The Integron: Adaptation On Demand

Escudero, José Antonio; Loot, Céline; Nivina, Aleksandra; Mazel, Didier

doi:10.1128/microbiolspec.mdna3-0019-2014

Cited by 128 publications

(163 citation statements)

References 138 publications

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“…It is possible that the prevalence of small CDSs in cassettes reflects constraints during cassette genesis. The process of de novo cassette formation is largely unknown, and the proposed hypotheses have many incongruities (discussed in reference 7). Thus, we can only speculate on the underlying processes and related constraints.…”

Section: Discussionmentioning

confidence: 99%

Differences in Integron Cassette Excision Dynamics Shape a Trade-Off between Evolvability and Genetic Capacitance

Loot

Nivina

Cury

et al. 2017

mBio

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Integrons ensure a rapid and “on demand” response to environmental stresses driving bacterial adaptation. They are able to capture, store, and reorder functional gene cassettes due to site-specific recombination catalyzed by their integrase. Integrons can be either sedentary and chromosomally located or mobile when they are associated with transposons and plasmids. They are respectively called sedentary chromosomal integrons (SCIs) and mobile integrons (MIs). MIs are key players in the dissemination of antibiotic resistance genes. Here, we used in silico and in vivo approaches to study cassette excision dynamics in MIs and SCIs. We show that the orientation of cassette arrays relative to replication influences attC site folding and cassette excision by placing the recombinogenic strands of attC sites on either the leading or lagging strand template. We also demonstrate that stability of attC sites and their propensity to form recombinogenic structures also regulate cassette excision. We observe that cassette excision dynamics driven by these factors differ between MIs and SCIs. Cassettes with high excision rates are more commonly found on MIs, which favors their dissemination relative to SCIs. This is especially true for SCIs carried in the Vibrio genus, where maintenance of large cassette arrays and vertical transmission are crucial to serve as a reservoir of adaptive functions. These results expand the repertoire of known processes regulating integron recombination that were previously established and demonstrate that, in terms of cassette dynamics, a subtle trade-off between evolvability and genetic capacitance has been established in bacteria.

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Section: Discussionmentioning

confidence: 99%

Differences in Integron Cassette Excision Dynamics Shape a Trade-Off between Evolvability and Genetic Capacitance

Loot

Nivina

Cury

et al. 2017

mBio

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“…Mobile genetic elements, including plasmids, IS and integrons, play important roles in rapid lateral spread of antibiotic resistance (Escudero, Loot, Nivina, & Mazel, 2015;Frost, Leplae, Summers, & Toussaint, 2005). A key finding of this microcosm study is that the different patterns of MGEs respond to different Zn level.…”

Section: Impacts Of Zn Exposure On Relative Abundance Of Mges In Soilmentioning

confidence: 94%

Co‐selection for antibiotic resistance genes is induced in a soil amended with zinc

Yang

Yanpeng

Wang

et al. 2019

Soil Use and Management

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The likelihood of co‐selection for antibiotic resistance induced by heavy metals is a potential threat to human health, however, direct evidence of heavy metal‐induced co‐selection of antibiotic resistance is lacking in soil. By using a metagenomic sequencing approach, zinc (Zn) driven co‐selection of antibiotic resistance genes (ARGs) in soil was investigated through a microcosm experiment where Zn salts were added at different levels. The results showed that the abundance and diversity of ARGs had a tendency to increase along the gradient of increasing Zn contents, with the maximum values recorded in the soil amended with 800 mg Zn kg−1. The abundance of mobile genetic elements (MGEs) such as integrons and insertion sequences was significantly increased by Zn exposure. Network analysis demonstrated significant associations between ARGs and MGEs, suggesting that Zn treatment might enhance the potential for horizontal transfer of ARGs. Furthermore, structural equation models revealed that the types of ARGs were primarily driven by variations in bacterial compositions and Zn exposure, followed by integrons. Thus, these results indicate that added Zn salts considerably changed the diversity, abundance and mobility potential of antibiotic resistance, and imply that application of amendments containing high levels of Zn to soil could be causing the emergence and release of ARGs to the environment, and should be carefully monitored.

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“…Sedentary chromosomal integrons encompass hundreds of integron classes and can carry a much larger number of gene cassettes of mostly unknown functions. Some Vibrio species carry hundreds of cassettes within a single integron cassette array (Chen et al, 2003;Escudero et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

High diversity and rapid spatial turnover of integron gene cassettes in soil

Ghaly

Geoghegan

Alroy

et al. 2019

Environmental Microbiology

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Summary Integrons are genetic elements that promote rapid adaptation in bacteria by capturing exogenous, mobile gene cassettes. Recently, a subset of gene cassettes has facilitated the global spread of antibiotic resistance. However, outside clinical settings, very little is known about their diversity and spatial ecology. To address this question, we sequenced integron gene cassettes from soils sampled across Australia and Antarctica. We recovered 44 970 open reading frames that encoded 27 215 unique proteins, representing an order of magnitude more cassettes than previous sequencing efforts. We found that cassettes have extremely high local richness, significantly greater than previously predicted, with estimates ranging from 4000 to 18 000 unique cassettes per 0.3 g of soil. We show that cassettes have a heterogeneous distribution across space, and that they exhibit rapid turnover with distance. Similarity between samples drops to between 0.1% and 10% at distances of as little as 100 m. Together, these data provide key insights into the ecology and size of the gene cassette metagenome.

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The Integron: Adaptation On Demand

Cited by 128 publications

References 138 publications

Differences in Integron Cassette Excision Dynamics Shape a Trade-Off between Evolvability and Genetic Capacitance

Differences in Integron Cassette Excision Dynamics Shape a Trade-Off between Evolvability and Genetic Capacitance

Co‐selection for antibiotic resistance genes is induced in a soil amended with zinc

High diversity and rapid spatial turnover of integron gene cassettes in soil

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