Treffer: MetaCherchant: analyzing genomic context of antibiotic resistance genes in gut microbiota.

Title:
MetaCherchant: analyzing genomic context of antibiotic resistance genes in gut microbiota.
Authors:
Olekhnovich EI; Federal Research and Clinical Centre of Physical and Chemical Medicine, Federal Medical and Biological Agency of Russia, Moscow, Russian Federation., Vasilyev AT; ITMO University, Saint Petersburg, Russian Federation.; JetBrains Research, Russian Federation., Ulyantsev VI; ITMO University, Saint Petersburg, Russian Federation., Kostryukova ES; Federal Research and Clinical Centre of Physical and Chemical Medicine, Federal Medical and Biological Agency of Russia, Moscow, Russian Federation., Tyakht AV; Federal Research and Clinical Centre of Physical and Chemical Medicine, Federal Medical and Biological Agency of Russia, Moscow, Russian Federation.; ITMO University, Saint Petersburg, Russian Federation.
Source:
Bioinformatics (Oxford, England) [Bioinformatics] 2018 Feb 01; Vol. 34 (3), pp. 434-444.
Publication Type:
Journal Article; Research Support, Non-U.S. Gov't
Language:
English
Journal Info:
Publisher: Oxford University Press Country of Publication: England NLM ID: 9808944 Publication Model: Print Cited Medium: Internet ISSN: 1367-4811 (Electronic) Linking ISSN: 13674803 NLM ISO Abbreviation: Bioinformatics Subsets: MEDLINE
Imprint Name(s):
Original Publication: Oxford : Oxford University Press, c1998-
MeSH Terms:
Software*, Bacteria/*genetics , Drug Resistance, Bacterial/*genetics , Gastrointestinal Microbiome/*genetics , Metagenomics/*methods, Algorithms ; Humans
Entry Date(s):
Date Created: 20171102 Date Completed: 20181226 Latest Revision: 20181226
Update Code:
20250114
DOI:
10.1093/bioinformatics/btx681
PMID:
29092015
Database:
MEDLINE

Weitere Informationen

Motivation: Antibiotic resistance is an important global public health problem. Human gut microbiota is an accumulator of resistance genes potentially providing them to pathogens. It is important to develop tools for identifying the mechanisms of how resistance is transmitted between gut microbial species and pathogens.
Results: We developed MetaCherchant-an algorithm for extracting the genomic environment of antibiotic resistance genes from metagenomic data in the form of a graph. The algorithm was validated on a number of simulated and published datasets, as well as applied to new 'shotgun' metagenomes of gut microbiota from patients with Helicobacter pylori who underwent antibiotic therapy. Genomic context was reconstructed for several major resistance genes. Taxonomic annotation of the context suggests that within a single metagenome, the resistance genes can be contained in genomes of multiple species. MetaCherchant allows reconstruction of mobile elements with resistance genes within the genomes of bacteria using metagenomic data. Application of MetaCherchant in differential mode produced specific graph structures suggesting the evidence of possible resistance gene transmission within a mobile element that occurred as a result of the antibiotic therapy. MetaCherchant is a promising tool giving researchers an opportunity to get an insight into dynamics of resistance transmission in vivo basing on metagenomic data.
Availability and Implementation: Source code and binaries are freely available for download at https://github.com/ctlab/metacherchant. The code is written in Java and is platform-independent.
Cotanct: ulyantsev@rain.ifmo.ru.
Supplementary Information: Supplementary data are available at Bioinformatics online.
(© The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com)