Prologue

To a great extent, the Forum on Microbial Threats (hereinafter, the Forum) owes its very existence to the life and legacies of the late Dr. Joshua Lederberg. Dr. Lederberg’s death on February 2, 2008, marked the departure of a central figure of modern science. It is in his honor that the Forum hosted this public workshop on “microbial evolution and co-adaptation” on May 20 and 21, 2008.

Along with the late Robert Shope and Stanley C. Oaks, Jr., Lederberg organized and co-chaired the 1992 Institute of Medicine (IOM) study, Emerging Infections: Microbial Threats to Health in the United States (IOM, 1992). The Emerging Infections report helped to define the factors and dynamic relationships that lead to the emergence of infectious diseases. The recommendations of this report (IOM, 1992) addressed both the recognition of and interventions against emerging infections. This IOM report identified major unmet challenges in responding to infectious disease outbreaks and monitoring the prevalence of endemic diseases, and ultimately led to the Forum’s creation in 1996 (Morse, 2008). As the first chair of the Forum, 1996–2001, Dr. Lederberg was instrumental in establishing it as a venue for the discussion and scrutiny of critical—and sometimes contentious—scientific and policy issues of shared concern related to research on and the prevention, detection, and management of infectious diseases and dangerous pathogens.

Lederberg’s influence may readily be appreciated in the 2005 Forum workshop Ending the War Metaphor: The Changing Agenda for Unraveling the Host-Microbe Relationship (IOM, 2006a). Its central theme was derived from a comprehensive essay entitled “Infectious History” that he published several years earlier in Science (Lederberg, 2000; reprinted as Appendix WO-1). Under the heading, “Evolving Metaphors of Infection: Teach War No More,” Lederberg argued that “[w]e should think of each host and its parasites as a superorganism with the respective genomes yoked into a chimera of sorts.” Thus began a discussion that developed the concept of the microbiome—a term Lederberg coined to denote the collective genome of an indigenous microbial community—as a forefront of scientific inquiry (Hooper and Gordon, 2001; Relman and Falkow, 2001).

Having reviewed the shortcomings and consequences of the war metaphor of infection, Lederberg suggested, in the same essay, a “paradigm shift” in the way we collectively identify and think about the microbial world around us, replacing notions of aggression and conflict with a more ecologically—and evolutionarily—informed view of the dynamic relationships among and between microbes, hosts, and their environments (Lederberg, 2000). This perspective recognizes the participation of every eukaryotic organism—moreover, every eukaryotic cell—in partnerships with microbes and microbial communities, and acknowledges that microbes and their hosts are ultimately interdependent upon one another for survival. It also encourages the exploration and exploitation of these ecological relationships in order to increase agricultural productivity and to improve animal, human, and environmental health.

The agenda of the present workshop demonstrates the extent to which conceptual and technological developments have, within a few short years, advanced our collective understanding of microbial genetics, microbial communities, and microbe-host-environment relationships. Through invited presentations and discussions, participants explored a range of topics related to microbial evolution and co-adaptation, including: methods for characterizing microbial diversity; model systems for investigating the ecology of host-microbe interactions and microbial communities at the molecular level; microbial evolution and the emergence of virulence; the phenomenon of antibiotic resistance and opportunities for mitigating its public health impact; and an exploration of current trends in infectious disease emergence as a means to anticipate the appearance of future novel pathogens.

Organization of the Workshop Summary

This workshop summary was prepared for the Forum membership by the rapporteurs and includes a collection of individually authored papers² and commentary. Sections of the workshop summary not specifically attributed to an individual reflect the views of the rapporteurs and not those of the Forum on Microbial Threats, its sponsors, or the IOM. The contents of the unattributed sections are based on presentations and discussions at the workshop.

The workshop summary is organized into chapters as a topic-by-topic summation of the presentations and discussions that took place at the workshop. Its purpose is to present lessons from relevant experience, to delineate a range of pivotal issues and their respective problems, and to offer potential responses as discussed and described by workshop participants.

Although this workshop summary provides an account of the individual presentations, it also reflects an important aspect of the Forum philosophy. The workshop functions as a dialogue among representatives from different sectors and allows them to present their beliefs about which areas may merit further attention. The reader should be aware, however, that the material presented here expresses the views and opinions of the individuals participating in the workshop and not the deliberations and conclusions of a formally constituted IOM study committee. These proceedings summarize only the statements of participants in the workshop and are not intended to be an exhaustive exploration of the subject matter or a representation of consensus evaluation.

Scientist

“Joshua Lederberg has been the dominant force that shaped our thinking, responses, and intellectual understanding of microbes for much of the last half of the twentieth century,” Mahmoud remarked. From his early, Nobel Prize–winning work on bacterial recombination, accomplished while he was barely 20, through the last years of his life, when he continued to provide much sought-after advice to global policy makers on emerging infectious diseases and biological warfare, Lederberg extended his command of microbiology to profoundly influence a host of related fields, including biotechnology, artificial intelligence, bioinformatics, and exobiology. Exobiology, the study of extraterrestrial life, was one among many widely used terms coined by Lederberg, according to Stephen Morse. He also noted along with several other participants that the hero of the classic science fiction novel The Andromeda Strain⁴ (Crichton, 1969), Dr. Jeremy Stone, may well have been based on Lederberg. Ultimately, Lederberg viewed his wide-ranging scientific interests through the lens of evolution. According to Morse, the unifying theme of Lederberg’s scientific studies was to characterize sources of genetic diversity and natural selection.

Nowhere is Lederberg’s comprehensive view of microbial evolution and its consequences more evident than in his essay, “Infectious History” (Lederberg, 2000), which informed the workshop’s agenda and serves as a framework for this workshop overview. Referring to that landmark publication as “the Bible of infectious diseases,” Mahmoud observed that it laid out “fundamental concepts that we are still debating about [including] the evolutionary biology and the ecology of microbes.”

From his earliest years, Lederberg embodied scientific curiosity and innovation, David Hamburg noted. He recalled Lederberg’s knack for “turning an issue on its head, and thereby illuminating it,” and added that he “took deep, deep satisfaction in discovery, his own and others,” which was apparent in his relentless questioning. Lederberg “was a great challenger of the scientific community to pursue many ramifications of questions that appeared to be, at least for the time being, answered but were never answered for him,” Hamburg said. “This inter-related set of attributes characterized Josh all his life and had much to do with his great accomplishments.”

Hamburg recounted that Lederberg entered medical school at Columbia University with this intense curiosity and sense of discovery, as well as a desire to improve the lot of humanity and to relieve human suffering. Fascinated with bacterial genetics, however, Lederberg took a one-year leave from medical school to work on Escherichia coli with Edward Tatum, at Yale University, in 1946. “This was groundbreaking, highly imaginative work on the nature of microorganisms, especially their mechanisms of inheritance,” Hamburg said. “It opened up bacterial genetics, including the momentous discovery of genetic recombination,” a line of inquiry that paved the way for Lederberg’s being awarded the Nobel Prize in Physiology or Medicine in 1958, along with Tatum and George Beadle for “discoveries concerning genetic recombination and the organization of the genetic material of bacteria.”

Following an extremely successful first year of research in Tatum’s laboratory, Lederberg decided to take another year away from medical school and continue to explore bacterial genetics. “We lost the budding physician in Joshua Lederberg by the end of the second year, because he was offered a faculty position at the University of Wisconsin,” Mahmoud explained, “but that did not stop Joshua Lederberg from being at the forefront of those concerned about human health and well-being.”

According to Forum member Jo Handelsman, professor of bacteriology at the University of Wisconsin, Lederberg’s influence reverberates to this day. “He left behind the great legacy of his research and the spirit of a truly great mind in science,” she said, as well as stories that have attained the status of “urban legends.” At Wisconsin, Lederberg also established the legendary habit of appearing to sleep during seminars, after which he would ask difficult and probing questions. This habit was still in evidence in the early 1990s during his co-chairmanship of the first IOM study on emerging infections, according to Forum member Enriqueta (Queta) Bond, president of the Burroughs Wellcome Fund. “I was the executive officer at the Institute of Medicine when the first Emerging Infections report was done,” she recalled. “I remember coming to one of the first meetings of the committee, and … Josh would sit there and you would think, ‘Is he awake? He’s supposed to be chairing this committee.’ … Then you would get the zingers from Josh: just the perfect question to move the agenda, develop the next topic, and so forth.”

Indeed, Morse said, Lederberg “was never happier than when he was absorbing knowledge and questioning it. I like to think of this, with all of us here, as being an important part of Josh’s legacy,” he added. Hamburg recalled Lederberg’s “rare capacity to range widely with open eyes and open mind, and also dig deeply at times into specialized topics; to combine these capacities in research, education, and intellectual synthesis led to so much fruitful stimulation in a variety of fields.”

“He believed that there are no limits to what the human mind can accomplish, especially when its power is hitched to a willingness to think boldly and unconventionally, and to hard work,” Mahmoud said. “Until almost the day he died, Joshua could be found in his office, in his apartment, working. His mind was always thinking, always probing, always questioning.” Indeed, during his last days, Lederberg offered insightful advice to his longtime friend Hamburg, who was editing the final draft of his recently published book, Preventing Genocide: Practical Steps Toward Early Detection and Effective Action (Hamburg, 2008). “We had a couple of very intensive hours in which he asked his usual penetrating questions and clarified key issues, and then was obviously quite exhausted,” Hamburg recalled. “We were prepared to take him back home. He said, ‘No. I’d like to rest for an hour or so and come back. I have one more chapter I want to discuss.’”

“We did that,” Hamburg continued. “It was vintage Josh. He mobilized himself to address an important problem with a friend that he valued and made an important contribution. The final changes in the book—all improvements—were due to that conversation.”

Academic

Another tribute to Lederberg’s remarkable capacities was institutional innovation, Hamburg observed. When Lederberg created departments of genetics in the medical schools at the University of Wisconsin and Stanford University, Hamburg recalled, “[the field of] genetics had been marginal or nonexistent in medical schools. There was a widely shared assumption, in the middle of the twentieth century, that genetics might be intrinsically interesting, but it would never have much practical significance for medicine.”

