Julian Davies is affiliated with TerraGen Diversity, Inc. and The University of British Columbia, Vancouver, BC, Canada, and is President-Elect of ASM.

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In Praise of Antibiotics

These "wonder drugs" revolutionized the treatment of infectious diseases-but they cannot be taken for granted

Julian Davies

The use of antibiotics, often considered one of the wonders of the modern world, has had dramatic effects on the practice of medicine, the pharmaceutical industry, and microbiology. Prior to the discovery of antibiotics, the treatment of infectious diseases was empirical, at best. Various types of antimicrobial agents, including extracts of plants, fungi, and lichens, were employed for thousands of years in primitive populations without any scientific knowledge of what was being used. Even in the early part of the twentieth century, therapy for infectious diseases was based essentially on patient isolation and chicken soup.

Table 1

However, the seminal work of Joseph Lister, Louis Pasteur, Robert Koch, and others-identifying microbes as agents of disease and devising means for avoiding infections by the use of disinfectants and antiseptics-made possible rational approaches to the treatment of infectious diseases. True antimicrobial therapy became available only in the 1930s with the discovery of the sulfonamides by Gerhardt Domagk (Table 1). Subsequently, these synthetic agents were found, through the work of D. D. Woods, to be competitive inhibitors of the enzymic incorporation of p-aminobenzoic acid into the folic acid biosynthetic pathway. Thus the sulfonamides became the first targets of primitive attempts at rational drug modification.

Surprisingly, no infectious disease has been eliminated by the use of antibiotics, even though vaccines against viruses such as those causing smallpox, polio, and measles have proved very successful. Many of the bacteria that caused human suffering pre-1950 are still making people sick, and we have come to the woeful realization that the use of antibiotics has even contributed to the recent phenomenon of emerging infections.

Pencillins Mark True Start of Antibiotic Era

Penicillin really changed the way that medicine was practiced. Starting in the mid-1940s, antibiotic therapy and prophylaxis became the norm in medical practice, and, ever since, several generations of physicians, surgeons, and their patients have relied on antibiotics. Their use has become pervasive in all types of disease treatment for one reason or another, rightly or wrongly.

Antibiotics played a key role in the development of the modern pharmaceutical industry. Prior to World War II, the industry was a relatively small spinoff from the heavy chemical industry, and chemists continue to exert strong influence in the business. However, the discovery of penicillin, and thereafter streptomycin, tetracycline, gentamicin, amphotericin, erythromycin, and other therapeutic compounds from microbes helped transform the pharmaceutical business into one in which natural products are produced by fermentation processes.

The penicillin story has been revisited many times. While details of this antibiotic discovery story are often debated, there is no question that the work of Alexander Fleming, Howard Florey, Ernst Chain, and their colleagues was paramount in initiating the antibiotic era.

Waksman and Fleming

From the point of view of human benefit, never was a Nobel prize so justifiably awarded as was the award to Selman Waksman for the discovery of streptomycin and other antibiotics produced from Streptomyces spp. Waksman and his talented team (many of whom went on to make important antibiotic discoveries in their own right) developed the concept of systematic screening of microbial culture products for biological activity, a technology which has provided the foundation of the antibiotic industry, and for this alone his name should rank high in any pantheon of microbiology.

Antibiotics Influenced Pharmaceutical Industry Developments

The well-known pharmaceutical companies such as Squibb, Merck, Lederle, and Eli Lilly have a long history, but there is little doubt that a decisive event in their evolution into "big pharma" was the discovery that low-molecular-weight products of microbes have potent antibacterial activity.

The introduction of fermentation methods to the industry was also a milestone; the recognition that microbes could be employed as biosynthetic factories on a large scale to generate not only antibiotics and other biologicals, but also a variety of useful products such as enzymes, amino acids, and vitamins, was the genesis of the biotechnology industry. This was nowhere more apparent than in Japan; ironically, in the 1950s when the Japanese fermentation industry was just developing, the country suffered the first major epidemics of antibiotic-resistant dysentery, subsequently shown to be the result of an unexpected genetic phenomenon-horizontal gene transfer between microbial strains.

