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Are humans increasing bacterial
evolvability?
Michael R. Gillings1 and H.W. Stokes2
1
2
Genes to Geoscience Research Centre, Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia
The ithree Institute, University of Technology, Sydney, Harris Street and Broadway, Sydney, NSW 2007, Australia
Attempts to control bacterial pathogens have led to an
increase in antibiotic-resistant cells and the genetic elements that confer resistance phenotypes. These cells
and genes are disseminated simultaneously with the
original selective agents via human waste streams. This
might lead to a second, unintended consequence of
antimicrobial therapy; an increase in the evolvability
of all bacterial cells. The genetic variation upon which
natural selection acts is a consequence of mutation,
recombination and lateral gene transfer (LGT). These
processes are under selection, balancing genomic integrity against the advantages accrued by genetic innovation. Saturation of the environment with selective
agents might cause directional selection for higher rates
of mutation, recombination and LGT, producing unpredictable consequences for humans and the biosphere.
Human effects on evolution
Humans are probably the greatest evolutionary force on
the planet [1]. Anthropogenic impacts are having significant long-term effects on the atmosphere, hydrosphere and
terrestrial ecosystems. These effects, in turn, exert selective pressures on all components of the biosphere. Direct
selection on organisms occurs through harvesting, artificial selection and attempts to control parasites, pests and
pathogens. One of the most dramatic pieces of evidence for
the influence of humans on evolutionary processes lies in
the rapid selection of antimicrobial resistance in bacterial
pathogens [2].
The question must now be asked whether the use and
dissemination of antimicrobial agents is having secondorder effects across the microbial biosphere. That is, are
humans inadvertently selecting for lineages that have an
increased potential for evolution [3,4]? Characteristics,
such as basal mutation rate, rates of recombination, protection against uptake of foreign DNA and the general
propensity for LGT, all affect the rate at which genetic
variation can be generated, some of which might be adaptive [5,6]. Differences in these traits are likely to exhibit
variation in populations and be subject to balancing
selection (Figure 1). With the current and widespread
dissemination of antimicrobial agents, humans might be
subjecting bacteria to directional selection for increased
evolvability [3,4,6]. In this review, we set the background
to this problem and examine the evidence that human
Corresponding author: Gillings, M.R. ([email protected]).
Keywords: evolution; antibiotic resistance; integron; plasmid; transposon; CRISPR;
lateral gene transfer; pollution; xenogenetic element.
346
activities might be altering the fundamental tempo of
bacterial evolution.
Antibiotics, resistance genes and pollution
Selection for antimicrobial resistance in human-dominated
ecosystems has resulted in the fixation of novel, complex
DNA vectors that can contain multiple antibiotic resistance
genes, often coupled with genes for resistance to disinfectants and/or heavy metals (Figure 2) [7,8]. Diverse, complex
DNA elements have now reached high frequencies in the
pathogens and commensals of humans and their domestic
animals. Each of these individually identifiable genetic
elements originally arose from a single event in a single
bacterial cell. Descendants of these elements have homogenous DNA sequences and structural signatures that can
identify them as originating from anthropogenic sources.
[9]. Thus, when these elements are detected in natural
ecosystems, they can be attributed to pollution from human-dominated ecosystems [10,11]. Such DNA elements
can be usefully thought of as xenogenetic pollution, analogous to pollution with xenobiotic compounds, but with one
crucial difference: their ability to replicate [12,13].
Resistance elements from human sources are now
spreading into the environment, where they are increasing
Glossary
Allochthonous bacteria: cells that originate outside the ecosystem where they
are currently found.
Autochthonous bacteria: cells indigenous to an ecosystem or location.
Biofilm: an aggregation of microorganisms growing in a matrix of polysaccharide and protein on a solid substrate.
Co-selection: when different resistance determinants on the same genetic
element are all fixed via hitchhiking, owing to selection by exposure to any one
selective agent.
CRISPR–Cas system: a system conferring acquired immunity in Bacteria and
Archaea. DNA segments are captured from invading plasmids or bacteriophage and expressed upon re-invasion. The transcribed RNA binds to, and
interferes with, the incoming foreign DNA.
