Highlights
- •Nanopore sequencing can provide a same day result for respiratory infection on ICU.
- •Nanopore 16S sequencing was able to identify causative pathogen in 32/33 cases.
- •Providing a sequenced negative result adds value to patient management.
- •Further work is required to standardise and automate this technology for routine use.
Summary
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.
Keywords
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Article info
Publication history
Published online: June 16, 2021
Accepted:
June 9,
2021
Identification
Copyright
© 2021 The British Infection Association. Published by Elsevier Ltd. All rights reserved.
