{"references": ["Alcock BP, Huynh W, Chalil R et al. CARD 2023: expanded curation, support for machine learning,\u00a0and resistome prediction at the Comprehensive Antibiotic Resistance Database. Nucleic Acids Res 2023;51:D690\u20139.", "Bonin N, Doster E, Worley H et al. MEGARes and AMR++, v3.0: an updated comprehensive database of antimicrobial resistance determinants and an improved software pipeline for classification using high-throughput sequencing. Nucleic Acids Res 2023;51:D744\u201352.", "Bortolaia V, Kaas RS, Ruppe E et al. ResFinder 4.0 for predictions of phenotypes from genotypes. J Antimicrob Chemother 2020;75:3491\u2013500.", "Daruka L, Czikkely MS, Szili P et al. Antibiotics of the future are prone to resistance in Gram-negative pathogens. Revis 2023.", "Feldgarden M, Brover V, Gonzalez-Escalona N et al. AMRFinderPlus and the Reference Gene Catalog facilitate examination of the genomic links among antimicrobial resistance, stress response, and virulence. Sci Rep 2021;11, DOI: 10.1038/s41598-021-91456-0.", "Gschwind R, Ugarcina\u00a0Perovic S, Weiss M et al. ResFinderFG v2.0: a database of antibiotic resistance genes obtained by functional metagenomics. Nucleic Acids Res 2023:gkad384.", "Gupta SK, Padmanabhan BR, Diene SM et al. ARG-ANNOT, a New Bioinformatic Tool To Discover Antibiotic Resistance Genes in Bacterial Genomes. Antimicrob Agents Chemother 2014;58:212\u201320.", "Pal C, Bengtsson-Palme J, Rensing C et al. BacMet: antibacterial biocide and metal resistance genes database. Nucleic Acids Res 2014;42:D737\u201343."]}

PanRes database of antimicrobial resistance genes Many different collections of antimicrobial resistance genes (ARGs) have been collected and used for various purposes. In order to develop a workflow for mass screening of public metagenomes, we recently gathered up and filtered in a number of these gene collections to produce PanRes. For details, please see the methods section in the following publication: "ARGfinder - a pipeline for large-scale analysis of antimicrobial resistance genes and their flanking regions in metagenomic datasets" Briefly, the PanRes gene collection is gathered from a combination of other resistance gene collections into one, so each unique sequence has an "pan_" identifier (PanRes_genes). A separate table (PanRes_data) provides an overview of all the genes, their origin database and which genes cluster together in high-identity clusters. A number of previously published collections of ARGs were used in the creation of PanRes (See references): ResFinder (downloaded 2023-01-20, (Bortolaia et al. 2020)), ResFinderFG (version 2.0, (Gschwind et al. 2023)) CARD (version 3.2.5, (Alcock et al. 2023)) MegaRes (version 3.0.0, (Bonin et al. 2023)) AMRFinderPlus (version 3.11/2022-12-19.1, (Feldgarden et al. 2021)) ARGANNOT (V6_July2019, (Gupta et al. 2014)) The 'CsabaPal' collection (Provided by Csaba Pál and Zoltán Farkas in November 2022, Daruka et al. 2023)) BacMet (version 1.1, (Pal et al. 2014))