Rossella Baldan1, Penelope R Cliff2, Sarah Burns1, Adela Medina2, Graeme C Smith2, Rahul Batra1, Alberto Cerda2, Rebekah Wilson2, Tammy Merrill2, Shona J Lewis2, Amita Patel1, Dakshika Jeyaratnam3, Duncan L Wyncoll4, Nicholas Barrett4, Meera A Chand5, Jonathan D Edgeworth6. 1. Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, King's College London, St Thomas' Hospital, Westminster Bridge Road, London, UK; Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK. 2. Infection Sciences, Viapath, St Thomas' Hospital, London, UK. 3. South London Specialist Virology Centre, King's College Hospital NHS Foundation Trust, London, UK. 4. Department of Critical Care, Guy's and St Thomas' NHS Foundation Trust, London, UK. 5. Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK; Department of Critical Care, Guy's and St Thomas' NHS Foundation Trust, London, UK; National Infection Service, Public Health England, London, UK; Health Protection Research Unit in Respiratory Infections, Imperial College London, London, UK. 6. Centre for Clinical Infection and Diagnostics Research, Department of Infectious Diseases, King's College London, St Thomas' Hospital, Westminster Bridge Road, London, UK; Department of Infectious Diseases, Guy's and St Thomas' NHS Foundation Trust, London, UK; Infection Sciences, Viapath, St Thomas' Hospital, London, UK. Electronic address: Jonathan.Edgeworth@gstt.nhs.uk.
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.
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.
Authors: Emma Whittle; Jennifer A Yonkus; Patricio Jeraldo; Roberto Alva-Ruiz; Heidi Nelson; Michael L Kendrick; Thomas E Grys; Robin Patel; Mark J Truty; Nicholas Chia Journal: mSphere Date: 2022-02-16 Impact factor: 4.389