Translational demand is not a major source of plasmid-associated fitness costs

Plasmids are key drivers of bacterial evolution because they are crucial agents for the horizontal transfer of adaptive traits, such as antibiotic resistance. Most plasmids entail a metabolic burden that reduces the fitness of their host if there is no selection for plasmid-encoded genes. It has been hypothesized that the translational demand imposed by plasmid-encoded genes is a major mechanism driving the fitness cost of plasmids. Plasmid-encoded genes typically present a different codon usage from host chromosomal genes. As a consequence, the translation of plasmid-encoded genes might sequestrate ribosomes on plasmid transcripts, overwhelming the translation machinery of the cell. However, the pervasiveness and origins of the translation-derived costs of plasmids are yet to be assessed. Here, we systematically altered translation efficiency in the host cell to disentangle the fitness effects produced by six natural antibiotic resistance plasmids. We show that limiting translation efficiency either by reducing the number of available ribosomes or their processivity does not increase plasmid costs. Overall, our results suggest that ribosomal paucity is not a major contributor to plasmid fitness costs. This article is part of the theme issue ‘The secret lives of microbial mobile genetic elements’.

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Herbicide selection promotes antibiotic resistance in soil microbiomes

Molecular Biology and Evolution ◽

10.1093/molbev/msab029 ◽

2021 ◽

Author(s):

Hanpeng Liao ◽

Xi Li ◽

Qiue Yang ◽

Yudan Bai ◽

Peng Cui ◽

...

Keyword(s):

Antibiotic Resistance ◽

Resistance Genes ◽

Agricultural Soils ◽

Soil Microbial Communities ◽

Antibiotic Resistance Genes ◽

Cell Membrane Permeability ◽

Herbicide Application ◽

Soil Microbial ◽

Resistance Plasmids ◽

Selection For

Abstract Herbicides are one of the most widely used chemicals in agriculture. While they are known to be harmful to non-target organisms, the effects of herbicides on the composition and functioning of soil microbial communities remain unclear. Here we show that application of three widely used herbicides—glyphosate, glufosinate and dicamba—increase the prevalence of antibiotic resistance genes (ARGs) and mobile genetic elements (MGEs) in soil microbiomes without clear changes in the abundance, diversity and composition of bacterial communities. Mechanistically, these results could be explained by a positive selection for more tolerant genotypes that acquired several mutations in previously well-characterized herbicide and antibiotic resistance genes. Moreover, herbicide exposure increased cell membrane permeability and conjugation frequency of multidrug resistance plasmids, promoting ARG movement between bacteria. A similar pattern was found in agricultural soils across eleven provinces in China, where herbicide application, and the levels of glyphosate residues in soils, were associated with increased ARG and MGE abundances relative to herbicide-free control sites. Together, our results show that herbicide application can enrich ARGs and MGEs by changing the genetic composition of soil microbiomes, potentially contributing to the global antimicrobial resistance problem in agricultural environments.

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Mutation supply and the repeatability of selection for antibiotic resistance

10.1101/114322 ◽

2017 ◽

Author(s):

Thomas van Dijk ◽

Sungmin Hwang ◽

Joachim Krug ◽

J. Arjan G.M. de Visser ◽

Mark P. Zwart

Keyword(s):

