Resistance can be active (i.e., the result of a specific evolutionary pressure to adapt a counterattack mechanism against an antibiotic or class of antibiotics) or passive (where resistance is a consequence of general adaptive processes that are not necessarily linked to a given class of antibiotic; e.g., the nonspecific barrier afforded by the outer membrane of Gram-negative bacteria). Bacteria achieve active drug resistance through three major mechanisms: (1) efflux of the antibiotic from the cell via a collection of membrane-associated pumping proteins; (2) modification of the antibiotic target (e.g., through mutation of key binding elements such as ribosomal RNA or even by reprogramming of biosynthetic pathways such as in resistance to the glycopeptide antibiotics); and (3) via the synthesis of modifying enzymes that selectively target and destroy the activity of antibiotics. All of these mechanisms require new genetic programming by the cell in response to the presence of antibiotics. In fact, in several cases, the antibiotics or their action actually genetically regulate the expression of resistance genes. Therefore, bacterial cells expend a considerable amount of energy and genetic space to actively resist antibiotics. — Gerard D. Write (2005) (p. 1452)

Towards developing a consideration of evolutionary biology from a distinctly microbiological perspective, we address in this chapter the fairly broad idea of the evolution by microorganisms to resist various detrimental environmental phenomena such as antibiotics, antivirals, immune systems, predation, environmental toxins, etc. In this way we can consider important evolutionary biological principles, such as mutation, migration, genetic drift, and natural selection, all within a context of what for many is a defining aspect of microbial evolution. Indeed, together with the evolution of pathogenesis, the closest that medical microbiology typically comes to considering issues of evolutionary ecology is to ponder the superlative potential for microorganisms to not only do what we would prefer that they would not do but to accomplish these unfortunately tendencies directly in the face of our efforts to keep these organisms at bay. I begin, however, with a recap of the microorganism-centered material found in previous chapters. I then turn to consideration of what factors microorganisms evolve resistance to, and then the role of natural selection in this evolution since mechanisms of resistance would not exist were it not for selective benefits associated with that resistance.


Table: Terms and Concepts Pertaining to Resistance Evolution.

(highlighted terms are new but all discussions are unique to this table)

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Active resistance Acquired ability to interfere with the action of environmental toxins, poisons, and degradants.
Such as in terms of antibiotic resistance. Acquisition here is either via mutation (mostly chromosomal resistance) or horizontal gene transfer (mostly extrachromosomal resistance). It is "active" because something has to happen for resistance to become manifest, that is, some change (particularly evolutionary) from the otherwise basal, sensitive state.
Adaptive evolution

Product of positive/directional selection.
Resistance evolution can be viewed as an example of adaptive evolution, with resistance genes acquired either mutationally or via horizontal gene transfer, and then retained particularly given antibiotic-mediated hard selection. Note, though, that adaptive evolution of resistance is not limited to antibiotic resistance. Note too that retention of resistance in the absence of presence of the selecting agent (such as the antibiotic) also can be a consequence of adaptive evolution, here in terms of selection for the presence of compensatory mutations which serve to reduce costs associated with expressing resistance mechanisms and particularly to the extent that costs of loss of resistance mechanisms leads to costs associated with retaining such compensating mutations. Adaptive integration of resistance mechanisms into an organism's physiology, that is, can be costly undo.
Antibiotic resistance

Presence of innate or acquired means by which bacteria avoid the cytotoxic impact of antibacterial chemotherapeutic agents.
Antibiotic resistance more broadly represents an ability of bacteria to evade the action of toxins, poisons, and degradants particularly as produced by other microorganisms. Note in any case that antibiotic resistance is a property of bacteria since it is only bacteria that, by definition, are affected by antibiotics, though other microorganisms or organisms generally also are impacted by toxins, poisons, and other degradants. In any case, these resistance mechanisms can be acquired or instead can represent innate aspects of organisms.
Acquired resistance

Mutational or horizontal gene transfer-conferred ability to interfere with the action of environmental toxins, poisons, and degradants.
Acquired resistance can be equated with active resistance. It is one of two general mechanisms by which, for example, bacteria may display antibiotic resistance, the other being innate resistance. Mutationally acquired resistance typically is chromosomally encoded while horizontal gene transfer-acquired resistance typically is extrachromosomally encoded, i.e., as carried by plasmids.
Clonal interference

