Bugs & drugs…

Zones of inhibition around antibiotic infused disksText books commonly state that in the natural environment antibiotics are a means by which bacteria (and yeasts) reduce competition for resources, by creating a ‘zone of inhibition’ around themselves—kind of like unleashing a smelly fart to stop people sitting too closely. However, antibiotics can also be seen as part a more complex system of cell to cell communication/signalling in microbial communities, in fact, they can also be food. When used at the concentrations we employ therapeutically, they can either stop bacterial growth, or kill outright. Just because they can have this effect, doesn’t mean that this is what they evolved to do—’antibiotic’ is simply the name we give to the few (of many) small organic molecules produced by bacteria that happen to have an effect on a particular group of bacteria against which it (along with many other molecules) was screened.

When present at low concentrations, small organic molecules (including antibiotics) have been found to produce a whole range of metabolic activity in neighbouring cells, stimulating surrounding cells to change their behaviour, increase their mutation frequency, or increase the transfer of mobile pieces of DNA. At many levels, using antibiotics incorrectly stimulates exactly what we don’t want to happen—it gives bacteria a kick up the arse, gets them talking and sharing information, including resistance to one or multiple antibiotics. The resistance can therefore be seen as an adaptation of a mechanism by which a bacterial cell can control its exposure to these small molecules, including antibiotics.

I mention this because it is a perspective that makes us think a little differently about the problem we’re trying to solve. Without an understanding of the subtleties in the war of drugs and bugs, we’re not going to get far. So for this post I just want to do a quick foray into the bugs and drugs background and mention something about the cocktail of conditions that we need to watch out for.

Antibiotics, and resistance to them, is not a new thing…

For a billion plus years there have been penicillin-like molecules out there, and for an equal amount of time there have been mechanisms to resist/control the effect of the same antibiotics. Numerous studies have shown that even a cursory screening of garden soil reveals a plethora of resistance determinants (genes or mutations that confer resistance), many of which may have not been (or may never be) documented in a clinical setting.

It’s probably useful, before I go any further, to distinguish between several forms of antibiotic resistance as, generally speaking, bacteria can become resistant to antibiotics in several ways, which are not altogether mutually exclusive:

i. They can evolve an enzyme (usually co-opted from a pre-existing family of enzymes present within the original cell where the gene appeared), these either modify or cut up the antibiotic molecules;

ii. Another form of resistance occurs when component of the of the cell that the antibiotic normally attacks becomes mutated, these can often result from one or several mutations of the gene encoding that component;

iii. Some bacterial cells can exist in a form that is impenetrable to antibiotics, by surrounding themselves in a sticky goo (biofilm); or they can pump out (efflux) the antibiotics from the cell just as fast as they enter.

iv. As I will discuss in a forthcoming post, some members of a bacterial population are simply not perturbed by antibiotics, yet not via a genetic or heritable mechanism, although one form of such ‘killing avoidance’ is the formation of biofilm, as in (iii).

Just to confuse matters, in some cases the resistance described in (ii) and (iii) can also be spread. There are examples of genes encoding pumps that can be transferred from one bacterium to another. Furthermore, mutated genes that are immune to the effect of an antibiotic, as described by (ii), can also be spread. One example from my own field is resistance to an antibiotic called mupirocin in Staphylococci spp. Mupirocin, which can be useful for treating some MRSA infections, attacks a crucial enzyme that makes a type of RNA needed to make proteins. Bacteria could become resistant if they mutate the specific enzyme that the antibiotic disrupts, but they can also acquire an alternative copy of this mutant enzyme from another cell. Many of the enzymes from (i) may have started life on a chromosome long ago, but have since taken up residence on segments of DNA that can be moved around, which I will come on to now.

The worrying cocktail…

So resistance determinants of many flavours are out there, but several factors need to be in play before we start worrying about finding them in an untreatable infection.

1. There needs to be ecological contact, a shared contact between the source of a gene encoding resistance, and the pathogen. Often there is no such link, but there is one place at least for which such contact is primer territory, sewage outlets. Here human pathogens can share an environment with environmental reservoirs (free-living environmental bacteria) of natural antibiotic resistance, or indeed, not so natural antibiotic resistance (where resistance has evolved due to improper use of antibiotics in agriculture). However, just because bacteria share the same space, doesn’t mean they will share genetic information. This is the next factor.

2. Promiscuous mobile genetic elements. In addition to the chromosomal DNA, which is the large molecule of DNA in every cell that encodes the blueprints of that organism, there are also small(er) pieces of DNA that can move around. Sometimes they just move around within the chromosome – snipping themselves out and then inserting themselves somewhere else. Other times they can be autonomous, i.e. in control of their own destiny and taking care of their own replication. Some of these DNAs can move themselves from one organism to another; some can move themselves and other small bits of DNA that happen to be around. In this way, a fully evolved mechanism of resistance to a particular antibiotic can be inherited, and established, within a bacterial generation (a matter of hours).

