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Abstract

Background

Influenza virus presents a considerable challenge to public health by causing seasonal epidemics and occasional pandemics. Nanopore metagenomic sequencing has the potential to be deployed for near-patient testing, providing rapid infection diagnosis, rationalising antimicrobial therapy, and supporting infection-control interventions.

Aim

To evaluate the applicability of this sequencing approach as a routine laboratory test for influenza in clinical settings.

Methods

We conducted Oxford Nanopore Technologies (Oxford, United Kingdom (UK)) metagenomic sequencing for 180 respiratory samples from a UK hospital during the 2018/19 influenza season, and compared results to routine molecular diagnostic standards (Xpert Xpress Flu/RSV assay; BioFire FilmArray Respiratory Panel 2 assay). We investigated drug resistance, genetic diversity, and nosocomial transmission using influenza sequence data.

Results

Compared to standard testing, Nanopore metagenomic sequencing was 83% (75/90) sensitive and 93% (84/90) specific for detecting influenza A viruses. Of 59 samples with haemagglutinin subtype determined, 40 were H1 and 19 H3. We identified an influenza A(H3N2) genome encoding the oseltamivir resistance S331R mutation in neuraminidase, potentially associated with an emerging distinct intra-subtype reassortant. Whole genome phylogeny refuted suspicions of a transmission cluster in a ward, but identified two other clusters that likely reflected nosocomial transmission, associated with a predominant community-circulating strain. We also detected other potentially pathogenic viruses and bacteria from the metagenome.

Conclusion

Nanopore metagenomic sequencing can detect the emergence of novel variants and drug resistance, providing timely insights into antimicrobial stewardship and vaccine design. Full genome generation can help investigate and manage nosocomial outbreaks.

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This work is licensed under a Creative Commons Attribution 4.0 International License.
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2021-07-08
2024-12-21
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Nanopore metagenomic sequencing of influenza virus directly from respiratory samples: diagnosis, drug resistance and nosocomial transmission, United Kingdom, 2018/19 influenza season
<p class="citation"> <span>Citation style for this article:</span> <span class="meta-value authors"> <a href="/search?value1=Yifei+Xu&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Xu Yifei</a>, <a href="/search?value1=Kuiama+Lewandowski&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Lewandowski Kuiama</a>, <a href="/search?value1=Louise+O+Downs&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Downs Louise O</a>, <a href="/search?value1=James+Kavanagh&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Kavanagh James</a>, <a href="/search?value1=Thomas+Hender&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Hender Thomas</a>, <a href="/search?value1=Sheila+Lumley&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Lumley Sheila</a>, <a href="/search?value1=Katie+Jeffery&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Jeffery Katie</a>, <a href="/search?value1=Dona+Foster&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Foster Dona</a>, <a href="/search?value1=Nicholas+D+Sanderson&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Sanderson Nicholas D</a>, <a href="/search?value1=Ali+Vaughan&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Vaughan Ali</a>, <a href="/search?value1=Marcus+Morgan&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Morgan Marcus</a>, <a href="/search?value1=Richard+Vipond&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Vipond Richard</a>, <a href="/search?value1=Miles+Carroll&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Carroll Miles</a>, <a href="/search?value1=Timothy+Peto&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Peto Timothy</a>, <a href="/search?value1=Derrick+Crook&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Crook Derrick</a>, <a href="/search?value1=A+Sarah+Walker&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Walker A Sarah</a>, <a href="/search?value1=Philippa+C+Matthews&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Matthews Philippa C</a>, <a href="/search?value1=Steven+T+Pullan&option1=author&noRedirect=true" class="nonDisambigAuthorLink">Pullan Steven T</a></span>. Nanopore metagenomic sequencing of influenza virus directly from respiratory samples: diagnosis, drug resistance and nosocomial transmission, United Kingdom, 2018/19 influenza season. <a href="/content/ecdc">Euro Surveill.</a> 2021;26(27):pii=2000004. <a href="https://doi.org/10.2807/1560-7917.ES.2021.26.27.2000004" title="doi link" target="_blank">https://doi.org/10.2807/1560-7917.ES.2021.26.27.2000004</a> <span class="ES_Article_citation"> <span class="generated">Received</span>: 22 Dec 2019;&nbsp;&nbsp; <span class="generated">Accepted</span>: 08 May 2020 </span> </p>
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