Nanopore metagenomics enables rapid clinical diagnosis of bacterial lower respiratory infection

• Published in: Nature biotechnology 2019-07, Vol.37 (7), p.783-792
• Main Authors: Charalampous, Themoula, Kay, Gemma L., Richardson, Hollian, Aydin, Alp, Baldan, Rossella, Jeanes, Christopher, Rae, Duncan, Grundy, Sara, Turner, Daniel J., Wain, John, Leggett, Richard M., Livermore, David M., O’Grady, Justin
• Format: Article
• Language: English
• Subjects: 631/326/2521; 631/61/212/2142; 631/61/514/2254; Agriculture; Anti-Bacterial Agents - pharmacology; Antibiotic resistance; Antibiotics; Bacteria; Bacteria - drug effects; Bacteria - genetics; Bacteria - isolation & purification; Bioinformatics; Biomedical and Life Sciences; Biomedical Engineering/Biotechnology; Biomedicine; Biotechnology; Bronchitis - diagnosis; Bronchitis - microbiology; Culture; Deoxyribonucleic acid; Depletion; Diagnosis; DNA; DNA sequencing; DNA, Bacterial - genetics; Drug Resistance, Bacterial - genetics; Genome, Bacterial; High-Throughput Nucleotide Sequencing - methods; Humans; Identification methods; Life Sciences; Metagenomics - methods; Nanopores; Pathogens; Pilot Projects; Pneumonia, Bacterial - diagnosis; Pneumonia, Bacterial - microbiology; Porosity; Respiratory tract infection; Saponins; Sensitivity analysis; Sensitivity and Specificity
• ISSN: 1087-0156; 1546-1696; 1546-1696
• DOI: 10.1038/s41587-019-0156-5

The gold standard for clinical diagnosis of bacterial lower respiratory infections (LRIs) is culture, which has poor sensitivity and is too slow to guide early, targeted antimicrobial therapy. Metagenomic sequencing could identify LRI pathogens much faster than culture, but methods are needed to remove the large amount of human DNA present in these samples for this approach to be feasible. We developed a metagenomics method for bacterial LRI diagnosis that features efficient saponin-based host DNA depletion and nanopore sequencing. Our pilot method was tested on 40 samples, then optimized and tested on a further 41 samples. Our optimized method (6 h from sample to result) was 96.6% sensitive and 41.7% specific for pathogen detection compared with culture and we could accurately detect antibiotic resistance genes. After confirmatory quantitative PCR and pathobiont-specific gene analyses, specificity and sensitivity increased to 100%. Nanopore metagenomics can rapidly and accurately characterize bacterial LRIs and might contribute to a reduction in broad-spectrum antibiotic use. Nanopore sequencing coupled with a metagenomics framework that effectively removes human DNA from samples enables rapid bacterial LRI diagnosis.