Molecular epidemiology of streptococcus pneumoniae

Abstract

Streptococcus pneumoniae, also named pneumococci, is often part of the normal flora in the nasopharynx of healthy children. However, pneumococci are also a major cause of morbidity and mortality world-wide, and colonization is required for pneumococci to cause severe invasive diseases such as septicaemia and meningitis. By focusing on the effects of conjugated pneumococcal vaccines (PCVs) on carriage and infections caused by Streptococcus pneumoniae, this thesis aims to further the understanding of why pneumococci sometimes cause severe disease.

PCVs were introduced into the childhood vaccination program in Stockholm in 2007 and replaced by PCV13 in 2010. To show the potential effect of PCVs, we collected carriage isolates and invasive pneumococcal isolates from before and after vaccine introduction, as well as clinical information about the patients. Pneumococcal isolates were characterized by molecular epidemiological typing methods such as serotyping, pulsed-field gel electrophoresis (PFGE), and multi-locus sequence typing (MLST). Before vaccine introduction serotype 6B was a dominant serotype both in carriage and invasive disease. The invasive disease potential (IDP) for serotypes and clonal types was calculated before the vaccine introduction and it was revealed that not only did the IDP differ between serotypes and clonal types, but also within clonal types as determined by MLST. Three PFGE patterns within CC138 (serotype 6B) that differed in the invasive disease potential were identified. Whole genome sequencing of four representative isolates was performed. Intra-clonal variants were found that reflected different prophage content, and major differences were observed in pneumococcal surface antigens that may affect virulence in vivo (mouse model) and invasive disease potential in children.

Moreover, we found that the invasive disease potential to be lower for non-PCV13 serotypes as compared to vaccine-type strains. Patients infected with non-PCV13 strains had more often underlying diseases, and were less likely to have pneumonia. Adults tended to have a higher mortality. Furthermore, patients infected with pneumococci belonging to clonal types only expressing non-PCV13 capsules had a higher risk of septicemia and mortality.

After vaccine introduction we observed that the serotype distribution changed and non-vaccine types emerged both in invasive disease and in carriage. Serotype 22F and serotype 3 were now the most commonly found serotypes causing invasive pneumococcal disease due to expansion of certain clonal types. Serotype 11A increased in asymptomatic children. In addition, serotype 11A was found to be the most common serotype in patients with lower respiratory tract infection (LRTI) in Europe. Furthermore, we found that the closely related species Streptococcus pseudopneumoniae may cause LRTI.

In summary, the results presented in this thesis illuminate and clarify the need for new pneumococcal vaccines, covering more serotypes and clonal types. A universal vaccine, based on for example one or more proteins found in all clinical isolates, might eradicate all pneumococci with the potential of becoming invasive.