Waste Water Based Epidemiological Surveillance (WBE)

This is the workflow we employ in the analysis of sequences with the goal of tracking pathogens of public health interest so as to inform on rapid response. Because a quick turn around is needed, the computational steps taken and fast to ensure feedback is provided in time.

Overview

This pipeline was developed based on Nextflow + Singularity to analysisd shotgun metagenomic NGS data for monitoring pathogens in wastewater across selected sites in Mombasa and Kisumu, Kenya. The work was done at ILRI through its Genomics Platform.

Analysis Workflow

  • Modular steps: Prefetch → QC → Assembly → Taxonomy → AMR
  • Containerised with BioContainers

  • Automated MultiQC reports & Slack alerts

  • Sequence data from Illumina NextSeq is processed through a custom pipeline similar to nf-core/MAG: QC, human filtering, and taxonomic classification with Kraken2 and Centrifuge.
  • Taxonomic reports are merged and filtered via pavian in R to generate relative and absolute abundance profiles.

Pathogens of Interest

Lists of target organisms are curated and updated. See:

  • Pathogenic Bacteria
  • Pathogenic Viruses
  • Pathogenic Parasites

Antimicrobial resistance gene detection using CARD/RGI is also under development.

Resources

This project is under active development. For details, see the Bioinformatics Workflow pdf.

References