The blocking of fixation of a genotype among two or more competing genotypes possessing similar fitness within a population.
Though perhaps hypothetical, there certainly exists a potential for more than one allele that confers antibiotic resistance to compete within a population, particularly following exposure to antibiotics (or, more generally, exposure to any environmental toxin, poison, etc.). In addition, the more complex the environment – varying such as in terms of antibiotic densities over both space and time – then the more likely that any one allele might confer exceptional fitness benefits may be diminished. That is, different alleles may be better suited to different environmental conditions, many of which could exist simultaneously across a microorganism population. Indeed, different alleles could confer different levels of resistance to different antibiotics. The resulting competition between alleles existing in different genotypes could result in the fixation of none, that is, as a consequence of what is described as clonal interference.
Compensatory mutation

Mutation that reduces the negative consequences of another mutation.
Compensatory mutations can play a role in the adaptation of bacteria to the acquisition of antibiotic resistance, or instead to acquisition of resistance to other environmental aspects. Such resistance-conferring genes basically can be pleiotropic, conferring advantages (i.e., resistance) as well as disadvantages (basically the costs of conferring resistance). Compensatory mutations in turn can serve to reduce disadvantages, though with the caveat that compensatory mutations themselves potentially may be disadvantageous to carry in the absence of whatever it is that they are compensating for. Thus, loss of antibiotic resistance by a bacterium is not always trivially achieved once compensating mutations have accumulated.
Convergent evolution

Appearance of similar but not identical adaptations that are a response to similar selective pressures.
One example of convergent evolution is acquired resistance across multiple populations, such as in response to the treatment of bacterial communities with broadly acting antibiotic agents. In particular, it is possible for similar mutations to confer antibiotic resistance within different lineages. Alternatively, and contrasting convergent evolution in a very relevant way, it is possible instead to acquire resistance via horizontal gene transfer, with two lineages potentially acquiring similar or even identical resistance mechanisms. This, by definition, is not as a consequence of convergent evolution but instead the resulting similarities are a consequence of common descent of the genes in question. Though with this is common descent other than via vertical inheritance, nevertheless convergent evolution is requires an independence of evolutionary histories rather than the possession of genes that are similar or identical by descent..
Chromosomal resistance

Antagonism, especially by bacteria to antibiotics, that is associated with changes to existing and especially non-plasmid-borne genes.
Chromosomal resistance is a kind of acquired resistance that is associated especially with mutations, versus due to horizontal gene transfer. Chromosomal resistance particularly involves modification of, for example, antibiotic targets such that antibiotic binding and/or inhibitory effects no longer are as effective. This is active resistance in the sense that it is not innate but nonetheless is not typically active in the sense of energy expenditure or otherwise catalytic action on the part of the resistance mechanism (which instead is often associated with extrachromosomally encoded resistance mechanisms).
Divergent evolution

Descent with modification resulting in increasing dissimilarity between two or more species.
Contrasting convergent evolution, divergent evolution from the perspective of resistance evolution would represent differing solutions to more or less common selective forces for such mechanisms. In addition, acquisition of differing compensatory mutations that otherwise serve to address costs associated with resistance evolution can follow differing evolutionary paths. Lineages too can diverge in response to differing selective pressures (e.g., exposure to different antibiotics) but also as a consequence of random processes that are in addition to the stochasticity of mutation acquisition, i.e., genetic drift. They also can vary in terms of how horizontal gene transfer may or may not be manifest, that is, with genetic migration also leading to potentially stochastic divergence between lineages given a relative rarity of horizontal gene transfer (i.e., where some individuals receive specific, new alleles whereas other individuals do not).

Strength of natural selection relative to genetic drift as measured particularly in terms of fixed mutations in populations.
Note that synonymous versus nonsynonymous substitutions are only relevant to changes found in gene reading frames. Mutations to antibiotic resistance that are found, for example, in ribosomal RNA genes, which lack codons, thus cannot be distinguished into adaptive (fixation due to natural selection) versus non-adaptive (fixation by drift) by these means.

