Widespread clinical use of antibiotics first began in the 1950s. The availability of these “miracle drugs,” as they were called at the time, caused great excitement for both physicians and the public as a whole. They came at a time when the medical community was gaining greater control over infectious diseases than ever before. In clinics and hospitals, hygienic practices such as handwashing and disinfectant use were reducing the risk of disease transmission. In the community, improved nutrition made people better able to resist infections, while less crowded conditions and the availability of clean water helped reduce the spread of disease. Meanwhile, newly developed vaccines were protecting against some much-feared diseases. Despite all this, bacterial infections, such as pneumonia, tuberculosis, cholera, and syphilis, continued to take a heavy toll, and infectious diseases were still a leading cause of death. Antibiotics appeared to be the superweapon that would give humans the final decisive victory over bacteria.

In this early euphoria over the success of antibiotics, scientists and policy makers alike concluded that bacterial infections were no longer a threat and turned their attention to other problems, such as cancer, heart disease, and viral infections. For the next three decades, bacteria were of interest mainly as tractable model systems for studying physiology, genetics, and ecology, and as a source of tools for the new molecular biology and genetic engineering technologies that were revolutionizing all of biology. Confidence that bacterial diseases were completely under control was bolstered by a glut of new antibiotics on the market. Indeed, there was a pervasive perception among the medical community and the public as a whole that bacterial infectious diseases were no longer a problem since they could now be readily and effectively treated with antibiotics.

Unnoticed by all but a few researchers in the field and some pharmaceutical companies, the first cracks soon began to appear in the protective shield against bacterial diseases. This danger became more evident in the late 1970s. Antibiotics were no longer the highly profitable products they had once been, especially not compared to heart medications or tranquilizers, which needed to be taken daily for long periods of time. Additionally, new antibiotics were becoming harder to discover and more expensive to develop. One pharmaceutical company after another quietly cut back or dismantled its antibiotic discovery program. For a while, these cracks appeared not to matter, as there were enough new antibiotics that still worked on the bacteria that had become resistant to the old standbys like penicillin. Warnings from scientists that bacteria were becoming more resistant to antibiotics were largely ignored.

During the late 1980s, however, scientists and health officials began to notice an alarming increase in difficult-to-treat bacterial infections. By 1995, infectious diseases became one of the top five causes of death in the United States. Even with the AIDS epidemic in full swing, most infectious disease deaths were still caused by bacterial diseases, such as pneumonia and bacterial bloodstream infections (sepsis). Why was the incidence of bacterial pneumonia and sepsis increasing? For one, the population as a whole was aging, and older people are more susceptible to these diseases. For another, modern medicine had created a large and growing population of patients whose immune systems were temporarily disrupted due to cancer chemotherapy or immunosuppressive therapy following organ transplants, as well as due to other immune-compromising illnesses such as AIDS.

A development that caught many in the medical community by surprise was the appearance of new diseases that were dubbed emerging infectious diseases. In the past, scientists had assumed that any microorganism capable of causing disease would surely have done so by now, given the hundreds of thousands of years humans have occupied the planet. This view overlooked two important facts. First, bacteria can very rapidly change their genetic makeup to take advantage of new opportunities. Members of some bacterial populations are hypermutable, allowing them to try many genetic combinations to find the one most appropriate for the current environment experienced by that bacterium. Many bacteria can also acquire genes conferring new virulence traits or resistance to antibiotics from other related or even unrelated bacteria through a phenomenon known as horizontal gene transfer (HGT). Second, changing human practices, such as increased global travel, widespread use of air-conditioning, and the appearance of crowded intensive care wards in big hospitals, brought susceptible people into contact with microorganisms that had not previously had the opportunity to cause human infections.

A new category of disease-causing bacteria was recognized: opportunistic pathogens. These bacteria normally do not cause disease in healthy people, but can infect and cause disease in individuals whose defenses are compromised in some way. In fact, many of these pathogens are found normally in or on the human body and thus had been assumed to be innocuous. Others are bacteria commonly found in soil or aquatic environments. During the early antibiotic era, these soil bacteria were thought to be beneficial to humans because scientists were finding that many of them were producers of antibiotics. However, these bacteria were suddenly being seen as the only bacterium isolated from the blood, lungs, feces, or wounds of seriously ill patients. They also tend to exhibit a troubling, not-so-friendly characteristic. Because of the antibiotics present in their natural environment, they are often intrinsically resistant to a variety of antibiotics, which made infections by these opportunistic bacteria challenging to treat.

Scientists and physicians reluctantly began to realize that a decisive human victory over bacteria had not occurred. Not only were known pathogens changing to be more resistant to antibiotics or better able to cause disease, but also new pathogens with markedly different virulence traits were emerging. The infectious disease picture was changing in a way that made it increasingly difficult to predict new patterns of bacterial disease. The serious threat of antibiotic-resistant bacteria to human health both in the United States and the world was documented in 2013 by reports from the Centers for Disease Control and Prevention (CDC) and the World Health Organization (WHO).

Bacteria, a Formidable Ancient Life Form

The brief foregoing account of how bacterial diseases have come into prominence as a major global health problem explored the recent past. However, to understand fully why no one should have been surprised by this development and why bacteria are such formidable opponents, it is necessary to take a closer look at the long history of bacteria, during which they were constantly forced to evolve and adapt to new conditions.

Today, we realize that Earth is a microbial planet. Bacteria were probably the first form of life to appear on Earth, about 3.5 to 4 billion years ago (Figure 1-1). Bacteria and another type of prokaryote, the archaea, ruled the world unchallenged for at least a billion years before the first eukaryotes appeared. During this period, they helped create the global geochemical cycles that made Earth habitable for larger life forms. Bacteria and archaea are master recyclers. Bacteria put the first molecular oxygen in Earth’s atmosphere, thereby creating the ozone layer, which protected Earth’s surface from the deadly radiation that had previously bombarded it, making life on Earth’s surface possible. By adding molecular oxygen to the atmosphere, bacteria created conditions that permitted the later evolution of oxygen-utilizing creatures, including humans.

Figure 1-1. Overview of microbial evolution. Microorganisms appeared 3.5 to 4 billion years ago and changed Earth such that eukaryotes could evolve.

In the course of their long history, bacteria developed a variety of metabolic capabilities that allowed them to survive under an impressive variety of conditions. There are bacteria that can obtain energy by oxidizing sulfides, reducing sulfate, oxidizing ammonia, reducing nitrate, and oxidizing methane—to name only a few of the vast number of metabolic types represented in the bacterial world. Bacteria also learned how to maximize the plasticity of their genomes, constantly acquiring new DNA and mutating or rearranging existing genes, thereby creating new capabilities that enabled them to colonize the many niches on Earth. So far, no part of Earth has been found to be free of bacteria and archaea. They are in arctic ice, the deep subsurface of landmasses, the surfaces and depths of the oceans, and boiling hot springs. The genetic plasticity that enabled evolution of such metabolically diverse organisms continues to serve bacteria today as they face new challenges and opportunities.

About a billion years after bacteria first appeared on Earth, the first eukaryotes, the single-celled protozoa, emerged. Disease-causing bacteria are often capable of doing so because they have developed strategies for evading phagocytosis (engulfment) or for surviving inside phagocytic cells. Evolution of such strategies could have begun soon after the appearance of the first protozoa, well in advance of the appearance of animals and humans. Some of the toxic proteins that disease-causing bacteria use to kill human cells might have originally evolved to allow bacteria to evade or survive feeding by their protozoal adversaries. Today, scientists are finding that some bacterial pathogens that are harmful to humans normally live inside amoebas in nature. If this view of bacterial evolution is correct, then there are likely to be more unidentified disease-causing bacteria in nature than we currently know.

