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Goldman M, Zhao C, Pollard KS. Improved detection of microbiome-disease associations via population structure-aware generalized linear mixed effects models (microSLAM). PLoS Comput Biol 2025; 21:e1012277. [PMID: 40424276 DOI: 10.1371/journal.pcbi.1012277] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2024] [Accepted: 05/13/2025] [Indexed: 05/29/2025] Open
Abstract
Microbiome association studies typically link host disease or other traits to summary statistics measured in metagenomics data, such as diversity or taxonomic composition. But identifying disease-associated species based on their relative abundance does not provide insight into why these microbes act as disease markers, and it overlooks cases where disease risk is related to specific strains with unique biological functions. To bridge this knowledge gap, we developed microSLAM, a mixed-effects model and an R package that performs association tests that connect host traits to the presence/absence of genes within each microbiome species, while accounting for strain genetic relatedness across hosts. Traits can be quantitative or binary (such as case/control). MicroSLAM is fit in three steps for each species. The first step estimates population structure across hosts. Step two calculates the association between population structure and the trait, enabling detection of species for which a subset of related strains confer risk. To identify specific genes whose presence/absence across diverse strains is associated with the trait, step three models the trait as a function of gene occurrence plus random effects estimated from step two. Applying microSLAM to 710 gut metagenomes from inflammatory bowel disease (IBD) samples, we discovered 56 species whose population structure correlates with IBD, meaning that different lineages are found in cases versus controls. After controlling for population structure, 20 species had genes significantly associated with IBD. Twenty-one of these genes were more common in IBD patients, while 32 genes were enriched in healthy controls, including a seven-gene operon in Faecalibacterium prausnitzii that is involved in utilization of fructoselysine from the gut environment. The vast majority of species detected by microSLAM were not significantly associated with IBD using standard relative abundance tests. These findings highlight the importance of accounting for within-species genetic variation in microbiome studies.
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Affiliation(s)
- Miriam Goldman
- Department of Epidemiology & Biostatistics, University of California San Francisco, San Francisco, California, United States of America
- Institute of Data Science & Biotechnology, Gladstone Institutes, San Francisco, California, United States of America
| | - Chunyu Zhao
- Institute of Data Science & Biotechnology, Gladstone Institutes, San Francisco, California, United States of America
- Chan Zuckerberg Biohub, Data Science, San Francisco, California, United States of America
| | - Katherine S Pollard
- Department of Epidemiology & Biostatistics, University of California San Francisco, San Francisco, California, United States of America
- Institute of Data Science & Biotechnology, Gladstone Institutes, San Francisco, California, United States of America
- Chan Zuckerberg Biohub, Data Science, San Francisco, California, United States of America
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2
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Blanco P, Trigo da Roza F, Toribio-Celestino L, García-Pastor L, Caselli N, Morón Á, Ojeda F, Darracq B, Vergara E, Amaro F, San Millán Á, Skovgaard O, Mazel D, Loot C, Escudero J. Chromosomal integrons are genetically and functionally isolated units of genomes. Nucleic Acids Res 2024; 52:12565-12581. [PMID: 39385642 PMCID: PMC11551772 DOI: 10.1093/nar/gkae866] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Revised: 09/17/2024] [Accepted: 09/23/2024] [Indexed: 10/12/2024] Open
Abstract
Integrons are genetic elements that increase the evolvability of bacteria by capturing new genes and stockpiling them in arrays. Sedentary chromosomal integrons (SCIs) can be massive and highly stabilized structures encoding hundreds of genes, whose function remains generally unknown. SCIs have co-evolved with the host for aeons and are highly intertwined with their physiology from a mechanistic point of view. But, paradoxically, other aspects, like their variable content and location within the genome, suggest a high genetic and functional independence. In this work, we have explored the connection of SCIs to their host genome using as a model the Superintegron (SI), a 179-cassette long SCI in the genome of Vibrio cholerae N16961. We have relocated and deleted the SI using SeqDelTA, a novel method that allows to counteract the strong stabilization conferred by toxin-antitoxin systems within the array. We have characterized in depth the impact in V. cholerae's physiology, measuring fitness, chromosome replication dynamics, persistence, transcriptomics, phenomics, natural competence, virulence and resistance against protist grazing. The deletion of the SI did not produce detectable effects in any condition, proving that-despite millions of years of co-evolution-SCIs are genetically and functionally isolated units of genomes.
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Affiliation(s)
- Paula Blanco
- Molecular Basis of Adaptation, Departamento de Sanidad Animal, Universidad Complutense de Madrid, Madrid 28040, Spain
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - Filipa Trigo da Roza
- Molecular Basis of Adaptation, Departamento de Sanidad Animal, Universidad Complutense de Madrid, Madrid 28040, Spain
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - Laura Toribio-Celestino
- Departamento de Microbiología Microbiana, Centro Nacional de Biotecnología–CSIC, Madrid 28049, Spain
| | - Lucía García-Pastor
- Molecular Basis of Adaptation, Departamento de Sanidad Animal, Universidad Complutense de Madrid, Madrid 28040, Spain
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - Niccolò Caselli
- Departamento de Química Física, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - Álvaro Morón
- Departamento de Genética, Fisiología y Microbiología, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - Francisco Ojeda
- Molecular Basis of Adaptation, Departamento de Sanidad Animal, Universidad Complutense de Madrid, Madrid 28040, Spain
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - Baptiste Darracq
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, 75015 Paris, France
- Sorbonne Université, ED515, F-75005 Paris, France
| | - Ester Vergara
- Molecular Basis of Adaptation, Departamento de Sanidad Animal, Universidad Complutense de Madrid, Madrid 28040, Spain
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - Francisco Amaro
- Departamento de Genética, Fisiología y Microbiología, Facultad de Ciencias Biológicas, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - Álvaro San Millán
- Departamento de Microbiología Microbiana, Centro Nacional de Biotecnología–CSIC, Madrid 28049, Spain
| | - Ole Skovgaard
- Department of Science and Environment, Roskilde University, 4000 Roskilde, Denmark
| | - Didier Mazel
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, 75015 Paris, France
| | - Céline Loot
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, 75015 Paris, France
| | - José Antonio Escudero
- Molecular Basis of Adaptation, Departamento de Sanidad Animal, Universidad Complutense de Madrid, Madrid 28040, Spain
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Madrid 28040, Spain
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3
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Blanco P, Hipólito A, García-Pastor L, Trigo da Roza F, Toribio-Celestino L, Ortega A, Vergara E, San Millán Á, Escudero J. Identification of promoter activity in gene-less cassettes from Vibrionaceae superintegrons. Nucleic Acids Res 2024; 52:2961-2976. [PMID: 38214222 PMCID: PMC11014356 DOI: 10.1093/nar/gkad1252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Revised: 12/18/2023] [Accepted: 12/26/2023] [Indexed: 01/13/2024] Open
Abstract
Integrons are genetic platforms that acquire new genes encoded in integron cassettes (ICs), building arrays of adaptive functions. ICs generally encode promoterless genes, whose expression relies on the platform-associated Pc promoter, with the cassette array functioning as an operon-like structure regulated by the distance to the Pc. This is relevant in large sedentary chromosomal integrons (SCIs) carrying hundreds of ICs, like those in Vibrio species. We selected 29 gene-less cassettes in four Vibrio SCIs, and explored whether their function could be related to the transcription regulation of adjacent ICs. We show that most gene-less cassettes have promoter activity on the sense strand, enhancing the expression of downstream cassettes. Additionally, we identified the transcription start sites of gene-less ICs through 5'-RACE. Accordingly, we found that most of the superintegron in Vibrio cholerae is not silent. These promoter cassettes can trigger the expression of a silent dfrB9 cassette downstream, increasing trimethoprim resistance >512-fold in V. cholerae and Escherichia coli. Furthermore, one cassette with an antisense promoter can reduce trimethoprim resistance when cloned downstream. Our findings highlight the regulatory role of gene-less cassettes in the expression of adjacent cassettes, emphasizing their significance in SCIs and their clinical importance if captured by mobile integrons.
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Affiliation(s)
- Paula Blanco
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid 28040, Spain
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - Alberto Hipólito
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid 28040, Spain
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - Lucía García-Pastor
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid 28040, Spain
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - Filipa Trigo da Roza
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid 28040, Spain
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - Laura Toribio-Celestino
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid 28049, Spain
| | - Alba Cristina Ortega
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - Ester Vergara
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid 28040, Spain
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Madrid 28040, Spain
| | - Álvaro San Millán
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CNB-CSIC), Madrid 28049, Spain
- Centro de Investigación Biológica en Red de Epidemiología y Salud Pública (CIBERESP), Instituto de Salud Carlos III, Madrid 28222, Spain
| | - José Antonio Escudero
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid 28040, Spain
- VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Madrid 28040, Spain
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Richard E, Darracq B, Littner E, Millot GA, Conte V, Cokelaer T, Engelstädter J, Rocha EPC, Mazel D, Loot C. Belt and braces: Two escape ways to maintain the cassette reservoir of large chromosomal integrons. PLoS Genet 2024; 20:e1011231. [PMID: 38578806 PMCID: PMC11023631 DOI: 10.1371/journal.pgen.1011231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 04/17/2024] [Accepted: 03/19/2024] [Indexed: 04/07/2024] Open
Abstract
Integrons are adaptive devices that capture, stockpile, shuffle and express gene cassettes thereby sampling combinatorial phenotypic diversity. Some integrons called sedentary chromosomal integrons (SCIs) can be massive structures containing hundreds of cassettes. Since most of these cassettes are non-expressed, it is not clear how they remain stable over long evolutionary timescales. Recently, it was found that the experimental inversion of the SCI of Vibrio cholerae led to a dramatic increase of the cassette excision rate associated with a fitness defect. Here, we question the evolutionary sustainability of this apparently counter selected genetic context. Through experimental evolution, we find that the integrase is rapidly inactivated and that the inverted SCI can recover its original orientation by homologous recombination between two insertion sequences (ISs) present in the array. These two outcomes of SCI inversion restore the normal growth and prevent the loss of cassettes, enabling SCIs to retain their roles as reservoirs of functions. These results illustrate a nice interplay between gene orientation, genome rearrangement, bacterial fitness and demonstrate how integrons can benefit from their embedded ISs.
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Affiliation(s)
- Egill Richard
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, Paris, France
- Sorbonne Université, ED515, Paris, France
| | - Baptiste Darracq
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, Paris, France
- Sorbonne Université, ED515, Paris, France
| | - Eloi Littner
- Sorbonne Université, ED515, Paris, France
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, France
- DGA CBRN Defence, Vert-le-Petit, France
| | - Gael A. Millot
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, France
| | - Valentin Conte
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, Paris, France
| | - Thomas Cokelaer
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, France
- Institut Pasteur, Université Paris Cité, Plateforme Technologique Biomics, Paris, France
| | - Jan Engelstädter
- School of the Environment, The University of Queensland, Brisbane, Australia
| | - Eduardo P. C. Rocha
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, France
| | - Didier Mazel
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, Paris, France
| | - Céline Loot
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Unité Plasticité du Génome Bactérien, Paris, France
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5
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Qi Q, Ghaly TM, Rajabal V, Gillings MR, Tetu SG. Dissecting molecular evolution of class 1 integron gene cassettes and identifying their bacterial hosts in suburban creeks via epicPCR. J Antimicrob Chemother 2024; 79:100-111. [PMID: 37962091 DOI: 10.1093/jac/dkad353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 10/30/2023] [Indexed: 11/15/2023] Open
Abstract
OBJECTIVES Our study aimed to sequence class 1 integrons in uncultured environmental bacterial cells in freshwater from suburban creeks and uncover the taxonomy of their bacterial hosts. We also aimed to characterize integron gene cassettes with altered DNA sequences relative to those from databases or literature and identify key signatures of their molecular evolution. METHODS We applied a single-cell fusion PCR-based technique-emulsion, paired isolation and concatenation PCR (epicPCR)-to link class 1 integron gene cassette arrays to the phylogenetic markers of their bacterial hosts. The levels of streptomycin resistance conferred by the WT and altered aadA5 and aadA11 gene cassettes that encode aminoglycoside (3″) adenylyltransferases were experimentally quantified in an Escherichia coli host. RESULTS Class 1 integron gene cassette arrays were detected in Alphaproteobacteria and Gammaproteobacteria hosts. A subset of three gene cassettes displayed signatures of molecular evolution, namely the gain of a regulatory 5'-untranslated region (5'-UTR), the loss of attC recombination sites between adjacent gene cassettes, and the invasion of a 5'-UTR by an IS element. Notably, our experimental testing of a novel variant of the aadA11 gene cassette demonstrated that gaining the observed 5'-UTR contributed to a 3-fold increase in the MIC of streptomycin relative to the ancestral reference gene cassette in E. coli. CONCLUSIONS Dissecting the observed signatures of molecular evolution of class 1 integrons allowed us to explain their effects on antibiotic resistance phenotypes, while identifying their bacterial hosts enabled us to make better inferences on the likely origins of novel gene cassettes and IS that invade known gene cassettes.
