Diagnosis of lower respiratory tract infections using nanopore sequencing

Themoula Charalampous, Hollian Richardson, Gemma Kay, Rossella Baldan, Christopher Jeanes, Daniel Turner, John Wain, David Livermore, Richard Leggett, Justin O'Grady

Research output: Contribution to journalAbstractpeer-review


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.
Original languageEnglish
Article numberPA5308
Number of pages2
JournalEuropean Respiratory Journal
Issue numberSuppl.
Early online date19 Nov 2018
Publication statusPublished - 2018
Event28th International Congress of the European Respiratory Society (ERS) - Paris, France
Duration: 15 Sep 201819 Sep 2018

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