Efflux pumps: proteins located in cell membranes that are responsible for
exporting toxic compounds from cells.
Evolvability: the potential for lineages to generate novel genetic variation;
affected by basal rates of mutation, recombination and LGT.
Integron: a gene capture and expression system often found embedded in
mobile elements, such as plasmids and transposons.
Lateral gene transfer (LGT): the movement of genetic material between
bacterial cells other than by vertical descent.
Plasmid: a circular DNA that can replicate independently of the bacterial
chromosome and can be transferred between both cells and species.
SOS response: a global response to DNA damage, resulting in transcriptional
activation of genes for DNA repair and low-fidelity polymerases, among others.
Transposon: a DNA element that can move between locations in a host.
Xenogenetic elements: novel DNA elements that have fixed in populations,
largely as a result of human use of selective agents.
0169-5347/$ – see front matter . Crown Copyright ß 2012 Published by Elsevier Ltd. All rights reserved. doi:10.1016/j.tree.2012.02.006 Trends in Ecology and Evolution, June 2012, Vol. 27, No. 6
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Review
Trends in Ecology and Evolution June 2012, Vol. 27, No. 6
(a)
tet R,A,C,D
Plasmid R100
Tn 10
Tn 9-like
cat
Δ
Δ
(b)
Tn 21
Number of cells in population
Transient increase
Transposon backbone
mer operon
Tn 402
intI1
aadA1
IS1326
qacE
sul1
IS1353
TRENDS in Ecology & Evolution
(c)
Directional selection
Rate at which
diversity is generated
Figure 2. The mosaic structure of xenogenetic elements. DNA elements that have
fixed in populations as a consequence of human use of antimicrobial agents often
have a mosaic structure, being assembled from diverse genetic modules, each
with a different evolutionary history. This schematic presents an overview of the
modules that comprise R100, a self-transmissible plasmid containing multiple
resistance determinants. At the base of the figure, gene cassettes encoding
aminoglycoside resistance (aadA1) and disinfectant resistance (qacE) were
captured by the class 1 integron (intI1), which itself inserted into transposon
Tn402. Subsequently, the Tn402 module was modified by insertion of a gene for
sulfonamide resistance (sul1) and deletion of part of qacE1 and the tni
transposition genes (marked with Ds). This module was sequentially invaded by
two insertion elements, IS1356 and IS1353. Transposon Tn402 inserted into
another transposon backbone that carried a mercury resistance operon (mer) to
generate the transposon known as Tn21. The Tn21 transposon was itself inserted
into the chloramphenicol resistance (cat) transposon Tn9. In turn, Tn9 is carried on
the plasmid R100, which also carries another transposon (Tn10) conferring
tetracycline resistance (tetR,A,C,D). It is likely that all these events, with the
exception of the capture of the mer operon, were fixed by selection during the
antibiotic era. The plasmid R100 carries genes for self transmissibility (tra) and
independent replication (rep). Data are summarized from NCBI Reference
Sequence: NC_002134 and Liebert et al. [79].
TRENDS in Ecology & Evolution
Figure 1. How antimicrobial agents affect both short- and long-term evolvability in
Bacteria. (a) Mechanisms that generate genetic diversity, such as rates of mutation,
recombination and lateral gene transfer (LGT) exhibit variation among members of
a population. (b) Short-term exposure to an antimicrobial agent causes transient
increases in these rates for each individual cell (dotted line), through mechanisms
such as induction of the SOS response. (c) Selection for lineages with inherently
higher rates of generation of genetic diversity results in long-term changes in the
basal rates of mutation, recombination and LGT in subsequent generations
(dashed line).
autochthonous and allochthonous bacteria to a wide range of
concentrations of selective agents, from therapeutic to subinhibitory levels [20–22]. Hence, there is a consistent zone of
selection spreading out from human activities, and this in
turn promotes the fixation of advantageous mutations and
LGT events [23–25].
in abundance [14,15]. Over the past decade, resistance genes
and their LGT vectors have been reported from a range of
wild animals and in environments far removed from the
direct influence of antibiotics [6,16]. The dissemination of
bacteria that carry xenogenetic DNA elements and antibiotic resistance genes is mediated by waste streams emanating from human activity [17,18]. Simultaneously, waste
streams also release significant concentrations of antibiotics, disinfectants and heavy metals [12,19]. Such compounds then form a concentration gradient, exposing both
The nature of antibiotics and resistance genes
What are antibiotics and what is their function in the
general environment?
