ArticleGenome medicine2020
PathoSPOT genomic epidemiology reveals under-the-radar nosocomial outbreaks.
Article in Genome medicine, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 15 papers.
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Who cites it
15 citing papers in PubMed.
- Sampling and Host-Strain Interactions Shape Detection of Staphylococcus aureus Transmission in Hospitals.The Journal of infectious diseases · 2026Article
- Genome sequencing for prevention of health-care-associated bacterial infections.Nature reviews. Microbiology · 2026Review
- Implementation and outcomes of a rapid response genomic hospital epidemiology programme at an academic medical centre over 7 years.The Lancet. Microbe · 2026Review
- Evaluation of Fourier transform infrared spectroscopy as a first-line surveillance typing tool forFrontiers in antibiotics · 2026Article
- Decoding the evolutionary history of ST30Frontiers in microbiology · 2025Article
- ST105 Lineage of MRSA: An Emerging Implication for Bloodstream Infection in the American and European Continents.Antibiotics (Basel, Switzerland) · 2024Review
- Forensic Microbiology: When, Where and How.Microorganisms · 2024Review
- Article
- Economic and health impact modelling of a whole genome sequencing-led intervention strategy for bacterial healthcare-associated infections for England and for the USA.Microbial genomics · 2023Article
- Unsuspected Clonal Spread of Methicillin-Resistant Staphylococcus aureus Causing Bloodstream Infections in Hospitalized Adults Detected Using Whole Genome Sequencing.Clinical infectious diseases : an official publication of the Infectious Diseases Society of America · 2022Article
- Whole-Genome Sequencing Surveillance and Machine Learning of the Electronic Health Record for Enhanced Healthcare Outbreak Detection.Clinical infectious diseases : an official publication of the Infectious Diseases Society of America · 2022Article
- Everybody nose: molecular and clinical characteristics of nasal colonization during active methicillin-resistant Staphylococcus aureus bloodstream infection.BMC infectious diseases · 2022Article
- Whole-genome sequencing surveillance and machine learning for healthcare outbreak detection and investigation: A systematic review and summary.Antimicrobial stewardship & healthcare epidemiology : ASHE · 2022Review
- NGSocomial Infections: High-Resolution Views of Hospital-Acquired Infections Through Genomic Epidemiology.Journal of the Pediatric Infectious Diseases Society · 2021Review
- The impact of genomics on precision public health: beyond the pandemic.Genome medicine · 2021Article
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Authors and funding
19 authors.
Funding
Abstract
backgroundWhole-genome sequencing (WGS) is increasingly used to map the spread of bacterial and viral pathogens in nosocomial settings. A limiting factor for more widespread adoption of WGS for hospital infection prevention practices is the availability of standardized tools for genomic epidemiology.
methodsWe developed the Pathogen Sequencing Phylogenomic Outbreak Toolkit (PathoSPOT) to automate integration of genomic and medical record data for rapid detection and tracing of nosocomial outbreaks. To demonstrate its capabilities, we applied PathoSPOT to complete genome surveillance data of 197 MRSA bacteremia cases from two hospitals during a 2-year period.
resultsPathoSPOT identified 8 clonal clusters encompassing 33 patients (16.8% of cases), none of which had been recognized by standard practices. The largest cluster corresponded to a prolonged outbreak of a hospital-associated MRSA clone among 16 adults, spanning 9 wards over a period of 21 months. Analysis of precise timeline and location data with our toolkit suggested that an initial exposure event in a single ward led to infection and long-term colonization of multiple patients, followed by transmissions to other patients during recurrent hospitalizations.
conclusionsWe demonstrate that PathoSPOT genomic surveillance enables the detection of complex transmission chains that are not readily apparent from epidemiological data and that contribute significantly to morbidity and mortality, enabling more effective intervention strategies.
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