AlbaTraDIS: Comparative analysis of large datasets from parallel transposon mutagenesis experiments

Area of Science:

• Microbiology
• Genomics
• Bioinformatics

Background:

• Understanding bacterial survival mechanisms under stress, like antimicrobial presence, is crucial but incomplete.
• Transposon directed insertion-site sequencing (TraDIS) is a powerful method for identifying genes involved in bacterial fitness and survival.
• Analyzing multiple TraDIS datasets simultaneously presents a significant analytical challenge.

Purpose of the Study:

• To develop a software application, AlbaTraDIS, for rapid, large-scale comparative analysis of TraDIS experiments.
• To predict the impact of transposon insertions on nearby genes and identify genes involved in conditional stress survival.
• To facilitate the identification of commonalities in bacterial stress responses across different conditions.

Main Methods:

• Development of AlbaTraDIS, a Python 3 software application for analyzing multiple TraDIS datasets.
• Application of AlbaTraDIS to analyze gene requirements for Escherichia coli survival in varying Triclosan concentrations.
• Experimental validation of predicted phenotypes for newly identified Triclosan resistance loci.

Main Results:

• AlbaTraDIS successfully identified known Triclosan resistance genes, including the primary target fabI.
• The software implicated several new loci in Triclosan resistance.
• Experimental validation confirmed the predicted roles of selected novel loci in bacterial survival.

Conclusions:

• AlbaTraDIS offers a simple, rapid method for large-scale analysis of transposon mutagenesis data.
• This tool enhances the utility of TraDIS for understanding bacterial stress responses and identifying resistance mechanisms.
• AlbaTraDIS is the first available tool capable of performing large-scale comparative analysis of multiple TraDIS experiments.