Genomic surveillance of invasive Streptococcus pneumoniae isolates in the period pre-PCV10 and post-PCV10 introduction in Brazil. Issue 10 (5th October 2021)

• Record Type: Journal Article
• Authors: Almeida, Samanta C. G.; Lo, Stephanie W.; Hawkins, Paulina A.; Gladstone, Rebecca A.; Cassiolato, Ana Paula; Klugman, Keith P.; Breiman, Robert F.; Bentley, Stephen D.; McGee, Lesley; Brandileone, Maria-Cristina de C.
• Is Part Of: Microbial genomics. Volume 7:Issue 10(2021)
• Publication Date: 2021-10-05
• Subjects: Brazil -- genomic surveillance -- global pneumococcal sequence cluster -- Multi-locus sequencing typing -- PCV10 -- Streptococcus pneumoniae; Microbial genomics -- Periodicals; 572.8629
• DOI: 10.1099/mgen.0.000635
• Languages: English
• ISSNs: 2057-5858

Abstract

Abstract : In 2010, Brazil introduced the 10-valent pneumococcal conjugate vaccine (PCV10) into the national children's immunization programme. This study describes the genetic characteristics of invasive Streptococcus pneumoniae isolates before and after PCV10 introduction. A subset of 466 [pre-PCV10 (2008–2009): n =232, post-PCV10 (2012–2013): n =234;<5 years old: n =310, ≥5 years old: n =156] pneumococcal isolates, collected through national laboratory surveillance, were whole-genome sequenced (WGS) to determine serotype, pilus locus, antimicrobial resistance and genetic lineages. Following PCV10 introduction, in the <5 years age group, non-vaccine serotypes (NVT) serotype 3 and serotype 19A were the most frequent, and serotypes 12F, 8 and 9 N in the ≥5 years old group. The study identified 65 Global Pneumococcal Sequence Clusters (GPSCs): 49 (88 %) were GPSCs previously described and 16 (12 %) were Brazilian clusters. In total, 36 GPSCs (55 %) were NVT lineages, 18 (28 %) vaccine serotypes (VT) and 11 (17 %) were both VT and NVT lineages. In both sampling periods, the most frequent lineage was GPSC6 (CC156, serotypes 14/9V). In the <5 years old group, a decrease in penicillin ( P =0.0123) and cotrimoxazole ( P <0.0001) resistance and an increase in tetracycline ( P =0.019) were observed. Penicillin nonsusceptibility was predicted in 40 % of the isolates; 127 PBP combinations were identified (51 predicted MIC≥0.125 mg l −1 ); cotrimoxazole ( fol A and/or fol P alterations), macrolide ( mef and/or ermB ) and tetracycline ( tet M, tet O or tet S / M) resistance were predicted in 63, 13 and 21.6 % of pneumococci studied, respectively. The main lineages associated with multidrug resistance in the post-PCV10 period were composed of NVT, GPSC1 (CC320, serotype 19A), and GPSC47 (ST386, serotype 6C). The study provides a baseline for future comparisons and identified important NVT lineages in the post-PCV10 period in Brazil.