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O031 - EMERGENCE OF A STREPTOCOCCUS PNEUMONIAE SEROTYPE 3 CAPSULE VARIANT AMONGST CARRIAGE ISOLATES IN THE 8 YEARS SINCE PCV13 INTRODUCTION IN BLANTYRE, MALAWI (ID 574)
Abstract
Background
Several studies worldwide showed limited PCV13 efficacy against carriage of serotype 3 Streptococcus pneumoniae. Serotype 3 lineages vary substantially geographically and show tendency to recombine. We hypothesised that the apparent serotype 3 vaccine escape, in the context of reduced carriage of other vaccine serotypes (VTs), could be due to the emergence of nasopharyngeal niche-adapted lineages.
Methods
The genome and CPS locus sequences of 556 serotype-3 isolates (from Africa, Asia, Europe and America) were analysed. ML-phylogeny, antimicrobial resistance (tetM, mefA, ermB, cat gene presence and pbpX allelic profiles) and MLST profiles were calculated. Colony morphology was observed in microaerophilic and anaerobic conditions, and opsonophagocytosis of representative isolates was assessed using conjugate vaccine induced sera.
Results
We identified a serotype-3 CPS locus variant in 82% of Blantyre isolates (2015-2019), characterized by an 8-gene cluster deletion and unchanged colony morphology. ST700 is the dominant genotype with these characteristics: it was identified in invasive disease, and we observed higher resistance to opsonophagocytosis than other serotype 3 strains commonly carried in Blantyre. ST700 strains are characterised by a higher MIC to penicillin, significant genome reduction, and unique virulence gene profiles, including pathogenicity islands carrying bacteriocin synthesis genes and ABC-transporters.
Conclusions
We highlight the emergence of an AMR serotype 3 variant, characterised by a shorter, yet functional, CPS locus, genome reduction and a unique genetic and phenotypic profile which may enhance colonisation and disease. We propose that these characteristics have the potential to confer competitive advantage to this lineage, which should be considered when designing the next generation of pneumococcal vaccines.