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Affiliation(s)
- Qin Qi
- School of Natural Sciences, 14 Eastern Road, Macquarie University, Sydney, NSW, Australia
| | - Timothy M Ghaly
- School of Natural Sciences, 14 Eastern Road, Macquarie University, Sydney, NSW, Australia
| | - Vaheesan Rajabal
- ARC Centre of Excellence for Synthetic Biology, 14 Eastern Road, Macquarie University, Sydney, NSW, Australia
| | - Michael R Gillings
- School of Natural Sciences, 14 Eastern Road, Macquarie University, Sydney, NSW, Australia
- ARC Centre of Excellence for Synthetic Biology, 14 Eastern Road, Macquarie University, Sydney, NSW, Australia
| | - Sasha G Tetu
- School of Natural Sciences, 14 Eastern Road, Macquarie University, Sydney, NSW, Australia
- ARC Centre of Excellence for Synthetic Biology, 14 Eastern Road, Macquarie University, Sydney, NSW, Australia
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Ghaly TM, Rajabal V, Penesyan A, Coleman NV, Paulsen IT, Gillings MR, Tetu SG. Functional enrichment of integrons: Facilitators of antimicrobial resistance and niche adaptation. iScience 2023; 26:108301. [PMID: 38026211 PMCID: PMC10661359 DOI: 10.1016/j.isci.2023.108301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Revised: 10/11/2023] [Accepted: 10/19/2023] [Indexed: 12/01/2023] Open
Abstract
Integrons are genetic elements, found among diverse bacteria and archaea, that capture and rearrange gene cassettes to rapidly generate genetic diversity and drive adaptation. Despite their broad taxonomic and geographic prevalence, and their role in microbial adaptation, the functions of gene cassettes remain poorly characterized. Here, using a combination of bioinformatic and experimental analyses, we examined the functional diversity of gene cassettes from different environments. We find that cassettes encode diverse antimicrobial resistance (AMR) determinants, including those conferring resistance to antibiotics currently in the developmental pipeline. Further, we find a subset of cassette functions is universally enriched relative to their broader metagenomes. These are largely involved in (a)biotic interactions, including AMR, phage defense, virulence, biodegradation, and stress tolerance. The remainder of functions are sample-specific, suggesting that they confer localised functions relevant to their microenvironment. Together, they comprise functional profiles different from bulk metagenomes, representing niche-adaptive components of the prokaryotic pangenome.
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Affiliation(s)
- Timothy M. Ghaly
- School of Natural Sciences, Macquarie University, New South Wales 2109, Australia
| | - Vaheesan Rajabal
- School of Natural Sciences, Macquarie University, New South Wales 2109, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, New South Wales 2109, Australia
| | - Anahit Penesyan
- School of Natural Sciences, Macquarie University, New South Wales 2109, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, New South Wales 2109, Australia
| | - Nicholas V. Coleman
- School of Natural Sciences, Macquarie University, New South Wales 2109, Australia
| | - Ian T. Paulsen
- School of Natural Sciences, Macquarie University, New South Wales 2109, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, New South Wales 2109, Australia
| | - Michael R. Gillings
- School of Natural Sciences, Macquarie University, New South Wales 2109, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, New South Wales 2109, Australia
| | - Sasha G. Tetu
- School of Natural Sciences, Macquarie University, New South Wales 2109, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, New South Wales 2109, Australia
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AL-Muzahmi M, Rizvi M, AL-Quraini M, AL-Muharrmi Z, AL-Jabri Z. Comparative Genomic Analysis Reveals the Emergence of ST-231 and ST-395 Klebsiella pneumoniae Strains Associated with the High Transmissibility of blaKPC Plasmids. Microorganisms 2023; 11:2411. [PMID: 37894068 PMCID: PMC10608898 DOI: 10.3390/microorganisms11102411] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2023] [Revised: 09/21/2023] [Accepted: 09/23/2023] [Indexed: 10/29/2023] Open
Abstract
Conjugative transposons in Gram-negative bacteria have a significant role in the dissemination of antibiotic-resistance-conferring genes between bacteria. This study aims to genomically characterize plasmids and conjugative transposons carrying integrons in clinical isolates of Klebsiella pneumoniae. The genetic composition of conjugative transposons and phenotypic assessment of 50 multidrug-resistant K. pneumoniae isolates from a tertiary-care hospital (SQUH), Muscat, Oman, were investigated. Horizontal transferability was investigated by filter mating conjugation experiments. Whole-genome sequencing (WGS) was performed to determine the sequence type (ST), acquired resistome, and plasmidome of integron-carrying strains. Class 1 integrons were detected in 96% of isolates and, among integron-positive isolates, 18 stains contained variable regions. Horizontal transferability by conjugation confirmed the successful transfer of integrons between cells and WGS confirmed their presence in conjugative plasmids. Dihydrofolate reductase (dfrA14) was the most prevalent (34.8%) gene cassette in class 1 integrons. MLST analysis detected predominantly ST-231 and ST-395. BlaOXA-232 and blaCTX-M-15 were the most frequently detected carbapenemases and beta-lactamases in the sequenced isolates. This study highlighted the high transmissibility of MDR-conferring conjugative plasmids in clinical isolates of K. pneumoniae. Therefore, the wise use of antibiotics and the adherence to effective infection control measures are necessary to limit the further dissemination of multidrug-resistant bacteria.
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Affiliation(s)
| | - Meher Rizvi
- Department of Microbiology and Immunology, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat 123, Oman;
| | - Munawr AL-Quraini
- Microbiology and Immunology Diagnostic Laboratory, Department of Microbiology and Immunology, Sultan Qaboos University Hospital, Muscat 123, Oman; (M.A.-Q.); (Z.A.-M.)
| | - Zakariya AL-Muharrmi
- Microbiology and Immunology Diagnostic Laboratory, Department of Microbiology and Immunology, Sultan Qaboos University Hospital, Muscat 123, Oman; (M.A.-Q.); (Z.A.-M.)
| | - Zaaima AL-Jabri
- Department of Microbiology and Immunology, College of Medicine and Health Sciences, Sultan Qaboos University, Muscat 123, Oman;
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Gheibzadeh MS, Manyumwa CV, Tastan Bishop Ö, Shahbani Zahiri H, Parkkila S, Zolfaghari Emameh R. Genome Study of α-, β-, and γ-Carbonic Anhydrases from the Thermophilic Microbiome of Marine Hydrothermal Vent Ecosystems. BIOLOGY 2023; 12:770. [PMID: 37372055 DOI: 10.3390/biology12060770] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/17/2023] [Accepted: 05/17/2023] [Indexed: 06/29/2023]
Abstract
Carbonic anhydrases (CAs) are metalloenzymes that can help organisms survive in hydrothermal vents by hydrating carbon dioxide (CO2). In this study, we focus on alpha (α), beta (β), and gamma (γ) CAs, which are present in the thermophilic microbiome of marine hydrothermal vents. The coding genes of these enzymes can be transferred between hydrothermal-vent organisms via horizontal gene transfer (HGT), which is an important tool in natural biodiversity. We performed big data mining and bioinformatics studies on α-, β-, and γ-CA coding genes from the thermophilic microbiome of marine hydrothermal vents. The results showed a reasonable association between thermostable α-, β-, and γ-CAs in the microbial population of the hydrothermal vents. This relationship could be due to HGT. We found evidence of HGT of α- and β-CAs between Cycloclasticus sp., a symbiont of Bathymodiolus heckerae, and an endosymbiont of Riftia pachyptila via Integrons. Conversely, HGT of β-CA genes from the endosymbiont Tevnia jerichonana to the endosymbiont Riftia pachyptila was detected. In addition, Hydrogenovibrio crunogenus SP-41 contains a β-CA gene on genomic islands (GIs). This gene can be transferred by HGT to Hydrogenovibrio sp. MA2-6, a methanotrophic endosymbiont of Bathymodiolus azoricus, and a methanotrophic endosymbiont of Bathymodiolus puteoserpentis. The endosymbiont of R. pachyptila has a γ-CA gene in the genome. If α- and β-CA coding genes have been derived from other microorganisms, such as endosymbionts of T. jerichonana and Cycloclasticus sp. as the endosymbiont of B. heckerae, through HGT, the theory of the necessity of thermostable CA enzymes for survival in the extreme ecosystem of hydrothermal vents is suggested and helps the conservation of microbiome natural diversity in hydrothermal vents. These harsh ecosystems, with their integral players, such as HGT and endosymbionts, significantly impact the enrichment of life on Earth and the carbon cycle in the ocean.
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Affiliation(s)
- Mohammad Sadegh Gheibzadeh
- Department of Energy and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran 14965/161, Iran
| | - Colleen Varaidzo Manyumwa
- Research Unit in Bioinformatics (Rubi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa
| | - Özlem Tastan Bishop
- Research Unit in Bioinformatics (Rubi), Department of Biochemistry and Microbiology, Rhodes University, Grahamstown 6140, South Africa
| | - Hossein Shahbani Zahiri
- Department of Energy and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran 14965/161, Iran
| | - Seppo Parkkila
- Faculty of Medicine and Health Technology, Tampere University, 33520 Tampere, Finland
- Fimlab Ltd., Tampere University Hospital, 33520 Tampere, Finland
| | - Reza Zolfaghari Emameh
- Department of Energy and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran 14965/161, Iran
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9
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Krin E, Baharoglu Z, Sismeiro O, Varet H, Coppée JY, Mazel D. Systematic transcriptome analysis allows the identification of new type I and type II Toxin/Antitoxin systems located in the superintegron of Vibrio cholerae. Res Microbiol 2023; 174:103997. [PMID: 36347445 DOI: 10.1016/j.resmic.2022.103997] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/27/2022] [Accepted: 10/28/2022] [Indexed: 11/07/2022]
Abstract
Vibrio cholerae N16961 genome encodes 18 type II Toxin/Antitoxin (TA) systems, all but one located inside gene cassettes of its chromosomal superintegron (SI). This study aims to investigate additional TA systems in this genome. We screened for all two-genes operons of uncharacterized function by analyzing previous RNAseq data. Assays on nine candidates, revealed one additional functional type II TA encoded by the VCA0497-0498 operon, carried inside a SI cassette. We showed that VCA0498 antitoxin alone and in complex with VCA0497 represses its own operon promoter. VCA0497-0498 is the second element of the recently identified dhiT/dhiA superfamily uncharacterized type II TA system. RNAseq analysis revealed that another SI cassette encodes a novel type I TA system: VCA0495 gene and its two associated antisense non-coding RNAs, ncRNA495 and ncRNA496. Silencing of both antisense ncRNAs lead to cell death, demonstrating the type I TA function. Both VCA0497 and VCA0495 toxins do not show any homology to functionally characterized toxins, however our preliminary data suggest that their activity may end up in mRNA degradation, directly or indirectly. Our findings increase the TA systems number carried in this SI to 19, preferentially located in its distal end, confirming their importance in this large cassette array.
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Affiliation(s)
- Evelyne Krin
- Institut Pasteur, Université Paris Cité, CNRS UMR 3525, Unité de Plasticité du Génome Bactérien, 28 rue du Docteur Roux, F-75015 Paris, France.
| | - Zeynep Baharoglu
- Institut Pasteur, Université Paris Cité, CNRS UMR 3525, Unité de Plasticité du Génome Bactérien, 28 rue du Docteur Roux, F-75015 Paris, France.
| | - Odile Sismeiro
- Institut Pasteur, Université Paris Cité, Transcriptome and EpiGenome, Biomics Center for Innovation and Technological Research, 28 rue du Docteur Roux, F-75015 Paris, France.
| | - Hugo Varet
- Institut Pasteur, Université Paris Cité, Transcriptome and EpiGenome, Biomics Center for Innovation and Technological Research, 28 rue du Docteur Roux, F-75015 Paris, France.
| | - Jean-Yves Coppée
- Institut Pasteur, Université Paris Cité, Transcriptome and EpiGenome, Biomics Center for Innovation and Technological Research, 28 rue du Docteur Roux, F-75015 Paris, France.
| | - Didier Mazel
- Institut Pasteur, Université Paris Cité, CNRS UMR 3525, Unité de Plasticité du Génome Bactérien, 28 rue du Docteur Roux, F-75015 Paris, France.
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10
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Ghaly TM, Tetu SG, Penesyan A, Qi Q, Rajabal V, Gillings MR. Discovery of integrons in Archaea: Platforms for cross-domain gene transfer. SCIENCE ADVANCES 2022; 8:eabq6376. [PMID: 36383678 PMCID: PMC9668308 DOI: 10.1126/sciadv.abq6376] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2022] [Accepted: 10/19/2022] [Indexed: 06/16/2023]
Abstract
Horizontal gene transfer between different domains of life is increasingly being recognized as an important evolutionary driver, with the potential to increase the pace of biochemical innovation and environmental adaptation. However, the mechanisms underlying the recruitment of exogenous genes from foreign domains are mostly unknown. Integrons are a family of genetic elements that facilitate this process within Bacteria. However, they have not been reported outside Bacteria, and thus their potential role in cross-domain gene transfer has not been investigated. Here, we discover that integrons are also present in 75 archaeal metagenome-assembled genomes from nine phyla, and are particularly enriched among Asgard archaea. Furthermore, we provide experimental evidence that integrons can facilitate the recruitment of archaeal genes by bacteria. Our findings establish a previously unknown mechanism of cross-domain gene transfer whereby bacteria can incorporate archaeal genes from their surrounding environment via integron activity. These findings have important implications for prokaryotic ecology and evolution.
