BacAnt

BacAnt annotates antimicrobial resistance genes (ARGs) and mobile genetic elements (MGEs), including insertion sequences, integrons, and transposons, in bacterial genome sequences to support analysis of resistance mechanisms and epidemiology.

Key Features:

• Integrated annotation: Simultaneously annotates ARGs and MGEs (insertion sequences, integrons, transposons) within bacterial genome sequences.
• GenBank export: Automatically generates GenBank files from annotated data for downstream analyses and visualization (e.g., Easyfig).
• WGS support: Processes whole genome sequencing (WGS) data to predict ARGs and MGEs from bacterial genomes.
• Scalability: Pipeline is designed to handle large datasets efficiently.

Scientific Applications:

• Clinical microbiology: Identification of resistance mechanisms in clinical bacterial isolates by annotating ARGs and associated MGEs.
• Epidemiological surveillance: Tracking the spread of resistant strains through joint ARG and MGE annotation from WGS data.
• Comparative genomics: Enabling comparative analyses of genomic regions containing ARGs and MGEs using exported GenBank files.

Methodology:

Annotations are produced by leveraging databases Resfinder, ISfinder, INTEGRALL, and The Transposon Registry; the pipeline annotates bacterial DNA sequences, generates GenBank files from annotations, and is implemented to handle large datasets efficiently.