The ‘faecal’ bank…

Welcome to The Gene Gym on SciLogs.com.

I’m going to take great license to wander around numerous areas that overlap, nudge, cajole and nestle up against the main theme of my blog, which is of course bug and drugs.

So firstly, a brain dump:

A colleague and I once – rather drunkenly – planned a letter to The Lancet [a popular medical journal] in which we describe a means by which one might ‘bank’ a sample of ones faecal matter [shit] (comprising a cross-section of a healthy gut microflora), prior to departing on an exotic holiday, or undergoing antibiotic treatment. The premise was that any insult or injury arising from catching a bout of traveller’s Delhi-Belly, or depletion of the gut flora from chemotherapy, could be abated by having your original gut flora restored from your earlier banked sample. The service would naturally be called, the ‘Shit Bank’. Continue reading “The ‘faecal’ bank…”

Re-awakening enemy sleepers…

The idea of an enemy sleeper agent is a central plot device in many a spy novel or movie, and certainly the idea of going to ground behind enemy lines is not unheard of in many theatres of conflict. The idea in all cases is to remain undetected until re-activated to cause harm behind enemy defences.

The trick to identifying if there are latent sleepers operating is to try and re-activate them and get them to reveal themselves. Cue any number of spy stories about false radio signals or targets to lure sleepers into the open.

Curiously, it is a similar strategy that is being used in novel treatments for infections from two disparate areas of chemotherapy, one in the treatment of HIV and the other the treatment of persistent bacterial infections.

Continue reading “Re-awakening enemy sleepers…”

Where I am quoted not quite correctly….

I was recently called by an editor at NewScientist asking for some background on the field of fitness in bacteria, and particularly the issue of multi-resistant bacteria persisting in the environment (or clinic) in the absence of antibiotic selection. The reason for the question arose due to the upcoming publishing of an interesting paper in PLoS Genetics:

Silva RF, Mendonça SCM, Carvalho LM, Reis AM, Gordo I, et al. 2011 Pervasive Sign Epistasis between Conjugative Plasmids and Drug-Resistance Chromosomal Mutations. PLoS Genet 7(7): e1002181. doi: “10.1371/journal.pgen.1002181 “:http://dx.doi.org/10.1371/journal.pgen.1002181

Following this, I have been quoted in a NewScientist Health News item, and as I don’t feel my response is quite in the context I gave it, I thought I would give a more detailed account. I spoke to NewScientist last Wednesday (the paper in question wasn’t due to be published until the following day), but I was told that in the study the authors had observed that antibiotic resistance can have a positive effect on bacterial fitness, even in the absence of selection. I was asked whether this was a surprise to me, and more generally about research in bacterial fitness. What I perhaps should have done was ask specifically whether the paper was still embargoed and whether I could have more particulars of the study, because I could not have anticipated the particular nature of the study in question.

Continue reading “Where I am quoted not quite correctly….”

No action today, no antibiotics tomorrow…

YOU may have missed the fact that today was a World Health Day devoted to antibiotics; if you hadn’t, then it is, or at least was. In any case, it’s more or less over now and the issue can sink into the din of background noise.

As Frank Swain put it in in his well researched, and typically pithy, Guardian article today:

Health experts have been ringing the alarm over antimicrobial resistance for so long that it seems to have become part of our collective background noise, like the endless rasp of waves on the shore. And like stupid tourists, we sleep in the sun while the tide comes in.

A little pithiness is warranted, because if we find ourselves still in this situation in 2021, I’m going to be either, a) A disgruntled cash-strapped senior lecturer / reader / professor with a serious Cassandra complex; b) long since departed from research due to lack of funding; or c) dead, or missing a limb, due to an untreatable bacterial infection, or grieving over the same in a loved one.

I’ve written previously about some of the reasons we don’t have new drugs, and we can keep re-stating these issues ad nauseam, but it doesn’t mean anything will actually change. The broad response of governments following the ReAct meeting in Stockholm last year was more words, then an eerie silence. Similarly, in a meeting of the British Society for Antimicrobial Chemotherapy (BSAC), bylined ‘The Urgent Need’, more words were said amongst people who already familiar with those words, following which there has also been an eerie silence.

Continue reading “No action today, no antibiotics tomorrow…”

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.

Continue reading “Bugs & drugs…”

Surviving antibiotics…

Killing avoidance strategies

A couple of recent research papers remind me that I promised to talk a little about a phenomenon by which bacteria can avoid being killed by antibiotics, without actually being resistant in the classical sense, i.e. they can’t actually grow in elevated concentrations of the antibiotics they survive, and those cells that do survive give rise to populations that are no more, or less, likely to survive next time.