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Affiliation(s)
- Timothy M. Ghaly
- School of Natural Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Sasha G. Tetu
- School of Natural Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Anahit Penesyan
- School of Natural Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Qin Qi
- School of Natural Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Vaheesan Rajabal
- School of Natural Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Michael R. Gillings
- School of Natural Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, New South Wales 2109, Australia
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11
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Hipólito A, García-Pastor L, Blanco P, Trigo da Roza F, Kieffer N, Vergara E, Jové T, Álvarez J, Escudero J. The expression of aminoglycoside resistance genes in integron cassettes is not controlled by riboswitches. Nucleic Acids Res 2022; 50:8566-8579. [PMID: 35947699 PMCID: PMC9410878 DOI: 10.1093/nar/gkac662] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 07/11/2022] [Accepted: 07/22/2022] [Indexed: 12/24/2022] Open
Abstract
Regulation of gene expression is a key factor influencing the success of antimicrobial resistance determinants. A variety of determinants conferring resistance against aminoglycosides (Ag) are commonly found in clinically relevant bacteria, but whether their expression is regulated or not is controversial. The expression of several Ag resistance genes has been reported to be controlled by a riboswitch mechanism encoded in a conserved sequence. Yet this sequence corresponds to the integration site of an integron, a genetic platform that recruits genes of different functions, making the presence of such a riboswitch counterintuitive. We provide, for the first time, experimental evidence against the existence of such Ag-sensing riboswitch. We first tried to reproduce the induction of the well characterized aacA5 gene using its native genetic environment, but were unsuccessful. We then broadened our approach and analyzed the inducibility of all AgR genes encoded in integrons against a variety of antibiotics. We could not observe biologically relevant induction rates for any gene in the presence of several aminoglycosides. Instead, unrelated antibiotics produced mild but consistently higher increases in expression, that were the result of pleiotropic effects. Our findings rule out the riboswitch control of aminoglycoside resistance genes in integrons.
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Affiliation(s)
- Alberto Hipólito
- Departamento de Sanidad Animal, Facultad de Veterinaria de la Universidad Complutense de Madrid, Spain,VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Spain
| | - Lucía García-Pastor
- Departamento de Sanidad Animal, Facultad de Veterinaria de la Universidad Complutense de Madrid, Spain,VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Spain
| | | | | | - Nicolas Kieffer
- Departamento de Sanidad Animal, Facultad de Veterinaria de la Universidad Complutense de Madrid, Spain,VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Spain
| | - Ester Vergara
- Departamento de Sanidad Animal, Facultad de Veterinaria de la Universidad Complutense de Madrid, Spain,VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Spain
| | - Thomas Jové
- INSERM, CHU Limoges, RESINFIT, University of Limoges, Limoges, France
| | - Julio Álvarez
- Departamento de Sanidad Animal, Facultad de Veterinaria de la Universidad Complutense de Madrid, Spain,VISAVET Health Surveillance Centre, Universidad Complutense de Madrid, Spain
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12
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Song X, Lin Z, Yuan W. Toxin-antitoxin systems in pathogenic Vibrio species: a mini review from a structure perspective. 3 Biotech 2022; 12:125. [PMID: 35542053 DOI: 10.1007/s13205-022-03178-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2022] [Accepted: 03/31/2022] [Indexed: 11/01/2022] Open
Abstract
Toxin-antitoxin (TA) genetic modules have been found to widely exist in bacterial chromosomes and mobile genetic elements. They are composed of stable toxins and less stable antitoxins that can counteract the toxicity of toxins. The interactions between toxins and antitoxins could play critical roles in the virulence and persistence of pathogenic bacteria. There are at least eight types of TA systems which have been identified in a variety of bacteria. Vibrio, a genus of Gram-negative bacteria, is widespread in aquatic environments and can cause various human diseases, such as epidemic cholera. In this review, we mainly explore the structures and functions of TA modules found in common Vibrio pathogens, mainly V. cholerae, for better understanding of TA action mechanisms in pathogenic bacteria.
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13
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Unbridled Integrons: A Matter of Host Factors. Cells 2022; 11:cells11060925. [PMID: 35326376 PMCID: PMC8946536 DOI: 10.3390/cells11060925] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Revised: 03/03/2022] [Accepted: 03/04/2022] [Indexed: 12/29/2022] Open
Abstract
Integrons are powerful recombination systems found in bacteria, which act as platforms capable of capturing, stockpiling, excising and reordering mobile elements called cassettes. These dynamic genetic machineries confer a very high potential of adaptation to their host and have quickly found themselves at the forefront of antibiotic resistance, allowing for the quick emergence of multi-resistant phenotypes in a wide range of bacterial species. Part of the success of the integron is explained by its ability to integrate various environmental and biological signals in order to allow the host to respond to these optimally. In this review, we highlight the substantial interconnectivity that exists between integrons and their hosts and its importance to face changing environments. We list the factors influencing the expression of the cassettes, the expression of the integrase, and the various recombination reactions catalyzed by the integrase. The combination of all these host factors allows for a very tight regulation of the system at the cost of a limited ability to spread by horizontal gene transfer and function in remotely related hosts. Hence, we underline the important consequences these factors have on the evolution of integrons. Indeed, we propose that sedentary chromosomal integrons that were less connected or connected via more universal factors are those that have been more successful upon mobilization in mobile genetic structures, in contrast to those that were connected to species-specific host factors. Thus, the level of specificity of the involved host factors network may have been decisive for the transition from chromosomal integrons to the mobile integrons, which are now widespread. As such, integrons represent a perfect example of the conflicting relationship between the ability to control a biological system and its potential for transferability.
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14
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Ghaly TM, Gillings MR, Penesyan A, Qi Q, Rajabal V, Tetu SG. The Natural History of Integrons. Microorganisms 2021; 9:2212. [PMID: 34835338 PMCID: PMC8618304 DOI: 10.3390/microorganisms9112212] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 10/22/2021] [Accepted: 10/23/2021] [Indexed: 11/17/2022] Open
Abstract
Integrons were first identified because of their central role in assembling and disseminating antibiotic resistance genes in commensal and pathogenic bacteria. However, these clinically relevant integrons represent only a small proportion of integron diversity. Integrons are now known to be ancient genetic elements that are hotspots for genomic diversity, helping to generate adaptive phenotypes. This perspective examines the diversity, functions, and activities of integrons within both natural and clinical environments. We show how the fundamental properties of integrons exquisitely pre-adapted them to respond to the selection pressures imposed by the human use of antimicrobial compounds. We then follow the extraordinary increase in abundance of one class of integrons (class 1) that has resulted from its acquisition by multiple mobile genetic elements, and subsequent colonisation of diverse bacterial species, and a wide range of animal hosts. Consequently, this class of integrons has become a significant pollutant in its own right, to the extent that it can now be detected in most ecosystems. As human activities continue to drive environmental instability, integrons will likely continue to play key roles in bacterial adaptation in both natural and clinical settings. Understanding the ecological and evolutionary dynamics of integrons can help us predict and shape these outcomes that have direct relevance to human and ecosystem health.
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Affiliation(s)
- Timothy M. Ghaly
- Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia; (T.M.G.); (A.P.); (Q.Q.); (V.R.)
| | - Michael R. Gillings
- Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia; (T.M.G.); (A.P.); (Q.Q.); (V.R.)
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW 2109, Australia;
| | - Anahit Penesyan
- Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia; (T.M.G.); (A.P.); (Q.Q.); (V.R.)
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW 2109, Australia;
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
| | - Qin Qi
- Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia; (T.M.G.); (A.P.); (Q.Q.); (V.R.)
| | - Vaheesan Rajabal
- Department of Biological Sciences, Macquarie University, Sydney, NSW 2109, Australia; (T.M.G.); (A.P.); (Q.Q.); (V.R.)
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW 2109, Australia;
| | - Sasha G. Tetu
- ARC Centre of Excellence in Synthetic Biology, Macquarie University, Sydney, NSW 2109, Australia;
- Department of Molecular Sciences, Macquarie University, Sydney, NSW 2109, Australia
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15
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Predicting the taxonomic and environmental sources of integron gene cassettes using structural and sequence homology of attC sites. Commun Biol 2021; 4:946. [PMID: 34373573 PMCID: PMC8352920 DOI: 10.1038/s42003-021-02489-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Accepted: 07/16/2021] [Indexed: 11/08/2022] Open
Abstract
Integrons are bacterial genetic elements that can capture mobile gene cassettes. They are mostly known for their role in the spread of antibiotic resistance cassettes, contributing significantly to the global resistance crisis. These resistance cassettes likely originated from sedentary chromosomal integrons, having subsequently been acquired and disseminated by mobilised integrons. However, their taxonomic and environmental origins are unknown. Here, we use cassette recombination sites (attCs) to predict the origins of those resistance cassettes now spread by mobile integrons. We modelled the structure and sequence homology of 1,978 chromosomal attCs from 11 different taxa. Using these models, we show that at least 27% of resistance cassettes have attCs that are structurally conserved among one of three taxa (Xanthomonadales, Spirochaetes and Vibrionales). Indeed, we found some resistance cassettes still residing in sedentary chromosomal integrons of the predicted taxa. Further, we show that attCs cluster according to host environment rather than host phylogeny, allowing us to assign their likely environmental sources. For example, the majority of β-lactamases and aminoglycoside acetyltransferases, the two most prevalent resistance cassettes, appear to have originated from marine environments. Together, our data represent the first evidence of the taxonomic and environmental origins of resistance cassettes spread by mobile integrons.
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16
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Vit C, Richard E, Fournes F, Whiteway C, Eyer X, Lapaillerie D, Parissi V, Mazel D, Loot C. Cassette recruitment in the chromosomal Integron of Vibrio cholerae. Nucleic Acids Res 2021; 49:5654-5670. [PMID: 34048565 PMCID: PMC8191803 DOI: 10.1093/nar/gkab412] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Revised: 04/26/2021] [Accepted: 05/03/2021] [Indexed: 01/16/2023] Open
Abstract
Integrons confer a rapid adaptation capability to bacteria. Integron integrases are able to capture and shuffle novel functions embedded in cassettes. Here, we investigated cassette recruitment in the Vibrio cholerae chromosomal integron during horizontal transfer. We demonstrated that the endogenous integrase expression is sufficiently triggered, after SOS response induction mediated by the entry of cassettes during conjugation and natural transformation, to mediate significant cassette insertions. These insertions preferentially occur at the attIA site, despite the presence of about 180 attC sites in the integron array. Thanks to the presence of a promoter in the attIA site vicinity, all these newly inserted cassettes are expressed and prone to selection. We also showed that the RecA protein is critical for cassette recruitment in the V. cholerae chromosomal integron but not in mobile integrons. Moreover, unlike the mobile integron integrases, that of V. cholerae is not active in other bacteria. Mobile integrons might have evolved from the chromosomal ones by overcoming host factors, explaining their large dissemination in bacteria and their role in antibioresistance expansion.
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Affiliation(s)
- Claire Vit
- Institut Pasteur, Unité Plasticité du Génome Bactérien, CNRS UMR3525, Paris, France.,Sorbonne Université, Collège doctoral, F-75005 Paris, France
| | - Egill Richard
- Institut Pasteur, Unité Plasticité du Génome Bactérien, CNRS UMR3525, Paris, France.,Sorbonne Université, Collège doctoral, F-75005 Paris, France
| | - Florian Fournes
- Institut Pasteur, Unité Plasticité du Génome Bactérien, CNRS UMR3525, Paris, France
| | - Clémence Whiteway
- Institut Pasteur, Unité Plasticité du Génome Bactérien, CNRS UMR3525, Paris, France
| | - Xavier Eyer
- Institut Pasteur, Unité Plasticité du Génome Bactérien, CNRS UMR3525, Paris, France
| | - Delphine Lapaillerie
- CNRS, UMR5234, Fundamental Microbiology and Pathogenicity laboratory, University of Bordeaux. Département de Sciences Biologiques et Médicales, Bordeaux, France.,Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), France
| | - Vincent Parissi
- CNRS, UMR5234, Fundamental Microbiology and Pathogenicity laboratory, University of Bordeaux. Département de Sciences Biologiques et Médicales, Bordeaux, France.,Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), France
| | - Didier Mazel
- Institut Pasteur, Unité Plasticité du Génome Bactérien, CNRS UMR3525, Paris, France
| | - Céline Loot
- Institut Pasteur, Unité Plasticité du Génome Bactérien, CNRS UMR3525, Paris, France
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17
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Lundbäck IC, McDougall FK, Dann P, Slip DJ, Gray R, Power ML. Into the sea: Antimicrobial resistance determinants in the microbiota of little penguins (Eudyptula minor). INFECTION GENETICS AND EVOLUTION 2020; 88:104697. [PMID: 33370595 DOI: 10.1016/j.meegid.2020.104697] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 12/11/2020] [Accepted: 12/22/2020] [Indexed: 12/30/2022]
Abstract
Terrestrial and aquatic birds have been proposed as sentinels for the spread of antimicrobial resistant bacteria, but few species have been investigated specifically in the context of AMR in the marine ecosystem. This study contrasts the occurrence of class 1 integrons and associated antimicrobial resistance genes in wild and captive little penguins (Eudyptula minor), an Australian seabird with local population declines. PCR screening of faecal samples (n = 448) revealed a significant difference in the prevalence of class 1 integrons in wild and captive groups, 3.2% and 44.7% respectively, with genes that confer resistance to streptomycin, spectinomycin, trimethoprim and multidrug efflux pumps detected. Class 1 integrons were not detected in two clinically relevant bacterial species, Klebsiella pneumoniae or Escherichia coli, isolated from penguin faeces. The presence of class 1 integrons in the little penguin supports the use of marine birds as sentinels of AMR in marine environments.
