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16 results for “Integrons”
Off-target integron activity leads to rapid plasmid compensatory evolution in response to antibiotic selection pressure
Integrons are mobile genetic elements that have played an important role in the dissemination of antibiotic resistance. As shown previously (Souque et al, 2021), the integron can generate under stress combinatorial variation in resistance cassette expression by cassette re-shuffling, accelerating the evolution of resistance. However, the flexibility of the integron integrase site recognition motif hints at potential off-target effects of the integrase on the rest of the genome that may have important evolutionary consequences. Here we test this hypothesis by selecting for increased piperacillin resistance populations of <em>P.aeruginosa</em> with a mobile integron containing a hard-to-mobilise beta-lactamase cassette to minimize the potential for adaptive cassette re-shuffling. We found that integron activity can both decrease overall survival rate but also improve the fitness of the surviving populations. Off-target inversions mediated by the integron accelerated plasmid adaptation by disrupting costly conjugative genes otherwise mutated in control populations lacking a functional integrase. Plasmids containing integron-mediated inversions were associated with lower plasmid costs and higher stability than plasmids carrying mutations, albeit at a cost of reduced conjugative ability. These findings highlight the potential for integrons to create structural variation that can drive bacterial evolution, and they provide an interesting example showing how antibiotic pressure can drive the loss of conjugative genes.
Data for: Identification of integrons and gene cassette-associated recombination sites in bacteriophage genomes
<p>Bacteriophages are versatile mobile genetic elements that play key roles in driving the evolution of their bacterial hosts through horizontal gene transfer. Phages co-evolve with their bacterial hosts and have plastic genomes with extensive mosaicism. In this study, we present bioinformatic and experimental evidence that temperate and virulent (lytic) phages carry integrons, including integron-integrase genes, attC/attI recombination sites and gene cassettes. Integrons are normally found in Bacteria, where they capture, express and re-arrange mobile gene cassettes via integron-integrase activity. We demonstrate experimentally that a panel of attC sites carried in virulent phage can be recognized by the bacterial class 1 integron-integrase (IntI1) and then integrated into the paradigmatic attI1 recombination site using an attC x attI recombination assay. With an increasing number of phage genomes projected to become available, more phage-associated integrons and their components will likely be identified in the future. The discovery of integron components in bacteriophages establishes a new route for lateral transfer of these elements and their cargo genes between bacterial host cells.</p>
Uncovering bacterial hosts of class 1 integrons in an urban coastal aquatic environment with a single-cell fusion-polymerase chain reaction technology
<p>Horizontal gene transfer (HGT) is a key driver of bacterial evolution via transmission of genetic materials across taxa. Class 1 integrons are genetic elements that correlate strongly with anthropogenic pollution and contribute to the spread of antimicrobial resistance (AMR) genes via HGT. Despite their significance to human health, there is a shortage of robust, culture-free surveillance technologies for identifying uncultivated environmental taxa that harbour class 1 integrons. We developed a modified version of epicPCR (emulsion, paired isolation and concatenation PCR) that links class 1 integrons amplified from single bacterial cells to taxonomic markers from the same cells in emulsified aqueous droplets. Using this single-cell genomic approach and Nanopore sequencing, we successfully assigned class 1 integron gene cassette arrays containing mostly AMR genes to their hosts in coastal water samples that were affected by pollution. Our work presents the first application of epicPCR for targeting variable, multi-gene loci of interest. We also identified the <em>Rhizobacter</em> genus as novel hosts of class 1 integrons. These findings establish epicPCR as a powerful tool for linking taxa to class 1 integrons in environmental bacterial communities and offer the potential to direct mitigation efforts towards hotspots of class 1 integron-mediated dissemination of AMR.</p>
Data from: Dissecting molecular evolution of class 1 integron gene cassettes and their bacterial hosts in suburban creeks via epicPCR
