EuroPneumo Special Issue / pneumonia 2015 Oct 21;7:I–72

types, except 15B/C. Over 1000 STs were observed; the most prevalent (n = 275) was the highly clonal ST217, expressing

serotype 1, exclusively from the African continent. Eight of the 13 major lineages defined by hierBAPS, were present in all

nine countries for which >100 isolates had been sequenced, whilst the remaining 5 lineages were present in ≥7 of these

countries. All 13 lineages exhibited multiple serotypes but ≤3 serotypes accounted for >50% of isolates in each lineage.

Although most lineages were widespread, serotype/genotype profiles varied between countries, potentially overstated

by any sampling biases. As PCV use expands globally, characterising lineage and serotype distribution is valuable

for assessing changes in pneumococcal diversity, which could potentially impact the effectiveness of pneumococcal

prevention and control measures.

*On behalf of all Global Pneumococcal Sequencing project partners:


Investigating the pneumococcal phageome using a diverse genome


Caroline L Harrold, Andries J van Tonder, Angus McDonnell, Ben A Edwards, Angela B


University of Oxford, Oxford, UK

Bacteriophages are viruses that infect bacteria: many bacterial species are infected by bacteriophages and the

bacteriophages often confer benefits to their host by providing genes that encode toxins or other virulence factors.

Pneumococcal bacteriophages were first identified in 1975. Bacteriophages may play an important role in pneumococcal

biology and evolution; however, prevalence data has been limited and relatively little is known about their effects on the

pneumococcal host. We have a large and diverse global dataset of 336 pneumococcal whole genome sequences (WGS)

obtained from 31 different countries between 1916 and 2008. Preliminary analysis of this dataset used bioinformatics

tools to interrogate the pneumococcal genomes for sequence-based evidence of bacteriophages. With the view to

build a pneumococcal phageome reference database of pneumococcal bacteriophage sequences, the dataset was

screened for evidence of bacteriophage DNA using an in-house pipeline and a reference database of previously

characterised streptococcal bacteriophage genomes. Initial analyses revealed that 86% of the pneumococcal genomes

had bacteriophage DNA integrated within them, with 48 different bacteriophage types identified. In many cases the

pneumococcal genomes contained DNA from >1 bacteriophage type: 22 genomes contained 2 full length bacteriophages,

and 13 genomes contained ≥5 full length and partial bacteriophages. The results of the screen led to the identification of

10 novel bacteriophages. Four of the novel bacteriophages showed considerable sequence similarity to each other, but

were unlike the other 6 novel bacteriophages, and were widespread throughout our collection of South African isolates,

suggesting that they are a common feature of the South African pneumococcal population. These results suggest that

bacteriophage sequences in the pneumococcus are much more prevalent and diverse than previously recognised, and

that they are likely to be contributing to pneumococcal genome evolution.


Molecular pneumococcal capsular typing using whole genome

sequencing: moving the Streptococcus pneumoniae reference service

into the genomic era

Georgia Kapatai, Carmen Sheppard, Ali Al-Shahib, David Litt, Norman Fry, Anthony Underwood,

Timothy Harrison

Public Health England, London, UK

We describe a novel bioinformatics method for accurate prediction of 88/92 (95.7%) Streptococcus pneumoniae

serotypes using WGS data. Our project is part of a large modernisation strategy within Public Health England aiming

to replace the current phenotypic pneumococcal species confirmation and serotyping reference service with a unified

WGS pipeline. Our bioinformatics pipeline integrating several components provides a comprehensive S. pneumoniae

workflow delivering species identification, MLST typing and capsular typing for each isolate. The “capsular typing” tool

pneumonia 2015 Volume 7


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