In terms of phenotype, the impact of one genetic locus on another genetic locus.
Compensating mutations often are epistatic, at least with regard to organism fitness (as a phenotype), that is, if they modify the fitness impact of otherwise detrimental mutations that are located at different loci. The coping by an organism to having acquired antibiotic resistance mechanisms, either mutationally or via horizontal gene transfer, thus can be viewed at least in part in light of such epistatic mechanisms. In other words, the acquisition of new alleles or genes by an organism potentially can interfere with the functioning of existing alleles, genes, and gene products, which by definition as pre-existing genes are located at different loci and thus implying epistatic interactions, with subsequent compensating mutations such as in the pre-existing genes potentially serving to reduce such epistatic conflicts. The genome thus evolves better accommodate new additions, becoming a more streamlined and thereby effective whole, though a cost of such integration of new genes is that subsequent loss of those genes also can be disruptive to the functioning in this case of remaining functions.
Extrachromosomal resistance

Antagonism, such as by bacteria to antibiotics, that is associated with particularly with plasmid-borne genes.
Though much can be said about mutational acquisition of antibiotic resistance, in fact the greatest challenge in terms of antibiotic resistance is the acquisition of resistance plasmids, that is, which can be transferred as whole genes from one bacterium to another to confer, for example, enzymatically effected antibiotic resistance in the recipient bacterium. This extrachromosomal resistance is both active and acquired.

Process by which an allele becomes the only allele found at a given locus within a gene pool.
Within bacterial populations, the ongoing application of antibiotics at sufficient levels can have the effect of either driving the bacterial population to extinction (re: hard selection) or instead select to the point of fixation of those population members that have acquired resistance mechanisms through either mutation or horizontal gene transfer. Note though that fixation does not imply that the bacterial population has necessarily recovered in numbers to pre-antibiotic application levels but instead solely that sensitive bacteria will no longer be present within the directly antibiotic-treated population.
General mutator

Organism that displays a substantially reduced replication fidelity in comparison to parental or otherwise equivalent strains.
Chromosomal resistance is more likely to be acquired the greater an organism's mutation rate and consequently is more likely to be attained, all else held constant, by general mutators versus less mutation-prone individuals. Presumably extrachromosomal resistance, once acquired, might also be evolutionarily refined more rapidly within general mutator strands versus during carriage by strains with standard replication fidelities.
Hard selection

Additional levels of mortality experienced by a population that can result in population extinction absent successful adaptation.
An all but defining example of hard selection is that imposed by antibiotics on sensitive bacterial populations. Given sufficient antibacterial dosing, these bacterial populations either possess sufficient genetic variation – particularly in terms of antibiotic-resistance alleles – or instead populations are driven to extinction. Of course, from the perspective of the medical treatment the latter is a good thing. Note that it is following the application of antibiotics that bacterial population average resistance is lowered and it is with the selection for antibiotic resistance-conferring alleles that increases in bacterial population average fitness, in the face of antibiotic treatment, are observed.
Historical contingency

Constraints on adaptation that stem from complications as well as limitations associated with an organism's current genotype or population's current genotypes.
The potential to acquire resistance due either to mutation or horizontal gene transfer is a function in part of the existing genotype of the target organism, as too is the cost of harboring as well as subsequently compensating for specific resistance alleles. Different bacterial populations, for example, thus have differing potentials to acquire resistance to antibiotics such as in the course of antibiotic treatment, and these differences can be attributed directly to what can be described as historical contingency.
Hitchhiking (Genetic hitchhiking)

Increase in the frequency of certain alleles based solely on their linkage to other alleles.
The selection for resistance phenotypes among organisms will have the effect of selecting for whatever other alleles those organisms happen to carry. From the perspective of bacterial communities, for example, the application of antibiotics has the effect of selecting for those species or strains that either are inherently more resistant or which instead possess some potential to acquire robust resistance mechanisms. These tendencies can increase frequencies, within communities, of organisms that otherwise can effect pathogenesis, such as Clostridium difficile in the gastrointestine. These often innately (that is, passively) resistant organisms can possess mechanisms of pathogenesis that are independent of their ability to resist antibiotics, but where those mechanisms nonetheless are genetically linked to their antibiotic-resistance tendencies. (Note, by the way, that by invoking "communities" in this example I am providing an ecological rather than strictly evolutionary scenario, that is, competition between species rather than necessarily evolution within species.)
Horizontal gene transfer

Movement of alleles between individual organisms but other than from parent to offspring.
Extrachromosomal resistance mechanisms inherently are associated with horizontal gene transfer, in this case the acquisition of plasmids via either conjugation (usually) or instead transduction (lower likelihood but probably still important). So-called resistance plasmids typically will carry multiple genes that confer resistance separately to multiple factors such as multiple antibiotics.
Passive resistance

Innate ability to interfere with the action of environmental toxins, poisons, and degradants.
Passive here refers to lack of any change in order for an organism to display resistance phenotypes. Typically this is either because the organisms lack targets for degradants or instead are configured in such a way that degradants, such as antibiotics, are unable to reach targets for their action, e.g., such as due to the presence of an outer membrane.

