Virulence Mechanisms of Bacterial Pathogens, Fifth Edition

Why do organisms “eat”? This core question drives the study of biochemistry—specifically metabolism. The short answer to this seemingly simple question is 2-fold: first, eating provides cells with the physical building blocks for the generation of cellular components (i.e., growth of the physical cell; something must come from something); second, eating is the way to extract energy to do cellular work (i.e., powering the process of growth; work is never done for free). These two processes—catabolism and anabolism—are inextricably linked. The pathways of catabolism, such as glycolysis and the tricarboxylic acid (TCA) cycle, which break down molecules for energy metabolism, also branch off into anabolic pathways that generate building blocks for the cell. Bacterial metabolism is dynamic and flexible, with different bacterial species encoding different metabolic capacities within their genomes. Thus, the canonical TCA cycle may function fully in one bacterial species, while another bacterium, missing a key enzyme of the cycle now uses the other TCA enzymes in branched oxidative and reductive pathways. Moreover, depending on the availability of carbon sources or oxygen, even if a bacterium encodes all of the enzymes for respiration, with its high-energy yield, the less energy-efficient but faster process of fermentation may predominate. Thus, the flexible metabolic space of rapidly evolving bacterial genomes enables many different ways for bacteria to take advantage of nutrients in complex environments for robust replication.

Iron is essential to nearly all life forms on Earth, required for the proper function of enzymes involved in, for example, respiration, photosynthesis, the tricarboxylic acid cycle, nitrogen fixation, electron transport, and amino acid synthesis. The utility of iron in biological processes hinges on its chemical properties as a transition metal, engaging in single electron transfers to interconvert between the ferrous (Fe2+) and ferric (Fe3+) states. While this clearly makes iron advantageous, the same property provides the explanation for why excess, or “free,” iron is inherently toxic. Ferrous iron–catalyzed Fenton chemistry results in the generation of the highly toxic hydroxyl radical (OH•) that can compromise cellular integrity through damage to lipids, proteins, and nucleic acids.

Microbiology has gathered much attention in recent years in part thanks to major scientific advancements in the microbiome field. Large-scale projects such as the NIH-funded Human Microbiome Project ( 1 – 3 ) provide extensive catalogues of the microbes that live in and on the human body. Statements like “the human body is home to bacteria that outnumber human cells by more than 10:1” or “the genetic content of these bacteria can be 100x that of the human genome” are often used by mainstream media and are known to the general public. Vast explorations of the human and nonhuman microbiomes are to a large extent boosted by recent breakthroughs in DNA sequencing and community metagenomics ( 4 – 6 ), and the many studies that have emerged reveal an expanding role of multispecies host-associated microbial communities in several host functions ( 7 , 8 ). Arguably, one of the most notable functions of commensal microbiota, i.e., nonpathogenic microbes, is protecting the host from colonization by other microbes ( 9 ). This is an exciting area of research that aims to address open questions in pathogenesis such as why individuals exposed to the same pathogen can differ in their levels of infection. It can also explain why patients can have increased risk of infections after antibiotic therapy destroys the commensal microbiota that would naturally protect against pathogen invasion.

