Staphylococcus aureus: superbug, super genome?

doi:10.1016/j.tim.2004.06.004

Trends in Microbiology

Volume 12, Issue 8, 1 August 2004, Pages 378-385

https://doi.org/10.1016/j.tim.2004.06.004 Get rights and content

Abstract

Staphylococcus aureus is a common cause of infection in both hospitals and the community, and it is becoming increasingly virulent and resistant to antibiotics. The recent sequencing of seven strains of S. aureus provides unprecedented information about its genome diversity. Subtle differences in core (stable) regions of the genome have been exploited by multi-locus sequence typing (MLST) to understand S. aureus population structure. Dramatic differences in the carriage and spread of accessory genes, including those involved in virulence and resistance, contribute to the emergence of new strains with healthcare implications. Understanding the differences between S. aureus genomes and the controls that govern these changes is helping to improve our knowledge of S. aureus pathogenicity and to predict the evolution of super-superbugs.

Section snippets

S. aureus comparative genomics

Pairwise comparisons of S. aureus chromosomes reveals that they are colinear to each other and that they consist of a stable component that contains genes present in all of the stains and also a variable component that encompasses genes found in some of the strains (Figure 1). Preliminary investigation of the genetic diversity of S. aureus strains by DNA microarray analysis suggests that ∼22% of S. aureus genomes are composed of variable regions [16]. It was further identified that much of the

Core genome

The five S. aureus genomes range in size from 2.820 Mb to 2.903 Mb and are predicted to contain between 2592 and 2748 protein coding sequences. In silico analysis suggests that the core genome makes up ∼75% of any S. aureus genome and is highly conserved between isolates (Figure 1). Gene order is also conserved and the similarity of individual genes between the five isolates is typically 98–100% at the amino acid level. As would be expected, the majority of genes comprising the core genome are

Accessory genome

The accessory genome accounts for ∼25% of any S. aureus genome, and mostly consists of mobile (or once mobile) genetic elements that transfer horizontally between strains. These elements include bacteriophages, pathogenicity islands, chromosomal cassettes, genomic islands, plasmids and transposons (Figure 1; Table 3). Preliminary evidence suggests that some of these elements move between isolates at high frequency, whereas others move infrequently, if at all.

Many of these genetic elements carry

S. aureus pathogenicity islands (SaPI)

SaPI often carry superantigen genes, such as toxic shock syndrome toxin (tst) and enterotoxins B and C, implicated in toxic shock and food poisoning. Seven SaPIs in human isolates (SaPIn1 [13], SaPIm1 [13], SaGIm [13], νSa3(MW2) [14], SaPI1 [30], SaPI3 [31] and SaPI4 [15]) and two in bovine isolates (SaPIbov [32] and SaPIbov2 [33]) have now been sequenced. Again, we can classify the human SaPIs into four groups on the basis of integrase homology and insertion site, and it is notable that no

Concluding remarks

The sequencing projects provide an enormous wealth of data, therefore, outlining all the benefits derived from them would be a huge task. In terms of understanding pathogenicity, they provide a finite list of putative virulence genes that can be exploited in laboratory studies, bioinformatic analyses and population studies. Through comparative genomics we are developing a better understanding of the ability of this organism to evolve and adapt. The emerging picture of the genome is one of a

Acknowledgements

We would like to thank Ed Feil for his useful comments and for providing permission for the use of Figure 2.

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Trends in Microbiology

Staphylococcus aureus: superbug, super genome?

Abstract

Section snippets

S. aureus comparative genomics

Core genome

Accessory genome

S. aureus pathogenicity islands (SaPI)

Concluding remarks

Acknowledgements

Curr. Opin. Microbiol.

Trends Microbiol.

Lancet

Lancet

Lancet

Trends Microbiol.

Gene

Gene

Gene

J. Biol. Chem.

Trends Microbiol.

FEMS Microbiol. Lett.

Frequency of isolation and antimicrobial resistance of Gram-negative and Gram-positive bacteria from patients in intensive care units of 25 European university hospitals participating in the European arm of the SENTRY Antimicrobial Surveillance Program 1997-1998

Eur. J. Clin. Microbiol. Infect. Dis.

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J. Antimicrob. Chemother.

Staphylococcus aureus resistant to vancomycin - United States, 2002

MMWR Morb. Mortal. Wkly. Rep.

Infection with vancomycin-resistant Staphylococcus aureus containing the vanA resistance gene

N. Engl. J. Med.

Vancomycin resistant Staphylococcus aureus—New York, 2004

MMWR Morb. Mortal. Wkly. Rep.

Dominance of EMRSA-15 and-16 among MRSA causing nosocomial bacteraemia in the UK: analysis of isolates from the European Antimicrobial Resistance Surveillance System (EARSS)

J. Antimicrob. Chemother.

Community-acquired methicillin-resistant Staphylococcus aureus in children with no identified predisposing risk

J. Am. Med. Assoc.

Community-acquired methicillin-resistant Staphylococcus aureus infections in France: Emergence of a single clone that produces Panton-Valentine leukocidin

Clin. Infect. Dis.

Evolutionary genomics of Staphylococcus aureus: Insights into the origin of methicillin-resistant strains and the toxic shock syndrome epidemic

Proc. Natl. Acad. Sci. U. S. A.

How clonal is Staphylococcus aureus?

J. Bacteriol.

The evolutionary history of methicillin-resistant Staphylococcus aureus (MRSA)

Proc. Natl. Acad. Sci. U. S. A.

Genetic variation among hospital isolates of methicillin-sensitive Staphylococcus aureus: Evidence for horizontal transfer of virulence genes

J. Clin. Microbiol.