BacARscan

BacARscan detects and characterizes antibiotic resistance genes (ARGs) in metagenomic, genomic, and proteomic datasets to support surveillance and analysis of antimicrobial resistance.

Key Features:

• Extensive ARG models: Contains 254 ARG models annotated with resistance profiles against diverse antibiotic classes and detailed descriptions of resistance mechanisms.
• Benchmarked accuracy: Benchmarking on combined datasets of antibiotic-resistant (AR) and non-antibiotic-resistant proteins reported 92% precision and a 95% F-measure in distinguishing ARGs from homologous non-resistance proteins.
• NGS fragmentation handling: Addresses challenges from next-generation sequencing (NGS), including detection in fragmented genome databases resulting from incomplete assembly.
• Multi-omics compatibility: Operates on metagenomic, genomic, and proteomic data and on short-read genomic and proteomic sequences.
• Gut microbiome and ESKAPE analysis: Demonstrated efficacy in identifying ARGs within the gut microbiome and in short-read sequences from ESKAPE pathogens.
• Clinical metagenomic relevance: Capable of analyzing clinical metagenomic data and serving as a complementary resource to whole-genome sequencing (WGS) for identifying ARGs in clinical samples.

Scientific Applications:

• Resistance surveillance: Supports surveillance and epidemiological studies of antibiotic resistance emergence and spread in clinical and environmental contexts.
• Microbiome research: Enables profiling and analysis of ARG distributions within the gut microbiome.
• Clinical AMR investigations: Complements WGS-based analyses for identifying ARGs in clinical metagenomic samples to inform antimicrobial resistance investigations.
• Pathogen-focused studies: Facilitates detection of ARGs in ESKAPE pathogens from short-read genomic and proteomic datasets.

Methodology:

Uses a library of 254 annotated ARG models for detection and characterization and was benchmarked against combined datasets of antibiotic-resistant (AR) and non-antibiotic-resistant proteins to evaluate precision and F-measure.