Humanity’s uphill battle against antibiotic resistance

By: Zuri Sullivan

Antibiotic resistance is a public health crisis that has received lots of attention recently, and for good reason. One only need read Maryn McKenna’s essay in Medium to understand the gravity of the situation. The advent of antibiotics in the 20th century, in addition to improvements in sanitation and other medical advances, saw a doubling of life expectancy in the United States. If widespread antibiotic resistance were to render these miracle drugs virtually useless, we could return to the dismal reality of our grandparents’ childhood, where apparently innocuous infections like strep throat could spell a death sentence.  And for every antibiotic currently on the market, there exist bacteria that are resistant to it.

So how does antibiotic resistance arise? The emergence of antibiotic resistance is actually a real-time illustration of evolution. When Charles Darwin published On the Origin of Species in 1859, he put forth the theory of natural selection, which became the basis for what we now call evolutionary biology. The basic principle is as follows:

  • Variation arises amongst organisms due to random genetic mutations
  • The environment that organisms are exposed to determines whether this mutation is beneficial (makes them more fit, or able to reproduce) or detrimental (makes them less fit)
  • When a mutation confers a fitness benefit, the organisms that possess this mutation reproduce more, passing down the variation to their offspring
  • Thus, over generations, beneficial mutations become more frequent in the entire population

Antibiotic resistance is an example of a variation that could arise in a population of bacteria. When the population is exposed to antibiotics, this mutation confers a fitness benefit to the mutant. The antibiotic kills the non-mutant bacteria, while the mutant survives, and gives rise to mutant offspring. Not only can resistant bacteria spread antibiotic resistance genes to their offspring, but they can also pass them to their neighbors through a process called horizontal gene transfer. Over time, the entire population of bacteria becomes resistant to the antibiotic. When this happens inside a person’s body, it can mean that the drugs that their doctor prescribes to treat an infection may not be effective.

The gravity of the situation is clear—antibiotic resistant infections account for about 23,000 deaths per year in the US alone, and are estimated to cost us as much as $35 billion annually. Though the problem is obvious, the solution is much less so. Many have been proposed, from restricting the use of antibiotics in agriculture, (the vast majority of antibiotics sold in the US are bought by the agriculture industry), limiting the inappropriate use of antibiotics in medicine, to reducing antibiotic treatment regimens to the lowest level possible to improve a patient’s health. The most obvious solution, and the one scientists have been working on since antibiotic resistance was first described in 1940, is discovering new antibiotics.

Unfortunately, this endeavor has produced limited success. In the past 50 years, there has only been one new class of antibiotics introduced into clinical practice; the overwhelming majority of antibiotics developed in the last several decades have been variations on existing compounds. And for most new drugs, resistance arises so quickly that antibiotic-resistant bacteria can be detected in the population years before the antibiotic even hits the market. It would seem that humans are fighting a losing battle against bacteria.

A glimmer of hope came earlier this year, when researchers from Northeastern University published a study in Nature describing the discovery of a new antibiotic without detectable resistance. The new compound, teixobactin, was found to be effective against a number of disease-causing bacteria, including Staphylococcus aureus (staph) and Mycobacterium tuberculosis (TB). Not surprisingly, this discovery generated a lot of excitement in the scientific and medical communities. But some wonder whether the development of resistance against new and exciting drugs is just a matter of time.

The answer could come from a surprising source: bacterial DNA isolated from the remains of woolly mammoths, massive, now-extinct relatives of modern elephants who walked the earth during the Pleistocene Epoch over 30,000 years ago. A 2011 study in Nature described the detection of bacterial antibiotic resistance genes in samples isolated from woolly mammoths and other ancient animals from the Pleistocene. Based on what I’ve told you already, this seems crazy. After all, antibiotic resistance is driven by the use of antibiotics, and humans have only been using antibiotics for about 100 years. So why would bacteria from 30,000 years ago be evolving resistance to antibiotics?

It turns out that humans weren’t the first organisms to realize that antibiotics are a good way to kill bacteria. Bacteria themselves were the original inventors of antibiotics, and they’ve been using them to kill each other for millions of years. That’s right—our modern antibiotics are the product of millions of years of interbacterial warfare. Humans only discovered antibiotics in the 20th century, but bacteria have been using them for much longer than that. For as long as these weapons have existed, their targets have been devising ways to evade them. If resisting antibiotics is a fundamental component of what it means to be a successful bacterium, can antibiotic resistance ever really be eliminated? 

