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doi:10.1111/j.1558-5646.2011.01531.x
TRAGEDY OF THE COMMONS AMONGANTIBIOTIC RESISTANCE PLASMIDSJeff Smith1,2,3
1Department of Biology, Emory University, Atlanta, Georgia 303022E-mail: [email protected].
Received July 28, 2011
Accepted November 21, 2011
As social interactions are increasingly recognized as important determinants of microbial fitness, sociobiology is being enlisted
to better understand the evolution of clinically relevant microbes and, potentially, to influence their evolution to aid human
health. Of special interest are situations in which there exists a “tragedy of the commons,” where natural selection leads to a
net reduction in fitness for all members of a population. Here, I demonstrate the existence of a tragedy of the commons among
antibiotic resistance plasmids of bacteria. In serial transfer culture, plasmids evolved a greater ability to superinfect already-
infected bacteria, increasing plasmid fitness when evolved genotypes were rare. Evolved plasmids, however, fell victim to their
own success, reducing the density of their bacterial hosts when they became common and suffering reduced fitness through
vertical transmission. Social interactions can thus be an important determinant of evolution for the molecular endosymbionts of
bacteria. These results also identify an avenue of evolution that reduces proliferation of both antibiotic resistance genes and their
bacterial hosts.
KEY WORDS: Cheating, conflict, cooperation, horizontal gene transfer, selfish genetic elements, symbiosis, virulence.
The tragedy of the commons is an economic analogy that describes
how individuals, acting rationally and in their own self-interest,
can overexploit a shared resource even when it is in no one’s
long-term interest to do so (Hardin 1968). It was introduced to
contrast with Adam Smith’s claim that economic self-interest
leads individuals, as if “led by an invisible hand,” to promote
the public interest (Smith 1776). The analogy has been imported
into evolutionary biology, where it refers to a situation in which
competition reduces the resource over which individuals compete,
leading to a reduction in fitness for all members of the population
or group (reviewed in Dionisio and Gordo 2006; Rankin et al.
2007). The net effect is that, somewhat counterintuitively, natural
selection reduces population-mean fitness. Rankin et al. (2007)
distinguish between “collapsing” tragedies in which a resource
is entirely depleted and “component” tragedies that reduce mean
3Current address: Department of Biology, Washington University in
St. Louis, Campus Box 1137, One Brookings Drive, St. Louis, Missouri
63130–4899.
group fitness but fall short of total collapse. Because avoiding a
tragedy seems to require that individuals give up personal fitness
to benefit the larger group, the analogy is often invoked in the
context of the evolution of cooperation.
The potential for tragedies of the commons among
pathogenic microbes has been appreciated for some time. The-
oretical models have proposed that competition among pathogen
genotypes within a host allows aggressively reproducing strains
to gain short-term advantage but may also shorten the duration of
infection due to increased host death or immune clearance. The
host is thus a resource that is shared among coinfecting strains,
and optimal infectious transmission may require cooperative re-
straint (Lewontin 1970; Axelrod and Hamilton 1981; Levin and
Pimental 1981; Bremermann and Pickering 1983; Nowak and
May 1994; May and Nowak 1995; Frank 1996). Another kind of
social dilemma occurs when the success of microbial infections
depends on the production of costly diffusible products whose
benefits can also be obtained by nonproducing “cheater” strains
(Brown 1999; Chao et al. 2000; Smith 2001; West et al. 2007;
1 2 6 9C© 2012 The Author(s). Evolution C© 2012 The Society for the Study of Evolution.Evolution 66-4: 1269–1274
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Buckling and Brockhurst 2008). Microbial sociobiology may
thus be able to help us better understand how selection acts on
pathogenic traits and to predict whether pathogen evolution in
response to medical interventions will lead to desirable or unde-
sirable outcomes (Foster 2005; Kohler et al. 2010). Some have
even suggested that we may be able to influence pathogen evo-
lution to aid human health, for example, by using intervention
strategies that select for less-virulent pathogens (Dieckmann et
al. 2002) or introducing cheater strains to sabotage infections
(Brown et al. 2009; Marriott and Dimmock 2010).