Our view of antibiotics is anthropocentric. Antibiotics
encompass an eclectic range of structural and molecular
families, united only by their ability to inhibit microbial
growth at high concentrations. In natural ecosystems, antibiotics might act as signaling or regulatory molecules,
and are generally produced at subinhibitory concentrations
that might mediate interspecies competition, rather than at
the lethal concentrations used in antibiotic therapy [21,26].
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Low concentrations of these molecules are known to induce a
cascade of transcriptional responses [27,28]. Consequently,
bacteria exhibit a biphasic dose-response curve, with adaptive and beneficial transcriptional responses at low concentrations, whereas higher concentrations are in most cases
lethal or inhibitory [20].
Humans manufacture and distribute millions of metric
tons of antibiotics, although it is difficult to obtain precise
estimates on their production and use [29]. A significant
proportion of antibiotics for human and veterinary use are
excreted and released unchanged into the environment,
where they can be both persistent and mobile [30,31]. The
majority of the environmental load of antibiotics appears to
originate from commercial production [32]. The diverse roles
that antibiotic compounds play in natural microbial ecosystems will all be affected by this additional antibiotic exposure and, furthermore, selection for traits that deal with
antibiotic exposure is probably occurring on a global scale,
encompassing both terrestrial and aquatic ecosystems.
Where do antibiotic resistance genes come from?
Most antibiotic classes were originally discovered in bacteria from soil, so it should not be surprising that these
same bacteria can carry genes for resistance, and that
these genes protect them from potential effects of the
antibiotics that they produce. Where examined, the resistance genes and DNA vectors currently found in pathogens can often be traced back to environmental organisms
[26,33,34]. Databases of antibiotic resistance determinants now list >20 000 genes [35], but even this might
be a small fraction of the total number of resistance genes
and their precursors in environmental bacteria [36,37].
Analysis of metagenomic DNA from soil and permafrost
reveals diverse and ancient lineages of genes for resistance to antibiotics, such as aminoglycosides, tetracyclines, glycopeptides and b-lactams, all pre-dating the
antibiotic era [38,39].
Therefore, natural microbial ecosystems contain a vast
pool of potential resistance genes that can be acquired by
pathogens. Vectors, such as plasmids, that move resistance
genes between bacterial lineages, have captured many of
these genes since the advent of the antibiotic era, because
bacteria isolated before the medical use of antibiotics have
similar plasmid backbones, but without resistance determinants [40]. If resistance genes are captured by LGT
vectors, then their transmission between bacterial cells
and species is enhanced.
How do bacteria become antibiotic resistant?
Some bacteria are intrinsically resistant to antibiotics
through possession of efflux pumps or biodegradative
enzymes that eliminate or degrade antibiotics, respectively
[32,34]. In other cases, mutation of existing genes changes
the target molecule of the antibiotic, or diverse genes can be
co-opted to detoxify or avoid antibiotic effects, including
genes encoding efflux mechanisms, catabolic enzymes or
cell surface properties [21,32]. However, many, if not most,
bacterial species are not intrinsically resistant to antibiotics. These species can acquire resistance genes through
LGT, when existing resistance genes cross species boundaries [6,26].
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Some bacteria are able to take up DNA from their
general environment (transformation), including DNA
that encodes resistance determinants. Resistance genes
are rarely found in bacteriophages, but they can move DNA
between cells (transduction), and their mechanisms for
integration into host chromosomes have certainly been
co-opted by diverse genetic elements that carry resistance
and virulence genes [32]. However, direct physical transfer
of DNA between cells (conjugation) is the best studied and
possibly most important process by which LGT takes place.