The discovery of antibiotics and the maturation of the antibiotic industry illustrates well the marriage of basic and applied science in the development of industrial microbiology. The birth and growth of this field are linked to the production of antibiotics by the pharmaceutical industry on a large scale, while the massive production of antibiotics by fermentation processes would not have been possible without extensive basic research in microbial genetics, physiology, and engineering.

Consider the special contributions of the John Innes group, led by David Hopwood, to our understanding of streptomycetes. Their development of molecular genetic techniques for manipulating Streptomyces coelicolor is creating a store of information about this colorful microbe. In turn, those insights are now being applied to studies of the organization and genetic regulation of the pathways of antibiotic synthesis, which hold great promise for the discovery of novel anti-infective agents in the future. In addition, work on S. coelicolor has provided important fundamental knowledge about the complex developmental processes of prokaryotes; a detailed understanding of these biological transitions has implications for all organisms.

Antibiotics Influence Medicine, Public Health Perceptions

The use of antibiotics has certainly changed public perceptions of infectious disease and its treatment. This change has not been an entirely positive development in the sense that some people regard antibiotics as a panacea, employing them for so many different purposes. Through the use of antibiotics in nonhuman applications such as agriculture and aquaculture, antibiotic-resistant microbes are near-ubiquitous.

The widespread distribution of such microorganisms has many implications, not only in terms of the maintenance of the resistance gene pool, but also in contributing to the spread of antibiotic-resistant organisms in the food chain. The recent spate of cases of human infection by animal-derived antibiotic-resistant strains of Salmonella typhimurium DT1O4 and glycopeptide-resistant enterococci attest to this.

Likewise, and in no small measure, the concepts of "Give me an antibiotic, doc" and "Take two of these and call me in the morning" have contributed to inappropriate and unnecessary use with coincident development of antibiotic resistance, perhaps not killing, but certainly threatening, the goose that lays the golden eggs.

Impact of Antibiotics on Microbes in Environment

What about the targets of all this antibiotic activity? The release of millions of metric tons of antibiotics into the biosphere over the last five decades has surely brought profound consequences for the microbial population. Might some microbial species have disappeared, especially in those areas of greatest exposure to the use of antimicrobial agents, such as hospitals and farms and in the vicinity of pharmaceutical production and disposal plants?

The extent of the effect of antibiotics on microbial diversity will never be known, mostly because the methods to count and provide inventories of natural microbial populations (both cultivable and noncultivable) accurately and completely have only recently been developed. Even today it is not possible to assess the deleterious effects of exposure to an antibiotic on the totality of a population of 5,000 to 10,000 microbial species (the estimated number in a soil sample).

While most microbes survive exposure to antibiotics, many of them change form either as mutants or recombinants. However, some microbial species undoubtedly are lost in certain areas, including species which possibly played key roles in the microbial community, perhaps involved in organic recycling or other ecological functions. There is great concern about the conservation of visible biological diversity, but the microbial world is given short shrift by world authorities who are concerned with preserving biodiversity. After all, what percentage of the population recognizes the critical roles of microbes in the maintenance of all life on the planet? Does anyone besides microbiologists believe that microbes are beautiful?!

Likewise, there is little real understanding of the importance of antimicrobial agents in nature. As natural products of microbes, many of these agents presumably were present in one form or another in the environment for billions of years, and some of these organic molecules may well have been components of primordial soups, as products of an enormous combinatorial chemistry experiment.

Complex Secondary Metabolism Presents Untapped Opportunities

The complexity of the biosynthetic pathways of secondary metabolites and the mechanisms of their regulation still present a huge intellectual challenge to geneticists, biochemists, microbial physiologists, and other specialists. The gene clusters frequently include multiple and divergent transcription control systems, with both specific and global regulatory processes being implicated. The production of secondary metabolites plays a critical role in the lifestyles of many microbes, and the relationship of secondary metabolism with bacterial growth and development is a topic of increasing interest.

One can only guess at the numbers of secondary metabolites that microorganisms produce. According to laboratory studies, a single Streptomyces species may produce upwards of 100 low-molecular-weight compounds. Thus, in the aggregate, diverse microbial species may be producing tens of millions of naturally occurring low-molecular-weight compounds throughout the biosphere.