“In teaching and in institution building, Lederberg emphasized the mutually beneficial interplay of basic and clinical research,” Hamburg continued. Lederberg, he said, helped clinical departments at Stanford University’s School of Medicine build interdisciplinary groups and identify research opportunities and promising lines of innovation. He fostered many lines of inquiry within his own Department of Genetics at Stanford—including molecular genetics, cellular genetics, clinical genetics, population genetics, immunology, neurobiology, and exobiology (particularly in relation to the National Aeronautics and Space Admininstration’s [NASA’s] Mariner and Viking missions to Mars)—and hired a superb group of internationally-known researchers, including Walter Bodmer and Eric Shooter from the United Kingdom, Luca Cavalli-Sforza from Italy, and Gus Nossal from Australia, Hamburg recalled. He also recruited from within the university, including speaker Stanley Cohen, who eventually succeeded Lederberg as chairman of the genetics department at Stanford. By taking this action, Hamburg said, Lederberg “was not robbing another department, but rather opening up an opportunity that Stan [Cohen] wanted and needed, and, of course, in which he made tremendous contributions.”

While at Stanford, Lederberg also made a major contribution to undergraduate education, establishing a cross-disciplinary program in human biology that remains one of the university’s most sought-after majors. Hamburg—who as chairman of Stanford’s psychiatry and behavioral science department, assisted in this effort along with Donald Kennedy, then the chairman of Stanford’s biology department—remarked that the program might not have had such a long and illustrious history if Lederberg had not insisted that it include endowed chairs.

Following his years at Stanford, Lederberg’s “rich experience, knowledge, skill, and wisdom were brought to bear on Rockefeller University under his presidency, broadening the scope of its great faculty, opening new opportunities for young people, and greatly improving the facilities,” Hamburg said. Although admitting that he did not at first think university administration was the best use of his friend’s talents, Hamburg recognized that Lederberg adapted well to his new responsibilities and proved adept both as a financial and a human resources manager who was deeply concerned about the personal well-being of his faculty.

While it seems that nothing was too big for Lederberg to tackle, Forum member Gerald Keusch of Boston University described how he had benefited from Lederberg’s willingness to address what might have seemed a small issue. During the mid-1990s, National Institutes of Health (NIH) director Harold Varmus was thinking about the impact on NIH of shrinking the number of institutes and centers, beginning with the Fogarty International Center. “Harold is a very smart person and knew there were going to be problems in trying to change the status quo. How to proceed? You form a committee to give you the recommendation that allows you to go ahead and act,” Keusch recalled. “So he asked Josh and Barry Bloom⁵ to do a review of the Fogarty and all international programs at the NIH.” Lederberg and Bloom proceeded to conduct an exhaustive study, which ultimately recommended that the Fogarty be strengthened, not disbanded. As a result, a new position was created—for which Keusch was hired—to direct the Fogarty International Center and serve as the NIH’s associate director for international research.

After five years in this position, Keusch asked Lederberg and Bloom to return and review the Fogarty’s progress. Although unwell and not traveling as he once had, Lederberg did not hesitate “to come back to do an honest, objective review and [once again] come out strongly in favor of the Fogarty’s international mission,” Keusch said. “You might have thought, in 1996, that Fogarty and the international programs at NIH would not have attracted [Lederberg’s] attention. But they did, and I think the Fogarty is certainly the better for it, [as] is NIH.”

Global Citizen

Achieving the Nobel Prize at the age of 33 gave Lederberg a global perspective that he fully embraced in the subsequent half-century, according to Mahmoud. In so doing, Lederberg undertook multiple roles, including advisor to governments, institutions, and industry, as well as educator of the general public.

“Every president from John F. Kennedy to the current administration sought Joshua’s advice and consultation,” Hamburg said. “He chaired and studied issues from space science to human and artificial intelligence, to human-microbe interplay.” Lederberg advised many agencies in the United States, most notably the NIH, the Centers for Disease Control and Prevention (CDC), the National Science Foundations (NSF), NASA, the Office of Science and Technology Policy (OSTP), and the Department of the Navy. He also served as an advisor to the World Health Organization (WHO) and was particularly influential as that organization attempted to establish regional surveillance centers for emerging infectious diseases. Forum member James Hughes, of Emory University, remarked that Lederberg was “very engaged in Geneva, to the point that he took it upon himself to meet with the director-general of the WHO at the time, Dr. Hiroshi Nakajima. I am sure this is one of the reasons that WHO went on to develop its emerging infections focus.”

“Josh used to go to Washington sometimes three times a week, back and forth, to give scientific advice,” Morse recalled. “He was the model of the scientific adviser. His advice was honest and dispassionate and in no way self-interested. His interest was furthering the cause of science and humanity.” Morse observed Lederberg had been concerned that samples obtained from space or spaceships might contain extraterrestrial life forms. NASA asked Lederberg how to decontaminate such samples and what precautions should be taken with them. “He gave very freely of his advice,” Morse said. “This led, I think, to one of the most interesting job descriptions I have ever seen. NASA created a position called ‘planetary quarantine officer.’⁶ Those of us who talk about emerging infections on this world have to realize that Josh’s purview extended far beyond that.”

Emerging infections on Earth did, however, feature prominently in Lederberg’s advisory efforts, as many participants readily acknowledged. According to Mahmoud, “It was Josh, and Josh alone, who articulated and brought to the forefront of the scientific agenda the subject of emerging and reemerging infections.”

Concern about emerging infections has grown following the appearance of new diseases, such as HIV/AIDS, and the reemergence of others, such as dengue, and from appreciation of the complex determinants of their emergence—including microbial adaptation to new hosts (HIV infection, severe acute respiratory syndrome [SARS]), population immunity pressures (influenza A), travel (acute hemorrhagic conjunctivitis), animal migration and movement (West Nile virus infection, H5N1 avian influenza), microbial escape from antibiotic pressures (multidrug-resistant and extensively drug-resistant tuberculosis), mechanical dispersal (Legionnaires’ disease), and others (panel, Figure WO-1; Morens et al., 2008).⁷

FIGURE WO-1

Newly emerging, reemerging or resurging, and deliberately emerging diseases. (A) Selected emerging diseases of public-health importance in the past 30 years (1977–2007), with representative examples of where epidemics occurred. (B) Selected emerging (more...)

Lederberg was also “a pioneer in biological warfare and bioterrorism defense, applying his farsighted vision to efforts to understand the danger and find ways to cope with it,” Morse said, long before that threat was widely acknowledged. “He strongly influenced the negotiation of the biological weapons disarmament treaty.”⁸

When Lederberg first voiced his concerns regarding emerging microbial threats in the late 1980s, Mahmoud recalled, “half of the scientific community was just smiling [as if to say], ‘the old man is just babbling about the subject.’” Instead, the advent of “a fundamental platform,” the 1992 IOM report, “really opened the way for a new way of thinking about microbes … [and also] forced the whole community to come back, in 2003, for the second report on the subject.” Lederberg also co-chaired the committee that produced this second report, Microbial Threats to Health (IOM, 2003), along with current Forum co-chair, Margaret (“Peggy”) A. Hamburg of the Nuclear Threat Initiative/Global Health and Security Initiative (and daughter of David Hamburg).

At an early conference on emerging viruses, in 1989, “somebody asked Josh, when should we declare that a virus is a new species or a new unknown virus?” Morse recalled, to which Lederberg gave the Solomonic answer, “When it matters.” “That was very much Josh’s way, to cut through all of the red tape and all of the inconsistencies and see straight to the heart of the matter,” Morse concluded.

Lederberg strongly believed in educating the public about science and encouraging public discussion of complex and politically and emotionally charged topics, Peggy Hamburg said. The tangible evidence of this belief can be found in the columns on science and society that Lederberg wrote for The Washington Post between 1966 and 1971, and that have been collected by the National Library of Medicine at its website, “Profiles in Science” (NLM, 2008). As David Hamburg remembered, “many in the scientific community thought, why would a person of his gifts devote that kind of time to the public?” Lederberg believed, however, that an informed public was essential not only for good science policy, but ultimately for human survival, Hamburg said. It should be noted that many of his columns in The Washington Post addressed the health implications of environmental conditions.

Forum member Terence Taylor, director of the International Council for Life Sciences, asked Dr. David Hamburg to speculate on what Lederberg would say to the next U.S. president if he had been asked to name priorities for enhancing scientific advice to the nation’s leadership. Hamburg observed that Lederberg “had a fundamental concern about the relationship between scientific expertise and political leadership. On the one hand, he thought it was enormously important for our political leaders to have access to and appreciation of the scientific community…. However, he was equally concerned that we as scientists might inadvertently mislead political leaders, with even the best of intentions.”

Hamburg believed that Lederberg would stress the importance of a diversity of expert advice, through processes that invite experts from different arenas to challenge each other. “He never, I think, to the end of his life, was satisfied that we had found the right formula for that,” Hamburg added, “but I’m sure he would tell the new president, ‘Make much more use of the scientific community than your predecessor has done and do it with much less ideology or political slant…. Don’t just pick people you know, but reach out to get people that you don’t know and have never heard of that you have some reason to believe are excellent.’” Moreover, Hamburg said, Lederberg would encourage further efforts toward improving the yet-unresolved and vital relationship between scientific expertise and political leadership.

“I simply know of no eminent scientist of such immense stature, who gave so much serious analysis of public policy and social problems,” Hamburg concluded. “Our country and the world are in his debt. Those of us here today profoundly appreciate what he did, not just for science, but for humanity. His life exemplified the finest attributes of the great institution in which we meet today to honor his memory.”

Mentor, Colleague, and Friend

In the course of remembering Lederberg’s prodigious accomplishments, workshop participants also reflected upon the ways in which he had touched their lives and careers, further revealing his extraordinary character. Forum co-chair Peggy Hamburg—whose experiences with Lederberg evolved from those of a young daughter of a colleague (exploring tidal pools) to that of a professional peer (co-chairing the IOM Committee on Microbial Threats to Health in the 21st Century)—recalled a man who “loved to go out and walk and talk and study the life on the beach and in the tide pools and see what you could discover in there and how it changed.” He was also the first person she knew who owned a computer: “I remember being brought over and sort of ushered into the room, as though it was almost a temple.” As a child, Lederberg seemed to her “the epitome of a mad scientist.” However, “as I got older and learned more, I realized that he was, in fact, this extraordinary presence in the field of science.”

Peggy Hamburg went on to observe, “I would say that one of the things that I actually appreciated most about Josh was that even though he had gotten to know me when I was just a kid, he was able to make the transition—and I don’t know exactly when it happened—to really treating me as a peer and a colleague. That is, I think, quite extraordinary, particularly in someone of his generation.”

