srst2

srst2 identifies antibiotic resistance (AR) genes and related variants in bacterial genomes by performing local BLAST-based sequence comparisons against the ARG-ANNOT database of 1,689 AR genes to detect known determinants, point mutations, and to link novel sequences to known families.

Key Features:

• Curated database: Contains 1,689 antibiotic resistance genes with nucleotide and protein sequences compiled from published literature and sourced from NCBI GenBank.
• BLAST-based sequence comparison: Uses a local BLAST program to compare query sequences to the ARG-ANNOT database.
• Sensitivity and specificity: Achieved 100% sensitivity and 100% specificity in a blind test using 100 random sequences, including partial gene sequences.
• Novel gene linkage: Links novel AR gene sequences to known families, exemplified by associating the rmtF aminoglycoside-modifying enzyme sequence with rmt family segments of 17–40 bp using significant E values.
• Genome-scale throughput: Processes bacterial genomes with an average analysis time of approximately 3.35 ± 0.13 minutes per genome.
• Enhanced detection of AR determinants: Identified more AR genes than Resfinder in comparative analyses of 178 Acinetobacter baumannii and 20 Staphylococcus aureus genomes and detected 11 point mutations in target genes known to confer resistance.

Scientific Applications:

• Genomic surveillance: Rapid annotation of AR genes for monitoring the distribution and emergence of resistance determinants in bacterial populations.
• Epidemiological studies: Comparative genomic analyses to track AR gene prevalence and variability across isolates and outbreaks.
• Mechanistic studies of resistance: Detection of known resistance determinants and point mutations to inform studies of antibiotic resistance mechanisms.
• Clinical microbiology and public health: Identification of known and novel AR determinants to support diagnostics, surveillance, and intervention strategies.

Methodology:

Performs local BLAST-based comparisons of query sequences against the ARG-ANNOT database (1,689 genes) using nucleotide and protein sequences sourced from NCBI GenBank, evaluates matches by E values, and reports detections including partial-sequence hits and point mutations.