The first paper comes from the lab of Prof. Tony Coates at the Centre for Infection at St. George’s, University of London. Prof. Coates has for a long time been heavily involved in research into the treatment of latent and persistent infections, most notably T.B./tuberculosis. His research team (as indeed are mine) are trying to understand why some antibiotics that kill actively growing bacteria of a particular species have no effect on cells of the same species that aren’t actively growing; almost akin to the bit in Jurassic Park where T. rex kills the lawyer who’s running, but wouldn’t have done had the lawyer stood still §.

One of the reasons for this is that, historically, most drug discovery has been focussed on targeting actively growing cells, but what we are increasingly finding is that persistent infections can be mediated by a recalcitrant population of slow-growing or non-growing cells.

Whilst the idea of targeting non-growing bacteria is not a wholly new idea (you can find a review on the subject by Prof. Coates in my ‘Further reading’), it does seem that together with the report’s first author, Dr Yanmin Hu, their spin-out company (Helperby Therapeutics) has developed a platform and proof of principle drug that is now in trials, demonstrating the utility of such an approach. They have identified an antibiotic compound that has potent anti-Staphylococcal activity, but importantly, acts specifically against non-multiplying cells.

In a second paper, brought to my attention by Ed Yong, the Collins lab in Boston has identified that a sub-population of super-resistant bacteria act in a charitable manner to other members of the colony that are less resistant. Whilst the super-resistant cells could satisfy their own selfishness by merely allowing all their less-resistant siblings to die out, the bacteria in this case have a mutation that maintains their production of indole (a signalling molecule) when normally its production would be shut down on exposure to the antibiotic. When released by the cell, indole stimulates non-resistant cells to enter a state of phenotypic resistance or ‘antibiotic survival’, even though continued-production of indole incurs a fitness cost.

Why might they do this?

Well, for one of the reasons that is very much the subject of my blog, bacterial fitness. As I have mentioned before, antibiotic resistance can have a fitness cost, which means that cells committing themselves to this ‘path of resistance’ may find themselves at a disadvantage come the time when the antibiotic is no longer around. The subject of my research is to document the various ways in which antibiotic resistant Staph. aureus mitigate these fitness costs so that they get to remain resistant and just as competitive as they ever were in the absence of antibiotic. It seems that in the case of the Collins’ lab’s charitable bacteria, they may mitigate the fitness cost of antibiotic resistance at a population level by maintaining the presence of non-resistant cells that can come to the fore once the antibiotic is removed.

“These few drug-resistant mutants, by enhancing the survival capacity of the overall population in stressful environments, may also help to preserve the potential for the population to return to its genetic origins should the stress prove transient. Efforts to monitor and combat antibiotic resistance are complicated by these bet-hedging survival strategies and other forms of bacterial cooperation.”

So what I want to do is briefly introduce the types of ‘antibiotic survival’ strategies seen in bacteria. It goes without saying that future drug discovery that targets the molecular/physiological underpinning for these strategies (once we’ve identified what these are!) will be important for the clinical management of infection.

Resistance or ‘killing avoidance’?

I’ve discussed in a previous post what I might describe as mechanisms of antibiotic resistance, i.e. producing a enzyme that modifies or chews up the antibiotic; or changing the component of the cell so that the antibiotic targeted to that component no longer has any effect, or pumping the antibiotic out of the cell before it does any damage.

It was recognised early on, in the heyday of antibiotics, that penicillin could kill most bacteria in a culture, but could not sterilise a culture. This has been observed with numerous antibiotic compounds, thus at a practical level you cannot achieve a 100% kill with antibiotics. Now this isn’t generally a problem for a healthy individual, as it is at this point the immune system takes over and clears away the remaining cells. However, many people receiving antibiotics aren’t well, they may be immuno-compromised, or suffering from a deep-seated infection. The persistence of a bacterial infection becomes a perfect breeding ground for classical antibiotic resistance, with each resurgence of the infection from surviving cells increasing the probability that resistance may evolve; and thus is thought to play a significant role in the failure of antibacterial treatment.

1. INDIFFERENCE. Bacteria can avoid being killed by being in a stationary phase (non-growing or metabolically inactive). This is actually the default repose of bacteria in the environment, only submitting to bursts of growth in the presence of nutrients. Most current (and old) antibiotics are specific to the particular cell components and processes of actively growing cells, there is no reason to expect that such antibiotics would have any killing effect on cells not engaging in these processes.