As one might expect, Lederberg’s leisure interests were largely intellectual, including technology in all its forms and reading widely and voraciously (he had a particular fondness for the Times Literary Supplement), according to Morse. “A kind of recreation for him was to meet someone about whom he had heard good things, in a completely, even wildly different field … and through conversation with that person, to get some idea of what was going on in many different fields,” David Hamburg recalled.

He was also a phenomenal correspondent, as attested by many workshop participants who received handwritten notes, telephone calls, and e-mails from him over the years. Lederberg had special memo pads upon which he would write notes that were challenged and challenging to many people, Hamburg included. “At first I thought he was just picking on me,” he said. “He explained to me that he didn’t really expect that the person receiving it would respond or necessarily act on it, but he thought from what he knew of the person’s interest that this was something that he or she ought to know about. It was kind of a way of needling us all to broaden our horizons.”

When he became director of what was then the Hospital Infections Program at the Centers for Disease Control and Prevention, Hughes was at first amazed to be receiving notes from Lederberg, who had been a figure of awe to Hughes as a medical student at Stanford. Then, Hughes said, “I began to get notes from him asking very interesting and challenging questions that I had never been asked before and that, of course, I never knew the answers to and had great difficulty finding anyone else who knew the answers to his questions.”

Speaker Bruce Levin, of Emory University, was equally challenged by communications he received from Lederberg. “It was always a delight for me to receive those e-mails,” he said. “The questions Josh asked would sometimes keep me busy for a day, making me think about things I thought I knew, but really didn’t. While I don’t know whether he got much out of my answers, I know I learned a great deal by thinking about his questions.”

“Josh’s notes have always been insightful,” added Cohen. “I can’t imagine how he found the time to write all of the notes he has written to all of us over so many years, and keep track of our interests, and pick out exactly the relevant things to say at particular times…. I really miss them.”

Speakers Mark Woolhouse, of the University of Edinburgh, and Margaret McFall-Ngai, of the University of Wisconsin, were both surprised to hear from Lederberg when their work caught his attention. In Woolhouse’s case, it was a catalog of human pathogen species (see Woolhouse and Gaunt in Chapter 5), which caused him to reflect that while his group employs various forms of sophisticated mathematics and modeling in many of their studies, “Josh Lederberg liked our work because we can count. So when somebody of that eminence says he likes your work because you can count, you count some more.”

McFall-Ngai was a young associate professor, in 1998, when Lederberg e-mailed her after reading a piece she wrote for the American Zoologist (McFall-Ngai, 1998). “At first I thought it was spam,” she admitted. “Why would Joshua Lederberg write to me? I was getting ready to trash it and I thought, okay, I’ll open this up. It started an e-mail volley between him and me, several back-and-forths, about the role of beneficial microbes.”

In Memoriam

Recalling his own childhood in Egypt, Mahmoud observed that imposing monuments, such as the Great Sphinx, were a testament to the enormous egos of the rulers who ordered their construction. “They wanted to be sure that long after they were gone, people would be able to gaze upon their mighty works and remember that a great man once ruled here,” he said. “Joshua Lederberg, of course, needs no [such] monuments to ensure that his life and work are long remembered. In a very real sense, his accomplishments are embedded in the DNA of many whose lives have been shaped because of his work. That work and those concepts will be passed on to every generation yet to come, long after the Great Sphinx has crumbled into dust.”

“Joshua believed very strongly in the work of this Forum,” Mahmoud continued. “He had great confidence in the ability of scientists and researchers to continue to solve some of the riddles that still confront science in the fight against infectious diseases. By remembering him with this tribute, we are also remembering the many things that his life and career can teach all of us. I hope that every time we meet at this Forum, Joshua Lederberg will be an inspiration and a reminder that our work can truly change the world, just as his life and career certainly did.”

Communities of Microbes and Genes

Exploring the Human Microbiome⁹

Microbes colonize the human body during its first weeks to years of life and establish themselves in relatively stable communities in its various microhabitats (Dethlefsen et al., 2007). The human microbiome is far from being fully appreciated or definitively described. Research to date suggests that while site-specific communities (such as skin, mouth, intestinal lumen, small intestine, and large bowel, to name a few) of most individual humans contain characteristic microbial families and genera, the exact mix of species and strains of microbes present in any given individual may be as unique as a fingerprint. The microbiomes of other terrestrial vertebrates are dominated by organisms related to, but distinct from, those found in humans. This suggests that host species have co-evolved with their microbial flora and fauna.

Through their explorations of the human microbiome, Relman and coworkers seek to understand the role of indigenous microbial communities associated with human health, disease, and the various transition states in between. By understanding essential features of symbiotic relationships between microbial communities and their human hosts, they hope eventually to be able to predict host phenotypes—such as health status—that are associated with particular features of indigenous communities, and potentially manipulate these communities to restore or preserve health. This effort is at an early stage of development, with research focused on identifying elements of microbial communities that can be monitored and measured to assess physical and metabolic interactions within and among microbial communities and between human and microbial cells.

One such important, and measurable, characteristic of microbial communities is their diversity, as reflected in the number of different ribosomal RNA sequences present in a given location in the human body. These highly-conserved sequences also reveal microbial ancestry and phylogenetic relatedness, permitting the construction of phylogenetic trees (see Relman in Chapter 2, especially Figure 2-1). The organisms represented by these sequences remain largely uncultivated. Sequences derived by Relman and coworkers in 2005, from the microbial inhabitants of human colonic tissue, suggested that approximately 80 percent had not yet been cultured, and about 60 percent had not been previously described (Eckburg et al., 2005).

This analysis also revealed a striking diversity of microbes at the genus and species level, but affiliated with relatively few phyla, a pattern apparently common among indigenous microbial communities of vertebrates, but not among microbial communities found in external environments. The dearth of microbial phyla on or within the human body probably results from multiple influences, including selection, environmental factors, and even early opportunistic environmental exposures to particular microorganisms. Further, samples collected from various locations in the gut of several subjects revealed greater variation in the diversity of microbial communities between these hosts than was present within an individual host (Eckburg et al., 2005). Similarly distinct gut communities were found by Relman and coworkers in each of 14 babies, whose feces were sampled periodically throughout the first year of life (Palmer et al., 2007). The composition and temporal patterns of the microbial communities varied widely from baby to baby, especially early in the first year of life, but the patterns converged by the end of the first year towards a distinct signature for each baby, as well as towards a generic adult signature (Figure WO-2).

FIGURE WO-2

Temporal profiles of the most abundant level 3 taxonomic groups. Level 3 taxonomic groups were selected for display if their mean (normalized) relative abundance across all baby samples was greater than 1 percent. The x-axis indicates days since birth (more...)

Clinical problems associated with the human microbiota include chronic peridontitis, Crohn’s disease and other forms of inflammatory bowel disease, tropical sprue, antibiotic-associated diarrhea, bacterial vaginosis, and premature labor and delivery (see Relman in Chapter 2). Considerable evidence suggests that the indigenous microbiota is altered during states of infectious disease, especially those diseases that involve the mucosal or skin surfaces that serve as a contact boundary. In some cases, it appears that the indigenous microbiota propagates the disease process. Treatment of such clinical problems with antibiotics, or diversion of the luminal flow away from a segment of bowel, reduces inflammation and other symptoms. These features suggest a system in which the collective microbial community acts as a pathogen, and in which disease results from community disturbance, rather than from infection by a specific organism or group of organisms. It also invites an ecological view of infectious disease control that seeks to restore community equilibrium following disturbance.

In order to study the effects of such disturbances, Relman and coworkers have examined patterns of microbial diversity in the human gut before, during, and after deliberate, periodic, exposure of healthy human subjects to the antibiotic ciprofloxacin. They identified approximately 5,800 different species or strains of bacteria from these samples, of which only 6 percent had been seen before. All three subjects studied so far showed significant reduction in the number of bacterial species present following antibiotic treatment, the result of which was a partial elimination of the differences in community structure that distinguished the three host individuals.

“What makes the human microbiome so intrinsically interesting, at least to me, is the degree to which it may reflect who we are as individuals and as a host species,” Relman said, and this individuality has implications for health and disease. While the human microbiome remains largely uncharacterized, Relman held out hope that, thanks to the progress of microbiology since van Leeuwenhoek, we now possess sufficient experimental technology and clinical opportunities to explore the microscopic terra incognita¹⁰ within and upon us all.

Biofilms and the Processes That Shape Them

Microbe-microbe relationships include nutritional interactions (e.g., the stepwise processing of plant polysaccharides in the human gut by members of the microbiota) and genetic exchanges that occur through transformation, phage transduction, and conjugation (IOM, 2006a). The last of these processes, bacterial conjugation, first described by Lederberg and coworkers, earned him the Nobel Prize in 1958. Indeed, horizontal gene transfer—also known as lateral gene transfer (Eisen, 2000)—among members of some microbial communities appears to be an extremely pervasive process, but perhaps not to the extent as to call into question whether the concept of speciation applies to communal microbes (Eppley et al., 2007).

Investigations of microbial biofilm communities—which grow on substrates such as rocks in freshwater streams, drains, and teeth¹¹—are providing insights into the ecological and evolutionary processes that shape microbial communities. The microbial constituents of the biofilm known as dental plaque include hundreds of species and strains of bacteria,¹² as well as various methanogens (Archaea) whose collective metabolic activities are associated with gum disease and tooth decay (Lepp et al., 2004). Biofilms containing iron- and sulfuroxidizing microbes also thrive in mines and in watersheds where mine wastes drain, resulting in the release of acids and toxic metals into creeks and streams (Banfield, 2008a). This process, called acid mine drainage (AMD), impairs biodiversity and ecological productivity in aquatic ecosystems and, in some cases, precludes inhabitation by macroorganisms altogether (Klemow, 2008). Horizontal gene exchange appears to help microbes in these biofilms adapt to this extreme environment (Lo et al., 2007).

Banfield and coworkers use mine-derived biofilms as a model system to examine how relatively simple microbial communities (that is, communities dominated by a few types of organisms) organize themselves and how their members interact with each other and their physical surroundings (Banfield, 2008b). Biofilms “grow”—that is, they add or accumulate increasingly large populations of microbes—in stages. In this setting, a biofilm nucleus begins at a stream’s margins and extends across the water’s surface toward its center, while simultaneously increasing in thickness. In her workshop presentation, Banfield described her group’s efforts to characterize this process by comparing genomic and protein profiles of biofilms at early and late stages of development.