What are all these molecules doing in nature? They must serve biochemical functions, suggesting that some fraction of them behaves as antibiotics while others act as inter- and intra-cellular signalling molecules. From a practical standpoint, we can assume that secondary metabolites provide a rich if not inexhaustible source of biochemically diverse small molecules whose roles are unknown and whose potential has not been fully exploited.

Table 2

This biological "space" is almost totally unexplored, meaning that this vast unexamined assemblage of molecules, biosynthetic pathways, and evolutionary functions represents a great but largely untapped scientific opportunity. Take, for example, the use of antibiotics as "chemical mutants," supplying inhibitors to block the biochemical reactions of cells (often reversibly) and thereby to study processes of cellular biochemistry and physiology in the same way that traditional genetic methods have been used (Table 2). In this application, antibiotics serve as a powerful set of reagents that we can expect to play an increasing role in functional genomics. For instance, they will help investigators to identify the characteristics of unidentified genes from different bacterial species.

A Dose of Rationality Could Enhance Quest for Antibiotics

However successful, past searches for effective antibiotics have also been regrettably irrational, in the sense that very little was done during the early days to establish detailed structure-activity relationships for many of these agents. To this day, precious few of the reactions between low-molecular-weight secondary metabolites and target microbial cell components have been analyzed in any detail. Thus, the modes of action of antibiotics and their targets (receptors) are still poorly understood at the molecular level. Although many investigators are claiming that they are designing drugs or lead compounds rationally, no one has exploited natural products to their full extent. Thus, the horn of plenty has hardly been touched.

Meanwhile, antibiotics continue to influence microbiology in many ways, affecting industrial, academic, and public perceptions of the discipline. The incredibly rapid development of antibiotic resistance in particular is having a profound impact on medical and food microbiology, epidemiology, ecology, genetics, biochemistry, and diagnostics. Studies of antibiotic-resistant microbes in all their forms have created a subdiscipline of microbiology that links those working in industry, academia, medicine, and agriculture-not always harmoniously.

No discussion of the past 50 years of antibiotic history can overlook the mortal combat between terrestrial microbes and the antimicrobial agents that humans have released into the environment. In one sense, the past half-century provides a capsule of microbial evolution, the survival of the oldest living organisms in the face of yet another catastrophic situation.

Antibiotic-resistant bacteria have increased greatly in number (compared to their sensitive relatives), in direct proportion to the extent of that antibiotic use. This shift came about in part because microorganisms embody prodigious (and now well-studied) attributes of genetic versatility: they have the ability to mutate, transfer genetic information, and integrate stably a plethora of resistance determinants from a vast microbial gene pool.

Antibiotic Resistance Also Reflects Biodiversity

Table 3

These diverse "resistance" determinants keep antibiotics from penetrating cells in some cases or pump them out in others. Alternatively, the antibiotics may be sequestered, detoxified by hydrolytic cleavage or by modification, or otherwise rendered inactive. The target site for the antibiotic may be altered to protect it or amplified to maintain an active metabolic function of the host (Table 3). All in all, nigh on 200 genes involved in antibiotic resistance have so far been identified, and there may be many more to be found.

In the absence of specific resistance genes, some microbes undergo mutations that make them refractory to antibiotics. Early microbial geneticists did not know about horizontal gene transfer and its implications for antibiotic resistance. Moreover, despite accurate predictions from a few scientists, including Alexander Fleming, most microbiologists did not anticipate losses in efficacy from the development of antibiotic resistance.

By now, however, the consequences of extensive antibiotic use are now painfully evident: resistance is rampant in the microbial population, and many of the most effective agents are becoming useless. Some experts even suggest that, at least in particular situations, we may revert to the preantibiotic era. That is, sometimes no useful therapeutic agents will be available for the treatment of specific infectious diseases. In the case of infection with certain types of organisms, such as vancomycin-resistant enterococci or multidrug-resistant mycobacteria, this prediction is now close to being realized.

Countering Antibiotic Resistance

There have been numerous proposals suggesting ways to counteract this trend toward antibiotic resistance and thus to ameliorate the public health crisis that threatens us. One answer lies in the discovery of new antibiotics by chemical synthesis or by natural product screening. Indeed, traditional approaches for identifying and developing antibiotic agents are now being supplemented by newer approaches, including the systematic genetic and chemical manipulation of biosynthetic pathways.