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Affiliation(s)
- Ida C Lundbäck
- Department of Biological Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, Australia
| | - Fiona K McDougall
- Department of Biological Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, Australia
| | - Peter Dann
- Conservation Department, Phillip Island Nature Parks, Victoria, Australia
| | - David J Slip
- Department of Biological Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, Australia; Taronga Conservation Society, Sydney, Australia
| | - Rachael Gray
- Sydney School of Veterinary Science, Faculty of Science, The University of Sydney, Australia
| | - Michelle L Power
- Department of Biological Sciences, Faculty of Science and Engineering, Macquarie University, Sydney, Australia.
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18
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Escudero JA, Nivina A, Kemble HE, Loot C, Tenaillon O, Mazel D. Primary and promiscuous functions coexist during evolutionary innovation through whole protein domain acquisitions. eLife 2020; 9:58061. [PMID: 33319743 PMCID: PMC7790495 DOI: 10.7554/elife.58061] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2020] [Accepted: 12/14/2020] [Indexed: 11/13/2022] Open
Abstract
Molecular examples of evolutionary innovation are scarce and generally involve point mutations. Innovation can occur through larger rearrangements, but here experimental data is extremely limited. Integron integrases innovated from double-strand- toward single-strand-DNA recombination through the acquisition of the I2 α-helix. To investigate how this transition was possible, we have evolved integrase IntI1 to what should correspond to an early innovation state by selecting for its ancestral activity. Using synonymous alleles to enlarge sequence space exploration, we have retrieved 13 mutations affecting both I2 and the multimerization domains of IntI1. We circumvented epistasis constraints among them using a combinatorial library that revealed their individual and collective fitness effects. We obtained up to 104-fold increases in ancestral activity with various asymmetrical trade-offs in single-strand-DNA recombination. We show that high levels of primary and promiscuous functions could have initially coexisted following I2 acquisition, paving the way for a gradual evolution toward innovation.
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Affiliation(s)
- José Antonio Escudero
- Institut Pasteur, Unité de Plasticité du Génome Bactérien, Département Génomes et Génétique, Paris, France.,CNRS, UMR3525, Paris, France.,Molecular Basis of Adaptation, Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad Complutense de Madrid, Madrid, Spain.,VISAVET Health Surveillance Centre. Universidad Complutense Madrid. Avenida Puerta de Hierro, Madrid, Spain
| | - Aleksandra Nivina
- Institut Pasteur, Unité de Plasticité du Génome Bactérien, Département Génomes et Génétique, Paris, France.,CNRS, UMR3525, Paris, France.,Université Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - Harry E Kemble
- Infection, Antimicrobials, Modelling, Evolution, INSERM, UMR 1137, Université Paris Diderot, Université Paris Nord, Paris, France
| | - Céline Loot
- Institut Pasteur, Unité de Plasticité du Génome Bactérien, Département Génomes et Génétique, Paris, France.,CNRS, UMR3525, Paris, France
| | - Olivier Tenaillon
- Infection, Antimicrobials, Modelling, Evolution, INSERM, UMR 1137, Université Paris Diderot, Université Paris Nord, Paris, France
| | - Didier Mazel
- Institut Pasteur, Unité de Plasticité du Génome Bactérien, Département Génomes et Génétique, Paris, France.,CNRS, UMR3525, Paris, France
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19
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Dias MF, de Castro GM, de Paiva MC, de Paula Reis M, Facchin S, do Carmo AO, Alves MS, Suhadolnik ML, de Moraes Motta A, Henriques I, Kalapothakis E, Lobo FP, Nascimento AMA. Exploring antibiotic resistance in environmental integron-cassettes through intI-attC amplicons deep sequencing. Braz J Microbiol 2020; 52:363-372. [PMID: 33247398 DOI: 10.1007/s42770-020-00409-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 11/19/2020] [Indexed: 02/08/2023] Open
Abstract
INTRODUCTION Freshwater ecosystems provide propitious conditions for the acquisition and spread of antibiotic resistance genes (ARGs), and integrons play an important role in this process. MATERIAL AND METHODS In the present study, the diversity of putative environmental integron-cassettes, as well as their potential bacterial hosts in the Velhas River (Brazil), was explored through intI-attC and 16S rRNA amplicons deep sequencing. RESULTS AND DISCUSSION: ORFs related to different biological processes were observed, from DNA integration to oxidation-reduction. ARGs-cassettes were mainly associated with class 1 mobile integrons carried by pathogenic Gammaproteobacteria, and possibly sedentary chromosomal integrons hosted by Proteobacteria and Actinobacteria. Two putative novel ARG-cassettes homologs to fosB3 and novA were detected. Regarding 16SrRNA gene analysis, taxonomic and functional profiles unveiled Proteobacteria, Bacteroidetes, Firmicutes, and Actinobacteria as dominant phyla. Betaproteobacteria, Alphaproteobacteria, and Actinobacteria classes were the main contributors for KEGG orthologs associated with resistance. CONCLUSIONS Overall, these results provide new information about environmental integrons as a source of resistance determinants outside clinical settings and the bacterial community in the Velhas River.
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Affiliation(s)
- Marcela França Dias
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Avenida Antônio Carlos 6627, Belo Horizonte, MG, 31270-901, Brazil.,Departamento de Biologia, Universidade de Aveiro, Aveiro, Portugal
| | - Giovanni Marques de Castro
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Avenida Antônio Carlos 6627, Belo Horizonte, MG, 31270-901, Brazil
| | | | - Mariana de Paula Reis
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Avenida Antônio Carlos 6627, Belo Horizonte, MG, 31270-901, Brazil
| | - Susanne Facchin
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Avenida Antônio Carlos 6627, Belo Horizonte, MG, 31270-901, Brazil
| | - Anderson Oliveira do Carmo
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Avenida Antônio Carlos 6627, Belo Horizonte, MG, 31270-901, Brazil
| | - Marta Salgueiro Alves
- Departamento de Biologia, Universidade de Aveiro, Aveiro, Portugal.,CESAM, Universidade de Aveiro, Aveiro, Portugal
| | - Maria Luíza Suhadolnik
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Avenida Antônio Carlos 6627, Belo Horizonte, MG, 31270-901, Brazil
| | - Amanda de Moraes Motta
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Avenida Antônio Carlos 6627, Belo Horizonte, MG, 31270-901, Brazil
| | - Isabel Henriques
- CESAM, Universidade de Aveiro, Aveiro, Portugal.,Departamento de Ciências da Vida, Faculdade de Ciências e Tecnologia, Universidade de Coimbra, Coimbra, Portugal
| | - Evanguedes Kalapothakis
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Avenida Antônio Carlos 6627, Belo Horizonte, MG, 31270-901, Brazil
| | - Francisco Pereira Lobo
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Avenida Antônio Carlos 6627, Belo Horizonte, MG, 31270-901, Brazil
| | - Andréa Maria Amaral Nascimento
- Departamento de Genética, Ecologia e Evolução, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Avenida Antônio Carlos 6627, Belo Horizonte, MG, 31270-901, Brazil.
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20
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Manolov A, Konanov D, Fedorov D, Osmolovsky I, Vereshchagin R, Ilina E. Genome Complexity Browser: Visualization and quantification of genome variability. PLoS Comput Biol 2020; 16:e1008222. [PMID: 33035207 PMCID: PMC7577506 DOI: 10.1371/journal.pcbi.1008222] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Revised: 10/21/2020] [Accepted: 08/05/2020] [Indexed: 12/30/2022] Open
Abstract
Comparative genomics studies may be used to acquire new knowledge regarding genome architecture, which defines the rules for combining sets of genes in the genome of living organisms. Hundreds of thousands of prokaryotic genomes have been sequenced and assembled. However, computational tools capable of simultaneously comparing large numbers of genomes are lacking. We developed the Genome Complexity Browser, a tool that allows the visualization of gene contexts, in a graph-based format, and the quantification of variability for different segments of a genome. The graph-based visualization allows the inspection of changes in gene contents and neighborhoods across hundreds of genomes, simultaneously, which may facilitate the identification of conserved and variable segments of operons or the estimation of the overall variability associated with a particular genome locus. We introduced a measure called complexity, to quantify genome variability. Intraspecies and interspecies comparisons revealed that regions with high complexity values tended to be located in areas that are conserved across different strains and species. The comparison of genomes among different bacteria and archaea species has revealed that many species frequently exchange genes. Occasionally, such horizontal gene transfer events result in the acquisition of pathogenic properties or antibiotic resistance in the recipient organism. Previously, the probabilities of gene insertions were found to vary, with unequal distributions along a chromosome. At some loci, referred to as hotspots, changes occur with much higher frequencies compared with other regions of the chromosome. We developed a computational method and a software tool, called Genome Complexity Browser, that allows the identification of genome variability hotspots and the visualization of changes. We compared the localization of various hotspots and revealed that some demonstrate conserved localizations, even across species, whereas others are transient. Our tool allows users to visually inspect the patterns of gene changes in graph-based format, which presents the visualization in a format that is both compact and informative.
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Affiliation(s)
- Alexander Manolov
- Federal Research and Clinical Center of Physical and Chemical Medicine, Federal Medical and Biological Agency of Russia, Moscow, Russian Federation
- * E-mail:
| | - Dmitry Konanov
- Federal Research and Clinical Center of Physical and Chemical Medicine, Federal Medical and Biological Agency of Russia, Moscow, Russian Federation
| | - Dmitry Fedorov
- Federal Research and Clinical Center of Physical and Chemical Medicine, Federal Medical and Biological Agency of Russia, Moscow, Russian Federation
| | - Ivan Osmolovsky
- Federal Research and Clinical Center of Physical and Chemical Medicine, Federal Medical and Biological Agency of Russia, Moscow, Russian Federation
| | - Rinat Vereshchagin
- Federal Research and Clinical Center of Physical and Chemical Medicine, Federal Medical and Biological Agency of Russia, Moscow, Russian Federation
| | - Elena Ilina
- Federal Research and Clinical Center of Physical and Chemical Medicine, Federal Medical and Biological Agency of Russia, Moscow, Russian Federation
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The Peril and Promise of Integrons: Beyond Antibiotic Resistance. Trends Microbiol 2020; 28:455-464. [PMID: 31948729 DOI: 10.1016/j.tim.2019.12.002] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 11/13/2019] [Accepted: 12/09/2019] [Indexed: 12/11/2022]
Abstract
Integrons are bacterial genetic elements that can capture, rearrange, and express mobile gene cassettes. They are best known for their role in disseminating antibiotic-resistance genes among pathogens. Their ability to rapidly spread resistance phenotypes makes it important to consider what other integron-mediated traits might impact human health in the future, such as increased virulence, pathogenicity, or resistance to novel antimicrobial strategies. Exploring the functional diversity of cassettes and understanding their de novo creation will allow better pre-emptive management of bacterial growth, while also facilitating development of technologies that could harness integron activity. If we can control integrons and cassette formation, we could use integrons as a platform for enzyme discovery and to construct novel biochemical pathways, with applications in bioremediation or biosynthesis of industrial and therapeutic molecules. Integron activity thus holds both peril and promise for humans.
