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Michael R Gillings - One of the best experts on this subject based on the ideXlab platform.
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Bats as reservoirs of antibiotic resistance determinants: A survey of class 1 integrons in Grey-headed Flying Foxes (Pteropus poliocephalus).
Infection Genetics and Evolution, 2019Co-Authors: Fiona Mcdougall, Michael R Gillings, Wayne Boardman, Michelle L. PowerAbstract:Abstract Increasing reports of antimicrobial resistance in wildlife highlight the significance of a One Health approach to managing resistance. We investigated the prevalence and diversity of class 1 integrons, a Genetic determinant of resistance, in grey-headed flying foxes, a large fruit bat species belonging to the order Chiroptera. Class 1 integrons were detected in both wild flying foxes (5.3%) and captive flying foxes (41.2%) housed in wildlife rehabilitation facilities. Genes encoding resistance to aminoglycosides, trimethoprim and beta-lactams, and Qac efflux pumps were detected. Analysis of conserved integron elements and Gene Cassette arrays indicate the direction of integron transfer is from humans to flying foxes. The detection of two novel Gene Cassette arrays (5′CS-qacH-aacA34-blaOXA-21-3′CS and 5′CS-qacF-3′CS strongly suggests acquisition of Genes from the environmental resistome into class 1 integrons within the flying fox microbiota. The dynamics of class 1 integrons in flying foxes indicates bats have a role in the emergence of novel antibiotic resistance determinants.
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Impact of Wastewater Treatment on the Prevalence of Integrons and the Genetic Diversity of Integron Gene Cassettes.
Applied and environmental microbiology, 2018Co-Authors: Qing-lin Chen, Dong Zhu, Yong-guan Zhu, Michael R GillingsAbstract:ABSTRACT The integron platform allows the acquisition, expression, and dissemination of antibiotic resistance Genes within Gene Cassettes. Wastewater treatment plants (WWTPs) contain abundant resistance Genes; however, knowledge about the impacts of wastewater treatment on integrons and their Gene Cassettes is limited. In this study, by using clone library analysis and high-throughput sequencing, we investigated the abundance of class 1, 2, and 3 integrons and their corresponding Gene Cassettes in three urban WWTPs. Our results showed that class 1 integrons were most abundant in WWTPs and that wastewater treatment significantly reduced the abundance of all integrons. The WWTP influents harbored the highest diversity of class 1 integron Gene Cassettes, whereas class 3 integron Gene Cassettes exhibited highest diversity in activated sludge. Most of the Gene Cassette arrays detected in class 1 integrons were novel. Aminoglycoside, beta-lactam, and trimethoprim resistance Genes were highly prevalent in class 1 integron Gene Cassettes, while class 3 integrons mainly carried beta-lactam resistance Gene Cassettes. A core class 1 integron resistance Gene Cassette pool persisted during wastewater treatment, implying that these resistance Genes could have high potential to spread into environments through WWTPs. These data provide new insights into the impact of wastewater treatment on integron pools and highlight the need for surveillance of resistance Genes within both class 1 and 3 integrons. IMPORTANCE Wastewater treatment plants represent a significant sink and transport medium for antibiotic resistance bacteria and Genes spreading into environments. Integrons are important Genetic elements involved in the evolution of antibiotic resistance. To better understand the impact of wastewater treatment on integrons and their Gene Cassette contexts, we conducted clone library construction and high-throughput sequencing to analyze Gene Cassette contexts for class 1 and class 3 integrons during the wastewater treatment process. This study comprehensively profiled the distribution of integrons and their Gene Cassettes (especially class 3 integrons) in influents, activated sludge, and effluents of conventional municipal wastewater treatment plants. We further demonstrated that while wastewater treatment significantly reduced the abundance of integrons and the diversity of associated Gene Cassettes, a large fraction of integrons persisted in wastewater effluents and were consequentially discharged into downstream natural environments.
