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Review and Comparison of Antimicrobial Resistance Gene Databases

As the prevalence of antimicrobial resistance genes is increasing in microbes, we are facing the return of the pre-antibiotic era. Consecutively, the number of studies concerning antibiotic resistance and its spread in the environment is rapidly growing. Next generation sequencing technologies are w...

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Detalles Bibliográficos
Autores principales: Papp, Márton, Solymosi, Norbert
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8944830/
https://www.ncbi.nlm.nih.gov/pubmed/35326803
http://dx.doi.org/10.3390/antibiotics11030339
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author Papp, Márton
Solymosi, Norbert
author_facet Papp, Márton
Solymosi, Norbert
author_sort Papp, Márton
collection PubMed
description As the prevalence of antimicrobial resistance genes is increasing in microbes, we are facing the return of the pre-antibiotic era. Consecutively, the number of studies concerning antibiotic resistance and its spread in the environment is rapidly growing. Next generation sequencing technologies are widespread used in many areas of biological research and antibiotic resistance is no exception. For the rapid annotation of whole genome sequencing and metagenomic results considering antibiotic resistance, several tools and data resources were developed. These databases, however, can differ fundamentally in the number and type of genes and resistance determinants they comprise. Furthermore, the annotation structure and metadata stored in these resources can also contribute to their differences. Several previous reviews were published on the tools and databases of resistance gene annotation; however, to our knowledge, no previous review focused solely and in depth on the differences in the databases. In this review, we compare the most well-known and widely used antibiotic resistance gene databases based on their structure and content. We believe that this knowledge is fundamental for selecting the most appropriate database for a research question and for the development of new tools and resources of resistance gene annotation.
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spelling pubmed-89448302022-03-25 Review and Comparison of Antimicrobial Resistance Gene Databases Papp, Márton Solymosi, Norbert Antibiotics (Basel) Review As the prevalence of antimicrobial resistance genes is increasing in microbes, we are facing the return of the pre-antibiotic era. Consecutively, the number of studies concerning antibiotic resistance and its spread in the environment is rapidly growing. Next generation sequencing technologies are widespread used in many areas of biological research and antibiotic resistance is no exception. For the rapid annotation of whole genome sequencing and metagenomic results considering antibiotic resistance, several tools and data resources were developed. These databases, however, can differ fundamentally in the number and type of genes and resistance determinants they comprise. Furthermore, the annotation structure and metadata stored in these resources can also contribute to their differences. Several previous reviews were published on the tools and databases of resistance gene annotation; however, to our knowledge, no previous review focused solely and in depth on the differences in the databases. In this review, we compare the most well-known and widely used antibiotic resistance gene databases based on their structure and content. We believe that this knowledge is fundamental for selecting the most appropriate database for a research question and for the development of new tools and resources of resistance gene annotation. MDPI 2022-03-04 /pmc/articles/PMC8944830/ /pubmed/35326803 http://dx.doi.org/10.3390/antibiotics11030339 Text en © 2022 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Review
Papp, Márton
Solymosi, Norbert
Review and Comparison of Antimicrobial Resistance Gene Databases
title Review and Comparison of Antimicrobial Resistance Gene Databases
title_full Review and Comparison of Antimicrobial Resistance Gene Databases
title_fullStr Review and Comparison of Antimicrobial Resistance Gene Databases
title_full_unstemmed Review and Comparison of Antimicrobial Resistance Gene Databases
title_short Review and Comparison of Antimicrobial Resistance Gene Databases
title_sort review and comparison of antimicrobial resistance gene databases
topic Review
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8944830/
https://www.ncbi.nlm.nih.gov/pubmed/35326803
http://dx.doi.org/10.3390/antibiotics11030339
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