Using metagenomic¹³ methods, Banfield and coworkers have constructed near-complete collective genomes from several different mine-derived biofilm communities (see Chapter 2 Overview). These proved to be dominated by members of bacterial Leptospirillum groups II and III, but the biofilm communities also contained several uncultivated Archaea species, as well as some novel organisms. In comparisons of 27 early- and late-stage biofilms, the researchers found that early biofilms, which were dominated—in some cases, almost exclusively—by Leptospirillum group II, later developed into more complex communities with more diverse members, including greater numbers of Leptospirillum group III bacteria and more species of Archaea.

To examine how this changing cast of organisms functions in the community, and how their functions change as the community develops, the researchers used proteomic¹⁴ methods to determine whether, much like the community’s taxonomic composition, the genes being expressed by its members changed over the course of development (see Chapter 2 Overview). Significant shifts in protein expression correlated with the sequential domination of the community by two different but closely-related strains from Leptospirillum group II. This result suggests that different suites of proteins, as well as genotypes, perform different functions at different times in these communities, Banfield concluded.

Further characterization by Banfield and coworkers of 27 biofilms of various stages of development, sampled from eight different microenvironments at the same iron mine, revealed the presence of six distinct genotypes (Lo et al., 2007); each contained blocks of sequence from the two closely-related Leptospirillum group II strains. Many of the biofilm samples were found to contain only one genotype; others had several (Denef et al., 2009). The researchers also examined the distribution of genotypes across the eight sampling sites (Figure WO-3). Over the course of more than two years, they consistently found the same genotype at one site—despite the fact that biofilms at this site would have had constant exposure to other genotypes. Thus, Banfield concluded, there appeared to be strong local selection for this particular genotype, which has “achieved a fine level of adaptation to environmental opportunity” (Figure WO-3).

FIGURE WO-3

Six genotypes of Leptospirillum group II bacteria were detected in the Richmond Mine (Iron Mountain, CA) by proteomic-inferred genome typing and inferred to have arisen via homologous recombination between parental genotypes. The types (shown schematically (more...)

Banfield’s group has also examined the role of viruses in biofilms, and particularly the viral “predators” of the dominant bacterial species in these communities. Their investigations were inspired by recent reports (Makarova et al., 2006; Mojica et al., 2005) that the genomes of most Bacteria and Archaea contain repeat regions, known as clustered regularly interspaced short palindromic repeats (CRISPRs). Derived from coexisting viruses, CRISPRs appear to provide immunity (perhaps via RNA interference) to their possessors for the virus of its derivation. Thus, Banfield said, “a microbe has a level of immunity to a virus, so long as it has the spacers that match it or silence it. It has been shown experimentally by the Danisco Group that should a mutation occur such that the spacer is no longer effective, the virus may proliferate and the microbe will suffer” (Barrangou et al., 2007). However, she added, another component of the bacterial system, CRISPR-associated proteins, rapidly sample the local viral DNA and incorporate new spacers, conferring the population with a range of immunity levels to different mutant viruses as they arise (Tyson and Banfield, 2008).

Taking advantage of the correspondence in CRISPR sequences between viruses and their host microbes (see Chapter 2 Overview), Banfield and coworkers identified the sequences of viruses that target Bacteria and Archaea present in acid mine drainage biofilms (Andersson and Banfield, 2008; Figure WO-4). Their investigation revealed a picture of microbial interaction within the biofilm, where a “cloud of viruses” maintains high levels of sequence diversity by various means in order to defeat host microbes, while the hosts counter by rapidly acquiring viral spacers, and, thereby, immunity. Overall, Banfield said, this dynamic system is probably in stasis; nevertheless, she added, “it’s clearly an example of co-evolution in a virus and host community.”

FIGURE WO-4

Virus-host associations in AMD biofilms. Putative viral (SNC) contigs were clustered based on tetranucleotide frequencies (left panel), and CRISPRs were clustered based on patterns of SNC contig matching (right panel). Columns in the left panel represent (more...)

Models of Coexistence and Cooperation

Quoting Heinrich Anton de Bary¹⁵ in his 1879 monograph Die Erscheinung der Symbios, Ané defined symbiosis as “a prolonged living-together of different organisms that is beneficial for at least one of them.” He noted that this general description applies to a continuum of interactions ranging from the extreme of strict mutualism, which benefits both partners, to the opposite extreme of parasitism, which benefits one partner and is detrimental to the other (Figure WO-5). Individual symbioses evolve over time, and under the influence of a variety of environmental, physiological, and developmental factors.

FIGURE WO-5

The symbiotic continuum. SOURCE: Figure courtesy of John Meyer, North Carolina State University.

In order to capture certain aspects of this complexity and gain insights into the bases of symbioses, biologists develop models of colonization. These fall into two main categories, according to McFall-Ngai: constructed models, based on germ-free hosts such as mice and zebrafish, which allow investigators to study colonization as microbes are introduced in a controlled manner (see, for example, IOM, 2006a); and natural models, which permit researchers to observe the process of colonization, typically by only a few microbial phylotypes, as it occurs naturally in a variety of hosts and sites. Existing models of the latter type include the guts of certain insects (such as the gypsy moth, described below, and by Handelsman in Chapter 4), as well as the two systems described in workshop presentations and discussed below: plant roots and the light organ of the Hawaiian squid.

Plant Root Symbionts

In relationships somewhat analogous to those that exist between mammals and their gastrointestinal microbiota, plants establish mutualistic associations with several microorganisms (see Chapter 2 Overview). The roots of most higher plant species form arbuscular mycorrhiza, associations with specific fungal species that significantly improves the plant’s ability to acquire phosphorus, nitrogen, and water from the soil (Brelles-Mariño and Ané, 2008). This type of interaction dates back approximately 460 million years and has played a central role in the evolution of land plants, according to Ané.

A more recent association, over the past 60 million years, involves legumes and nitrogen-fixing bacteria named rhizobia. The bacteria induce and colonize new organs on the plant’s roots, called nodules; there, they receive energy in the form of carbon from the plant and convert atmospheric nitrogen to ammonia for the plant’s use. This partnership furnishes much of Earth’s biologically available nitrogen and boosts productivity in non-leguminous crops that are grown in rotation with legumes.

Symbiotic relationships between plants and bacteria or fungi are established through chemical and genetic “cross-talk.” As shown in Figure WO-6, legume roots release compounds that trigger nitrogen-fixing rhizobia to express modified chitin oligomers called Nod factors, which in turn facilitate infection of the root by the bacteria, as well as nodule development (Brelles-Mariño and Ané, 2008; Riely et al., 2006). Plants also produce chemical signals called strigolactones that increase branching of fungal hyphae, and thereby increase their contact with arbuscular mycorrhizal fungi. The fungi release diffusible compounds known as Myc factors, which, when recognized by the plant, activate symbiosis-related genes.

FIGURE WO-6

Symbiotic relationship between plants and bacteria. Legume roots release compounds that trigger nitrogen-fixing rhizobia to express modified chitin oligomers called Nod factors, which in turn facilitate infection of the root by the bacteria, as well as (more...)

The discovery that a largely shared signaling pathway makes possible both arbuscular mycorrhization and legume nodulation—despite their apparent differences—has led to the conclusion that plants have a single, highly-conserved genetic program for recognizing beneficial microbes, according to Ané. Both microbial Nod and Myc factors also appear to have common features, including the ability to promote plant growth, which may benefit microbes by increasing the availability of infection sites, he said.

Plant-microbe symbioses do not exist in a vacuum, but are challenged by “cheaters” and parasites (see Chapter 2 Overview). The cheaters include individual rhizobial colonists of legume nodules that do not fix nitrogen efficiently, and thereby act as parasites, receiving carbohydrates without offering anything in return (and without expending the considerable energy involved in fixing nitrogen), Ané explained. However, their hosts appear to have ways of detecting these microbial freeloaders and “sanctioning” them. Some researchers have hypothesized that the plant decreases oxygen supplies to under-performing nodules (Kiers et al., 2003). While the actual mechanism remains unknown, Ané said, he suspects that the plant may starve the cheaters by reducing their access to carbohydrates.

Parasites on plant roots include root-knot nematodes, nearly ubiquitous pathogens that account for up to 10 percent of global crop loss, according to Ané. Evidence suggests that these nematodes infect legume roots by using genetic pathways adapted for rhizobial colonization, perhaps by producing molecular mimics of Nod factors (Weerasinghe et al., 2005). Human pathogens, including Salmonella and E. coli O157:H7, also take advantage of the symbiotic signaling pathway to colonize legume roots, such as alfalfa sprouts, that have been linked to several outbreaks of foodborne illness (Taormina et al., 1999). Characterizing the plant and microbe genes involved in these infections, and understanding how these pathogens override or constrain the plant’s defenses against invading microbes, may reveal ways to prevent such outbreaks.

The Squid and the Bacterium

The Hawaiian squid Euprymna scolopes forms a persistent association with the gram-negative luminous bacterium Vibrio fischeri (Nyholm and McFall-Ngai, 2004). Incorporated in the squid’s light organ, the bacterium emits luminescence that resembles moonlight and starlight filtering through ocean waters, camouflaging the squid—a nocturnal animal—from predators. In her presentation, McFall-Ngai described the process by which the bacterium colonizes the squid’s light organ, which begins within an hour after hatching and appears to occur in stages, each enabling greater specificity between host and symbiont, as shown in Figure WO-7. McFall-Ngai referred to this progression as “a fairly well-orchestrated minuet between the host and the symbiont” that induces the maturation of the squid’s light organ, as well as developmental changes that appear to exclude colonization of the organ by other bacterial cells. She noted that much of this process is signaled by microbe-associated molecular patterns (MAMPs).¹⁶

FIGURE WO-7

The “winnowing.”. This model depicts the progression of light-organ colonization as a series of steps, each more specific for symbiosis-competent Vibrio fischeri. (a) In response to gram-positive and gram-negative bacteria (alive or dead) (more...)

Using a range of molecular approaches, McFall-Ngai and coworkers are engaged in characterizing the colonization of the squid light organ and the maintenance of its symbionts in exacting detail, “to get an hour-by-hour view of the conversation that the host has with its bacterial partner,” McFall-Ngai explained. Among the many squid genes that are transcriptionally upregulated in response to colonization by V. fisheri, the researchers identified 18 genes that are also upregulated during the colonization of both mouse and zebrafish guts, as determined in constructed models (Chun et al., 2008; see McFall-Ngai in Chapter 2). These shared genes encode proteins that are components of cellular pathways involved in transcriptional regulation, oxidative stress, and apoptosis—responses that typically have been associated with pathogenesis, McFall-Ngai noted. Instead, she said, these pathways constitute a “language of symbiosis,” by which a host “talks” to a bacterial colonist, which in most cases is not a pathogen (see the following section for an extended discussion of microbial pathogenesis and the host response).