Candida species are the most common commensal fungus that coexists with hundreds of species of bacteria in the human body. Between 24 and 70% of humans harbor Candida species in various body niches, including the oral and vaginal mucosa and the skin ( 1 ). Out of over 150 Candida species, Candida albicans is the principal pathogenic species that causes infections, especially in patient populations with immune dysfunction due to HIV infection, malignancy, immunosuppressive therapy, and organ transplantation. Therefore, these opportunistic infections of Candida in topical or systemic forms have become widespread and account for 8 to 10% of bloodstream infections in hospitals ( 2 ). Nearly 70% of denture wearers experience denture stomatitis, or inflammation of oral mucosa covered by denture prostheses, with C. albicans being a primary etiological factor ( 3 , 4 ). Almost 75% of the female population has experienced an episode of vulvovaginal candidiasis at least once in their lifetime, and many have recurring episodes ( 5 ). In many of these conditions, there is a phenotypic change for Candida from harmless commensal to invasive pathogen. Adhesion to various surfaces, morphogenesis, phenotypic and genotypic switching, and production of lytic enzymes are major virulence mechanisms facilitating this conversion ( 6 ). However, properties of the host are also commiserate in enabling Candida to act as an invasive pathogen since compromise in the interleukin-17 (IL-17)/Th17 arm of the host immune response (e.g., AIDS, Job’s syndrome, etc.) or an imbalance in the host microbiome ( 7 ) both can contribute to candidiasis ( 7 ). During this shift, commensal or transient organisms living with Candida species in various locations may play diverse roles in the process of pathogenesis; environmental bacteria may also be introduced via catheters, cannulae, and prosthetic appliances and interact with the already present Candida. Such interactions may be detrimental to the health of the human host, leading to mortality.

Microbial endocrinology represents the intersection of two seemingly disparate fields: microbiology and neurobiology ( Fig 1 ). The field of microbial endocrinology was founded in 1993 when the term was first coined by Lyte ( 1 , 2 ) based on experimental data obtained the prior year ( 3 , 4 ). Although the concept of microbial endocrinology was founded just over 2 decades ago ( 1 , 3 – 5 ), there has been published evidence by numerous investigators over the preceding 6 decades going back to 1930 ( 6 ), that demonstrate the validity of uniting the fields of microbiology and neurobiology as a conceptual framework with which to understand interactions between the microbiota and the host in the pathogenesis of infectious disease. It should be appreciated, however, that approaching microbiology through an interdisciplinary “lens” such as microbial endocrinology has relevance outside of the field of infectious disease. As will be discussed in this article, the ability of microorganisms to not only respond to, but also produce the very same neurochemicals that are more typically thought in the context of mammalian systems, means that host interactions with microorganisms are much more interactive than previously envisioned. This is the basis of microbial endocrinology ( 1 , 2 , 7 – 9 ). As such, microbial endocrinology has found applications outside of infectious disease (where it has its developmental roots) including other aspects of host health such as the ability of the gut microbiota to influence the brain and behavior through the microbiota-gut-brain axis ( 10 – 12 ). This review will address how and why the fields of microbiology and neurobiology should intersect and what the relevance of this interaction is for infectious disease.

Many pathogenic bacteria transit between free-living lifestyles and the markedly different environments presented by their hosts. This requires detection, integration, and response to different external and intracellular conditions and subsequent realignment of physiology and metabolism, as well as virulence factor expression via coordinated gene expression changes. Signals detected by pathogens include not only changes in temperature, pH, or nutrient availability, but also cues from the host and neighboring bacteria. How virulence genes are regulated at the transcriptional level has been studied extensively, and the regulons of several master regulators of virulence and survival gene transcription have been described in detail ( 1 , 2 ). This has provided insight into both general regulatory mechanisms used by bacteria, and the lifestyles of pathogenic species.

One essential prokaryotic cell function is the transport of proteins from the cytoplasm into other compartments of the cell, the environment, and/or other bacteria or eukaryotic cells—a process known as protein secretion. Prokaryotes have developed numerous ways of transporting protein cargo between locations, which largely involve the assistance of dedicated protein secretion systems. Protein secretion systems are essential for the growth of bacteria and are used in an array of processes. Some secretion systems are found in almost all bacteria and secrete a wide variety of substrates, while others have been identified in only a small number of bacterial species or are dedicated to secreting only one or a few proteins. In certain cases, these dedicated secretion systems are used by bacterial pathogens to manipulate the host and establish a replicative niche. Other times, they are required to take advantage of an environmental niche, perhaps by secreting proteins that help bacteria to compete with nearby microorganisms. There are several different classes of bacterial secretion systems, and their designs can differ based on whether their protein substrates cross a single phospholipid membrane, two membranes, or even three membranes, where two are bacterial and one is a host membrane. Due to the specificity of expression of some of these secretion systems in bacterial pathogens, antimicrobials are being developed against these systems to augment our current repertoire of antibiotics. This topic is discussed in Section VII, “Targeted Therapies”.