Low-level gene flow between species.
Extrachromosomally acquired resistance, that is, as acquired via horizontal gene transfer, can be viewed as a form of introgression, and particularly so to the extent that resistance mechanisms are acquired from donor organisms that are of a different species than recipient species. In fact, such inter-specific movement of antibiotic-resistance alleles, particularly as carried on plasmids, is thought to be quite common across communities, if not necessarily an "everyday" occurrence on a per capita basis.
Muller's ratchet

Manifestation of genetic drift where, in small, non-sexual populations, there will be a tendency for the wild-type genotype to be lost.
Though not necessarily resistance mechanisms, some of the lifestyles that pathogens acquire that may serve at least in part as mechanisms of resistance especially to immune systems can have a secondary effect of isolating these organisms into small populations that are both prone to genetic drift and less amenable to sexual processes. As a consequence, Muller's Ratchet can be at least seemingly rampant in such populations, resulting in genetic deterioration of genomes. This appears to be the case, for example, with the pathogen, Mycobacterium tuberculosis.
Mutational meltdown

Inability of natural selection to remove deleterious mutations from a population faster than those mutations arise without otherwise driving the population to extinction.
Mutational meltdown generally will occur if mutation rates are sufficiently high within a population, such as can occur given exposure to mutagens. An implicit or explicit assumption of non-linearity of the fitness impact associated with mutation accumulation may be associated with concepts of mutational meltdown such that relatively small increases in mutation frequencies may be catastrophic to population survival. Mutational meltdown may be associated with the application of certain antiviral compounds to treat especially RNA virus infections.
Neutral mutation

Change in the base sequence of a genome that has little effect on fitness of the so-affected organism as compared with the parental sequence.
It is especially neutral mutations, or alleles, that will be expected to increase in frequency within clonal populations due to genetic hitchhiking. This is more so than detrimental mutations (or alleles) given that neutral mutations by definition do not negatively impact the fitness of the genotypes within which they are found and therefore will not (again by definition) have a negative impact on the ascent (selective sweep) of genotypes in the course of periodic selection. (This is also more than newly arising beneficial mutations since neutral mutations are expected to be somewhat more numerous than beneficial ones.) Thus, upon acquisition and/or utilization of resistance alleles, there will be additional, linked alleles that may be carried to fixation in addition to the resistance alleles themselves, and many of those alleles will confer selectively neutral fitness benefits. These ideas as tied to those of genetic hitchhiking are highly similar to the impact of genetic drift on allele frequency or fixation, though are not dependent in the same way on genetic bottlenecking or founder effects but instead are dependent particularly on clonal population structures.
Parallel evolution

Changes in phenotype or genotype that are similar or even identical within closely related but nonetheless independently evolving lineages.
Mutational acquisition of resistance mechanisms that are identical but nonetheless a consequence of independent mutational events – that is, as may be observed when following isogenic but otherwise independently evolving lineages – would represent an example of parallel evolution. Indeed, any time you subject independently evolving but otherwise isogenic populations to hard selection, and those populations respond evolutionarily either similarly or identically, then that response can be viewed as an example of parallel evolution, at least as viewed at the level of phenotype. Alternatively, to the extent the independently evolving lineages are increasingly less isogenic then this mechanism of independent but otherwise similar or identical evolution may be described instead as representing a convergent evolution.
Periodic selection

Deterministic increases in the representation of certain genotypes within clonal populations.
With periodic selection it is particularly the genotype that represents the unit of selection, that is, entire genomes, rather than necessarily independent alleles. Nonetheless, specific beneficial alleles can certainly drive the ascent of their associated genotypes, even if the rest of the alleles found in those genotypes can be deemed neutral or even moderately detrimental. This scenario is explicitly the case with the ascent of organisms that have acquired resistance in response to exposure of a population to hard selection, such as mediated by antibiotic treatment. Antibiotic resistance-conferring alleles thus can sweep through populations (i.e., as a selective sweep), but if a population is clonal it nonetheless is the genotype as a whole that is carried in that sweep. Antibiotic resistance thus 6often arises within populations, in response to antibiotic treatment, as a consequence of periodic selection.