“What I think this demands of biologists … is to go back and question our basic premises about how bacteria and animals work together, what virulence factors really are, and such host behaviors as inflammation, tolerance, and carriage,” she concluded. “The horizon, then, is how these characters of host and symbiont are controlled to result in a mutualistic, commensal, or beneficial association.”

The Nature of Bacterial Pathogenicity

As Lederberg’s observation above suggests, and studies of indigenous microbial communities attest, coexistence between host and microbe is a dynamic equilibrium (Blaser, 1997; Lederberg, 2000). In the case of microbes that cause persistent, asymptomatic infections, physiological or genetic changes in either host or microbe may shift the relationship toward microbial invasion of host tissue, which typically results in an immune response that destroys the invading microbes, but which may also injure or kill the host (Dethlefsen et al., 2007; Merrell and Falkow, 2004).

Research in the decades following Lederberg’s ground-breaking work on bacterial conjugation has revealed the following fundamental characteristics of bacterial pathogens, as noted by Falkow (see also Chapter 3):

• Bacteria manipulate the normal functions of host cells in ways that benefit the bacteria (see Falkow’s Figure 3-1 in Chapter 3).
• Horizontal gene transfer via mobile genetic elements has shaped the evolution of bacterial specialization.
• Pathogenicity is generally conferred through the inheritance of blocks of genes, called pathogenicity islands.

In order to establish themselves within their hosts, reproduce, and find a new suitable host, pathogenic and commensal bacteria alike must overcome many similar challenges posed by the host’s immune system and by competition with other microbes. Pathogens have an inherent ability—largely conferred by the products of pathogenicity islands, known as virulence factors—to breach host barriers and defenses that commensals cannot penetrate, Falkow explained. When pathogenic bacteria cross the intestinal epithelium of their mammalian hosts, usually through areas known as Peyer’s patches, they are engulfed by phagocytes: immune cells that destroy invaders by digesting them. Successful pathogens are able to avoid this fate and survive and sometimes replicate within phagocytes, however, and thereafter are distributed to the liver and spleen. Some pathogens establish persistent, systemic—and sometimes asymptomatic—infections in their hosts and may be shed for the remainder of the host’s life. “In my view,” Falkow said, “pathogens choose to live in a dangerous place [exposed to the host’s immune system] to avoid competition and to get nutrients.”

However, Falkow also observed, several members of the human bacterial microbiota that typically live uneventfully in the nasopharynx—including Streptococcus pneumoniae, Neisseria meningitidis, Haemophilus influenzae type b, and Streptococcus pyogenes—sometimes cause disease. These microbes have virulence factors, suggesting that they interact with the host’s immune system, and they persistently infect a significant proportion of the human population, the vast majority of whom are asymptomatic carriers. The existence of such “commensal pathogens” suggests that virulence factors represent one form of a larger class of adaptive factors that allow microbes to colonize and survive in particular niches, and that these factors have been selected on this basis, rather than for their ability to produce disease in host organisms. Indeed, Falkow remarked, it may also be the case that the continual interaction of persistent, asymptomatic bacterial infections with the host immune system keeps it “primed for defensive action.”

The conceptualization of virulence factors as colonization factors underlies the larger notion of a distinction between pathogenicity and disease, Falkow observed. “I submit that medicine’s focus on disease really distracts us from understanding the biology of pathogenicity,” he said. “Disease does not encompass the biological aspects of pathogenicity and the evolution of the host-parasite relationship.” Thus, he continued, “If the nature of microbial pathogenicity is schizophrenic—characterized by inconsistent or contradictory elements—then it is important to study every aspect of its biology, and not be distracted by its role in causing disease.”

Microbial Virulence and the Host Response

Just as there is more to microbial pathogenicity than disease, there is more to infectious disease than the actions of virulence factors on host cells and systems. Rather, as workshop presenter Bruce Levin, of Emory University, bluntly asserted, virulence almost always results from “screw-ups” by the host’s immune system. These immunological failings include responding more vigorously than needed, as occurs in bacterial sepsis; responding incorrectly to a pathogen, as occurs in lepromatous leprosy; or responding to the wrong signals, as occurs in toxic shock syndrome (see Margolis and Levin, 2008, reprinted in Chapter 3). “Sometime in the future, we will look at antimicrobial chemotherapy as a primitive approach to treating infections; we will treat diseases such as sepsis and meningitis by controlling the host response,” Levin predicted. “It’s going to be a hard job, and we can’t do it by episodic dosing. Effective treatment will require real-time monitoring and response to changes in the immune response. I believe it will be possible to treat infections in this way, but to do so we have to know a lot more about the immune response and its control than we do now.”

Tying this “it’s the host’s fault” perspective into existing hypotheses for the evolution of virulence, which focus primarily on the parasite, raises some interesting issues (see Margolis and Levin in Chapter 3). According to “conventional wisdom,” as described by May and Anderson (1983), virulence is an early stage in the association between a parasite and its host after which, over the course of evolution, a successful parasite “learns” not to bite the hand that feeds it. Levin suggested that the host, too, could evolve such that its immune system “learns” not to overreact to the parasite, and that eventually, on “equilibrium day,” all such host-parasite relationships would achieve mutualism (Levin et al., 2000). He also considered the trade-off hypothesis, which postulates that a too-virulent parasite will kill its host too rapidly to permit efficient transmission. Natural selection in the parasite population, therefore, favors some—but not too much—virulence. Levin further wondered whether this trade-off could be achieved by the parasite evolving restraint in its production of agents that inflame the host’s immune system.

By contrast, in his prepared remarks Levin presented experimental findings suggesting that the host effects of certain bacterial products (e.g., Shiga toxin produced by Escherichia coli O157:H7; Steinberg and Levin, 2007) appear to have evolved coincidentally as virulence determinants, having been selected for different functions and the advantages that they confer upon a microbe. Other virulent microbes (e.g., Falkow’s “commensal pathogens”) may have been selected within the host, under local circumstances that favor more pathogenic members of a colonizing population, even if they are at a disadvantage in the community of hosts, Levin said.

But how to account, in evolutionary terms, for the disadvantages of host “immunoperversity”: the tendency to overreact to pathogens, resulting in host morbidity and mortality? This phenomenon may be an artifact of the relative slowness of human evolution, Levin explained, coupled with the low efficiency of infectious disease-mediated selection in our species. It may also result from selection pressures associated with maintaining a large microbiota, McFall-Ngai suggested. “By and large, the invertebrates (with the exception of the termites and the cockroaches, which do have large consortia) generally have very limited persistent coevolved interactions with microbes,” she said. Thus, it is possible that the adaptive immune system of jawed vertebrates evolved as a mechanism by which to control the large populations of microbes—a task that may require extreme responses that occasionally result in disease.

Pathogen Evolution, as Illustrated by Salmonella

Setting aside the inconsistencies and contradictions inherent to pathogenicity, Falkow and fellow workshop speakers Gordon Dougan and Julian Parkhill, of the Wellcome Trust Sanger Institute in Cambridge, United Kingdom, described approaches to discovering how certain microbes have evolved to cause disease in their hosts (see Chapter 3). In particular, each presentation discussed bacterial pathogens of the genus Salmonella. Serovars¹⁹ of Salmonella enterica include S. typhimurium, which infects a wide range of hosts and is a major cause of gastroenteritis in humans, and S. typhi, the human-specific agent of the systemic infection typhoid fever (Lawley et al., 2006; Monack et al., 2004b).

In humans, S. typhimurium infections are generally (but not always) contained within the intestinal epithelium, while S. typhi evades destruction by the immune system and is transported, via the liver and spleen, to the gall bladder and bone marrow, in which the bacteria can persist (Figure WO-8; Monack et al., 2004b). Thus, significant numbers of people infected with typhoid—including those asymptomatically infected with S. typhi—become chronic carriers of the pathogen and reservoirs of a disease that poses a considerable threat to public health. From the perspective of S. typhi, however, this “stealth” strategy is essential to its survival. Workshop presentations described how evolution—both ancient and recent—has shaped pathogenicity in Salmonella, from its initial acquisition of genes that confer invasiveness to the loss of gene function in some serovars, leading to a reduction in host range and increasing virulence, to the recent challenge of antibiotics, which the bacterium has quickly met with resistance.

FIGURE WO-8

Comparison of pathogenesis of infection associated with Salmonella typhimurium versus S. typhi (human restricted). SOURCE: Reprinted from Young et al. (2002) with permission from Macmillan Publishers Ltd. Copyright 2002.

Loss of Function Leads to Specialization

While bacterial pathogenicity is associated with the acquisition of novel virulence genes (typically through horizontal transfer), research by Parkhill and colleagues indicates that host-restricted, virulent pathogens such as S. typhi have evolved those characteristics following a loss of function in genes that control interactions with host cells (thereby limiting their host range) and that modulate the expression of virulence factors (see Box WO-2 and Chapter 3). The genomes of S. typhi and another systemic, host-restricted pathogen, S. paratyphi A—each independently descended from S. enterica—contain approximately 200 inactivated genes, of which about 30 are common to both serovars. Many of these encode functions involved in determining virulence or host range. Most of these shared pseudogenes, however, do not bear the same inactivating mutations, suggesting that their loss conferred a selective advantage.

BOX WO-2

Host-Restriction Versus Virulence in Bordetella spp.

Antibiotic Resistance: Origins and Countermeasures

Reports of antibiotic-resistant bacterial infections followed within a few years of the first widespread use of penicillin at the close of World War II. By the mid-1950s, multidrug-resistant bacterial strains began to emerge (Figure WO-9) and have since become ubiquitous. Indeed, mortality rates due to bacterial infections threaten to return to the levels of the pre-antibiotic era, according to speaker Julian Davies of the University of British Columbia.

FIGURE WO-9

The relationship between antibiotic resistance development in Shigella dysentery isolates in Japan and the introduction of antimicrobial therapy between 1950 and 1965. In 1955, the first case of plasmid determined resistance was characterized. MDR = multidrug (more...)

Perhaps these developments could have been anticipated based on Lederberg’s work on bacterial conjugation, a key route by which plasmids carrying drug-resistance genes are horizontally transferred between bacteria. Certainly, the ongoing impact of antibiotic resistance has confirmed the importance of understanding its evolutionary, genetic, and ecological origins, as several workshop presentations attested.

