Table 3.
Reference databases for antibiotic resistance genes.
| Database | Comments | Latest Update | Information contained | Website | Ref. |
|---|---|---|---|---|---|
| ARDB | No longer being maintained. All information has moved to CARD. | July 2009 |
13,293 genes, 377 types, 257 antibiotics, 632 genomes, 933 species and 124 genera | https://ardb.cbcb.umd.edu/ | 43 |
| ARGO | Data was restricted to β-lactamase, tetracycline, and vancomycin genes. | Unclear | 555 β-lactamases and 115 vancomycin resistance genes reported before 2004. | http://www.argodb.org/ | 44 |
| ARG-ANNOT | Based on a local BLAST program in Bio-Edit software, allowing offline analysis. | Unclear | 1,689 antibiotic resistance genes | No longer available | 45 |
| CARD | This is one of the most extensive AMR sequence databases, covering intrinsic, mutation-driven, and acquired resistance, including mobile genetic elements. | April 2019 | 2570 reference sequences, 1233 SNPs, 7305 plasmids, 5524 chromosomes | https://card.mcmaster.ca/ | 46 |
| Lahey Clinic database | This database provides comprehensive information on β-lactamase genes. | May 2019 | β-lactamase classification and amino acid sequences for TEM, SHV, and OXA genes. | https://www.lahey.org/ | 47 |
| SARG | The redundant sequences were removed and query sequence detection optimized. | June 2018 | 9080 sequence belonged to 189 ARGs subtypes. | http://smile.hku.hk/SARGs | 38 |
| MERGEM | This database contains resistance genes suitable for k-mer filtering. | Unclear | The website is no longer maintained | http://www.mergem.genome.ulaval.ca/ | 48 |
| RED-DB | Both partial and complete coding sequences are available. | May 2019 |
10,742 non-redundant genes covering ten antibiotic classes. | http://www.fibim.unisi.it/REDDB | - |
| ResFams | Database of proteins encoding drug resistance, organized by ontology. | Feb 2018 | 2,454 unique sequences, presenting 54 Resfams protein families. | http://www.dantaslab.org/resfams | 49 |
| AMRFinder | Database of AMR protein and gene nomenclature with hidden Markov models | June 2019 | 4,579 AMR protein sequences and more than 560 hidden Markov models. | https:/www.ncbi.nlm.nih.gov/pathogens/antimicrobial-resistance/AMRFinder/ | 50 |
ARDB, Antibiotic Resistance Gene Database; CARD, The Comprehensive Antibiotic Resistance Database; MERGEM, Mobile Elements and Resistance Genes database Enhanced for Metagenomics; RED-DB, Resistance Determinants Database; SARG, Structured Antibiotic Resistance Genes.