This is called horizontal gene transfer, as opposed to vertical gene transfer, which is how your parents passed their DNA to you, or when a cell divides to produce daughter cells. Horizontal gene transfer in humans might resemble you placing your hand on your cousin’s shoulder and inheriting their hair colour (though presumably this isn’t going to improve your chances of survival). Of course, over evolutionary history we have been subject to horizontal gene transfer, with numerous human genes being derived from viral genes.

3. Multidrug resistance. Mupirocin resistance, which I described above, is limited both in terms of what other bacteria it can spread to, and is also unlikely to confer cross-resistance to related antibiotics. However, some resistance determinants, such as NDM-1, confer resistance that can be readily employed by other bacteria, and confer resistance to numerous antibiotics.

Thus what the NDM-1 report (raised in my last post) describes is a heady cocktail ripe for troubled times:

Ecological contact + promiscuous mobile genetic elements + multidrug resistance = not good. These tick all the boxes for a situation that should be carefully monitored, as you would any invading pest species in a zoological sense.

NDM-1 is of course not the first determinant to raise concerns in this manner. Within my own neighbourhood of bacteria (the Staphylococci), a resistance determinant identified in 2008 called ‘cfr‘ was found to mediate resistance to several different classes of antibiotics, including Linezolid—a purely synthetic and important anti-MRSA antibiotic. It also be found on a plasmid, one of those potentially movable bits of DNA I mentioned, thus we might anticipate its propensity for spreading, though how much time this will take is anyone’s guess. I’ll discuss this further as part of a later post on surveillance of antibiotic resistance.

The future…

In the early days of antimicrobial chemotherapy we devoted a lot of time to identifying compounds that work, with often very little understanding of actually how they work. Over time we identified the (comparatively few) principle cell components that antibiotics attack (structure/function of DNA, protein synthesis, cell wall/membrane integrity; and at least one metabolic pathway), but even so there are still numerous compounds in use for which we don’t have a clear molecular mechanism for their action, even if we know that they broadly interfere with.

A later development was an understanding of how bacterial resistance mechanisms work, their broad functioning being as I described earlier, but again there is much work to be done to understand the molecular mechanism behind it. Mechanisms of action and mechanisms of resistance are both areas focussed on in the lab where I work.

There is a great need to develop new antibiotics, of that there is no doubt. Part of the frustration in the the field of antibiotic chemotherapy is that we don’t have a huge array of drugs to play with, and this severely curtails our options. I don’t doubt that somewhere out there, there are chemical compounds that can do the job, some may even be sat on shelves as undeveloped test compounds because we don’t have a the developmental infrastructure that makes their bringing to market (economically) worthwhile; others, are currently being held up by technical licensing issues and legal contests between discoverers and developers, such as with oritavancin, which showed potent activity against Staphylococcus aureus in biofilms.

We already employ strategies to improve the lifespan of antibiotics: using them as cocktails with other antibiotics, monitoring and isolating patients with resistant bacteria (I’ll discuss these in later posts). However these are complicated because antibiotic chemotherapy is complicate, rife with side-effects and strict dosing regimes, and can be quite expensive. For such reasons, these strategies are not universally practised (worldwide) for socio-economic reasons, and such strategies in any case tend to be reactive (being employed only in serious cases, or when complications arise) rather than pro-active. If we’re not working to the same strategic plan worldwide, then we will fall foul of the formula I’ve just discussed: Ecological contact, promiscuous genetic elements and multidrug resistance.

Without continuing investment in research to understand each of these processes, trying to solve the problem of antibiotic resistance will be as hard as trying to play Subbuteo wearing boxing gloves.

I will of course continue to expand on these themes in coming posts, but I’m sure you’re all itching to know what this all has to do with bacterial fitness, and gene gyms; well next time…

Further reading:

I thought I’d name and fame some of the big names working in the field whose research I will be discussing, and point you in the direction of material that isn’t behind a paywall (where possible).

Yim et al. (2007) Antibiotics as signalling molecules. Phil. Trans. R. Soc. B (2007) 362, 1195-1200 [ link to pdf ]

– Julian Davies is a mine of information about antibiotics and developed the thesis of antibiotics as signalling molecules.

Wright, G.D. (2007) The antibiotic resistome: the nexus of chemical and genetic diversity. Nature Reviews Microbiology 5: 175-186 [ link to pdf ]

– Gerry Wright has written some fascinating articles on the evolution of antibiotic resistance. You can listen to him giving an interview on U.S. National Public Radio (NPR) following the discovery that rather than being killed by antibiotics, some soil bacteria actually eat them.

Payne et al. (2007) Drugs for bad bugs: confronting the challenges of antibacterial discovery. Nature Reviews Drug Discovery 6: 29-40 [ link to pdf ]

– From the Infectious Diseases Centre of Excellence for Drug Discovery at GlaxoSmithKline, this is a sobering read on the learning outcomes from seven years of focussed, high-throughput antibiotic drug discovery, detailing the scientific and technical challenges to drug discovery.

[This post was restored from a WayBackWhen archive. It was originally posted to a blog called ‘The Gene Gym” that began life on the Nature Network in 2010, and then moved to Spekrum’s SciLogs platform.]

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