Here, I demonstrate the existence of a tragedy of the com-
mons in a clinically relevant system at an even smaller level of bi-
ological organization—among the plasmids of bacteria. Plasmids
are mobile genetic elements that often carry genes for resistance
to antibiotics and are major determinants of resistance among bac-
terial pathogens and opportunistic infections (Frost et al. 2005; Su
et al. 2008). Plasmids reproduce independently of chromosomes
and are typically inherited by both daughter cells after division.
Many plasmids can also transmit themselves infectiously among
cells. Plasmid fitness thus has two components: one through ver-
tical transmission and another through horizontal transmission.
Because plasmid ecology and evolution is somewhat decoupled
from that of their bacterial hosts (Boyd and Hartl 1997), with both
positive and negative effects on host fitness (Bouma and Lenski
1988; Modi and Adams 1991; Turner et al. 1998; Dahlberg and
Chao 2003; Dionisio et al. 2005), plasmids can be thought of as
molecular endosymbionts of bacteria.
I previously described an experiment in which plasmids
evolved an increased ability to “superinfect” bacteria already in-
fected with incompatible plasmids (Fig. 1A; smith 2011). Here,
I test theoretical predictions that within-host competition caused
by superinfection creates a tragedy of the commons. I measure the
fitness of evolved plasmids in direct competition with the ances-
tral genotype, including both vertical and horizontal transmission
components of fitness, and measure how evolved plasmids affect
host abundance.
Materials and MethodsCULTURE CONDITIONS
All bacteria were cultured in 10 mL Davis minimal media sup-
plemented with 1000 μg/mL glucose and 20 μg/mL uracil, in-
cubated at 37◦C in 50 mL conical flasks shaking at 200 rpm.
Where indicated, cultures were passaged with 100-fold dilution
(0.1 mL into 9.9 mL fresh media). These are the same conditions
as the previous evolution experiment (smith 2011). Cell densi-
ties were estimated from colony counts on tetrazolium arabinose
(TA) plates (Levin et al. 1977), on which Ara+ colonies appear
white and Ara− colonies appear red. The evolution experiment
and fitness assays were performed in antibiotic-free media, but
Figure 1. (A) Plasmids evolved in serial transfer culture (Smith
2011). All host bacteria were infected, but plasmids can spread
by superinfecting already-infected hosts (inset). (B) An evolved
plasmid genotype invades populations of the ancestral plasmid
through superinfection. The evolved plasmid is highly virulent,
slowing growth of infected hosts and reducing population density
when it becomes common. Solid line: cells infected with ancestral
plasmid. Dashed line: introduced donor strain of hosts infected
with evolved plasmid. Dotted line: transconjugant cells that have
acquired evolved plasmids via superinfection. Lines and error bars
are geometric mean ± range of data (n = 4). (C) In control com-
petitions between differently marked versions of the ancestral
plasmid, some superinfection occurs but transconjugants remain
rare.
antibiotic resistances were used as genetic markers of plasmid
and host genotype. Where indicated, antibiotics were included
in plates at the following concentrations: kanamycin (Km) at
25 μg/mL, chloramphenicol (Cm) at 25 μg/mL, rifampin (Rif) at
10 μg/mL, and nalidixic acid (Nal) at 2.0 μg/mL.
BACTERIA STRAINS AND PLASMIDS
All bacterial strains used here are derivatives of Escherichia coli
strain MG1655 obtained from the National Type Culture Collec-
tion. NalR and RifR strains were obtained as spontaneous mutants
after plating on Nal or Rif TA medium, respectively. Plasmid
R1–19 (Meynell and Datta 1967) was obtained from B. Levin
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(Emory University). Plasmid R1–19K, a CmS mutant of R1–19,
was obtained from K. Nordstrom (Uppsala University).
