BioPharm Executive: The Coming Antibiotic Crisis: Should Biotech Follow Its Gut?

Published: Nov 27, 2013

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November 27, 2013

By Karl Thiel for

A special editorial in the November issue of The Lancet warned that emerging, antibiotic-resistant superbugs could undo a century worth of medical advances and plunge us back into the pre-antibiotic era, when infection often meant death.

This warning, while both blunt and alarming, is nothing new. At least as far back as 2000, a joint task force of FDA, the CDC, and the NIH was issuing a similar warning, noting that drug companies have largely turned their backs on developing new antibiotics. Indeed, that Lancet editorial builds by a new warning from the CDC issued in September, which for the first time put a number on deaths stemming from antibiotic resistance--23,000 annually and more than 2 million illnesses. The warnings continue, of course, because too little has been done to counter a growing threat. "Rarely has modern medicine faced such a grave threat," say the authors.

Too little has been done, but not nothing (see Golden Handshakes and Bench to Clinic). While major pharma companies still largely ignore antibiotic research as not profitable enough, smaller companies are looking at next-generation drugs or in some cases alternative therapies. A handful of companies, for instance, are plugging away at bacteriophage therapy--viruses selected for their ability to destroy specific bacteria. But despite technical successes, these companies face an uphill battle in developing a consistent, approvable product and haven't yet found much commercial validation or attracted much investment.

Perhaps a newer area will fare better: The human microbiome. Heightened interest in the microbiome can probably be dated to April 2011, when a study showing that humanity fits into one of three basic profiles of intestinal flora was published in Nature. What the researchers called the "enterotype" was likened to blood type--a durable characteristic that distinguishes us from birth (or at least shortly thereafter), and that comes in one of three flavors characterized by a preponderance of bacteria from one of three genera: Bacteroides, Prevotella, or Ruminococcus.

Subsequent research has indicated that maybe the distinction isn't so clear cut, and populations of these three bacteria, as well as others, may exist on a continuum in most people. Also now questioned is the original researchers' contention that enterotype doesn't appear to be related to a person's age, gender, nationality, or diet; as is the hypothesis that one's enterotype may be fixed for life.

All this makes for an interesting area for potential commercial therapeutics. Flagship Ventures announced this month that Seres Health, which has been operating in stealth mode for the past two years, has emerged with funding and a therapeutic platform. It joins two other venture-backed microbiome companies, Second Genome and Vedanta BioSciences. Interestingly, Seres was cofounded by Noubar Afeyan, who I mentioned last month--as the co-founder of ProNutria, a company screening for potentially therapeutic proteins found in the human diet.

Seres is initially going after C. difficile infection, a bacterial infection frequently acquired in hospitals that is difficult to treat at the best of times. Exactly what Seres' angle is I don't know, but it's a good bet that it relates to another area of study with a somewhat longer pedigree--fecal transplant. First described in 1958, this is exactly what it sounds like, and has been used therapeutically on a limited basis for at least 20 years. Thought to work by altering the makeup of an individuals microbiome, fecal transplant is a cheap and effective tool for combating C. difficile--but faces some pretty serious PR problems, as well as some logistical challenges.

On the other hand, a discovery platform based on the success of fecal transplant in treating C. difficile could not only make that treatment easier, but also play a role in other illnesses thought to be related to variations in the microbiome--everything from irritable bowel syndrome, ulcerative colitis, and celiac disease to even rheumatoid arthritis, diabetes, and obesity.

That explains the interest of venture capital in this area, and C. diff looks like it could be the low-hanging fruit--the success of reintroducing healthy gut flora is pretty well established here. Unfortunately, that's only a small part of our growing problem with antibiotic resistance. It may take mounting complications and deaths before drug companies and VCs become more interested.

-Karl Thiel

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