Tools
Tools
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
Abstract
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 Sep 2024 14:43 |
| URI: | https://ueaeprints.uea.ac.uk/id/eprint/75443 |
| DOI: | 10.1183/13993003.congress-2018.PA5308 |
Actions (login required)
 |
View Item |