Evolved plasmids come from a previously described exper-
iment in which hosts were infected with R1–19 and passaged in
daily serial transfer culture (smith 2011). In that paper’s termi-
nology, evolved plasmids were sampled from population N1 after
100 generations of evolution. This population was chosen because
it contains evolved plasmids that retained resistance to chloram-
phenicol. The original evolution experiment allowed both plas-
mids bacteria to evolve. The plasmids studied here were among
the very first evolved genotypes to appear. They appeared very
rapidly in the original experiment (∼14 days), before evolved host
genotypes were detected or would be expected to reach apprecia-
ble frequency. These plasmids, then, evolved primarily in the
ancestral host genotype. Plasmids from later on in the evolution
experiment would be more likely to have evolved in evolved hosts.
Individual plasmid genotypes were sampled from the evolved
population and moved onto a common ancestral host background.
To accomplish this, frozen stocks of the evolved population (Ara−)
and an ancestral plasmid-free host (js171; Ara+ RifR) were sep-
arately grown for one day then coinoculated into fresh media
and grown another day, during which evolved plasmids infected
plasmid-free hosts. These cultures were then plated onto TA Rif
Cm to select for ancestral hosts infected with an evolved plasmid.
Random colonies were resuspended in saline, used to inoculate
each of four flasks, and incubated for one day. These four cul-
tures were then used as replicate test strains in the fitness assays
described below. As a control, test strains were also made using
ancestral plasmids from an ancestral host strain (js42; Ara− NalR)
instead of the evolved population.
PLASMID ASSAYS
Plasmid fitness was measured by competing plasmids in serial
passage culture against a differently marked version of the an-
cestral plasmid. For these assays, test strain cultures were diluted
1000-fold in saline, mixed at equal volume with overnight cultures
of an ancestral host infected with the competitor plasmid (js244;
Ara− NalR R1–19K), and passaged one day. Some genotypes
were passaged for additional days to follow plasmid/host popu-
lation dynamics. Total cell densities were calculated from colony
counts on TA plates. Densities of all infected cells were calculated
from colony counts on TA Km plates. Densities of donor strains
for evolved plasmids were calculated from Ara+ colony counts
on TA Cm or TA Rif Cm plates. Densities of transconjugant cells
newly infected with the evolved plasmid were calculated from
Ara− colony counts on TA Cm or TA Nal Cm plates. Densities
of cells infected with the differently marked ancestral plasmid
were calculated as total infected density minus transconjugant
density.
A mathematical model of population dynamics predicted in
the fitness assays is included as Supporting Information. Plas-
mid fitness was calculated in terms of absolute fitness per serial
transfer. If n is the density of cells infected with a given genotype
immediately after dilution and n′ is the density of cells infected
with that same genotype after one day’s growth, then the ab-
solute fitness of that genotype over the whole growth cycle is
w = n′/n. The vertical transmission component of plasmid fitness
was measured by calculating w using only the densities of the
donor strain for tested plasmids (i.e., excluding transconjugants).
Relative fitness was calculated as the ratio of tested to competitor
fitness wtest/wcompetitor.
To measure how plasmids affect host populations, test strains
were passaged one day. Population densities were calculated from
colony counts on TA plates.
As an additional measure of plasmid fitness through vertical
transmission, test strains were competed against plasmid-resistant
strain js177 (smith 2011). Against a resistant host, plasmid fitness
is primarily determined by its effect on the survival and reproduc-
tion of hosts who have inherited their infections vertically. For
these assays, overnight cultures of test strains and resistant hosts
were mixed at equal volume and passaged one day. Densities
of plasmid-infected test hosts were calculated from Ara+ colony
counts on TA or TA Rif plates. Densities of resistant hosts were
calculated from Ara− colony counts on TA plates. Fitness were
calculated as above, only now with the resistant host strain as the
competitor.
STATISTICS
All data were analyzed using R 2.8.1 (R Development Core Team
2011). Statistical models were fit to log10 relative fitness or log10
host density. Differences between differently marked versions of
the ancestral plasmid were tested using two-tailed one-sample
t-tests (t.test procedure). To test differences between the ancestral
and evolved plasmids as a group, data were fit to linear mixed
effects models by maximum likelihood (lme procedure). Signif-
icance was determined using likelihood ratio tests on models fit
with or without ancestral/evolved status as a fixed effect. Plasmid
genotype was modeled as a random effect nested within ances-
tral/evolved status, allowing evolved genotypes to vary in fitness
in addition to an overall difference between evolved plasmids
and the ancestor. Differences between individual evolved plas-
mids and the ancestor were tested using two-sample t-tests (t.test
procedure). These tests were one-tailed because of a prior expec-
tation for the direction of effects under a tragedy of the commons.
