ArticleJournal of global antimicrobial resistance2019
Use of online tools for antimicrobial resistance prediction by whole-genome sequencing in methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant enterococci (VRE).
Article in Journal of global antimicrobial resistance, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed, 27 citations in OpenAlex.
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- Comparative genomics of Vibrio toranzoniae strains.International microbiology : the official journal of the Spanish Society for Microbiology · 2025Article
- Development of a One-Step Multiplex qPCR Assay for Detection of Methicillin and Vancomycin Drug Resistance Genes in Antibiotic-Resistant Bacteria.Pathogens (Basel, Switzerland) · 2024Article
- Comparative genomics of Vibrio toranzoniae strains.Research square · 2024Article
- Whole genome sequencing of methicillin-resistant Staphylococcus aureus clinical isolates from Terengganu, Malaysia, indicates the predominance of the EMRSA-15 (ST22-SCCmec IV) clone.Scientific reports · 2024Article
- Current Uses and Future Perspectives of Genomic Technologies in Clinical Microbiology.Antibiotics (Basel, Switzerland) · 2023Review
- Mechanisms of high-level fosfomycin resistance in Staphylococcus aureus epidemic lineage ST5.The Journal of antimicrobial chemotherapy · 2022Article
- Next Generation and Other Sequencing Technologies in Diagnostic Microbiology and Infectious Diseases.Genes · 2022Review
- Methodology for laboratory-based antimicrobial resistance surveillance in animals.Veterinary world · 2022Review
- Recent Developments in Phenotypic and Molecular Diagnostic Methods for Antimicrobial Resistance Detection inDiagnostics (Basel, Switzerland) · 2022Review
- mSphere of Influence: Whole-Genome Sequencing, a Vital Tool for the Interruption of Nosocomial Transmission.mSphere · 2021Article
- Assessing the Potential for Unintended Microbial Consequences of Routine Chlorhexidine Bathing for Prevention of Healthcare-associated Infections.Clinical infectious diseases : an official publication of the Infectious Diseases Society of America · 2021Review
- Staphylococcus aureus whole genome sequence-based susceptibility and resistance prediction using a clinically amenable workflow.Diagnostic microbiology and infectious disease · 2020Article
- Whole Genome Sequencing Differentiates Presumptive Extended Spectrum Beta-Lactamase ProducingMicroorganisms · 2020Article
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Authors and funding
10 authors at 1 institution in 1 country.
Funding
Abstract
objectivesThe antimicrobial resistance (AMR) crisis represents a serious threat to public health and has resulted in concentrated efforts to accelerate development of rapid molecular diagnostics for AMR. In combination with publicly available web-based AMR databases, whole-genome sequencing (WGS) offers the capacity for rapid detection of AMR genes. Here we studied the concordance between WGS-based resistance prediction and phenotypic susceptibility test results for methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant enterococci (VRE) clinical isolates using publicly available tools and databases.
methodsClinical isolates prospectively collected at the University of Pittsburgh Medical Center between December 2016 and December 2017 underwent WGS. The AMR gene content was assessed from assembled genomes by BLASTn search of online databases. Concordance between the WGS-predicted resistance profile and phenotypic susceptibility as well as the sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) were calculated for each antibiotic/organism combination, using the phenotypic results as gold standard.
resultsPhenotypic susceptibility testing and WGS results were available for 1242 isolate/antibiotic combinations. Overall concordance was 99.3%, with a sensitivity, specificity, PPV and NPV of 98.7% (95% CI 97.2-99.5%), 99.6% (95% CI 98.8-99.9%), 99.3% (95% CI 98.0-99.8%) and 99.2% (95% CI 98.3-99.7%), respectively. Additional identification of point mutations in housekeeping genes increased the concordance to 99.4%, sensitivity to 99.3% (95% CI 98.2-99.8%) and NPV to 99.4% (95% CI 98.4-99.8%).
conclusionWGS can be used as a reliable predicator of phenotypic resistance both for MRSA and VRE using readily available online tools.
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