Presence of more than one allele at a given locus within a gene pool.
Alleles that are present within populations at very low levels in association with a mutation-selection balance may or may not be easily detected and therefore may not be viewed as contributing to a polymorphism within a population, a.k.a., genetic variation. Nonetheless, to the extent that such alleles exist then application of a selective agent, such as antibiotics, may demonstrate their presence in the course of positive selection. Importantly, it is particularly within relatively large populations (e.g., "millions") that this effect is best seen, such as can be seen during bacterial infections. Large bacterial or virus populations thus often can harbor large amounts of genetic variation, even if technically it may be difficult to argue that this variation is sufficiently prevalent that it can be described as contributing to a polymorphism.
Positive selection

Used here mostly equivalently to that of directional selection.
Explicitly, selection for resistance mechanisms, by whatever it is that resistance is mediated against, represents positive selection. Following antibiotic treatment the frequency of resistance within populations thus increases, though this occurs explicitly as a consequence of reductions in the frequency of sensitive genotypes/alleles conferring instead sensitivity. Allele frequencies, that is, directionally change from domination by sensitive alleles to dominance instead by resistance alleles.
Purifying selection

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Deterministic (non-random) reductions in already rare alleles from populations.
Selection for loss of antibiotic sensitivity well into antibiotic treatment can be viewed as a form of purifying selection. Thus, even given mutation or instead plasmid loss that results in loss of resistance by some members of populations, there is otherwise no net increase in frequency of antibiotic sensitivity, with such sensitivity instead maintained at a mutation-selection balance (particularly, given sufficient antibiotic presence then sensitivity is lost as soon as it arises). This concept is taken advantage of in practical terms in genetic engineering by employing antibiotic-resistance genes to assure plasmid stability within bacterial populations within the laboratory, with those bacteria that have, for example, lost transforming plasmids also quickly lost from the population (indeed, mechanisms that assure plasmid retention within wild bacterial populations can be viewed as being maintained by equivalent purifying selection mechanisms). Alternatively, it means that in the face of ongoing antibiotic treatment there can be little retention of otherwise sensitive bacterial populations.
Selective sweep

Increase in frequency of an allele due to that allele's beneficial impact on the fitness of carriers.
Selective sweeps are seen particularly in the course of hard selection such as to resistance to antimicrobial agents or immune systems. Thus one sees selective sweeps of, for example, antiviral-resistance alleles, antibacterial-resistance alleles, and in terms of immune-system escape. This is particularly as seen with the confined and otherwise limited populations that are present within a single host during infection of that host, with populations potentially coming to be completely dominated by particular resistance alleles once those alleles become useful.
Selectively neutral marker

Especially alleles and associated phenotypes that allow a simple distinguishing among the genotypes of laboratory organisms but without otherwise substantively impacting especially experimental evolution procedures.
Antibiotic-resistance genes/alleles can be readily employed as either selectively neutral or nearly so markers. This is seen with simple gene cloning as well as a means of distinguishing among lineages during competition experiments. Specifically, these markers should be selectively neutral during experiments or during propagation, but should be amenable to selection during enumeration or otherwise when separation of carrying organisms from non-carriers is desired. In this case it is positive selection (in a microbiological sense) that is employed to separate marker carriers from those organisms that do not carry the marker. Alternatively, it is possible to employ markers that do not enhance survival under certain, selective conditions, but instead allow for a visual distinguishing among genotypes, such as in terms of the carriage of the β-galactosidase gene by bacteria, which results in blue colonies during growth in the presence of the compound known informally as X-gal.
Soft selection

Deterministic evolution that can result in increases in the relative fitness of certain individuals but not the absolute fitness of associated populations.
A resistance mechanism that can be viewed as effecting soft selection rather than hard selection is resistance to bacteriocins. These are antibacterial entities that can be produced by conspecifics towards elimination of sensitive individuals of the same species. Here there is no net gain in average fitness of the population even if all sensitive individuals are eliminated since it is resistant members of the same population that are effecting the selection. Indeed, there can even be a reduction in population average fitness to the extent that resistant individuals are less fit than sensitive ones given an absence of the selecting bacteriocin. Such interspecific competition represents the essential characteristic of soft selection, and this is versus hard selection which is imposed upon populations instead from sources other than the population itself.