Pathogen resistance can track with drug penetration, not just with drug number or variety

Here's an interesting paper from a multi-institution group looking at a perpetual problem in antibacterial and antiviral drug therapy - the emergence of mutations and resistance. As one of the authors describes it on her blog, the project started when the team realized that while the conventional wisdom about multiple drugs working better because of increased barriers to multiple mutations in the pathogen is correct, the mechanism for this seemed to be rather fuzzy, especially because the data seemed to show that multiple mutations arise not in tuples but as singles, one at a time.

The authors essentially divided the body into different compartments with viruses and bacteria and then assumed differential penetration of drugs in multidrug therapy into these compartments. They built a mathematical model to track the emergence of mutations as a function of exposure to various drugs. What they found is that imperfect drug penetration into a compartment can allow mutations against that drug to arise one at a time, and quite speedily at that. Thus, even if multiple drugs are being administered, the pathogen may not be exposed to these drugs simultaneously at the relevant concentrations in every compartment: as indicated in the title of the paper, even if the treatment may therefore consist of multitherapy in principle, it leads to "spatial monotherapy" in practice leading to the focused exposure of certain compartments only to single drugs at a time.

The study is interesting because it shows that mutations and resistance may not only be a function of drug number and variety but could also result from the drugs not making it to their site of action effectively - it's something that's not surprising in retrospect but it's nice to firm up this belief with a model. It also means that simply administering multiple drugs may not curb resistance if those drugs have vastly different penetration profiles.

If this hypothesis is true however, then you would see some correlation between drug penetration profiles and resistance mutations and not just with the diversity and number of drugs - in part it could explain why certain combinations of drugs even from similar classes work better than others (for instance, it could potentially explain why protease inhibitor X + RT inhibitor Y work better than protease inhibitor A + RT inhibitor B). I am assuming that this kind of cell and compartment penetration data does exist for certain drugs so it would be interesting to model it and track such potential correlations.

My E. coli brother's keeper

Would an anti-indole work?

Antibiotic resistance is one of the best examples of evolution in real-time and it’s also one of the most serious medical problems of our time. Emerging resistance in bacteria like MRSA threatens to bring on a wave of epidemics that may remind us of past, more unseemly times.

Given the threat that antibiotic resistance poses, it is paramount to understand the mechanisms behind this process. While considerable progress has been made in understanding the genetic basis of mutations that confer antibiotic resistance, much less is known about the population dynamics of bacteria that evolve this kind of resistance. Now, in the cover story of the latest issue of Nature, researchers from Boston University discover a novel and remarkable mechanism by which bacteria acquire resistance. The mechanism is effectively a form of bacterial altruism.

The researchers start by challenging successive generations of E. coli in a bioreactor with increasing concentrations of the antibiotic norfloxacin, which inhibits DNA synthesis by binding to DNA gyrase. Around the tenth generation or so, they notice something interesting. Not all bacteria have evolved resistance to the antibiotic, but there’s a very small population of bacteria with high resistance. However, in the next few generations, the other bacteria also seem to acquire this resistance. What’s going on?

It turns out that the small populations of bacteria which are highly resistant are actually ‘teaching’ their fellow bacteria to become resistant. They are doing this by a remarkably simple mechanism- by secreting the molecule indole into their environment. This indole acts as a signaling molecule that is mopped up by the other bacteria. The result is the activation of a variety of resistance mechanisms, including increased production of drug transporter proteins which are well-known to confer resistance by extruding drug molecules out.

Now indole is well-known as a component of signaling molecules. For instance, indole-3-acetic acid (IAA) plays many important signaling roles in plants and encourages cell growth and division. The detection of indole by itself was not surprising in this case, since all the bacteria secreted indole as part of their regular metabolism in the beginning. But what was surprising was the mechanism; as the antibiotic stressed out the bacteria, most of them essentially weakened and stopped indole-secretion with the exception of this small cadre of selfless individuals who kept on generating the molecular signal. Since production of indole in times of stress clearly requires an investment of energy, this was a bona fide case of bacterial altruism; sacrifice one’s own fitness to increase that of the group.

Ultimately though, we don’t want to just understand such novel mechanisms of antibiotic resistance but want to thwart them. Based on this mechanism I had an idea. If indole is so important for bacteria to acquire resistance, then one logical way to counter resistance would be to introduce an ‘anti-indole’ in their environment and mix it up with the natural molecule to cause confusion. This anti-indole would be a molecule resembling indole- an indole mimic and antagonist- that would effectively compete with indole for uptake, without causing any of the resulting effects.

Most likely this molecule would be a very close analog of indole, perhaps indole with a hydroxyl or fluoro group on it. Any small modification of indole would do, as long as it’s enough to confuse the bacteria. Of course we would also need to worry about bioavailability and toxicity, but I don’t see why the basic strategy would be completely unfeasible and why a proof-of-principle experiment could not be done in a petri dish.

Lee HH, Molla MN, Cantor CR, & Collins JJ (2010). Bacterial charity work leads to population-wide resistance. Nature, 467 (7311), 82-5 PMID: 20811456