Direct Detection of Shigella in Stool Specimens by Use of a Metagenomic Approach.

The underestimation of 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 via a metagenomics approach. Three groups of samples were selected from diarrheal cases from the Global Enteric Multicenter Study: nine culture-positive and qPCR-positive (culture qPCR) samples, nine culture-negative but qPCR-positive (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 × 10 ± 5.6 × 10 high-quality reads were generated for each sample. We used Kraken software to compare the read counts specific to "" among the three groups. The proportions of -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, = 0.627) and distinct from the culture qPCR group (0.17 ± 0.15%, < 0.05). The read counts of sequences previously targeted by enteroinvasive (EIEC) qPCR assays, namely, , , , , , and , were also similar between the culture qPCR and culture qPCR groups and distinct from the culture qPCR groups ( < 0.001). Kraken performed well versus other methods: its precision and recall of were excellent at the genus level but variable at the species level. In summary, metagenomic sequencing indicates that /EIEC qPCR-positive samples are similar to those of culture-positive samples in sequence composition, thus supporting qPCR as an accurate method for detecting .