Metagenomic analysis of viruses in feces from unsolved outbreaks of gastroenteritis in humans

Nicole E. Moore, Jing Wang, Joanne Hewitt, Dawn Croucher, Deborah A. Williamson, Shevaun Paine, Seiha Yen, Gail E. Greening, Richard J. Hall

Research output: Contribution to journalArticlepeer-review

31 Scopus citations

Abstract

The etiology of an outbreak of gastroenteritis in humans cannot always be determined, and ∼25% of outbreaks remain unsolved in New Zealand. It is hypothesized that novel viruses may account for a proportion of unsolved cases, and new unbiased high-throughput sequencing methods hold promise for their detection. Analysis of the fecal metagenome can reveal the presence of viruses, bacteria, and parasites which may have evaded routine diagnostic testing. Thirty-one fecal samples from 26 gastroenteritis outbreaks of unknown etiology occurring in New Zealand between 2011 and 2012 were selected for de novo metagenomic analysis. A total data set of 193 million sequence reads of 150 bp in length was produced on an Illumina MiSeq. The metagenomic data set was searched for virus and parasite sequences, with no evidence of novel pathogens found. Eight viruses and one parasite were detected, each already known to be associated with gastroenteritis, including adenovirus, rotavirus, sapovirus, and Dientamoeba fragilis. In addition, we also describe the first detection of human parechovirus 3 (HPeV3) in Australasia. Metagenomics may thus provide a useful audit tool when applied retrospectively to determine where routine diagnostic processes may have failed to detect a pathogen.

Original languageEnglish (US)
Pages (from-to)15-21
Number of pages7
JournalJournal of clinical microbiology
Volume53
Issue number1
DOIs
StatePublished - Jan 1 2015

All Science Journal Classification (ASJC) codes

  • Microbiology (medical)

Fingerprint Dive into the research topics of 'Metagenomic analysis of viruses in feces from unsolved outbreaks of gastroenteritis in humans'. Together they form a unique fingerprint.

Cite this