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Baquero F, Coque TM, Martínez JL, Aracil-Gisbert S, Lanza VF. Gene Transmission in the One Health Microbiosphere and the Channels of Antimicrobial Resistance. Front Microbiol 2019; 10:2892. [PMID: 31921068 PMCID: PMC6927996 DOI: 10.3389/fmicb.2019.02892] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2019] [Accepted: 12/02/2019] [Indexed: 12/12/2022] Open
Abstract
Antibiotic resistance is a field in which the concept of One Health can best be illustrated. One Health is based on the definition of communication spaces among diverse environments. Antibiotic resistance is encoded by genes, however, these genes are propagated in mobile genetic elements (MGEs), circulating among bacterial species and clones that are integrated into the multiple microbiotas of humans, animals, food, sewage, soil, and water environments, the One Health microbiosphere. The dynamics and evolution of antibiotic resistance depend on the communication networks linking all these ecological, biological, and genetic entities. These communications occur by environmental overlapping and merging, a critical issue in countries with poor sanitation, but also favored by the homogenizing power of globalization. The overwhelming increase in the population of highly uniform food animals has contributed to the parallel increase in the absolute size of their microbiotas, consequently enhancing the possibility of microbiome merging between humans and animals. Microbial communities coalescence might lead to shared microbiomes in which the spread of antibiotic resistance (of human, animal, or environmental origin) is facilitated. Intermicrobiome communication is exerted by shuttle bacterial species (or clones within species) belonging to generalist taxa, able to multiply in the microbiomes of various hosts, including humans, animals, and plants. Their integration into local genetic exchange communities fosters antibiotic resistance gene flow, following the channels of accessory genome exchange among bacterial species. These channels delineate a topology of gene circulation, including dense clusters of species with frequent historical and recent exchanges. The ecological compatibility of these species, sharing the same niches and environments, determines the exchange possibilities. In summary, the fertility of the One Health approach to antibiotic resistance depends on the progress of understanding multihierarchical systems, encompassing communications among environments (macro/microaggregates), among microbiotas (communities), among bacterial species (clones), and communications among MGEs.
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Affiliation(s)
- Fernando Baquero
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain
| | - Teresa M. Coque
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain
| | - José-Luis Martínez
- Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas (CSIC), Madrid, Spain
| | - Sonia Aracil-Gisbert
- Department of Microbiology, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain
| | - Val F. Lanza
- Bioinformatics Unit, Ramón y Cajal University Hospital, Ramón y Cajal Institute for Health Research (IRYCIS), Madrid, Spain
- CIBER in Epidemiology and Public Health (CIBERESP), Madrid, Spain
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23
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Shen Y, Stedtfeld RD, Guo X, Bhalsod GD, Jeon S, Tiedje JM, Li H, Zhang W. Pharmaceutical exposure changed antibiotic resistance genes and bacterial communities in soil-surface- and overhead-irrigated greenhouse lettuce. ENVIRONMENT INTERNATIONAL 2019; 131:105031. [PMID: 31336252 DOI: 10.1016/j.envint.2019.105031] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/14/2019] [Revised: 06/29/2019] [Accepted: 07/16/2019] [Indexed: 06/10/2023]
Abstract
New classes of emerging contaminants such as pharmaceuticals, antibiotic resistant bacteria (ARB), and antibiotic resistance genes (ARGs) have received increasing attention due to rapid increases of their abundance in agroecosystems. As food consumption is a direct exposure pathway of pharmaceuticals, ARB, and ARGs to humans, it is important to understand changes of bacterial communities and ARG profiles in food crops produced with contaminated soils and waters. This study examined the level and type of ARGs and bacterial community composition in soil, and lettuce shoots and roots under soil-surface or overhead irrigation with pharmaceuticals-contaminated water, using high throughput qPCR and 16S rRNA amplicon sequencing techniques, respectively. In total 52 ARG subtypes were detected in the soil, lettuce shoot and root samples, with mobile genetic elements (MGEs), and macrolide-lincosamide-streptogramin B (MLSB) and multidrug resistance (MDR) genes as dominant types. The overall abundance and diversity of ARGs and bacteria associated with lettuce shoots under soil-surface irrigation were lower than those under overhead irrigation, indicating soil-surface irrigation may have lower risks of producing food crops with high abundance of ARGs. ARG profiles and bacterial communities were sensitive to pharmaceutical exposure, but no consistent patterns of changes were observed. MGE intl1 was consistently more abundant with pharmaceutical exposure than in the absence of pharmaceuticals. Pharmaceutical exposure enriched Proteobacteria (specifically Methylophilaceae) and decreased bacterial alpha diversity. Finally, there were significant interplays among bacteria community, antibiotic concentrations, and ARG abundance possibly involving hotspots including Sphingomonadaceae, Pirellulaceae, and Chitinophagaceae, MGEs (intl1 and tnpA_1) and MDR genes (mexF and oprJ).
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Affiliation(s)
- Yike Shen
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, United States; Environmental Science and Policy Program, Michigan State University, East Lansing, MI 48824, United States; Institute for Integrative Toxicology, Michigan State University, East Lansing, MI 48824, United States
| | - Robert D Stedtfeld
- Department of Civil and Environmental Engineering, Michigan State University, East Lansing, MI 48823, United States
| | - Xueping Guo
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, United States; Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824, United States; College of Environmental Science and Engineering, Tongji University, Shanghai 200092, China
| | - Gemini D Bhalsod
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, United States; Cook County Unit, University of Illinois Extension, Arlington Heights, IL 60004, United States
| | - Sangho Jeon
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, United States; National Institute of Agricultural Sciences, Rural Development Administration, Wanju 54875, Republic of Korea
| | - James M Tiedje
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, United States; Center for Microbial Ecology, Michigan State University, East Lansing, MI 48824, United States
| | - Hui Li
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, United States
| | - Wei Zhang
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI 48824, United States; Environmental Science and Policy Program, Michigan State University, East Lansing, MI 48824, United States.
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Cathelicidin Peptides Restrict Bacterial Growth via Membrane Perturbation and Induction of Reactive Oxygen Species. mBio 2019; 10:mBio.02021-19. [PMID: 31506312 PMCID: PMC6737244 DOI: 10.1128/mbio.02021-19] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Antimicrobial peptides (AMPs) are an important part of the mammalian innate immune system in the battle against microbial infection. How AMPs function to control bacteria is not clear, as nearly all activity studies use nonphysiological levels of AMPs. We monitored peptide action in live bacterial cells over short time frames with single-cell resolution and found that the primary effect of cathelicidin peptides is to increase the production of oxidative molecules that cause cellular damage in Gram-positive and Gram-negative bacteria. All metazoans produce antimicrobial peptides (AMPs) that have both broad antimicrobial and immunomodulatory activity. Cathelicidins are AMPs that preferentially kill Gram-negative bacteria in vitro, purportedly by assembling into higher-order structures that perforate the membrane. We utilized high-resolution, single-cell fluorescence microscopy to examine their mechanism of action in real time. Engineered cathelicidins rapidly bound to Gram-negative and Gram-positive cells and penetrated the cytoplasmic membrane. Rapid failure of the peptidoglycan superstructure in regions of active turnover caused leakage of cytoplasmic contents and the formation of membrane-bound blebs. A mutation anticipated to destabilize interactions between cathelicidin subunits had no effect on bactericidal activity, suggesting that cathelicidins have activities beyond perforating the membrane. Nanomolar concentrations of cathelicidins, although not bactericidal, reduced the growth rate of Gram-negative and Gram-positive bacteria. The cells exhibited expression changes in multiple essential processes, including protein synthesis, peptidoglycan biosynthesis, respiration, and the detoxification of reactive oxygen species (ROS). Time-lapse imaging revealed that ROS accumulation preceded bleb formation, and treatments that reduced cellular ROS levels overcame these bactericidal effects. We propose that that the primary effect of cathelicidins is to induce the production of ROS that damage bacterial molecules, leading to slowed growth or cell death. Given their low circulating levels in vivo, AMPs may serve to slow bacterial population expansion so that cellular immunity systems can respond to and battle the infection.
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Narendrakumar L, Gupta SS, Johnson JB, Ramamurthy T, Thomas S. Molecular Adaptations and Antibiotic Resistance inVibrio cholerae: A Communal Challenge. Microb Drug Resist 2019; 25:1012-1022. [DOI: 10.1089/mdr.2018.0354] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Affiliation(s)
- Lekshmi Narendrakumar
- Cholera and Biofilm Research Laboratory, Rajiv Gandhi Centre for Biotechnology, Kerala, India
- Research Scholar, University of Kerala, Kerala, India
| | | | - John B. Johnson
- Viral Disease Biology, Rajiv Gandhi Centre for Biotechnology, Kerala, India
| | | | - Sabu Thomas
- Cholera and Biofilm Research Laboratory, Rajiv Gandhi Centre for Biotechnology, Kerala, India
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Ghaly TM, Geoghegan JL, Alroy J, Gillings MR. High diversity and rapid spatial turnover of integron gene cassettes in soil. Environ Microbiol 2019; 21:1567-1574. [PMID: 30724441 DOI: 10.1111/1462-2920.14551] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2018] [Accepted: 01/30/2019] [Indexed: 12/01/2022]
Abstract
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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Affiliation(s)
- Timothy M Ghaly
- Department of Biological Science, Macquarie University, Sydney, NSW, 2109, Australia
| | - Jemma L Geoghegan
- Department of Biological Science, Macquarie University, Sydney, NSW, 2109, Australia
| | - John Alroy
- Department of Biological Science, Macquarie University, Sydney, NSW, 2109, Australia
| | - Michael R Gillings
- Department of Biological Science, Macquarie University, Sydney, NSW, 2109, Australia
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Almasian P, Amani J, Arani FB, Nazarian S, Kazemi R, Tabrizi NM. Preparation of chitosan nanoparticle containing recombinant StxB antigen of EHEC and evaluation its immunogenicity in BALB/c mice. IRANIAN JOURNAL OF MICROBIOLOGY 2018; 10:361-370. [PMID: 30873263 PMCID: PMC6414748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
BACKGROUND AND OBJECTIVES Escherichia coli O157:H7 is one of the most important food pathogens that produces colitis and bloody urine in humans. The Stx2B subunit is considered as one of the candidates for vaccine due to its immunogenic and adjuvant properties. Designing a mucosal vaccine using nanoparticles for protecting the antigen against degradation and controlling the release of antigen are important. The objective of the current study was to prepare nanoparticles containing the Stx2B subunit of E. coli O157:H7 and evaluation of its immunogenicity in the mouse model. MATERIALS AND METHODS E. coli BL21 DE3 and pET28a-stxB were used for expression of the stx2b gene. After inducing gene expression, purification of the Stx2b protein was performed. Then, chitosan nanoparticle containing recombinant Stx2B was prepared and administered to BALB/c mice. IgA and IgG titers in serum and IgA titers in feces of immunized and control mice were evaluated by the ELISA method. RESULTS After expression and purification of the Stx2B recombinant protein, an expected band of 13 kDa was observed on the SDS-PAGE gel and confirmed by Western Blot analysis. The size of the nanoparticle containing Stx2B was 290 nm. In the immunized mice, IgG and IgA titers were significantly increased. The immunized mice were challenged against E. coli O157:H7 Stx+ and the shedding analysis showed that colonization of bacteria in the intestinal tract decreased. CONCLUSION Oral administration of nanoparticles containing Stx2B as a candidate for the vaccine can induce a systemic and mucosal immune response against Stx2 toxin and can provide acceptable protection.
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Affiliation(s)
- Pegah Almasian
- Department of Genetics and Biotechnology, School of Biological Sciences, Varamin-Pishva Branch, Islamic Azad University, Varamin, Iran
| | - Jafar Amani
- Applied Microbiology Research Center, Systems Biology and Poisonings Institute, Baqiyatallah University of Medical Sciences, Tehran, Iran
| | - Fahimeh Baghban Arani
- Department of Genetics and Biotechnology, School of Biological Sciences, Varamin-Pishva Branch, Islamic Azad University, Varamin, Iran
| | - Shahram Nazarian
- Department of Biology, Faculty of Sciences, Imam Hossein University, Tehran, Iran
| | - Rouhollah Kazemi
- Department of Agricultural Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran, Iran
| | - Niloufar Mirzaee Tabrizi
- Department of Genetics and Biotechnology, School of Biological Sciences, Varamin-Pishva Branch, Islamic Azad University, Varamin, Iran
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Guanhua Y, Wang C, Wang X, Ma R, Zheng H, Liu Q, Zhang Y, Ma Y, Wang Q. Complete genome sequence of the marine fish pathogen Vibrio anguillarum and genome-wide transposon mutagenesis analysis of genes essential for in vivo infection. Microbiol Res 2018; 216:97-107. [DOI: 10.1016/j.micres.2018.08.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 08/21/2018] [Accepted: 08/23/2018] [Indexed: 12/14/2022]
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Sultan I, Rahman S, Jan AT, Siddiqui MT, Mondal AH, Haq QMR. Antibiotics, Resistome and Resistance Mechanisms: A Bacterial Perspective. Front Microbiol 2018; 9:2066. [PMID: 30298054 PMCID: PMC6160567 DOI: 10.3389/fmicb.2018.02066] [Citation(s) in RCA: 162] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2018] [Accepted: 08/13/2018] [Indexed: 12/28/2022] Open
Abstract
History of mankind is regarded as struggle against infectious diseases. Rather than observing the withering away of bacterial diseases, antibiotic resistance has emerged as a serious global health concern. Medium of antibiotic resistance in bacteria varies greatly and comprises of target protection, target substitution, antibiotic detoxification and block of intracellular antibiotic accumulation. Further aggravation to prevailing situation arose on observing bacteria gradually becoming resistant to different classes of antibiotics through acquisition of resistance genes from same and different genera of bacteria. Attributing bacteria with feature of better adaptability, dispersal of antibiotic resistance genes to minimize effects of antibiotics by various means including horizontal gene transfer (conjugation, transformation, and transduction), Mobile genetic elements (plasmids, transposons, insertion sequences, integrons, and integrative-conjugative elements) and bacterial toxin-antitoxin system led to speedy bloom of antibiotic resistance amongst bacteria. Proficiency of bacteria to obtain resistance genes generated an unpleasant situation; a grave, but a lot unacknowledged, feature of resistance gene transfer.