To correct for multiple comparisons, tests were only considered
significant below the Bonferoni cutoff level for four comparisons
of P = (0.05/4) = 0.0125.
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ResultsWhen I introduced evolved plasmids at low frequency into popula-
tions of bacterial hosts infected with a differently marked version
of the ancestral plasmid, evolved plasmids rapidly increased in
frequency by superinfecting hosts previously infected with the
ancestral plasmid genotype (Fig. 1B shows one example). In con-
trol competitions between two differently marked ancestral plas-
mid genotypes, very little superinfection occurred (Fig. 1C). I
calculated the relative fitness of the ancestral and four evolved
plasmid genotypes over the first transfer of these experiments,
when evolved plasmids were still rare (Fig. 2A). In the control
competitions, the ancestral plasmid was slightly but significantly
less fit than its competitor (t = −9.8, df = 3, P = 0.0022), possi-
bly due to the different genetic markers. Evolved plasmids were
much more fit than the ancestor when compared together as a
group (LR = 9.2, P = 0.0024) or individually (E1: t = 11.4, df =3.0, P = 6.8 × 10−4; E2: t = 16.3, df = 3.1, P = 2.0 × 10−4; E3:
t = 50.7, df = 3.7, P = 1.1 × 10−6; E4: t = 12.5, df = 3.1, P =4.5 × 10−4).
Over the course of several passages, evolved plasmids in-
creased in frequency. When they became common, cultures
were visibly delayed becoming turbid (an indicator of bacterial
density), and host population densities were severely reduced
(Fig. 1B). To investigate this effect further, I separately cultured
hosts infected with either evolved or ancestral plasmid genotypes
(Fig. 2B). Compared to the ancestral plasmid, evolved plasmids as
a group reduced host densities by one or two orders of magnitude
(LR = 7.7, P = 0.0057). Compared individually, two evolved
genotypes showed significant reduction (E2: t = −10.2, df = 3.1,
P = 8.3 × 10−4; E4: t = −4.6, df = 3.0, P = 0.0094) whereas
the other two were only significant before correcting for multiple
comparisons (E1: t = −3.1, df = 3.0, P = 0.025; E3: t = −3.0,
df = 3.0, P = 0.028).
Although the overall frequency of evolved plasmids
increased in competition experiments, the frequency of the orig-
inally infected host strain decreased (Fig. 1B). In ancestral con-
trols, the frequency of these “donor” hosts changed relatively lit-
tle (Fig. 1C). I estimated the vertical transmission component of
plasmid fitness from the change in donor frequency over the first
transfer (Fig. 2C). Compared as a group to the ancestral control,
evolved plasmids had reduced fitness through vertical transmis-
sion (LR = 4.2, P = 0.039). Compared individually, two had
significantly reduced fitness (E2: t = −8.3, df = 3.2, P = 0.0015;
E4: t = −4.5, df = 3.1, P = 0.0096), one was only significant
before correcting for multiple comparisons (E3: t = −2.5, df =3.2, P = 0.041), and one was almost significant (E1: t = −2.2,
df = 3.0, P = 0.058).
As another measure of plasmid fitness through vertical trans-
mission, I competed infected hosts against a bacterial strain
Figure 2. Plasmid evolution creates a tragedy of the commons.
(A) Evolved plasmids are more fit than their ancestor when rare
but (B) reduce host population density when common. (C) Evolved
plasmids have reduced fitness through vertical transmission when
measured against the ancestral plasmid genotype or (D) a plasmid-
resistant host strain. Points: replicate fitness measurements. Bars:
geometric mean of replicates for each plasmid genotype (n = 4).