Antibiotic resistance genes are usually transferred as
components of larger genetic elements, such as plasmids,
transposons, integrons, genomic islands or integrative
conjugative elements (ICEs) [6,32].
Clinical strategies have exacerbated the resistance
problem. Historically, antimicrobials were designed to
have a broad spectrum of activity, thus allowing treatment
to commence without accurate identification of the pathogen. However, exposure to broad-spectrum antibiotics
exerts strong selection pressure on a correspondingly
broad range of bacterial species. This drives selection of
LGT events in diverse pathogens, commensals and environmental bacteria, none of which might have been the
original target of antibiotic therapy. It also promotes the
dissemination of resistant bacterial clones, which then aids
the dispersal of resistance genes and the genetic elements
that carry them.
Evidence that humans are selecting for increased
evolvability
Antimicrobial exposure and its effects on mutation rate
Oxidative stress is induced when bacteria are exposed to
antibiotics, even at sublethal levels. Reactive oxygen species (ROS) then induce the SOS response (Box 1), which in
turn activates multiple pathways, including the expression
of error-prone DNA polymerases that can introduce mistakes during DNA replication [41,42]. Consequently, one
Box 1. Genetic systems involved in regulation of bacterial
genetic diversity
The SOS response
The SOS response is a system that is triggered by DNA damage,
detectable as the presence of single-stranded DNA. Such damage
might be generated by radiation, toxins or ROS. Single-stranded
DNA binds to RecA, activating it and causing cleavage of the LexA
repressor protein, consequently allowing expression of genes in the
SOS regulon. This activity not only repairs the DNA damage, but
also increases the basal mutation rate through expression of errorprone polymerases. The SOS response also increases the basal rate
of LGT and recombination [77,78].
The CRISPR–Cas system
The CRISPR–Cas system [58] is a form of acquired immunity in
prokaryotes that reflects past exposure to invading DNA elements.
Short sections of DNA from invading bacteriophage or plasmids are
captured as part of a tandem array bounded by palindromic repeat
elements. Expression of these DNAs generates RNA guides that
target complementary sequences in invading DNAs, and mark them
for destruction in a manner analogous, but unrelated to interfering
RNA in eukaryotes. The efficiency of defense against different
laterally transferred DNAs is determined by the diversity of RNA
guides, and this varies among individual cells [58,59].
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unintended adverse effect of antibiotic pollution is a general increase in the standing rate of mutation in exposed
bacteria (Figure 1b), potentially generating adaptive
changes, including resistance mutations. In retrospect, it
is not surprising that bacteria can exhibit responses to
stressful environments that include mechanisms for increasing genetic variability. Such first-order responses
should cease when the environment becomes less stressful.
However, there is also good evidence that bacterial
populations contain cells with a range of inherently different basal mutation rates, including some hypermutable
strains. Mutation rates are under balancing selection, with
the costs of replication fidelity being weighed against the
potentially damaging effects of mutations [43]. During
stresses such as antibiotic exposure, ‘mutator’ strains generate more variation, some of which might be adaptive.
This leads to second-order selection, where mutator alleles
can hitchhike, based on their linkage to newly formed
adaptive mutations [44,45]. Theoretical studies predict
that the frequencies of such mutators will increase in
asexual populations under conditions where adaptation
is important [46], a prediction that has been verified
experimentally [47]. Consequently, the consistent lowlevel selective pressures maintained by antibiotic pollution
might have two major adverse effects: an increase in stress
induced mutagenesis within individual cells (Figure 1b),
and second-order selection for lineages with inherently
higher rates of mutation (Figure 1c) [3–5]. Higher mutation rates do incur a fitness cost, and reversion to a less
mutable phenotype is likely if environmental conditions
become less adverse.
Antimicrobial exposure and its effects on recombination
rate
Another method for generating genetic variation in bacteria is via recombination. Even under subinhibitory antibiotic exposures, rates of homologous recombination are
known to increase [48]. Such activity might recombine
different adaptive point mutations, obviating the need
for serial mutations to occur [5]. As mentioned above, a
wide range of antibiotics induce the SOS response, which
has also recently been shown to control the expression of
integron integrase and, thus, to enhance recombination at
this locus [49].
