Background

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.

Methods

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).

Results

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.

Conclusions

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.

Background

In 2010, Brazil introduced PCV10 into the national children’s immunization program. This study describes the genomic population structure of invasive SPN before and after PCV10 introduction.

Methods

As part of Global Pneumococcal Sequencing (GPS) project, 466 (pre-PCV10:n=232, post-PCV10:n=234; <5-year-olds:n=310, ≥5-year-olds:n=156) invasive SPN collected through national laboratory surveillance were whole-genome sequenced.

Results

The study identified 65 GPS clusters (GPSCs): 49 (88%) GPS previously described and 16 (12%) were Brazilian clusters. 36 GPSCs (55%) were non-PCV10 lineages, 11 (17%) PCV10/non-PCV10 and 18 (28%) PCV10. In both periods, the most frequent lineage was GPSC6/CC156/PMEN3/14-9V. Post-vaccine non-PCV10 lineages GPSC16/CC66/9N-15A, GPSC12/CC180/PMEN3/3 and GPSC32/CC218/PMEN24/12F increased; in <5-year-olds, GPSC1/CC320/DLV-PMEN14/19A, GPSC47/CC386/DLV-PMEN20/6C and GPSC51/CC458/3; and ≥5-year-olds GPSC3/CC53/PMEN33/8 were predominant (Figure-1).

SPN penicillin nonsusceptibility was predicted in 40%; 127 PBP combinations were identified (51 predicted MIC≥0.125mg/L); cotrimoxazole (folA+folP alterations), macrolide (mef/ermB/ermB+mef) and tetracycline (tetM/tetO/tetS/M) resistance were predicted in 46%, 13% and 21% SPN, respectively. In <5-year-olds, a penicillin (p=0.0169) and cotrimoxazole (p<0.0001) resistance reduction and an increase in tetracycline (p=0.019) were observed. Post-PCV10, PBP15-12-18(2mg/L) was frequent in lineage GPSC6/CC156/PMEN3/14-9V; among <5-year-olds the PBP13-11-16(4mg/L) in GPSC1/CC320/DLV-PMEN14/19A and PBP2-53-77(0.125mg/L) in GPSC47/ST386/DLV-PMEN20/6C were predominant.

Conclusions

Post-PCV10, important non-PCV10 lineages, GPSC1/CC320/DLV-PMEN14/19A and GPSC47/ST386/DLV-PMEN20/6C associated with multidrug resistance and GPSC12/CC180/PMEN31/3, GPSC3/CC53/PMEN33/8 and GPSC32/CC218/PMEN24/12F were identified in Brazil.

Background

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.

Methods

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).

Results

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.

Conclusions

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.