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Affiliation(s)
- Insha Sultan
- Department of Biosciences, Jamia Millia Islamia, New Delhi, India
| | - Safikur Rahman
- Department of Medical Biotechnology, Yeungnam University, Gyeongsan, South Korea
| | - Arif Tasleem Jan
- School of Biosciences and Biotechnology, Baba Ghulam Shah Badshah University, Rajouri, India
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Sulca MA, Orozco R, Alvarado DE. Antimicrobial resistance not related to 1,2,3 integrons and Superintegron in Vibrio spp. isolated from seawater sample of Lima (Peru). MARINE POLLUTION BULLETIN 2018; 131:370-377. [PMID: 29886960 DOI: 10.1016/j.marpolbul.2018.04.050] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 03/28/2018] [Accepted: 04/18/2018] [Indexed: 06/08/2023]
Abstract
Antimicrobial resistance (AMR) in microorganisms has been attributed to integrons, which have the ability to capture antimicrobial resistance gene cassettes and express them in their hosts. 170 strains of Vibrio spp. were isolated from Lima (Peru) seawater samples and identified by biochemical tests and PCR. AMR profiles were generated using 15 standard antibiotics. The presence of class 1, 2 and 3 integrons and Superintegron in these strains were also investigated by PCR. Ten species of Vibrio were identified with V. alginolyticus the most frequent. All strains were resistant to antibiotics, especially to penicillin group. No resistance to norfloxacin or tetracycline was observed. Class 1, 2 and 3 integrons were not found, only one Superintegron containing the mutT gene was identified in V. cholerae L22 strain. This indicated that AMR is not related to integrons as mentioned previously and that these strains can be reservoirs of resistance genes in marine environments.
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Affiliation(s)
- Marcos A Sulca
- Molecular Microbiology and Biotechnology Laboratory, Faculty of Biological Science, National University of San Marcos, Lima, Peru; Aquatic Microbiology Laboratory, Alexander von Humboldt Aquaculture Research Center - IMARPE, Lima, Peru.
| | - Rita Orozco
- Aquatic Microbiology Laboratory, Alexander von Humboldt Aquaculture Research Center - IMARPE, Lima, Peru
| | - Débora E Alvarado
- Molecular Microbiology and Biotechnology Laboratory, Faculty of Biological Science, National University of San Marcos, Lima, Peru
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31
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Martini MC, Quiroga MP, Pistorio M, Lagares A, Centrón D, Del Papa MF. Novel environmental class 1 integrons and cassette arrays recovered from an on-farm bio-purification plant. FEMS Microbiol Ecol 2017; 94:4781311. [DOI: 10.1093/femsec/fix190] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 12/27/2017] [Indexed: 11/12/2022] Open
Affiliation(s)
- María Carla Martini
- IBBM (Instituto de Biotecnología y Biología Molecular), CCT-CONICET-La Plata, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calle 115 entre 49 y 50, 1900, La Plata, Argentina
| | - María Paula Quiroga
- Instituto de Microbiología y Parasitología Médica, Universidad de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Tecnológicas (IMPaM, UBA-CONICET), Paraguay 2155, 1121, Ciudad Autónoma de Buenos Aires, Argentina
| | - Mariano Pistorio
- IBBM (Instituto de Biotecnología y Biología Molecular), CCT-CONICET-La Plata, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calle 115 entre 49 y 50, 1900, La Plata, Argentina
| | - Antonio Lagares
- IBBM (Instituto de Biotecnología y Biología Molecular), CCT-CONICET-La Plata, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calle 115 entre 49 y 50, 1900, La Plata, Argentina
| | - Daniela Centrón
- Instituto de Microbiología y Parasitología Médica, Universidad de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Tecnológicas (IMPaM, UBA-CONICET), Paraguay 2155, 1121, Ciudad Autónoma de Buenos Aires, Argentina
| | - María Florencia Del Papa
- IBBM (Instituto de Biotecnología y Biología Molecular), CCT-CONICET-La Plata, Departamento de Ciencias Biológicas, Facultad de Ciencias Exactas, Universidad Nacional de La Plata, Calle 115 entre 49 y 50, 1900, La Plata, Argentina
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Differences in Integron Cassette Excision Dynamics Shape a Trade-Off between Evolvability and Genetic Capacitance. mBio 2017; 8:mBio.02296-16. [PMID: 28351923 PMCID: PMC5371416 DOI: 10.1128/mbio.02296-16] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
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.IMPORTANCE The integron system confers upon bacteria a rapid adaptation capability in changing environments. Specifically, integrons are involved in the continuous emergence of bacteria resistant to almost all antibiotic treatments. The international situation is critical, and in 2050, the annual number of deaths caused by multiresistant bacteria could reach 10 million, exceeding the incidence of deaths related to cancer. It is crucial to increase our understanding of antibiotic resistance dissemination and therefore integron recombination dynamics to find new approaches to cope with the worldwide problem of multiresistance. Here, we studied the dynamics of recombination and dissemination of gene encoding cassettes carried on integrons. By combining in silico and in vivo analyses, we show that cassette excision is highly regulated by replication and by the intrinsic properties of cassette recombination sites. We also demonstrated differences in the dynamics of cassette recombination between mobile and sedentary chromosomal integrons (MIs and SCIs). For MIs, a high cassette recombination rate is favored and timed to conditions when generating diversity (upon which selection can act) allows for a rapid response to environmental conditions and stresses. In contrast, for SCIs, cassette excisions are less frequent, limiting cassette loss and ensuring a large pool of cassettes. We therefore confirm a role of SCIs as reservoirs of adaptive functions and demonstrate that the remarkable adaptive success of integron recombination system is due to its intricate regulation.
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Nivina A, Escudero JA, Vit C, Mazel D, Loot C. Efficiency of integron cassette insertion in correct orientation is ensured by the interplay of the three unpaired features of attC recombination sites. Nucleic Acids Res 2016; 44:7792-803. [PMID: 27496283 PMCID: PMC5027507 DOI: 10.1093/nar/gkw646] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2016] [Revised: 07/05/2016] [Accepted: 07/10/2016] [Indexed: 01/29/2023] Open
Abstract
The integron is a bacterial recombination system that allows acquisition, stockpiling and expression of cassettes carrying protein-coding sequences, and is responsible for the emergence and rise of multiresistance in Gram-negative bacteria. The functionality of this system depends on the insertion of promoterless cassettes in correct orientation, allowing their expression from the promoter located upstream of the cassette array. Correct orientation is ensured by strand selectivity of integron integrases for the bottom strand of cassette recombination sites (attC), recombined in form of folded single-stranded hairpins. Here, we investigated the basis of such strand selectivity by comparing recombination of wild-type and mutated attC sites with different lengths, sequences and structures. We show that all three unpaired structural features that distinguish the bottom and top strands contribute to strand selectivity. The localization of Extra-Helical Bases (EHBs) directly favors integrase binding to the bottom strand. The Unpaired Central Spacer (UCS) and the Variable Terminal Structure (VTS) influence strand selectivity indirectly, probably through the stabilization of the bottom strand and the resulting synapse due to the nucleotide skew between the two strands. These results underscore the importance of the single-stranded nature of the attC site that allows such tight control over integron cassette orientation.
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Affiliation(s)
- Aleksandra Nivina
- Institut Pasteur, Bacterial Genome Plasticity Unit, 75724 Paris, France CNRS UMR3525, 75724 Paris, France Paris Descartes, Sorbonne Paris Cité, Paris, France
| | - José Antonio Escudero
- Institut Pasteur, Bacterial Genome Plasticity Unit, 75724 Paris, France CNRS UMR3525, 75724 Paris, France
| | - Claire Vit
- Institut Pasteur, Bacterial Genome Plasticity Unit, 75724 Paris, France CNRS UMR3525, 75724 Paris, France
| | - Didier Mazel
- Institut Pasteur, Bacterial Genome Plasticity Unit, 75724 Paris, France CNRS UMR3525, 75724 Paris, France
| | - Céline Loot
- Institut Pasteur, Bacterial Genome Plasticity Unit, 75724 Paris, France CNRS UMR3525, 75724 Paris, France
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Abstract
Similar to other genera and species of bacteria, whole genomic sequencing has revolutionized how we think about and address questions of basic Vibrio biology. In this review we examined 36 completely sequenced and annotated members of the Vibrionaceae family, encompassing 12 different species of the genera Vibrio, Aliivibrio, and Photobacterium. We reconstructed the phylogenetic relationships among representatives of this group of bacteria by using three housekeeping genes and 16S rRNA sequences. With an evolutionary framework in place, we describe the occurrence and distribution of primary and alternative sigma factors, global regulators present in all bacteria. Among Vibrio we show that the number and function of many of these sigma factors differs from species to species. We also describe the role of the Vibrio-specific regulator ToxRS in fitness and survival. Examination of the biochemical capabilities was and still is the foundation of classifying and identifying new Vibrio species. Using comparative genomics, we examine the distribution of carbon utilization patterns among Vibrio species as a possible marker for understanding bacteria-host interactions. Finally, we discuss the significant role that horizontal gene transfer, specifically, the distribution and structure of integrons, has played in Vibrio evolution.
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Cury J, Jové T, Touchon M, Néron B, Rocha EP. Identification and analysis of integrons and cassette arrays in bacterial genomes. Nucleic Acids Res 2016; 44:4539-50. [PMID: 27130947 PMCID: PMC4889954 DOI: 10.1093/nar/gkw319] [Citation(s) in RCA: 196] [Impact Index Per Article: 21.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 04/13/2016] [Indexed: 12/13/2022] Open
Abstract
Integrons recombine gene arrays and favor the spread of antibiotic resistance. Their broader roles in bacterial adaptation remain mysterious, partly due to lack of computational tools. We made a program – IntegronFinder – to identify integrons with high accuracy and sensitivity. IntegronFinder is available as a standalone program and as a web application. It searches for attC sites using covariance models, for integron-integrases using HMM profiles, and for other features (promoters, attI site) using pattern matching. We searched for integrons, integron-integrases lacking attC sites, and clusters of attC sites lacking a neighboring integron-integrase in bacterial genomes. All these elements are especially frequent in genomes of intermediate size. They are missing in some key phyla, such as α-Proteobacteria, which might reflect selection against cell lineages that acquire integrons. The similarity between attC sites is proportional to the number of cassettes in the integron, and is particularly low in clusters of attC sites lacking integron-integrases. The latter are unexpectedly abundant in genomes lacking integron-integrases or their remains, and have a large novel pool of cassettes lacking homologs in the databases. They might represent an evolutionary step between the acquisition of genes within integrons and their stabilization in the new genome.
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Affiliation(s)
- Jean Cury
- Microbial Evolutionary Genomics, Institut Pasteur, 28, rue Dr Roux, Paris, 75015, France CNRS, UMR3525, 28, rue Dr Roux, Paris, 75015, France
| | - Thomas Jové
- Univ. Limoges, INSERM, CHU Limoges, UMR_S 1092, F-87000 Limoges, France
| | - Marie Touchon
- Microbial Evolutionary Genomics, Institut Pasteur, 28, rue Dr Roux, Paris, 75015, France CNRS, UMR3525, 28, rue Dr Roux, Paris, 75015, France
| | - Bertrand Néron
- Centre d'Informatique pour la Biologie, C3BI, Institut Pasteur, Paris, France
| | - Eduardo Pc Rocha
- Microbial Evolutionary Genomics, Institut Pasteur, 28, rue Dr Roux, Paris, 75015, France CNRS, UMR3525, 28, rue Dr Roux, Paris, 75015, France
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Tiruvayipati S, Bhassu S. Host, pathogen and the environment: the case of Macrobrachium rosenbergii, Vibrio parahaemolyticus and magnesium. Gut Pathog 2016; 8:15. [PMID: 27114742 PMCID: PMC4843205 DOI: 10.1186/s13099-016-0097-1] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Accepted: 03/18/2016] [Indexed: 12/18/2022] Open
Abstract
Macrobrachium rosenbergii is well-known as the giant freshwater prawn, and is a commercially significant source of seafood. Its production can be affected by various bacterial contaminations. Among which, the genus Vibrio shows a higher prevalence in aquatic organisms, especially M. rosenbergii, causing food-borne illnesses. Vibrio parahaemolyticus, a species of Vibrio is reported as the main causative of the early mortality syndrome. Vibrio parahaemolyticus infection in M. rosenbergii was studied previously in relation to the prawn's differentially expressed immune genes. In the current review, we will discuss the growth conditions for both V. parahaemolyticus and M. rosenbergii and highlight the role of magnesium in common, which need to be fully understood. Till date, there has not been much research on this aspect of magnesium. We postulate a model that screens a magnesium-dependent pathway which probably might take effect in connection with N-acetylglucosamine binding protein and chitin from V. parahaemolyticus and M. rosenbergii, respectively. Further studies on magnesium as an environment for V. parahaemolyticus and M. rosenbergii interaction studies will provide seafood industry with completely new strategies to employ and to avoid seafood related contaminations.