Integrons are genetic elements that capture gene cassettes by site-specific recombination. In clinically important
bacteria, integrons typically carry up to six cassettes, usually encoding antibiotic resistance determinants, linked in a
tandem array. Environmental bacteria have integrons that
can have tandem arrays containing hundreds of cassettes,
often of unknown function. Newly acquired cassettes are
inserted adjacent to the integron integrase gene and are
expressed by an associated promoter. As cassette arrays
lengthen by repeated acquisition of new cassettes, the distal
cassettes can become transcriptionally silent as their distance from the promoter increases [50].
Environmental stress, such as exposure to antimicrobial
agents, enhances integrase-mediated recombination of integron cassettes. This has two consequences important for
bacterial adaptation: first, there is a heightened potential
for acquiring new cassettes; and second, existing cassettes
Trends in Ecology and Evolution June 2012, Vol. 27, No. 6
can be rearranged to bring distal cassettes into more proximal positions (adjacent to the integrase gene), where they
can be more readily expressed [51,52]. Under such circumstances, bacterial populations can generate diversity at the
integron locus by altering cassette order and content, precisely at times when innovation might be advantageous. The
generation of genomic diversity by this mechanism has
implications for the development of antibiotic resistance,
and might also be a mechanism whereby environmental
conditions can generate diversity, out of which locally
adapted variants can emerge after selection [53].
Antimicrobial exposure and its effects on LGT
One of the most important means of acquiring antimicrobial resistance is via LGT. Again, it should not be surprising that under conditions where innovation is adaptive, the
stress-induced SOS response is associated with various
mechanisms that increase the potential for LGT
(Figure 1b). For instance, antibiotic exposure improves
the ability of Streptococcus to acquire foreign DNA by
transformation [54]. The SOS response can also induce
lateral transfer of pathogenicity islands [55], and of antibiotic resistance genes themselves, in a mechanism whereby the use of individual antibiotics might actually promote
the lateral spread of diverse resistance genes, including
those for unrelated antibiotics [56].
Propensity for LGT can exhibit considerable variation,
even among otherwise indistinguishable isolates collected
from small areas [57]. If the propensity for acquisition of
foreign DNA varies in populations, then under conditions
of antimicrobial pressure, lineages with increased propensity have a survival advantage. Again, an unintended
adverse effect of antimicrobial pollution might be selection
for lineages with increased rates of LGT and, thus, increased evolutionary flux (Figure 1c).
The propensity for LGT is likely to be under balancing
selection, because bacteria must protect themselves
against invasion by parasitic DNA elements, while still
being able to take advantage of occasional advantageous
transfer events. The dissemination of antimicrobial agents
now gives an increased advantage to lineages that are
more amenable to lateral transfer, with selection favoring
those variants with inherently higher rates (Figure 1c).
There are several mechanisms that exclude foreign
DNA from bacteria, including restriction-modification systems, surface exclusion and sugar non-specific nucleases.
One would predict that under scenarios where increased
rates of lateral transfer were advantageous, lineages with
compromised defenses against LGT would have a selective
advantage. An important confirmation of this prediction
has recently been published, dealing with a novel mechanism for exclusion of foreign DNA, the clustered regularly
interspaced short palindromic repeats (CRISPR)–Cas system (Box 1) [58]. The efficiency of defense against different
laterally transferred DNAs is determined by CRISPR activity and diversity, and this varies among individual cells
[58,59]. Where the advantage of acquiring foreign DNA
outweighs the risks associated with invasion by parasitic
DNA, CRISPR systems might be selected against. Consistent with this notion, antibiotic resistance and the possession of active CRISPR loci are inversely correlated in
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enterococci, suggesting that antibiotic exposure has selected for lineages with compromised defenses against LGT
[60].
Co-selection as a mechanism for fixation
The plasmids and other DNAs that are laterally transferred between bacterial lineages are often complex
mosaics of genetic elements with different evolutionary
histories (Figure 2) [6,61,62]. Individual plasmids can
carry diverse antibiotic resistance genes embedded within
an integron, which itself can be inserted into a transposon.
