ISMapper: identifying transposase insertion sites in bacterial genomes from short read sequence data.

Area of Science:

• Genomics
• Bioinformatics
• Microbiology

Background:

• Insertion sequences (IS) are transposable elements prevalent in bacterial genomes.
• Identifying IS locations is crucial for epidemiology and antibiotic resistance prediction.
• Multiple IS copies complicate genome assembly and site identification.

Purpose of the Study:

• To present ISMapper, a novel mapping-based tool.
• To identify the site and orientation of IS insertions in bacterial genomes.
• To analyze paired-end short read data directly.

Main Methods:

• Developed ISMapper, a mapping-based computational tool.
• Validated ISMapper using simulated and real Illumina short read data.
• Tested ISMapper on 20 genomes across 13 species and 32 distinct IS.

Main Results:

• ISMapper achieved 97% accuracy on simulated reads and 98% on real reads.
• Accurate IS insertion detection was possible with >20x read depth, with >50x for confident calls.
• Confirmed ISAba1 insertions in Acinetobacter baumannii, including those linked to cephalosporin resistance.
• Profiled IS6110 insertions in Mycobacterium tuberculosis, revealing lineage-specific patterns.

Conclusions:

• ISMapper offers a rapid, accurate, and robust method for IS insertion site identification.
• The tool effectively utilizes short read data across diverse bacterial species.
• ISMapper enhances genomic analysis for epidemiological and resistance studies.