2. TOLERANCE. Those antibiotics that do kill bacteria don’t necessarily do so directly; they initiate a series of events, a cascade of physiological responses, which ultimately result in cell death. Unlike indifference, tolerance is not linked to the growth/metabolic state of the bacteria, but instead result from genetic changes that uncouple the killing activity of the drug from its inhibitory activity. In the clinic, tolerance seems to be specific to certain bacteria, and even then only in response to particualr antibiotics targeting the bacteria cell-wall.

3. PERSISTENCE. In a bacterial population there exists a sub-population of ‘persister’, cells that regardless of the growth state of the population as a whole, continue to exist in a stationary or growth-retarded state. It may be that persisters avoid antibiotic killing in the same way that indifferent bacteria do, but whilst there are some antibiotics that can kill indifferent cells, they don’t kill persisters; this suggests that something different is going on in these cells, and there is increasing evidence to suggest that there are defined genetic differences implicated in persistence, including changes within the stress-response pathways, but what these are (and what they do exactly) remains to be seen.

4. BIOFILMS. Finally, and most stubbornly, there is the issue of biofilms. Biofilms are like a condominium (or halls of residence) of bacteria, a structured environment where the bugs are surrounded by a gelatinous matrix of sugar chains and many other macromolecules. They are involved in some 80% of human infections and represent a major cause of antibiotic treatment failure. Within the matrix the bacteria avoid antibiotic killing through indifference and persistence, thought to be brought on by the low oxygen and low nutrient environment; the matrix also provides some protection from certain classes of antibiotics, as well as the immune system. Even if a large number of matrix surface cells are killed off, the matrix structure survives and can be re-populated by the surviving cells. For some bacteria the biofilm environment stimulates them to massively increase their rate of mutation, which can increase the rate at which antibiotic resistance can evolve.

So what do we do?

Well again it comes down to idealism versus pragmatism. The current system of drug discovery is fraught and inefficient enough without an additional burden of esoteric and poorly understood mechanisms of bacterial antibiotic survival. I do think there is some merit in drug discovery targeted at non-growing indifferent bacteria, this is particularly important in the treatment of T.B. The problem is going to be that many of these killing avoidance strategies differ between pathogens and between the particular environment in which they’re found, and also that in the absence of any ongoing preventative treatment, such as potential vaccines, by the time an infection manifests itself the antibiotic survival systems are likely to already be in place.

Other than indifference, biofilms are a system worth addressing in the immediate term. We have amassed a huge amount of data on biofilms, and demonstrated that they are of great clinical importance, thus efforts should be made to increase the number of biofilm busting compounds we have available.

Many people are familiar with antibiotic resistance, but I’m interested to hear (especially from other biologists) how much people knew about such antibiotic survival strategies. Also, as ever, please feel free to ask questions at any level. This (rather long) post barely touches the surface of this subject, there’s plenty more to be said!

^§^ The theory that T. rex would only ‘see’ moving objects is probably a little outdated.

Further reading

As always I will try to find open access material where available, and will update those references that aren’t as and when they do.

_Hu et al. (2010) A New Approach for the Discovery of Antibiotics by Targeting Non-Multiplying Bacteria: A Novel Topical Antibiotic for Staphylococcal Infections. PLoS ONE 5: e11818._
Open access ]

_Coates, A. et al. (2002) The future challenge facing the development of new antimicrobial drugs. Nature Reviews Drug Discovery 1: 895-910._
Free pdf ]

_Lee, H. et al. (2010) Bacterial charity work leads to population-wide resistance. Nature 467, 82-85._
[Sorry, article behind a paywall] – You can read Ed Yong’s post on it though.

Levin, B.R. and Rozen, D.E. (2006) Non-inhertied antibiotic resistance. Nat Rev Microbiol 4: 556-562.
free pdf ]

– A very useful grounding to the subject of phenotypic resistance, as it was understood back in 2006.

Lewis, K. (2010) Persister cells. Annu. Rev. Microbiol. 64: 357-72.
[Sorry, another paywall paper ]

– Good review of bacterial persistence.

[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.]

Science Online 2010 (and some science)

This Friday I will be getting up horrendously early in the morning to catch a train to London. Here I’ll be meeting the many wonderful and varied people who are attending Science Online London 2010, this time at the British Museum Library. I went along to last year’s event in the Royal Institution, and thoroughly enjoyed it. It gave me an opportunity to put a face (and an accent) to most of the bloggers I’d been reading for some time, and meet a huge number of new faces. Also like last year I be at the wonderfully informal FringeFrivolous rooftop debate.