Evolved plasmid E4 is the genotype shown in Figure 1B.
resistant to plasmid infection (Fig. 2D). In these experiments, host
strains infected with evolved plasmids were less fit than those
infected with the ancestral plasmid when compared as a group
(LR = 6.1, P = 0.014) or when compared individually (E1: t =−4.0, df = 3.5, P = 0.011; E2: t = −8.2, df = 5.7, P = 1.1 ×10−4; E3: t = −7.2, df = 5.1, P = 3.8 × 10−4; E4: t = −5.6,
df = 4.4, P = 0.0018).
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DiscussionA tragedy of the commons occurs when natural selection favors
traits that diminish the resource over which individuals compete,
leading to a net reduction in fitness for all individuals (Rankin
et al. 2007). By this standard, plasmid evolution in these ex-
periments followed a tragedy of the commons. Greater ability
to superinfect already-infected bacteria increased the fitness of
evolved plasmids when rare and directly competing with the an-
cestral type. Evolved plasmids, however, fell victim to their own
success. When they were common, they severely reduced the den-
sity of the bacterial hosts on which they depend. They also had
reduced fitness through vertical transmission, the majority com-
ponent of fitness when plasmid genotypes are locally common.
Selection favored plasmid traits, therefore, that led to a net de-
crease in population-mean fitness. Tragedies of the commons can
therefore occur among the mobile genetic elements of bacteria
that so often carry and disseminate genes for antibiotic resistance
and pathogen virulence (Frost et al. 2005).
In this system, the tragedy follows from plasmids failing to
use hosts prudently. Abolishing plasmid-borne resistance to su-
perinfection can cause membrane damage and host death when
plasmids are common (Ou 1980). Following the classification
system of Rankin et al. (2007), hosts are a preexisting resource
whose optimal usage requires cooperative restraint. In this sense,
the tragedy is similar to those predicted to exist in host/pathogen
systems (Lewontin 1970; Axelrod and Hamilton 1981; Levin and
Pimental 1981; Bremermann and Pickering 1983; Frank 1996;
Read and Taylor 2001). Evidence for such a tragedy is lack-
ing among human pathogens (Read et al. 2002), but similar ef-
fects have been seen in nonpathogenic microbes (MacLean 2008;
Eshelman et al. 2011).
A different form of social dilemma occurs when individuals
compete by producing less of a costly public good (West et al.
2007; Buckling and Brockhurst 2008). The Pseudomonas bacteria
that infect cystic fibrosis patients, for example, evolve to produce
fewer secreted products that increase proliferation within hosts
(Kohler et al. 2009; Rumbaugh et al. 2009; Kohler et al. 2010).
Viral infection success can also be reduced by “defective inter-
fering particles” that produce less of a gene product necessary
for replication but can use products produced by other viruses
(Marriott and Dimmock 2010). So far, there is no evidence for a
public goods dilemma among the plasmids in these experiments.
If the primary effect of superinfection, for example, was to favor
defective interfering genotypes, one would expect evolved plas-
mids to impose less of a metabolic burden on hosts, increasing
host density and increasing fitness through vertical transmission.
Two clinically desirable outcomes were seen in the evo-
lution experiments from which these plasmids were isolated—
reduced bacterial proliferation and rapid loss of antibiotic resis-
tance (smith 2011). Other studies of plasmid evolution, however,
have often found that resistance persists long after antibiotic se-
lection is removed (Bouma and Lenski 1988; Modi and Adams
1991; Turner et al. 1998; Dahlberg and Chao 2003; Dionisio
et al. 2005). Future work to clarify the genetic and environmental
causes of these different outcomes could help us understand how
to enlist evolution as an aid, rather than a hindrance, in the fight
against antibiotic resistant bacteria.
ACKNOWLEDGMENTSD. Queller, D. Rozen, and J. Strassmann provided helpful discussion andcomments on the manuscript. This research was supported by NIH grantGM33782–17 to B. Levin (Emory University).
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Associate Editor: S. Gandon
Supporting InformationThe following supporting information is available for this article:
Figure S1. Population dynamics expected in serial transfer assay of plasmid fitness.
Table S1. Parameter values used in numerical solutions.
Supporting Information may be found in the online version of this article.
Please note: Wiley-Blackwell is not responsible for the content or functionality of any supporting information supplied by the
authors. Any queries (other than missing material) should be directed to the corresponding author for the article.
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