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Recovery and evolutionary analysis of complete integron Gene Cassette arrays from Vibrio
BMC Evolutionary Biology, 2006Co-Authors: Yan Boucher, Camilla L Nesbø, Michael J Joss, Andrew Robinson, Bridget C Mabbutt, Michael R Gillings, W Ford Doolittle, H. W. StokesAbstract:Background Integrons are Genetic elements capable of the acquisition, rearrangement and expression of Genes contained in Gene Cassettes. Gene Cassettes Generally consist of a promoterless Gene associated with a recombination site known as a 59-base element (59-be). Multiple insertion events can lead to the assembly of large integron-associated Cassette arrays. The most striking examples are found in Vibrio , where such Cassette arrays are widespread and can range from 30 kb to 150 kb. Besides those found in completely sequenced genomes, no such array has yet been recovered in its entirety. We describe an approach to systematically isolate, sequence and annotate large integron Gene Cassette arrays from bacterial strains. Results The complete Vibrio sp . DAT722 integron Cassette array was determined through the streamlined approach described here. To place it in an evolutionary context, we compare the DAT722 array to known vibrio arrays and performed phyloGenetic analyses for all of its components (integrase, 59-be sites, Gene Cassette encoded Genes). It differs extensively in terms of genomic context as well as Gene Cassette content and organization. The phyloGenetic tree of the 59-be sites collectively found in the Vibrio Gene Cassette pool suggests frequent transfer of Cassettes within and between Vibrio species, with slower transfer rates between more phyloGenetically distant relatives. We also identify multiple cases where non-integron chromosomal Genes seem to have been assembled into Gene Cassettes and others where Cassettes have been inserted into chromosomal locations outside integrons. Conclusion Our systematic approach greatly facilitates the isolation and annotation of large integrons Gene Cassette arrays. Comparative analysis of the Vibrio sp . DAT722 integron obtained through this approach to those found in other vibrios confirms the role of this Genetic element in promoting lateral Gene transfer and suggests a high rate of Gene gain/loss relative to most other loci on vibrio chromosomes. We identify a relationship between the phyloGenetic distance separating two species and the rate at which they exchange Gene Cassettes, interactions between the non-mobile portion of bacterial genomes and the vibrio Gene Cassette pool as well as intragenomic translocation events of integrons in vibrios.
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Recovery and evolutionary analysis of complete integron Gene Cassette arrays from Vibrio
BMC evolutionary biology, 2006Co-Authors: Yan Boucher, Camilla L Nesbø, Michael J Joss, Andrew Robinson, Bridget C Mabbutt, Michael R Gillings, W Ford Doolittle, H. W. StokesAbstract:Integrons are Genetic elements capable of the acquisition, rearrangement and expression of Genes contained in Gene Cassettes. Gene Cassettes Generally consist of a promoterless Gene associated with a recombination site known as a 59-base element (59-be). Multiple insertion events can lead to the assembly of large integron-associated Cassette arrays. The most striking examples are found in Vibrio, where such Cassette arrays are widespread and can range from 30 kb to 150 kb. Besides those found in completely sequenced genomes, no such array has yet been recovered in its entirety. We describe an approach to systematically isolate, sequence and annotate large integron Gene Cassette arrays from bacterial strains. The complete Vibrio sp. DAT722 integron Cassette array was determined through the streamlined approach described here. To place it in an evolutionary context, we compare the DAT722 array to known vibrio arrays and performed phyloGenetic analyses for all of its components (integrase, 59-be sites, Gene Cassette encoded Genes). It differs extensively in terms of genomic context as well as Gene Cassette content and organization. The phyloGenetic tree of the 59-be sites collectively found in the Vibrio Gene Cassette pool suggests frequent transfer of Cassettes within and between Vibrio species, with slower transfer rates between more phyloGenetically distant relatives. We also identify multiple cases where non-integron chromosomal Genes seem to have been assembled into Gene Cassettes and others where Cassettes have been inserted into chromosomal locations outside integrons. Our systematic approach greatly facilitates the isolation and annotation of large integrons Gene Cassette arrays. Comparative analysis of the Vibrio sp. DAT722 integron obtained through this approach to those found in other vibrios confirms the role of this Genetic element in promoting lateral Gene transfer and suggests a high rate of Gene gain/loss relative to most other loci on vibrio chromosomes. We identify a relationship between the phyloGenetic distance separating two species and the rate at which they exchange Gene Cassettes, interactions between the non-mobile portion of bacterial genomes and the vibrio Gene Cassette pool as well as intragenomic translocation events of integrons in vibrios.
