Staphylococcus is a genus of Gram positive bacteria including at least 40 species. These include:
- Staphylococcus aureus is an important nosocomial and community-acquired pathogen. S. aureus is the most common cause of hospital acquired infection, causing clinical disease in 2% of all patient admissions in the UK. Not only does it cause enormous numbers of infections, but S. aureus in hospitals are becoming increasingly resistant to antibiotics. In several industrialised nations including parts of Europe, the US and Japan, 40-60% of all hospital S. aureus are now resistant to methicillin (methicillin-resistant Staphylococcus aureus, MRSA).
- Staphylococcus lugdunensis is a commensal of man and can cause serious invasive infections. This bacterium accounts for 5-10% of cases of invasive endocarditis
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.
- Comparative genomics of EMRSA-15, EMRSA-16, ST239, ST5, ST398
- Comparative genomics of isolates from a transmission study on an ITU
- Other reference genomes: MSHR 1132 (ST75), BB155 (ST152) and LGA251 (ST425)
- Genomics of BSAC resistance surveillance project - see bsacsurv.org for details and availability
- 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
Rosy Reynolds, British Society for Antimicrobial Chemotherapy
This work has been funded by the Wellcome Trust.
We are sequencing the genome of a Staphylococcus lugdenensis strain N920143, a breast abscess isolate, in collaboration with Tim Foster, Trinity College, Ireland.
Published Genome Data
The Sanger Institute completed the sequencing of the genomes of six Staphylococcus aureus 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.
- Evolution of MRSA During Hospital Transmission and Intercontinental Spread
- Discovery of sequence diversity in Staphylococcus aureus ST22 and ST36
- Genetic diversity in Staphylococcus aureus (European collection)
- Determination of the genome sequence of Staphylococcus lugdunensis strain 1003
- Discovery of sequence diversity in Staphylococcus aureus ST22 (global collection)
- Discovery of sequence diversity in Staphylococcus aureus ST398
- Staphylococcus aureus ST239 diversity
- Staphylococcus aureus ST239 diversity (Turkey)
- Major lineages of healthcare-associated methicillin-resistant Staphylococcus aureus in Singapore
- Staphylococcus aureus (MRSA) transmission in a London hospital
- Evolution of MRSA in a single institution over a 12 year period
- Diversity of MRSA
- Diversity of MRSA II
- MRSA sequencing test
- Staphylococcus aureus (MSSA) study
- Staphylococcus aureus (BSAC) study
- Genomic characterisation of early UK MRSA isolates
- Generation of draft genomes for supershedder and bacteriotherapy bacteria
- MRSA library sequencing
- Staphylococcus aureus (USFL) study
- Staphylococcus aureus (EOE) study
- Staphylococcus aureus (CSARH & CSASH) study
- Clostridium difficile 078 diversity
- Population structure of a very early branching Staphylococcus aureus lineage
- Virulent Australian Staphylococcus aureus ST93; population structure, transmission dynamics and clinical correlates
- Staphylococcus aureus (MPROS) study
- Staphylococcus aureus lineages from the Indian subcontinent: emergence and global transmission
- Antimicrobial resistance modifiers studied by TraDIS
- Staphylococcus aureus (MRSA) hospital samples
- Staphylococcus aureus global survey
- Staphylococcus aureus ST239 diversity in Thailand
- Veterinary hospital MRSA infection study
- Staphylococcus aureus genome sequencing study
- TraDIS to study novel antibiotic targets
- Staphylococcus aureus (erythromycin resistant strains) study
- Whole genome sequencing of 1200 bacterial strains isolated from healthy faecal transplant donors and recurrent C. difficile patients
- Staphylococcus aureus (MRSA) study
- Staphylococcus aureus (National Collection) sequencing
- TraDIS method optimisation and validation
- NCTC 3000
- Staphylococcus aureus samples from PHE collection
- Staphylococcus aureus small colony variants sequencing study
- Sequencing bacterial genomes
- Sequencing MRSA samples (HICF)
- Genomic characterization of bladder bacteria from healthy and infected women
- Transcriptomic analysis of investigation of the Type VII protein secretion system in Staphylococcus aureus
- Bloodstream surveillence across Africas
- Lung Culturomics
- Multi-drug resistant organisms in acute hospitals and intermediate and long term care facilities
- Sequencing Staphylococcus aureus samples from Thailand (HICF)
- Application of whole genome sequencing to investigate Staphylococcus aureus outbreaks in Ghana
- Sequencing Staphylococcus aureus samples (UKCRC)
- Sequencing a modified Staphylococcus aureus strain
- Staphylococcal Reference Laboratories (SRL) - S. aureus Structured Surveys
- Scottish Healthcare Associated Infection Prevention Institute (SHAIPI)
- ‘Silent’ antibiotic resistance genes: an overlooked issue of considerable importance in antibacterial chemotherapy?
- Human Gastrointestinal Microbiota Diversity
- Composition of the human micobiome in granulomatosis with polyangiitis: A pilot study
- Kenyan MRSA seq
- Commensal bacterial genomes from health and disease