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Background Pneumococcus kills over one million children annually and over 90 % of these deaths occur in low-income countries especially in Sub-Saharan Africa (SSA) where HIV exacerbates the disease burden. In SSA, serotype 1 pneumococci particularly the endemic ST217 clone, causes majority of the pneumococcal disease burden. To understand the evolution of the virulent ST217 clone, we analysed ST217 whole genomes from isolates sampled from African and Asian countries. Methods We analysed 226 whole genome sequences from the ST217 lineage sampled from 9 African and 4 Asian countries. We constructed a whole genome alignment and used it for phylogenetic and coalescent analyses. We also screened the genomes to determine presence of antibiotic resistance conferring genes. Results Population structure analysis grouped the ST217 isolates into five sequence clusters (SCs), which were highly associated with different geographical regions and showed limited intracontinental and intercontinental spread. The SCs showed lower than expected genomic sequence, which suggested strong purifying selection and small population sizes caused by bottlenecks. Recombination rates varied between the SCs but were lower than in other successful clones such as PMEN1. African isolates showed higher prevalence of antibiotic resistance genes than Asian isolates. Interestingly, certain West African isolates harbored a defective chloramphenicol and tetracycline resistance-conferring element (Tn5253) with a deletion in the loci encoding the chloramphenicol resistance gene (cat pC194), which caused lower chloramphenicol than tetracycline resistance. Furthermore, certain genes that promote colonisation were absent in the isolates, which may contribute to serotype 1’s rarity in carriage and consequently its lower recombination rates. Conclusions The high phylogeographic diversity of the ST217 clone shows that this clone has been in circulation globally for a long time, which allowed its diversification and adaptation in different geographical regions. Such geographic adaptation reflects local variations in selection pressures in different locales. Further studies will be required to fully understand the biological mechanisms which makes the ST217 clone highly invasive but unable to successfully colonise the human nasopharynx for long durations which results in lower recombination rates. Electronic supplementary material The online version of this article (doi:10.1186/s12879-016-1987-z) contains supplementary material, which is available to authorized users.

Streptococcus pneumoniae causes a high burden of invasive pneumococcal disease (IPD) globally, especially in children from resource-poor settings. Like many bacteria, the pneumococcus can import DNA from other strains or even species by transformation and homologous recombination, which has allowed the pneumococcus to evade clinical interventions such as antibiotics and pneumococcal conjugate vaccines (PCVs). Pneumococci are enclosed in a complex polysaccharide capsule that determines the serotype; the capsule varies in size and is associated with properties including carriage prevalence and virulence. We determined and quantified the association between capsule and recombination events using genomic data from a diverse collection of serotypes sampled in Malawi. We determined both the amount of variation introduced by recombination relative to mutation (the relative rate) and how many individual recombination events occur per isolate (the frequency). Using univariate analyses, we found an association between both recombination measures and multiple factors associated with the capsule, including duration and prevalence of carriage. Because many capsular factors are correlated, we used multivariate analysis to correct for collinearity. Capsule size and carriage duration remained positively associated with recombination, although with a reduced P value, and this effect may be mediated through some unassayed additional property associated with larger capsules. This work describes an important impact of serotype on recombination that has been previously overlooked. While the details of how this effect is achieved remain to be determined, it may have important consequences for the serotype-specific response to vaccines and other interventions.IMPORTANCE: The capsule determines >90 different pneumococcal serotypes, which vary in capsule size, virulence, duration, and prevalence of carriage. Current serotype-specific vaccines elicit anticapsule antibodies. Pneumococcus can take up exogenous DNA by transformation and insert it into its chromosome by homologous recombination. This mechanism has disseminated drug resistance and generated vaccine escape variants. It is hence crucial to pneumococcal evolutionary response to interventions, but there has been no systematic study quantifying whether serotypes vary in recombination and whether this is associated with serotype-specific properties such as capsule size or carriage duration. Larger capsules could physically inhibit DNA uptake, or given the longer carriage duration for larger capsules, this may promote recombination. We find that recombination varies among capsules and is associated with capsule size, carriage duration, and carriage prevalence and negatively associated with invasiveness. The consequence of this work is that serotypes with different capsules may respond differently to selective pressures like vaccines.

