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

Autor: Jeremy M. Rock, James C. Sacchettini, Sarah M. Fortune, Marta Fernandez-Suarez, Michael R. Chase, Sebastien Gagneux, Inna Krieger, Thomas R. Ioerger, Allison F. Carey
Jazyk: angličtina
Rok vydání: 2018
Předmět:
0301 basic medicine
Mutagenesis and Gene Deletion Techniques
Antitubercular Agents
Gene Expression
Antibiotics
Drug Resistance
Multiple
Bacterial
Mobile Genetic Elements
Medicine and Health Sciences
lcsh:QH301-705.5
Genetics
biology
Antimicrobials
Fungal genetics
High-Throughput Nucleotide Sequencing
Drugs
Genomics
3. Good health
Actinobacteria
Phenotypes
Phenotype
Research Article
lcsh:Immunologic diseases. Allergy
030106 microbiology
Immunology
Virulence
Research and Analysis Methods
Microbiology
Mycobacterium tuberculosis
03 medical and health sciences
Genetic Elements
Bacterial Proteins
Microbial Control
Virology
Humans
Tuberculosis
Molecular Biology Techniques
Molecular Biology
Gene
Pharmacology
Whole genome sequencing
Whole Genome Sequencing
Bacteria
Organisms
Transposable Elements
Correction
Biology and Life Sciences
Computational Biology
Genome Analysis
Genomic Libraries
biology.organism_classification
030104 developmental biology
lcsh:Biology (General)
Antibiotic Resistance
Mutation
DNA Transposable Elements
Parasitology
Transposon mutagenesis
Antimicrobial Resistance
Mobile genetic elements
lcsh:RC581-607
Genome
Bacterial
Mycobacterium Tuberculosis
Transposon Mutagenesis
Zdroj: PLoS Pathogens, Vol 14, Iss 3, p e1006939 (2018)
PLoS Pathogens
ISSN: 1553-7374
1553-7366
Popis: 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.
Author summary Tuberculosis, caused by the bacterium Mycobacterium tuberculosis (Mtb), remains a serious global health problem, causing ~1.5 million deaths a year world-wide. Like other bacterial pathogens, diversity among strains of Mtb contributes to differences in infection outcomes, vaccine efficacy, and response to antibiotic treatment. Currently, the important genetic differences that contribute to variation among Mtb strains remain poorly understood. In this study, we applied a functional genomics technique called TnSeq to a panel of Mtb clinical strains to investigate the genetic basis of strain diversity. We identified a number of genes that are differentially required for growth in culture among these strains. Some of these genes are involved in the response to antibiotics, including the first-line antitubercular agent isoniazid and a novel antitubercular drug currently in development. We found that the genetic differences between strains uncovered by TnSeq predicted responses to these antibiotics. Our results demonstrate the utility of TnSeq for identifying clinically relevant differences among Mtb strains.
Databáze: OpenAIRE
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