ArticleClinical infectious diseases : an official publication of the Infectious Diseases Society of America2022
Whole-Genome Sequencing Surveillance and Machine Learning of the Electronic Health Record for Enhanced Healthcare Outbreak Detection.
Article in Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 75 papers.
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Who cites it
75 citing papers in PubMed.
- Differential virulence potential of different clades of multidrug-resistantMicrobiology spectrum · 2026Article
- Genomic analysis of intrahospital transmission of carbapenem-resistant Gram-negative bacteria: a multicentre study in Japan.Microbial genomics · 2026Article
- Culture-enriched metagenomic sequencing reveals within-patient diversity and transmission of vancomycin-resistantMicrobial genomics · 2026Article
- Can Artificial Intelligence Transform Early Warning for Antimicrobial-Resistant Outbreak Clones? Approaches, Gaps, and Opportunities: A Scoping Review.Antibiotics (Basel, Switzerland) · 2026Review
- Genomic Epidemiology of Antibiotic-Resistant Bacteria Sampled from Metropolitan Wastewater.Microorganisms · 2026Article
- Differential virulence potential of different clades of multidrug-resistantmedRxiv : the preprint server for health sciences · 2026Article
- Advocating the potential of artificial intelligence for syndrome discovery in syndromic surveillance systems: A scoping review.iScience · 2026Review
- Culture-enriched metagenomic sequencing reveals within-patient diversity and transmission of vancomycin-resistantmedRxiv : the preprint server for health sciences · 2026Article
- Connections betweenInfection and immunity · 2026Article
- Identifying intra-hospital Norovirus GII transmission using whole-genome sequencing.Genome medicine · 2026Article
- Healthcare worker long-sleeved attire contamination: a prospective observational study.Infection control and hospital epidemiology · 2026Observational
- Real-Time Genomic Surveillance for Enhanced Healthcare Outbreak Detection and Control: Clinical and Economic Impact.Clinical infectious diseases : an official publication of the Infectious Diseases Society of America · 2026Article
- Regression-based modeling of pairwise genomic linkage data identifies risk factors for healthcare-associated pathogen transmission: application to carbapenem-resistantMicrobiology spectrum · 2026Article
- Artificial intelligence enhances genomic surveillance in healthcare outbreak investigations.Infection control and hospital epidemiology · 2026Article
- Implementation and outcomes of a rapid response genomic hospital epidemiology programme at an academic medical centre over 7 years.The Lancet. Microbe · 2026Review
- Feasibility of AI-driven disease surveillance systems at international airports in sub-Saharan Africa: a narrative review.Frontiers in public health · 2026Review
- Beyond contact precautions: unmasking environmental and antibiotic drivers of ESBL-E in the ICU.Annals of intensive care · 2026Article
- Leveraging real-time genomic surveillance to combat infectious diseases and antimicrobial resistance in cancer patients.Frontiers in public health · 2026Article
- Methods for cost-efficient, whole genome sequencing surveillance for enhanced detection of outbreaks in a hospital setting.PloS one · 2026Article
- Genomic pitfalls in hospital surveillance: unexpected Enterobacter cloacae clustering without epidemiological link highlights the need for cautious core genome MLST analysis interpretation.Antimicrobial resistance and infection control · 2025Article
15 more citing papers are in PubMed but not listed here.
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22 authors.
Funding
Abstract
backgroundMost hospitals use traditional infection prevention (IP) methods for outbreak detection. We developed the Enhanced Detection System for Healthcare-Associated Transmission (EDS-HAT), which combines whole-genome sequencing (WGS) surveillance and machine learning (ML) of the electronic health record (EHR) to identify undetected outbreaks and the responsible transmission routes, respectively.
methodsWe performed WGS surveillance of healthcare-associated bacterial pathogens from November 2016 to November 2018. EHR ML was used to identify the transmission routes for WGS-detected outbreaks, which were investigated by an IP expert. Potential infections prevented were estimated and compared with traditional IP practice during the same period.
resultsOf 3165 isolates, there were 2752 unique patient isolates in 99 clusters involving 297 (10.8%) patient isolates identified by WGS; clusters ranged from 2-14 patients. At least 1 transmission route was detected for 65.7% of clusters. During the same time, traditional IP investigation prompted WGS for 15 suspected outbreaks involving 133 patients, for which transmission events were identified for 5 (3.8%). If EDS-HAT had been running in real time, 25-63 transmissions could have been prevented. EDS-HAT was found to be cost-saving and more effective than traditional IP practice, with overall savings of $192 408-$692 532.
conclusionsEDS-HAT detected multiple outbreaks not identified using traditional IP methods, correctly identified the transmission routes for most outbreaks, and would save the hospital substantial costs. Traditional IP practice misidentified outbreaks for which transmission did not occur. WGS surveillance combined with EHR ML has the potential to save costs and enhance patient safety.
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