After PCV10 introduction into the national children’s immunization program in 2010 in Brazil, Spn19A increased as cause of DPI and NCC. This study describes the genomic population structure of Spn19A before and after PCV10 introduction.
Spn19A (n=454) collected from <5-year and ≥50-year through national laboratory surveillance (DPI:n=403) and from 1-<2-year NCC (n=51) were MLST characterized (pre-PCV10:n=68, post-PCV10:n=386). Of these, 50 Spn19A (pre-PCV10:n=20, post-PCV10:n=30) were whole-genome sequenced (WGS).
This study identified 8 clonal complexes (CCs), with the prevalent lineages CC1118 (51.5%, 35/68) and MDR-CC320 (60.9%, 235/386) in pre-PCV10 and post-PCV10 periods, respectively. The WGS showed 11 GPS clusters (GPSCs), with GPSC1 (32.0%, 16/50) and GPSC204 (30.0%, 15/50) prevalent and related to MDR-CC320 and CC1118, respectively. GPSC1/CC320 (87.5%, 14/16) lineage was associated to penicillin (MIC≥2.0µg/mL) and ceftriaxone (MIC≥1.0µg/mL) nonsusceptibility, presenting pbp1a+pbp2b+pbp2x mutations, and 100.0% (16/16) of cotrimoxazole resistance (folA+folP alterations). Only in the GPSC1/CC320 lineage was identified the pilus-1 and pilus-2 genes and the transposon Tn2010, which carry macrolide (mefE+msrD+ermB) and tetracycline (tetM) resistance genes.
The study showed the expansion of the lineage GPSC1/CC320-Spn19A-MDR after PCV10 introduction in Brazil. Besides vaccine impact, the presence of MDR and the pilus-1 and pilus-2 genes could collaborate with the expansion.