Type III secretion systems (T3SSs) afford Gram-negative bacteria an intimate means of altering the biology of their eukaryotic hosts—the direct delivery of effector proteins from the bacterial cytoplasm to that of the eukaryote ( 1 , 2 ). T3SSs utilize a conserved set of homologous gene products to assemble the nanosyringe “injectisomes” capable of traversing the three plasma membranes, peptidoglycan layer, and extracellular space that form a barrier to the direct delivery of proteins from bacterium to host. While the injectisome is architecturally similar across disparate Gram-negative organisms, its applications are a study in diversity: T3SSs are employed by both symbionts and pathogens; they target animals, plants, and protists; and they are used to manipulate a wide array of cellular activities and pathways.

Bacterial type IV secretion systems (T4SSs) are widely distributed among Gram-negative and Gram-positive bacteria. These systems contribute in various ways to infection processes among clinically important pathogens, including Helicobacter pylori, Brucella and Bartonella species, Bordetella pertussis, and Legionella pneumophila ( 1 – 3 ). The list of pathogens employing T4SSs to subvert host cellular pathways for establishment of a replication niche continues to expand, making these machines an important subject of study for defining critical features of disease progression and development of strategies aimed at suppressing T4SS function ( 4 ). Also of importance, studies of T4SSs and effector functions have coincidentally and appreciably augmented our understanding of basic cellular processes in the human host.

Gram-negative bacteria are surrounded by two membranes, called the outer and inner membranes. The space between these membranes, the periplasm, is spanned by a polymeric glycopeptide network, the peptidoglycan. This net has a closely defined mesh size and is attached to the outer and inner membranes by various proteins in the different Gram-negative organisms, leading to an even distance between the two membranes. Proteins that are to be transported to the outer membrane or the extracellular space thus have to cross various obstacles on their way; this process is mediated by a number of highly specialized secretion systems, mostly classified by Roman numerals from type I to type VII (see other chapters in this book for a comprehensive review of these systems). More secretion systems, or new variations of the ones previously described, are still found on a regular basis, making a comprehensive listing almost impossible. The major systems that are either well described and/or widely present in many Gram-negative species can be classified into two general architectures: those that span both membranes and the periplasm as one large secretion complex and those where the individual membranes are crossed using independent (i.e., not physically connected) secretion machineries. Type V secretion systems are part of the latter systems.

The type VI secretion system (T6SS), a Gram-negative secretion pathway ( 1 , 2 ), delivers effectors upon direct contact with a target cell ( 3 , 4 ). Death of the target cell is the primary outcome that follows the delivery of the lethal effectors, which are translocated from the attacker cell cytoplasm into the periplasm of the target cell via a T6S apparatus in a contact-dependent process ( 5 , 6 ). It is well known that bacteria release bactericidal agents such as bacteriocins and antibiotics into the extracellular environment as a means to indiscriminately eliminate bacterial competitors ( 7 ). In addition, it is now understood that many Gram-negative bacteria also use the T6SS to directly antagonize bacteria in close proximity ( 5 ). Direct antagonism of neighboring cells can provide a selective advantage for bacteria in their natural habitat in dense biofilm communities or during a multicellular lifestyle that requires direct contact and cooperation ( 8 , 9 ). As a consequence, bacteria benefit from a specific mechanism that depends on cell–cell contact to discriminate between one another and eliminate nonself bacteria, potential cheaters, or competitors from the population. In particular, lethal action of the T6 contractile puncturing device provides a specific advantage for bacteria that possess the T6SS to discriminate, recognize, and kill competitors.

