Background

Streptococcus pneumoniae naturally undergoes fluctuations in genotype. We previously showed a high residual prevalence of vaccine serotype (VT) pneumococci (18% in under 5’s) 7 years after PCV13 introduction in Malawi. In this context, we hypothesised the emergence and fixation of S. pneumoniae lineages with genetic traits conveying a competitive advantage in the nasopharyngeal niche.

Methods

1826 S. pneumoniae genomes were analysed from isolates collected during rolling cross-sectional carriage surveys in Blantyre, 4-7 years after PCV13 introduction. The metabolic core-genome includes 175 discrete metabolic genotypic profiles (metabolic types, MTs). Relative fitness was assessed by in-vitro growth and adhesive potential evaluated using Detroit 562 nasopharyngeal epithelial cells.

Results

High residual pneumococcal carriage is characterised by persistent MTs in VT (e.g. 3 and 23F) and emerging new MTs in non-VT (NVT; 38 and 23B). Increase in AMR MTs among 38 and 23B was observed. Emerging MTs show characteristic sequences of virulence genes and are characterised phenotypically by higher growth potential and propensity for better adherence to NP cell. We identified convergent evolution between MTs isolated in different countries, result of genetic bottlenecks.

Conclusions

This shift in metabolic genotypes, antimicrobial resistance and colonization adaptations may facilitate vaccine escape.

Background

Serotype 2 was a major cause of pneumococcal pneumonia about 100 years ago and then disappeared. Recently, serotype 2 re-emerged in many countries, including Bangladesh and associated with meningitis. This study aims to understand genomic and epidemiological characteristics of newly emerged serotype 2 strains.

Methods

Whole-genome sequencing was performed on 146 isolates (invasive= 125, carriage= 8 and other= 5, unknown= 8) collected between 1989 and 2017. Data were analyzed for comparative genomics, antimicrobial resistance and molecular typing.

Results

Isolates were from 16 countries, mostly in Asia (n=93), Africa (n=23) and Oceania (n=26). Bangladesh (n=66) and Papua New Guinea (n=26) contributed 63% of the isolates. Among the known clinical conditions, 80% (91/113) were from meningitis. All isolates belonged to GPSC96 lineage and descended from two predominant sequence types: ST74 found in Asia and Africa, and ST1504 found in Papua New Guinea and Israel. Almost all isolates were sensitive to all antibiotics. No significant genetic differences were detected between invasive and carriage isolates.

Conclusions

Our findings don’t explain why the recent increase in serotype 2 occurred but exclude an outbreak or emergence of an antimicrobial-resistant strain as the cause. These isolates have unusually high propensity to be invasive, mostly causing meningitis.

Background

Streptococcus pneumoniae serotype-1 is the predominant cause of invasive pneumococcal disease in sub-Saharan Africa, but the mechanism behind its increased invasiveness is not well understood.

Methods

To identify factors that make key contributions to serotype-1 disease pathogenesis, we used a BALB/c model of pneumococcal pneumonia. Disease severity of infection with African serotype-1 (ST217 and ST3081) was compared to serotypes 2 (D39), 5, 6B and 7F.

Results

BALB/c mice are normally highly resistant to pneumococcal pneumonia with little to no bacterial dissemination from lungs into the bloodstream, resulting in 100% survival rates. However, when BALB/c mice were intranasally infected with serotype-1 ST217, 100% mortality was observed with high levels of bacteraemia within 24 hours. Mice challenged with all other serotypes survived.

We show that serotype-1 produces pneumolysin in large quantities, rapidly released due to high levels of bacterial autolysis. This released pneumolysin induces substantial levels of cellular cytotoxicity and breakdown of tight junctions between cells, allowing a route for rapid bacterial dissemination from the respiratory tract into blood; offering an explanation for increased serotype-1 invasiveness.

Conclusions

In conclusion, serotype-1 virulence was driven by rapid bacterial autolysis, which led to the release of large quantities of pneumolysin, enabling rapid bacterial dissemination into the bloodstream.