Elsewhere on the same plasmid, there can be genes for
resistance to heavy metals or disinfectants [6]. The significance of this mosaic structure lies in the fact that exposure
to a single selective agent fixes the plasmid, and co-selects
all the associated genes through simple linkage. Thus,
selection for a particular plasmid can be mediated by
exposure to any one of the selective agents for which it
carries resistance determinants, and simultaneous exposure to multiple agents enhances this effect.
Concern has been raised that long-standing environmental pollution with metals can co-select for antibiotic
resistance genes that reside on the same plasmid [7].
Certainly, the abundance of integrons and transposons
increases proportionally to discharge rates from wastewater treatments that contain contaminating heavy metals
[63,64]. Similarly, widespread pollution with disinfectants
can co-select for plasmids carrying antibiotic resistance
genes [65,66], and probably had a role in the original
selection of the most common class of integron in clinical
pathogens [67].
Hotspots for LGT
Humans create hotspots for LGT and the assembly of novel
genetic elements. In particular, wastewater and effluents
bring pathogens, commensal organisms and environmental bacteria together in locations that also contain significant quantities of selective agents, such as antibiotics,
heavy metals and disinfectants. Sewage treatment plants
carry a high diversity of plasmids, transposons, integrons
and genes for resistance to selective agents [17,18]. Consequently, there is ample opportunity for interactions between diverse elements, and for movement of DNA
between species, coupled with the selective pressures to
fix these outcomes in host bacteria. Sewage treatment
plants then become a reactor for assembling complex
DNA elements that contain genes encoding resistance to
metals, disinfectants and antibiotics, and can promote
dissemination of these newly formed assemblages to diverse species [18].
Within wastewaters and sewage sludge, many LGT
events are likely to occur between bacteria that form
biofilms, and biofilms more generally are a hotspot for
lateral exchanges [68]. Exposure of bacteria to subinhibitory concentrations of antibiotics enhances biofilm formation, which then protects the cells within the biofilm from
the antibiotic effect. This in turn allows more time for
beneficial mutations to occur, while also increasing cell
density and enhancing LGT [69]. Biofilms allow dynamic
exchange of gene cassettes between integrons resident in
different cells [70,71]. Other biofilms, such as those within
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animal digestive systems, or in aquatic ecosystems, the
rhizosphere and phyllosphere, are also hotspots for lateral
exchanges [22,68]. All these locations are exposed to subinhibitory levels of antibiotics and other selective agents.
Creation of these hotspots provides the means and opportunity for rapid bacterial evolution.
Complex DNA elements and emergent properties
Examination of plasmids collected from before the antibiotic era [40] makes it clear that their structural complexity
has increased as a result of human activities. The selective
pressures imposed on bacteria have promoted the assembly of complex, mosaic structures that can be thought of as
being xenogenetic. Contemporary plasmids often contain
diverse antibiotic resistance determinants linked to resistance genes for metals and disinfectants, embedded in a
mosaic of transposons and insertion elements (Figure 2)
[18].
Each of the modules comprising these structures has a
different evolutionary history, and modules can be freely
exchanged between different DNA elements. This creates a
situation where identical DNA segments can be widely
distributed among different plasmid backbones, generating lateral exchange communities [8]. The existence of
homologous sequences on different mobile DNA elements
allows recombination events to occur, such that these
elements can effectively promote their own diversity
[72]. This modularity generates emergent properties
through combinatorial assembly, the dynamic interactions
of genes and their vectors, and persistent selection by
diverse agents.
Combinatorial assembly and its consequent emergent
properties are also becoming features of recent chromosomal evolution in bacteria. This can be illustrated using
two emerging opportunistic pathogens, Pseudomonas
aeruginosa and Acinetobacter baumannii. The reference
strain of P. aeruginosa, PAO1, was isolated during the
1950s, and has a genome size of 6.3 Mb, in comparison with
contemporary strains that typically contain 6.6–6.9 Mb.