Bacterial secretion systems were initially studied in the Gram-negative bacterium Escherichia coli K-12. When researchers started to explore protein secretion in different Gram-negative bacteria and especially in bacterial pathogens, it was clear that E. coli K-12 was not able to present us with a complete picture of protein secretion systems. Type II, type III, and type IV secretion systems were quickly discovered and revolutionized host-pathogen interaction studies. Gram-negative bacteria need these specialized secretion systems to transport proteins across two membranes (also called a diderm cell envelope). The presence of this complex cell envelope not only means that two membranes have to be crossed, but an additional problem is that there is no energy source at the outer membrane. This means that alternative mechanisms for protein transport need to be present, such as coupling the energy of the inner membrane to protein transport across the outer membrane or crossing the entire cell envelope in a single step. Although the discovery of different secretion systems in Gram-negative bacteria was a major breakthrough, the downside has been that secretion systems in other bacteria have been neglected. It was generally thought that secretion in other bacteria, which are generally monoderm, would completely depend on the universal Sec or Tat system. Only in recent years has this idea begun shifting, and again it started by studying pathogens, i.e., the pathogenic mycobacteria.

Bacterial pathogens are exposed to a variety of stressful conditions while spreading to and colonizing new hosts to cause infection. Gastrointestinal pathogens such as Campylobacter, Escherichia, Helicobacter, Listeria, Salmonella, and Shigella species encounter numerous stresses during host colonization and infection. During transit through the gastrointestinal tract these pathogens are exposed to physical stresses (pH and osmotic stresses) as well as noxious substances (reactive oxygen and nitrosative species). Bacteria respond to these stresses by altering their transcriptome/proteome in an adaptive manner to either overcome the stress or resist the stress long enough to transition to more favorable conditions. The following sections will present the current state of knowledge for each stress response mentioned above and how these defenses contribute to bacterial virulence.

Antimicrobial peptides (AMPs) are small (<10 kDa) soluble host defense peptides that play an important role in the mammalian innate immune response, helping to prevent infection by inhibiting pathogen growth on skin and mucosal surfaces and subsequent dissemination to normally sterile sites. These natural antibiotics are produced by many cell types including epithelial cells, leukocytes (neutrophils, macrophages, dendritic cells, and mast cells), platelets, endothelial cells, and adipocytes in response to tissue damage or infectious stimuli and are found in body fluids and secretions including saliva, urine, sweat, and breast milk. To date, more than 2,000 AMPs have been identified from a wide variety of organisms including bacteria, insects, plants, amphibians, birds, reptiles, and mammals including humans ( 1 , 2 ). Whereas prokaryotic AMPs are produced as a competitive strategy to facilitate the acquisition of nutrients and promote niche colonization ( 3 ), AMPs produced by higher organisms are generally conceived to carry out immune defense functions. In humans, the principal AMPs are hydrophobic molecules composed of ∼10 to 50 amino acid residues with a net positive charge, which exhibit varying degrees of broad-spectrum bioactivity against Gram-positive and Gram-negative bacteria, fungi, protozoan parasites, and certain enveloped viruses ( 4 , 5 ). AMPs may be expressed constitutively or induced in response to infection (e.g., proinflammatory cytokines, toll-like receptor [TLR] signaling) ( 6 ) and are commonly produced as propeptides that undergo subsequent proteolytic processing to the mature bioactive peptide ( 7 ). AMPs with central roles in host defense are active at micromolar to nanomolar concentrations and facilitate microbial killing through perturbation of the cytoplasmic membrane ( 8 ). Several important human pathogens display significant resistance to AMPs, which appears to play a key role in their potential to produce serious invasive infections.

Ross and Thompson’s 1910 report of periodic spikes of Trypanosoma gambiense parasitemia ( 1 ), made possible by the relatively large size of the parasite, which allowed quantitation using light microscopy, was seminal in understanding how pathogens persist and led to later studies defining how trypanosomes and numerous other pathogens use antigenic variation to evade host immunity and clearance. Antigenic variation is a strategy used by a broad diversity of microbial pathogens to persist within mammalian hosts, from small RNA viruses, notably the human immunodeficiency virus (HIV), to large eukaryotic parasites with multiple chromosomes, illustrated by trypanosomal and malarial parasites ( 2 , 3 ). Using a variety of genetic mechanisms to generate antigenic variants, immune evasion results in the infected host serving as a microbial reservoir for subsequent transmission. Unlike respiratory and gastrointestinal pathogens that have essentially continual opportunities for transmission, arthropod vector-borne and sexually transmitted pathogens have episodic transmission opportunities. Correspondingly, both vector-borne and sexually transmitted agents are overrepresented among antigenically variant pathogens ( 3 , 4 ).

