IntegronFinder 2.0: Identification and Analysis of Integrons across Bacteria, with a Focus on Antibiotic Resistance in Klebsiella
Integrons are flexible gene-exchanging platforms that contain multiple cassettes encoding accessory genes whose order is shuffled by a specific integrase. Integrons embedded within mobile genetic elements often contain multiple antibiotic resistance genes that they spread among nosocomial pathogens...
| Main Authors: | , , , , , |
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| Format: | Article |
| Language: | English |
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MDPI AG
2022-03-01
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| Series: | Microorganisms |
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| Online Access: | https://www.mdpi.com/2076-2607/10/4/700 |
| _version_ | 1797444775807287296 |
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| author | Bertrand Néron Eloi Littner Matthieu Haudiquet Amandine Perrin Jean Cury Eduardo P. C. Rocha |
| author_facet | Bertrand Néron Eloi Littner Matthieu Haudiquet Amandine Perrin Jean Cury Eduardo P. C. Rocha |
| author_sort | Bertrand Néron |
| collection | DOAJ |
| description | Integrons are flexible gene-exchanging platforms that contain multiple cassettes encoding accessory genes whose order is shuffled by a specific integrase. Integrons embedded 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 4000 <i>Klebsiella pneumoniae</i> genomes for the presence of integrons and antibiotic resistance genes within them. Our data show that <i>K. pneumoniae</i> 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 on multiple public platforms. |
| first_indexed | 2024-03-09T13:16:25Z |
| format | Article |
| id | doaj.art-60d097f8e95e40d780b8b6111baca133 |
| institution | Directory Open Access Journal |
| issn | 2076-2607 |
| language | English |
| last_indexed | 2024-03-09T13:16:25Z |
| publishDate | 2022-03-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Microorganisms |
| spelling | doaj.art-60d097f8e95e40d780b8b6111baca1332023-11-30T21:34:48ZengMDPI AGMicroorganisms2076-26072022-03-0110470010.3390/microorganisms10040700IntegronFinder 2.0: Identification and Analysis of Integrons across Bacteria, with a Focus on Antibiotic Resistance in KlebsiellaBertrand Néron0Eloi Littner1Matthieu Haudiquet2Amandine Perrin3Jean Cury4Eduardo P. C. Rocha5Bioinformatics and Biostatistics Hub, Institut Pasteur, Université de Paris Cité, 75015 Paris, FranceMicrobial Evolutionary Genomics, Institut Pasteur, Université de Paris Cité, CNRS UMR3525, 75015 Paris, FranceMicrobial Evolutionary Genomics, Institut Pasteur, Université de Paris Cité, CNRS UMR3525, 75015 Paris, FranceBioinformatics and Biostatistics Hub, Institut Pasteur, Université de Paris Cité, 75015 Paris, FranceMicrobial Evolutionary Genomics, Institut Pasteur, Université de Paris Cité, CNRS UMR3525, 75015 Paris, FranceMicrobial Evolutionary Genomics, Institut Pasteur, Université de Paris Cité, CNRS UMR3525, 75015 Paris, FranceIntegrons are flexible gene-exchanging platforms that contain multiple cassettes encoding accessory genes whose order is shuffled by a specific integrase. Integrons embedded 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 4000 <i>Klebsiella pneumoniae</i> genomes for the presence of integrons and antibiotic resistance genes within them. Our data show that <i>K. pneumoniae</i> 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 on multiple public platforms.https://www.mdpi.com/2076-2607/10/4/700integronantibiotic resistancebioinformaticsgenomics |
| spellingShingle | Bertrand Néron Eloi Littner Matthieu Haudiquet Amandine Perrin Jean Cury Eduardo P. C. Rocha IntegronFinder 2.0: Identification and Analysis of Integrons across Bacteria, with a Focus on Antibiotic Resistance in Klebsiella Microorganisms integron antibiotic resistance bioinformatics genomics |
| title | IntegronFinder 2.0: Identification and Analysis of Integrons across Bacteria, with a Focus on Antibiotic Resistance in Klebsiella |
| title_full | IntegronFinder 2.0: Identification and Analysis of Integrons across Bacteria, with a Focus on Antibiotic Resistance in Klebsiella |
| title_fullStr | IntegronFinder 2.0: Identification and Analysis of Integrons across Bacteria, with a Focus on Antibiotic Resistance in Klebsiella |
| title_full_unstemmed | IntegronFinder 2.0: Identification and Analysis of Integrons across Bacteria, with a Focus on Antibiotic Resistance in Klebsiella |
| title_short | IntegronFinder 2.0: Identification and Analysis of Integrons across Bacteria, with a Focus on Antibiotic Resistance in Klebsiella |
| title_sort | integronfinder 2 0 identification and analysis of integrons across bacteria with a focus on antibiotic resistance in klebsiella |
| topic | integron antibiotic resistance bioinformatics genomics |
| url | https://www.mdpi.com/2076-2607/10/4/700 |
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