Development and evaluation of a nanopore 16S rRNA gene sequencing service for same day targeted treatment of bacterial respiratory infection in the intensive care unit

Rossella Baldan, Penelope R. Cliff, Sarah Burns, Adela Medina, Graeme C. Smith, Rahul Batra, Alberto Cerda, Rebekah Wilson, Tammy Merrill, Shona J. Lewis, Amita Patel, Dakshika Jeyaratnam, Duncan L. Wyncoll, Nicholas Barrett, Meera A. Chand, Jonathan D. Edgeworth*

*Corresponding author for this work

    Research output: Contribution to journalArticlepeer-review

    Abstract

    Objectives: Assess the feasibility and impact of nanopore-based 16S rRNA gene sequencing (Np16S) service on antibiotic treatment for acute severe pneumonia on the intensive care unit (ICU).

    Methods: Speciation and sequencing accuracy of Np16S on isolates with bioinformatics pipeline optimisation, followed by technical evaluation including quality checks and clinical-reporting criteria analysing stored respiratory samples using single-sample flow cells. Pilot service comparing Np16S results with all routine respiratory tests and impact on same-day antimicrobial prescribing.

    Results: Np16S correctly identified 140/167 (84%) isolates after 1h sequencing and passed quality control criteria including reproducibility and limit-of-detection. Sequencing of 108 stored respiratory samples showed concordance with routine culture in 80.5% of cases and established technical and clinical reporting criteria. A 10-week same-day pilot Np16S service analysed 45 samples from 37 patients with suspected community (n=15) or hospital acquired (n=30) pneumonia. Np16S showed concordance compared with all routine culture or molecular tests for 27 (82%) of 33 positive samples. It identified the causative pathogen in 32/33 (97%) samples and contributed to antimicrobial treatment changes for 30 patients (67%).

    Conclusions: This study demonstrates feasibility of providing a routine same-day nanopore sequencing service that makes a significant contribution to early antibiotic prescribing for bacterial pneumonia in the ICU.

    Original languageEnglish
    Pages (from-to)167-174
    Number of pages8
    JournalJournal of Infection
    Volume83
    Issue number2
    Early online date17 Jun 2021
    DOIs
    Publication statusPublished - Aug 2021

    Bibliographical note

    Funding Information: This study was funded/supported by the National Institute for Health Research (NIHR) Biomedical Research Centre based at Guy's and St Thomas' NHS Foundation Trust and King's College London, programme of Infection and Immunity [RJ112/N027] and the NIHR Collaboration for Leadership in Applied Health Research and Care (CLAHRC) South London at King's College Hospital NHS Foundation Trust, awarded to JDE, and the Viapath Innovation Grant awarded to PC.

    The authors want to thank the staff of the clinical microbiology laboratory for helping to collect the isolates included in this study. The authors are grateful to the infection physicians, Drs Carolyn Hemsley and John Klein, for helping to identify the most clinically relevant species and to Dr Fearghal Tucker and Lisa Bryan from Viapath Infection Sciences for providing support to the study. The authors would also like to thank Natalie Groves from Public Health England for her bioinformatics expertise and the strategy adopted to parse Centrifuge results.

    Open Access: No Open Access licence

    Publisher Copyright: © 2021 The British Infection Association. Published by Elsevier Ltd. All rights reserved.

    Citation: Rossella Baldan, Penelope R. Cliff, Sarah Burns, Adela Medina, Graeme C. Smith, Rahul Batra, Alberto Cerda, Rebekah Wilson, Tammy Merrill, Shona J. Lewis, Amita Patel, Dakshika Jeyaratnam, Duncan L. Wyncoll, Nicholas Barrett, Meera A. Chand, Jonathan D. Edgeworth, Development and evaluation of a nanopore 16S rRNA gene sequencing service for same day targeted treatment of bacterial respiratory infection in the intensive care unit, Journal of Infection,
    Volume 83, Issue 2, 2021, Pages 167-174, ISSN 0163-4453.

    DOI: https://doi.org/10.1016/j.jinf.2021.06.014.

    Keywords

    • 16S rRNA
    • Bacterial infections
    • LRTI
    • Nanopore flongle
    • Rapid diagnostics

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