As bacteria evolved diverse metabolic specialties, acquisition of bacteria or archaea as coinhabitants (endosymbionts) enabled eukaryotes to expand their metabolic diversity as well. Eukaryotes acquired bacterial endosymbionts (now known as mitochondria) that allowed them to gain energy through respiration and to regulate cellular metabolism, thereby also enabling them to become multicellular. Cells of what would later become plants acquired photosynthetic bacteria as endosymbionts (now known as chloroplasts), again conferring on them the ability to harness energy from the sun through photosynthesis. Some plants went even further and also recruited into their root cells prokaryotic endosymbionts (both bacterial and archaeal), which could fix atmospheric nitrogen into nitrogenous compounds that the plant could then use as fertilizer.

As animals and eventually people emerged, bacteria were quick to take advantage of the warm, moist environment offered by their intestinal tracts. In turn, many of these bacteria helped to provide nutrients for the animal or human host by metabolizing the intestinal contents. There is no point in a human life span, except for the brief time the fetus spends in the uterus, during which the human body is not heavily colonized by large numbers of bacteria, especially on the skin, in the mouth, in the intestinal tract, and in the vaginal tract. These bacteria are highly adapted to their niches in and on the human body. However, their constant presence puts them in a position to take advantage of any breach in the defenses protecting the interior tissues and bloodstream from bacterial invasion.

Although some eukaryotic microbes such as algae have a photosynthetic lifestyle, many others, especially amoebas and other protozoa, live by feeding on bacteria and archaea. An interesting aspect of this protozoal grazing that has attracted particular attention recently is that protozoa have properties that are remarkably similar to human phagocytic cells, cells that form an important part of the defenses of the human body. Some of these human phagocytic cells function mainly to engulf, break down, and clear bacteria in blood and tissues. Of these, some then present components of broken-down bacteria to the cells of the immune system.

When animals and humans finally appeared on the evolutionary scene, bacteria immediately took advantage of them as rich niches in which to grow. To a bacterium accustomed to the vagaries of the external environment, where ambient temperature and availability of water and nutrients can vary widely (and unpredictably), a warm-blooded animal whose body temperature is stably maintained and whose lifestyle involves constantly collecting food and water from the environment must be as close as it gets to bacterial heaven. As such, it should not be surprising that the bodies of humans and animals carry dense bacterial loads, especially in the mouth, intestinal tract, and vaginal tract. Small wonder that the human or animal body is often referred to in the scientific literature as the host and that the interaction between a bacterium and its host is referred to as a host-microbe relationship.

Until recently, scientists studying the evolution of insects, animals, and humans almost completely ignored the selective pressure exerted by the long-term presence of the large and diverse populations of bacteria with their hosts. Now, a rapidly expanding area of research has emerged that is devoted to studying the coevolution of hosts with their resident microbial communities, also known as microbiomes. As will become evident in the next few chapters, the effects of microbial pressure can be seen clearly in the design of human skin, eyes, lungs, intestinal tract, vaginal tract, and in particular the immune system. Overwhelming evidence points to the vital role that microbiomes play in both promoting health and modulating disease susceptibility and severity. For the first time, we are also realizing the importance of considering the ancestry of both the host and the microbe when considering pathogenic potential (Box 1-1).

Box 1-1.

Sharing an Ancestral Relationship with Your Resident Pathogen Can Prevent Stomach Ulcers and Cancer

After more than two decades of controversy and intense experimental investigation, it is now well-established that Helicobacter pylori, a bacterium that colonizes the stomach of nearly half of the world’s population, is the leading cause of gastric inflammation, which can lead to stomach ulcers and in a small percentage of infected individuals (<1%) stomach cancer. Extensive phylogenetic evidence suggests that H. pylori bacteria are about as old as modern humans and that since leaving Africa with their hosts these bacteria have diversified geographically in parallel with their human hosts. But until recently, researchers had a hard time correlating the prevalence of H. pylori infections with the incidence of cancer.

The first clue that other factors were at play came from comparing disease prevalence in two populations of Colombians, located about 200 kilometers from each other, with similar levels of H. pylori infection. In this study, the researchers compared H. pylori strains colonizing a coastal population of largely African ancestry (58%) having a low incidence of gastric cancer (∼6 per 100,000) with those from a mountain population of mostly Amerindian descent (68%), in which gastric cancer is more common (∼150 per 100,000). The results showed that Colombians of African ancestry infected with African bacterial strains had low incidence of disease, while Colombians of Amerindian ancestry infected with African strains had a high risk of cancer. Indeed, the more Amerindian ancestry an individual had and the more African-like the H. pylori strains harbored by that individual were, the more likely that person was to have severe gastric disease.

So, it looks like the longer you have coevolved with your resident pathogen, the less likely you are to progress to a diseased state. These findings further support a popular theory of pathogenesis that chronic pathogens that spread through vertical transmission from parent to child are predicted to become less virulent over time as a consequence of coevolution.

Sources:

Moodley Y, Linz B, Bond RP, Nieuwoudt M, Soodyall H, Schlebusch CM, Bernhöft S, Hale J, Suerbaum S, Mugisha L, van der Merwe SW, Achtman M. 2012. Age of the association between Helicobacter pylori and man. PLoS Pathog 8:e1002693.[PubMed][CrossRef]

Kodaman N, Pazos A, Schneider BG, Piazuelo MB, Mera R, Sobota RS, Sicinschi LA, Shaffer CL, Romero-Gallo J, de Sablet T, Harder RH, Bravo LE, Peek RM Jr, Wilson KT, Cover TL, Williams SM, Correa P. 2014. Human and Helicobacter pylori coevolution shapes the risk of gastric disease. Proc Natl Acad Sci USA 111:1455–1460.[PubMed][CrossRef]

Pressing Current Infectious Disease Issues

Having made this digression into ancient history, let us now return to the present and examine some bacterial infections that are at the forefront of burning public health issues. These include emerging infectious diseases, increasing problems with large outbreaks of foodborne and waterborne infections, hospital-acquired (nosocomial) infections, disease transmission, antibiotic resistance, microbiota shift diseases, pathogen evolution, and bioterrorism.

Emerging and Reemerging Infectious Diseases

The emergence of apparently new bacterial diseases and the reemergence of old diseases thought to be under control (at least in developed countries) was an unpleasant shock to the health care community. Emerging and reemerging infectious diseases illustrate an important principle. Disease patterns change, both because bacteria change by acquiring new traits through genetic mutation and horizontal gene transfer and because changing human activities can create new opportunities for bacteria to cause disease.

Not all diseases are truly emerging in the sense of being completely new to the human population. In some cases, the disease symptoms have been around for a long time as a known disease, but the bacterial cause has only recently been identified. A good example of this phenomenon is gastric ulcers, which are now known to be caused largely by the bacterium Helicobacter pylori. This bacterium eluded notice previously because the methods for cultivating and identifying it had not yet become common practice and because many medical researchers were convinced that no bacteria could colonize the human stomach. In this sense, many of these diseases are “emerging” in terms of public awareness but not in the minds of the scientists who study them.

Old diseases can return if the conditions change to favor their reemergence. For example, the increased use of antibiotics in hospital settings with inadequate stewardship has led to known pathogens, such as Clostridium difficile, Klebsiella pneumoniae, Streptococcus pneumoniae, and methicillin-resistant Staphylococcus aureus (MRSA), acquiring new antibiotic-resistance traits that now challenge measures to control their spread. Unfortunately, noncompliance with hygiene practices by health care workers promotes the spread of these bacteria among susceptible hosts.

As another example, tuberculosis made a comeback in developed countries, such as the United States and Europe during the 1990s. Its reemergence was due to several causes. One was the dismantling of the preventive infrastructure that had been developed in the 1950s to contain the spread of this insidious disease. Another was the presence of unprecedentedly large populations of highly susceptible individuals in crowded settings, such as prisons and homeless shelters. Further complicating matters were the emergence of other illnesses, such as AIDS, that suppress the immune system of afflicted individuals and the development of resistance to the traditional anti-tuberculosis drugs, which had not been updated or improved since their original introduction because no one thought tuberculosis would return.

