PubMed · 15414368
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1950-05-06. EPIDEMIOLOGICAL notes.. https://pubmed.ncbi.nlm.nih.gov/15414368/
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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.
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The precautionary principle calls on decisionmakers to take preventive action in light of evidence indicating that there is a potential for harm to public health and the environment, even though the nature and magnitude of harm are not fully understood scientifically. Critics of the precautionary principle frequently argue that unbridled application of the principle leads to unintended damage to health and ecosystems (risk tradeoffs) and that precautious decision making leaves us vulnerable to "false-positive" risks that divert resources away from "real risks." The 1991 cholera epidemic in Peru is often cited as an example of these pitfalls of the precautionary principle. It has been mistakenly argued that application of the precautionary principle caused decisionmakers to stop chlorinating the water supply due to the risks of disinfection byproducts (DBPs), resulting in the epidemic. Through analyses of investigations conducted in the cities of Iquitos and Trujillo, Peru, literature review, and interviews with leading Peruvian infectious disease researchers, we determined that the epidemic was caused by a much more complex set of circumstances, including poor sanitation conditions, poor separation of water and waste streams, and inadequate water treatment and distribution systems. The evidence indicates that no decision was made to stop chlorinating on the basis of DBP concerns and that concerns raised about DBPs masked more important factors limiting expansion of chlorination. In fact, outside of Peru's capital Lima, chlorination of drinking water supplies at the time of the epidemic was limited at best. We conclude that the Peruvian cholera epidemic was not caused by a failure of precaution but rather by an inadequate public health infrastructure unable to control a known risk: that of microbial contamination of water supplies.