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The Gene Cassette metagenome is a basic resource for bacterial genome evolution.
Environmental microbiology, 2003Co-Authors: Andrew J. Holmes, Bridget C Mabbutt, Michael R Gillings, Blair S Nield, K. M. Helena Nevalainen, Harold W. StokesAbstract:Summary Lateral Gene transfer has been proposed as a fundamental process underlying bacterial diversity. Transposons, plasmids and phage are widespread and have been shown to significantly contribute to lateral Gene transfer. However, the processes by which disparate Genes are assembled and integrated into the host regulatory network to yield new phenotypes are poorly known. Recent discoveries about the integron/Gene Cassette system indicate it has the potential to play a role in this process. Gene Cassettes are small mobile elements typically consisting of a promoterless orf and a recombination site. Integrons are capable of acquisition and re-arrangement of Gene Cassettes and of the expression of their associated Genes. The potential of the integron/Gene Cassette system is thus largely determined by the diversity contained within the Cassette pool and the rate at which integrons sample this pool. We show here using a polymerase chain reaction (PCR) approach by which the environmental Gene Cassette (EGC) metagenome can be directly sampled that this metagenome contains both protein-coding and non-protein coding Genes. Environmental Gene Cassette-associated recombination sites showed greater diversity than previously seen in integron arrays. Class 1 integrons were shown to be capable of accessing this Gene pool through tests of recombinational activity with a representative range of EGCs. We propose that Gene Cassettes represent a vast, prepackaged Genetic resource that could be thought of as a metagenomic template for bacterial evolution.
Francoisxavier Weill - One of the best experts on this subject based on the ideXlab platform.
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Variant Salmonella genomic island 1-L antibiotic resistance Gene cluster in Salmonella enterica serovar Newport
Antimicrobial Agents and Chemotherapy, 2006Co-Authors: Axel Cloeckaert, Benoit Doublet, Karine Praud, Marie Demartin, Francoisxavier WeillAbstract:We report a new Salmonella genomic island 1 variant antibiotic resistance Gene cluster called SGI1-L in a Salmonella enterica serovar Newport isolate containing a dfrA15 Gene Cassette conferring resistance to trimethoprim. The isolate carried another class 1 integron containing the aacC5 and aadA7 Gene Cassettes conferring resistance to gentamicin and streptomycin/spectinomycin, respectively
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variant salmonella genomic island 1 antibiotic resistance Gene cluster containing a novel 3 n aminoglycoside acetyltransferase Gene Cassette aac 3 id in salmonella enterica serovar newport
Antimicrobial Agents and Chemotherapy, 2004Co-Authors: Benoit Doublet, Francoisxavier Weill, Laetitia Fabre, Elisabeth Chaslusdancla, Axel CloeckaertAbstract:Salmonella genomic island 1 (SGI1) harbors an antibiotic resistance Gene cluster and was previously identified in the multidrug-resistant Salmonella enterica serovars Typhimurium DT104, Agona, Paratyphi B, and Albany. This antibiotic resistance Gene cluster is a complex class 1 integron and most often confers resistance to ampicillin (Ap), chloramphenicol (Cm)/florfenicol (Ff), streptomycin (Sm)/spectinomycin (Sp), sulfonamides (Su), and tetracycline (Tc) (ApCmFfSmSpSuTc profile). Recently, variant SGI1 antibiotic resistance Gene clusters conferring different antibiotic resistance profiles have been identified in several S. enterica serovars and were classified as SGI1-A to -G. We identified a new variant SGI1 antibiotic resistance Gene cluster in two multidrug-resistant S. enterica serovar Newport strains isolated from humans in France. In these strains, the Sm/Sp resistance Gene Cassette aadA2 inserted at the first attI1 site was replaced by two other aminoglycoside resistance Gene Cassettes. The first one contains a new resistance Gene encoding an AAC(3)-I aminoglycoside 3-N-acetyltransferase that confers resistance to gentamicin (Gm) and sisomicin (Sc). This Gene has been named aac(3)-Id. The second one harbors the Sm/Sp resistance Gene aadA7. This Gene Cassette replacement in the SGI1 complex integron of serovar Newport strains constitutes a new variant SGI1 antibiotic resistance Gene cluster named SGI1-H. The occurrence of SGI1 in different S. enterica serovars, now including serovar Newport, strengthens the hypothesis of horizontal transfer of SGI1.
