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Forecasting the dissemination of antibiotic resistance genes across bacterial genomes

Antibiotic resistance spreads among bacteria through horizontal transfer of antibiotic resistance genes (ARGs). Here, we set out to determine predictive features of ARG transfer among bacterial clades. We use a statistical framework to identify putative horizontally transferred ARGs and the groups o...

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Autores principales: Ellabaan, Mostafa M. H., Munck, Christian, Porse, Andreas, Imamovic, Lejla, Sommer, Morten O. A.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Nature Publishing Group UK 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8065159/
https://www.ncbi.nlm.nih.gov/pubmed/33893312
http://dx.doi.org/10.1038/s41467-021-22757-1
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author Ellabaan, Mostafa M. H.
Munck, Christian
Porse, Andreas
Imamovic, Lejla
Sommer, Morten O. A.
author_facet Ellabaan, Mostafa M. H.
Munck, Christian
Porse, Andreas
Imamovic, Lejla
Sommer, Morten O. A.
author_sort Ellabaan, Mostafa M. H.
collection PubMed
description Antibiotic resistance spreads among bacteria through horizontal transfer of antibiotic resistance genes (ARGs). Here, we set out to determine predictive features of ARG transfer among bacterial clades. We use a statistical framework to identify putative horizontally transferred ARGs and the groups of bacteria that disseminate them. We identify 152 gene exchange networks containing 22,963 bacterial genomes. Analysis of ARG-surrounding sequences identify genes encoding putative mobilisation elements such as transposases and integrases that may be involved in gene transfer between genomes. Certain ARGs appear to be frequently mobilised by different mobile genetic elements. We characterise the phylogenetic reach of these mobilisation elements to predict the potential future dissemination of known ARGs. Using a separate database with 472,798 genomes from Streptococcaceae, Staphylococcaceae and Enterobacteriaceae, we confirm 34 of 94 predicted mobilisations. We explore transfer barriers beyond mobilisation and show experimentally that physiological constraints of the host can explain why specific genes are largely confined to Gram-negative bacteria although their mobile elements support dissemination to Gram-positive bacteria. Our approach may potentially enable better risk assessment of future resistance gene dissemination.
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spelling pubmed-80651592021-05-11 Forecasting the dissemination of antibiotic resistance genes across bacterial genomes Ellabaan, Mostafa M. H. Munck, Christian Porse, Andreas Imamovic, Lejla Sommer, Morten O. A. Nat Commun Article Antibiotic resistance spreads among bacteria through horizontal transfer of antibiotic resistance genes (ARGs). Here, we set out to determine predictive features of ARG transfer among bacterial clades. We use a statistical framework to identify putative horizontally transferred ARGs and the groups of bacteria that disseminate them. We identify 152 gene exchange networks containing 22,963 bacterial genomes. Analysis of ARG-surrounding sequences identify genes encoding putative mobilisation elements such as transposases and integrases that may be involved in gene transfer between genomes. Certain ARGs appear to be frequently mobilised by different mobile genetic elements. We characterise the phylogenetic reach of these mobilisation elements to predict the potential future dissemination of known ARGs. Using a separate database with 472,798 genomes from Streptococcaceae, Staphylococcaceae and Enterobacteriaceae, we confirm 34 of 94 predicted mobilisations. We explore transfer barriers beyond mobilisation and show experimentally that physiological constraints of the host can explain why specific genes are largely confined to Gram-negative bacteria although their mobile elements support dissemination to Gram-positive bacteria. Our approach may potentially enable better risk assessment of future resistance gene dissemination. Nature Publishing Group UK 2021-04-23 /pmc/articles/PMC8065159/ /pubmed/33893312 http://dx.doi.org/10.1038/s41467-021-22757-1 Text en © The Author(s) 2021 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) .
spellingShingle Article
Ellabaan, Mostafa M. H.
Munck, Christian
Porse, Andreas
Imamovic, Lejla
Sommer, Morten O. A.
Forecasting the dissemination of antibiotic resistance genes across bacterial genomes
title Forecasting the dissemination of antibiotic resistance genes across bacterial genomes
title_full Forecasting the dissemination of antibiotic resistance genes across bacterial genomes
title_fullStr Forecasting the dissemination of antibiotic resistance genes across bacterial genomes
title_full_unstemmed Forecasting the dissemination of antibiotic resistance genes across bacterial genomes
title_short Forecasting the dissemination of antibiotic resistance genes across bacterial genomes
title_sort forecasting the dissemination of antibiotic resistance genes across bacterial genomes
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8065159/
https://www.ncbi.nlm.nih.gov/pubmed/33893312
http://dx.doi.org/10.1038/s41467-021-22757-1
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