Cheaters never prosper, not even bacteria

We all know that cheating is wrong, but some people do it anyway. I know I had my fair share of classmates growing up who would try to copy my homework (perils of being a nerd). Big or small, cheating has consequences. If you’re caught peeking at someone’s answers while taking a test, you’ll probably get a zero.

The existence of consequences for cheating makes sense in the context of social cooperation— rules and laws facilitate our happy coexistence, and thus need to be enforced. It turns out that the phenomenon of social cooperation isn’t unique to humans. Biologists have also observed that animals living in groups can have complex social structures that are regulated by rules to prevent cheating, and “police” who enforce the rules. In ant colonies, for example, worker ants are policed (link) by occasional violent attacks to prevent individual workers from cheating. In this case, cheating means a single worker ant reproducing more than would be good for the colony as a whole. By policing these cheaters, the overall harmony of the colony is maintained.

While scientists have long known that animals exhibit cooperative behavior, a recent study published in Proceedings of the National Academy of Sciences showed that bacteria do the same thing. A team led by Dr. Peter Greenberg from the University of Washington studied social behavior in a species of bacteria called Pseudomonas aeruginosa. All social groups need a means of communication. Humans use language, among other things, to communicate with one another. In P. aeruginosa (and, in fact, all bacteria), communication is mediated by a process called quorum sensing.

In a legislative body, quorum refers to the minimum number of members that must be present at a meeting to make its proceedings valid. Bacteria are able to sense quorum, or how many bacteria of the same species around them, by sending out molecules that can then be recognized by special receptors on other bacteria. If you’re an individual bacterium, these receptors tell how many of your buddies are nearby by detecting the concentration of these quorum sensing molecules. When quorum sensing is intact, the entire population of bacteria benefits by being able to coordinate their behavior. If there’s a certain valuable resource around, like a nutrient, the whole population benefits if the nutrient is equally shared. In order to make sure they share equally with each other, the bacteria need to be able to sense how many other bacteria are around, which they accomplish through quorum sensing.

Unfortunately, this system is subject to cheating. After all, these nutrients are really yummy to the bacteria, and they don’t always want to share. It’s like if you brought a bunch of cupcakes to school to celebrate your birthday, but then realized that the cupcakes are delicious and you’d actually just rather sit at home and eat them all yourself. P. aeruginosa is able to cheat when it loses the ability for quorum sensing. This occurs by random a mutation event, but subsequently allows an individual bacterium to take up nutrients and reproduce independently of its buddies. This is great for the cheater (the bacterium that loses the ability for quorum sensing), but bad for the population as a whole, so the population needs a way of controlling this cheating behavior.

 It turns out that cooperating P. aeuroginosa, those that don’t cheat and maintain the capacity for quorum sensing, police the activity of the cheaters by producing a toxic molecule called cyanide. The same gene that mediates quorum sensing is also implicated in the detoxification of cyanide. So cheaters are punished for their behavior by losing the ability to break down cyanide produced by cooperators. The cheaters die, the cooperators prosper, and all is right with the world. 

Sisterhood of the Traveling Genes

By: Helen Beilinson

Unlike humans, bacteria reproduce asexually (yet another reason why I’m happy I’m not a bacterium). This means that one bacterium splits itself into two, giving rise to two daughter cells. The two asexual offspring have the same genome as their one parent. Although keeping the same genome as your parent has a lot of benefits (moms always know best), it can also lead to problems; the lack of new genes sometimes makes it hard for bacteria to adapt to changing environments. Luckily for them, bacteria have found lots of ways of acquiring new genes to survive new environments. One such strategy is getting genes from other bacteria through a process called ‘horizontal gene transfer’ (as opposed to ‘vertical gene transfer’ where parents give genes to their offspring). Horizontal gene transfer doesn’t just occur between bacterial species—it has also happened between bacteria and eukaryotes, which are much more complex organisms. And recently, scientists from the University of Washington found that horizontal gene transfer has brought bacterial genes into animal genomes.

