Whole-Genome Enrichment Provides Deep Insights into Vibrio cholerae Metagenome from an African River

Abstract

The detection and typing of Vibrio cholerae in natural aquatic environments encounter major methodological challenges related to the fact that the bacterium is often present in environmental matrices at very low abundance in nonculturable state. This study applied, for the first time to our knowledge, a whole-genome enrichment (WGE) and next-generation sequencing (NGS) approach for direct genotyping and metagenomic analysis of low abundant V. cholerae DNA (<50 genome unit/L) from natural water collected in the Morogoro river (Tanzania). The protocol is based on the use of biotinylated RNA baits for target enrichment of V. cholerae metagenomic DNA via hybridization. An enriched V. cholerae metagenome library was generated and sequenced on an Illumina MiSeq platform. Up to 1.8 × 107 bp (4.5× mean read depth) were found to map against V. cholerae reference genome sequences representing an increase of about 2500 times in target DNA coverage compared to theoretical calculations of performance for shotgun metagenomics. Analysis of metagenomic data revealed the presence of several V. cholerae virulence and virulence associated genes in river water including major virulence regions (e.g. CTX prophage and Vibrio pathogenicity island-1) and genetic markers of epidemic strains (e.g. O1-antigen biosynthesis gene cluster) that were not detectable by standard culture and molecular techniques. Overall, besides providing a powerful tool for direct genotyping of V. cholerae in complex environmental matrices, this study provides a ‘proof of concept’ on the methodological gap that might currently preclude a more comprehensive understanding of toxigenic V. cholerae emergence from natural aquatic environments.

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Acknowledgements

We are particularly indebted to Dr. Alison Devault (MYcroarray, USA) for helpful assistance and advice in WGE analysis. This work was supported by the European FP7 project ‘Protecting the health of Europeans by improving methods for the detection of pathogens in drinking water and water used in food preparation’—AQUAVALENS (grant number 311846). The HORIZON2020 project ‘Preventing and mitigating farmed bivalve disease—VIVALDI (grant number 678589)’ is also acknowledged.

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Correspondence to L. Vezzulli.

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L. Vezzulli and C. Grande contributed equally to this work.

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Vezzulli, L., Grande, C., Tassistro, G. et al. Whole-Genome Enrichment Provides Deep Insights into Vibrio cholerae Metagenome from an African River. Microb Ecol 73, 734–738 (2017). https://doi.org/10.1007/s00248-016-0902-x

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Keywords

  • Vibrio cholerae
  • Africa
  • Next-generation sequencing
  • Whole-genome enrichment