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TnSeq of Mycobacterium tuberculosis clinical isolates reveals strain-specific antibiotic liabilities

Once considered a phenotypically monomorphic bacterium, there is a growing body of work demonstrating heterogeneity among Mycobacterium tuberculosis (Mtb) strains in clinically relevant characteristics, including virulence and response to antibiotics. However, the genetic and molecular basis for mos...

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Autores principales: Carey, Allison F., Rock, Jeremy M., Krieger, Inna V., Chase, Michael R., Fernandez-Suarez, Marta, Gagneux, Sebastien, Sacchettini, James C., Ioerger, Thomas R., Fortune, Sarah M.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5854444/
https://www.ncbi.nlm.nih.gov/pubmed/29505613
http://dx.doi.org/10.1371/journal.ppat.1006939
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author Carey, Allison F.
Rock, Jeremy M.
Krieger, Inna V.
Chase, Michael R.
Fernandez-Suarez, Marta
Gagneux, Sebastien
Sacchettini, James C.
Ioerger, Thomas R.
Fortune, Sarah M.
author_facet Carey, Allison F.
Rock, Jeremy M.
Krieger, Inna V.
Chase, Michael R.
Fernandez-Suarez, Marta
Gagneux, Sebastien
Sacchettini, James C.
Ioerger, Thomas R.
Fortune, Sarah M.
author_sort Carey, Allison F.
collection PubMed
description Once considered a phenotypically monomorphic bacterium, there is a growing body of work demonstrating heterogeneity among Mycobacterium tuberculosis (Mtb) strains in clinically relevant characteristics, including virulence and response to antibiotics. However, the genetic and molecular basis for most phenotypic differences among Mtb strains remains unknown. To investigate the basis of strain variation in Mtb, we performed genome-wide transposon mutagenesis coupled with next-generation sequencing (TnSeq) for a panel of Mtb clinical isolates and the reference strain H37Rv to compare genetic requirements for in vitro growth across these strains. We developed an analytic approach to identify quantitative differences in genetic requirements between these genetically diverse strains, which vary in genomic structure and gene content. Using this methodology, we found differences between strains in their requirements for genes involved in fundamental cellular processes, including redox homeostasis and central carbon metabolism. Among the genes with differential requirements were katG, which encodes the activator of the first-line antitubercular agent isoniazid, and glcB, which encodes malate synthase, the target of a novel small-molecule inhibitor. Differences among strains in their requirement for katG and glcB predicted differences in their response to these antimicrobial agents. Importantly, these strain-specific differences in antibiotic response could not be predicted by genetic variants identified through whole genome sequencing or by gene expression analysis. Our results provide novel insight into the basis of variation among Mtb strains and demonstrate that TnSeq is a scalable method to predict clinically important phenotypic differences among Mtb strains.
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spelling pubmed-58544442018-03-28 TnSeq of Mycobacterium tuberculosis clinical isolates reveals strain-specific antibiotic liabilities Carey, Allison F. Rock, Jeremy M. Krieger, Inna V. Chase, Michael R. Fernandez-Suarez, Marta Gagneux, Sebastien Sacchettini, James C. Ioerger, Thomas R. Fortune, Sarah M. PLoS Pathog Research Article Once considered a phenotypically monomorphic bacterium, there is a growing body of work demonstrating heterogeneity among Mycobacterium tuberculosis (Mtb) strains in clinically relevant characteristics, including virulence and response to antibiotics. However, the genetic and molecular basis for most phenotypic differences among Mtb strains remains unknown. To investigate the basis of strain variation in Mtb, we performed genome-wide transposon mutagenesis coupled with next-generation sequencing (TnSeq) for a panel of Mtb clinical isolates and the reference strain H37Rv to compare genetic requirements for in vitro growth across these strains. We developed an analytic approach to identify quantitative differences in genetic requirements between these genetically diverse strains, which vary in genomic structure and gene content. Using this methodology, we found differences between strains in their requirements for genes involved in fundamental cellular processes, including redox homeostasis and central carbon metabolism. Among the genes with differential requirements were katG, which encodes the activator of the first-line antitubercular agent isoniazid, and glcB, which encodes malate synthase, the target of a novel small-molecule inhibitor. Differences among strains in their requirement for katG and glcB predicted differences in their response to these antimicrobial agents. Importantly, these strain-specific differences in antibiotic response could not be predicted by genetic variants identified through whole genome sequencing or by gene expression analysis. Our results provide novel insight into the basis of variation among Mtb strains and demonstrate that TnSeq is a scalable method to predict clinically important phenotypic differences among Mtb strains. Public Library of Science 2018-03-05 /pmc/articles/PMC5854444/ /pubmed/29505613 http://dx.doi.org/10.1371/journal.ppat.1006939 Text en © 2018 Carey et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Carey, Allison F.
Rock, Jeremy M.
Krieger, Inna V.
Chase, Michael R.
Fernandez-Suarez, Marta
Gagneux, Sebastien
Sacchettini, James C.
Ioerger, Thomas R.
Fortune, Sarah M.
TnSeq of Mycobacterium tuberculosis clinical isolates reveals strain-specific antibiotic liabilities
title TnSeq of Mycobacterium tuberculosis clinical isolates reveals strain-specific antibiotic liabilities
title_full TnSeq of Mycobacterium tuberculosis clinical isolates reveals strain-specific antibiotic liabilities
title_fullStr TnSeq of Mycobacterium tuberculosis clinical isolates reveals strain-specific antibiotic liabilities
title_full_unstemmed TnSeq of Mycobacterium tuberculosis clinical isolates reveals strain-specific antibiotic liabilities
title_short TnSeq of Mycobacterium tuberculosis clinical isolates reveals strain-specific antibiotic liabilities
title_sort tnseq of mycobacterium tuberculosis clinical isolates reveals strain-specific antibiotic liabilities
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5854444/
https://www.ncbi.nlm.nih.gov/pubmed/29505613
http://dx.doi.org/10.1371/journal.ppat.1006939
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