The biochemical mechanisms by which bacteria achieve resistance are many and varied, and the genes to accomplish each of them can be acquired by horizontal transfer, Davies said. Mechanisms conferring resistance include increased efflux of antibiotic, enzymatic inactivation, target modification, target overexpression, sequestration, and intracellular localization. Yet although we have gained considerable understanding of the biochemical and genetic bases of antibiotic resistance, we have failed dismally to control the development of antibiotic resistance, or to stop its transfer among bacterial strains, Davies observed. Novel antibiotics are unlikely to be developed without significant financial incentives for the pharmaceutical industry, which has largely abandoned infectious disease therapeutic discovery for more profitable targets, such as chronic conditions (Spellberg et al., 2008). Workshop participants considered a variety of means to address these considerable challenges, including investigating the environmental origins of antibiotic resistance, identifying sources of novel antibiotics, and developing alternatives to conventional antibiotic therapies.

Patterns of Emergence

The Pathogens

Woolhouse and coworkers used a rigorous, formal methodology to produce and refine their catalog of the nearly 1,400 recognized human pathogen species, of which the 87 “novel” species constitute a subset (see Woolhouse and Gaunt in Chapter 5). As shown in Figure WO-13, while known human pathogens are dominated by bacterial species, the vast majority of novel pathogen species are viruses. Indeed, the researchers identified four attributes of these novel pathogens that they expect will describe most future emergent microbes: a preponderance of RNA viruses; pathogens with nonhuman animal reservoirs; pathogens with a broad host range; and pathogens with some (perhaps initially limited) potential for human-to-human transmission (Woolhouse and Gaunt, 2007). “These new pathogens that we are reporting are coming from the same sorts of places, the same sorts of animal populations, we have always shared our viruses and other pathogens with,” Woolhouse explained, adding that host proximity, not taxonomy, seems to be the main driver for pathogens to jump between host species.

FIGURE WO-13

While known human pathogens are dominated by bacterial species, the vast majority of novel pathogen species are viruses. SOURCE: Adapted from data in Woolhouse and Gaunt (2007).

Potential for Prediction

The considerable knowledge gained over recent years regarding ecological and evolutionary processes that drive disease emergence makes possible the measurement and prediction of future patterns of disease emergence, Daszak asserted. “I’m not going to try to say that we can predict in great detail where, when, and what the next new emerging disease is going to be,” he said, “but I think we can use ecological approaches to make some predictions about future trends.” Bringing together information from genetic sequencing, phylogenetic analyses, and ecological studies, Daszak’s group has produced predictions on disease emergence on scales ranging from the local to the global (see Daszak in Chapter 5).

At the global level, Daszak and coworkers developed a predictive model identifying regions (“hotspots”) where new infectious diseases are likely to emerge (Jones et al., 2008). From a database of 335 emerging infectious disease (EID) “events”²² that occurred between 1940 and 2004, the researchers found that zoonoses were responsible for a majority (60 percent) of these events, of which 72 percent originated in wildlife—including SARS and Ebola hemorrhagic fever. Bacteria caused more than 50 percent of these disease events, and many were associated with the development of antibiotic resistance. The hotspots shown in Figure WO-14 were identified based on correlations between the disease events and five socio-economic, environmental, and ecological variables. Concentrated in lower-latitude developing countries, these areas largely lack infectious disease surveillance and control efforts, which are disproportionately focused on the world’s healthiest, wealthiest citizens. Thus, Daszak concluded, “we are misal-locating our global efforts to deal with emerging infections.”

FIGURE WO-14

Global distribution of relative risk of an EID event. Maps are derived for EID events caused by (a) zoonotic pathogens from wildlife; (b) zoonotic pathogens from nonwildlife; (c) drug-resistant pathogens; and (d) vector-borne pathogens. SOURCE: Reprinted (more...)

Our Wits Versus Their Genes

Discussion at the workshop’s conclusion (and immediately following the session on emerging infectious diseases) brought together many of Lederberg’s passions, in the tradition of Infectious History (Lederberg, 2000). As Daszak remarked of the potential for predicting the next emerging zoonosis, “I think this is the next ‘Holy Grail’ for emerging disease, a way to fuse different disciplines: evolution, ecology, virology, microbiology.” Workshop participants explored how best to pursue this prize, as well as the larger objective of anticipating, detecting, and responding to emerging infectious threats, and the even greater goal of developing a truly comprehensive understanding of the relationships between and among microbes and host species.

The Incubation of a Scientific Discipline

Many people laid the groundwork for the germ theory. Even the terrified masses touched by the Black Death (bubonic plague) in Europe after 1346 had some intimation of a contagion at work. But they lived within a cognitive framework in which scapegoating, say, of witches and Jews, could more “naturally” account for their woes. Breaking that mindset would take many innovations, including microscopy in the hands of Anton van Leeuwenhoek. In 1683, with one of his new microscopes in hand, he visualized bacteria among the animalcules harvested from his own teeth. That opened the way to visualize some of the dreaded microbial agents eliciting contagious diseases.

There were pre-germ-theory advances in therapy, too. Jesuit missionaries in malaria-ridden Peru had noted the native Indians’ use of Cinchona bark. In 1627, the Jesuits imported the bark (harboring quinine, its anti-infective ingredient) to Europe for treating malaria. Quinine thereby joined the rarified pharmacopoeia—including opium, digitalis, willow (Salix) bark with its analgesic salicylates, and little else—that prior to the modern era afforded patients any benefit beyond placebo.

Beginning in 1796, Edward Jenner took another major therapeutic step—the development of vaccination—after observing that milkmaids exposed to cowpox didn’t contract smallpox. He had no theoretical insight into the biological mechanism of resistance to the disease, but vaccination became a lasting prophylactic technique on purely empirical grounds. Jenner’s discovery had precursors. “Hair of the dog” is an ancient trope for countering injury and may go back to legends of the emperor Mithridates, who habituated himself to lethal doses of poisons by gradually increasing the dose. We now understand more about a host’s immunological response to a cross-reacting virus variant.

Sanitary reforms also helped. Arising out of revulsion over the squalor and stink of urban slums in England and the United States, a hygienic movement tried to scrub up dirt and put an end to sewer stenches. The effort had some health impact in the mid-19th century, but it failed to counter diseases spread by fleas and mosquitoes or by personal contact, and it often even failed to keep sewage and drinking water supplies separated. It was the germ theory—which is credited to Pasteur (a chemist by training) and Koch (ultimately a German professor of public health)—that set a new course for studying and contending with infectious disease. Over the second half of the 19th century, these scientists independently synthesized historical evidence with their own research into the germ theory of disease.

Pasteur helped reveal the vastness of the microbial world and its many practical applications. He found microbes to be behind the fermentation of sugar into alcohol and the souring of milk. He developed a heat treatment (pasteurization, that is) that killed microorganisms in milk, which then no longer transmitted tuberculosis or typhoid. And he too developed new vaccines. One was a veterinary vaccine against anthrax. Another was against rabies and was first used in humans in 1885 to treat a young boy who had been bitten by a rabid dog.

One of Koch’s most important advances was procedural. He articulated a set of logical and experimental criteria, later restated as “Koch’s Postulates,” as a standard of proof for researchers’ assertions that a particular bacterium caused a particular malady. In 1882, he identified the bacterium that causes tuberculosis; a year later he did the same for cholera. Koch also left a legacy of students (and rivals) who began the systematic search for disease-causing microbes: The golden age of microbiology had begun.

Just as the 19th century was ending, the growing world of microbes mushroomed beyond bacteria. In 1892, the Russian microbiologist Dmitri Ivanowski, and in 1898, the Dutch botanist Martinus Beijerinck, discovered exquisitely tiny infectious agents that could pass through bacteria-stopping filters. Too small to be seen with the conventional microscope, these agents were described as “filtrable [sic] viruses.”

With a foundation of germ theory in place even before the 20th century, the study of infectious disease was ready to enter a new phase. Microbe hunting became institutionalized, and armies of researchers systematically applied scientific analyses to understanding disease processes and developing therapies.

During the early acme of microbe hunting, from about 1880 to 1940, however, microbes were all but ignored by mainstream biologists. Medical microbiology had a life of its own, but it was almost totally divorced from general biological studies. Pasteur and Koch were scarcely mentioned by the founders of cell biology and genetics. Instead, bacteriology was taught as a specialty in medicine, outside the schools of basic zoology and botany. Conversely, bacteriologists scarcely heard of the conceptual revolutions in genetic and evolutionary theory.

Bacteriology’s slow acceptance was partly due to the minuscule dimensions of microbes. The microscopes of the 19th and early 20th centuries could not resolve internal microbial anatomy with any detail. Only with the advent of electron microscopy in the 1930s did these structures (nucleoids, ribosomes, cell walls and membranes, flagella) become discernible. Prior to that instrumental breakthrough, most biologists had little, if anything, to do with bacteria and viruses. When they did, they viewed such organisms as mysteriously precellular. It was still an audacious leap for René Dubos to entitle his famous 1945 monograph “The Bacterial Cell.”

The early segregation of bacteriology and biology per se hampered the scientific community in recognizing the prospects of conducting genetic investigation with bacteria. So it is ironic that the pivotal discovery of molecular genetics—that genetic information resides in the nucleotide sequence of DNA—arose from studies on serological types of pneumococcus, studies needed to monitor the epidemic spread of pneumonia.

This key discovery was initiated in 1928 by the British physician Frederick Griffith. He found that extracts of a pathogenic strain of pneumococcus could transform a harmless strain into a pathogenic one. The hunt was then on to identify the “transforming factor” in the extracts. In 1944, Oswald Avery, Colin MacLeod, and Maclyn McCarty reported in the Journal of Experimental Medicine that DNA was the transforming factor. Within a few years, they and others ruled out skeptics’ objections that protein coextracted with the DNA might actually be the transforming factor.

Those findings rekindled interest in what was really going on in the life cycle of bacteria. In particular, they led to my own work in 1946 on sexual conjugation in Escherichia coli and to the construction of chromosome maps emulating what had been going on in the study of the genetics of fruit flies, maize, and mice for the prior 45 years. Bacteria and bacterial viruses quickly supplanted fruit flies as the test-bed for many of the subsequent developments of molecular genetics and the biotechnology that followed. Ironically, during this time, we were becoming nonchalant about microbes as etiological agents of disease.

