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•Examined norovirus concentrations in shellfish associated with norovirus illness.•RT-ddPCR determined between 44 and 4,267 norovirus GC/g digestive tissue.•<200 norovirus GC/g digestive tissue in 40% (8/20) shellfish.•RNase treatment led to reductions in titre of approximately 50%.•Provides valuable evidence for risk assessment of contaminated shellfish.

ABSTRACTThe 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 novometagenomic 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.

ABSTRACTShiga toxin-producing Escherichia coliO84 isolates (n= 22) were examined using culture- and molecularly based methods in order to compare their phenotypic and genotypic characteristics. These analyses directly linked Shiga toxin-producing Escherichia coliO84 isolates from cattle and sheep with human isolates indicating that New Zealand livestock may be a reservoir of infection.