ArticleClinical infectious diseases : an official publication of the Infectious Diseases Society of America2019
Whole-genome Sequencing Provides Data for Stratifying Infection Prevention and Control Management of Nosocomial Influenza A.
Article in Clinical infectious diseases : an official publication of the Infectious Diseases Society of America, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 19 papers, 1 of them a synthesis that pooled it.
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Who cites it
19 citing papers in PubMed, 1 synthesis or guideline pooled it.
- Detection of respiratory viruses directly from clinical samples using next-generation sequencing: A literature review of recent advances and potential for routine clinical use.Reviews in medical virology · 2022Pooled it
- Beyond traditional outbreak investigation: Using genomic data for enhanced detection of COVID-19 disease clusters in Utah.PloS one · 2026Article
- The potential of genomic epidemiology: capitalizing on its practical use for impact in the healthcare setting.Frontiers in public health · 2025Article
- Feasibility and clinical utility of local rapid Nanopore influenza A virus whole genome sequencing for integrated outbreak management, genotypic resistance detection and timely surveillance.Microbial genomics · 2023Article
- Culture-Independent Workflow for Nanopore MinION-Based Sequencing of Influenza A Virus.Microbiology spectrum · 2023Article
- Investigating Epidemiologic and Molecular Links Between Patients With Community- and Hospital-Acquired Influenza A: 2017-2018 and 2019-2020, Michigan.Open forum infectious diseases · 2023Article
- Article
- From Clinical Specimen to Whole Genome Sequencing of A(H3N2) Influenza Viruses: A Fast and Reliable High-Throughput Protocol.Vaccines · 2022Article
- Article
- The Impact of Real-Time Whole-Genome Sequencing in Controlling Healthcare-Associated SARS-CoV-2 Outbreaks.The Journal of 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
- Nanopore metagenomic sequencing of influenza virus directly from respiratory samples: diagnosis, drug resistance and nosocomial transmission, United Kingdom, 2018/19 influenza season.Euro surveillance : bulletin Europeen sur les maladies transmissibles = European communicable disease bulletin · 2021Article
- Viral metagenomics reveals the presence of novel Zika virus variants in Aedes mosquitoes from Barbados.Parasites & vectors · 2021Article
- Rapid feedback on hospital onset SARS-CoV-2 infections combining epidemiological and sequencing data.eLife · 2021Article
- Epidemic situation of the complex seasonality of imported influenza A and B virus transmission in Guangxi ports of ChinaTurkish journal of medical sciences · 2021Article
- Epidemiological and clinical characteristics of community-acquired and nosocomial influenza cases and risk factors associated with complications: A four season analysis of all adult patients admitted in a tertiary hospital.Influenza and other respiratory viruses · 2021Observational
- Using Whole Genome Sequences to Investigate Adenovirus Outbreaks in a Hematopoietic Stem Cell Transplant Unit.Frontiers in microbiology · 2021Article
- A Systematic Review Analyzing the Prevalence and Circulation of Influenza Viruses in Swine Population Worldwide.Pathogens (Basel, Switzerland) · 2020Review
- Third-Generation Sequencing in the Clinical Laboratory: Exploring the Advantages and Challenges of Nanopore Sequencing.Journal of clinical microbiology · 2019Review
Corrections and comments
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Authors and funding
6 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundInfluenza A virus causes annual epidemics in humans and is associated with significant morbidity and mortality. Haemagglutinin (HA) and neuraminidase (NA) gene sequencing have traditionally been used to identify the virus genotype, although their utility in detecting outbreak clusters is still unclear. The objective of this study was to determine the utility, if any, of whole-genome sequencing over HA/NA sequencing for infection prevention and control (IPC) in hospitals.
methodsWe obtained all clinical samples from influenza (H1N1)-positive patients at the Great Ormond Street Hospital between January and March 2016. Samples were sequenced using targeted enrichment on an Illumina MiSeq sequencer. Maximum likelihood trees were computed for both whole genomes and concatenated HA/NA sequences. Epidemiological data was taken from routine IPC team activity during the period.
resultsComplete genomes were obtained for 65/80 samples from 38 patients. Conventional IPC analysis recognized 1 outbreak, involving 3 children, and identified another potential cluster in the haemato-oncology ward. Whole-genome and HA/NA phylogeny both accurately identified the previously known outbreak cluster. However, HA/NA sequencing additionally identified unrelated strains as part of this outbreak cluster. A whole-genome analysis identified a further cluster of 2 infections that had been previously missed and refuted suspicions of transmission in the haemato-oncology wards.
conclusionsWhole-genome sequencing is better at identifying outbreak clusters in a hospital setting than HA/NA sequencing. Whole-genome sequencing could provide a faster and more reliable method for outbreak monitoring and supplement routine IPC team work to allow the prevention of transmission.
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