ArticleJournal of clinical microbiology2015
Application of whole-genome sequencing for bacterial strain typing in molecular epidemiology.
Article in Journal of clinical microbiology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 160 papers, 1 of them a synthesis that pooled it.
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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.
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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.
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Who cites it
160 citing papers in PubMed, 1 synthesis or guideline pooled it, 288 citations in OpenAlex.
- Diagnostic Performance of Metagenomic Next-Generation Sequencing (mNGS) and Culture in Infected Pancreatic Necrosis: A Systematic Review and Meta-Analysis.Digestive diseases and sciences · 2026Pooled it
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- Performance of the IR Biotyper, Nanopore, and Illumina sequencing to discriminateMicrobiology spectrum · 2026Article
- Comparing whole-genome sequencing to pulsed-field gel electrophoresis for vancomycin-resistantMicrobiology spectrum · 2026Article
- Genomic characterization and pathogenicity validation of Mycoplasma ovipneumoniae strains from diseased sheep: insights into potential pathogenic mechanisms of GSWW364.Veterinary research · 2026Article
- East AsianJournal of veterinary science · 2026Article
- Methicillin-ResistantInternational journal of molecular sciences · 2026Review
- From Culture to Sequencing: Evolving Strategies for the Diagnosis of Pediatric Spondylodiscitis.Orthopaedic surgery · 2026Review
- Mammaliicoccus sciuri as a sentinel for antimicrobial resistance and virulence: genomic epidemiology, transmission dynamics, and control in the one health era.Veterinary research communications · 2026Review
- Genetic diversity and within-farm transmission of Staphylococcus aureus from ewes in Norway.BMC microbiology · 2026Article
- Emergence of Dalbavancin, Vancomycin, and Daptomycin Cross-resistance in MRSA During Long-term LVAD Suppression With Vancomycin Followed by Dalbavancin: Genomic Insights and Synergy With Cefadroxil.Open forum infectious diseases · 2026Article
- The Brief Case: Adjudication of discrepant genotypic and phenotypic antimicrobial susceptibility testing results in a patient withJournal of clinical microbiology · 2026Review
- Integrated FTIR and Whole-Genome Sequencing Reveal Scale-Dependent Genotype-Phenotype Relationships in Multidrug-ResistantPathogens (Basel, Switzerland) · 2026Article
- Culture and Adaptation of Pseudomonas aeruginosa During Early Infection in Children With Cystic Fibrosis.The Journal of infectious diseases · 2026Article
- Unveiling aAnimals : an open access journal from MDPI · 2025Article
- Study Protocol for Genomic Epidemiology Investigation of Intensive Care Unit Patient Colonization by Antimicrobial-Resistant ESKAPE Pathogens.Methods and protocols · 2025Article
- Human microbiome acquisition and transmission.Nature reviews. Microbiology · 2025Review
- Diversity versus clonality in carbapenem-resistant A. baumannii: a two-year surveillance study in four intensive care units at a large teaching hospital in Rome, Italy.Antimicrobial resistance and infection control · 2025Article
- Article
- Molecular Epidemiology Clinical Manifestations, Decolonization Strategies, and Treatment Options of Methicillin-ResistantPathogens (Basel, Switzerland) · 2025Review
100 more citing papers are in PubMed but not listed here.
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Authors and funding
6 authors at 1 institution in 1 country.
Funding
Abstract
Nosocomial infections pose a significant threat to patient health; however, the gold standard laboratory method for determining bacterial relatedness (pulsed-field gel electrophoresis [PFGE]) remains essentially unchanged 20 years after its introduction. Here, we explored bacterial whole-genome sequencing (WGS) as an alternative approach for molecular strain typing. We compared WGS to PFGE for investigating presumptive outbreaks involving three important pathogens: vancomycin-resistant Enterococcus faecium (n=19), methicillin-resistant Staphylococcus aureus (n=17), and Acinetobacter baumannii (n=15). WGS was highly reproducible (average≤0.39 differences between technical replicates), which enabled a functional, quantitative definition for determining clonality. Strain relatedness data determined by PFGE and WGS roughly correlated, but the resolution of WGS was superior (P=5.6×10(-8) to 0.016). Several discordant results were noted between the methods. A total of 28.9% of isolates which were indistinguishable by PFGE were nonclonal by WGS. For A. baumannii, a species known to undergo rapid horizontal gene transfer, 16.2% of isolate pairs considered nonidentical by PFGE were clonal by WGS. Sequencing whole bacterial genomes with single-nucleotide resolution demonstrates that PFGE is prone to false-positive and false-negative results and suggests the need for a new gold standard approach for molecular epidemiological strain typing.
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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.