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

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 sele...

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Detalles Bibliográficos
Autores principales: Liu, Jie, Almeida, Mathieu, Kabir, Furqan, Shakoor, Sadia, Qureshi, Shahida, Zaidi, Anita, Li, Shan, Tamboura, Boubou, Sow, Samba O., Mandomando, Inacio, Alonso, Pedro L., Ramamurthy, Thandavarayan, Sur, Dipika, Kotloff, Karen, Nataro, James, Levine, Myron M., Stine, O. Colin, Houpt, Eric
Formato: Online Artículo Texto
Lenguaje:English
Publicado: American Society for Microbiology 2018
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5786726/
https://www.ncbi.nlm.nih.gov/pubmed/29118177
http://dx.doi.org/10.1128/JCM.01374-17
Descripción
Sumario: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 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(8) ± 5.6 × 10(7) 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.