Foodborne and Waterborne Infections

Many foodborne and waterborne infections fit into the category of emerging or reemerging infectious diseases. We treat this subject as a separate category because of its unique impact on the public perception of disease risks. Ironically, as food and water supplies have become cleaner, the public’s concern about their integrity has increased rather than decreased. A review of news articles from the past few years makes this quite evident. The integrity of the food and water supplies is a nonnegotiable issue as far as the public is concerned.

From the 1960s through the 1980s, the public’s main concern about the food supply was pesticide residues and other chemical adulterants that might cause cancer. This problem has been largely solved by more stringent regulations and testing, which limit the amount of pesticide residues and other harmful chemicals that might be found in food sold for human consumption. More recently, concern has arisen about another hazard that had been around all along but had not been perceived as a threat: foodborne bacterial diseases.

The catalyst for the abrupt swing in public concern regarding food safety was Escherichia coli O157:H7, a type of E. coli that can cause kidney failure and death, especially in children. Widespread media attention was first drawn to this problem in 1993, when an outbreak of disease was caused by undercooked, contaminated hamburger meat dispensed by an American fast-food chain. Although there had been prior outbreaks in the previous decade, many in the beef and fast-food industries and most of the general public had never heard of E. coli up to this point. In total, this outbreak involved 732 cases, including 4 deaths, from 73 restaurants in a number of western states before the source of the outbreak was identified and the contaminated meat was recalled. Since then, there have been many more cases of E. coli O157:H7 infections spread by undercooked meat, radish sprouts, lettuce, spinach, and even apple juice. The apple juice incident, during which 65 cases with 1 death were reported, nearly bankrupted the company that had produced the contaminated juice, which had not been pasteurized. The lesson that juice was not exempt from bacterial contamination was learned very quickly by the industry, and it is now rare to see unpasteurized juices in supermarkets.

Earlier in the 20th century, before the advent of centralized food processing and distribution, foodborne disease outbreaks tended to be confined to church socials, family gatherings, or business-sponsored employee picnics (Box 1-2). As the food industry became more centralized, however, a different pattern of foodborne disease emerged: the multistate (or even multicountry) outbreak of foodborne disease derived from a single source. The nature of foodborne outbreaks has changed considerably from the days of the church social outbreaks, and the effect on the public has been dramatic. In the case of the E. coli O157:H7 outbreak described above, a single processing plant was the source. Contaminated radish sprouts caused another outbreak of E. coli O157:H7 in Japanese schoolchildren. The seeds used by the Japanese sprouting companies came from a single source in the northwestern United States, where the initial contamination event probably occurred. In 2006, E. coli O157:H7-contaminated spinach grown in California and used by consumers in spinach salads was spread throughout the United States. In 2009, E. coli O157:H7 showed up yet again, this time in refrigerated cookie dough sold throughout the United States.

Box 1-2.

Bioterrorism Hits Oregon Salad Bars

In 1984, a large outbreak of salmonellosis involving at least 750 people occurred in The Dalles, the county seat of Wasco County in Oregon. At the time, a religious commune was at odds with local residents over land-use restrictions placed on the commune in an attempt by the townspeople to eliminate it. Members of the commune felt that the outcome of an upcoming election was critical to their future ability to grow. In an apparent attempt to disrupt the election, commune members planned to cause an outbreak of salmonellosis that would keep people home from the polls. The outbreak was a trial run to determine the best way to create the most havoc. At least 10 restaurants were involved, with the salad bar being the main site of intentional contamination. Contamination attempts were also made at local grocery stores, but the restaurant salad bars were the most effective source of disease. Unfortunately for commune members, their trial run was too successful and attracted the attention of the Public Health Department and the police.

Even so, it took nearly a year to trace the epidemic source and to suspect intentional contamination. Such events are fortunately quite rare, so intentional contamination was not even considered at first as a possible explanation for the outbreak. Careful questioning of the victims led investigators to deduce that salad bars had been the main source of the outbreak. Further interrogation of commune members by police and FBI agents revealed that the commune members had been the perpetrators of the outbreak. The commune had its own laboratory, where the strain of Salmonella enterica serovar Typhimurium was grown and prepared for inoculation of the salad bars. Commune members had apparently gotten the strain by ordering it from the American Type Culture Collection (ATCC), a widely respected repository of bacterial strains that distributes strains to scientific laboratories for a modest fee. Nearly 2 years after the outbreak, two commune members were sentenced to 1 to 2 years in prison for conspiring to tamper with consumer products. An earlier episode of product tampering involving introduction of cyanide into Tylenol capsules had been responsible for a rash of antitampering legislation. These antitampering laws were used to prosecute the commune members. As a precaution against misuse of its cultures, the ATCC has tightened restrictions on obtaining certain bacterial stocks.

Source:

Török TJ, Tauxe RV, Wise RP, Livengood JR, Sokolow R, Mauvais S, Birkness KA, Skeels MR, Horan JM, Foster LR. 1997. A large community outbreak of salmonellosis caused by intentional contamination of restaurant salad bars. JAMA 278:389–395.[PubMed][CrossRef]

Similar to foodborne diseases, outbreaks of waterborne disease continue to occur, despite advances in water management and sanitation; however, they tend to be more localized in nature. Most of the waterborne outbreaks that have made the news lately were caused by aging pipes and water treatment plants or by mammal and bird fecal material in water reservoirs. Over half of all waterborne illnesses in the United States in recent years have been associated with contamination of drinking water with Legionella, a Gram-negative bacterium commonly found in soil and aquatic environments. Other microbes associated with waterborne outbreaks are E. coli and Campylobacter bacteria and the parasites Giardia and Cryptosporidium. The media picked up on this contamination problem, as was seen on a cover of Time magazine (August 3, 1998) showing E. coli cascading out of a kitchen tap. The event that stimulated this particular media response was an outbreak that occurred among 61 residents of Alpine, Wyoming (total population 470), who drank tap water on one particular weekend. Wild animals had probably contaminated the spring that was the source of the town’s tap water.

An often-overlooked aspect of waterborne infectious microorganisms is that contaminated water can also produce a contaminated food product if that water is used to wash the food. In most cases, water used to wash dirt off fruits and vegetables prior to shipping is not tap water quality and is instead what is referred to as “gray water”: water processed to remove the worst contamination but not microbiologically sterile. In some foodborne outbreaks, the contamination may actually have come from water used to wash the food. At first, vegetarians felt safe because foodborne diseases were so often spread by meat. But nowadays most people concerned with ensuring food safety consider any foods that are consumed raw, such as fruits and vegetables, a potentially more serious threat to public health. If meat or other food is properly cooked, the contamination problem is solved, but even careful washing is not always sufficient to render contaminated raw fruits or vegetables safe.

Modern Medicine as a Source of New Diseases

Modern medicine has made impressive breakthroughs in therapies for many human diseases. Surgeons now routinely transplant new organs into patients whose own organs are failing. Cancer chemotherapy is becoming more and more effective. This progress has come at a cost, however. Transplant patients and patients receiving cancer chemotherapy have suppressed immune systems due to the medications they are taking. This immunosuppression is temporary in the case of cancer patients and ends when the chemotherapy is finished, but transplant patients take their immunosuppressive therapy for life. Also, there are a large number of individuals suffering from infectious diseases, such as human immunodeficiency virus (HIV), that are immunosuppressive. Not surprisingly, these immunocompromised patients can become infected with bacteria never before suspected to be able to cause human disease.

Other bacteria cause disease not because the patient is immunocompromised, but because a physical barrier against bacterial invasion is bypassed. For example, accidental perforation of the colon during surgery releases gut bacteria into tissue and blood. Patients with certain types of respiratory infections may have ventilator tubes inserted to keep their airways open, which can allow bacteria to bypass some of the defenses of the respiratory tract to directly enter the lungs. Likewise, catheters enable bacteria to bypass the normal cleansing flow of urine to gain access to the bladder.

