7:675-685.

Carriço, J.A., C. Silva-Costa, J. Melo-Cristino, F. R. Pinto, H. de Lencastre, J.S. Almeida, M.Ramirez. 2006. Illustration of a common framework for relating multiple typing methods by application to macrolide- resistant Streptococcus pyogenes. J. Clin. Microbiol. 44:2524-2532.

Pinho, M. D., J. Melo-Cristino, M. Ramirez, and the Portuguese group for the study of streptococcal infections. 2006. Clonal relationships between invasive and noninvasive lancefield group C and G Streptococci and emm-specific differences in invasiveness. J. Clin. Microbiol. 44:841-846.

Silva-Costa, C., M. Ramirez, and J. Melo-Cristino. 2005. Rapid inversion of the prevalences of macrolide resistance phenotypes paralleled by a diversification of T and emm types among Streptococcus pyogenes in Portugal. Antimicrob. Agents Chemother. 49:2109-2111.

Serrano, I., J. Melo-Cristino, J. A. Carriço, and M. Ramirez. 2005. Characterization of the genetic lineages responsible for pneumococcal invasive disease in Portugal. J. Clin. Microbiol. 43:1706-1715.