ARG-ANNOT, a new bioinformatic tool to discover antibiotic resistance genes in bacterial genomes
Open accessAbstract
ARG-ANNOT (Antibiotic Resistance Gene-ANNOTation) is a new bioinformatic tool that was created to detect existing and putative new antibiotic resistance (AR) genes in bacterial genomes. ARG-ANNOT uses a local BLAST program in Bio-Edit software that allows the user to analyze sequences without a Web interface. All AR genetic determinants were collected from published works and online resources; nucleotide and protein sequences were retrieved from the NCBI GenBank database. After building a database that includes 1,689 antibiotic resistance genes, the software was tested in a blind manner using 100 random sequences selected from the database to verify that the sensitivity and specificity were at 100% even when partial sequences were queried. Notably, BLAST analysis results obtained using the rmtF gene sequence (a new aminoglycoside-modifying enzyme gene sequence that is not included in the database) as a query revealed that the tool was able to link this sequence to short sequences (17 to 40 bp) found in other genes of the rmt family with significant E values. Finally, the analysis of 178 Acinetobacter baumannii and 20 Staphylococcus aureus genomes allowed the detection of a significantly higher number of AR genes than the Resfinder gene analyzer and 11 point mutations in target genes known to be associated with AR. The average time for the analysis of a genome was 3.35 ± 0.13 min. We have created a concise database for BLAST using a Bio-Edit interface that can detect AR geneti…
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Basic local alignment search tool
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“The five DBs screened for genes of interest were: 1) ARG-ANNOT v4 (Gupta et al., 2014), 2) CGE resfinder DB (Bortolaia et al., 2020), 3) CGE toxfinder DB (Camacho et al., 2009), 4) Virulence Factor setB DB (Chen et al., 2005) and 5) CGE virulence-finder DB (Camacho et al., 2009).”
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“The presence of putative AMR genes was ascertained using ABRicate [82] against the following databases: NCBI AMRFinderPlus [83], CARD [84], Resfinder [85], ARG-ANNOT [86], MEGARES [87], and EcOH [88].”
- Authors
- Gupta, S. K., Padmanabhan, B. R., Diene, S. M., Lopez-Rojas, R., Kempf, M., Landraud, L., & Rolain, J.-M.
- Affiliations
- Centre National de la Recherche Scientifique (FR)
- Unité de Recherche sur les Maladies Infectieuses et Tropicales Emergentes, UMR CNRS 7278—IRD 198 IHU, Méditerranée Infection, Faculté de Médecine et de Pharmacie, Aix-Marseille Université, Marseille, France
- Servicio de Enfermedades Infecciosas, Hospitales Universitarios Virgen del Rocıo, Seville, Spain
- Centre Hospitalier Universitaire d'Angers (FR)
- Inserm (FR)
- Venue
- Antimicrobial Agents and Chemotherapy
- Publisher
- American Society for Microbiology
- Published
- 2014-01
- Volume
- 58
- Issue
- 1
- Pages
- 212-220
- ISSN
- 0066-4804 (ISSN-L)
- 1098-6596
- PMC
- PMC3910750
- OpenAlex
- W2118688136
- Cited by
- 1,476
- References
- 2
- Citations by year
- 2026: 108 · 2025: 127 · 2024: 141 · 2023: 117 · 2022: 159 · 2021: 190 · 2020: 153 · 2019: 144 · 2018: 119 · 2017: 93 · 2016: 84 · 2015: 32 · 2014: 8 · 2013: 1
- FWCI
- 19.19
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Locations
- Antimicrobial Agents and Chemotherapy (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- HAL (submittedVersion)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Medicine › Antibiotic Resistance in Bacteria
- Health Sciences › Medicine › Infectious Diseases › Antimicrobial Resistance in Staphylococcus
- Life Sciences › Immunology and Microbiology › Applied Microbiology and Biotechnology › Antibiotic Use and Resistance
- Keywords
- antibiotic resistance genes, bacterial genomes, BLAST database, aminoglycoside-modifying enzymes, Acinetobacter baumannii, Staphylococcus aureus
- MeSH terms
- Drug Resistance, Microbial, Software, Genome, Bacterial, Computational Biology, Databases, Genetic
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