Direct detection of shigella in stool specimens by use of a metagenomic approach

Authors

Jie Liu, University of Virginia, Charlottesville, Virginia, USA.
Mathieu Almeida, University of Maryland, College Park, Maryland, USA.
Furqan Kabir, Aga Khan UniversityFollow
Sadia Shakoor, Aga Khan UniversityFollow
Shahida Qureshi, Aga Khan UniversityFollow
Anita K. M. Zaidi, Aga Khan UniversityFollow
Shan Li, University of Maryland, Baltimore, Maryland, USA.
Boubou Tamboura, Centre pour le Développement des Vaccins, Bamako, Mali
Samba O. Sow, Centre pour le Développement des Vaccins, Bamako, Mali
Inacio Mandomando, Centro de Investigação em Saúde da Manhiça, Maputo, Mozambique

Document Type

Article

Department

Paediatrics and Child Health; Pathology and Microbiology; Pathology and Laboratory Medicine

Abstract

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 × 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.

Comments

Pagination are not provided by the author/publisher

Publication (Name of Journal)

Journal of Clinical Microbiology

Recommended Citation

Liu, J., Almeida, M., Kabir, F., Shakoor, S., Qureshi, S., Zaidi, A., Li, S., Tamboura, B., Sow, S. O., Mandomando, I. (2018). Direct detection of shigella in stool specimens by use of a metagenomic approach. Journal of Clinical Microbiology, 56(2), e01374-17.
Available at: https://ecommons.aku.edu/pakistan_fhs_mc_women_childhealth_paediatr/949

Creative Commons License

This work is licensed under a Creative Commons Attribution 4.0 International License.