Feasibility and clinical utility of local rapid Nanopore influenza A virus whole genome sequencing for integrated outbreak management, genotypic resistance detection and timely surveillance
Rattachement africain : gb. Niveau de preuve : code pays fourni par la source.
Le résumé fourni par la source
Rapid respiratory viral whole genome sequencing (WGS) in a clinical setting can inform real-time outbreak and patient treatment decisions, but the feasibility and clinical utility of influenza A virus (IAV) WGS using Nanopore technology has not been demonstrated. A 24 h turnaround Nanopore IAV WGS protocol was performed on 128 reverse transcriptase PCR IAV-positive nasopharyngeal samples taken over seven weeks of the 2022-2023 winter influenza season, including 25 from patients with nosocomial IAV infections and 102 from patients attending the Emergency Department. WGS results were reviewed collectively alongside clinical details for interpretation and reported to clinical teams. All eight segments of the IAV genome were recovered for 97/128 samples (75.8 %) and the haemagglutinin gene for 117/128 samples (91.4 %). Infection prevention and control identified nosocomial IAV infections in 19 patients across five wards. IAV WGS revealed two separate clusters on one ward and excluded transmission across different wards with contemporaneous outbreaks. IAV WGS also identified neuraminidase inhibitor resistance in a persistently infected patient and excluded avian influenza in a sample taken from an immunosuppressed patient with a history of travel to Singapore which had failed PCR subtyping. Accurate IAV genomes can be generated in 24 h using a Nanopore protocol accessible to any laboratory with SARS-CoV-2 Nanopore sequencing capacity. In addition to replicating reference laboratory surveillance results, IAV WGS can identify antiviral resistance and exclude avian influenza. IAV WGS also informs management of nosocomial outbreaks, though molecular and clinical epidemiology were concordant in this study, limiting the impact on decision-making.
Ce résumé expose les affirmations des auteurs. BNTIC ne l’interprète pas comme une validation indépendante des résultats.
Le contrôle bibliographique ouvert
DOI retrouvé dans Crossref DOI retrouvé ; titre concordant.
- Titre Crossref
- Feasibility and clinical utility of local rapid Nanopore influenza A virus whole genome sequencing for integrated outbreak management, genotypic resistance detection and timely surveillance
- Date Crossref
- 17/08/2023
- Éditeur
- Microbiology Society
- Type
- journal-article
Ce recoupement confirme des métadonnées liées au DOI. Il ne confirme ni la méthode ni les conclusions de l’étude, et il ne compte pas comme une seconde source scientifique indépendante.
Où se fait cette recherche
-
Guy's and St Thomas' NHS Foundation Trust pays non établi dans la noticeÉtablissement de santé
-
King's College London Department of Infectious Diseases pays non établi dans la noticeUniversité ou école supérieure
-
Centre for Clinical Diagnostics & Infectious Disease Research pays non établi dans la noticeÉtablissement de santé
-
Guy’s & St. Thomas’ NHS Foundation Trust Department of Infection pays non établi dans la noticeOrganisation à but non lucratif
-
Infection Sciences pays non établi dans la noticeInstitution
-
United Kingdom Health Security Agency (UKHSA) pays non établi dans la noticeOrganisme public
Guy's and St Thomas' NHS Foundation Trust, Department of Infectious Diseases — King's College London et Centre for Clinical Diagnostics & Infectious Disease Research, avec 3 autres affiliations.
Une affiliation ne permet pas de déduire la nationalité d’un auteur.