1. History of the Staphylococcus aureus

Richard A. Proctor

The history of Staphylococcus aureus and the history of bacterial infectious diseases parallel one another. S. aureus was one of the first pathogens described, which is not surprising as it was and is still one of the most common and feared infections in humans. This chapter traces the history of S. aureus from 1880 to the present.

2. Clinical Significance in Humans

Mathias Herrmann and Mark S. Smeltzer

This chapter is intended to provide a broad overview of the staphylococci as a cause of human infections. Several key points must be made in this regard beginning with the observation that all staphylococcal species are generally adapted to live on humans and/or other animal species as commensals. However, all also exhibit some capacity to cause infection, and therefore can all be considered opportunistic pathogens. Nevertheless, the single most prominent pathogen in the context of human infections is Staphylococcus aureus, which has the capacity to cause a remarkably diverse array of infections ranging from superficial skin and soft tissue abscesses to life-threatening infections including bacteremia, endocarditis, and osteomyelitis. The prominence of S. aureus as a human pathogen is clearly linked to two factors, the first being that it is a commensal inhabitant of 30-50% of the population and is therefore available to cause disease when given the opportunity, and the second being its ability to produce a diverse array of virulence factors when called upon under selective pressure from the host to do so. The staphylococci are also highly adaptable at a genetic and phenotypic level, a primary manifestation of the first being the recent emergence of methicillin-resistant strains even among isolates associated with community-acquired infections, and a primary manifestation of the second being that these isolates exhibit phenotype characteristics that threaten the definition of S. aureus as an opportunistic pathogen. This brings up the additional key point that the epidemiology and pathogenesis of S. aureus infections has changed significantly in recent years. This is reflected in reports that now distinguish between classic healthcare-associated strains and those associated with community-acquired infections, with resistance to methicillin and its derivatives (e.g. oxacillin) being a common and troubling characteristic of both groups. However, the goal here is not to detail this diversity but rather to provide a broad overview of the staphylococci, with a specific emphasis on S. aureus, as both a commensal inhabitant of humans and as a human pathogen.

3. Staphylococcus: Clinical Significance in Animals

John Dustin Loy

The staphylococci are important pathogens of a many animal species including domestic and wild mammals and birds. Many of the animal associated staphylococci have undergone extensive host adaptation to animals and specific body sites. Like human infections, infections in animals with staphylococci frequent the skin and mucous membranes and given the opportunity can cause severe invasive disease and septicemia. They also possess numerous virulence factors and mechanisms that enable a diverse number of clinical manifestations and disease syndromes in host species. The introduction of molecular phylogenetics into veterinary clinical microbiology has found diversity among what were thought to only be a handful of clinically important species, and significant taxonomic changes have occurred. Like human medicine, challenges are also being faced by veterinary clinicians as methicillin resistance is emerging in animal infections. This chapter describes the role of staphylococci in animal disease, important virulence factors associated with animal disease, treatment of significant veterinary infections, as well as antimicrobial resistance in staphylococci associated with animals

4. Staphylococcal Variation and Evolution

Jodi A. Lindsay

A staphylococcal genome carries all of the information responsible for behaviour of that cell. The genome sequence of each staphylococcal isolate can vary substantially from other isolates, even those that cause similar disease. And S. aureus populations as a whole are not stagnant, but constantly evolving. The population structure of S. aureus groups isolates into independent lineages, each with unique combinations of surface, regulatory and immune evasion genes. Individual isolates also acquire and lose mobile genetic elements (MGEs) encoding virulence, resistance and host-adaptation factors. Transfer of DNA within populations is controlled by molecular machinery that partially dictates how the species evolves. Selection, such as by antimicrobials or host-specificity, leads to the emergence and spread of successful clones in particular environments. Other staphylococcal species also show evidence of lineages and MGEs that shape populations. Improving technology for sequencing and comparing genomes is allowing analysis of thousands of isolates and will ensure this is a rapidly growing area of research. Investigation of the diversity and selection of staphylococcal genomic variation leads to greater understanding of physiology, host-pathogen interactions, epidemiology and the development of better therapeutic and public health strategies.