Opportunistic pathogens that normally do not cause disease are able to cause disease because some defense of the body that normally keeps them at bay has been breached, giving them the opportunity to cause infection. For an interesting example of an opportunist from an unexpected source, see Box 1-3. The term “opportunist” makes such bacteria seem somehow less dangerous than “real” disease-causing bacteria. Do not be fooled by the seemingly innocuous nature of the opportunists! In most developed countries, a person is far more likely to die from an opportunistic infection than from the epidemic diseases that serve as the public’s mental image of infectious diseases.

Box 1-3.

Enterprising Bacteria Always on the Alert for New Infection Opportunities

An example of how bacteria can rapidly act to take advantage of new opportunities is provided by an outbreak of pneumonia in an intensive care ward. Many of the patients were very ill and were on respirators to support breathing. The type of respirator being used required that a tube be inserted deep into the airway of the lungs, an ideal conduit to carry bacteria deep into the lung, bypassing the normal respiratory defenses. After a number of previous cases of respirator-associated lung infections, hospital personnel have learned to be very careful not to contaminate the respirator itself or to allow bacterial contaminants to enter the air being forced into the lung.

No one, however, thought about mouthwash. Since patients on respirators are often unable to attend to their own dental hygiene, hospital staff workers use mouthwash to clean and freshen the mouth every day. The cause of the lung infections was identified as Burkholderia (formerly Pseudomonas) cepacia. Although this bacterial species is known to cause infections in people with lung diseases, such as cystic fibrosis, it is generally considered to be a relatively innocuous soil bacterium. In fact, B. cepacia is used as a biocontrol agent to degrade herbicides, such as 2,4,5-trichlorophenoxyacetic acid (2,4,5-T, a toxic defoliant also known as Agent Orange). The bacterium is ubiquitous in soil and water, but in this case apparently managed to contaminate many lots of the mouthwash, which did not contain alcohol to discourage bacterial growth. In effect, the hospital workers taking care of the patients on respirators were inoculating the patients’ teeth and gums daily with a contaminated mouthwash solution, which placed the bacteria in an ideal location to gain access to the lungs.

Source:

Centers for Disease Control and Prevention (CDC). 1998. Nosocomial Burkholderia cepacia infection and colonization associated with intrinsically contaminated mouthwash—Arizona, 1998. MMWR Morb Mortal Wkly Rep 47:926–928.[PubMed]

Another way in which modern medicine has affected the infectious disease picture is by increasing the human life span. The increasing number of elderly people, whose immune defenses are beginning to decline and who are more likely to be receiving therapies that undermine the defenses of their bodies, provides an expanding population of individuals highly susceptible to diseases. Put these elderly people in crowded conditions, such as those experienced in nursing homes, and an even greater opportunity is created for infectious diseases to spread.

Postsurgical and Other Wound Infections

Most recent studies of wound infections have focused on the infections that can be a serious complication of surgery (postsurgical infections). In the preantibiotic era, infections were a major complication of surgery. Regardless of how skillful the surgeon, an infection could kill the recipient of the most successful surgery. This may have been the origin of the grim old joke that the surgery was a success, but the patient died. Antibiotics changed all this and made routine surgery possible because antibiotics eliminated any bacteria that might have managed to penetrate the barrier of the surgical scrub and other hygienic procedures.

The first shadow in this rosy picture appeared when surgeons and other health care workers began taking patient survival for granted and became more lax in their time-consuming hygienic practices. Hospitals trying to save money began cutting budgets for nurses and janitors, individuals responsible for the cleanliness characteristic of hospitals in developed countries. To make matters worse, the bacteria often causing postsurgical problems tend to be resistant to antibiotics. These postsurgical infections have consequences for both patients and hospitals. Patients risk damage to major organs or even death, while hospitals and insurance companies bear significantly higher financial costs to care for these patients.

Not long ago, the state of Pennsylvania made history by publishing postsurgical infection data from its hospitals. Until this unprecedented move to transparency, infection rates in hospitals were secrets guarded almost as fiercely as classified CIA files. The reason is easy to understand. No hospital wants potential users of its facilities, especially people getting elective surgery, to identify the hospital as a place where people go in healthy and come out sick or even dead. The Pennsylvania figures confirmed what everyone in the infectious disease community already knew: patients who contract a postsurgical infection, especially one caused by antibiotic-resistant bacteria, cost over four times more to treat than people who do not contract an infection. Unfortunately, this type of statistic has attracted a lot more attention than the suffering of the patients involved. The good news is that this increased transparency has led to improved antibiotic stewardship and hygiene practices, which in the long run will help individuals who go into hospitals.

Recently, however, attention has once again focused on another old problem: war-related infections. Accounts of the antibiotic revolution often point out how a combination of antibiotics and improved surgical interventions enable the treatment of wound infections that once killed soldiers more frequently than the trauma of the wounds themselves. World War I was the last war in which infectious diseases—not just wound infections but also diarrhea and pneumonia—were the main cause of soldiers’ deaths.

An ominous development in the past decade or so has been the appearance of a soil bacterium, Acinetobacter baumannii, first as a wound infection problem in soldiers and now as a dangerous hospital-acquired infection. A. baumannii was not a stranger to microbiologists, as there had been a few outbreaks in intensive care wards, but A. baumannii began to attract real attention around 2003 when it started showing up in military hospitals during the Iraq War. Its claim to fame is that it was one of the first bacteria to be called “panresistant” because it is resistant to almost all antibiotics. Before the emergence of panresistant A. baumannii, the worst threat in terms of antibiotic resistance was another soil bacterium, Pseudomonas aeruginosa, which has long been known as an infectious disease problem in burn victims and cystic fibrosis patients. A number of other soil bacteria and bacteria normally found in or on the human body (such as MRSA, mentioned previously) also seem to be resistant to multiple antibiotics. Unfortunately, these ubiquitous bacteria have emerged as common causes of hospital-acquired infections.

A new understanding of antibiotic resistance is that the physiological state of a bacterium can be as important as its complement of resistance genes. Many bacteria can form biofilms, multilayer groupings of bacteria that are held together by a sticky polysaccharide matrix secreted by the bacteria. Biofilms are found in many places in nature, most notably in areas such as streams, where the fast flow of water makes it necessary for bacteria to resort to biofilm formation to stay in a particular site. In hospital patients, biofilms seem to form very readily on plastic or metal implants. Although we do not yet fully understand the reason, bacteria in these biofilms are significantly less susceptible to antibiotics and are therefore quite difficult to eliminate. All too frequently, patients with a biofilm-contaminated implant have to undergo additional surgery to remove the implant so that antibiotics can be used to eliminate any remaining bacteria. After the infection is cleared, a second implantation can be attempted.

Bioterrorism

No discussion of current infectious disease issues would be complete without mention of bioterrorism. Germ warfare—the use of infectious microorganisms as weapons—is an old idea that has, fortunately, never worked very well. The nature of germ warfare has changed in recent years. In the past, the purpose of germ warfare was to kill or incapacitate large numbers of soldiers. Recently, the aim of terrorists’ actions has changed. Now, the goal is to frighten the general population (hence the name “bioterrorism”). A small number of deaths are sufficient to achieve this goal.

Among bacteria, Bacillus anthracis, the causative agent of anthrax disease, has been identified as a particularly useful weapon by bioterrorists. B. anthracis, as a spore-forming Gram-positive bacterium, is easier to store and “weaponize” than a more fragile organism, such as the Gram-negative Yersinia pestis, the causative agent of bubonic plague. In spore form, B. anthracis is also easier to handle than the highly contagious smallpox virus. The U.S. Army was worried enough about possible anthrax attacks to administer the anthrax vaccine to soldiers going to Iraq and Afghanistan. This sparked controversy because the efficacy and safety of the available anthrax vaccines were contentious issues at the time. Unfortunately, the anthrax attacks through the U.S. postal system in late 2001 only served to exacerbate the fear and solidify the realization that bioterrorism is a reality that we must now address.

