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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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2
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Papa-Ezdra R, Outeda M, Cordeiro NF, Araújo L, Gadea P, Garcia-Fulgueiras V, Seija V, Bado I, Vignoli R. Outbreak of Pseudomonas aeruginosa High-Risk Clone ST309 Serotype O11 Featuring blaPER-1 and qnrVC6. Antibiotics (Basel) 2024; 13:159. [PMID: 38391545 PMCID: PMC10885872 DOI: 10.3390/antibiotics13020159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 12/26/2023] [Accepted: 12/27/2023] [Indexed: 02/24/2024] Open
Abstract
Pseudomonas aeruginosa is a leading cause of hospital-acquired infections worldwide. Biofilm production, antibiotic resistance, and a wide range of virulence factors contribute to their persistence in nosocomial environments. We describe an outbreak caused by a multidrug-resistant P. aeruginosa strain in an ICU. Antibiotic susceptibility was determined and blaPER-1 and qnrVC were amplified via PCR. Clonality was determined using PFGE and biofilm formation was studied with a static model. A combination of antibiotics was assessed on both planktonic cells and biofilms. WGS was performed on five isolates. All isolates were clonally related, resistant to ceftazidime, cefepime, amikacin, and ceftolozane-tazobactam, and harbored blaPER-1; 11/19 possessed qnrVC. Meropenem and ciprofloxacin reduced the biofilm biomass; however, the response to antibiotic combinations with rifampicin was different between planktonic cells and biofilms. WGS revealed that the isolates belonged to ST309 and serotype O11. blaPER-1 and qnrVC6 were associated with a tandem of ISCR1 as part of a complex class one integron, with aac(6')-Il and ltrA as gene cassettes. The structure was associated upstream and downstream with Tn4662 and flanked by direct repeats, suggesting its horizontal mobilization capability as a composite transposon. ST309 is considered an emerging high-risk clone that should be monitored in the Americas.
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Affiliation(s)
- Romina Papa-Ezdra
- Departamento de Bacteriología y Virología, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Av. Alfredo Navarro 3051, CP 11600 Montevideo, Uruguay
| | - Matilde Outeda
- Departamento de Laboratorio Clínico, Área Microbiología, Hospital de Clínicas, Facultad de Medicina, Universidad de la República, Av. Italia s/n, CP 11600 Montevideo, Uruguay
| | - Nicolás F Cordeiro
- Departamento de Bacteriología y Virología, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Av. Alfredo Navarro 3051, CP 11600 Montevideo, Uruguay
| | - Lucía Araújo
- Departamento de Bacteriología y Virología, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Av. Alfredo Navarro 3051, CP 11600 Montevideo, Uruguay
| | - Pilar Gadea
- Departamento de Laboratorio Clínico, Área Microbiología, Hospital de Clínicas, Facultad de Medicina, Universidad de la República, Av. Italia s/n, CP 11600 Montevideo, Uruguay
| | - Virginia Garcia-Fulgueiras
- Departamento de Bacteriología y Virología, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Av. Alfredo Navarro 3051, CP 11600 Montevideo, Uruguay
| | - Verónica Seija
- Departamento de Laboratorio Clínico, Área Microbiología, Hospital de Clínicas, Facultad de Medicina, Universidad de la República, Av. Italia s/n, CP 11600 Montevideo, Uruguay
| | - Inés Bado
- Departamento de Bacteriología y Virología, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Av. Alfredo Navarro 3051, CP 11600 Montevideo, Uruguay
| | - Rafael Vignoli
- Departamento de Bacteriología y Virología, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Av. Alfredo Navarro 3051, CP 11600 Montevideo, Uruguay
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3
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Loot C, Millot GA, Richard E, Littner E, Vit C, Lemoine F, Néron B, Cury J, Darracq B, Niault T, Lapaillerie D, Parissi V, Rocha EPC, Mazel D. Integron cassettes integrate into bacterial genomes via widespread non-classical attG sites. Nat Microbiol 2024; 9:228-240. [PMID: 38172619 DOI: 10.1038/s41564-023-01548-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 11/07/2023] [Indexed: 01/05/2024]
Abstract
Integrons are genetic elements involved in bacterial adaptation which capture, shuffle and express genes encoding adaptive functions embedded in cassettes. These events are governed by the integron integrase through site-specific recombination between attC and attI integron sites. Using computational and molecular genetic approaches, here we demonstrate that the integrase also catalyses cassette integration into bacterial genomes outside of its known att sites. Once integrated, these cassettes can be expressed if located near bacterial promoters and can be excised at the integration point or outside, inducing chromosomal modifications in the latter case. Analysis of more than 5 × 105 independent integration events revealed a very large genomic integration landscape. We identified consensus recombination sequences, named attG sites, which differ greatly in sequence and structure from classical att sites. These results unveil an alternative route for dissemination of adaptive functions in bacteria and expand the role of integrons in bacterial evolution.
