Nanopore metagenomic sequencing to investigate nosocomial transmission of human metapneumovirus from a unique genetic group among haematology patients in the United Kingdom

偏肺病毒 基因组 传输(电信) 生物 变性肺病毒 纳米孔测序 基因组 背景(考古学) 呼吸道感染 病毒学 医学 计算生物学 内科学 遗传学 基因 计算机科学 电信 呼吸系统 古生物学
作者
Yifei Xu,Kuiama Lewandowski,Katie Jeffery,Louise Downs,Dona Foster,Nicholas D. Sanderson,James Kavanagh,Ali Vaughan,Claudia Salvagno,Richard Vipond,Miles W. Carroll,Robert Danby,Timothy E. A. Peto,Derrick W. Crook,A. Sarah Walker,Philippa C. Matthews,Steven T. Pullan
出处
期刊:Journal of Infection [Elsevier BV]
卷期号:80 (5): 571-577 被引量:17
标识
DOI:10.1016/j.jinf.2020.02.003
摘要

Abstract

Background

Human metapneumovirus (HMPV) infection causes a spectrum of respiratory tract disease, and may be a significant pathogen in the context of immunocompromise. Here, we report direct-from-sample metagenomic sequencing of HMPV using Oxford Nanopore Technology.

Methods

We applied this sequencing approach to 25 respiratory samples that had been submitted to a clinical diagnostic laboratory in a UK teaching hospital. These samples represented 13 patients under the care of a haematology unit over a 20-day period in Spring 2019 (two sampled twice), and ten other patients elsewhere in the hospital between 2017–2019.

Results

We generated HMPV reads from 20/25 samples (sensitivity 80% compared to routine diagnostic testing) and retrieved complete HMPV genomes from 15/20 of these. Consensus sequences from Nanopore data were identical to those generated by Illumina, and represented HMPV genomes from two distinct sublineages, A2b and B2. Sequences from ten haematology patients formed a unique genetic group in the A2b sublineage, not previously reported in the UK. Among these, eight HMPV genomes formed a cluster (differing by ≤3 SNPs), likely to reflect nosocomial transmission, while two others were more distantly related and may represent independent introductions to the haematology unit.

Conclusion

Nanopore metagenomic sequencing can be used to diagnose HMPV infection, although more work is required to optimise sensitivity. Improvements in the use of metagenomic sequencing, particularly for respiratory viruses, could contribute to antimicrobial stewardship. Generation of full genome sequences can be used to support or rule out nosocomial transmission, and contribute to improving infection prevention and control practices.
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