Rapid Metagenomic Next-Generation Sequencing during an Investigation of Hospital-Acquired Human Parainfluenza Virus 3 Infections

Abstract

Metagenomic next-generation sequencing (mNGS) is increasingly used for the unbiased detection of viruses, bacteria, fungi, and eukaryotic parasites in clinical samples. Whole-genome sequencing (WGS) of clinical bacterial isolates has been shown to inform hospital infection prevention practices, but this technology has not been utilized during potential respiratory virus outbreaks. Here, we report on the use of mNGS to inform the real-time infection prevention response to a cluster of hospital-acquired human parainfluenza 3 virus (HPIV3) infections at a children's hospital. Samples from 3 patients with hospital-acquired HPIV3 identified over a 12-day period on a general medical unit and 10 temporally associated samples from patients with community-acquired HPIV3 were analyzed. Our sample-to-sequencer time was <24 h, while our sample-to-answer turnaround time was <60 h with a hands-on time of approximately 6 h. Eight (2 cases and 6 controls) of 13 samples had sufficient sequencing coverage to yield the whole genome for HPIV3, while 10 (2 cases and 8 controls) of 13 samples gave partial genomes and all 13 samples had >1 read for HPIV3. Phylogenetic clustering revealed the presence of identical HPIV3 genomic sequence in the two of the cases with hospital-acquired infection, consistent with the concern for recent transmission within the medical unit. Adequate sequence coverage was not recovered for the third case. This work demonstrates the promise of mNGS for providing rapid information for infection prevention in addition to microbial detection.

The role of next generation sequencing in infection prevention in human parainfluenza virus 3 infections in immunocompromised patients

“…In our experience, and as recently reported, NGS offers a significantly higher discriminatory value as an epidemiologic tool, and can be used to gather real-time information and identification of transmission linkages to assist in infection prevention in these highly immunocompromised patients (9,10). A challenge going forward will be developing bioinformatics tools which will allow this sequencing information to be available to clinical providers in a rapid and actionable timeframe.…”

A decade of RNA virus metagenomics is (not) enough

“…The benefit of the protocol is the minimal hands-on time, low cost given the dilutability of the transposase, ease of dual-indexing, and direct compatibility with Illumina sequencers. The protocol can be performed in as little as 4-6 h and is amenable to automation (Greninger et al, 2017b(Greninger et al, , 2017c. Variants include the use of additional PCR cycles or amplification prior to tagmentation.…”

The phylogenetic approach for viral infectious disease evolution and epidemiology: An updating review

“…A first report on the use of metagenomics NGS for the investigation of a nosocomial outbreak by parainfluenza virus 3 was published by Greninger et al in 2016 . By Bayesian phylogenetic analysis, these authors demonstrated that two strains causing HAI have the same sequence confirming the hypothesis of a possible transmission within the medical ward where the two patients were admitted.…”

“…By Bayesian phylogenetic analysis, these authors demonstrated that two strains causing HAI have the same sequence confirming the hypothesis of a possible transmission within the medical ward where the two patients were admitted. Authors concluded that NGS and WGS represent important tools for pathogen transmission investigation and a significant advance in clinical care providing pathogen detection with high resolution and reliability …”