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Affiliation(s)
- Céline Loot
- Institut Pasteur, Université Paris Cité, CNRS UMR 3525, Unité Plasticité du Génome Bactérien, Paris, France.
| | - Gael A Millot
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, France
| | - Egill Richard
- Institut Pasteur, Université Paris Cité, CNRS UMR 3525, Unité Plasticité du Génome Bactérien, Paris, France
- Sorbonne Université, Collège Doctoral, Paris, France
| | - Eloi Littner
- Sorbonne Université, Collège Doctoral, Paris, France
- DGA CBRN Defence, Vert-le-Petit, France
- Institut Pasteur, Université Paris Cité, CNRS UMR 3525, Microbial Evolutionary Genomics, Paris, France
| | - Claire Vit
- Institut Pasteur, Université Paris Cité, CNRS UMR 3525, Unité Plasticité du Génome Bactérien, Paris, France
- Sorbonne Université, Collège Doctoral, Paris, France
| | - Frédéric Lemoine
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, France
| | - Bertrand Néron
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, France
| | - Jean Cury
- Université Paris-Saclay, Inria, Laboratoire de Recherche en Informatique, CNRS UMR 8623, Orsay, France
| | - Baptiste Darracq
- Institut Pasteur, Université Paris Cité, CNRS UMR 3525, Unité Plasticité du Génome Bactérien, Paris, France
- Sorbonne Université, Collège Doctoral, Paris, France
| | - Théophile Niault
- Institut Pasteur, Université Paris Cité, CNRS UMR 3525, Unité Plasticité du Génome Bactérien, Paris, France
- Sorbonne Université, Collège Doctoral, Paris, France
| | - Delphine Lapaillerie
- Université de Bordeaux, Fundamental Microbiology and Pathogenicity Laboratory, CNRS UMR 5234, Département de Sciences Biologiques et Médicales, Bordeaux, France
- Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), Bordeaux, France
| | - Vincent Parissi
- Université de Bordeaux, Fundamental Microbiology and Pathogenicity Laboratory, CNRS UMR 5234, Département de Sciences Biologiques et Médicales, Bordeaux, France
- Viral DNA Integration and Chromatin Dynamics Network (DyNAVir), Bordeaux, France
| | - Eduardo P C Rocha
- Institut Pasteur, Université Paris Cité, CNRS UMR 3525, Microbial Evolutionary Genomics, Paris, France
| | - Didier Mazel
- Institut Pasteur, Université Paris Cité, CNRS UMR 3525, Unité Plasticité du Génome Bactérien, Paris, France
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4
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Baltazar-Cruz J, Rojas-Rios R, Larios-Serrato V, Mendoza-Sanchez I, Curiel-Quesada E, Pérez-Valdespino A. A Class 4-like Chromosomal Integron Found in Aeromonas sp. Genomospecies paramedia Isolated from Human Feces. Microorganisms 2023; 11:2548. [PMID: 37894206 PMCID: PMC10609294 DOI: 10.3390/microorganisms11102548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 09/29/2023] [Accepted: 10/12/2023] [Indexed: 10/29/2023] Open
Abstract
Integrons are genetic elements that store, express and exchange gene cassettes. These elements are characterized by containing a gene that codes for an integrase (intI), a cassette integration site (attI) and a variable region holding the cassettes. Using bioinformatics and molecular biology methods, a functional integron found in Aeromonas sp. 3925, a strain isolated from diarrheal stools, is described. To confirm the integron class, a phylogenetic analysis with amino acid sequences was conducted. The integrase was associated to class 4 integrases; however, it is clearly different from them. Thus, we classified the associated element as a class 4-like integron. We found that the integrase activity is not under the control of the SOS or catabolic repression, since the expression was not increased in the presence of mitomycin or arabinose. The class-4-like integron is located on the chromosome and contains two well-defined gene cassettes: aadA1 that confers resistance to streptomycin and lpt coding for a lipoprotein. It also includes eight Open Reading frames (ORFs) with unknown functions. The strain was characterized through a Multilocus Phylogenetic Analyses (MLPA) of the gyrB, gyrA, rpoD, recA, dnaJ and dnaX genes. The phylogenetic results grouped it into a different clade from the species already reported, making it impossible to assign a species. We resorted to undertaking complete genome sequencing and a phylogenomic analysis. Aeromonas sp. 3925 is related to A. media and A. rivipollensis clusters, but it is clearly different from these species. In silico DNA-DNA hybridization (isDDH) and Average Nucleotide Identity (ANI) analyses suggested that this isolate belongs to the genomospecies paramedia. This paper describes the first class 4-like integron in Aeromonas and contributes to the establishment of genomospecies paramedia.
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Affiliation(s)
- Jesús Baltazar-Cruz
- Department of Biochemistry, Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Col. Santo Tomás, Mexico City 11340, Mexico; (J.B.-C.); (R.R.-R.); (V.L.-S.)
| | - Rogelio Rojas-Rios
- Department of Biochemistry, Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Col. Santo Tomás, Mexico City 11340, Mexico; (J.B.-C.); (R.R.-R.); (V.L.-S.)
| | - Violeta Larios-Serrato
- Department of Biochemistry, Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Col. Santo Tomás, Mexico City 11340, Mexico; (J.B.-C.); (R.R.-R.); (V.L.-S.)
| | - Itza Mendoza-Sanchez
- Department of Environmental & Occupational Health, Texas A&M University School of Public Health, College Station, TX 77843, USA;
| | - Everardo Curiel-Quesada
- Department of Biochemistry, Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Col. Santo Tomás, Mexico City 11340, Mexico; (J.B.-C.); (R.R.-R.); (V.L.-S.)
| | - Abigail Pérez-Valdespino
- Department of Biochemistry, Escuela Nacional de Ciencias Biológicas del Instituto Politécnico Nacional, Prolongación de Carpio y Plan de Ayala S/N, Col. Santo Tomás, Mexico City 11340, Mexico; (J.B.-C.); (R.R.-R.); (V.L.-S.)
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