An alternative bacterial choice of bioterrorists is Clostridium botulinum, another spore-forming bacterium that produces botulinum neurotoxin. Producing botulinum neurotoxin in your garage is inadvisable and can be extremely hazardous to your health, but this toxin is produced commercially (as Botox) for use in a variety of medical and cosmetic applications, ranging from correcting facial tics and strabismus (cross eyed) to eliminating wrinkles and preventing scarring from reconstructive surgery. Thus, it is conceivable that terrorists might hijack commercially produced Botox from factories that produce it. Whether emptying vials of toxin into a city’s water supply would actually result in any deaths is not clear, as dilution and breakdown of the purified toxin protein in the environment will occur. It is, however, better to err on the side of caution. The most recent concern, though so far only theoretical, is that botulinum toxin might be deliberately introduced into milk, juice, or soft drinks during processing.

A New Respect for Prevention

Major changes that hold great promise for the future have been occurring in the approach to controlling infectious diseases. Traditionally, medical establishments in developed countries have opted for a treatment-based approach. Although vaccinations were given to prevent some diseases and doctors used antibiotics prophylactically to prevent others, such as postsurgical infections or infections in cancer chemotherapy patients, the most common approach to treating infectious diseases was to wait for an infected person to seek medical help before intervening in the disease process. This approach has been criticized for being expensive and for allowing diseases to gain a foothold in the body before action is taken—a delay that in some cases results in long-term damage to the patient, even if the treatment successfully eliminates the infecting bacterium from the body.

Treatment-based approaches have also become much less effective as increasingly resistant bacteria make it more difficult to choose the appropriate antibiotic treatment. To better combat this escalating problem, it is important to understand the reasons for the rise in antibiotic resistance, particularly in hospital settings. If a bacterial infection is not cleared immediately, sepsis can kill a patient in just a few hours. Thus, since waiting for proper diagnostics can be fatal to the patient, the physicians’ responses have generally been to use more advanced, broad-spectrum antibiotics to treat all bacterial infections, regardless of whether they might be treatable with less expensive, narrow-spectrum antibiotics. Adding the diagnostic testing to the decision process also raises the overall cost of the clinical visit, something that not only delays treatment, but also is actively discouraged by health insurance companies. Physicians have been advised to use the frontline antibiotics first, but also to send samples to the microbiological laboratory for antibiotic resistance evaluation and then adjust the therapy if laboratory results indicate another, more appropriate treatment regimen. Nevertheless, the overall result is increased selective pressure on the bacteria to develop resistance against the frontline antibiotics.

A far preferable approach to controlling a disease is preventing it in the first place. This approach has been successful in ensuring the safety of food and water. Now, more and more public health officials, hospital managers, and executives of health management organizations (HMOs) are rediscovering that prevention is also far more effective—and far less expensive—than treatment after infection has occurred. Prevention is suddenly center stage again. But, for a preventive approach to work, it is first necessary to have extensive information about the epidemiology of disease (i.e., information about disease patterns, their geographic distribution, and determinants of health-related states). It is also necessary to have a large-scale networking infrastructure in place that can serve as an early warning system to detect signals indicating new disease trends. Led by the CDC and the WHO, a variety of such epidemiological surveillance programs have been implemented to monitor the appearance of new diseases, the increased incidence of existing diseases, and the occurrence of antibiotic-resistant bacteria. Indeed, the CDC website (http://www.cdc.gov/) is now an extensive portal for the latest information about various infectious diseases, including scientific and medical information about a disease and its causative agent, up-to-date disease trends, precautionary measures, and travel alerts.

The CDC has been monitoring a subset of particularly problematic infectious diseases for years, but the list of diseases covered had been far from exhaustive. Now, many more infectious diseases, such as infections with pathogenic E. coli and Chlamydia, have been placed on the list of reportable diseases. A problem the CDC has had to cope with is that reporting of diseases is voluntary on the part of state public health departments. Overworked and underfunded state health departments have sometimes, understandably, given reporting of diseases a low priority. The CDC and the National Institutes of Health (NIH) are fighting to alert government agencies to the importance of having consistently funded monitoring programs. Many of the recent pandemics, such as SARS, West Nile virus, Ebola, and various avian and swine flus, have lent urgency to these efforts.

Surveillance: An Early Warning System

An example of a CDC surveillance program that was established in 1995 is Foodnet, a program that tries to count all cases of foodborne disease, such as those caused by Salmonella, E. coli O157:H7, Vibrio cholerae, Listeria, and Campylobacter, in 10 selected states in the United States and then to estimate from these data the incidence of these diseases nationwide. Attempts are also being made in several areas to monitor antibiotic-resistant pathogens. Prior to the introduction of Foodnet, the CDC had abundant information about large outbreaks of foodborne disease, but had no idea how many isolated cases of foodborne disease occur, so it was difficult to track sources of contamination. Based on the information gathered so far by Foodnet, the outlook is not positive. Although contamination of foods by some pathogens, such as E. coli O157:H7, has declined, there have been little or no recent reductions for most other infections. Indeed, Campylobacter and Vibrio infections have actually increased in recent years.

Monitoring disease prevalence is only the first step. Next must come effective action to control the further spread of disease. Due to limited shelf life, most perishable products must be shipped immediately for distribution. As such, companies generally wait until the final step in food processing to test foods for microbiological safety. However, it can take days to weeks for microbiological test results to be obtained. This scenario allows shipments of contaminated food to leave processing plants and reach points of distribution before the results of the tests are known. There are encouraging signs that programs for prevention of foodborne diseases are beginning to be implemented. For example, the Food and Drug Administration (FDA) and the United States Department of Agriculture (USDA) have now in place hazard analysis and critical control point (HACCP) programs.

Based on risk assessment, HACCP programs monitor the food and food safety practices at control points along the food production chain where contamination is most likely to occur. This approach not only lessens the likelihood that contaminated foods will be shipped, but also identifies contamination problems or situations that might lead to contamination early so that they can be rectified. At first the food industry was leery of the HACCP approach, viewing it as a needless and potentially expensive government intrusion, but the food industry has now become more enthusiastic about HACCP programs after seeing how expensive and injurious to the reputation of a company a large recall of contaminated products can be. A good HACCP program not only protects the public from disease, but also protects the company from recalls and lawsuits. Although there is still grumbling about specifics, the HACCP concept seems to be catching on.

Making Hospitals Safe for Patients

Fears concerning the prevalence of increasingly antibiotic-resistant bacteria have led to a number of changes in the way hospitals handle infectious disease cases. At one time, a surgeon could infect numerous patients and never even be informed of such incidents, let alone held accountable, due to lack of communication between physicians who care for patients during the postsurgical period and the surgeons who performed the operation. On top of that, hospitals with an infection control program would often delegate the job of infection control officer to someone of lower administrative authority who could not take action against doctors whose postsurgical infection record was poor or whose drug-prescribing practices were open to criticism. Now, this job is being taken much more seriously and is usually held by an infectious disease physician. Communication lines are also being improved.

Managed health care organizations, alarmed at the costs associated with infections involving antibiotic-resistant bacteria, have started cracking down on physician abuse or overuse of antibiotics. Ironically, cost-cutting measures by the health care plan bean counters, who had pressured physicians earlier to reduce drastically the number of laboratory tests they ordered, actually contributed to the resistance problem by encouraging physicians to use the strongest drugs available regardless of need. Thus, although there is still a certain amount of confusion and sending of contradictory signals between managers and physicians, awareness of the consequences have spurred positive changes in diagnostic and antibiotic prescription practices.

A somewhat less successful effort, so far, has been the campaign within hospitals to persuade health care workers to wash their hands after each patient and to implement other supposedly standard precautions, such as changing gloves when moving from one patient to another. Because many outbreaks of hospital-acquired infections likely spread by contact with health care workers, preventing transmission by this route has become an important priority. Unfortunately, health care workers have gotten out of the habit of washing their hands and instead rely on antibiotics. The high-stress atmosphere of a modern hospital, in which fewer health care workers are expected to treat more and sicker patients, has made it difficult to perform hygienic procedures by the book.

