Atlas of group A streptococcal vaccine candidates compiled using large-scale comparative genomics

Abstract

Group A Streptococcus (GAS; Streptococcus pyogenes) is a bacterial pathogen for which a commercial vaccine for humans is not available. Employing the advantages of high-throughput DNA sequencing technology to vaccine design, we have analyzed 2,083 globally sampled GAS genomes. The global GAS population structure reveals extensive genomic heterogeneity driven by homologous recombination and overlaid with high levels of accessory gene plasticity. We identified the existence of more than 290 clinically associated genomic phylogroups across 22 countries, highlighting challenges in designing vaccines of global utility. To determine vaccine candidate coverage, we investigated all of the previously described GAS candidate antigens for gene carriage and gene sequence heterogeneity. Only 15 of 28 vaccine antigen candidates were found to have both low naturally occurring sequence variation and high (>99%) coverage across this diverse GAS population. This technological platform for vaccine coverage determination is equally applicable to prospective GAS vaccine antigens identified in future studies.

Figure 1. Population structure and pangenome of 2,083 globally distributed GAS strains.

(a) Maximum-likelihood phylogenetic tree of 30,738 SNPs generated from an alignment of 416 core genes. Branch colours indicate bootstrap support according to the legend. Distinct genetic lineages (n = 299) are highlighted in alternating colours (blue and grey) from the tips of the tree. Coloured asterisks refer to the relative position of complete GAS reference genome sequences (existing references are shown in brown; 30 new reference genomes are shown in dark blue). Colour coded around the outside of the phylogenetic tree is the country of isolation for each isolate. (b) Pangenome accumulation curve of 2,083 GAS genomes based on clustering of protein sequence at 70% homology.

Figure 2. Antigenic variation within vaccine targets from 2,083 GAS genomes.

(a) Gene carriage (presence/absence) of vaccine antigens. (b) Amino acid sequence variation within 25 protein antigens for each of the 2,083 GAS genomes. Each ring represents a single antigen with protein similarity colour coded according to pairwise BlastP similarity: Black (>98%); Blue (between 95 – 98%); Red (between 90 - 95%); Pink (80 - 90%); Yellow (70 - 80%); Grey (<70%); and White (protein absence). Rings correspond to: 1) R28; 2) Sfb1; 3) Spa; 4) SfbII; 5) FbaA; 6) SpeA; 7) M1 (whole protein); (8) M1 (180bp N-terminal) 9) SpeC; 10) Sse; 11) Sib35; 12) ScpA; 13) SpyCEP; 14) PulA; 15) SLO; 16) Shr; 17) OppA; 18) SpeB; 19) Fbp54; 20) SpyAD; 21) Spy0651; 22) Spy0762; 23) Spy0942; 24) ADI; and 25) TF.

Figure 3. Global amino acid variation mapped onto the protein crystal structure of the mature GAS Streptolysin O and C5a peptidase.

(a) Frequency of amino acid variations within 2,083 genomes. (b) Schematic of the Streptolysin O and C5a peptidase open reading frame representing the location of amino acids within the mature enzymes (blue block). Model of the consensus sequence of the Streptolysin O (c) and C5a peptidase (d) mature enzymes. Plotted against the structure is the amino acid variation frequency within the 2,083 GAS genomes as represented in the colour gradient from 1% variable (blue) to 42% variable (red); invariant sites are coloured in light grey. Position of the top 5 most variable surface hotspots (“HS”) are annotated (as defined in Supplementary Tables 10 and 11). Active sites for each enzyme are indicated (cyan arrow).