Publications by authors named "Alfred F Florensa"
ResFinder - an open online resource for identification of antimicrobial resistance genes in next-generation sequencing data and prediction of phenotypes from genotypes.
Microb Genom
January 2022
Antimicrobial resistance (AMR) is one of the most important health threats globally. The ability to accurately identify resistant bacterial isolates and the individual antimicrobial resistance genes (ARGs) is essential for understanding the evolution and emergence of AMR and to provide appropriate treatment. The rapid developments in next-generation sequencing technologies have made this technology available to researchers and microbiologists at routine laboratories around the world.
View Article and Find Full Text PDFSummary: Here, we present an automated pipeline for Download Of NCBI Entries (DONE) and continuous updating of a local sequence database based on user-specified queries. The database can be created with either protein or nucleotide sequences containing all entries or complete genomes only. The pipeline can automatically clean the database by removing entries with matches to a database of user-specified sequence contaminants.
View Article and Find Full Text PDFArticle Synopsis
- WGS-based antimicrobial susceptibility testing (AST) can be as effective as traditional phenotypic methods, but its use is limited by the need for specialized bioinformatics skills.
- New tools like ResFinder and PointFinder have been improved to make them user-friendly for those with limited bioinformatics knowledge.
- Validation studies showed that ResFinder 4.0 achieved a high concordance rate (≥95%) in predicting antimicrobial resistance in various bacterial species, demonstrating its reliability for public health applications.