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

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 (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, 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.

Keywords: Brazil; Multi-locus sequencing typing; PCV10; Streptococcus pneumoniae; genomic surveillance; global pneumococcal sequence cluster.

Fig. 1.

Dynamics of Global Pneumococcal Sequence Clusters (GPSCs) among invasive isolates from children aged <5 years old over vaccine periods in Brazil. The number of invasive pneumococcal isolates, coloured by serotypes, is plotted by GPSC with stratification into two vaccine periods (pre-PCV10 and post-PCV10) and MLST CC. Solid fill represented the VT and NVT additional PCV13 serotypes while hatched patterns represented the NVT non-PCV serotypes. The antibiotic resistance pattern to penicillin, chloramphenicol, erythromycin, cotrimoxazole, tetracycline and MDR are present for each GPSC and in the entire period studied.

Fig. 2.

Dynamics of Global Pneumococcal Sequence Clusters (GPSCs) among invasive isolates from children aged ≥5 years old over vaccine periods in Brazil. The number of invasive pneumococcal isolates, coloured by serotypes, is plotted by GPSC with stratification into two vaccine periods (pre-PC10 and post-PCV10) and MLST CC. Solid fill represented the VT and NVT additional PCV13 serotypes while hatched patterns represented the NVT non-PCV serotypes. The antibiotic resistance pattern to penicillin, chloramphenicol, erythromycin, cotrimoxazole, tetracycline and MDR are present for each GPSC and in the entire period studied.

Fig. 3.

A timed-measured phylogeny of GPSC47 (ST386) isolates from Brazil and the other 15 countries from Gladstone et al. [14]. The phylogeny is built using BactDating [22] with 100 000 000 generations on a recombination-free SNP alignment generated by GUBBINs [21]. The most recent common ancestor (tMRCA) of the serotype 6C clade (all isolates are ST386) is estimated to emerge in around 2000 (95 % confidence interval: 1997–2003), and the capsular switching occurred among 1990–2003. The phylogeny and metadata can be interactively visualized at https://microreactorg/project/tmxT66fLq56uZb5VfA1BYC.

Fig. 4.

Distribution of pilus islets genes in the main GPSCs by vaccine period studied (n=150).