Antibiotic Resistance

HELEN
Is Antibiotic resistance really an example of evolution?
The short answer is no, it's not.

Antibiotic resistance is a product of a built-in ability for a bacteria to vary. However, that bacteria never changes its essential identity and is still recognized as being 'what it was and is.'

Before I quote some technical stuff, let me put it this way -- any organism which reproduces sexually has a great deal of variation available to the population, simply because mommy and daddy have different combinations of predominances in their genetic packages, and these can combine different ways, so that even each of their offspring are slightly different.

Asexually reproducing organisms, such as bacteria, which reproduce only by making copies of themselves, do not have this advantage. In short, if they could not mutate, they would all be the same all over the world. That means that we, as human beings with all our chemicals, could have easily destroyed all life everywhere in short order, as we all depend on bacteria for survival.

But bacteria and other asexually reproducing organisms have rapid mutation rates, primarily along 'hot spots' or special sections of their chromosomes. These mutations are often 'back and forth' mutations. But sometimes they are mutations involving the loss of information and sometimes they are mutations involving the duplication of all or part of a gene which might cause some changes in the organism.

Many mutant cells die. Many do not. Of those that do not, the ones that are best able to survive in a given environment do, and they reproduce, with the 'trial' mutations continuing.

This sounds like it could lead to evolution of a grand sort, but it doesn't. Not only do the cells themselves not change their basic identity, but the mutant cells often pay what is called a high 'cost' -- and it is this which is the subject of the material I am quoting here. It's a little technical, but I think most of it can be understood in theory by most reading it:

In July of this year [2001] a Danish group published findings supporting the idea that antibacterial resistance leads to a less robust bacteria (Aarestrup et al. Antimicrobial Agents and Chemotherapy vol45 pgs. 2054-2059). They show that removal of antibiotics from animal feed had a profound effect on the number of resistant isolates recovered from these animals. This has potentially profound implications on animal and human medicine. To quote, "The results discussed above represent the first documented effects of large-scale interventions to reduce the occurrence of antimicrobial resistance. They demonstrate that the exposure of humans to bacteria resistant to antimicrobial drugs and to resistance genes through food can be reduced effectively by intervention."

Here is another example of resistance to an antibiotic carrying with it a reduction in overall viability of the microbe.
The paper below was published in Publications of the National Academy of Sciences (USA), PNAS, online November 20, 2001.

Microbiology
Mutation frequency and biological cost of antibiotic resistance in Helicobacter pylori Britta Bjorkholm*,,, Maria Sjolund,?, Per G. Falk?, Otto G. Berg, Lars Engstrand*,?, and Dan I. Andersson*,** * Swedish Institute for Infectious Disease Control, 17182 Solna, Sweden; Department of Medicine, Karolinska Institute, 17182 Solna, Sweden; Department of Medical Sciences, University Hospital, 75185 Uppsala, Sweden; etc.

Among the several factors that affect the appearance and spread of acquired antibiotic resistance, the mutation frequency and the biological cost of resistance are of special importance. Measurements of the mutation frequency to rifampicin resistance in Helicobacter pylori strains isolated from dyspeptic patients showed that about 1/4 of the isolates had higher mutation frequencies than Enterobacteriaceae mismatch-repair defective mutants. This high mutation frequency could explain why resistance is so frequently acquired during antibiotic treatment of H. pylori infections. Inactivation of the mutS gene had no substantial effect on the mutation frequency, suggesting that MutS-dependent mismatch repair is absent in this bacterium. Furthermore, clarithromycin resistance conferred a biological cost, as measured by a decreased competitive ability of the resistant mutants in mice. In clinical isolates this cost could be reduced, indicating that compensation is a clinically relevant phenomenon that could act to stabilize resistant bacteria in a population.

** To whom reprint requests should be addressed. E-mail:
[email protected]


And the following comment from someone else who read the same email I got:

I have been thinking about antibiotic resistance as a support for evolution and I keep thinking of this comparison. Many of these examples of resistance are akin to destroying a function used by the foreign threat.

Examples
Antibiotic resistance might arise as a loss of a transporter or alteration of ribosome
Resistance to HIV might arise from a loss of CD4
Malaria resistance due to damaged hemoglobin etc
Conclusion: This shows we can obtain new functions by mutation and selection

In a way, we have an analogy in wartime where we might blow up a bridge to prevent the enemy from crossing.
Is the conclusion then that dynamite is good for building bridges?


From Helen: it appears, as well, that once selective pressure is removed, the mutant strains (those with the 'bridges blown up') can no longer compete with the wild, or parent strains, and almost always (I can't say 'always' because there might be rare exceptions) are overtaken and 'starved out' by the original strain in a natural environment.