Despite its slow emergence, bacteriology was already having a large impact. Its success is most obviously evidenced by the graying of the population. That public health has been improving—due to many factors, especially our better understanding of infectious agents—is graphically shown by the vital statistics. These began to be diligently recorded in the United States after 1900 in order to guide research and apply it to improving public health. The U.S. experience stands out in charts (Figure WO-15) depicting life expectancy at birth through the century. The average life-span lengthened dramatically: from 47 years in 1900 to today’s expectation of 77 years (74 years for males and 80 for females).²⁶ Similar trends are seen in most other industrialized countries, but the gains have been smaller in economically and socially depressed countries.

FIGURE WO-15

Longer life. Anti-infection medicine and other factors have helped dramatically lengthen the average life expectancy in the United States. SOURCE: Social Security Office of the Chief Actuary.

Other statistics reveal that the decline in mortality ascribable to infectious disease accounted for almost all of the improvement in longevity up to 1950, when life expectancy had reached 68. The additional decade of life expectancy for babies born today took the rest of the century to gain. Further improvements now appear to be on an asymptotic trajectory: Each new gain is ever harder to come by, at least pending unpredictable breakthroughs in the biology of aging.

The mortality statistics fluctuated considerably during the first half of the last century. Much of this instability was due to sporadic outbreaks of infections such as typhoid fever, tuberculosis, and scarlet fever, which no longer have much statistical impact. Most outstanding is the spike due to the great influenza pandemic of 1918–19 that killed 25 million people worldwide—comparable to the number of deaths in the Great War. Childhood immunization and other science-based medical interventions have played a significant role in the statistical trends also. So have public health measures, among them protection of food and water supplies, segregation of coughing patients, and personal hygiene. Overall economic growth has also helped by contributing to less crowded housing, improved working conditions (including sick leave), and better nutrition.

As infectious diseases have assumed lower rankings in mortality statistics, other killers—mostly diseases of old age, affluence, and civilization—have moved up the ladder. Heart disease and cancer, for example, have loomed as larger threats over the past few decades. Healthier lifestyles, including less smoking, sparer diets, more exercise, and better hygiene, have been important countermeasures. Prophylactic medications such as aspirin, as well as medical and surgical interventions, have also kept people alive longer.

The 1950s were notable for the “wonder drugs”—the new antibiotics penicillin, streptomycin, chloramphenicol, and a growing list of others that at times promised an end to bacteria-based disease. Viral pathogens have offered fewer routes to remedies, except for vaccines, such as Jonas Salk’s and Albert Sabin’s polio vaccines. These worked by priming immune systems for later challenges by the infectious agents. Old vaccines, including Jenner’s smallpox vaccine, also were mobilized in massive public health campaigns, sometimes with fantastic results. By the end of the 1970s, smallpox became the first disease to be eradicated from the human experience.

Confidence about medicine’s ability to fight infectious disease had grown so high by the mid-1960s that some optimists were portraying infectious microbes as largely conquered. They suggested that researchers shift their attention to constitutional scourges of heart disease, cancer, and psychiatric disorders. These views were reflected in the priorities for research funding and pharmaceutical development. President Nixon’s 1971 launch of a national crusade against cancer, which tacitly implied that cancer could be conquered by the bicentennial celebrations of 1976, was an example. Few people now sustain the illusion that audacious medical goals like conquering cancer or infectious disease can be achieved by short-term campaigns.

Wake-Up Calls

The overoptimism and complacency of the 1960s and 1970s was shattered in 1981 with the recognition of AIDS. Since then, the spreading pandemic has overtaken one continent after another with terrible costs. Its spread has been coincident with another wake-up call—the looming problem of antibiotic-resistant microbes. This was a predictable consequence of the evolutionary process operating on microbes challenged by the new selection pressure of antibiotics, arising in part from medical prescriptions and in part from unregulated sales and use in feed for crop animals.

AIDS’s causative agent, the human immunodeficiency virus (HIV), is a member of the retrovirus family. These viruses had been laboratory curiosities since 1911, when Francis Peyton Rous discovered the Rous sarcoma virus (RSV) in chickens. Early basic research on retroviruses later helped speed advances in HIV research. By the time AIDS began to spread, RSV had been studied for years as a model for cancer biology, because it could serve as a vector for transferring oncogenes into cells. That work accelerated the characterization of HIV as a retrovirus, and it also helped guide our first steps toward medications that slow HIV infection.

AIDS and HIV have spurred the most concentrated program of biomedical research in history, yet they still defy our counterattacks. And our focus on extirpating the virus may have deflected less ambitious, though more pragmatic, aims, including learning to live with the virus by nurturing in equal measure the immune system that HIV erodes. After all, natural history points to analogous infections in simians that have long since achieved a mutually tolerable state of equilibrium.

Costly experiences with AIDS and other infectious agents have led to widespread reexamination of our cohabitation with microbes. Increased monitoring and surveillance by organizations such as the U.S. Centers for Disease Control and Prevention (CDC) and the World Health Organization (WHO) have revealed a stream of outbreaks of exotic diseases. Some have been due to the new importation of microbes (such as cholera in the Southern Hemisphere); some to older parasites (such as Legionella) that have been newly recognized as pathogenic; and some to newly evolved antibiotic-resistant pneumonia strains.

Even maladies that had never before been associated with infectious agents recently have been revealed as having microbial bases. Prominent among these are gastric ulcers, which previously had been attributed almost entirely to stress and other psychosomatic causes. Closer study, however, has shown a Helicobacter to be the major culprit. Researchers are now directing their speculations away from stress and toward Chlamydia infection as a cause of atherosclerosis and coronary disease.

The litany of wake-up calls goes on. Four million Americans are estimated to be infected with hepatitis C, mainly by transfusion of contaminated blood products. This population now is at significant risk for developing liver cancer. Those harboring hepatitis C must be warned to avoid alcohol and other hepatotoxins, and they must not donate blood.

Smaller but lethal outbreaks of dramatic, hypervirulent viruses have been raising public fear. Among these are the Ebola virus outbreak in Africa in 1976 and again in 1995 and the hantavirus outbreak in the U.S. Southwest in 1993. In hindsight, these posed less of a public health risk than the publicity they received might have suggested. Still, studying them and uncovering ecological factors that favor or thwart their proliferation is imperative because of their potential to mutate into more diffusible forms.

Our vigilance is mandated also by the facts of life: The processes of gene reassortment in flu viruses, which are poorly confined to their canonical hosts (birds, swine, and people), goes on relentlessly and is sure to regenerate human-lethal variants. Those thoughts were central in 1997 when the avian flu H5N1 transferred into a score of Hong Kong citizens, a third of whom died. It is likely that the resolute actions of the Hong Kong health authorities, which destroyed 2 million chickens, stemmed that outbreak and averted the possibility of a worldwide spread of H5N1.

Complacency is not an option in these cases, as other vectors, including wildfowl, could become carriers. In Malaysia, a new infectious entity, the Nipah virus, killed up to 100 people last year; authorities there killed a million livestock to help contain the outbreak. New York had a smaller scale scare last summer with the unprecedented appearance of bird- and mosquito-borne West Nile encephalitis, although the mortality rate was only a few percent of those infected. We need not wonder whether we will see outbreaks like these again. The only questions are when and where?

These multiple wake-up calls to the infectious disease problem have left marks in vital statistics. From mid-century to 1982, the U.S. mortality index (annual deaths per 100,000) attributable to infection had been steady at about 30. But from 1982 to 1994, the rate doubled to 60. (Keep in mind that the index was 500 in 1900 and up to 850 in 1918–19 due to the Spanish flu epidemic.) About half of the recent rise in deaths is attributable to AIDS; much of the rest is due to respiratory disease, antibiotic resistance, and hospital-acquired infection.

Our Wits Versus Their Genes

As our awareness of the microbial environment has intensified, important questions have emerged. What puts us at risk? What precautions can and should we be taking? Are we more or less vulnerable to infectious agents today than in the past? What are the origins of pathogenesis? And how can we use deeper knowledge to develop better medical and public health strategies? Conversely, how much more can the natural history of disease teach us about fundamental biological and evolutionary mechanisms?

An axiomatic starting point for further progress is the simple recognition that humans, animals, plants, and microbes are cohabitants of the planet. That leads to refined questions that focus on the origin and dynamics of instabilities within this context of cohabitation. These instabilities arise from two main sources loosely definable as ecological and evolutionary.

Ecological instabilities arise from the ways we alter the physical and biological environment, the microbial and animal tenants (humans included) of these environments, and our interactions (including hygienic and therapeutic interventions) with the parasites. The future of humanity and microbes likely will unfold as episodes of a suspense thriller that could be titled Our Wits Versus Their Genes.

We already have used our wits to increase longevity and lessen mortality. That simultaneously has introduced irrevocable changes in our demographics and our own human ecology. Increased longevity, economic productivity, and other factors have abetted a global population explosion from about 1.6 billion in 1900 to its present level above 6 billion. That same population increase has fostered new vulnerabilities: crowding of humans, with slums cheek by jowl with jet setters’ villas; the destruction of forests for agriculture and suburbanization, which has led to closer human contact with disease-carrying rodents and ticks; and routine long-distance travel.

Travel around the world can be completed in less than 80 hours (compared to the 80 days of Jules Verne’s 19th-century fantasy), constituting a historic new experience. This long-distance travel has become quotidian: Well over a million passengers, each one a potential carrier of pathogens, travel daily by aircraft to international destinations. International commerce, especially in foodstuffs, only adds to the global traffic of potential pathogens and vectors. Because the transit times of people and goods now are so short compared to the incubation times of disease, carriers of disease can arrive at their destination before the danger they harbor is detectable, reducing health quarantine to a near absurdity.

Our systems for monitoring and diagnosing exotic diseases have hardly kept pace with this qualitative transformation of global human and material exchange. This new era of global travel will redistribute and mix people, their cultures, their prior immunities, and their inherited predispositions, along with pathogens that may have been quiescent at other locales for centuries.

This is not completely novel, of course. The most evident precedent unfolded during the European conquest of America, which was tragically abetted by pandemics of smallpox and measles imported into native populations by the invading armies. In exchange, Europeans picked up syphilis’s Treponema, in which Fracastoro discerned contagion at work.