The discovery, commercialization, and routine administration of antimicrobial compounds to treat infections revolutionized modern medicine and changed the therapeutic paradigm. Indeed, antibiotics have become one of the most important medical interventions needed for the development of complex medical approaches such as cutting-edge surgical procedures, solid organ transplantation, and management of patients with cancer, among others. Unfortunately, the marked increase in antimicrobial resistance among common bacterial pathogens is now threatening this therapeutic accomplishment, jeopardizing the successful outcomes of critically ill patients. In fact, the World Health Organization has named antibiotic resistance as one of the three most important public health threats of the 21st century ( 1 ).

Persistent bacterial infections such as brucellosis and typhoid fever are characterized by a long incubation period that leads to chronic, sometimes lifelong, debilitating disease with serious clinical manifestations ( 1 ). Therefore, chronic bacterial diseases have a significant impact on public health, due to the utilization of resources for long-term treatment of patients ( 2 ). Additionally, chronic infections affect the ability of the ill to provide for their families, resulting in a significant socioeconomic burden in affected countries ( 3 ).

The Staphylococcus genus includes a diverse group of commensals that colonize mammals on the skin or mucous membranes. Some of the best-known members of this genus, such as Staphylococcus aureus and Staphylococcus epidermidis, are also opportunistic pathogens and are responsible for a tremendous burden on the health care system ( 1 , 2 ). One of the reasons staphylococci are problematic is their well-known ability to attach to surfaces and develop into recalcitrant community structures, often referred to as “biofilms.” Generally, biofilms are defined as communities of cells encased within an exopolymeric matrix and attached to a surface, and they are recognized as being resistant to antimicrobial therapy and host defenses ( 3 ).

The Bacillus species are Gram-positive, spore-forming, facultative aerobes that are commonly found in the soil, sometimes associated with plants and nematodes. The Bacillus cereussensu lato clade of this well-studied genus contains pathogens and nonpathogens, with a complex taxonomy that in recent years has been continuously modified to reflect DNA sequence data. In addition to DNA sequence similarities and gene synteny, horizontal transfer of closely related plasmids is apparent among these ubiquitous soil bacteria ( 1 ). Member species of the B. cereussensu lato group include B. cereussensu stricto, B. anthracis, Bacillus thuringiensis, Bacillus mycoides, Bacillus pseudomycoides, Bacillus weihenstephanensis, and Bacillus cytotoxicus ( 2 – 10 ). Of these, the best-studied species are B. anthracis, B. cereussensu stricto, and B. thuringiensis. B. anthracis is the causative agent of anthrax in mammals, an often lethal disease. Human disease is generally acquired accidentally during outbreaks of anthrax in domestic livestock and wildlife, but has also been associated with bioterrorism ( 11 ). Certain strains of B. cereus can cause food poisoning in humans, while some strains of B. thuringiensis are lethal for invertebrates and are used as insecticides ( 12 , 13 ). Other species of the B. cereussensu lato group are only occasionally cited as disease-causing in mammals, but their potential virulence factors are not known.

