Streptococcus pneumoniae
Streptococcus pneumoniae (the pneumococcus) is a facultatively anaerobic Gram positive bacterium which normally resides harmlessly within the human nasopharynx but is a major cause of morbidity and mortality worldwide, causing diseases that range in severity from meningitis, septicaemia, and pneumonia to sinusitis and acute otitis media. Rates of carriage are highest in infants and the elderly and much lower in other adults.
Data Downloads
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. pneumoniaeSpain23F 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. pneumoniaeSpain23F 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.
Studies
- Streptococcus pneumoniae transcriptomics
- Genetic diversity on Streptococcus pneumoniae in Malawi 1
- Deep sequencing within the Streptococcus pneumoniae antibiotic resistant pandemic clone PMEN1
- Genetic diversity on Streptococcus pneumoniae in Malawi 2
- Discovery of sequence diversity in Streptococcus pneumoniae serotype 1
- Streptococcus pneumoniae serotype switching
- Pneumococcal in morbus diversity (QEH, Blantyre, Malawi)
- Streptococcus pneumoniae evolution
- Streptococcus pneumoniae ST180 diversity
- Streptococcus pneumoniae global lineages
- Population structure and diversity in non-encapsulated Streptococcus pneumoniae
- Streptococcus pneumoniae evolution and population structure during longitudinal sampling in a defined human population
- Streptococcus pneumoniae evolution and population structure during longitudinal sampling in a defined human population
- Streptococcus pneumoniae evolution and population structure during longitudinal sampling in a defined human population
- Streptococcus pneumoniae evolution and population structure during longitudinal sampling in a defined human population
- Streptococcus pneumoniae evolution and population structure during longitudinal sampling in a defined human population
- Streptococcus pneumoniae evolution and population structure during longitudinal sampling in a defined human population
- Whole genome sequencing of carried Streptococcus pneumoniae during the implementation of pneumococcal conjugate vaccines in the UK
- Population genomics of Streptococcus pneumoniae in the presence of vaccine and antimicrobial treatment
- Diversity of MRSA
- Streptococcus pneumoniae samples from Malawi
- Impact of HIV on nasopharyngeal carriage of Streptococcus pneumoniae
- Whole genome sequencing of pathogenic strains of Mycobacterium abscessus
- Global Pneumococcal Sequencing (GPS) study I
- Streptococcus pneumoniae genetic diversity and invasive pneumococcal disease
- Effect of mass macrolide treatment on pneumococcal population
- Microevolution of Neisseria meningitidis during clonal waves of colonization and disease - phase 2
- Veterinary hospital MRSA infection study
- Discovery of natural pneumococcal mutation rates during controlled colonisation of the human nasopharynx
- An epidemiological study to evaluate the impact of the 10-valent pneumococcal conjugate vaccine in a previously unvaccinated population
- Integration of the host and pathogen genetics in bacterial meningitis
- Genome sequence variation in a mouse model of invasive pneumococcal infection
- Indel detection in stressed pneumococci
- NCTC 3000
- Identifying pneumococcal genetic determinants for progression from colonisation to serious disease
- Genomic characterization of bladder bacteria from healthy and infected women
- Chest Array: Direct sequencing of selected bacterial strains from clinical samples
- Streptococcus pneumoniae from the pre-PCV7, PCV7 and PCV13 eras
- Bloodstream surveillence across Africas
- Lung Culturomics
- PacBio sequencing of samples from Global Pneumococcal Sequencing (GPS) study
- Pneumococcal adaptation in COPD Spain
- Deep sequencing of the Maela carriage cohort to study within-host evolution, pathogenesis and transmission epidemiology of Streptococcus pneumoniae
- Dutch pneumococcal carriage isolates
Streptococcus pneumoniae transcriptomics
Genetic diversity on Streptococcus pneumoniae in Malawi 1
Deep sequencing within the Streptococcus pneumoniae antibiotic resistant pandemic clone PMEN1
Genetic diversity on Streptococcus pneumoniae in Malawi 2
Discovery of sequence diversity in Streptococcus pneumoniae serotype 1
Streptococcus pneumoniae serotype switching
Sample | Strain | Run Accession |
---|---|---|
05-008 | 05-008 | ERR023543 |
14-034 | 14-034 | ERR023308 |
3027-Spneu | 3027 | ERR023544 |
3029 | 3029.0 | ERR023302 |
3221 | 3221.0 | ERR023542 |
BR1008 | BR1008 | ERR023539 |
BR1014 | BR1014 | ERR023303 |
BR1068 | BR1068 | ERR023540 |
CH2053 | CH2053 | ERR023307 |
MD5030 | MD5030 | ERR023305 |
MD5037 | MD5037 | ERR023304 |
ND6053 | ND6053 | ERR023541 |
ND6123 | ND6123 | ERR023538 |
PT8072 | PT8072 | ERR023306 |
Pneumococcal in morbus diversity (QEH, Blantyre, Malawi)
Sample | Strain | Run Accession |
---|---|---|
A30615 | A30615 | ERR024492 |
A32273 | A32273 | ERR024496 |
A34978 | A34978 | ERR024497 |
A35432 | A35432 | ERR024498 |
A35711 | A35711 | ERR024499 |
A35792 | A35792 | ERR024500 |
A36530 | A36530 | ERR024501 |
A37104 | A37104 | ERR024502 |
A37642 | A37642 | ERR024503 |
A37893 | A37893 | ERR024493 |
A40931 | A40931 | ERR024494 |
A41763 | A41763 | ERR024495 |
A42347 | A42347 | ERR024505 |
A43965 | A43965 | ERR024509 |
A47073 | A47073 | ERR024510 |
A52018 | A52018 | ERR024511 |
B10366 | B10366 | ERR024512 |
B11501 | B11501 | ERR024513 |
B11684 | B11684 | ERR024514 |
B11825 | B11825 | ERR024515 |
B11856 | B11856 | ERR024516 |
B12226 | B12226 | ERR024506 |
B12423 | B12423 | ERR024507 |
B12674 | B12674 | ERR024508 |
B12772 | B12772 | ERR024518 |
B14208 | B14208 | ERR024522 |
B14457 | B14457 | ERR024523 |
B15017 | B15017 | ERR024524 |
B16242 | B16242 | ERR024525 |
B18374 | B18374 | ERR024526 |
B18762 | B18762 | ERR024527 |
B9632 | B9632 | ERR024528 |
C11950 | C11950 | ERR024529 |
C12495 | C12495 | ERR024519 |
C12675 | C12675 | ERR024520 |
C15473 | C15473 | ERR024521 |
C15514 | C15514 | ERR024531 |
C9938 | C9938 | ERR024532 |
D31827 | D31827 | ERR024533 |
D33293 | D33293 | ERR024534 |
D33733 | D33733 | ERR024535 |
D40623 | D40623 | ERR024536 |
D40696 | D40696 | ERR024537 |
D46797 | D46797 | ERR024538 |