The Sanger Institute has a program of activities focused on Staphylococcus aureus including reference genomes, comparative genomics, deep sequencing within lineages, and also sampling populations.

Projects

• Other reference genomes: MSHR 1132 (ST75), BB155 (ST152) and LGA251 (ST425)
• Comparative genomics of EMRSA-15
• Comparative genomics of ST239
• Comparative genomics of EMRSA-16
• Comparative genomics of ST5
• Comparative genomics of ST398
• Comparative genomics of isolates from a transmission study on an ITU
• Transcriptomic studies

Collaborators (in no particular order)

Ed Feil, Bath University, UK

Sharon Peacock, Cambridge University, UK

Hermínia de Lencastre, The Rockefeller University, New York, USA

Hajo Grundmann, National Institute for Public Health and the Environment (RIVM), The Netherlands

Deborah Holt, Charles Darwin University, Australia

Philip Giffard, Charles Darwin University, Australia

Raymond Ruimy, University Paris, France

Jonathan Edgeworth, Guy's and St Thomas' Hospital, UK

Jodi Lindsay, St George's Medical School, UK

Brian Spratt, Imperial College, UK

Mark Enright, Imperial College, UK

Mark Holmes, Cambridge University, UK

Mark Achtman, University of Cork, Ireland

Simon Foster, University of Sheffield, UK

Funding

This work has been funded by the Wellcome Trust.

Published Genome Data

The Sanger Institute completed the sequencing of the genomes of six Staphylococcus aureus strains.

Published Strains

MRSA252 is a representative of the epidemic EMRSA-16 lineage endemic in UK hospitals. The strain has been typed as sequence type (ST)36 by MLST. The MRSA252 genome is composed of a single circular chromosome of 2,902,619 bp, and was sequenced in collaboration with Prof. Tim Foster of the Department of Microbiology, Trinity College, Dublin, Prof. Brian Spratt of the Department of Infectious Disease Epidemiology, Imperial College School of Medicine, Dr. Mark Enright of the Department of Biology and Biochemistry, University of Bath, and Dr. Nicholas Day and Dr. Sharon Peacock of the John Radcliffe Hospital, Oxford. The fully annotated genome is available from the EMBL/GenBank databases with accession number BX571856.

MSSA476 is methicillin-sensitive strain, and was isolated from a patient in the community who developed severe invasive disease. MSSA476 belongs to a major global lineage associated with community-acquired disease. The strain has been typed as sequence type (ST)1 by MLST. The MSSA476 genome is composed of a single circular chromosome of 2,799,802 bp, and a plasmid (pSAS) of 20,652 bp, and was sequenced in collaboration with the same collaberators as those for MRSA252. The fully annotated chromosome is available from the EMBL/GenBank databases with accession number BX571857. Similarly, the fully annotated plasmid is available with accession number BX571858.

TW20 is a representative of a highly transmissible MRSA outbreak that occurred on an intensive care unit in a large London hospital. The strain has been typed as sequence type (ST)239 by MLST. The S. aureus strain TW20 genome is composed of a single circular chromosome of 3,075,806 bp and two plasmids (pTW20_1 and pTW20_2) of 29,585 bp and 3,011 bp, and was sequenced in collaboration with with Dr. Jonathan Edgeworth, Dept. of Infection, Guy's and St Thomas' Hospital, London and Dr. Jodi Lindsay, Centre for Infection & Molecular Medicine, St George's Medical School, London. The fully annotated chromosome is available from the EMBL/GenBank databases with accession number FN433596. Similarly, the fully annotated plasmids are available with accession numbers FN433597 and FN433598.

HO 5096 0412 (EMRSA-15) is a strain endemic to UK hospitals. The EMRSA-15 genome consists of a single circular chromosome of 2,832,299 bp and a plasmid of 2473 bp. It was sequenced in collaboration with Dr. Mark Enright, Dept. of Infectious Disease Epidemiology, Imperial College, London. The fully annotated chromosome is available from the EMBL/GenBank databases with accession number HE681097. A preliminary gene prediction of the plasmid may be downloaded in Artemis format.

MSHR1132 is a northern Australian isolate belonging to the divergent clonal complex 75 lineage. The MSHR1132 genome consists of a single circular chromosome of 2,762,785 bp and a plasmid of 24,853 bp. It was sequenced in collaboration with Dr. Ed Feil, Department of Biology and Biochemistry, University of Bath and Dr. Phil Giffard and Dr. Bart Currie of Menzies School of Health Research, Charles Darwin University, Darwin, Northern Territory, Australia. The fully annotated chromosome is available from the EMBL/GenBank databases with accession number FR821777. Similarly the fully annotated plasmid is available with accession number FR821778.

Strain LGA251 has a genome consisting of a single circular chromosome of 2,750,834 bp and a plasmid of 2993 bp. It was sequenced in collaboration with Dr Laura Garcia-Alvarez, Dr Cerian Webb, Dr Mark Holmes and Prof. Duncan Maskell from the Department of Veterinary Medicine, University of Cambridge. ftp site. The fully annotated chromosome is available from the EMBL/GenBank databases with accession number FR821779. Similarly the fully annotated plasmid is available with accession number FR821780.