For my own part, I have always been enthusiastic about communicating science. As to whether I succeed at this (or not) in my writing I have absolutely no idea, but then again, as I am not a professional science communicator, it never quite seemed to matter. However, I do love to talk about science more. On the conference circuit I fair pretty well in giving talks, but outside of academia I have bent the ear of many a friend, and enjoyed the rare opportunity to hold the rapt attention of roomfuls of school children, or humanist societies. These make me feel great!

However, given the thematic nature of this blog and my mission being to keep the issue of bugs and drugs in the public domain, it’s time for me to put a more concerted effort into up-skilling on communicating ‘as a scientist, to the public’ (whether I get paid for it or not). Of course, we’re fortunate to have the likes of Maryn McKenna (the journalist and blogger behind ‘Superbug’, the book and blog) who hits the subject with her inimitable journalistic verve, but I can’t say I’ve encountered many scientists in the field giving their perspective.

I began this blog off the back of the NDM-1 story because whilst representative of an ongoing serious issue of multidrug resistant bacteria, it comes at a crucial time in the budgetary planning of future science funding. The recent media furore focussed on the lack of antibiotics (in between over-hyped commentary on cheap-ops in India), but failed to mention any of the reasons why most big industry doesn’t want to touch antibiotics with a barge pole (economic in-viability), or any of the academic involvement in resolving this problem (needless to say that it is the efforts of academic labs that we even know we have a problem!)

So what of it? Between 1995 – 2001, the team at one of the remaining biggest players, GlaxoSmithKline, spent $14m for each drug ‘lead’ identified over a period of 7 years (they identified 5 ‘leads’ in that time); remembering of course that a ‘lead’ may well never make it through clinical trials. One of the potential quick-fix options was screening of the pharmacopoeia, the pharmaceutical back-catalogue of drugs developed for everything from bone-loss to cardiac arrhythmia, for new leads. Companies have spent millions assaying such compounds, and derivatives thereof, to see if they can also hit a bacterial target. However, they haven’t yielded the kind of hits that were hoped. One of the reasons cited for this is that whilst the majority of therapeutic drugs obey Lipinski’s ‘rule of five’ (a set of molecular properties that define a good therapeutic drug), antibiotics don’t follow these rules.

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

Thus what are needed are truly novel chemicals; bat-shit crazy, funky, out of the box new chemicals developed by willing, well-founded and eager chemists…..but where are the chemists? Hell, where are the chemistry departments?

You might wonder that such problems are incumbent in all drug discovery, but then most ‘lifestyle’ drugs, the preferred pot of gold for big industry, have a relatively long shelf life. Not so antibiotics: most infections don’t last long, thus people don’t need many packets; physicians are told (correctly) to reserve their use only for bacterial infections (not colds/flu); moves are afoot to ban/scale back agricultural use = not much return for their investment. Then, just when the chips are down, resistance to your new drug is observed in the clinic and the death knell of the drug’s usable life is sounded.

Physicians and industry also want to treat a ‘disease’, not a multiplicity of different infections; but how do you treat a disease like pneumonia with a single antibiotic? Pneumonia can be caused by any of eight completely different bacteria (or multiples thereof), some species of which have as much in common with each other as a human does with a paramecium [ pdf ]. There is a fundamental disconnect between the popular models of drug development and the issues at hand with antibiotic development.

Of course, if industry sees no economic viability in antibiotic drug development, we need to sweeten the deal; one way to do this is offer public money. I hear you gasp, but think about it, this is a global issue and treatment programmes for HIV/AIDS, TB and malaria are the great success stories of what happens when public support, political clout, industrial partnership and a huge pot of cash collide. Of course, in these days of pharma-bad / dolphins-good, no-one is going to throw any public money at industry. One of the best accommodations is for partnerships between industry and academia. These are already a mainstay in microbiology (because if we relied on research council money we certainly wouldn’t still be here!), but it actually relies on the academic partner still being here.

Industrial partners can out-source a great deal of the legwork to academic partners for relatively low cost, increasing the network of players scanning for new drugs, informing new directions and finding. However, I can already run off a list of ten names of highly trained researchers in this field who have left the field over the past 8 years. At this time we’re facing another budgetary crisis in science funding and we must, at all costs, prevent a further loss of both industrial and academic research capacity involved in antibiotic research.

The public needs to be aware of the strong part academic research will have to play in developing new courses of action in the advent of new ‘superbugs’. For all the hope I have that there are academic solutions to better strategies of antibiotic use, anticipating and preventing resistance, better surveillance, and identifying new drug targets in bacteria (or better approaches to known targets), these are all rather like architect’s plans when what we need right now are some bricks in the oven.

Look forward to seeing everyone at Science Online 2010.

[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.]