The researchers, led by Joseph D. Moungos, published a study in a recent issue of Nature. They found a bacterial gene called Tae that has repeatedly entered eukaryotic lineages through horizontal gene transfer. Many bacteria have Tae proteins, which function as antimicrobials to kill other bacteria. To do this, Tae breaks down the layer of protection that surrounds the bacteria, called the cell wall. The bacteria that Tae targets actually have two cell walls—an inner wall and outer wall. Tae goes in between the two walls and breaks down a sugar-rich structural protein called peptidoglycan. By targeting peptidoglycan, Tae essentially makes the two cell walls collapse in on each other, killing the bacteria. This group found that at least six times in history, eukaryotes have gotten this gene from bacteria to use as their own. When they looked at the animal versions of the proteins, termed Dae, they discovered that their function in animals is the same as in bacteria; Dae proteins are antimicrobial agents that target peptidoglycan.

The experiments initially showing that Dae has antimicrobial function were performed in a test tube, outside an actual organism. To investigate whether Dae has antimicrobial function within organisms, this study looked at an animal that got Tae from bacteria—the deer tick. Deer ticks can spread the bacteria that cause Lyme disease, which results in fevers, headaches, and rashes, and can lead to more serious symptoms if untreated. Borrelia burgdorferi is one bacterium that can cause Lyme disease in humans. It moves from person to person by living in ticks and transmitted through tick bites. To see if Dae works as an antimicrobial in deer ticks, the scientists removed the Dae protein from the deer ticks and looked for changes in the amount of B. burgdorferi. Turns out that without Dae, deer ticks have more B. burgdorferi. Dae restricts the population size of B. burgdorferi can get in the deer tick by killing the bacteria.

 Collectively, bacteria harbor heaps of antimicrobial peptides. This group looked at one such protein in a defined animal species. If one protein has been transferred to eukaryotic genomes six times in the species that they looked at, this implies that with the thousands of other antimicrobial peptides and thousands of other animals, it is highly probable that many other bacterial genes have been transferred into animals. Who knows, maybe it wouldn’t be so bad being a little bacterial.

Roses are red, violets are blue, frogs are icky, but may be good for you

By: Zuri Sullivan

Sorry, kids, but if you kiss a frog, it’s highly unlikely that he’ll turn into a prince. The most you’ll probably get out of it is some icky frog skin slime on your mouth. That may sound terrible, but a new study published in Antimicrobial Agents and Chemotherapy suggests that some components of icky frog skin can have some unexpected benefits for our health.

As you might imagine, frogs are pretty distantly related from humans, and consequently, their immune systems work quite differently from ours. One thing we have in common, however, is that we both produce molecules specialized for killing bacteria, called antimicrobial peptides (AMPs). Humans produce lots of AMPs in their guts— last week, I wrote a story about how the helpful bacteria in our guts manage to survive in the face of these harsh molecules, while dangerous bacteria don’t. Unlike humans, frogs and other amphibians produce AMPs in their skin. To a certain extent, you could say they wear their immune systems on their backs.

Scientists haven’t quite figured out all of the ways that AMPs actually kill bacteria, but if the bacteria are susceptible to them, they work incredibly well. So from the bacteria’s perspective, AMPs are pretty nasty. From biomedical scientists’ perspective, however, this means that AMPs from a variety of species may be able to be used to treat bacterial infections when our own AMPs are inadequate.

This was the focus of the study I mentioned above, led by principal investigator David Craik at the University of Queensland in Australia. His research group wanted to know whether frog AMPs could be used to treat Staphylococcus aureus infection. You may know of Staphylococcus aureus by its more colloquial nickname, Staph. Staph infections are a major problem in hospitals, and the widespread use of antibiotics has led to the emergence of antibiotic resistant staph, also known as MRSA (for methicillin resistant Staphylococcus aureus). Antibiotics are great, but when misused or overused, they can promote the emergence of antibiotic resistant bacteria, necessitating the development of new antibiotics. It’s a vicious cycle, but AMPs could be new weapons in our anti-bacterial arsenal.

Can you really take AMPs from frog skin and use them to treat a staph infection? In mice, the answer seems to be yes. Dr. Craik’s group isolated AMPs from frogs, and studied their chemical structure. If they’d had to run out and catch a frog every time they wanted to do an experiment, the study would have taken forever, so they synthesized molecules that were very similar to the frog AMPs. These synthetic AMPs were then used to treat Staph-infected mice. Surprisingly, they worked! And not only that, but when they tested the compounds to find out if they were toxic to the mice, they seemed to be safe.

