Diagnosis of lower respiratory tract infections using nanopore sequencing

Charalampous, Themoula, Richardson, Hollian, Kay, Gemma, Baldan, Rossella, Jeanes, Christopher, Turner, Daniel, Wain, John, Livermore, David ORCID: https://orcid.org/0000-0002-9856-3703, Leggett, Richard and O'Grady, Justin (2018) Diagnosis of lower respiratory tract infections using nanopore sequencing. European Respiratory Journal, 52 (Suppl.). ISSN 0903-1936

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Background: According to WHO, lower respiratory tract infections (LRTI) are the deadliest communicable disease globally, causing 3.2 million deaths annually. Culture is the gold-standard diagnostic, but produces sub-optimal results and takes a minimum of 48hr. Poor diagnostics impact on patient management and treatment. Shotgun-metagenomics can overcome these issues, by reducing turnaround time and improving diagnostic accuracy. Aim: To develop a rapid metagenomics sequencing pipeline for the diagnosis of bacterial LRTIs directly from respiratory samples. Methods: Respiratory samples (sputum and aspirates) from patients with suspected bacterial LRTIs were used to develop and optimise a metagenomics pipeline which included: novel human DNA depletion, pathogen DNA extraction, library preparation and MinION sequencing. Pathogens and antibiotic resistance genes were identified in real-time by MinION sequencing and Epi2ME analysis (Antimicrobial Resistance pipeline) and were compared to clinical microbiology results. Results: The initial sample set (n=42) was 89% concordant with culture for pathogen detection. After optimisation (improving turnaround and sensitivity) the pipeline was tested on a second sample set (n=13) and was 100% concordant with culture. The turnaround time was 6hrs from sample to pathogen and acquired-resistance gene identification. Routine microbiology identified 2 MRSA positive samples, both of which were mecA gene positive using the developed metagenomics sequencing pipeline. Conclusion: LRTI pathogens and antibiotic resistance genes were identified within 6hrs with our pipeline, demonstrating that metagenomic sequencing has the potential to replace culture.

Item Type: Article
Faculty \ School: Faculty of Medicine and Health Sciences > Norwich Medical School
UEA Research Groups: Faculty of Medicine and Health Sciences > Research Groups > Public Health and Health Services Research (former - to 2023)
Faculty of Medicine and Health Sciences > Research Groups > Epidemiology and Public Health
Depositing User: LivePure Connector
Date Deposited: 03 Jun 2020 00:13
Last Modified: 25 Aug 2022 15:41
URI: https://ueaeprints.uea.ac.uk/id/eprint/75443
DOI: 10.1183/13993003.congress-2018.PA5308

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