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

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Item Type:Article
Title:Landscape of mobile genetic elements and their antibiotic resistance cargo in prokaryotic genomes
Creators Name:Khedkar, S. and Smyshlyaev, G. and Letunic, I. and Maistrenko, O.M. and Coelho, L.P. and Orakov, A. and Forslund, S.K. and Hildebrand, F. and Luetge, M. and Schmidt, T.S.B. and Barabas, O. and Bork, P.
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.
Keywords:Bacteria, Bacteriophages, DNA Transposable Elements, Microbial Drug Resistance, Horizontal Gene Transfer, Phylogeny, Recombinases / Genetics
Source:Nucleic Acids Research
Publisher:Oxford University Press
Page Range:3155-3168
Date:8 April 2022
Official Publication:https://doi.org/10.1093/nar/gkac163
PubMed:View item in PubMed

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