This doesn’t mean you should go out and lick a frog next time you’re feeling sick. As Helen and I tried to illustrate before, findings in mice need a lot of work to be extrapolated to humans. We know that a drug’s effect on mice is not always the same as its effect on humans, so clinical trials, despite being absurdly costly and tedious, are really important to make sure our drugs have the effects we want them to. AMPs are also expensive and difficult to synthesize, and scientists will need to find easier ways of making them if they want to try to use them to treat human infections.

Don’t give up on frog AMPs yet, though. With time, scientists may be able to turn them into real treatments for human infections. And in the meantime, you can put them to good use by applying the old Russian method of dipping a frog in unpasteurized milk to keep it from spoiling.

Why don’t we kill our microbiota?

By: Zuri Sullivan

If you didn’t already know that humans are colonized by trillions of bacteria, that these bacteria make up much more of our bodies than our own cells, and that they play an important role in our physiology, health, and disease, then you probably didn’t read Helen’s piece about the microbiota and defense against viruses. The “microbiota” refers to the collection of microorganisms that live in and on our bodies. A search for “microbiota” returns close to 14,000 academic papers. To call this a current hot topic would be a massive understatement. Why are scientists so excited about the microbiota? First, major technological advances have allowed scientists to begin unraveling the complex community of bacteria, fungi, and viruses that colonize our bodies. Additionally, mounting evidence suggests that the microbiota can influence nearly every aspect of our physiology, which raises important questions about its interactions with other cells and tissues in our bodies. 

There’s a lot to be learned about the microbiota and its functions, but one of the biggest unanswered questions in the field is why all of these bacteria are overlooked by our immune system. Most of us know the immune system as the mechanism by which our body eliminates disease-causing agents, or pathogens. These pathogens are bacteria, viruses, and fungi—the same organisms that make up the microbiota. One of the biggest unanswered questions regarding the microbiota is why our immune system doesn’t eliminate our own microbial population, but does eliminate those microbes that are pathogenic. The initiation of an immune response against an invading species relies on the detection of pathogen associated molecular patterns (PAMPs). PAMPs are molecular structures that are present in microorganisms, but not in host cells. For example, a particular sugar-like molecule, lipopolysaccharide (LPS) is present on the surface of some bacteria, but absent from mammalian cells. Thus, by targeting attacks against cells that have LPS, the immune system can efficiently target a wide array of bacteria without risking damage to host cells. In addition to being distinctly non-mammalian, another critical feature of PAMPs is that they are conserved amongst microbes. This means that PAMPs tend to be molecules that serve critical functions for microbial survival, and thus they are seen in an array of microbial species, including pathogens (microbes that make us sick) and commensals (microbes that have neutral or beneficial effects on our health). This raises an important conundrum: if the immune system recognizes PAMPs that are common to all microbes, why don’t we attack commensals?

A paper published last week in Science provides an exciting clue to how our commensal bacteria survive some of the host’s innate defenses. They looked at antimicrobial peptides, which are chemicals made by immune cells that can directly kill bacteria. They’re like antibiotics made by your own body, and they are an important innate defense mechanism against bacterial infection. The team of researchers asked whether commensal bacteria might be resistant to antimicrobial peptides, which would allow them to survive in the host. Their hypothesis was that commensal bacteria that are adapted to live in our bodies might have evolved mechanisms to tolerate antimicrobial peptides, while pathogens have not.

They found that a common commensal species, Bacteroidetes thetaiotamicron  (B. theta) was more resistant to a particular antimicrobial peptide than pathogenic bacteria. Next, they identified the B. theta gene that was responsible for antimicrobial peptide resistance, a gene called LpxF. They then asked what role this gene played in the ability of this commensal organism to survive the host immune response to a pathogenic bacteria.

This was an important question, because it illustrates an important principle about how the microbiota helps us protect ourselves from pathogenic bacteria. When we’re infected with an intestinal pathogen, gut immune cells detect the infection and induce many defense mechanisms, one of which is the secretion of antimicrobial peptides. These antimicrobial peptides need to be able to target the pathogen, while sparing the commensals that provides other benefits to the host. Thus, by having a gene that confers resistance to antimicrobial peptides, the commensal has an advantage over the pathogen in the context of an immune response.