<p>Horizontal gene transfer (HGT) of class 1 integrons plays a key role in the dissemination of antimicrobial resistance (AMR) with clinical consequences worldwide. Class 1 integrons in clinical pathogens are commonly associated with AMR genes and embedded in mobile genetic elements. Over time, these mobile class 1 integrons have spread to diverse environmental bacterial hosts via HGT. We applied a single-cell fusion PCR-based technique to link class 1 integron gene cassette arrays to the phylogenetic markers in their bacterial hosts. Class 1 integrons and associated gene cassettes were detected in <em>Alpha</em>- and <em>Gammaproteobacteria </em>hosts from freshwater samples from two creeks in suburban Sydney. Molecular and bioinformatic characterisations of altered gene cassettes generated new insights into mechanisms that contribute to the evolution of class 1 integron gene cassettes. Here, we present experimental and bioinformatic evidence for key signatures of molecular evolution of gene cassettes, including the gain of a regulatory 5'-untranslated region (5'-UTR), the loss of <em>attC </em>recombination sites between adjacent gene cassettes, and the invasion of a 5'-UTR by an insertion sequence (IS) element. Notably, our experimental testing of a new variant of the aminoglycoside adenylyltransferase encoding <em>aadA11 </em>gene cassette demonstrated that the gain of 5'-UTR contributed to a 3-fold increase in the minimum inhibitory concentration of streptomycin relative to the ancestral reference gene cassette. Understanding these signatures of molecular evolution allows us to explain their effects on AMR phenotypes and offers the potential to better predict evolutionary trajectories of class 1 integrons.</p>
Data from: Dissecting molecular evolution of class 1 integron gene cassettes and identifying their bacterial hosts in suburban creeks via epicPCR
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Uncovering bacterial hosts of class 1 integrons in an urban coastal aquatic environment with a single-cell fusion-polymerase chain reaction technology
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Data from: Vegetable phylloplane microbiomes harbour class 1 integrons in novel bacterial hosts and drive the spread of chlorite resistance
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Off-target integron activity leads to rapid plasmid compensatory evolution in response to antibiotic selection pressure
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Data for: Identification of integrons and gene cassette-associated recombination sites in bacteriophage genomes
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Integron array MICs and cassettes transcription data
<p>Mobile integrons are widespread genetic platforms that allow bacteria to modulate the expression of antibiotic resistance cassettes by shuffling their position from a common promoter. Antibiotic stress induces the expression of an integrase that excises and integrates cassettes, and this unique recombination and expression system is thought to allow bacteria to 'evolve on demand' in response to antibiotic pressure. To test this hypothesis, we inserted a custom three cassette integron into <em>P. aeruginosa</em>, and used experimental evolution to measure the impact of integrase activity on adaptation to gentamicin. Crucially, integrase activity accelerated evolution by increasing the expression of a gentamicin resistance cassette through duplications and by eliminating redundant cassettes. Importantly, we found no evidence of deleterious off-target effects of integrase activity. Our results show that integrons accelerate resistance evolution by rapidly generating combinatorial variation in cassette composition while maintaining genomic integrity, and they highlight the importance of semi-conservative cassette excision for integron dynamics.</p>
Integron array MICs and cassettes transcription data
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Copy Number of an Integron-Encoded Antibiotic Resistance Locus Regulates a Virulence and Opacity Switch in Acinetobacter baumannii AB5075
GEO Series GSE156206. Acinetobacter baumannii. 6 samples. Type: Expression profiling by high throughput sequencing.
INterest of the Negative Predictive Value of Integrons in Choosing a Narrow-spectrum Empirical anTibiotic Treatment vs Usual Empirical Antibiotic Treatment for Urinary Tract infectionS in the PEDiatri
ClinicalTrials.gov study NCT05066854. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Prevalence of Digestive Carriage of Integrons
ClinicalTrials.gov study NCT01985217. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Dynamic of the Acquisition of Antibiotic Resistance in Integrons in Neonatology Newborns
ClinicalTrials.gov study NCT02434679. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Chromosomal integrons are genetically and functionally isolated units of genomes
GEO Series GSE247496. Vibrio cholerae. 12 samples. Type: Expression profiling by high throughput sequencing.
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