Now that antibiotics are becoming less effective, hygienic practices have become more important than ever, yet there is still considerable disparity among hospitals regarding compliance. An article published in the Wall Street Journal (April 5, 2006) described some of the methods used by hospitals to increase hand hygiene among health care workers. The methods included educational programs, monitoring of activities, disciplinary action, and even dismissal for failure to comply. A more recent trend, the use of alcohol-based antimicrobial gels by health care workers, is starting to make a difference because these gels are more effective than soap and water, require only 15 to 30 seconds of application, and, unlike soaps, do not cause skin dryness.

And Now for Some Good News: You’ve Got a Bacterial Infection!

Who would have thought that a person could be happy to learn that he or she had a bacterial infection? Yet, this is exactly what has happened to people suffering from ulcers and some other chronic infections. The doctrine for decades has been that infectious diseases are acute diseases that develop rapidly and run their course quickly, whereas chronic diseases—diseases that last for long periods of time without resolving—are caused by an autoimmune response, a genetic disorder, or some environmental factor. Examples of chronic diseases are heart disease, Alzheimer’s disease, and cancer. Now, one might ask the question: what if microbes caused these diseases and others like them? They might then be curable by antimicrobial agents or preventable by vaccines or other measures!

The discovery that many cases of liver cancer are caused by the hepatitis B virus made it possible to prevent this type of cancer by an antihepatitis B vaccine. Similarly, the discovery that most gastric and duodenal ulcers and some stomach cancers were caused by bacteria led to a revolution in the way patients with gastric diseases are now treated. More recently, cervical cancer was linked to the presence of human papilloma virus (HPV), and vaccination against HPV is now encouraged for women to prevent cervical cancer. Such examples have spawned a revolution that has led to the reinvestigation of virtually every chronic disease, from heart disease to schizophrenia, for possible microbial or viral origin.

The Helicobacter pylori Revolution

Not all is gloom and doom on the infectious disease front. Frustration over the inability of immunologists to find cures for autoimmune diseases or the inability of physiologists to find cures for heart disease has yielded to optimism as scientists begin to suspect that bacteria or other infectious agents may cause many of these diseases. To most people, taking lifelong medication that does not necessarily prevent the disease is not an acceptable “cure.” Because microbiologists have by far the best track record for cures, the new rallying cry has become “Let’s find the microbe that causes this intractable disease so we can cure it!”

The landmark that dramatically changed the way people think about chronic diseases was the discovery that most gastric inflammation and ulcers are caused by the Gram-negative bacterium H. pylori. This discovery led to a simple antibiotic combination therapy that cures gastritis and ulcers. Although some people have recurrences, the rate of recurrences is far lower than that for conventional treatments, which addressed the symptoms rather than the cause of the disease. Because having ulcers for a prolonged period increases the risk of developing gastric cancer, a particularly dangerous form of cancer, an effective treatment for ulcers should also help reduce the incidence of gastric cancer.

This discovery generated great enthusiasm among gastroenterologists, but when this information first came out, there was one major sector of the health care system that did not share in the celebration: the pharmaceutical companies. Ulcer medications, which had to be taken daily for life—costing patients thousands of dollars a year—were suddenly replaced by a single course of antibiotics that cost as little as $200 per treatment. Seeking to cut their losses, the pharmaceutical companies are now marketing their former prescription ulcer drugs as nonprescription heartburn medications.

The Aftermath

Getting the medical community to accept the idea that bacteria could cause ulcers took many years of acrimonious scientific debate, but once the idea was accepted, first by the research community and then by clinicians, it only took a short time for the world at large to understand that the implications of this discovery went far beyond ulcers. Suddenly, they recalled that if a disease is caused by a bacterium, then it could usually be cured with antibiotics, especially if diagnosed early enough. What followed was a veritable gold rush to find a bacterial cause for other diseases with unknown origins.

A partial list of the diseases currently being reexamined for possible bacterial origins is provided in Table 1-1. The scope of this list conveys better than anything else the boundless optimism that surged through the medical community once the implications of H. pylori as a cause of ulcers were fully appreciated. Table 1-1 indicates that some of these causal associations are well-established, whereas others are still controversial and may not pan out as a direct cause. Yet if even a few of these diseases become curable due to having bacterial origins, a treatment revolution will have occurred. More details about some of these associations will be given in subsequent chapters. It is striking how rapidly great skepticism (about H. pylori as a cause of ulcers) metamorphosed into great optimism about the likelihood of making further discoveries of similar magnitude.

Table 1-1. Some diseases currently suspected of being caused by bacteria

Microbiota Shift Diseases

A category of bacterial disease that defies conventional classification consists of diseases that are not caused by a single bacterial pathogen, but rather by a shift in the composition of a bacterial population of some part of the human body. Although the natural microbial populations (microbiota, formerly called microflora) of the human body are usually protective, certain shifts in the composition of these populations can have pathological consequences. Diseases of this type are referred to as microbiota shift diseases. In chapter 5, “The Normal Human Microbiota,” examples of microbiota shift diseases are described in more detail, but for present purposes, one example should suffice: bacterial vaginosis.

Bacterial vaginosis is the term used to describe a shift in the vaginal microbiota from a predominantly Gram-positive population, dominated by Lactobacillus species, to a population of Gram-negative anaerobes. For a long time, this condition was not taken seriously by physicians because the only symptoms, if there were symptoms at all, were a sparse discharge, some discomfort, and in some women a fishy odor. Two papers in the New England Journal of Medicine in 1995 changed the status of bacterial vaginosis. One of these papers linked bacterial vaginosis with preterm births. This was an epidemiological association, not proof of a cause-and-effect relationship. The second paper described the result of an intervention study, in which antibiotics known to target Gram-negative anaerobes were administered to pregnant women with bacterial vaginosis, and the effect on the birth weight of the infant was determined. Antibiotic intervention that returned the vaginal microbiota to “normal” was associated with normal full-term births, whereas untreated women were significantly more likely to have preterm infants.

Soon after these first connections were made, bacterial vaginosis was linked to a higher risk of contracting HIV infections and other sexually transmitted diseases, just as chlamydial disease and gonorrhea had been shown previously. A major challenge for scientists trained in the analysis of diseases caused by a single species of microorganism is to learn how to deal technically and conceptually with polymicrobial diseases caused by shifts in bacterial populations consisting of hundreds of species. Undoubtedly, all of the species present are not equal contributors to the disease state, but the situation is far more complex than single-microbe infections.

A Brave New World of Pathogenesis Research

The H. pylori revolution captured the public imagination, but an even more important revolution has been the realization by research scientists that new molecular technologies are opening up a plethora of new opportunities to understand at the molecular level how infectious diseases develop. For several decades after the discovery of antibiotics, during a period in which a number of new vaccines were developed, it seemed sufficient to simply treat or prevent bacterial diseases. As long as antibiotics worked and vaccines were widely available, controlling bacterial infections at the practical level did not require in-depth information about the bacterium-host interaction. As physicians and scientists became concerned about increasing antibiotic resistance, there was a growing realization that a better understanding of the detailed interactions between the human body and the bacterial pathogen might lead to new treatment strategies.

Additionally, there was recognition that there are some diseases whose symptoms are caused by bacterially produced toxins that are not effectively treated by antibiotics. A good example is anthrax, a disease caused by Bacillus anthracis. The symptoms of this disease are caused by a protein toxin, produced and secreted as the bacteria multiply in the body. If the disease is diagnosed immediately and the right antibiotic is administered, the disease can be controlled. However, antibiotics do not inactivate the toxin, and if antibiotic therapy is delayed for even a few days, enough anthrax toxin will have been produced to cause death.

In the case of a disease called septic shock that develops when bacteria enter and proliferate in the bloodstream (sepsis), a nonprotein component of the Gram-negative bacterial cell surface, lipopolysaccharide (LPS) (see Box 1-4), acts as a toxin that leads to organ damage and death. Here too, antibiotics are only effective if they are administered very early in the infection before the bacteria lyse and release too much of this toxic material. Although anthrax is not a significant threat (other than as a potential bioweapon), septic shock continues to kill tens of thousands of people each year in the United States alone. As discussed in later chapters, new understanding has recently emerged about how the human body responds to LPS, as well as to nonprotein surface components of Gram-positive bacteria, such as lipoteichoic acid (LTA). There is growing hope that this knowledge will make possible new and more effective therapies.

