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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Whole genome \"TraDIS-Xpress\" assay to determine gene roles during growth of E. coli in different concentrations of the antibiotics trimethoprim and sulfamethoxazole

ABSTRACT: To assay every gene in the E. coli genome to identify those that contribute to increased or decreased susceptibility to the antibiotics trimethoprim and sulfamethoxazole. This will help to define more accurately those bacterial cell mechanisms that contribute to these phenomena and provide information that will contribute to the development of new antibiotics, or compounds or known antibiotics that synergise with those already in clinical use. Thus, this set of experiments confirmed that AZT, widely known for its antiviral activity, acts synergistically with trimehoprim.

INSTRUMENT(S): NextSeq 550

ORGANISM(S): Escherichia coli str. K-12 substr. MG1655

SUBMITTER: Arthur Turner

PROVIDER: E-MTAB-9305 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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TraDIS-Xpress: a high-resolution whole-genome assay identifies novel mechanisms of triclosan action and resistance.

Yasir Muhammad M Turner A Keith AK Bastkowski Sarah S Baker David D Page Andrew J AJ Telatin Andrea A Phan Minh-Duy MD Monahan Leigh L Savva George M GM Darling Aaron A Webber Mark A MA Charles Ian G IG

Genome research 20200212 2

Understanding the genetic basis for a phenotype is a central goal in biological research. Much has been learnt about bacterial genomes by creating large mutant libraries and looking for conditionally important genes. However, current genome-wide methods are largely unable to assay essential genes which are not amenable to disruption. To overcome this limitation, we developed a new version of "TraDIS" (transposon directed insertion-site sequencing) that we term "TraDIS-Xpress" that combines an in ...[more]

PMID: 32051187

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TraDIS-Xpress to determine E. coli response to Piperacillin and Tazobactam separately and in combination

Project description:Found how E. coli responds to the commonly prescribed antibiotic-inhibitor combination piperacillin and tazobactam, separately and in combination. TraDIS-Xpress was performed following the protocol outlined by Yasir et al 2020 Genome Research. The results suggest tazobactam triggers the activity of multidrug efflux systems that have been previously seen to confer clinical resistance to multiple classes of antibiotics.

2023-08-31 | E-MTAB-13226 | biostudies-arrayexpress

Genome wide analysis of genes involved in efflux function and regulation within Escherichia coli and Salmonella enterica serovar Typhimurium

Project description:Expression of efflux pumps is a key feature of most cells which are resistant to multiple antibiotics. This study used TraDIS-Xpress, a genome wide transposon mutagenesis technology to identify genes in Escherichia coli and Salmonella Typhimurium involved in drug efflux and its regulation. We exposed mutant libraries to the canonical efflux substrate acriflavine in the presence and absence of the efflux inhibitor phenylalanine-arginine β-naphthylamide. Comparisons between conditions identified efflux specific and drug specific responses. Known efflux associated genes were easily identified including: AcrAB-TolC, MarA, RamA and SoxS confirming specificity of the response. Further genes encoding cell envelope maintenance enzymes and products involved with stringent response activation, DNA housekeeping, respiration and glutathione biosynthesis were also identified as affecting efflux activity in both species. We identified a conserved set of pathways crucial for efflux activity in these experimental conditions which expands the list of genes known to impact efflux efficacy.

2022-11-12 | E-MTAB-12353 | biostudies-arrayexpress

LoRTIS: A long read method for analysis of large transposon mutant libraries

Project description:Transposon insertion site sequencing (TIS) is a powerful method for associating genotype to phenotype. However, all TIS methods described to date use short nucleotide sequence reads which cannot uniquely determine the locations of transposon insertions within repeating genomic sequences where the repeat units are longer than the sequence read length. To overcome this limitation, we have developed a TIS method using Oxford Nanopore sequencing technology that generates and uses long nucleotide sequence reads; we have called this method LoRTIS (Long Read Transposon Insertion-site Sequencing). This experiment data contains sequence files generated using Nanopore and Illumina platforms. Biotin1308.fastq.gz and Biotin2508.fastq.gz are fastq files generated from nanopore technology. Rep1-Tn.fastq.gz and Rep1-Tn.fastq.gz are fastq files generated using Illumina platform. In this study, we have compared the efficiency of two methods in identification of transposon insertion sites.

2022-05-30 | E-MTAB-11351 | biostudies-arrayexpress

Whole genome TraDIS-Xpress assay to determine gene roles during growth of E. coli in different concentrations of the beta-lactam antibiotic meropenem

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The transcriptional response of Pasteurella multocida to three classes of antibiotics

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