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O072 - THE METABOLIC, VIRULENCE AND ANTIMICROBIAL RESISTANCE PROFILES OF COLONIZING STREPTOCOCCUS PNEUMONIAE SHIFT AFTER PCV13 INTRODUCTION IN URBAN MALAWI (ID 571)
Streptococcus pneumoniae naturally undergoes genotypic fluctuations. We previously showed a high residual prevalence of vaccine serotype (VT) pneumococci (18% in under 5’s) 7 years after PCV13 introduction in Malawi. Here, we address the hypothesis that following vaccine introduction in high disease and carriage settings, adapted pneumococcal genotypes emerge with the potential to facilitate vaccine escape.
2804 S. pneumoniae isolates were collected and sequenced during rolling cross-sectional carriage surveys in Blantyre, 4-8 years after PCV13 introduction. We identified the serotype and the antimicrobial resistance characteristics genomically. Further, we developed a pipeline to cluster the bacterial population based on its metabolic core genes (Metabolic Genotypes, MTs). Relative fitness was assessed by in vitro growth and epithelial adhesion/invasion using Detroit 562 nasopharyngeal cells.
We show marked changes in S. pneumoniae carriage population genetics. 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). These metabolic genotypes show distinct virulence and antimicrobial resistance (AMR) profiles, including genes responsible for metabolism and carbohydrate transport, and toxin-antitoxin systems located in an integrative-conjugative region suggestive of horizontal gene transfer. We identified convergent evolution between MTs isolated in different countries, result of genetic bottleneck. These emergent genotypes were found to have differential growth, haemolytic, or epithelial adhesion/invasion traits that may confer advantage in the nasopharyngeal niche.
This vaccine-induced shift in metabolic genotypes, antimicrobial resistance and colonization adaptations extends beyond simple serotype replacement, could further undermine vaccine control and promote the spread of AMR.