Axel Cloeckaert - One of the best experts on this subject based on the ideXlab platform.
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Variant Salmonella genomic island 1-L antibiotic resistance Gene cluster in Salmonella enterica serovar Newport
Antimicrobial Agents and Chemotherapy, 2006Co-Authors: Axel Cloeckaert, Benoit Doublet, Karine Praud, Marie Demartin, Francoisxavier WeillAbstract:We report a new Salmonella genomic island 1 variant antibiotic resistance Gene cluster called SGI1-L in a Salmonella enterica serovar Newport isolate containing a dfrA15 Gene Cassette conferring resistance to trimethoprim. The isolate carried another class 1 integron containing the aacC5 and aadA7 Gene Cassettes conferring resistance to gentamicin and streptomycin/spectinomycin, respectively
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variant salmonella genomic island 1 antibiotic resistance Gene cluster containing a novel 3 n aminoglycoside acetyltransferase Gene Cassette aac 3 id in salmonella enterica serovar newport
Antimicrobial Agents and Chemotherapy, 2004Co-Authors: Benoit Doublet, Francoisxavier Weill, Laetitia Fabre, Elisabeth Chaslusdancla, Axel CloeckaertAbstract:Salmonella genomic island 1 (SGI1) harbors an antibiotic resistance Gene cluster and was previously identified in the multidrug-resistant Salmonella enterica serovars Typhimurium DT104, Agona, Paratyphi B, and Albany. This antibiotic resistance Gene cluster is a complex class 1 integron and most often confers resistance to ampicillin (Ap), chloramphenicol (Cm)/florfenicol (Ff), streptomycin (Sm)/spectinomycin (Sp), sulfonamides (Su), and tetracycline (Tc) (ApCmFfSmSpSuTc profile). Recently, variant SGI1 antibiotic resistance Gene clusters conferring different antibiotic resistance profiles have been identified in several S. enterica serovars and were classified as SGI1-A to -G. We identified a new variant SGI1 antibiotic resistance Gene cluster in two multidrug-resistant S. enterica serovar Newport strains isolated from humans in France. In these strains, the Sm/Sp resistance Gene Cassette aadA2 inserted at the first attI1 site was replaced by two other aminoglycoside resistance Gene Cassettes. The first one contains a new resistance Gene encoding an AAC(3)-I aminoglycoside 3-N-acetyltransferase that confers resistance to gentamicin (Gm) and sisomicin (Sc). This Gene has been named aac(3)-Id. The second one harbors the Sm/Sp resistance Gene aadA7. This Gene Cassette replacement in the SGI1 complex integron of serovar Newport strains constitutes a new variant SGI1 antibiotic resistance Gene cluster named SGI1-H. The occurrence of SGI1 in different S. enterica serovars, now including serovar Newport, strengthens the hypothesis of horizontal transfer of SGI1.
Tialynn Ashman - One of the best experts on this subject based on the ideXlab platform.
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repeated translocation of a Gene Cassette drives sex chromosome turnover in strawberries
PLOS Biology, 2018Co-Authors: Jacob A Tennessen, Shannon C K Straub, Rajanikanth Govindarajulu, Aaron Liston, Tialynn AshmanAbstract:Turnovers of sex-determining systems represent important diversifying forces across eukaryotes. Shifts in sex chromosomes—but conservation of the master sex-determining Genes—characterize distantly related animal lineages. Yet in plants, in which separate sexes have evolved repeatedly and sex chromosomes are typically homomorphic, we do not know whether such translocations drive sex-chromosome turnovers within closely related taxonomic groups. This phenomenon can only be demonstrated by identifying sex-associated nucleotide sequences, still largely unknown in plants. The wild North American octoploid strawberries (Fragaria) exhibit separate sexes (dioecy) with homomorphic, female heterogametic (ZW) inheritance, yet sex maps to three different chromosomes in different taxa. To characterize these turnovers, we identified sequences unique to females and assembled their reads into contigs. For most octoploid Fragaria taxa, a short (13 kb) sequence was observed in all females and never in males, implicating it as the sex-determining region (SDR). This female-specific “SDR Cassette” contains both a Gene with a known role in fruit and pollen production and a novel retroGene absent on Z and autosomal chromosomes. PhyloGenetic comparison of SDR Cassettes revealed three clades and a history of repeated translocation. Remarkably, the translocations can be ordered temporally due to the capture of adjacent sequence with each successive move. The accumulation of the “souvenir” sequence—and the resultant expansion of the hemizygous SDR over time—could have been adaptive by locking Genes into linkage with sex. Terminal inverted repeats at the insertion borders suggest a means of movement. To our knowledge, this is the first plant SDR shown to be translocated, and it suggests a new mechanism (“move-lock-grow”) for expansion and diversification of incipient sex chromosomes.
