Microbiology: A New Golden Age of Antibiotic Discovery?

A new golden age of antibiotic discovery is needed. The good news is that we may be on the verge of one

By Brandoch Cook

The accomplishments of biomedical science in the past two generations have been staggering and profound. Some highlights include the unraveling of cancer biology, from oncogene and tumor suppressor functions to tumor immunology and the promise of biologics; the unlocking of literally billions of avenues of new information via genomic sequencing of humans, mice, yeast, microbes, and seemingly everything in between; and the uncoupling of genetics from destiny, with first the knockout mouse and later the at-will interrogative and architectural power of CRISPR and induced pluripotency. However, our ability to translate these and other revelations into broadly transformative medicine rests on a fragile skein of protection from infectious agents both exotic and mundane.

There is a recent upsurge in hospital-oriented contractions of multidrug-resistant bacterial infections. There’s also been a resurgence of long-defeated microbial foes such as gonorrhea, syphilis, and tuberculosis. This long-term trend has been gathering momentum, with approximately two million infections and 23,000 deaths annually in the United States and an associated health care cost of $20 billion. Without the aid of novel antimicrobial drugs, the arc will skyrocket upward, with perhaps a 10-fold increase by the year 2050. Simply and obviously put, a new golden age of antibiotic discovery is needed. The good news is that we may be on the verge of one.

The original golden age was spurred by the widespread use of penicillin and streptomycin by the end of World War II to mitigate battlefield and communicable infections. Over the next quarter century, 20 distinct classes of antibiotic compounds were discovered, primarily via screening for natural metabolic products in actinomycetes in soil samples. Thus, although pathogenic species typically begin demonstrating resistance to new antibiotics within two years, the steady profusion of novel products, along with modified analogs of existing ones, allowed medicine to outflank microbes for almost 50 years. Unfortunately, the microbes quietly spent that time catching up, for several reasons: (1) medical crises prompted regulatory changes that prolonged clinical trial and approval processes, greatly increasing the associated cost and failure rates of new drugs before entry to market; (2) microbiology research programs and academic departments turned their attention to tropical and emerging diseases, resulting in a scientific detraining of potential future antibiotic investigators; and (3) stagnation in government funding for antibiotic research and an exodus from the field by the pharma giants to target more profitable ventures combined to promote the design of analogs at the expense of novel compound discovery.

This third point is perhaps most salient, because analog design is intrinsically a finite endeavor, strictly bounded by the ingenuity of medicinal chemists, whereas natural product discovery is potentially limitless, especially because approximately 99 percent of bacterial species have never been cultivated in laboratory settings. This is partly due to the great plate count anomaly, the observation that bacterial cultivation generates substantially fewer colonies than can be detected microscopically within samples allowed to grow ungoverned in their natural environment. Therefore, there is evidently something special, beyond current understanding, brewing within either the direct surroundings or the close interactions between adjacent symbiotic or competitive species. The anomaly has been conquered only empirically in isolated instances through modification of growth media. This stepwise approach, while informative, is laborious and in the end inadequate when it comes to target-driven drug discovery. However, a recent innovation has bypassed it and perhaps rendered the anomaly obsolete, allowing the propagation and analysis of previously uncultivable species.

The isolation chip (iChip) is a microwell diffusion chamber device containing a restrictive membrane that traps individual bacterial cells within each well after they are extracted from the environment, for instance from the soil or sea floor. A portion of the native environment is removed along with the sample and maintained surrounding the iChip to promote normal bacterial growth in a way not feasible with agar or liquid media. The result is a many fold increase in efficiency of cultivation, and the approach has yielded the novel antibiotic class teixobactin, which can kill S. aureus, among other pathogenic species. NovoBiotic Pharmaceuticals (Cambridge, MA) is currently developing products with this technology, but its founders note that the iChip can be produced for minimal cost using readily available materials such as pipette tip boxes and 3-D printers. This opens up great possibilities for individual laboratories to contribute supportive innovation, for instance via bacterial coculture using more permissive membranes to identify novel metabolic products that are activated through competition or cooperation of adjacent microbes.

Additionally, metagenomics approaches have stimulated antibiotic discovery. While the efforts of the Human Genome Project received the bulk of the press, the full genomic sequence of S. coelicolor was quietly revealed. This is a nonpathogenic species with a large genome (for bacteria), and one of the resulting discoveries was the existence of silent synthetic gene clusters that can be activated by coculture to produce novel secondary metabolites. The new antibiotic class of malacidins was discovered by metagenomics strategies to identify calciumdependent genes. The benefit of this type of approach is that it is largely culture-independent and allows one to derive diverse information directly from an environmental sample. For example, Oxford Nanopore Technologies (Oxford, England) has combined its benchtop sequencer MinION™ with an iChip culture platform to allow direct and rapid identification of previously uncultivable species and, by extension, potential novel metabolites and synthetic gene clusters.

There are several small companies, including Entasis Therapeutics (Waltham, MA) and Melinta Therapeutics (Chapel Hill, NC), in startup, venture, and early product phases dedicated to these and other strategies. Additionally, there are open-source genome-mining platforms, including Anti-SMASH, NaPDoS, and MIBiG, that are constantly evolving and improving and provide metadata such as annotation on synthetic gene clusters and secondary metabolites. They and others are at the leading edge of what may turn out to be a second golden age of antibiotic discovery. Most excitingly, this territory is open and new to innovators and researchers, as it has yet to be consumed by the large biomedical research suppliers or the major biotech and pharma firms that continue to leave the field.


For additional resources on microbiology, including useful articles and a list of manufacturers, visit www.labmanager.com/microbiology 

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Scientific Apps

Published: December 7, 2018

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