Scientific article
OA Policy
English

Landscape of mobile genetic elements and their antibiotic resistance cargo in prokaryotic genomes

Published inNucleic Acids Research, vol. 50, no. 6, p. 3155-3168
Publication date2022-04-08
First online date2022-03-22
Abstract

Prokaryotic Mobile Genetic Elements (MGEs) such as transposons, integrons, phages and plasmids, play important roles in prokaryotic evolution and in the dispersal of cargo functions like antibiotic resistance. However, each of these MGE types is usually annotated and analysed individually, hampering a global understanding of phylogenetic and environmental patterns of MGE dispersal. We thus developed a computational framework that captures diverse MGE types, their cargos and MGE-mediated horizontal transfer events, using recombinases as ubiquitous MGE marker genes and pangenome information for MGE boundary estimation. Applied to ∼84k genomes with habitat annotation, we mapped 2.8 million MGE-specific recombinases to six operational MGE types, which together contain on average 13% of all the genes in a genome. Transposable elements (TEs) dominated across all taxa (∼1.7 million occurrences), outnumbering phages and phage-like elements (<0.4 million). We recorded numerous MGE-mediated horizontal transfer events across diverse phyla and habitats involving all MGE types, disentangled and quantified the extent of hitchhiking of TEs (17%) and integrons (63%) with other MGE categories, and established TEs as dominant carriers of antibiotic resistance genes. We integrated all these findings into a resource (proMGE.embl.de), which should facilitate future studies on the large mobile part of genomes and its horizontal dispersal.

Funding
  • Biotechnology and Biological Sciences Research Council - [BBS/E/F/000PR10353]
  • Federal Ministry of Education and Research - [FKZ 01Kl1706]
  • European Molecular Biology Laboratory -
  • Shanghai Municipal Science and Technology - [2018SHZDZX01]
  • European Research Council - [ERC-AdG-669830]
  • EMBARK JPIAMR -
  • Earlham Institute (Funder) - [EI-G-FH]
  • German Network for Bioinformatics Infrastructure - [031L0181A]
Citation (ISO format)
KHEDKAR, Supriya et al. Landscape of mobile genetic elements and their antibiotic resistance cargo in prokaryotic genomes. In: Nucleic Acids Research, 2022, vol. 50, n° 6, p. 3155–3168. doi: 10.1093/nar/gkac163
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Article (Published version)
Identifiers
ISSN of the journal0305-1048
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