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Affiliation(s)
- Suma Tiruvayipati
- Department of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia
| | - Subha Bhassu
- Department of Genetics and Molecular Biology, Institute of Biological Sciences, Faculty of Science, University of Malaya, 50603 Kuala Lumpur, Malaysia ; Centre of Biotechnology for Agriculture (CEBAR), University of Malaya, Kuala Lumpur, Malaysia
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37
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Abstract
The integron is a powerful system which, by capturing, stockpiling, and rearranging new functions carried by gene encoding cassettes, confers upon bacteria a rapid adaptation capability in changing environments. Chromosomally located integrons (CI) have been identified in a large number of environmental Gram-negative bacteria. Integron evolutionary history suggests that these sedentary CIs acquired mobility among bacterial species through their association with transposable elements and conjugative plasmids. As a result of massive antibiotic use, these so-called mobile integrons are now widespread in clinically relevant bacteria and are considered to be the principal agent in the emergence and rise of antibiotic multiresistance in Gram-negative bacteria. Cassette rearrangements are catalyzed by the integron integrase, a site-specific tyrosine recombinase. Central to these reactions is the single-stranded DNA nature of one of the recombination partners, the attC site. This makes the integron a unique recombination system. This review describes the current knowledge on this atypical recombination mechanism, its implications in the reactions involving the different types of sites, attC and attI, and focuses on the tight regulation exerted by the host on integron activity through the control of attC site folding. Furthermore, cassette and integrase expression are also highly controlled by host regulatory networks and the bacterial stress (SOS) response. These intimate connections to the host make the integron a genetically stable and efficient system, granting the bacteria a low cost, highly adaptive evolution potential "on demand".
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Unmasking the ancestral activity of integron integrases reveals a smooth evolutionary transition during functional innovation. Nat Commun 2016; 7:10937. [PMID: 26961432 PMCID: PMC4792948 DOI: 10.1038/ncomms10937] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 02/03/2016] [Indexed: 12/28/2022] Open
Abstract
Tyrosine (Y)-recombinases have evolved to deliver mechanistically different reactions on a variety of substrates, but these evolutionary transitions are poorly understood. Among them, integron integrases are hybrid systems recombining single- and double-stranded DNA partners. These reactions are asymmetric and need a replicative resolution pathway, an exception to the canonical second strand exchange model of Y-recombinases. Integron integrases possess a specific domain for this specialized pathway. Here we show that despite this, integrases are still capable of efficiently operating the ancestral second strand exchange in symmetrical reactions between double-stranded substrates. During these reactions, both strands are reactive and Holliday junction resolution can follow either pathway. A novel deep-sequencing approach allows mapping of the crossover point for the second strand exchange. The persistence of the ancestral activity in integrases illustrates their robustness and shows that innovation towards new recombination substrates and resolution pathways was a smooth evolutionary process. The integron integrases have evolved to perform recombination of single and double stranded DNA. Here the authors show that the ancestral pathway is still functional at double stranded sites, revealing the evolution towards the modern resolution pathway.
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Ravi A, Avershina E, Foley SL, Ludvigsen J, Storrø O, Øien T, Johnsen R, McCartney AL, L’Abée-Lund TM, Rudi K. The commensal infant gut meta-mobilome as a potential reservoir for persistent multidrug resistance integrons. Sci Rep 2015; 5:15317. [PMID: 26507767 PMCID: PMC4623605 DOI: 10.1038/srep15317] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2015] [Accepted: 09/21/2015] [Indexed: 02/08/2023] Open
Abstract
Despite the accumulating knowledge on the development and establishment of the gut microbiota, its role as a reservoir for multidrug resistance is not well understood. This study investigated the prevalence and persistence patterns of an integrase gene (int1), used as a proxy for integrons (which often carry multiple antimicrobial resistance genes), in the fecal microbiota of 147 mothers and their children sampled longitudinally from birth to 2 years. The study showed the int1 gene was detected in 15% of the study population, and apparently more persistent than the microbial community structure itself. We found int1 to be persistent throughout the first two years of life, as well as between mothers and their 2-year-old children. Metagenome sequencing revealed integrons in the gut meta-mobilome that were associated with plasmids and multidrug resistance. In conclusion, the persistent nature of integrons in the infant gut microbiota makes it a potential reservoir of mobile multidrug resistance.
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Affiliation(s)
- Anuradha Ravi
- Norwegian University of Life Sciences, Chemistry, Biotechnology and Food science department (IKBM), Campus Ås, Ås 1432, Norway
| | - Ekaterina Avershina
- Norwegian University of Life Sciences, Chemistry, Biotechnology and Food science department (IKBM), Campus Ås, Ås 1432, Norway
| | - Steven L. Foley
- National Center for Toxicological Research, U.S. Food and Drug Administration, Division of Microbiology, Jefferson, AR 72079
| | - Jane Ludvigsen
- Norwegian University of Life Sciences, Chemistry, Biotechnology and Food science department (IKBM), Campus Ås, Ås 1432, Norway
| | - Ola Storrø
- Department of Public Health and General Practice, Norwegian University of Science and Technology, 9491 Trondheim, Norway
| | - Torbjørn Øien
- Department of Public Health and General Practice, Norwegian University of Science and Technology, 9491 Trondheim, Norway
| | - Roar Johnsen
- Department of Public Health and General Practice, Norwegian University of Science and Technology, 9491 Trondheim, Norway
| | - Anne L. McCartney
- Microbial Ecology & Health Group, Department of Food and Nutritional Sciences, University of Reading, Reading, UK
| | - Trine M. L’Abée-Lund
- Norwegian University of Life Sciences, Department of Food safety and Infection Biology, Campus Adamstuen, Oslo 0454, Norway
| | - Knut Rudi
- Norwegian University of Life Sciences, Chemistry, Biotechnology and Food science department (IKBM), Campus Ås, Ås 1432, Norway
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Deng Y, Bao X, Ji L, Chen L, Liu J, Miao J, Chen D, Bian H, Li Y, Yu G. Resistance integrons: class 1, 2 and 3 integrons. Ann Clin Microbiol Antimicrob 2015; 14:45. [PMID: 26487554 PMCID: PMC4618277 DOI: 10.1186/s12941-015-0100-6] [Citation(s) in RCA: 231] [Impact Index Per Article: 23.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Accepted: 08/14/2015] [Indexed: 11/30/2022] Open
Abstract
As recently indiscriminate abuse of existing antibiotics in both clinical and veterinary treatment leads to proliferation of antibiotic resistance in microbes and poses a dilemma for the future treatment of such bacterial infection, antimicrobial resistance has been considered to be one of the currently leading concerns in global public health, and reported to widely spread and extended to a large variety of microorganisms. In China, as one of the currently worst areas for antibiotics abuse, the annual prescription of antibiotics, including both clinical and veterinary treatment, has approaching 140 gram per person and been roughly estimated to be 10 times higher than that in the United Kingdom, which is considered to be a potential area for the emergence of “Super Bugs”. Based on the integrons surveillance in Guangzhou, China in the past decade, this review thus aimed at summarizing the role of integrons in the perspective of both clinical setting and environment, with the focus on the occurrence and prevalence of class 1, 2 and 3 integrons.
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Affiliation(s)
- Yang Deng
- College of Light Industry and Food Sciences, South China University of Technology, Guangzhou, 510640, China.
| | - Xuerui Bao
- College of Light Industry and Food Sciences, South China University of Technology, Guangzhou, 510640, China.
| | - Lili Ji
- College of Light Industry and Food Sciences, South China University of Technology, Guangzhou, 510640, China.
| | - Lei Chen
- Institute of Agro-products Processing, Anhui Academy of Agricultural Sciences, Hefei, 230031, China.
| | - Junyan Liu
- College of Light Industry and Food Sciences, South China University of Technology, Guangzhou, 510640, China.
| | - Jian Miao
- College of Light Industry and Food Sciences, South China University of Technology, Guangzhou, 510640, China.
| | - Dingqiang Chen
- Department of Laboratory Medicine, First Affiliated Hospital of Guangzhou Medical College, Guangzhou, 510120, China.
| | - Huawei Bian
- The Third Affiliated Hospital of Sun Yat-sen University, Guangzhou, 510630, China.
| | - Yanmei Li
- Guangzhou Women and Children's Medical Center, 9 Jinsui Road, Guangzhou, 510620, China.
| | - Guangchao Yu
- First Affiliated Hospital of Jinan University, Guangzhou, 510620, China.
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41
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Wang Q, Lu Q, Mao D, Cui Y, Luo Y. The horizontal transfer of antibiotic resistance genes is enhanced by ionic liquid with different structure of varying alkyl chain length. Front Microbiol 2015; 6:864. [PMID: 26379641 PMCID: PMC4550778 DOI: 10.3389/fmicb.2015.00864] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Accepted: 08/07/2015] [Indexed: 01/24/2023] Open
Abstract
Antibiotic resistance genes (ARGs) have become a global health concern. In our previous study, an ionic liquid (IL) 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIm][PF6]) had been proven to facilitate the dissemination of ARGs in the environment. However, enhanced alkyl group chain length or the substitution of alkyl groups with the cation ring corresponded with increased antimicrobial effects. In this study, we investigated how different structures of ILs with 4, 6, and 8 C atoms in the longer alkyl chain on the imidazolium cations facilitated the dissemination of ARGs. The promotion of plasmid RP4 transfer frequency decreased with [CnMIM][BF4] increasing the alkyl chain length from 4 carbon atoms to 8 carbon atoms on the imidazolium cations, which is observed with [BMIM][BF4] (n = 4, 5.9 fold) > HMIM][BF4] (n = 6, 2.2 fold) > [OMIM][BF4] (n = 8, 1.7 fold). This illustrates that [CnMIM][BF4] with increasing the alkyl chain length exert decreasing ability in facilitating plasmid RP4 horizontal transfer, which is possibly related to IL-structure dependent toxicity. The IL-structure dependent plasmid RP4 transfer frequency was attributable to bacterial cell membrane permeability weaken with increasing alkyl chain length of [CnMIM][PF4], which was evidenced by flow cytometry. In freshwater microcosm, [CnMIm][BF4] promoted the relative abundance of the sulI and intI genes for 4.6 folds, aphA and traF for 5.2 folds higher than the untreated groups, promoting the propagation of ARGs in the aquatic environment. This is the first report that ILs with different structure of varying alkyl chain length facilitate horizontal transfer of plasmid RP4 which is widely distributed in the environment, and thus add the adverse effects of the environmental risk of ILs.
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Affiliation(s)
- Qing Wang
- School of Environmental Science and Engineering, Tianjin UniversityTianjin, China
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai UniversityTianjin, China
| | - Qian Lu
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai UniversityTianjin, China
| | - Daqing Mao
- School of Environmental Science and Engineering, Tianjin UniversityTianjin, China
| | - Yuxiao Cui
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai UniversityTianjin, China
| | - Yi Luo
- Ministry of Education Key Laboratory of Pollution Processes and Environmental Criteria, College of Environmental Science and Engineering, Nankai UniversityTianjin, China
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42
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Domingues S, Nielsen KM, da Silva GJ. Global dissemination patterns of common gene cassette arrays in class 1 integrons. Microbiology (Reading) 2015; 161:1313-37. [DOI: 10.1099/mic.0.000099] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
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43
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Abstract
Integrons are versatile gene acquisition systems commonly found in bacterial genomes. They are ancient elements that are a hot spot for genomic complexity, generating phenotypic diversity and shaping adaptive responses. In recent times, they have had a major role in the acquisition, expression, and dissemination of antibiotic resistance genes. Assessing the ongoing threats posed by integrons requires an understanding of their origins and evolutionary history. This review examines the functions and activities of integrons before the antibiotic era. It shows how antibiotic use selected particular integrons from among the environmental pool of these elements, such that integrons carrying resistance genes are now present in the majority of Gram-negative pathogens. Finally, it examines the potential consequences of widespread pollution with the novel integrons that have been assembled via the agency of human antibiotic use and speculates on the potential uses of integrons as platforms for biotechnology.
