Online Abstracts Basic Sciences - Genomics and Transmission A3 Genomics and Transmission



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.


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.


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.

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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.