Vibrio cholerae causes 3 to 5 million cases of cholera annually, resulting in 100,000 to 120,000 deaths ( 1 , 2 ). Infection occurs through the ingestion of contaminated water or food, primarily impacting regions that lack adequate sanitation and clean drinking water ( 3 , 4 ). The disease is characterized by watery diarrhea and rapid dehydration, which, if untreated, can lead to hypotonic shock and death within 12 hours of the first symptoms ( 3 , 4 ). Large outbreaks of the disease have occurred throughout the past two centuries, including several recent epidemics in Haiti, Vietnam, and Zimbabwe ( 5 – 7 ). Annual seasonal outbreaks also occur in many areas of the world where cholera is endemic, including countries in Asia, Africa, and the Americas, due to the ability of toxigenic V. cholerae to survive in the aquatic environment year-round ( 8 , 9 ). The timing and severity of seasonal outbreaks vary depending on a number of environmental factors, including rainfall, salinity, temperature, and plankton blooms ( 10 ).

“Lipids” is the inclusive name for a complex group of molecules composed predominantly of carbon, hydrogen, and oxygen (also nitrogen and phosphorus) that are insoluble in water but soluble in organic solvents. They are characterized as being hydrophobic or amphiphilic. Lipids include fatty acids, glycerolipids, glycerophospholipids, sphingolipids, glycolipids, sterols, polyketides, and prenol lipids. The structures of the lipids discussed in this review are shown in Fig. 1 . The functions of lipids were thought to be limited to being structural components of cell membranes and to being the main form of energy storage in cells. Aside from these important functions, lipids participate in key biological processes that include signaling, organization of the membrane, and trafficking from the membrane to the cytosol. In addition, lipid disorders are key to the pathogenesis of cardiovascular diseases and other metabolic disorders.

Bacterial pathogens that adopt an intracellular lifestyle often avoid many challenges that are faced by their extracellular counterparts. However, upon entering the host cell, they have a new set of trials with which to contend. Upon phagocytic uptake or entry by receptor-mediated endocytosis, they immediately traffic to a degradative subcellular compartment. Successful intracellular pathogens have adopted different strategies to avoid trafficking of their initial phagosome along the endocytic pathway to fusion with the lysosome, a subcellular compartment that has specifically evolved to degrade them. In this chapter, we will compare the different molecular mechanisms employed by four intracellular pathogens that have adopted distinct vacuolar niches and lifestyles. Many vacuolar pathogens alter their initial phagosomal compartment to stall or exit the endocytic pathway and thereby avoid elimination. Yet a few species require at least some interaction with lysosomes for completion of their infectious cycle. In this chapter, we will compare the strategies employed by Mycobacterium and Chlamydia to avoid lysosomal fusion with those of Brucella, whose vacuole interacts with lysosomes transiently, and Coxiella, a bacterium adapted to growth in a compartment that closely resembles a terminal phagolysosome.

Of the 56 million deaths reported worldwide in 2012, approximately 15 million are directly related to infectious diseases ( 1 ). The majority of annual deaths are related to bacterial infections such as tuberculosis, yellow and typhoid fever, cholera, shigellosis, pneumonia, etc. ( 1 ). Morbidity and mortality rates are highest in developing countries, where large numbers of infants and children count among the victims ( 2 ). In developed nations, infectious disease mortality falls most heavily on indigenous and disadvantaged minorities ( 3 ). The control of bacterial infectious diseases worldwide is an important task. Although antibiotics revolutionized the treatment of bacterial infections, increased resistance and the emergence of multidrug-resistant strains increasingly reduce their efficacy. This trend promotes an urgent need for better understanding of bacterial pathogenicity and resistance mechanisms, which will assist novel therapeutic and vaccination strategies.

Many infectious microbes spend all or some of their time within a host in an intracellular niche. Consequently, to maintain survival as a species these pathogens have evolved diverse mechanisms for overcoming a critical biological challenge they all face: how to exit the host cell. Historically, experimental research into the strategies adopted by intracellular pathogens to accomplish this task has been lacking, and many of our presumptions about how pathogens exit, or egress, from host cells were therefore largely speculative and unsupported by experimental data. Some explanations for our collective lack of knowledge include the difficulty of working with some of these organisms, especially in light of their often complex developmental growth cycles, the complexity and variation of the host cell types targeted by bacteria (exit mechanisms may be very different in macrophages than epithelial cells, for example), and the inadequacies of genetic manipulation of some bacteria. Finally, the general question of host cell exit has simply been overlooked by the field; earlier infection events such as attachment or entry are far easier to understand and investigate experimentally and have therefore attracted much of researchers’ attention.