Antibiotic Resistance ◽

Evolutionary Biology ◽

Selective Pressure ◽

Antibiotic Resistance Gene ◽

Driver Mutations ◽

Necessary Condition ◽

Beneficial Mutation ◽

Fitness Effects ◽

Selection For ◽

Simple Stochastic Model

AbstractWhether evolution can be predicted is a key question in evolutionary biology. Here we set out to better understand the repeatability of evolution, which is a necessary condition for predictability. We explored experimentally the effect of mutation supply and the strength of selective pressure on the repeatability of selection from standing genetic variation. Different sizes of mutant libraries of an antibiotic resistance gene, TEM-1 β-lactamase in Escherichia coli, were subjected to different antibiotic concentrations. We determined whether populations went extinct or survived, and sequenced the TEM gene of the surviving populations. The distribution of mutations per allele in our mutant libraries—generated by error-prone PCR—followed a Poisson distribution. Extinction patterns could be explained by a simple stochastic model that assumed the sampling of beneficial mutations was key for survival. In most surviving populations, alleles containing at least one known large-effect beneficial mutation were present. These genotype data also support a model which only invokes sampling effects to describe the occurrence of alleles containing large-effect driver mutations. Hence, evolution is largely predictable given cursory knowledge of mutational fitness effects, the mutation rate and population size. There were no clear trends in the repeatability of selected mutants when we considered all mutations present. However, when only known large-effect mutations were considered, the outcome of selection is less repeatable for large libraries, in contrast to expectations. Furthermore, we show experimentally that alleles carrying multiple mutations selected from large libraries confer higher resistance levels relative to alleles with only a known large-effect mutation, suggesting that the scarcity of high-resistance alleles carrying multiple mutations may contribute to the decrease in repeatability at large library sizes.

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Deep sequencing analysis of CRISPR-escaping plasmid transconjugants inEnterococcus faecalis

10.1101/220467 ◽

2017 ◽

Author(s):

Wenwen Huo ◽

Valerie J. Price ◽

Ardalan Sharifi ◽

Michael Q. Zhang ◽

Kelli L. Palmer

Keyword(s):

Antibiotic Resistance ◽

Enterococcus Faecalis ◽

Deep Sequencing ◽

Serial Passage ◽

Sequencing Analysis ◽

Gram Positive ◽

Antibiotic Selection ◽

Resistance Plasmids ◽

Selection For ◽

Over Time

AbstractEnterococcus faecalisis a Gram-positive bacterium that natively colonizes the human gastrointestinal tract and opportunistically causes life-threatening infections. Multidrug-resistant (MDR)E. faecalisstrains have emerged that are replete with mobile genetic elements (MGEs). SomeE. faecalisstrains possesses CRISPR-Cas systems, which reduce the conjugation frequency of pheromone-responsive plasmids. However, many transconjugants still arise, and we have demonstrated in previous studies thatE. faecaliscan transiently maintain both a functional CRISPR-Cas system and a CRISPR-Cas target. In this study, we used serial passage and deep sequencing to analyze CRISPR array dynamics over time in transconjugants which possess both a functional CRISPR-Cas system and a CRISPR-Cas target. In the presence of antibiotic selection for the plasmid, we found that plasmids ultimately escape CRISPR defense via the emergence of compromised CRISPR-Cas defense in host populations. As a consequence, these populations have enhanced abilities to acquire a second antibiotic resistance plasmid. In the absence of antibiotic selection, plasmids are lost from wild-type but not Δcas9host populations over time. We conclude that the adaptive immune system ofE. faecalisbecomes compromised under antibiotic selection for MGEs, generating populations with enhanced abilities to undergo horizontal gene transfer.ImportanceEnterococcus faecalisis a leading cause of hospital-acquired infections and known disseminator of drug resistance among Gram-positive bacteria. One of the main means of antibiotic resistance dissemination amongE. faecalispopulations is mediated by plasmids. We have previously shown that strains with an active CRISPR-Cas system can reduce plasmid acquisition and thus limit the transmission of antibiotic resistance determinants. In this study, we observed subpopulations with transient co-existence of active CRISPR-Cas and a plasmid target. Through serial passage and targeted sequencing analysis on these populations, we demonstrate that antibiotic treatment plays a key role in shaping theE. faecalisgenome, resulting in compromised genome defense that facilitates acquisition of other resistance plasmids. These results are significant because they show how antibiotic selection for a plasmid can alter the evolutionary trajectory ofE. faecalispopulations rendering them vulnerable to the acceptance of multiple resistance plasmids.

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Faculty Opinions recommendation of The rate of horizontal transmission of antibiotic resistance plasmids is increased in food preservation-stressed bacteria.

