Microbial Epidemiology

Enterococci                     Picture from Lab. Microbial Epidemiology

Two species Enterococcus faecalis and E. faecium are responsible for the majority of clinically relevant enterococcal infections. Since the isolation of the first vancomycin-resistant enterococci (VRE) in 1986  the incidence of enterococcal infections have been uncommon in European hospitals. However over the last five years the number of reports documenting a step up of the prevalence or outbreaks situations by VRE, especially E. faecium, have been frequent in several countries. According with the last data published by the European Antimicrobial Resistance Surveillance System-EARSS (www.rivm.nl/earss/) Portugal is one out of five European countries reporting more than 25% of VR E. faecium and high rates of both E. faecalis and E. faecium resistant to high concentrations of gentamicin.
The application of microbial standardized methods together with the utilization of molecular typing methods such as PCR, Multiplex PCR, Pulsed-field gel electrophoresis (PFGE), Multilocus Sequenced Type (MLST),  allow  to determinate the prevalence of enterococcal species, antimicrobial resistance rates, to establish virulence determinant profiles, as well to know the dynamic and fluctuations of the enterococcal clonal types circulating at the nosocomial setting. Epidemiological surveillance studies in high risk wards as intensive care units or haematological malignancies wards are very important to identifier the risk factors associated with the colonization and infection in these particular groups.

Clonal distribution of high level gentamicin-resistant and glycopeptide-resistant E. faecalis recovered from a Lisbon hospital over four years period. Establishment of a dominant clone and increase of vancomycin resistant  prevalence. (From Lab. Microbial Epidemiology).

Beta-haemolytic streptococci        Picture from D. Rolo. Master Degree Thesis.  FCT/UNL.      July 2007.

The Group A streptococcus (GAS) usually S. pyogenes is the most pathogenic bacterium among streptococcal species being the human body, the only known natural reservoir.
The primary sites for colonization of GAS involve the nasal and oropharyngeal mucosal epithelium of the upper respiratory tract and the superficial layers of the epidermis. The carrier state can persist for months and the organism remains capable of transmission to a new host, but with reduced efficiency. The mode of dissemination, mainly via droplets of respiratory secretions, makes crowded institutions, like day-care centers, propitious for the spread of pathogens. Although poorly understood, the carrier state is usually quite dynamic. Since carriers could be the source of infection, the study of the prevalence of healthy GAS carriers and the molecular epidemiology of the isolates may improve understanding about the origin and spread of this pathogen, allowing for more successful control measures. The immunization with the 7-valent pneumococcal conjugate vaccine may have impact not only on the replacement of vaccine serotypes with non-vaccine serotypes as well as on the composition of the nasopharyngeal flora. (In collaboration with Prof. I. Santos Sanches-FCT/UNL, and Prof. H. de Lencantre-ITQB/UNL).

The phenotypic and genotypic characterization of the beta-haemolytic streptococci strains includes molecular methodologies as for example T-typing, pulsed-field gel electrophoresis (PFGE), using  rare-cutter restriction enzymes, multilocus sequence typing (MLST) and  M protein genotyping (emm typing). 

Prevalence of nasopharyngeal colonization by  beta-haemolytic Streptococcus isolated from 569 nasopharyngeal samples recovered from healthy children attending day care centers (A, B, C, D, E, F, G, H, I, J, K) located at the Oeiras area. Period of sampling January-February 2006. (From C. Cabral. Degree Thesis. FCT/UNL. February 2007).