Metagenomic next-generation sequencing aids the diagnosis of viral infections in febrile returning travellers

JEROME, Hanna, TAYLOR, Callum, SREENU, Vattipally B, KLYMENKO, Tetyana, FILIPE, Ana Da Silva, JACKSON, Celia, DAVIS, Chris, ASHRAF, Shirin, WILSON-DAVIES, Eleri, JESUDASON, Natasha, DEVINE, Karen, HARDER, Lisbeth, AITKEN, Celia, GUNSON, Rory and THOMSON, Emma C (2019). Metagenomic next-generation sequencing aids the diagnosis of viral infections in febrile returning travellers. Journal of Infection.

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Link to published version:: https://doi.org/10.1016/j.jinf.2019.08.003
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    Abstract

    Objectives Travel-associated infections are challenging to diagnose because of the broad spectrum of potential aetiologies. As a proof-of-principle study, we used MNGS to identify viral pathogens in clinical samples from returning travellers in a single center to explore its suitability as a diagnostic tool. Methods Plasma samples from 40 returning travellers presenting with a fever of ≥38°C were sequenced using MNGS on the Illumina MiSeq platform and compared with standard-of-care diagnostic assays. Results In total, 11/40 patients were diagnosed with a viral infection. Standard of care diagnostics revealed 5 viral infections using plasma samples; dengue virus 1 (n = 2), hepatitis E (n = 1), Ebola virus (n = 1) and hepatitis A (n = 1), all of which were detected by MNGS. Three additional patients with Chikungunya virus (n = 2) and mumps virus were diagnosed by MNGS only. Respiratory infections detected by nasal/throat swabs only were not detected by MNGS of plasma. One patient had infection with malaria and mumps virus during the same admission. Conclusions MNGS analysis of plasma samples improves the sensitivity of diagnosis of viral infections and has potential as an all-in-one diagnostic test. It can be used to identify infections that have not been considered by the treating physician, co-infections and new or emerging pathogens. Summary Next generation sequencing (NGS) has potential as an all-in-one diagnostic test. In this study we used NGS to diagnose returning travellers with acute febrile illness in the UK, highlighting cases where the diagnosis was missed using standard methods.

    Item Type: Article
    Uncontrolled Keywords: Microbiology; 1103 Clinical Sciences
    Identification Number: https://doi.org/10.1016/j.jinf.2019.08.003
    SWORD Depositor: Symplectic Elements
    Depositing User: Symplectic Elements
    Date Deposited: 18 Sep 2019 11:08
    Last Modified: 03 Jul 2020 15:30
    URI: http://shura.shu.ac.uk/id/eprint/25123

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