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Prospective, Real-time Metagenomic Sequencing During Norovirus Outbreak Reveals Discrete Transmission Clusters.

ABSTRACT: BACKGROUND:Norovirus outbreaks in hospital settings are a common challenge for infection prevention teams. Given the high burden of norovirus in most communities, it can be difficult to distinguish between ongoing in-hospital transmission of the virus and new introductions from the community, and it is challenging to understand the long-term impacts of outbreak-associated viruses within medical systems using traditional epidemiological approaches alone. METHODS:Real-time metagenomic sequencing during an ongoing norovirus outbreak associated with a retrospective cohort study. RESULTS:We describe a hospital-associated norovirus outbreak that affected 13 patients over a 27-day period in a large, tertiary, pediatric hospital. The outbreak was chronologically associated with a spike in self-reported gastrointestinal symptoms among staff. Real-time metagenomic next-generation sequencing (mNGS) of norovirus genomes demonstrated that 10 chronologically overlapping, hospital-acquired norovirus cases were partitioned into 3 discrete transmission clusters. Sequencing data also revealed close genetic relationships between some hospital-acquired and some community-acquired cases. Finally, this data was used to demonstrate chronic viral shedding by an immunocompromised, hospital-acquired case patient. An analysis of serial samples from this patient provided novel insights into the evolution of norovirus within an immunocompromised host. CONCLUSIONS:This study documents one of the first applications of real-time mNGS during a hospital-associated viral outbreak. Given its demonstrated ability to detect transmission patterns within outbreaks and elucidate the long-term impacts of outbreak-associated viral strains on patients and medical systems, mNGS constitutes a powerful resource to help infection control teams understand, prevent, and respond to viral outbreaks.

SUBMITTER: Casto AM

PROVIDER: S-EPMC6735836 | biostudies-other | 2019 Aug

REPOSITORIES: biostudies-other

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Prospective, Real-time Metagenomic Sequencing During Norovirus Outbreak Reveals Discrete Transmission Clusters.

Casto Amanda M AM Adler Amanda L AL Makhsous Negar N Crawford Kristen K Qin Xuan X Kuypers Jane M JM Huang Meei-Li ML Zerr Danielle M DM Greninger Alexander L AL

Clinical infectious diseases : an official publication of the Infectious Diseases Society of America 20190801 6

<h4>Background</h4>Norovirus outbreaks in hospital settings are a common challenge for infection prevention teams. Given the high burden of norovirus in most communities, it can be difficult to distinguish between ongoing in-hospital transmission of the virus and new introductions from the community, and it is challenging to understand the long-term impacts of outbreak-associated viruses within medical systems using traditional epidemiological approaches alone.<h4>Methods</h4>Real-time metagenom ...[more]

PMID: 30576430

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Dataset Information

Prospective, Real-time Metagenomic Sequencing During Norovirus Outbreak Reveals Discrete Transmission Clusters.

Publications

Prospective, Real-time Metagenomic Sequencing During Norovirus Outbreak Reveals Discrete Transmission Clusters.

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