SynthesisThe Journal of antimicrobial chemotherapy2020
Large-scale assessment of antimicrobial resistance marker databases for genetic phenotype prediction: a systematic review.
Synthesis in The Journal of antimicrobial chemotherapy, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 57 papers.
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Who cites it
57 citing papers in PubMed.
- Application value and challenges associated with plasma cell-free DNA metagenomic sequencing technology in the diagnosis of infections in patients with hematological disorders.Blood science (Baltimore, Md.) · 2026Review
- Human wastewater contamination drives the emergence of multidrug-resistant bacteria in the Galápagos marine ecosystem.Nature communications · 2026Article
- Genomic Insights Into Antimicrobial Resistance and Virulence of Enterococcus avium Strains From Bovine Mastitis in Some Selected Dairy Farms of Bangladesh.Veterinary medicine and science · 2026Article
- Artificial intelligence for antimicrobial resistance: advancing reproducibility, interpretability, and clinical deployment.Briefings in bioinformatics · 2026Review
- Genomic landscape of antimicrobial resistance in India: findings from a multi-species surveillance study.npj antimicrobials and resistance · 2026Article
- Vancomycin resistance in gram-positive infections: evolutionary strategies of survival.Archives of microbiology · 2026Review
- Antimicrobial resistance databases: opportunities and challenges for public health.npj antimicrobials and resistance · 2026Review
- Metagenomic next-generation sequencing: new horizons in microbiology.Frontiers in cellular and infection microbiology · 2026Review
- Genomic screening of eight antibiotic-resistant Pseudomonas isolated from rainbow trout (Oncorhynchus mykiss).Access microbiology · 2026Article
- Interpreting antimicrobial resistance from bacterial whole-genome sequencing: prediction tools, database fragmentation, analytical trade-offs, and harmonized reporting.Frontiers in microbiology · 2026Review
- Comparative assessment of annotation tools reveals critical antimicrobial resistance knowledge gaps in Klebsiella pneumoniae.Scientific reports · 2025Article
- Phenotype-genotype discordance in antimicrobial resistance profiles of Gram-negative uropathogens recovered from catheter-associated urinary tract infections in Egypt.The Journal of antimicrobial chemotherapy · 2025Article
- Beyond the Resistome: Molecular Insights, Emerging Therapies, and Environmental Drivers of Antibiotic Resistance.Antibiotics (Basel, Switzerland) · 2025Review
- Development of a strain-specific PCR as a diagnostic tool for surveillance, detection, and monitoring of vancomycin-resistant Enterococcus faecium during outbreak.Antimicrobial resistance and infection control · 2025Article
- Metagenomics as a Transformative Tool for Antibiotic Resistance Surveillance: Highlighting the Impact of Mobile Genetic Elements with a Focus on the Complex Role of Phages.Antibiotics (Basel, Switzerland) · 2025Review
- Microbial cell-free DNA-sequencing as an addition to conventional diagnostics in neonatal sepsis.Pediatric research · 2025Article
- Integrating Metagenomic and Culture-Based Techniques to Detect Foodborne Pathogens and Antimicrobial Resistance Genes in Malaysian Produce.Foods (Basel, Switzerland) · 2025Article
- Next generation sequencing as a panacea for antibiotic susceptibility testing: yea or nay?Frontiers in public health · 2025Article
- Data-Driven Approaches in Antimicrobial Resistance: Machine Learning Solutions.Antibiotics (Basel, Switzerland) · 2024Article
- Exploring uncatalogued genetic variation in antimicrobial resistance gene families in Escherichia coli: an observational analysis.The Lancet. Microbe · 2024Observational
Corrections and comments
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5 authors.
Funding
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Abstract
backgroundAntimicrobial resistance (AMR) is a rising health threat with 10 million annual casualties estimated by 2050. Appropriate treatment of infectious diseases with the right antibiotics reduces the spread of antibiotic resistance. Today, clinical practice relies on molecular and PCR techniques for pathogen identification and culture-based antibiotic susceptibility testing (AST). Recently, WGS has started to transform clinical microbiology, enabling prediction of resistance phenotypes from genotypes and allowing for more informed treatment decisions. WGS-based AST (WGS-AST) depends on the detection of AMR markers in sequenced isolates and therefore requires AMR reference databases. The completeness and quality of these databases are material to increase WGS-AST performance.
methodsWe present a systematic evaluation of the performance of publicly available AMR marker databases for resistance prediction on clinical isolates. We used the public databases CARD and ResFinder with a final dataset of 2587 isolates across five clinically relevant pathogens from PATRIC and NDARO, public repositories of antibiotic-resistant bacterial isolates.
resultsCARD and ResFinder WGS-AST performance had an overall balanced accuracy of 0.52 (±0.12) and 0.66 (±0.18), respectively. Major error rates were higher in CARD (42.68%) than ResFinder (25.06%). However, CARD showed almost no very major errors (1.17%) compared with ResFinder (4.42%).
conclusionsWe show that AMR databases need further expansion, improved marker annotations per antibiotic rather than per antibiotic class and validated multivariate marker panels to achieve clinical utility, e.g. in order to meet performance requirements such as provided by the FDA for clinical microbiology diagnostic testing.
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