Paradigms of pathogenesis: targeting the mobile genetic elements of disease.

A century ago, Gertrude Stein told us that a rose is a rose is a rose, but today, modern genomics is telling us that a pathogen is not a pathogen. Advances in pathogenomics have greatly elucidated the genetic and molecular underpinnings of bacterial virulence and pathogenesis. This new knowledge of the evolution of pathogenic bacteria, and of the ways by which they acquire and maintain virulence, has increasingly indicated that not all bacterial pathogens are created equal. Evolutionarily speaking, there seem to be at least two broad categories of pathogenic bacteria: obligate pathogens that have evolved over time to become irreversibly specialized parasites and “Jekylland-Hyde pathogens,” still closely related to free-living bacteria, that have been rapidly but reversibly made pathogenic by mobile genetic elements. This distinction between full-scale genetic re-wiring and subtle genetic fine-tuning represents a fundamental contrast that may shed light on the past, present, and future evolution of pathogenic bacteria. More importantly, we might be able to use this knowledge of the paradigms of pathogenesis to develop novel strategies for combating some of today’s most significant bacterial pathogens. With the tremendous amount of information that has been generated by the genomics revolution, it is not surprising that new paradigms for the evolution of bacterial pathogens have emerged. One such paradigm is that bacteria can be pathogenic not because they possess defined “virulence factors” but because they have deleted genes detrimental to a pathogenic lifestyle (Maurelli et al., 1998) and/or have lost metabolic and regulatory genes required for a free-living state (Georgiades and Raoult, 2011). This principle of reductive evolution, which posits that certain bacteria gain virulence via massive gene deletion associated with increased specialization, has been most extensively documented amongst obligate intracellular pathogens and seems to represent a dominant evolutionary phenomenon of particularly specialized bacteria (Merhej et al., 2009). Nevertheless, massive gene loss is only a part of a larger picture for many other pathogenic bacteria. In fact, certain bacterial pathogens can be readily distinguished from nonpathogenic, free-living kin not by massive gene deletion but by specific virulence factors. Since non-pathogenic bacteria can chromosomally encode certain structural virulence factors previously considered unique to pathogens, such as type III and type VI secretion systems (Pallen and Wren, 2007), it is important to emphasize that the pathogenicity of these Jekylland-Hyde bacteria is largely mediated by mobile genetic elements such as bacteriophages and plasmids. The most prominent examples of these Jekyll-and-Hyde bacteria are those whose virulence factors, typically exotoxins and/or extracellular enzymes, are encoded by temperate bacteriophages. Free-living or commensal bacteria that pose little threat to human health can be rapidly transformed by lysogenic conversion into aggressively virulent pathogens. For example, uninfected strains of Clostridium botulinum, Corynebacterium diphtheriae, Escherichia coli, Staphylococcus aureus, Streptococcus pyogenes, and Vibrio cholerae are not usually dangerous, but those lysogens that acquire just a few exogenous genes from one or several virulence factor-encoding bacteriophage(s) can become highly virulent (Brussow et al., 2004). In this light, one could even make the case that the cholera toxinencoding bacteriophage CTXφ, not the bacterium V. cholerae, is the true causative agent of the disease we know as cholera. Similarly, a comparative genomic analysis of three taxonomic species within the genus Bacillus—B. anthracis, B. cereus, and B. thuringiensis—suggests that these three bacteria with vastly different ecological niches (acute pathogen, ubiquitous soil dweller, and insect commensal, respectively) are genetically a single species (Helgason et al., 2000). The genomes of these three bacteria are of similar sizes, and massive gene deletion does not explain B. anthracis’s extreme virulence compared to its kin; instead, its pathogenicity is largely a product of certain virulence factors encoded by two plasmids, without which anthrax is not fully virulent (Helgason et al., 2000). In all of these cases, the presence or absence of one or more virulence factor-encoding prophages and/or plasmids strongly influences their carriers’ virulence and pathogenicity. Of course, not all pathogenic bacteria can be neatly categorized into two camps: some pathogens, like Shigella spp., differ from their free-living kin both by gene deletion and by extrachromosomal virulence factors (Johnson, 2000). Indeed, these two paradigms of pathogenesis— gene deletion and the acquisition of mobile genetic elements—are not necessarily mutually exclusive because they operate over different scales of evolutionary time. In contrast to the classical evolution of bacteria, which occurs over many thousands and millions of years, horizontal gene transfer represents the fast mode of evolution, one by which prokaryotes can acquire new genes conferring unique traits, including virulence, in a very short time (Brussow et al., 2004). There are also undoubtedly other dynamics, such as epigenetics, that play important roles in the evolution and maintenance of virulence (Casadesus and Low, 2006). Nevertheless, it is important to recognize that the pathogenic bacteria confronting