This pipeline interprets results from ABRicate and mobileelementfinder CSV and .tab/.tabular outputs to analyze the colocation of antimicrobial resistance (AMR) genes and mobile genetic elements (MGEs). It is tailored for these two output formats but can be adapted for others.
The script identifies proximal instances between AMR genes and mobile elements, creating a numerical representation of the risk of gene mobility. While plasmid contigs are assumed mobile, the pipeline focuses on predicting the mobility of AMR genes within chromosomal structures by observing their proximity to MGEs.
- Ensure files are in either .tab/.tabular or .csv. Usually ABRicate results are in .tab while MGEfinder, mobileelementfinder and Integron finder are in .csv
- Install requirements to your own local venv
- Run python script and results will save to a local folder called Chromosome_maps
- Colocation Analysis: Parses and cross-checks AMR gene indices with IS segments to assess mobility risk.
- Visualization: Returns results using MatPlotLib, with Biopython formatting for prokaryotic genes.
- Transposase Identification: Maps transposase genes using TE identifiers, leveraging existing labels from IS and MGE Finder.
- Extensible: Designed to incorporate additional factors such as TEs, ICEs, and integrons into mobility prediction.
- ABRicate (CARD database) for AMR gene identification
- mobileelementfinder for locating insertion sequences (IS)
- Integron Finder (Galaxy or Local)
- MatPlotLib and Biopython for visualization
- IS: Insertion Sequence
- cn: Composite Transposon
- Tn: (Unit) Transposon
- MITE: Miniature Inverted Repeat
- ICE: Integrative Conjugative Element
- CIME: Cis-mobilizable Element
- IME: Integrative Mobilizable Element
- Integration of additional TE screeners
- Enhanced mapping of transposase proximity
- Support for more databases and output formats