Multitudes R Us: A Review of Ed Yong's I Contain Multitudes

If I were to break the history of infectious diseases medicine into periods I would say that infectious disease has moved into the period of the microbiome. This period, I believe, will be characterized by major discoveries regarding the role of the microbiome not only in health and disease but also establishing the role of the microbiome and its constituent microbes in various physiological functions in virtually every living organism on the planet. 

I have found no better way to understand the full implications of the microbiome than the masterful science journalist's Ed Yong's I Contain Multitudes: The Microbes Within Us and A Grander View of Life. 

This book, which is almost impossible to encapsulate because of the plethora of valuable information it contains, is a tour of the world of life with special attention and focus devoted to the role that microbes play in every organism's life. While the role of the microbiome is very well-established with certain human infections such as Clostridium difficile, Yong moves much further than these topics and explores the role of the microbiome in life more generally moving deftly from humans to corals to frogs. Some of the aspects of the book that I found exceptionally fascinating were his detailing of the various roles of the Wolbachia genus of bacteria as well as that of Sodalis.  

After finishing Yong's book, I am increasingly thinking that maybe we should stop discussing genomes and microbiomes and move to discussing the holobiome instead for understanding the "multitudes" and how they interact with us and other organisms likely holds many keys to unraveling the myriad mysteries of biology that remain to be solved

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Smog: What Lurks Within

The planet teems with bacteria in all niches imaginable, including the air we breath. Integrate this fact with the fact of the ubiquity of antibiotic resistant bacteria and it is not surprising that the air itself contains antibiotic resistant bacteria. A recent study, that the popular press has been reporting on, reveals that the smog (an amalgam of fog and particulate matter) of Beijing contains many antimicrobial resistance genes. 

Before anyone suits up in a gas mask before going outside (as if the air inside one's house is sterile), it is important to put the finding into context.

While the finding itself doesn't strike me as surprising, it does illustrate the magnitude and full scope of antibiotic resistance. I often emphasize that antibiotic resistance is a unrelenting process in nature that humans have exacerbated with injudicious use of antibiotics. Antibiotic resistance is how bacteria struggle and fight with other microbial species and everywhere you look resistance is present -- even in caves in which no human has set foot. It will always be present at some levels and that is why antibiotic stewardship that accounts for this fact and minimizes the acceleration of the process is crucial

What the implications are of this latest piece of research? I wonder if some of the community-acquired drug-resistant infections and colonization might be the result of acquisition from the air. This study noted the presence of antibiotic resistant genes -- not the presence of viable bacteria --- so follow up studies could attempt to cultivate antibiotic resistant bacteria from the air.

A Race Between Humans, Dogs, and Worms: Guinea Worm Eradication Setbacks

One of the principles of eradicating a human infectious disease from the planet is that the disease cannot have another host. For example, smallpox only infected humans. It could greatly complicate -- and likely derail -- an eradication effort if, in addition to finding and isolating infected humans, a wily animal species was added to the mix. 

The 2nd human infectious disease on the chopping block is Guinea Worm, or dracunculiasis. This infection, which is caused by an invasive worm which must be meticulously winded out of the body, has been beaten back to just a few African nations and, under the direction of President Carter's center, has been on its last legs (of course, worms don't have legs). The key to preventing infection is to keep those infected with the worm from placing themselves in water sources to prevent the worm from discharging its infectious form into the water in which others drink (filters are also used to prevent ingestion). 

In 2016, there have been just 19 cases in Chad, Ethiopia, and South Sudan. However those 19 cases are not the full picture as they represent a 25% increase over the same period in 2015 (there were a total of 22 cases in 2015). More ominous to me is the discovery that dogs and baboons are getting infected. It's almost as if the worm, sensing its impending annihilation, has pulled out all stops to stave off extinction and jumped into other species in a manner reminiscent of the demon spirit in the movie Fallen. This phenomenon could make it very hard to fully eradicate this pathogen as wild dogs, for example, can easily contaminate drinking water sources and undo the progress that has occurred with human cases.

Of course, it is no accident that the disease persists in only specific countries as the underlying problem is access to safe drinking water untainted by guinea worm. Civilization, then, is the ultimate way to eradicate this disease. If civilizing forces accelerate sufficiently to bring safe drinking water to the Chad, Ethiopia, and South Sudan, the issue of infections in dogs and other animals may not be so pivotal as feared. However, the provision of safe drinking water is a Herculean task and, if it proves unachievable in the near term, the race between humans, a worm, and dogs will carry more import for the human race than the Olympics.

Veterans of the War that Saved the World

Tonight was the dinner jointly organized by the UPMC Center for Health Security and Johns Hopkins University's Bloomberg School of Public Health in honor of DA Henderson, the founder of our center and a former dean of the school. 

It was an extraordinary event and one that I will remember for a lifetime. Sitting in a room of luminaries of public health including Army generals, two former CDC directors, an undersecretary of the Department of Homeland Security, and countless others would be an extraordinary conglomeration for anyone but DA. 

Scattered amongst the attendees were those that worked on the smallpox eradication campaign, DA's pathbreaking achievement that rid the planet of a murderous virus. Listening to these heroes trade stories from the 1960s and 1970s about how they, under DA's guidance and direction, vanquished this virus from remote corners of the planet -- a feat one of them called more important than the moon landing -- was inspirational. I imagine listening to true war stories of military veterans is a similar experience but I would argue the veterans I heard converse tonight are of a different sort: these were the veterans of the only successful war to save mankind from a virus that had killed with impunity until it met DA and with him as their commander-in-chief they saved the world.

Inferno: An Infernal Misconception of Virology and Infectious Disease

Despite my usual inability to pull myself away from a Dan Brown novel or their film versions, the latest of the film installments, Inferno -- which centers on a bioterrorist plan -- was an unfortunate exception. 

The novel version of Inferno was chock full of the trademark Dan Brown literary signatures that I love being immersed in, however its endorsement of the thoroughly debunked Malthusian doomsday prophecy was something that really detracted from the other aspects of the book that I particularly enjoyed, including its indictment of religiously-motivated opposition to birth control.

But, given the topics I gravitate to, I wanted to draw some attention to the actual virus attack scenario that drives the film's plot. NPR has already addressed the veracity of the technical aspects of the fictional virus and I definitely agree with the assessments of the renowned virologists they interviewed.  

A couple of points I want to emphasize:

A virus that kills 95% of the population, as the Inferno virus is alleged to do, would be a very hard feat. As I discussed in my Atlantic piece, the sheer diversity of the human immune response and the fact that humans emerged in a pathogen-laden environment creates an extremely high bar for any microbe to scale. To achieve a 95% kill rate within a matter of week is pure fiction without a true basis in fact. 

Another important aspect that merits comments is the ability of a rogue scientist to synthesize such a virus. Even if one grants that the person possesses all the tacit knowledge required to do such high level synthetic biology and genetic engineering, what properties are required for a 95% kill rate? Should the virus be transmitted via the airborne route, through body fluids, or through contact? Should it be enveloped or naked? What is the trade-off? 

My point is that fictional viruses are the stuff of fiction and should remain there. While a movie like Inferno will draw much-needed attention to the risks of bioterrorism and emerging infectious diseases, hopefully it does so without allowing fantasy virus characteristics to cloud people's conception of where the true risks lie.