ResFinder

ResFinder identifies acquired antimicrobial resistance (AMR) genes in bacterial whole-genome sequencing (WGS) data by aligning sequences to a resistance gene database using BLAST.

Key Features:

• Input compatibility: Accepts pre-assembled complete and partial genomes as well as short sequence reads from four different sequencing platforms.
• BLAST-based identification: Uses BLAST (Basic Local Alignment Search Tool) to align query sequences against a resistance gene database to detect AMR genes.
• Benchmark evaluation: Evaluated on 1,862 GenBank files containing 1,411 distinct resistance genes, demonstrating identification of genes with 100% identity to database entries.
• Phenotypic correlation: Validated against phenotypic testing of 23 de-novo-sequenced isolates across five bacterial species, showing strong agreement between in silico predictions and observed phenotypes.
• Chromosome and plasmid analysis: Evaluated on WGS chromosomes and plasmids from 30 isolates, including seven annotated for antimicrobial resistance, with annotations consistent with existing data.
• Database updates: Incorporates newly identified resistance genes through continuous updates to the reference database.

Scientific Applications:

• Surveillance and epidemiology: Detection of acquired AMR genes to monitor resistance patterns and dissemination.
• Genotype–phenotype comparisons: Comparison of in silico AMR gene predictions with phenotypic antimicrobial susceptibility testing.
• Genomic context analysis: Annotation of AMR genes on chromosomes and plasmids to study genetic context and mobility.
• Clinical decision support: Informing treatment considerations by identifying known acquired resistance determinants in clinical isolates.

Methodology:

Sequence alignment is performed using BLAST to compare pre-assembled genomes or short sequence reads against a resistance gene database and report matching acquired AMR genes with percent identity.