So, creationists, when you see the argument regarding antibacterial resistance being an example of evolution, remember that bacteria must mutate rapidly to survive as a population, and that ability is built into them. Most of their mutations are of the 'back and forth' variety. In other words, the mutation is undone as often as it occurs in the population. Of those mutations which do provide benefit in an environmentally pressured situation (such as the presence of an antibacterial agent), the cost to the organism appears inordinately high, allowing the parent, or wild-type, organism to overcome it as soon as the environmental pressure is removed (the antibacterial agent is gone).



THE BARBARIAN
The short answer is no, it's not.

The correct, answer, however, is "yes, it is". Let's go on.


Antibiotic resistance is a product of a built-in ability for a bacteria to vary.

In other words, DNA has a built-in ability to produce new information by mutation and recombination.


However, that bacteria never changes its essential identity and is still recognized as being 'what it was and is.'

Well, it's perfectly obvious that antibiotic-resistant bacteria are not the same thing as normal bacteria.
"Essential identity" is kind of a mystical, foggy phrase, that lends itself to obfuscation. Suffice to say that new kinds of antibiotic resistance evolve from time to time, and this new information is the result of changes in the genome that did not exist before.

Conjugation (a form of sexual reproduction found in many bacteria) is one way. There are other means of gene transfer besides that. Suffice to say that there's a good deal more going on than mere asexual reproduction among the little critters.


In short, if they could not mutate, they would all be the same all over the world.

Well, no, but mutation is a big part of it.
The general concept is that fitness only applies in context of the environment. So an antibiotic-resistant bacterium becomes adapted to an environment with the antibiotic. And it is less able to compete outside of that environment. That is true of all bacteria.

Antibiotic resistance might arise as a loss of a transporter or alteration of ribosome
Or it might involve the evolution of a new enzyme. This additional information would produce a substance to destroy the antibiotic molecule. This is one of many ways a bacterium can become antibiotic-resistant.
Here's a good link to a site that discusses the five major ways that bacteria can become antibiotic-resistant. You can see that several of them require that additional information be evolved by the bacterium to produce a new metabolite or metabolic pathway. http://www.plant.uoguelph.ca/safefood/ab-res/ab-res-ppr-wjp.htm#Types%20of%20Resist


In a way, we have an analogy in wartime where we might blow up a bridge to prevent the enemy from crossing.

Or we might build a gun to knock out his tanks. Analogues to both tactics occur in bacteria.


Is the conclusion then that dynamite is good for building bridges?

Evolution of new antibiotic-destroying enzymes is a good idea, as is building alternative metabolic pathways not damaged by antibiotics. Both of these are common ways that bacteria evolve new information to resist antibiotics.


From Helen:it appears, as well, that once selective pressure is removed, the mutant strains (those with the 'bridges blown up') can no longer compete with the wild, or parent strains, and almost always (I can't say 'always' because there might be rare exceptions) are overtaken and 'starved out' by the original strain in a natural environment.

As noted earlier, "fitness" only counts in terms of environment. One expects bacteria which have evolved to survive in high antibiotic concentrations, to be best fitted to that environment. No doubt, Helen is right, and some of these may still be highly competitive in other environments. Many soil bacteria, for example, are highly antibiotic resistant, because they are exposed to antibiotics from soil organisms like streptomyces.



HELEN
The PURPOSE of the lead post here was to show that mutations involving antibiotic resistance have an unacceptibly high cost -- a cost which precludes them being used as evidence of evolution (which is often done).


RUFUSATTICUS
The above statement makes no sense in light of real population genetics and evolutionary biology. The evolution of antibiotic resistance might have a high cost, but not having resistance has a higher cost if antibiotics are around. No population/lineage evolves in a vaccum. Environmental pressures are key in determining the fittest individuals. That is why blood disorders are more common in high malaria areas, and tropical peoples have darker skin than artic peoples.


MESK
Helen's discussion of the cost of antibiotic resistance is extremely misleading due to some quite selective data selection. It is true that, in many cases, antibiotic resistance is only advantageous in the presence of antibiotic and is often costly when the antibiotic is not present. This is hardly surprising: the bacteria have been strongly selected for antibiotic resistance, so even quite costly resistance mutations provide a selective advantage.

What Helen has failed to mention is that if bacteria are exposed to repeated periods of antibiotic exposure, interspersed with periods in the absence of antibiotic, the cost of antibiotic resistance decreases dramatically. Numerous experiments have shown a decrease in cost so extensive that there is eventually no competitive difference between resistant and wild-type bacteria in the absence of antibiotic - in other words, the "cost" has been reduced to zero by further mutations.

