PubMed · 14911438
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B MAEGRAITH. 1952. Cholera.. https://doi.org/10.1136/pgmj.28.317.158
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SUMMARY: Next Generation Sequencing is widely deployed in cholera-endemic regions, yet an end-to-end reproducible pipeline that unifies read QC, filtering, reference mapping, variant calling/annotation, recombination screening, and extraction of parsimony informative sites/variant codons, phylogenetic inference for downstream phylodynamic and epidemiological analyses have been lacking, slowing outbreak investigation and public health response. CholeraSeq is a high-throughput genomics pipeline for cholera genomic surveillance. It ingests consensus genomes, short read sequence data, draft assemblies, and scales seamlessly from local to cloud environments. To accelerate epidemiological context placement of new outbreak strains, we provide a curated ready-to-use core genome alignment compiled from public data, enabling flexible, fast, integration of new samples for outbreak investigations. AVAILABILITY AND IMPLEMENTATION: CholeraSeq is freely available on the GitHub platform https://github.com/CERI-KRISP/CholeraSeq. CholeraSeq is implemented in Nextflow with a modular design building upon the nf-core community standards.
Between 28 November 2003 and 23 February 2004, 4343 cases and 154 deaths from cholera (case-fatality rate 3.5%) were reported in Lusaka, Zambia. A case-control study was conducted in February 2004 to assess potential transmission routes and prevention strategies. Consumption of raw vegetables was significantly associated with cholera [adjusted odds ratio (aOR) 4.7, 95% confidence interval (CI) 1.7-13, P=0.003). Consumption of a local sardine-like fish was protective (aOR 0.3, 95% CI 0.1-0.7, P=0.008). Hand soap was present in 90% of control homes and 58% of case homes. Observed hand soap was a strongly protective factor (aOR 0.1, 95% CI 0.04-0.4, P=0.001). No water source or treatment practice was significantly associated with cholera. This study documents the importance of foodborne transmission of cholera, illustrates the protective role of hand washing in an epidemic setting, and identifies a novel possible protective factor, a local fish, which warrants further research.
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