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IntegronFinder 2.0: identification and analysis of integrons across Bacteria, with a focus on antibiotic resistance in Klebsiella

Bertrand Néron, Eloi Littner, View ORCID ProfileMatthieu Haudiquet, View ORCID ProfileAmandine Perrin, View ORCID ProfileJean Cury, View ORCID ProfileEduardo P.C. Rocha
doi: https://doi.org/10.1101/2022.02.28.482270
Bertrand Néron
1Institut Pasteur, Université de Paris, Bioinformatics and Biostatistics Hub, Paris, France
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Eloi Littner
2Institut Pasteur, Université de Paris, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, France
3DGA CBRN Defence Center, Vert-le-Petit, France
4Sorbonne Université, Collège Doctoral, Paris, France
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Matthieu Haudiquet
2Institut Pasteur, Université de Paris, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, France
5Ecole Doctoral FIRE–Programme Bettencourt, CRI, Paris, France
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Amandine Perrin
1Institut Pasteur, Université de Paris, Bioinformatics and Biostatistics Hub, Paris, France
2Institut Pasteur, Université de Paris, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, France
4Sorbonne Université, Collège Doctoral, Paris, France
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Jean Cury
2Institut Pasteur, Université de Paris, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, France
6Université Paris-Saclay, CNRS UMR 9015, INRIA, Laboratoire Interdisciplinaire des Sciences du Numérique, Orsay, France
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  • For correspondence: jean.cury@normalesup.org erocha@pasteur.fr
Eduardo P.C. Rocha
2Institut Pasteur, Université de Paris, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, France
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  • For correspondence: jean.cury@normalesup.org erocha@pasteur.fr
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Abstract

Integrons are mobile genetic elements that contain multiple cassettes encoding accessory genes whose order is shuffled by a specific integrase. Integrons within mobile genetic elements often contain multiple antibiotic resistance genes that they spread among nosocomial pathogens and contribute to the current antibiotic resistance crisis. However, most integrons are presumably sedentary and encode a much broader diversity of functions. IntegronFinder is a widely used software to identify novel integrons in bacterial genomes, but has aged and lacks some useful functionalities to handle very large datasets of draft genomes or metagenomes. Here, we present IntegronFinder version 2. We have updated the code, improved its efficiency and usability, adapted the output to incomplete genome data, and added a few novel functions. We describe these changes and illustrate the relevance of the program by analyzing the distribution of integrons across more than 20,000 fully sequenced genomes. We also take full advantage of its novel capabilities to analyze close to 4 thousand Klebsiella pneumoniae genomes for the presence of integrons and antibiotic resistance genes within them. Our data shows that K. pneumoniae has a large diversity of integrons and the largest mobile integron in our database of plasmids. The pangenome of these integrons contains a total of 165 different gene families with most of the largest families being related with resistance to numerous types of antibiotics. IntegronFinder is a free and open-source software available at https://github.com/gem-pasteur/Integron_Finder.

Competing Interest Statement

The authors have declared no competing interest.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC 4.0 International license.
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Posted March 02, 2022.
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IntegronFinder 2.0: identification and analysis of integrons across Bacteria, with a focus on antibiotic resistance in Klebsiella
Bertrand Néron, Eloi Littner, Matthieu Haudiquet, Amandine Perrin, Jean Cury, Eduardo P.C. Rocha
bioRxiv 2022.02.28.482270; doi: https://doi.org/10.1101/2022.02.28.482270
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IntegronFinder 2.0: identification and analysis of integrons across Bacteria, with a focus on antibiotic resistance in Klebsiella
Bertrand Néron, Eloi Littner, Matthieu Haudiquet, Amandine Perrin, Jean Cury, Eduardo P.C. Rocha
bioRxiv 2022.02.28.482270; doi: https://doi.org/10.1101/2022.02.28.482270

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