The literature reporting this decrease in cost following the initial acquisition of antibiotic resistance is quite extensive, and I am forced to conclude that Helen and her colleagues have failed to perform even a cursory examination of published work in this field before proclaiming this as "fact". Actually Helen's claims are far from factual, as I will show below.

I'll start with two review articles, since these present a suitably broad overview of a topic which has been the subject of quite intense research.

Firstly, Richard Lenski reviewed several studies on the costs of antibiotic resistance in a 1998 paper (the abstract of which can be found here). An excerpt from the abstract:

"An important question, therefore, is whether bacteria can overcome the cost of resistance by evolving adaptations that counteract the harmful side-effects of resistance genes. In fact, several experiments (in vitro and in vivo) show that the cost of antibiotic resistance can be substantially diminished, even eliminated, by evolutionary changes in bacteria over rather short periods of time. As a consequence, it becomes increasingly difficult to eliminate resistant genotypes simply by suspending the use of antibiotics."

Secondly, Lenski's findings are backed by a later review:

"Generally, resistance is associated with a cost, suggesting that the frequency of resistant bacteria might decline when the use of antibiotics is decreased. However, evolution to reduce these costs, without a concomitant loss of resistance, can occur and result in a stabilization of the resistant bacteria in the population. The rate and trajectory of this compensatory evolution is dependent on the bacterial species, the specific resistance mutation and the environmental conditions under which evolution occurs."

[Administrator: the link was accidently lost here. If Mesk still has it we can insert it.]

The actual mutations associated with both resistance and subsequent reduction of cost have been identified in some cases. An example:

"Fusidic acid resistance resulting from mutations in elongation factor G (EF-G) of Staphylococcus aureus is associated with fitness costs during growth in vivo and in vitro. In both environments, these costs can be partly or fully compensated by the acquisition of secondary intragenic mutations. Among clinical isolates of S. aureus, fusidic acid-resistant strains have been identified that carry multiple mutations in EF-G at positions similar to those shown experimentally to cause resistance and fitness compensation."

[Administrator: again, the abstracts in this post were lost. They had been embedded and when transferred, this was not noticed so that the links could be checked and added. Our apologies. We will be happy to insert the correct link if it can be supplied.]

But as my piece de resistance, allow me to present this lovely study of compensatory evolution (i.e. the reduction of the cost of antibiotic resistance) in E. coli:

"Adaptation to the costs of rif resistance was studied by following serial transfer cultures for several Rifr mutants both in the presence of rifampin and in the absence. For cultures evolved in the absence of rifampin, single clones isolated after 200 generations were more fit than their ancestor; we saw no association between increased fitness and changes in the level of rifampin resistance; and in all cases, increased fitness was due to compensatory mutations, rather than to reversion to drug sensitivity. However, in the parallel evolution experiments in the presence of rifampin, overall levels of resistance increased as did relative fitness—for all strains save one that had an initially high level of resistance."
[Administrator: ditto on the link here. Again, apologies are offered.]

Note: "rif" refers to the antibiotic rifampin, while "Rifr" (the final "r" should be superscript) indicates rifampin resistance.

The take home message from this article is clear, and directly and unequivocally contradicts Helen's claims: bacteria which evolve antibiotic resistance and are then grown in the absence of the antibiotic do not necessarily lose their resistance - instead, they undergo further mutations which reduce the cost of the resistance. Of the bacterial colonies grown in the absence of rifampin, not one lost their antibiotic resistance, but all of them increased in fitness (that is, the cost of resistance was reduced) by further, compensatory mutations.

That'll do for the moment. Helen, care to respond?


LATE CRETACEOUS
Helen
On several occasions you have discussed bacterial as though they reproduce asexually only. This is not the case. Certainly, on a petri dish loaded with nutrients and bathed in warmth, bacterial will reproduce in this way primarily.
However, in nature resources seldom come so easily. Bacteria also reproduce sexually, by a process called conjugation. Conjugation is often glossed over, or barely even mentioned, in most introductory texts on microbiology. Yet conjugation is quite significant.

Also, in the past you have mentioned that bacteria do not form complex or multicellular structures. Again, not true. In fact a co-worker of mine investigates biofilms - those slimey layers of gunk that develop on damp surfaces. They are made up of complex bacterial populations, composted of channels and specialized cells. Although these structures do not last very long, they do seem to be at the half way point between unicellular and multicellular life.