Summary of the genes found in the genetic recombination regions in clade SC2-WA. Genes present in the regions with recombination events in each clade are summarised. (DOCX 124Â kb)

Distribution of the accessory genes and antibiotic resistance conferring elements in the ST217 isolates. a) Maximum likelihood phylogeny of the isolates rooted using isolates from ST615 as an outgroup (not shown). b) Number of shared accessory open reading frames (ORFs) or genes between pairs of isolates in the phylogeny on the left side and at the top. c) Colour strips showing the continent and country of origin of the isolates and their SCs. d) A heatmap showing the number of shared accessory genes between each pair of isolates in the phylogeny (panel [a] and [e]). (PDF 4076Â kb)

Recombination events identified in the South East African clade (SC3-SEA). (a) Maximum likelihood phylogeny showing genetic relationship of the isolates in the SC. Color strips labeled (b) and (c) shows country and continent of origin of the isolates respectively. (d) Annotations in the reference serotype 1 genome. (e) Horizontal tracks from the phylogenetic tips represent each genome. The coloured blocks shows locations of the recombination events in the chromosome. Red blocks show shared recombination events identified in at least two isolate while the blue blocks show strain specific (unique) recombination events. (PDF 1077Â kb)

Summary of the genes found in the genetic recombination regions in clade SC1-SA. Genes present in the regions with recombination events in each clade are summarised. (DOCX 85Â kb)

Recombination events identified in the West African clade (SC2-WA). (a) Maximum likelihood phylogeny showing genetic relationship of the isolates in the SC. Color strips labeled (b) and (c) shows country and continent of origin of the isolates respectively. (d) Annotations in the reference serotype 1 genome. (e) Horizontal tracks from the phylogenetic tips represent each genome. The coloured blocks shows locations of the recombination events in the chromosome. Red blocks show shared recombination events identified in at least two isolate while the blue blocks show strain specific (unique) recombination events. (PDF 1452Â kb)

Estimated evolutionary parameters for all the clades. Each parameter estimate was calculated using MEGA. (DOC 80Â kb)

Summary of the genes found in the genetic recombination regions in clade SC3-SEA. Genes present in the regions with recombination events in each clade are summarised. (DOCX 133Â kb)

Clade specific phylogenies showing country of origin of the ST217 isolates. Maximum likelihood phylogenetic trees for clade (a) SC1-SA, (b) SC2-WA and (c) SC3-SEA. (PDF 292Â kb)

Recombination events identified in the South African clade (SC1-SA). (a) Maximum likelihood phylogeny showing genetic relationship of the isolates in the SC. Color strips labeled (b) and (c) shows country and continent of origin of the isolates respectively. (d) Annotations in the reference serotype 1 genome. (e) Horizontal tracks from the phylogenetic tips represent each genome. The coloured blocks shows locations of the recombination events in the chromosome. Red blocks show shared recombination events identified in at least two isolate while the blue blocks show strain specific (unique) recombination events. (PDF 641Â kb)

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Peptide-based immunotherapy (PIT) represents an attractive approach to develop safe interventions in food allergy, due to its attenuated risk of side-effects. The concept lies in the administration of allergen-derived peptides devoid of IgE-crosslinking activity, but with conserved T-cell determinants in order to maintain immunogenicity. In light of recent reports on the functions of regulatory T cells (Treg), it was hypothesized that T-cell epitope-containing peptides could induce regulatory mechanisms, capable of repressing an allergic response. Using the SPOTS® method, a 12-mer synthetic peptide library spanning the primary sequence of ovalbumin (OVA), a major egg allergen, was constructed and allowed identification of eight B-cell epitope regions. Optimization of an 'ex vivo' splenocyte proliferation assay led to recognition of three immunodominant and one minor T-cell determinants. Five groups of BALB/c mice were orally sensitized to OVA. Groups B, C and D were subsequently administered (s.c.) single synthetic peptides corresponding to OVA immunodominant T cell epitopes, while group E received a cocktail of the three peptides in equal amounts. Groups A and F served as negative (placebo) and positive (no peptide treatment) control groups, respectively. Following the peptide administration, mice were orally challenged with a high dose of OVA. Group B, C and E showed lower serum histamine and specific IgE levels compared to group A, and significantly lower anaphylactic scores were obtained in group E. Group D tended to show higher levels for these same parameters. Real-time RT-PCR analysis of mRNA gene expression in ileum indicated a dominant Th1-response in peptide-treated groups, supported by similar cytokine secretion profiles in splenocyte cultures (ELISA). Importantly, groups C and E were characterized by pronounced mRNA expressions of TGF-[beta] and FOXp3, suggesting the involvement of repressive mechanisms mediated by subsets of Treg cells. The suitability of a PIT approach in a food industrial context was assessed by orally administering egg-white protein hydrolyzates (