ArticleDiagnostic microbiology and infectious disease2020
Staphylococcus aureus whole genome sequence-based susceptibility and resistance prediction using a clinically amenable workflow.
Article in Diagnostic microbiology and infectious disease, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 13 papers.
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Who cites it
13 citing papers in PubMed.
- Review
- Automated whole genome sequencing platform for bacterial strain typing in clinical microbiology laboratories.Journal of clinical microbiology · 2025Article
- Integrative genomic characterization of five Pediococcus acidilactici strains reveals differing probiotic safety profiles.PloS one · 2025Article
- SMR peptide antagonizesMicrobiology spectrum · 2024Article
- Clinical and Genomic Characterization of Carbapenem-ResistantMicroorganisms · 2023Article
- Benchmarking of two bioinformatic workflows for the analysis of whole-genome sequenced Staphylococcus aureus collected from patients with suspected sepsis.BMC infectious diseases · 2023Observational
- Core Genome Multilocus Sequence Typing and Antibiotic Susceptibility Prediction from Whole-Genome Sequence Data of Multidrug-Resistant Pseudomonas aeruginosa Isolates.Microbiology spectrum · 2022Article
- Recent Developments in Phenotypic and Molecular Diagnostic Methods for Antimicrobial Resistance Detection inDiagnostics (Basel, Switzerland) · 2022Review
- NGSocomial Infections: High-Resolution Views of Hospital-Acquired Infections Through Genomic Epidemiology.Journal of the Pediatric Infectious Diseases Society · 2021Review
- Core Genome Multilocus Sequence Typing and Prediction of Antimicrobial Susceptibility Using Whole-Genome Sequences of Escherichia coli Bloodstream Infection Isolates.Antimicrobial agents and chemotherapy · 2021Article
- A Combined Phenotypic-Genotypic Predictive Algorithm for In Vitro Detection of Bicarbonate: β-Lactam Sensitization among Methicillin-ResistantAntibiotics (Basel, Switzerland) · 2021Article
- Comparative Transcriptomic Analysis of Staphylococcus aureus Associated with Periprosthetic Joint Infection under in Vivo and in Vitro Conditions.The Journal of molecular diagnostics : JMD · 2021Article
- Whole Genome Sequencing Provides an Added Value to the Investigation of Staphylococcal Food Poisoning Outbreaks.Frontiers in microbiology · 2021Article
Corrections and comments
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Authors and funding
5 authors.
Funding
Abstract
We used graphical user interface-based automated analytical tools from Next Gen Diagnostics (Mountain View, CA) and 1928 Diagnostics (Gothenburg, Sweden) to analyze whole genome sequence (WGS) data from 102 unique blood culture isolates of Staphylococcus aureus to predict antimicrobial susceptibly, with results compared to those of phenotypic susceptibility testing. Of 916 isolate/antibiotic combinations analyzed using the Next Gen Diagnostics tool, there were 9 discrepancies between WGS predictions and phenotypic susceptibility/resistance, including 8 for clindamycin and 1 for minocycline. Of 612 isolate/antibiotic combinations analyzed using the 1928 Diagnostics tool, there were 13 discrepancies between WGS predictions and phenotypic susceptibility/resistance, including 9 for clindamycin, 3 for trimethoprim-sulfamethoxazole, and 1 for rifampin. Trimethoprim-sulfamethoxazole was not assessed by Next Gen Diagnostics, and minocycline was not assessed by 1928 Diagnostics. There was complete concordance between phenotypic susceptibility/resistance and genotypic prediction of susceptibility/resistance using both analytical platforms for oxacillin, vancomycin, and mupirocin, as well as by the Next Gen Diagnostics analytical tool for levofloxacin (the 1928 Diagnostics tool did not assess levofloxacin). These results suggest that, from a performance standpoint, with some caveats, automatic bioinformatics tools may be acceptable to predict susceptibility and resistance to a panel of antibiotics for S. aureus.
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