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Integrative and Conjugative Elements (ICE) and Associated Cargo Genes within and across Hundreds of Bacterial Genera

View ORCID ProfileJames H Kaufman, View ORCID ProfileIgnacio Terrizzano, View ORCID ProfileGowri Nayar, Ed Seabolt, Akshay Agarwal, Ilya B Slizovskiy, View ORCID ProfileNoelle Noyes
doi: https://doi.org/10.1101/2020.04.07.030320
James H Kaufman
1IBM Research- Almaden, 650 Harry Road, San Jose, CA, 95126, USA
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  • For correspondence: jhkauf@us.ibm.com
Ignacio Terrizzano
1IBM Research- Almaden, 650 Harry Road, San Jose, CA, 95126, USA
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  • ORCID record for Ignacio Terrizzano
Gowri Nayar
1IBM Research- Almaden, 650 Harry Road, San Jose, CA, 95126, USA
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Ed Seabolt
1IBM Research- Almaden, 650 Harry Road, San Jose, CA, 95126, USA
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Akshay Agarwal
1IBM Research- Almaden, 650 Harry Road, San Jose, CA, 95126, USA
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Ilya B Slizovskiy
2Department of Veterinary Population Medicine, University of Minnesota, 1988 Fitch Ave, St. Paul, MN, 55108, USA
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Noelle Noyes
2Department of Veterinary Population Medicine, University of Minnesota, 1988 Fitch Ave, St. Paul, MN, 55108, USA
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Abstract

Horizontal gene transfer mediated by integrative and conjugative elements (ICE) is considered an important evolutionary mechanism of bacteria. It allows organisms to quickly evolve new phenotypic properties including antimicrobial resistance (AMR) and virulence. The rate of ICE-mediated cargo gene exchange has not yet been comprehensively studied within and between bacterial taxa. In this paper we report a big data analysis of ICE and associated cargo genes across over 200,000 bacterial genomes representing 1,345 genera. Our results reveal that half of bacterial genomes contain one or more known ICE features (“ICE genomes”), and that the associated genetic cargo may play an important role in the spread of AMR genes within and between bacterial genera. We identify 43 AMR genes that appear only in ICE genomes and never in non-ICE genomes. A further set of 95 AMR genes are found >5x more often in ICE versus non-ICE genomes. In contrast, only 29 AMR genes are observed more frequently (at least 5:1) in non-ICE genomes compared to ICE genomes. Analysis of NCBI antibiotic susceptibility assay data reveals that ICE genomes are also over-represented amongst phenotypically resistant isolates, suggesting that ICE processes are critical for both genotypic and phenotypic AMR. These results, as well as the underlying big data resource, are important foundational tools for understanding bacterial evolution, particularly in relation to important bacterial phenotypes such as AMR.

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-ND 4.0 International license.
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Posted August 03, 2020.
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Integrative and Conjugative Elements (ICE) and Associated Cargo Genes within and across Hundreds of Bacterial Genera
James H Kaufman, Ignacio Terrizzano, Gowri Nayar, Ed Seabolt, Akshay Agarwal, Ilya B Slizovskiy, Noelle Noyes
bioRxiv 2020.04.07.030320; doi: https://doi.org/10.1101/2020.04.07.030320
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Integrative and Conjugative Elements (ICE) and Associated Cargo Genes within and across Hundreds of Bacterial Genera
James H Kaufman, Ignacio Terrizzano, Gowri Nayar, Ed Seabolt, Akshay Agarwal, Ilya B Slizovskiy, Noelle Noyes
bioRxiv 2020.04.07.030320; doi: https://doi.org/10.1101/2020.04.07.030320

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