Box 1-4.

A Brief Review of the Surfaces of Gram-Negative and Gram-Positive Bacteria—One Membrane versus Two

For convenience, bacteria are often divided into two main groups, Gram positive and Gram negative, based on their ability to retain a purple dye after being washed with organic solvent such as methanol or acetone (this procedure of coloring bacteria is called Gram staining). The LPS is located at the surface of Gram-negative cells and is composed of lipid A (composed of fatty acids and a disaccharide), the core oligosaccharide, and the repeating-unit O-antigen polysaccharide (panel A). The LPS forms the surface of the outer membrane, whose inner layer is composed of phospholipids. The thin peptidoglycan (also called murein) of Gram-negative species is located in the periplasm between the inner and outer membrane.

In contrast, the cell wall of Gram-positive species lacks LPS and an outer membrane (panel B). The thick peptidoglycan is composed of multiple, cross–linked layers. A substantial amount of the Gram-positive cell wall is made up of another anionic polymer called wall teichoic acid (WTA, or TA) and lipoteichoic acid (LTA), both of which contain repeat units of ribitol or glycerol phosphate linked to amino sugars, sometimes to amino acids, such as D-alanine, and sometimes to ternary amines, such as phosphorylcholine. TA is covalently bonded to the peptidoglycan, whereas LTA is linked to a lipid anchor in the cellular membrane.

Other bacteria have cell walls with compositions that are a variation on one of these two types plus a few different components. For instance, the cell wall of mycobacteria, including Mycobacterium tuberculosis (the causative agent of tuberculosis), is similar to Gram-negative bacteria, but mycobacteria have a thick outer membrane comprised of two leaflets: an inner leaflet composed of arabinogalactan and mycolic acid (hence the name “mycobacteria”) and an outer leaflet composed of phosphoglycolipids (panel C). Further details can be found in The Physiology and Biochemistry of Prokaryotes, 4th Edition by David White, James Drummond, and Clay Fuqua (Oxford University Press, 2011).

It should be noted that the differences in bacterial surfaces and their components between Gram-positive and Gram-negative bacteria often dictate how they interact with their environments and, in particular, how they interact with their hosts. Importantly, the host immune system responds quite differently to these components. The properties conferred by these components necessitate that hosts have alternative strategies to recognize and combat Gram-negative versus Gram-positive pathogens. The presence of the outer membrane in Gram negatives also creates an extra challenge for the bacteria to export molecules on its surface and to secrete its toxins and other virulence factors into the external medium.

A different type of question is why different people respond differently to the same bacterium. In some cases, the human response can range all the way from a virtual lack of symptoms in some individuals to severe illness and death in others. Taking this issue one step further, prior exposure to one microbe can impact the nature and degree of response to subsequent exposure to another microbe. Indeed, it is now well-established that maternal exposure to pathogens or their components (e.g., LPS) modulates the immune competence and immune response of offspring in species ranging from insects to plants to birds and mammals. Clearly, it would be helpful to understand this range of reactions so that people who are most susceptible to an infectious agent could be quickly identified and given priority in treatment.

These and similar practical problems with controlling bacterial infections have driven a new interest in the interaction between bacteria and the human body at the molecular level. Fortunately, a cornucopia of new molecular tools and paradigms has become available that have made it possible to explore the host-pathogen interaction in a detailed way. It has even become more feasible to investigate infections that involve more than one species of bacteria or infections in which the bacterial pathogen acts in an area of the body, such as the mouth or small intestine, where there are many other bacteria that may influence the course of the disease.

The New Age of Genomics

Tremendous breakthroughs in DNA-sequencing technologies and bioinformatics now allow scientists to rapidly sequence, analyze, and study entire bacterial genomes (also known as genomics). There are now more than 13,000 complete genome sequences for bacteria, about half of which are from medically relevant bacteria, and there are over 175,000 incomplete or ongoing bacterial sequencing projects. These numbers and the pace of discovery are staggering considering that only a handful of complete bacterial genomes were available in the year 2000. At one time, it would have made sense to provide a list of available genome sequences, but additions to this list are coming so fast that the best solution is to provide the address of a website that keeps track of genomes that have been or are being sequenced: https://gold.jgi.doe.gov/.

Once a genome sequence becomes available, scientists examine the open reading frames (orfs) (i.e., the putative genes) one by one to try to assign each gene a name and function. In some cases, this process of genome annotation is easy, because the gene and its expressed protein product have already been characterized. In other cases, tentative identification of a gene is made on the basis of similarities to known genes or proteins present in other organisms that have been deposited into public repositories for DNA and protein sequences—DNA databases and protein databases, respectively. These automated assignments are useful but should be treated with some degree of caution, as many are based on relatively poor sequence matches. The best way to approach DNA sequence data is to realize that the function of a gene based on its sequence similarity to known genes is only a hypothesis that needs to be confirmed by more rigorous testing. A sobering fact is that even in the case of well-studied bacteria, such as E. coli and Salmonella, at least one-third of the genes in their genomes have no similarity to any known genes. A challenging job for future scientists is to determine the biological role of these genes of unknown function.

The way in which DNA sequence information can reveal surprising things about an organism is illustrated by the genome sequence of Borrelia burgdorferi, the spirochete that causes Lyme disease. Scientists noted that no genes corresponding to the usual iron-containing proteins normally found in bacteria were present in the genome of this organism. This suggested a radical hypothesis: that B. burgdorferi copes with the problem of low iron concentrations in the mammalian host by not using iron at all. Instead, its proteins use other metals that are abundant in humans, such as manganese. Scientists who were trained in an era in which every article on iron utilization by bacteria started by describing that all bacteria require iron were startled by this suggestion. Biochemical analyses confirmed, however, that indeed B. burgdorferi apparently does live without the need for iron, thus solving one problem most other pathogens have to confront: how to obtain iron in a host whose iron sequestration mechanisms keep the supply of available iron very low. As can be seen from this example, genome sequences not only provide valuable insights into unique bacterial metabolic processes, but also are excellent hypothesis-generating tools for understanding virulence mechanisms.

Along with the availability of complete genome sequences has come new technology enabling the high-throughput sequencing of an organism’s total RNA (RNA-seq, also called whole transcriptome shotgun sequencing). This technology has provided the means for scientists to measure the expression of thousands of genes in a single experiment. If the number of bacteria is high enough in a body site of a colonized or infected animal, RNA isolated from bacteria growing under these in vivo conditions can be obtained and analyzed by RNA-seq to assess the expression profile (i.e., the transcriptome) of different genes in the animal. Comparison of this expression profile with that obtained from bacteria grown outside of the host body has led, in turn, to the identification of genes that are only expressed during an infection and that might contribute to virulence in the host.

Another form of genomic analysis being used to detect and identify unknown pathogenic bacteria takes advantage of the fact that ribosomal RNA (rRNA) genes contain highly conserved regions of sequence separated by more variable regions. PCR primers that target conserved regions of the rRNA genes are used to amplify these genes from genomic DNA extracted from tissue suspected to contain an infectious organism. The PCR-amplified DNA is called an amplicon. Of course, if there are no bacteria present or if the level of bacterial DNA is too low, no PCR amplicon will be obtained; however, if an amplicon is obtained, its sequence can be determined and compared to the thousands of rRNA gene sequences now available in the DNA databases.

The variable regions of the 16S rRNA gene are particularly valuable in helping determine what known microbe is most similar to the one found in the diseased tissue. The next step is to establish whether the amplified DNA that comes from that organism is present in all cases in which there are similar symptoms of disease. The first unknown organism to be identified in this way was the bacterium that causes a rare intestinal disease called Whipple’s disease (Tropheryma whipplei). Currently, this approach is being used in an attempt to identify bacterial pathogen(s) thought to be responsible for other diseases with unknown causes (i.e., etiology), such as bacterial vaginosis, atherosclerosis, and inflammatory bowel disease.