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44
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Oliveira PH, Touchon M, Rocha EPC. The interplay of restriction-modification systems with mobile genetic elements and their prokaryotic hosts. Nucleic Acids Res 2014; 42:10618-31. [PMID: 25120263 PMCID: PMC4176335 DOI: 10.1093/nar/gku734] [Citation(s) in RCA: 220] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Revised: 07/29/2014] [Accepted: 07/30/2014] [Indexed: 01/21/2023] Open
Abstract
The roles of restriction-modification (R-M) systems in providing immunity against horizontal gene transfer (HGT) and in stabilizing mobile genetic elements (MGEs) have been much debated. However, few studies have precisely addressed the distribution of these systems in light of HGT, its mechanisms and its vectors. We analyzed the distribution of R-M systems in 2261 prokaryote genomes and found their frequency to be strongly dependent on the presence of MGEs, CRISPR-Cas systems, integrons and natural transformation. Yet R-M systems are rare in plasmids, in prophages and nearly absent from other phages. Their abundance depends on genome size for small genomes where it relates with HGT but saturates at two occurrences per genome. Chromosomal R-M systems might evolve under cycles of purifying and relaxed selection, where sequence conservation depends on the biochemical activity and complexity of the system and total gene loss is frequent. Surprisingly, analysis of 43 pan-genomes suggests that solitary R-M genes rarely arise from the degradation of R-M systems. Solitary genes are transferred by large MGEs, whereas complete systems are more frequently transferred autonomously or in small MGEs. Our results suggest means of testing the roles for R-M systems and their associations with MGEs.
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Affiliation(s)
- Pedro H Oliveira
- Institut Pasteur, Microbial Evolutionary Genomics, Département Génomes et Génétique, Paris, France CNRS, UMR3525, Paris, France
| | - Marie Touchon
- Institut Pasteur, Microbial Evolutionary Genomics, Département Génomes et Génétique, Paris, France CNRS, UMR3525, Paris, France
| | - Eduardo P C Rocha
- Institut Pasteur, Microbial Evolutionary Genomics, Département Génomes et Génétique, Paris, France CNRS, UMR3525, Paris, France
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45
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Zhang C, Pang B, Zhou Z, Wang H, Zhou H, Lu X, Du P, Zhang L, Li J, Cui Z, Chen C, Stokes HW, Kan B. The purifying trend in the chromosomal integron in Vibrio cholerae strains during the seventh pandemic. INFECTION GENETICS AND EVOLUTION 2014; 26:241-9. [PMID: 24905599 DOI: 10.1016/j.meegid.2014.05.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Revised: 05/14/2014] [Accepted: 05/17/2014] [Indexed: 12/31/2022]
Abstract
Chromosomal integron (CI) arrays in Vibrio spp. are generally large and display great variation. Here we determined the sequence of CI array in a toxigenic O139 Vibriocholerae strain and compared it with the arrays from the genome of different O1 biotypes available in GenBank. Then PCR scanning was used to determine the CI array variations in 83 epidemic O139 strains and subsequently these variations were compared with that found in toxigenic O1 El Tor strains in our previous work. Few differences were observed in the cohort of toxigenic O139 strains compared to the toxigenic O1 El Tor strains. On the basis of CI arrays, the toxigenic O1 El Tor and O139 strains isolated concurrently in recent years appear to be more similar to each other than to the O1 strains isolated in previous decades, suggesting a closer evolutionary relationship between them. Comparison of CI arrays in toxigenic O1 El Tor and O139 V. cholerae strains isolated between 1961 and 2009 revealed a purifying trend in the CI arrays in the chronological order during the seventh pandemic.
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Affiliation(s)
- Cuicai Zhang
- State Key Laboratory for Infectious Disease Prevention and Control, Department of Diarrheal Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, People's Republic of China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, People's Republic of China
| | - Bo Pang
- State Key Laboratory for Infectious Disease Prevention and Control, Department of Diarrheal Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, People's Republic of China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, People's Republic of China
| | - Zhemin Zhou
- The University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Haiyin Wang
- State Key Laboratory for Infectious Disease Prevention and Control, Department of Diarrheal Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, People's Republic of China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, People's Republic of China
| | - Haijian Zhou
- State Key Laboratory for Infectious Disease Prevention and Control, Department of Diarrheal Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, People's Republic of China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, People's Republic of China
| | - Xin Lu
- State Key Laboratory for Infectious Disease Prevention and Control, Department of Diarrheal Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, People's Republic of China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, People's Republic of China
| | - Pengcheng Du
- State Key Laboratory for Infectious Disease Prevention and Control, Department of Diarrheal Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, People's Republic of China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, People's Republic of China
| | - Lijuan Zhang
- State Key Laboratory for Infectious Disease Prevention and Control, Department of Diarrheal Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, People's Republic of China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, People's Republic of China
| | - Jie Li
- State Key Laboratory for Infectious Disease Prevention and Control, Department of Diarrheal Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, People's Republic of China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, People's Republic of China
| | - Zhigang Cui
- State Key Laboratory for Infectious Disease Prevention and Control, Department of Diarrheal Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, People's Republic of China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, People's Republic of China
| | - Chen Chen
- State Key Laboratory for Infectious Disease Prevention and Control, Department of Diarrheal Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, People's Republic of China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, People's Republic of China
| | - H W Stokes
- The ithree Institute, University of Technology, Sydney, New South Wales, Australia
| | - Biao Kan
- State Key Laboratory for Infectious Disease Prevention and Control, Department of Diarrheal Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, People's Republic of China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, People's Republic of China.
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46
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Ceccarelli D, Colwell RR. Vibrio ecology, pathogenesis, and evolution. Front Microbiol 2014; 5:256. [PMID: 24904566 PMCID: PMC4035559 DOI: 10.3389/fmicb.2014.00256] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Accepted: 05/10/2014] [Indexed: 11/13/2022] Open
Affiliation(s)
- Daniela Ceccarelli
- Department of Cell Biology and Molecular Genetics, Maryland Pathogen Research Institute, University of Maryland College Park, MD, USA
| | - Rita R Colwell
- Department of Cell Biology and Molecular Genetics, Maryland Pathogen Research Institute, University of Maryland College Park, MD, USA ; Department of Environmental Health Sciences, Johns Hopkins Bloomberg School of Public Health, Johns Hopkins University Baltimore, MD, USA
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Ravi A, Avershina E, Ludvigsen J, L'Abée-Lund TM, Rudi K. Integrons in the intestinal microbiota as reservoirs for transmission of antibiotic resistance genes. Pathogens 2014; 3:238-48. [PMID: 25437798 PMCID: PMC4243444 DOI: 10.3390/pathogens3020238] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2013] [Revised: 03/13/2014] [Accepted: 03/13/2014] [Indexed: 12/13/2022] Open
Abstract
The human intestinal microbiota plays a major beneficial role in immune development and resistance to pathogens. The use of antibiotics, however, can cause the spread of antibiotic resistance genes within the resident intestinal microbiota. Important vectors for this are integrons. This review therefore focuses on the integrons in non-pathogenic bacteria as a potential source for the development and persistence of multidrug resistance. Integrons are a group of genetic elements which are assembly platforms that can capture specific gene cassettes and express them. Integrons in pathogenic bacteria have been extensively investigated, while integrons in the intestinal microbiota have not yet gained much attention. Knowledge of the integrons residing in the microbiota, however, can potentially aid in controlling the spread of antibiotic resistance genes to pathogens.
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Affiliation(s)
- Anuradha Ravi
- Norwegian University of Life Sciences, Chemistry, Biotechnology and Food science department (IKBM), Campus Ås, Ås 1432, Norway.
| | - Ekaterina Avershina
- Norwegian University of Life Sciences, Chemistry, Biotechnology and Food science department (IKBM), Campus Ås, Ås 1432, Norway.
| | - Jane Ludvigsen
- Norwegian University of Life Sciences, Chemistry, Biotechnology and Food science department (IKBM), Campus Ås, Ås 1432, Norway.
| | - Trine M L'Abée-Lund
- Norwegian University of Life Sciences, Department of Food Safety and Infection Biology, Campus Adamstuen, Oslo 0454, Norway.
| | - Knut Rudi
- Norwegian University of Life Sciences, Chemistry, Biotechnology and Food science department (IKBM), Campus Ås, Ås 1432, Norway.
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Krin E, Cambray G, Mazel D. The superintegron integrase and the cassette promoters are co-regulated in Vibrio cholerae. PLoS One 2014; 9:e91194. [PMID: 24614503 PMCID: PMC3948777 DOI: 10.1371/journal.pone.0091194] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2013] [Accepted: 02/10/2014] [Indexed: 12/23/2022] Open
Abstract
Chromosome 2 of Vibrio cholerae carries a chromosomal superintegron, composed of an integrase, a cassette integration site (attI) and an array of mostly promoterless gene cassettes. We determined the precise location of the promoter, Pc, which drives the transcription of the first cassettes of the V. cholerae superintegron. We found that cassette mRNA starts 65 bp upstream of the attI site, so that the inversely oriented promoters Pc and Pint (integrase promoter) partly overlap, allowing for their potential co-regulation. Pint was previously shown to be induced during the SOS response and is further controlled by the catabolite repression cAMP-CRP complex. We found that cassette expression from Pc was also controlled by the cAMP-CRP complex, but is not part of the SOS regulon. Pint and Pc promoters were both found to be induced in rich medium, at high temperature, high salinity and at the end of exponential growth phase, although at very different levels and independently of sigma factor RpoS. All these results show that expression from the integrase and cassette promoters can take place at the same time, thus leading to coordinated excisions and integrations within the superintegron and potentially coupling cassette shuffling to immediate selective advantage.
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Affiliation(s)
- Evelyne Krin
- Institut Pasteur, Unité de Plasticité du Génome Bactérien, Département Génomes et Génétique, Paris, France
- CNRS, UMR 3525, Paris, France
| | - Guillaume Cambray
- Institut Pasteur, Unité de Plasticité du Génome Bactérien, Département Génomes et Génétique, Paris, France
| | - Didier Mazel
- Institut Pasteur, Unité de Plasticité du Génome Bactérien, Département Génomes et Génétique, Paris, France
- CNRS, UMR 3525, Paris, France
- * E-mail:
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Rapa RA, Labbate M. The function of integron-associated gene cassettes in Vibrio species: the tip of the iceberg. Front Microbiol 2013; 4:385. [PMID: 24367362 PMCID: PMC3856429 DOI: 10.3389/fmicb.2013.00385] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2013] [Accepted: 11/25/2013] [Indexed: 12/17/2022] Open
Abstract
The integron is a genetic element that incorporates mobile genes termed gene cassettes into a reserved genetic site via site-specific recombination. It is best known for its role in antibiotic resistance with one type of integron, the class 1 integron, a major player in the dissemination of antibiotic resistance genes across Gram negative pathogens and commensals. However, integrons are ancient structures with over 100 classes (including class 1) present in bacteria from the broader environment. While, the class 1 integron is only one example of an integron being mobilized into the clinical environment, it is by far the most successful. Unlike clinical class 1 integrons which are largely found on plasmids, other integron classes are found on the chromosomes of bacteria and carry diverse gene cassettes indicating a non-antibiotic resistance role(s). However, there is very limited knowledge on what these alternative roles are. This is particularly relevant to Vibrio species where gene cassettes make up approximately 1-3% of their entire genome. In this review, we discuss how emphasis on class 1 integron research has resulted in a limited understanding by the wider research community on the role of integrons in the broader environment. This has the capacity to be counterproductive in solving or improving the antibiotic resistance problem into the future. Furthermore, there is still a significant lack of knowledge on how gene cassettes in Vibrio species drive adaptation and evolution. From research in Vibrio rotiferianus DAT722, new insight into how gene cassettes affect cellular physiology offers new alternative roles for the gene cassette resource. At least a subset of gene cassettes are involved in host surface polysaccharide modification suggesting that gene cassettes may be important in processes such as bacteriophage resistance, adhesion/biofilm formation, protection from grazers and bacterial aggregation.
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Affiliation(s)
- Rita A Rapa
- ithree Institute, University of Technology Sydney, NSW, Australia ; Department of Medical and Molecular Biosciences, University of Technology Sydney, NSW, Australia
| | - Maurizio Labbate
- ithree Institute, University of Technology Sydney, NSW, Australia ; Department of Medical and Molecular Biosciences, University of Technology Sydney, NSW, Australia
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The integron integrase efficiently prevents the melting effect of Escherichia coli single-stranded DNA-binding protein on folded attC sites. J Bacteriol 2013; 196:762-71. [PMID: 24296671 DOI: 10.1128/jb.01109-13] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Integrons play a major role in the dissemination of antibiotic resistance genes among bacteria. Rearrangement of gene cassettes occurs by recombination between attI and attC sites, catalyzed by the integron integrase. Integron recombination uses an unconventional mechanism involving a folded single-stranded attC site. This site could be a target for several host factors and more precisely for proteins able to bind single-stranded DNA. One of these, Escherichia coli single-stranded DNA-binding protein (SSB), regulates many DNA processes. We studied the influence of this protein on integron recombination. Our results show the ability of SSB to strongly bind folded attC sites and to destabilize them. This effect was observed only in the absence of the integrase. Indeed, we provided evidence that the integrase is able to counterbalance the observed effect of SSB on attC site folding. We showed that IntI1 possesses an intrinsic property to capture attC sites at the moment of their extrusion, stabilizing them and recombining them efficiently. The stability of DNA secondary structures in the chromosome must be restrained to avoid genetic instability (mutations or deletions) and/or toxicity (replication arrest). SSB, which hampers attC site folding in the absence of the integrase, likely plays an important role in maintaining the integrity and thus the recombinogenic functionality of the integron attC sites. We also tested the RecA host factor and excluded any role of this protein in integron recombination.
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