Liu, Jie, Ph.D.; Almeida, Mathieu; Kabir, Furqan (Washington, D.C.: The American Society for Microbiology, 2017-11-08)
The underestimation of Shigella species as a cause of childhood diarrhea
disease has become increasingly apparent with quantitative PCR (qPCR)-based
diagnostic methods versus culture. We sought to confirm qPCR-based detection of
Shigella via a metagenomics approach. Three groups of samples were selected from
diarrheal cases from the Global Enteric Multicenter Study: nine Shigella culturepositive
and qPCR-positive (culture qPCR ) samples, nine culture-negative but qPCRpositive
(culture qPCR ) samples, and nine culture-negative and qPCR-negative
(culture qPCR ) samples. Fecal DNA was sequenced using paired-end Illumina
HiSeq, whereby 3.26 108 5.6 107 high-quality reads were generated for each
sample. We used Kraken software to compare the read counts specific to “Shigella”
among the three groups. The proportions of Shigella-specific nonhuman sequence
reads between culture qPCR (0.65 0.42%) and culture qPCR (0.55 0.31%)
samples were similar (Mann-Whitney U test, P 0.627) and distinct from the culture
qPCR group (0.17 0.15%, P 0.05). The read counts of sequences previously
targeted by Shigella/enteroinvasive Escherichia coli (EIEC) qPCR assays, namely,
ipaH, virA, virG, ial, ShET2, and ipaH3, were also similar between the culture qPCR
and culture qPCR groups and distinct from the culture qPCR groups (P
0.001). Kraken performed well versus other methods: its precision and recall of Shigella
were excellent at the genus level but variable at the species level. In summary,
metagenomic sequencing indicates that Shigella/EIEC qPCR-positive samples are similar
to those of Shigella culture-positive samples in Shigella sequence composition,
thus supporting qPCR as an accurate method for detecting Shigella.
The export option will allow you to export the current search results of the entered query to a file. Different
formats are available for download. To export the items, click on the button corresponding with the preferred download format.
By default, clicking on the export buttons will result in a download of the allowed maximum amount of items.
To select a subset of the search results, click "Selective Export" button and make a selection of the items you want to export.
The amount of items that can be exported at once is similarly restricted as the full export.
After making a selection, click one of the export format buttons. The amount of items that will be exported is indicated in the bubble next to export format.