Insights into Pathogen Evolution

A current preoccupation of many infectious disease researchers interested in deciphering the root causes of pathogen evolution and the dynamics of epidemics is to combine epidemiological and evolutionary knowledge about pathogen virulence gleaned from genomics. Application of mathematical modeling is then used to gain better understanding of pathogen physiology, ecology, and disease transmission. In formulating these models, the two most common assumptions are that pathogens evolve in response to selective pressures placed on them by their environment, namely the host—and, as we are beginning to learn, also the external environment—and that virulence (i.e., the deleterious effects of the pathogen on its host) is directly proportional to its ability to be transmitted.

Recent studies along these lines have provided new insights into the potential effects of imperfect vaccines and the reemergence of certain diseases once thought eradicated (or at least well-controlled) through vaccination, such as whooping cough. It has been a generally accepted premise that infection with one strain of a bacterial pathogen will significantly reduce the susceptibility of the host to subsequent infections with other related bacterial strains due to the host’s acquired immunity. However, these recent studies now indicate that the selective pressure of immunization may also be driving the evolution of pathogens like Bordetella pertussis, the bacterium responsible for whooping cough. Genomic sequence comparisons indicate that Bordetella strains, against which most of the current vaccines were designed and used extensively in developed countries, have now been replaced in the population by novel variant strains lacking key components previously recognized by the immune system to help clear the pathogen from the body. Experiments in mice further suggest that the existing vaccines are less protective against some of these new variants.

Modeling the Host-Pathogen Interaction in Experimental Animals

Studies of disease-causing bacteria growing under laboratory conditions need to be supplemented by studies in animal models. The most familiar type of infectious disease model is the laboratory rodent. Inbred strains of mice and rats are widely used as models for the infection process. The availability of animals with known genetic mutations in their defense systems has increased the utility of these rodent models. Numerous examples of the use of these models will be seen in later chapters of this book, including discussions of when it is appropriate to use animals in experimental schemes to study infectious diseases and the ethics of using vertebrate animals in experiments.

A new wrinkle on the animal model story is the increasing range of “animals” used, from the nematode Caenorhabditis elegans to the fruit fly Drosophila melanogaster and the zebra fish Danio rerio. Certainly, one motivation for using such models is the fact that the complex body of regulations and restrictions that has built up around the use of laboratory rodents and other warm-blooded animals is so complicated and expensive that only the best-funded laboratories can use them. However, more compelling reasons for the use of these new models are that so much is known about their genetics and that they are much more easily and rapidly genetically manipulated than mammals.

In the case of C. elegans, for example, the developmental origin and fate of every cell in the whole organism is known. Drosophila has a long history of use as a model for insect and human genetics, and many characterized mutants are available. In fact, a type of receptor on human neutrophils that is important for responding to bacterial infections (Toll-like receptors) was first discovered in Drosophila (Toll receptors). The zebra fish is a newer infection model, but it also has some of the same attractive features as the nematode and fruit fly models (e.g., small size, easy maintenance, short generation time, and ease of genetic manipulation). Zebra fish have the added advantage that they have somewhat more advanced host defense systems than the nematode and fruit fly and are thus a better model for the human immune system, particularly with regard to aquatic pathogens.

Given the genetic distance between these animals and mammals, a certain degree of care must be used in choosing the experimental questions and interpreting the results. For example, although nematodes, fruit flies, and zebra fish have phagocytic cell defenses that exhibit some similarities to that of humans, the systems are not identical and are evolutionarily distant from mammals. For example, insects and worms lack adaptive immune responses as are found in humans and other mammals, and so cannot be used to study antibody responses and inflammation. They also lack many of the immune signaling components present during infection in mammals. While zebra fish are genetically tractable vertebrate models with complete adaptive immune responses in adults, only a few of the immune components have been functionally studied thus far. Indeed, recent studies have also revealed questions regarding the evolutionary conservation of some of the processing and activation of inflammation in zebra fish. Nonetheless, these simple models can be used to generate hypotheses that can later be tested in laboratory rodents or other animals and, in some cases, humans.

Correlation Studies

Another type of modeling that has been used for a long time in epidemiological studies but is relatively new to pathogenesis studies is the statistical analysis of not just microbial populations, but also human and animal populations. At present, this type of modeling is still rather unsophisticated and based on seeking correlations between traits of the organism and outcomes of disease. In other words, the model can be used to ask whether the production of a particular protein is associated in a statistically significant fashion with various aspects of the disease progression in humans. This approach has the advantage of being easy to do because one merely needs to apply preexisting statistical methods. There are, however, two rather serious problems with this approach.

First, this kind of “modeling” is not modeling in the sense that this term is used in physics or chemistry, in which principles are first expressed mathematically in a way that generates specific predictions about the outcome of an experiment. Instead, correlation studies are usually performed without any clear idea of a theoretical connection between the parameters being tested. As such, finding a correlation does not prove cause and effect. There is an urban legend that illustrates this. A gentleman in California happened to pull down a shade in his apartment just before the onset of a particularly severe earthquake and remained convinced for the rest of his life that pulling down the shade had helped to cause the earthquake.

A second problem is that the items to be checked for correlation are chosen by the researcher, and there may or may not be some theoretical underpinnings to the choice. These problems do not necessarily make the correlation studies inappropriate, but these issues do emphasize the need for scrutiny. If the approach is treated as one for potentially generating hypotheses rather than as a method that provides a proof of cause and effect, then the objections disappear. As more mathematicians, physicists, and bioinformatists are becoming interested in applying their tools to study infectious diseases, more sophisticated modeling approaches are beginning to emerge.

As important as new technologies have been, the most important advance has been a new appreciation for the importance of focusing not just on the properties of a bacterium in a test tube, but also on the myriad ways in which the bacterium interacts with its environment and stimulates responses from the human body. In this book, we will place great emphasis on this bacterium-host interaction. It will become clear very quickly that although considerable progress has been made, there is much to be learned and many opportunities for readers of this book to participate in future research in the area of bacterial pathogenesis.

SELECTED READINGS

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Questions

1. The number of human deaths is often used as a standard for ranking human diseases in terms of importance. What, if anything, is wrong with this classification scheme?

2. Infectious diseases have obvious deleterious effects on the infected individual. Are there other consequences that reach beyond the infected person to his or her family and to society as a whole?

3. The United States and most developed countries have long had medical communities that focus on therapy rather than prevention. Why is this the case and under what conditions might this emphasis be appropriate? Why are scientists arguing for a return to a prevention-based health care system?

4. In our classification of emerging or reemerging infectious diseases, we treated antibiotic-resistant bacteria and E. coli O157:H7 as new diseases. Make the case for and against considering a member of an established disease-causing species that acquires a new trait as a new disease entity. What is the significance of such changes in bacterial pathogens and our ability to treat them?

5. The bacteria that cause the diseases cholera and tuberculosis are much more infectious than the so-called “opportunists.” Why then are these opportunists currently much more of a health concern in developed countries than cholera or tuberculosis?

6. Under what conditions—assuming no new epidemics—could infectious diseases suddenly move to the second or even first most common cause of deaths in the United States?

7. Do you think humans will ever win the battle against disease-causing bacteria? Why or why not? Is the use of warlike language to describe the relationship between humans and bacteria even accurate?

8. Microbiologists are fond of saying that only a tiny minority of bacteria causes disease. Are there reasons for thinking this might not be true?

9. In what sense are bacteria life-givers rather than life-takers? Is it possible that disease-causing bacteria might have a beneficial role in another context or even in their relationship with the human body?

10. There are many diseases that manifest in a variety of ways in different, apparently healthy individuals (e.g., a bacterium may cause a mild fever and malaise in one person, while causing life-threatening disease in another). What are some of the factors that may contribute to this phenomenon?

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