Evolution of invasive Streptococcus pneumoniae PMEN3 clone over 30 years in Barcelona, Spain

PMEN3 (Spain9V-156) is a major penicillin non-susceptible pneumococcal clone causing invasive pneumococcal disease (IPD) worldwide. To analyze the epidemiology and genetic evolution of this clone we studied 227 episodes of adult IPD detected in our institution (Bellvitge Hospital, Barcelona) over a thirty-year period (1987–2016). Whole genome sequencing (WGS) was performed in forty-six representative pneumococci, whose data allowed to distinguish six lineages and was subsequently used to design several experiments (partial MLST, PCR-RFLP analysis) to assign the remaining isolates to a lineage. Recombination events were mostly found in three regions: capsular operon (capsular switching) and adjacent regions (pbp2x, pbp1a), murM gene and the pbp2b–ddl region. Some of these genetic changes led to increase MICs of B-lactam antibiotics whereas others allowed the emergence of new successful serotype-variant lineages (serotypes 14 and 11A).Our study explored the patho-adaptative evolution of this clone over a thirty year-period and demonstrate successive genetic changes that allowed it to persist over time.