The Sanger Institute has a program of activities focused on Streptococcus pneumoniae including reference genomes, comparative genomics, deep sequencing within lineages and capsule biosynthesis loci sequencing.

Projects

• Sequencing of cps loci for 90 different serotypes.
• Genome of a representative of the S. pneumoniae^Spain23F sequence type 81 lineage
• Other reference genomes: INV104B (ST 227, serotype 1), INV200 (ST 9, serotype 14), OXC141 (ST 180, serotype 3), A45 (serotype 3)
• Comparative genomics within ST180 (strains 03_4156, 03_4183, 07_2838, 99_4038, 99_4039, 02_1198).
• Comparative genomics within serotype 1 (strains P1041, INV104B, 03_2672, 03_3038, 06_1370, NCTC7465)
• Deep sequencing within S. pneumoniae^Spain23F sequence type 81 lineage (200+ isolates)
• Repeat sequence analysis; annotation software can be downloaded here

Collaborators (in no particular order)

Brian Spratt, Imperial College, UK

Tim Mitchell, University of Glasgow, UK

Peter Andrew, University of Leicester, UK

Keith Klugman, Emory University, USA

Anne von Gottburg, NICD, South Africa

Lesley McGee, CDC, USA

Kwan Soo Ko, ARFID, South Korea

Steve Baker, OUCRU, Vietnam

Lotte Lambertsen, SSI, Denmark

Mark van der Linden, NRCS, Germany

Bruno Pichon, HPA, UK

Bill Hanage, Imperial College, UK

Margit Kaltoft, Streptococcus Unit, Statens Serum Institut, Denmark

Funding

This work has been funded by the Wellcome Trust and World Health Organisation

Published Genome Data

Published Sequence

S. pneumoniae type 23F (Spanish 23F-1), is a multiple antibiotic resistant pandemic strain. The genome has a size of 2,221,315 bp and was sequenced in collaboration with in collaboration with Prof. Tim Mitchell of the Division of Infection and Immunity, Institute of Biomedical and Life Sciences, University of Glasgow, and Prof. Peter William Andrew of the Department of Microbiology and Immunology, Univesity of Leicester. The fully annotated genome is available from the EMBL/GenBank databases with accession number FM211187.

The genomes of strains INV104B (ST 227, serotype 1), INV200 (ST 9, serotype 14) and OXC141 (ST 180, serotype 3) are fully sequenced, annotated and published. The fully annotated genomes are available from the EMBL/GenBank databases with accession numbers FQ312030, FQ312029 and FQ312027 respectively.

Shotgun and assembly data from these projects are also available from our ftp site.

The genome of strain SPNA45 is fully sequenced, annotated and published. The fully annotated genome is available from the EMBL/GenBank databases with accession number HE983624.

The fully assembled and published draft genomes of the following strains are also available from the EMBL/GenBank databases:

• SPN032672 with accession FQ312039
• SPN033038 with accession FQ312042
• SPN034156 with accession FQ312045
• SPN034183 with accession FQ312043
• SPN994038 with accession FQ312041
• SPN994039 with accession FQ312040

Assembled contigs of the following draft genomes have been published and made available from the EMBL/GenBank databases:

• SPN021198 with accessions CACH01000001-CACH01000022
• SPN061370 with accessions CACJ01000001-CACJ01000037
• SPN072838 with accessions CACI01000001-CACI01000025
• SPN1041 with accessions CACE01000001-CACE01000052
• SPN7465 with accessions CACF01000001-CACF01000026

Capsular Polysaccharide Biosynthetic Clusters

The Sanger Institute was funded by The World Health Organisation to sequence each of the 90 capsular polysaccharide (cps) biosynthetic clusters of S. pneumoniae in collaboration with Prof. Brian Spratt of the Department of Infectious Disease Epidemiology, Faculty of Medicine, Imperial College, London and Dr. Margit Kaltoft of the Streptococcus Unit, Statens Serum Institut, Denmark.

Knowledge of the full complement of capsule sequences should be important for surveillance and vaccine research.

Each cps cluster was amplified by long-PCR using primers in the conserved flanking dexB and aliA as described in Jiang et al., and the PCR product sequenced by the shotgun technique. Sizes range from 13844 to 30298 bp.

All 90 sequences are finished, annotated and published. Sequences are available for searching on our Blast Server. Sequences and preliminary annotations are available for download from our FTP site.