During the golden age of antibiotic discovery, from the 1930s through the 1960s, methods of antibiotic identification relied solely on scientific observation, and while chemical analogues such as amoxicillin, derived from penicillin, continued to be developed, they retained the same mechanisms of action and hence the same bacterial targets. Moreover, there are finite modifications that can ultimately be made to “old” classes of antibiotics. Consequently, only two new classes of antibiotics have been discovered in the past 40 years, and both entered the market early in the new millennium. The advent of the genomics revolution offered a new hope for the discovery of novel antimicrobial targets. Genomic strategies were utilized to identify potential antibacterial targets, namely those that, if inhibited, resulted in the death of the bacterium. Such targets were to be present in pathogenic strains of bacteria and absent from the human host; they could include metabolic pathways, receptor ligands, and virulence traits, to name a few. Despite the abundance of targets identified using this strategy, no new antibiotics have reached the marketplace as a result of the genomics approach. However, new antimicrobials with novel targets continue to be identified and contribute to the ongoing struggle against antimicrobial resistance that threatens to return humankind to a situation comparable to the preantibiotic era.

The discovery of penicillin in 1928 and its subsequent introduction as a therapeutic in the 1940s sparked the antibiotic era, ushering in effective treatment options for many common bacterial infections ( 1 ). Following the end of World War II, several pharmaceutical companies including Bayer, Merck, and Pfizer became household names through the discovery and clinical success of a number of additional antibiotics, which were identified by screening soil samples for antimicrobial activity ( 1 ). Compounds identified during this screening became the founding members of many now-ubiquitous groups of antibiotics, including the tetracycline, rifamycin, quinolone, and aminoglycoside families. In the early 1970s, declining rates of novel antibiotic discovery from microbial sources shifted the onus of antimicrobial development to synthetic chemists, who were tasked with designing and screening new compounds based on known principles of antibiotic design. These synthetic chemists were faced with many practical challenges, including poor penetration into bacterial cells, bacterial enzymes, and/or efflux pumps that degrade or expel the compounds, respectively, innate resistance mechanisms, and the requirement of high concentrations of some compounds that result in toxic side effects ( 2 , 3 ).

Tuberculosis (TB) is a global pandemic that ranks alongside HIV-AIDS and malaria as the leading cause of death by infectious disease, with the highest incidence rates observed in Southeast Asian, African, and Western Pacific countries ( 1 ). In 1993 the WHO declared TB to be a global health emergency and set the Millennium Development Goal of reducing the prevalence and mortality rates to 50% of those observed in 1990 by the 2015 deadline ( 2 ). Although the rates of new TB cases and mortality have declined over the past decade and are within reach of the 2015 target, the number of TB patients and the prevalence of drug-resistant strains are rising ( 3 ). Multidrug-resistant TB (MDR-TB) must be addressed now as a public health crisis to achieve the ambitious Millennium Development Goal target of complete elimination of TB as a public health concern by 2050 ( 4 ).

The mammalian gastrointestinal (GI) tract is comprised of several hundred species of microorganisms including bacteria, archaea, fungi, bacteriophages, eukaryotic viruses, and protozoa. This complex and eclectic ecosystem is collectively known as the gut microbiota. Bacteria are by far the most abundant constituent of the microbiota; studies using DNA shotgun sequencing analysis have estimated that bacteria make up approximately 98% of all metagenomic sequences in fecal samples of various mammals ( 1 , 2 ). The GI microbiota is acquired rapidly after birth and undergoes substantial compositional changes (from a more aerobic to a predominantly anaerobic flora) in the first 1 to 2 years of life before reaching a stable and symbiotic relationship with the host ( 3 ). It then remains dynamic but relatively stable throughout adulthood unless perturbed.