Medical defense against the interchange of infectious disease did not exist in the 16th century. In the 21st century, however, new medical technologies will be key parts of an armamentarium that reinforces our own immunological defenses. This dependence on technology is beginning to be recognized at high levels of national and international policy-making. With the portent of nearly instant global transmission of pathogenic agents, it is ever more important to work with international organizations like WHO for global health improvement. After all, the spread of AIDS in America and Europe in the 1980s and 1990s was due, in part, to an earlier phase of near obliviousness to the frightful health conditions in Africa. One harbinger of the kind of high-tech wit we will need for defending against outbreaks of infectious disease is the use of cutting-edge communications technology and the Internet, which already have been harnessed to post prompt global alerts of emerging diseases (see osi.oracle.com:8080/promed/promed.home).

Moving Targets

“Germs” have long been recognized as living entities, but the realization that they must inexorably be evolving and changing has been slow to sink in to the ideology and practice of the public health sector. This lag has early roots. In the 19th century, Koch was convinced that rigorous experiments would support the doctrine of monomorphism: that each disease was caused by a single invariant microbial species rather than by the many that often showed up in culture. He argued that most purported “variants” were probably alien bacteria that had floated into the petri dishes from the atmosphere.

Koch’s rigor was an essential riposte to careless claims of interconvertibility—for example, that yeasts could be converted into bacteria. It also helped untangle confusing claims of complex morphogenesis and life cycles among common bacteria. But strict monomorphism was too rigid, and even Koch eventually relented, admitting the possibility of some intrinsic variation rather than contamination. Still, for him and his contemporaries, variation remained a phenomenological and experimental nuisance rather than the essence of microbes’ competence as pathogens. The multitude of isolable species was confusing enough to the epidemic tracker; it would have been almost too much to bear to have to cope with constantly emerging variants with altered serological specificity, host affinity, or virulence.

Even today it would be near heresy to balk at the identification of the great plague of the 14th century with today’s Yersinia pestis; but we cannot readily account for its pneumonic transmission without guessing at some intrinsic adaptation at the time to aerosol conveyance. Exhumations of ancient remains might still furnish DNA evidence to test such ideas.

We now know and accept that evolutionary processes elicit changes in the genotypes of germs and of their hosts. The idea that infection might play an important role in natural selection sank in after 1949 when John B. S. Haldane conjectured that the prevalence of hemoglobin disorders in Mediterranean peoples might be a defense against malaria. That idea developed into the first concrete example of a hereditary adaptation to infectious disease.

Haldane’s theory preceded Anthony C. Allison’s report of the protective effect of heterozygous hemoglobinopathy against falciparum malaria in Africa. The side effects of this bit of natural genetic engineering are well known: When this beneficial polymorphism is driven to higher gene frequencies, the homozygous variant becomes more prevalent and with it the heavy human and societal burden of sickle cell disease.

We now have a handful of illustrations of the connection between infection and evolution. Most are connected to malaria and tuberculosis, which are so prevalent that genetic adaptations capable of checking them have been strongly selected. The same prevalence also makes their associated adaptations more obvious to researchers. A newly reported link between infection and evolution is the effect of a ccr5 (chemokine receptor) deletion, a genetic alteration that affords some protection against AIDS. It would be interesting to know what factors—another pathogen perhaps—may have driven that polymorphism in earlier human history.

One lesson to be gleaned from this coevolutionary dynamic is how fitful and sporadic human evolution is when our slow and plodding genetic change is pitted against the far more rapidly changing genomes of microbial pathogens.

We have inherited a robust immune system, but little has changed since its early vertebrate origins 200 million years ago. In its inner workings, immunity is a Darwinian struggle: a randomly generated diversification of leukocytes that collectively are prepared to duel with a lifetime of unpredictable invaders. But these duels take place in the host soma; successful immunological encounters do not become genetically inscribed and passed on to future generations of the host. By contrast, the germs that win the battles quickly proliferate their successful genes, and they can use those enhancements to go on to new hosts, at least in the short run.

The human race evidently has withstood the pathogenic challenges encountered so far, albeit with episodes of incalculable tragedy. But the rules of encounter and engagement have been changing; the same record of survival may not necessarily hold for the future. If our collective immune systems fail to keep pace with microbial innovations in the altered contexts we have created, we will have to rely still more on our wits.

Evolving Metaphors of Infection: Teach War No More

New strategies and tactics for countering pathogens will be uncovered by finding and exploiting innovations that evolved within other species in defense against infection. But our most sophisticated leap would be to drop the manichaean view of microbes—“We good; they evil.” Microbes indeed have a knack for making us ill, killing us, and even recycling our remains to the geosphere. But in the long run microbes have a shared interest in their hosts’ survival: A dead host is a dead end for most invaders too. Domesticating the host is the better long-term strategy for pathogens.

We should think of each host and its parasites as a superorganism with the respective genomes yoked into a chimera of sorts. The power of this sociological development could not be more persuasively illustrated than by the case of mitochondria, the most successful of all microbes. They reside inside every eukaryote cell (from yeast to protozoa to multicellular organisms), in which they provide the machinery of oxidative metabolism. Other bacteria have taken similar routes into plant cells and evolved there into chloroplasts—the primary harvesters of solar energy, which drive the production of oxygen and the fixed carbon that nourishes the rest of the biosphere.

These cases reveal how far collaboration between hosts and infecting microbes can go. In the short run, however, the infected host is in fact at metastable equilibrium: The balance could tip toward favorable or catastrophic outcomes.

On the bad side, the host’s immune response may be excessive, with autoimmune injuries as side effects. Microbial zeal also can be self-defeating. As with rogue cancer cells, deviant microbial cells (such as aggressive variants from a gentler parent population) may overtake and kill the host, thereby fomenting their own demise and that of the parent population.

Most successful parasites travel a middle path. It helps for them to have aggressive means of entering the body surfaces and radiating some local toxicity to counter the hosts’ defenses, but once established they also do themselves (and their hosts) well by moderating their virulence.

Better understanding of this balancing act awaits further research. And that may take a shift in priorities. For one, research has focused on hypervirulence. Studies into the physiology of homeostatic balance in the infected host qua superorganism have lagged. Yet the latter studies may be even more revealing, as the burden of mutualistic adaptation falls largely on the shoulders of the parasite, not the host. This lopsided responsibility follows from the vastly different evolutionary paces of the two. But then we have our wits, it is to be hoped, for drafting the last word.

To that end, we also need more sophisticated experimental models of infection, which today are largely based on contrived zoonoses (the migration of a parasite from its traditional host into another species). The test organism is usually a mouse, and the procedure is intended to mimic the human disease process. Instead, it is often a caricature.

Injected with a few bugs, the mouse goes belly up the next day. This is superb for in vivo testing of an antibiotic, but it bears little relation to the dynamics of everyday human disease.

Natural zoonoses also can have many different outcomes. In most cases, there will be no infection at all or only mild ones such as the gut ache caused by many Salmonella enteritidis species. Those relatively few infectious agents that cause serious sickness or death are actually maladapted to their hosts, to which they may have only recently gained access through some genetic, environmental, or sociological change. These devastatingly virulent zoonoses include psittacosis, Q fever, rickettsiosis, and hantavirus. Partly through lack of prior coevolutionary development with the new host, normal restraints fail.

I suggest that a successful parasite (one that will be able to remain infectious for a long time) tends to display just those epitopes (antigen fragments that stimulate the immune system) as will provoke host responses that (a) moderate but do not extinguish the primary infection, and (b) inhibit other infections by competing strains of the same species or of other species. According to this speculative framework, the symptoms of influenza evolved as they have in part to ward off other viral infections.

Research into infectious diseases, including tuberculosis, schistosomiasis, and even AIDS, is providing evidence for this view. So are studies of Helicobacter, which has been found to secrete antibacterial peptides that inhibit other enteric infections. We need also to look more closely at earlier stages of chronic infection and search for cross-protective factors by which microbes engage one another. HIV, for one, ultimately fails from the microbial perspective when opportunistic infections supervene to kill its host. That result, which is tragic from the human point of view, is a byproduct of the virus’s protracted duel with the host’s cellular immune system. The HIV envelope and those of related viruses also produce antimicrobials, although their significance for the natural history of disease remains unknown.

Now genomics is entering the picture. Within the past decade, the genomes of many microbes have been completely sequenced. New evidence for the web of genetic interchange is permeating the evolutionary charts. The functional analyses of innumerable genes now emerging are an unexplored mine of new therapeutic targets. It has already shown many intricate intertwinings of hosts’ and parasites’ physiological pathways. Together with wiser insight into the ground rules of pathogenic evolution, we are developing a versatile platform for developing new responses to infectious disease. Many new vaccines, antibiotics, and immune modulators will emerge from the growing wealth of genomic data.

The lessons of HIV and other emerging infections also have begun taking hold in government and in commercial circles, where the market opportunities these threats offer have invigorated the biotechnology industry. If we do the hard work and never take success for granted (as we did for a while during the last century), we may be able to preempt infectious disasters such as the influenza outbreak of 1918–1919 and the more recent and ongoing HIV pandemic.

Perhaps one of the most important changes we can make is to supercede the 20th-century metaphor of war for describing the relationship between people and infectious agents. A more ecologically informed metaphor, which includes the germs’-eye view of infection, might be more fruitful. Consider that microbes occupy all of our body surfaces. Besides the disease-engendering colonizers of our skin, gut, and mucous membranes, we are host to a poorly cataloged ensemble of symbionts to which we pay scant attention. Yet they are equally part of the superorganism genome with which we engage the rest of the biosphere.

The protective role of our own microbial flora is attested to by the superinfections that often attend specific antibiotic therapy: The temporary decimation of our home-team microbes provides entrée for competitors. Understanding these phenomena affords openings for our advantage, akin to the ultimate exploitation by Dubos and Selman Waksman of intermicrobial competition in the soil for seeking early antibiotics. Research into the microbial ecology of our own bodies will undoubtedly yield similar fruit.

Replacing the war metaphor with an ecological one may bear on other important issues, including debates about eradicating pathogens such as smallpox and polio. Without a clear strategy for sustaining some level of immunity, it makes sense to maintain lab stocks of these and related agents to guard against possible recrudescence. An ecological perspective also suggests other ways of achieving lasting security. For example, domestication of commensal microbes that bear relevant cross-reacting epitopes could afford the same protection as vaccines based on the virulent forms. There might even be a nutraceutical angle: These commensal epitopes could be offered as optional genetically engineered food additives, clearly labeled and meticulously studied.

Another relevant issue that can be recast in an ecological model is the rise in popularity of antibacterial products. This is driven by the popular idea that a superhygienic environment is better than one with germs—the “enemy” in the war metaphor. But too much antibacterial zeal could wipe out the very immunogenic stimulation that has enabled us to cohabit with microbes in the first place.