ArticleGenome biology and evolution2014
Dissecting vancomycin-intermediate resistance in staphylococcus aureus using genome-wide association.
Article in Genome biology and evolution, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 78 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
78 citing papers in PubMed.
- Integrated Genome-Wide Association Study and Machine Learning Approach for Characterizing the Determinants of Biofilm Formation in Staphylococcus aureus.Interdisciplinary sciences, computational life sciences · 2026Article
- Epistasis and co-adaptation in bacterial genome evolution.Nature reviews. Genetics · 2026Review
- A versatile multi-components mixed model for bacterial-Genome Wide association studies.Nature communications · 2026Article
- Article
- Advancing microbial risk assessment: perspectives from the evolution of detection technologies.NPJ science of food · 2025Review
- microGWAS: a computational pipeline to perform large-scale bacterial genome-wide association studies.Microbial genomics · 2025Article
- A dose-response model for statistical analysis of chemical genetic interactions in CRISPRi screens.PLoS computational biology · 2024Article
- Virulence attributes of successful methicillin-resistantClinical microbiology reviews · 2023Review
- Genome-Wide Association Studies (GWAS) Approaches for the Detection of Genetic Variants Associated with Antibiotic Resistance: A Systematic Review.Microorganisms · 2023Review
- Reduced ambiguity and improved interpretability of bacterial genome-wide associations using gene-cluster-centricMicrobial genomics · 2023Article
- Development of a Single-nucleotide Polymorphism Genotyping Assay for the Rapid Detection of Vancomycin-intermediate Resistance inAnnals of laboratory medicine · 2023Article
- Emerging resistance in Staphylococcus epidermidis during dalbavancin exposure: a case report and in vitro analysis of isolates from prosthetic joint infections.The Journal of antimicrobial chemotherapy · 2023Article
- Development of an Amplicon Nanopore Sequencing Strategy for Detection of Mutations Conferring Intermediate Resistance to Vancomycin in Staphylococcus aureus Strains.Microbiology spectrum · 2023Article
- Comparative Genomics Identifies Novel Genetic Changes Associated with Oxacillin, Vancomycin and Daptomycin Susceptibility in ST100 Methicillin-ResistantAntibiotics (Basel, Switzerland) · 2023Article
- Machine Learning for Antimicrobial Resistance Prediction: Current Practice, Limitations, and Clinical Perspective.Clinical microbiology reviews · 2022Review
- Antibiotic Exposure Leads to Reduced Phage Susceptibility in Vancomycin Intermediate Staphylococcus aureus (VISA).Antimicrobial agents and chemotherapy · 2022Article
- Reduced Chlorhexidine Susceptibility Is Associated with Tetracycline ResistanceAntimicrobial agents and chemotherapy · 2022Article
- Genome-Wide Association Study Reveals Host Factors Affecting Conjugation inMicroorganisms · 2022Article
- Vancomycin heteroresistance inFuture science OA · 2021Article
- Bioinformatics Accelerates the Major Tetrad: A Real Boost for the Pharmaceutical Industry.International journal of molecular sciences · 2021Review
18 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
8 authors.
Funding
Abstract
Vancomycin-intermediate Staphylococcus aureus (VISA) is currently defined as having minimal inhibitory concentration (MIC) of 4-8 µg/ml. VISA evolves through changes in multiple genetic loci with at least 16 candidate genes identified in clinical and in vitro-selected VISA strains. We report a whole-genome comparative analysis of 49 vancomycin-sensitive S. aureus and 26 VISA strains. Resistance to vancomycin was determined by broth microdilution, Etest, and population analysis profile-area under the curve (PAP-AUC). Genome-wide association studies (GWAS) of 55,977 single-nucleotide polymorphisms identified in one or more strains found one highly significant association (P = 8.78 E-08) between a nonsynonymous mutation at codon 481 (H481) of the rpoB gene and increased vancomycin MIC. Additionally, we used a database of public S. aureus genome sequences to identify rare mutations in candidate genes associated with VISA. On the basis of these data, we proposed a preliminary model called ECM+RMCG for the VISA phenotype as a benchmark for future efforts. The model predicted VISA based on the presence of a rare mutation in a set of candidate genes (walKR, vraSR, graSR, and agrA) and/or three previously experimentally verified mutations (including the rpoB H481 locus) with an accuracy of 81% and a sensitivity of 73%. Further, the level of resistance measured by both Etest and PAP-AUC regressed positively with the number of mutations present in a strain. This study demonstrated 1) the power of GWAS for identifying common genetic variants associated with antibiotic resistance in bacteria and 2) that rare mutations in candidate gene, identified using large genomic data sets, can also be associated with resistance phenotypes.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.