Faculty Opinions – Post-Publication Peer Review of the Biomedical Literature ◽

10.3410/f.1102325.558361 ◽

2008 ◽

Author(s):

Samuel Kariuki

Keyword(s):

Antibiotic Resistance ◽

Horizontal Transmission ◽

Food Preservation ◽

Resistance Plasmids

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Exogenous Isolation of Antibiotic Resistance Plasmids from Piggery Manure Slurries Reveals a High Prevalence and Diversity of IncQ-Like Plasmids

Applied and Environmental Microbiology ◽

10.1128/aem.66.11.4854-4862.2000 ◽

2000 ◽

Vol 66 (11) ◽

pp. 4854-4862 ◽

Cited By ~ 147

Author(s):

Kornelia Smalla ◽

Holger Heuer ◽

Antje Götz ◽

Dagmar Niemeyer ◽

Ellen Krögerrecklenfort ◽

...

Keyword(s):

Antibiotic Resistance ◽

Ralstonia Eutropha ◽

Blot Hybridization ◽

Restriction Pattern ◽

Pcr Analysis ◽

Dot Blot ◽

High Prevalence ◽

Resistance Plasmids ◽

Incq Plasmids ◽

K 12

ABSTRACT Antibiotic resistance plasmids were exogenously isolated in biparental matings with piggery manure bacteria as plasmid donors inEscherichia coli CV601 and Pseudomonas putidaUWC1 recipients. Surprisingly, IncQ-like plasmids were detected by dot blot hybridization with an IncQ oriV probe in severalP. putida UWC1 transconjugants. The capture of IncQ-like plasmids in biparental matings indicates not only their high prevalence in manure slurries but also the presence of efficiently mobilizing plasmids. In order to elucidate unusual hybridization data (weak or no hybridization with IncQ repB or IncQ oriTprobes) four IncQ-like plasmids (pIE1107, pIE1115, pIE1120, and pIE1130), each representing a different EcoRV restriction pattern, were selected for a more thorough plasmid characterization after transfer into E. coli K-12 strain DH5α by transformation. The characterization of the IncQ-like plasmids revealed an astonishingly high diversity with regard to phenotypic and genotypic properties. Four different multiple antibiotic resistance patterns were found to be conferred by the IncQ-like plasmids. The plasmids could be mobilized by the RP4 derivative pTH10 into Acinetobactersp., Ralstonia eutropha, Agrobacterium tumefaciens, and P. putida, but they showed diverse patterns of stability under nonselective growth conditions in different host backgrounds. Incompatibility testing and PCR analysis clearly revealed at least two different types of IncQ-like plasmids. PCR amplification of total DNA extracted directly from different manure samples and other environments indicated the prevalence of both types of IncQ plasmids in manure, sewage, and farm soil. These findings suggest that IncQ plasmids play an important role in disseminating antibiotic resistance genes.

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Specific phenotypic, genomic, and fitness evolutionary trajectories toward streptomycin resistance induced by pesticide co-stressors in Escherichia coli

ISME Communications ◽

10.1038/s43705-021-00041-z ◽

2021 ◽

Vol 1 (1) ◽

Author(s):

Yue Xing ◽

Xiaoxi Kang ◽

Siwei Zhang ◽

Yujie Men

Keyword(s):

Escherichia Coli ◽

Antibiotic Resistance ◽

Selective Pressure ◽

Fold Increase ◽

Streptomycin Resistance ◽

Evolutionary Stage ◽

Fitness Costs ◽

Evolutionary Trajectories ◽

K 12 ◽

Late Stages

AbstractTo explore how co-occurring non-antibiotic environmental stressors affect evolutionary trajectories toward antibiotic resistance, we exposed susceptible Escherichia coli K-12 populations to environmentally relevant levels of pesticides and streptomycin for 500 generations. The coexposure substantially changed the phenotypic, genotypic, and fitness evolutionary trajectories, resulting in much stronger streptomycin resistance (>15-fold increase) of the populations. Antibiotic target modification mutations in rpsL and rsmG, which emerged and dominated at late stages of evolution, conferred the strong resistance even with less than 1% abundance, while the off-target mutations in nuoG, nuoL, glnE, and yaiW dominated at early stages only led to mild resistance (2.5–6-fold increase). Moreover, the strongly resistant mutants exhibited lower fitness costs even without the selective pressure and had lower minimal selection concentrations than the mildly resistant ones. Removal of the selective pressure did not reverse the strong resistance of coexposed populations at a later evolutionary stage. The findings suggest higher risks of the selection and propagation of strong antibiotic resistance in environments potentially impacted by antibiotics and pesticides.

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