RT Journal Article SR Electronic T1 Integrative and Conjugative Elements (ICE) and Associated Cargo Genes within and across Hundreds of Bacterial Genera JF bioRxiv FD Cold Spring Harbor Laboratory SP 2020.04.07.030320 DO 10.1101/2020.04.07.030320 A1 James H Kaufman A1 Ignacio Terrizzano A1 Gowri Nayar A1 Ed Seabolt A1 Akshay Agarwal A1 Ilya B Slizovskiy A1 Noelle Noyes YR 2020 UL http://biorxiv.org/content/early/2020/08/03/2020.04.07.030320.abstract AB 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 StatementThe authors have declared no competing interest.