This was borne out in an experiment wherein the researchers added two different bacterial strains to the intestines of germ-free mice (mice who are raised to not have their own microbiota): wild-type (normal) B. theta or B. theta that were lacking LpxF (a mutant strain), and therefore lacked resistance to antimicrobial peptides. They then infected these mice with a known pathogen, Citerobacter rodentium. They found that while the LpxF mutant strain of B. theta was outcompeted by the pathogen, the wild-type B. theta survived the immune response.  

The findings of this study illustrate two important principles. First, they provide a mechanism that explains how a commensal bacterium survives a host defense mechanism that is directed against all bacteria. Second, they show that this survival mechanism helps commensal microbes compete with pathogens for colonization of the gut. These principles are relevant to both the continued understanding of the role of the microbiota in host defense, and in understanding the co-evolution of the immune system and commensal microbes. This co-evolutionary relationship, whereby our evolved mechanisms for eliminating bacteria are resisted by commensals that have evolved to live in our bodies, is important for the continued study of the microbiota and its impacts on our health. 

I Kid You Not, A Disease Exists That Makes You Drunk, Constantly

By: Ross Federman

A bar I used to frequent serves a delicious frozen drink known as a “Constant Buzz.”  It sounds like an appealing concept, a nice basal level of ongoing intoxication, but did you know that in some incredibly rare cases, individuals find themselves in this situation without any choice?  Auto-Brewery Syndrome (or gut fermentation syndrome) is a disease whereby patients literally brew alcohol in their guts.  Imagine not taking a single sip of beer, wine, or liquor, yet still constantly registering above the legal limit on any manner of blood alcohol or breathalyzer tests.  This is the unfortunate case for those rare few that find themselves with this disorder.

How does it happen?  It was a mystery for years.  In fact, it’s likely that some may have been incarcerated, fired from jobs, suspended from school, you name it, all because they were drunk against their will with no explanation to offer as to their erratic behavior.  Recently, we have gained significant insight into the nature of our gut microbiota and the profound role that it plays in human health.  The microbiota is usually discussed in terms of the species of bacteria that comprise it; yet other microorganisms are present, as well.  In most healthy microbiota, a small population of the commonplace fungal yeast species Saccharomyces cerevisiae lives in your gut with all the other microorganisms.  S. cerevisiae is also known as “Baker’s Yeast” and is the species often simply referred to as “yeast” in the majority of baking and beer brewing applications. You and everyone around you likely have some S. cerevisiae hanging around in your guts, and the amount of it is largely kept in check by your immune system, other microorganism species, and competition for nutrients.  However, in some rare cases, this population is not kept to the proper minimal levels and grows wildly out of control. 

At the heart of this phenomenon is the fermentation process.  It is found in both yeast and bacteria, though the specific fermentation products differ.  In both cases, sugars or carbohydrates are broken down to carbon dioxide in order for the microbes to produce energy in an environment lacking oxygen (such as our guts).  For bacteria, lactic acid is the second byproduct along with carbon dioxide, but in yeast, ethanol is produced in lieu of lactic acid.  Thus by increasing the ratio of S. cerevisiae to bacterial species in the gut, greater amounts of ethanol are produced, and past a certain threshold, the ethanol metabolic product seems to reach levels where it is in a great enough concentration to equate to imbibing ethanol in the form of an alcoholic beverage.  It should also be noted that this same fermentation process is used to achieve the alcohol content in said beverages, though this, of course, does not take place directly in our stomachs.

Even with a greater understanding of the microbiota, the precise nature of why these yeast populations can grow so large and lead to ongoing intoxication remains unknown. Cases are so rare that really everything we know about this disease is almost entirely anecdotal.  Perhaps the patients ate an absurd amount of sourdough after taking antibiotics that would have wiped out many of the bacteria just prior to yeast colonization?  Whatever oddball circumstance lead to this, the end result?  Enough yeast in your gut to lead to fermentation levels that are actually sufficient enough to influence blood alcohol levels.  Sounds pretty awesome if it only lasts for the three days you spend at Coachella, but week in and week out, it would probably get old pretty quickly.