5. Staphylococcal Virulence Factors

Patrick M. Schlievert

Staphylococcus aureus is a multi-dimensional pathogen that colonizes and infects only animals, including humans, with immune systems. The organism causes large numbers of infections worldwide, both relatively benign and highly serious, through its production of colonization factors and three tiers of virulence factors which interfere with immune function. Secreted superantigens and exfoliative toxins systemically interfere with immune function through dysregulation of cells and opening immune barriers, respectively. Secreted cytotoxins kill immune cells influxing into local areas of infection. At the same time, some microbial colonization factors sequester the organism in walled off sites, the hallmark of S. aureus infections, and in biofilms. Finally, if the immune system somehow bypasses these first two tiers of microbial resistance, S. aureus has capsules, other polysaccharides, and pigment as last lines of defense. This review discusses these virulence factors from the presumed staphylococcal point of view.

6. Staphylococcus aureus Metabolism and Physiology

Greg A. Somerville

All living organisms require endogenous and/or exogenous sources of biosynthetic precursors (e.g., nucleic acids, amino acids, carbohydrates, etc.) for polymerizing and assembly reactions that make DNA, RNA, proteins, and everything else required for life. In Staphylococcus aureus, the de novo synthesis of biosynthetic precursors requires thirteen biosynthetic intermediates (e.g., glucose-6-phosphate and oxaloacetate) and the coordinated action of numerous enzymes. The life-cycle of S. aureus is such that its environment is in a near constant state of flux. This flux has important implications because enzyme activity is altered in response to co-factor, substrate, and product availability, pH, temperature, post-translational modifications, and many other environmental and nutritional factors. In other words, changes in the environment precipitate changes in enzymatic activity, which alters the availability of biosynthetic precursors and the ability to synthesize cellular components. Understanding how environmental changes alter metabolism, begins with an understanding of metabolism.

7. Physiological Proteomics of Staphylococcus aureus: From the Protein Inventory to Stress Physiology and In Vivo adaptation

Susanne Engelmann, Stephan Fuchs and Michael Hecker

Here we present the different facets of proteomics turning it into a valuable tool for a more comprehensive understanding of metabolism and stress and starvation responses of Staphylococcus aureus. Relying on a combination of gel-based and gel-free proteomics procedures, new fields in staphylococci physiology such as phosphoproteomics, protein damage or proteolysis on a proteome wide scale are addressed. Finally, we show that stress/starvation proteomics signature libraries are essential diagnostic tools for the analysis of the physiological state of S. aureus cells under both in vitro and in vivo conditions.

8. Cell Wall Assembly and Physiology

Angelika Gründling

Staphylococcus aureus has a typical Gram-positive cell wall, which is composed of a thick peptidoglycan layer, cell surface proteins, teichoic acids and carbohydrate polymers. The functions of these different cell wall components are diverse: the peptidoglycan layer protects bacteria from osmotic lysis, cell surface proteins are required for adhesion, biofilm formation and immune evasion, and teichoic acids help to protect bacteria from the action of cationic antimicrobial peptides. Proper assembly of the different cell wall structures is not only essential for the pathogenesis of S. aureus but also for bacterial growth, and several antimicrobial agents target the synthesis of key cell wall components. In this chapter, the synthesis pathways and functions of the diverse cell wall components of S. aureus will be summarized, along with the action of important cell wall targeting antibiotics and the respective bacterial resistance mechanisms.

9. Transition Metal Ion Homeostasis

Jessica R. Sheldon, Ronald S. Flannagan, Mélissa Hannauer and David E. Heinrichs

The six 3D-block transition metals - iron, manganese, zinc, nickel, cobalt, and copper are biologically relevant to both prokaryotes and eukaryotes alike, serving as essential micronutrients while at the same time being potentially toxic in excess. As such, intricate mechanisms exist to control the availability of metal ions within the human host and in bacteria, in an effort to maintain homeostatic concentrations of these elements. Perturbations to metal ion availability within the host can impact both overall health, as well as susceptibility to infectious diseases, as bacteria, such as the staphylococci, express a plethora of acquisition systems that allow for the extraction of transition metals from the environment to fulfill their nutritional requirements. The host counters this effort to acquire metals with immune mechanisms that not only actively sequester transition metals, rendering them unavailable to support microbial growth, but also that harness the destructive redox potential of copper and zinc to intoxicate invading bacteria; these processes are collectively termed nutritional immunity. Importantly, exploitation of metal acquisition pathways in the staphylococci may represent a viable option for the realization of novel antimicrobials or vaccine based therapies that are desperately needed to combat important human staphylococcal pathogens such as S. aureus.

