Identifying bacterial airways infection in stable severe asthma using Oxford nanopore sequencing technologies

Jabeen, MF; Sanderson, N; Foster, D; Crook, D; Cane, J; Borg, C; Connolly, C; Thulborn, S; Pavord, I; Klenerman, P; Street, TL; Hinks, T

Journal article

Identifying bacterial airways infection in stable severe asthma using Oxford nanopore sequencing technologies

Abstract:: Previous metagenomic studies in asthma have been limited by inadequate sequencing depth for species-level bacterial identification and by heterogeneity in clinical phenotyping. We hypothesize that chronic bacterial airways infection is a key “treatable trait” whose prevalence, clinical phenotype and reliable biomarkers need definition. In this study, we have applied a method for Oxford Nanopore sequencing for the unbiased metagenomic characterization of severe asthma. We optimized methods to compare performance of Illumina MiSeq, Nanopore sequencing, and RT-qPCR on total sputum DNA extracts against culture/MALDI-TOF for analysis of induced sputum samples from highly phenotyped severe asthma during clinical stability. In participants with severe asthma (n = 23) H. influenzae was commonly cultured (n = 8) and identified as the dominant bacterial species by metagenomic sequencing using an optimized method for Illumina MiSeq and Oxford Nanopore. Alongside superior operational characteristics, Oxford Nanopore achieved near complete genome coverage of H. influenzae and demonstrated a high level of agreement with Illumina MiSeq data. Clinically significant infection was confirmed with validated H. influenzae plasmid-based quantitative PCR assay. H. influenzae positive patients were found to have sputum neutrophilia and lower FeNO. In conclusion, using an optimized method of direct sequencing of induced sputum samples, H. influenzae was identified as a clinically relevant pathogen in severe asthma and was identified reliably using metagenomic sequencing. Application of these protocols in ongoing analysis of large patient cohorts will allow full characterization of this clinical phenotype.

Publication status:: Published

Peer review status:: Peer reviewed

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APA Style

Jabeen, M. F., Sanderson, N., Foster, D., Crook, D., Cane, J., Borg, C., Connolly, C., Thulborn, S., Pavord, I., Klenerman, P., Street, T. L., & Hinks, T. (2022). Identifying bacterial airways infection in stable severe asthma using Oxford nanopore sequencing technologies. Microbiology Spectrum, 10(2).

MLA Style

Jabeen, M. F., et al. “Identifying Bacterial Airways Infection in Stable Severe Asthma Using Oxford Nanopore Sequencing Technologies.” Microbiology Spectrum, vol. 10, no. 2, American Society for Microbiology, 2022.

Chicago Style

Jabeen, MF, N Sanderson, D Foster, D Crook, J Cane, C Borg, C Connolly, et al. 2022. “Identifying Bacterial Airways Infection in Stable Severe Asthma Using Oxford Nanopore Sequencing Technologies.” Microbiology Spectrum 10 (2).
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