Streptococcus

Streptococcus is a genus of Gram positive bacteria belonging to the phylum Firmicutes. Species include:

• Streptococcus dysgalactiae: commonly found on the udders of cows with wild mastitis.

• Streptococcus equi': the causative agent of Strangles, the most common infectious disease of horses. The symptoms are severe, complications are common and, at present, there is no effective treatment or vaccine for the disease.

• Streptococcus pneumoniae (the pneumococcus) 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.

• Streptococcus pyogenes (Group A Strep) strains are associated with a wide variety of clinical manifestations, including streptococcal toxic-shock syndrome, acute rheumatic fever, scarlet fever, and others.

• Streptococcus suis which infects pigs and can occasionally cause serious infections in humans. Zoonotic infections occur sporadically in Europe and North America, but a recent major outbreak has been described in China with high levels of mortality.

• Streptococcus uberis: one of the main causes of bovine mastitis.

• Streptococcus zooepidemicus: the cause of Inflammatory Airway Disease (IAD) in horses.

Data Downloads

• FTP site

• S. equi BLAST server

• S. pneumoniae BLAST server

• S. pyogenes BLAST server

• S. suis BLAST server

• S. uberis BLAST server

• S. zooepidemicus BLAST server

S. equi

The Sanger Institute has completed the sequencing of and recently published the 2.25 Mb genome of S. equi strain 4047 in collaboration with Prof. Mike Kehoe, of the School of Cell and Molecular Biosciences, University of Newcastle, Duncan Maskell of the Centre for Veterinary Science, Dept. of Clinical Veterinary medicine, The University of Cambridge, and Dr. Neil Chanter of the Centre for Preventative Medicine, Animal Health Trust.

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.

S. pneumoniae

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

S. pyogenes

The Sanger Institute has completed the sequencing of and published the 1.84 Mb genome of Streptococcus pyogenes strain Manfredo (M5), in collaboration with Prof. Mike Kehoe, of the School of Cell and Molecular Biosciences, University of Newcastle. The strain chosen for this project is associated with acute rheumatic fever, and was isolated from a patient in Chicago in the late 1950's.

S. suis

We have sequenced the whole genome sequences of three Streptococcus suis strains from the same lineage: one from European pigs, and two from human cases from China and Vietnam.

The strains are:

• P1/7 was isolated from an ante-mortem blood culture from a pig dying with meningitis, and is sequence type (ST)1 by MLST
• BM407 was isolated from CSF from a human case of meningitis in Ho Chi Minh City, Vietnam in 2004, and is is ST1
• SC84 was isolated from a case of streptococcal toxic shock-like syndrome in Sichuan Province, China in 2005, and is is ST7, a single locus varient of ST1

We have also undertaken some deep sequencing within the ST1 lineages, examining human and pig isolates from in and around Ho Chi Minh City, Vietnam

Collaborators

Stephen Baker, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam

Constance Schultsz, Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam

S. uberis

The Sanger Institute has completed the sequencing of and published the 1.85 Mb genome of S. uberis strain 0140J in collaboration with Dr. Duncan Maskell of the Centre for Veterinary Science, Dept. of Clinical Veterinary Medicine, The University of Cambridge, Prof. Mike Kehoe of the School of Cell and Molecular Biosciences, University of Newcastle, Dr. Jamie Leigh and Dr. Phil Ward of the Institute for Animal Health, Compton, Prof. Christopher Dowson and Dr. Adrian Whatmore, of the Department of Biological Sciences, University of Warwick, and Dr. Neil Chanter of the Centre for Preventative Medicine, Animal Health Trust.

S. zooepidemicus

The Sanger Institute has completed the sequencing of and published the 2.15 Mb genome of S. zooepidemicus strain H70 in collaboration with Dr. Carl Robinson of the Animal Health Trust, and Dr. Duncan Maskell of the Centre for Veterinary Science, Dept. of Clinical Veterinary Medicine, The University of Cambridge.

Published Genome Data

S. equi

The fully annotated genome of S. equi strain 4047 is available from the EMBL/GenBank databases with accession number FM204883.

Shotgun and assembly data from this project are available from our FTP site.

S. pneumoniae

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.

S. pyogenes

The fully annotated genome of Streptococcus pyogenes strain Manfredo (M5) has been deposited in the EMBL/GenBank databases with accession number AM295007.

Shotgun and assembly data from this project are available from our ftp site.

S. suis

The sequences and annotations of the Streptococcus suis P1/7, SC84 and BM407 genomes have been deposited in the EMBL database under accession numbers AM946016, FM252031, FM252032 and FM252033 respectively.

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

S. uberis

The fully annotated genome of S. uberis strain 0140J has been deposited in the EMBL/GenBank databases with the accession number AM946015.

Shotgun and assembly data from this project are available from our FTP site.

S. zooepidemicus

The fully annotated genome has been deposited in the EMBL/GenBank databases with accession number FM204884.

Shotgun and assembly data from this project are available from our FTP site.