Changes in population genetic structure of serotype 19A Streptococcus pneumoniae after universal childhood use of the 10-valent pneumococcal conjugate vaccine in Brazil.

Background: The introduction of the 10-valent pneumococcal conjugate vaccine (PCV10) for nationwide childhood immunization in 2010 led to a significant reduction in colonization and invasive pneumococcal disease (IPD) by vaccine serotypes in young. However, non-vaccine serotypes have emerged, and serotype 19A is now the leading cause of IPD in Brazil.

Methods: We analyzed 32 serotype 19A isolates of Streptococcus pneumoniae recovered from children and adults who attended different health facilities in the state of Rio de Janeiro, Brazil, between 2010 and 2023. The capsular types of the isolates were determined by sequential multiplex PCR or by cpsB gene sequencing. All isolates were subjected to antimicrobial susceptibility testing and MLST.

Results: Of the 32 serotype 19A isolates, 29 (90.6 %) isolates were recovered from children aged ≤5 years and three (9.4 %) isolates were recovered from adults. Nineteen (59.4 %) isolates were associated with colonization, and 13 (40.6 %) isolates were from diseases. All isolates were susceptible to chloramphenicol, levofloxacin, linezolid, rifampin, and vancomycin. The highest frequencies of non-susceptibility (intermediate + resistant) were observed for sulfamethoxazole-trimethoprim (n = 30; 93.8 %), penicillin (n = 24; 75 %), and erythromycin (n = 23; 71.9 %). Twenty-two (68.8 %) isolates were multidrug resistant (MDR). MICs for penicillin among penicillin-non-susceptible pneumococci (PNSP) ranged from 0.12 to 8.0 μg/mL. MICs for erythromycin ranged from 0.064 to >256 μg/mL. MICs for ceftriaxone ranged from 0.023 to 4 μg/mL. The most common genetic lineages were ST733 (n = 7; 21.9 %), mostly found before and in the early years of PCV10 introduction, and CC320 (n = 25; 78.1 %), mostly found in the late-PCV10 period. All 25 isolates within CC320 were PNSP and mostly (n = 22; 88 %) MDR.

Conclusions: We observed a shift in antimicrobial susceptibility profiles and genetic lineages after long-term use of PCV, mostly PCV10, for routine childhood immunization, characterized by clonal expansion of the MDR lineage CC320.