10. Stress Responses in Staphylococcus aureus

Dorte Frees and Hanne Ingmer

Staphylococcus aures are prominent members of the normal flora of humans and animals, but are also a major cause of mild and severe infections. To persist and disseminate in the human host, and to survive in environmental settings, such as hospitals, S. aureus have developed a plethora of cellular stress responses allowing it to sense and adapt to its very different niches. The stress responses often involve dramatic cellular reprogramming, and the technological advances provided by the access to whole genome sequences have let to an unprecedented insight into the global reorganization of gene and protein expression following stress-exposure. Characterization of global gene responses has been very helpful both in identifying regulators sensing specific environmental stress signals and overlaps between different stress responses. In this chapter we review the recent progress in our understanding of the specific and general S. aureus stress responses, with a special emphasis on how stress responses contribute to virulence and antibiotic resistance in this important human pathogen.

11. Molecular Strategies of Staphylococcus aureus for Resisting Antibiotics

Susan Boyle-Vavra and Robert S Daum

Since there is no vaccine to prevent Staphylococcus aureus infection, clinicians must heavily rely on antibiotics to treat S. aureus infections. However, S. aureus has been able to elude every antibiotic that has been widely introduced into clinical practice. This Chapter summarizes some of the most important antibiotics that have been used in the therapy of S. aureus infection since the golden age of antibiotic discovery, starting with the introduction of penicillin in 1940s and methicillin in the 1960s. The emphasis of the chapter is placed on the variety of resistance mechanisms that S. aureus has evolved to elude antibiotics and the mobile genetic elements that allow horizontal transfer of resistance genes between strains and between species. S. aureus strains have become resistant to antibiotics by a wide variety of mechanisms. At the genetic level, resistance has occurred through acquiring point mutations in the chromosomal gene or genes encoding the antibiotic target or by horizontal gene exchange resulting in the acquisition of new genes that confer resistance. Examples of antibiotic resistance strategies that have evolved in S. aureus include: a) acquisition of spontaneous point mutations in the native target that decreases the binding of the antibiotic, b) acquisition of a gene encoding an enzyme that inactivates the antibiotic, c) acquisition of an antibiotic-insensitive target that can bypass the antibiotic's effect by replacing the function of the native target, d) acquisition of an enzyme that modifies the target thereby blocking access of the antibiotic to the target, e) expressing a protein or proteins that transport(s) a drug out of the cytoplasm (for instance via an efflux pump), thereby reducing its cytoplasmic concentration, f) acquiring mutations that alter the bacterial surface properties that, for instance, decrease the interaction of the antibiotic with the bacteria, g) ribosomal protection without target modification. Antibiotic strategies that target an essential process in bacteria place strong selective pressure that ultimately results in resistance. Strategies that potentiate reliable antibiotics or that delay resistance development could increase the lifespan and usefulness of old and new antimicrobial agents. Also, by better understanding how bacteria cause disease and death, it will be possible to design treatment strategies that ameliorate the toxic effects of the bacteria on the host rather than by directly killing the bacteria.

12. Genetic Regulation

Markus Bischoff and Pascale Romby

The ability of Stapylococcus aureus to accurately respond to changing environments is one of the prerequisites for its success as a versatile human pathogen. This bacterium is equipped with an armamentarium of virulence factors that facilitate adaptation to nearly all ecological niches within a host. In addition, this armamentarium allows S. aureus to counteract most of the immune response mechanisms used by the host to combat the invading pathogen. Regulation of this armamentarium is carried out by at least 112 transcription factors than can be divided into 36 regulatory families. The largest families of transcription factors found in S. aureus are one-component systems such as MarR-type, GntR/DeoR-type, and Xre-type of regulators, and two-component system response regulators. Alternative sigma factors, the third most common class of proteins involved in bacterial signal transduction, are underrepresented in S. aureus. Notably, less than half of S. aureus transcription factors have been functionally characterized, suggesting that our understanding of the regulatory network utilized by this pathogen to adapt to a changing environment is incomplete.

13. Immune Response to Staphylococcus aureus

Aisling F. Brown and Rachel M. McLoughlin

Staphylococcus aureus can act as either a harmless commensal or a potentially lethal pathogen. Disease is just one of a number of possible outcomes of host-microbe interactions. It is the interplay between both host and microbial factors that determines whether or not disease occurs and its severity. Here, we outline the main functions and elements of the host immune system and consider how they interact with S. aureus to shape clinical outcomes. We further discuss how the organism seeks to evade host immune mechanisms and review the immunodeficiency states that render certain hosts susceptible to S. aureus infection. Finally, we review the status of anti-S. aureus vaccine development and examine how we might modulate the immune response in order to improve the outcome of infection.