SSTAR, a Stand-Alone Easy-To-Use Antimicrobial Resistance Gene Predictor

ABSTRACT We present the easy-to-use Sequence Search Tool for Antimicrobial Resistance, SSTAR. It combines a locally executed BLASTN search against a customizable database with an intuitive graphical user interface for identifying antimicrobial resistance (AR) genes from genomic data. Although the da...

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Autores principales:	Tom J. B. de Man, Brandi M. Limbago
Formato:	article
Lenguaje:	EN
Publicado:	American Society for Microbiology 2016
Materias:	antimicrobial resistance genes porins BLAST SSTAR Microbiology QR1-502
Acceso en línea:	https://doaj.org/article/ca0e3c22f66a4091a567939a76b39c5c
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spelling	oai:doaj.org-article:ca0e3c22f66a4091a567939a76b39c5c2021-11-15T15:21:37ZSSTAR, a Stand-Alone Easy-To-Use Antimicrobial Resistance Gene Predictor10.1128/mSphere.00050-152379-5042https://doaj.org/article/ca0e3c22f66a4091a567939a76b39c5c2016-02-01T00:00:00Zhttps://journals.asm.org/doi/10.1128/mSphere.00050-15https://doaj.org/toc/2379-5042ABSTRACT We present the easy-to-use Sequence Search Tool for Antimicrobial Resistance, SSTAR. It combines a locally executed BLASTN search against a customizable database with an intuitive graphical user interface for identifying antimicrobial resistance (AR) genes from genomic data. Although the database is initially populated from a public repository of acquired resistance determinants (i.e., ARG-ANNOT), it can be customized for particular pathogen groups and resistance mechanisms. For instance, outer membrane porin sequences associated with carbapenem resistance phenotypes can be added, and known intrinsic mechanisms can be included. Unique about this tool is the ability to easily detect putative new alleles and truncated versions of existing AR genes. Variants and potential new alleles are brought to the attention of the user for further investigation. For instance, SSTAR is able to identify modified or truncated versions of porins, which may be of great importance in carbapenemase-negative carbapenem-resistant Enterobacteriaceae. SSTAR is written in Java and is therefore platform independent and compatible with both Windows and Unix operating systems. SSTAR and its manual, which includes a simple installation guide, are freely available from https://github.com/tomdeman-bio/Sequence-Search-Tool-for-Antimicrobial-Resistance-SSTAR- . IMPORTANCE Whole-genome sequencing (WGS) is quickly becoming a routine method for identifying genes associated with antimicrobial resistance (AR). However, for many microbiologists, the use and analysis of WGS data present a substantial challenge. We developed SSTAR, software with a graphical user interface that enables the identification of known AR genes from WGS and has the unique capacity to easily detect new variants of known AR genes, including truncated protein variants. Current software solutions do not notify the user when genes are truncated and, therefore, likely nonfunctional, which makes phenotype predictions less accurate. SSTAR users can apply any AR database of interest as a reference comparator and can manually add genes that impact resistance, even if such genes are not resistance determinants per se (e.g., porins and efflux pumps).Tom J. B. de ManBrandi M. LimbagoAmerican Society for Microbiologyarticleantimicrobial resistance genesporinsBLASTSSTARMicrobiologyQR1-502ENmSphere, Vol 1, Iss 1 (2016)
institution	DOAJ
collection	DOAJ
language	EN
topic	antimicrobial resistance genes porins BLAST SSTAR Microbiology QR1-502
spellingShingle	antimicrobial resistance genes porins BLAST SSTAR Microbiology QR1-502 Tom J. B. de Man Brandi M. Limbago SSTAR, a Stand-Alone Easy-To-Use Antimicrobial Resistance Gene Predictor
description	ABSTRACT We present the easy-to-use Sequence Search Tool for Antimicrobial Resistance, SSTAR. It combines a locally executed BLASTN search against a customizable database with an intuitive graphical user interface for identifying antimicrobial resistance (AR) genes from genomic data. Although the database is initially populated from a public repository of acquired resistance determinants (i.e., ARG-ANNOT), it can be customized for particular pathogen groups and resistance mechanisms. For instance, outer membrane porin sequences associated with carbapenem resistance phenotypes can be added, and known intrinsic mechanisms can be included. Unique about this tool is the ability to easily detect putative new alleles and truncated versions of existing AR genes. Variants and potential new alleles are brought to the attention of the user for further investigation. For instance, SSTAR is able to identify modified or truncated versions of porins, which may be of great importance in carbapenemase-negative carbapenem-resistant Enterobacteriaceae. SSTAR is written in Java and is therefore platform independent and compatible with both Windows and Unix operating systems. SSTAR and its manual, which includes a simple installation guide, are freely available from https://github.com/tomdeman-bio/Sequence-Search-Tool-for-Antimicrobial-Resistance-SSTAR- . IMPORTANCE Whole-genome sequencing (WGS) is quickly becoming a routine method for identifying genes associated with antimicrobial resistance (AR). However, for many microbiologists, the use and analysis of WGS data present a substantial challenge. We developed SSTAR, software with a graphical user interface that enables the identification of known AR genes from WGS and has the unique capacity to easily detect new variants of known AR genes, including truncated protein variants. Current software solutions do not notify the user when genes are truncated and, therefore, likely nonfunctional, which makes phenotype predictions less accurate. SSTAR users can apply any AR database of interest as a reference comparator and can manually add genes that impact resistance, even if such genes are not resistance determinants per se (e.g., porins and efflux pumps).
format	article
author	Tom J. B. de Man Brandi M. Limbago
author_facet	Tom J. B. de Man Brandi M. Limbago
author_sort	Tom J. B. de Man
title	SSTAR, a Stand-Alone Easy-To-Use Antimicrobial Resistance Gene Predictor
title_short	SSTAR, a Stand-Alone Easy-To-Use Antimicrobial Resistance Gene Predictor
title_full	SSTAR, a Stand-Alone Easy-To-Use Antimicrobial Resistance Gene Predictor
title_fullStr	SSTAR, a Stand-Alone Easy-To-Use Antimicrobial Resistance Gene Predictor
title_full_unstemmed	SSTAR, a Stand-Alone Easy-To-Use Antimicrobial Resistance Gene Predictor
title_sort	sstar, a stand-alone easy-to-use antimicrobial resistance gene predictor
publisher	American Society for Microbiology
publishDate	2016
url	https://doaj.org/article/ca0e3c22f66a4091a567939a76b39c5c
work_keys_str_mv	AT tomjbdeman sstarastandaloneeasytouseantimicrobialresistancegenepredictor AT brandimlimbago sstarastandaloneeasytouseantimicrobialresistancegenepredictor
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SSTAR, a Stand-Alone Easy-To-Use Antimicrobial Resistance Gene Predictor

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