Genomic surveillance of invasive Streptococcus pneumoniae isolates in the period pre-PCV10 and post-PCV10 introduction in Brazil

• Type of Material: Article
• Authors: Samanta CG Almeida, Adolfo Lutz Institute; Stephanie W Lo, Wellcome Sanger Institute; Paulina A Hawkins, Centers for Disease Control and Prevention, Atlanta; Rebecca A Gladstone, Wellcome Sanger Institute; Ana Paula Cassiolato, Adolfo Lutz Institute; Keith Klugman, Emory University; Robert Breiman, Emory University; Stephen D Bentley, Wellcome Sanger Institute; Lesley McGee, Centers for Disease Control and Prevention, Atlanta; Maria-Cristina de C Brandileone, Adolfo Lutz Institute
• Language: English
• Date: 2021-10-01
• Publisher: MICROBIOLOGY SOC
• Publication Version: Final Published Version
• Copyright Statement: © 2021 The Authors
• License: Creative Commons Attribution 4.0 International
• Final Published Version (URL): http://dx.doi.org/10.1099/mgen.0.000635
• Title of Journal or Parent Work: MICROBIAL GENOMICS
• Volume: 7
• Issue: 10
• Grant/Funding Information: This study was co-funded by the Bill and Melinda Gates Foundation (grant code OPP1034556), the Wellcome Sanger Institute (core Wellcome grants 098051 and 206194), and the USA Centres for Disease Control and Prevention. The funding sources had no role in isolate selection, analysis, or data interpretation.
• Keywords: Life Sciences & Biomedicine; UNITED-STATES; PCV10; SEROTYPE 19A; Genetics & Heredity; EVOLUTION; CLONES; RESPIRATORY PATHOGENS; Multi-locus sequencing typing; Science & Technology; PNEUMOCOCCAL CONJUGATE VACCINE; global pneumococcal sequence cluster; Brazil; genomic surveillance; Streptococcus pneumoniae; Microbiology; ANTIMICROBIAL RESISTANCE; CHILDREN; GENETIC-STRUCTURE; DISEASE
• Research Categories: Health Sciences, Public Health

Abstract

In 2010, Brazil introduced the 10-valent pneumococcal conjugate vaccine (PCV10) into the national children’s immunization pro-gramme. 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 <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 previ-ously 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 (folA and/or folP alterations), macrolide (mef and/ or ermB) and tetracycline (tetM, tetO or tetS/M) resistance were predicted in 63, 13 and 21.6% of pneumococci studied, respec-tively. 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.