Moreover, the genomic sequences of many bacterial pathogens are being determined, bringing great expectations that sophisticated bioinformatic analyses will provide new target reactions for the screening of potential inhibitors that may become new classes of antibiotics, which will be unaffected by the resistance mechanisms now present in bacterial pathogens.

Although microbial molecular diversity may provide potent new antimicrobial agents, their long-term success will depend in part on our ability to exert prudent controls over their use. If novel antibiotics are exploited as zealously as old antibiotics were over the past few decades, future efforts to treat human infectious diseases with these anticipated antibiotics will become compromised in the same way as they are now. It is to be hoped that we have now gotten the message and that future generations will be more prudent in their use of anti-infective agents.

Could we instead be facing the end of the golden age of antibiotics? I think not. Increasingly effective diagnostic methods and the institution of reliable early warning systems (with appropriately rapid responses) will aid in containing the problems of antibiotic resistance that we can expect to encounter in the immediate future. However, the longer-term treatment of infectious diseases will require the strong commitment of microbiologists in academia and industry to the application of increasing knowledge of the infectious disease process and characterization of host-pathogen interactions in parallel with better understanding of the biology of antibiotic-producing organisms.

Ironically, the use of antibiotics and subsequent development of antibiotic resistance have played a highly significant role in the development of the modern biotechnology industry. The discovery that antibiotic resistance is genetically transmissible, in the form of extrachromosomal elements (R plasmids), led Herbert Boyer and Stanley Cohen to transform E. coli, thereby demonstrating the underlying principles of genetic engineering. R plasmids served as vectors in their original recombinant DNA studies and continue to be used extensively for such purposes. Furthermore, the dominant selective markers used in the majority of horizontal gene transfer studies are largely derived from antibiotic-resistant bacterial pathogens. Even the dark cloud of antibiotic resistance has a small silver lining!

Key signs indicate that we are at a critical point in the history of antibiotic use. However, rather than being the beginning of the end, with a threat of returning to the pre-antibiotic era, this period can be takenas the end of the beginning, setting the stage for a new antibiotic era. To succeed, this new era needs to be based on creative approaches to the discovery and development of novel therapeutic agents, and it should be administered in an intellectual climate of better understanding of microbial pathogens and the diseases they cause and of procedures for treating those diseases. In addition, newer knowledge of the pathogens and their interactions with their hosts is likely to lead to the development of novel and more effective vaccines.

Only time will tell if these applications of the science of microbiology can enable humankind to maintain parity with our microbial adversaries.

SUGGESTED READING

Bucher, T., and H. Sies (ed.). 1969. Inhibitors: tools in cell research. Springer-Verlag, New York.

Ciba Foundation. 1997. Antibiotic resistance: origins, evolution, selection and spread. Ciba Foundation Symposium 207. John Wiley & Sons, Chichester, United Kingdom.

Davies, J. 1998. Aspects of the molecular genetics of antibiotics. In S. J. W. Busby, C. M. Thomas, and N. L. Brown (ed.), Molecular Microbiology, vol. 103. Springer-Verlag, Berlin.

Florey, H. W., E. Chain, N. G. Heatley, M. A. Jennings, A. G. Sanders, E. P. Abraham, and M. E. Florey. 1949. Antibiotics: a survey of penicillin, streptomycin, and other antimicrobial substances from fungi, actinomycetes, bacteria, and plants. Oxford University Press, London.

Gale, E. F., E. Cundliffe, P. E. Reynolds, M. H. Richmond, and M. J. Waring (ed.). 1981. The molecular basis of antibiotic action. John Wiley, Chichester, United Kingdom.

Hunter, P. A., G. K. Darby, and N. J. Russell (ed.). 1995. Fifty years of antimicrobials: past perspectives and future trends. Cambridge University Press, Cambridge.

Krause, R. M. (ed.). 1998. Emerging infections. Academic Press, New York.

Levy, S. B. 1992. The antibiotic paradox: how miracle drugs are destroying the miracle. Plenum Press, New York.

MAFF Report. 1998. A review of antimicrobial resistance in the food chain. Ministry of Agriculture, Fisheries and Food, London.

Moberg, C., and Z. A. Cohn (ed.). 1990. Launching the antibiotic era. Rockefeller University Press, New York.