Although PAO1 may have undergone some genome reduction during adaptation to laboratory conditions, the difference in DNA content in comparison to contemporary strains
is in part due to the latter containing large genomic islands
comprising a variety of genes for resistance and virulence
factors. Although the core genome of P. aeruginosa is highly
conserved, genomic islands are highly variable and capable
of LGT [73]. The origin of genomic islands and the related
ICEs appears to have arisen via recombination between
phages and conjugative plasmids, generating DNA elements that can integrate and excise from chromosomes
and are able to move between cells by conjugation [74].
The movement of ICEs into bacterial chromosomes
generates emerging and multidrug-resistant pathogens,
such as A. baumannii. During the 1970s, bacterial isolates
now referred to A. baumannii were generally susceptible to
antibiotics, but since then, this species has become a serious problem worldwide. The first resistance island described in A. baumanii contained 45 genes for antibiotic
or antimicrobial resistance together with diverse transposons, integrons and operons for mercury and arsenic resistance [75]. Recombination between different resistance
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islands has subsequently generated hybrids and variants
at an ever-increasing rate, such that nine new variants
have been described since 1997 from a single dominant
clone of this species [74,76]. The ability of such elements to
move between strains and species, coupled with their
extensive intersequence homology and transpositional machinery, ensures that they will continue to generate further
diversity and complexity [72]. This is a perfect example of
emergent properties. Although the original elements
might have been selected by antimicrobial therapy, the
diversity of accessory genes now found in genomic islands
ensures an ongoing evolution driven by a variety of selective forces, including antibiotic use.
Concluding remarks
Basal rates of mutation, recombination and LGT are all
under balancing selection in bacterial lineages, because
there is a fine balance between factors such as genomic
integrity and the ability to generate variation (benefits)
against DNA replication fidelity and invasion by parasitic
DNA elements (costs). Under stressful and variable conditions, this balance is likely to change in favor of lineages
that have increased rates of mutation, recombination and
LGT. This is because the descendants of such lineages are
more likely to generate the genetic innovation that enables
survival in the face of selection. Therefore, the saturation
of the environment with antimicrobial compounds could
drive selection for increased evolvability, and this might
have widespread consequences for both bacteria in natural
environments and for those of clinical relevance. It is
important to stress that any increase in evolvability
applies to the whole bacterial genome, not just to genes
dealing with antimicrobial agents, so the consequences of
the antibiotic era might eventually spread to affect all
bacterial genomes in the biosphere.
From a clinical perspective, the dissemination of multiple
antibiotic resistance genes among diverse bacteria establishes a situation where the possession of genes that enhance other phenotypes, such as virulence, transmission or
biofilm formation, confers a significant additional advantage. This will make existing pathogens more dangerous,
Box 2. Outstanding questions
What quantities of antimicrobial compounds are released into the
environment, and what is their half-life?
How does the standing concentration of antimicrobial agents
compare with those of the pre-antibiotic era?
How does exposure to antimicrobial agents affect mutation rates
and gene flux between organisms in both the short and long
term?
What is the fate of resistant organisms and their genes in the
environment?
Are particular organisms more likely to be affected by antimicrobial agents?
What methods can be used to monitor and quantify such genetic
changes?
What mechanisms are important in promoting the evolvability of
cell lineages?
Are increases in evolvability transient or more generally maintained?
How can the potential impact of antibiotic and resistance gene
pollution be reduced?
Trends in Ecology and Evolution June 2012, Vol. 27, No. 6
and might stimulate the emergence of new disease agents
from environmental organisms. The ongoing release of
selective agents into the biosphere is likely to affect bacterial evolvability on a global scale, and include environmental, commensal and pathogenic species. However, the
range and magnitude of second-order effects arising from
the antibiotic revolution cannot be reliably predicted,
because key questions about the process are still unanswered (Box 2).
Acknowledgments
We thank Andrew Beattie and Mark Westoby for comments on draft
versions of this manuscript, and apologize to all the authors of excellent
papers in this area who could not be cited owing to space restrictions. Work
in the authors’ laboratories was supported by the Australian Research
Council and the National Health and Medical Research Council of
Australia.
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