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repeated translocation of a Gene Cassette drives sex chromosome turnover in strawberries
bioRxiv, 2017Co-Authors: Jacob A Tennessen, Shannon C K Straub, Rajanikanth Govindarajulu, Aaron Liston, Tialynn AshmanAbstract:Turnovers of sex-determining systems represent important diversifying forces across eukaryotes. Shifts in sex chromosomes, but conservation of the master sex-determining Genes, characterize distantly-related animal lineages. Yet in plants, where separate sexes have evolved repeatedly and sex chromosomes are typically homomorphic, we do not know whether such translocations drive turnovers within closely related groups. This phenomenon can only be demonstrated by identifying sex-associated nucleotide sequences, still largely unknown in plants. The wild North American octoploid strawberries (Fragaria) exhibit separate sexes (dioecy) with homomorphic, female heterogametic (ZW) inheritance, yet sex maps to at least three different chromosomes. To characterize these turnovers, we sequenced the complete genomes of 60 plants of known sex from five Fragaria taxa. We identified 31-mers unique to females and assembled their reads into contigs. Remarkably, a short (13 kb) sequence is observed in nearly all females and never in male-fertile individuals, implicating it as the sex-determining region (SDR). This female-specific "SDR Cassette" contains both a Gene with a known role in fruit and pollen production and a novel retroGene absent on Z and autosomal chromosomes. Comparing SDR Cassettes across taxa reveals a history of repeated translocation, which can be ordered temporally due to the capture of adjacent sequence with each successive move. The accumulation of these "souvenirs" suggests an adaptive basis for the expanding (up to at least 23 kb) hemizygous region. This is the first plant SDR known to be translocated, and it suggests a new mechanism ("move-lock-grow") for expansion and diversification of incipient sex chromosomes.
Marco Scortichini - One of the best experts on this subject based on the ideXlab platform.
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Integron variability in Xanthomonas arboricola pv. juglandis and Xanthomonas arboricola pv. pruni strains.
Fems Microbiology Letters, 2008Co-Authors: Daniela Barionovi, Marco ScortichiniAbstract:The integron platform and the Gene Cassette arrays of 34 Xanthomonas arboricola pv. juglandis and of 47 Xanthomonas arboricola pv. pruni strains isolated from different geographical areas were screened to check their variability. Genetic variability of the strains was also tested by means of BOX-PCR. For two representative strains of the two pathovars, the integrase Gene intI and part of the flanking Gene ilvD were also cloned and sequenced. Whereas X. a . pv. pruni strains did not show relevant variability, six X. a . pv. juglandis strains isolated in Australia showed some differences in the Gene sequences. The ClustalW algorithm indicated that the majority of the X. a . pv. juglandis strains are closely related to X. a . pv. pruni , whereas the X. a . pv. juglandis strains isolated in Australia were more similar to Xanthomonas hortorum pv. pelargonii . Similarly, the Gene Cassette array pattern of the Australian strains, as well as that of the oldest strain maintained in culture, was different from the other strains. Also, three X. a . pv. pruni strains showed a different Cassette array pattern when compared with the majority of other strains but no relationships with geographical area of isolation or host plant was revealed. This study confirmed that in addition to species, integrons may Generate diversity also within two X. arboricola pathovars.