PubMed · 5566625
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G Thomas. 1971-08-14. Mass immunization technique.. https://doi.org/10.1136/bmj.3.5771.431
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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.
When John Snow undertook the studies of the cholera epidemic of 1854 in London, he was testing his theory of communicable disease, which had been enunciated in an oration delivered at the 80th anniversary of the Medical Society of London. Snow had been elected orator of the year for 1853 and, according to his biographer, had spent the better part of a year in preparation. The oration was titled, "On Continuous Molecular Changes, More Particularly in Their Relation to Epidemic Diseases." Although the text of this oration is readily available in the 1936 Commonwealth Fund facsimile reprint of Snow's more famous cholera studies, few modern epidemiologists are familiar with the work. In it, Snow lays out a theory which includes recognition that for each communicable disease there is a distinct and specific cause, that the causal agent is a living organism which is stable over many generations of propagation, that infection is necessary for communication to occur, and that the quantity of infectious material transmitted is increased by multiplication after infection to produce disease manifestations. Although Snow's theory is similar to Jacob Henle's formulations of a decade earlier, it is more precise, more comprehensive, and more explicit. On the basis of this work alone, Snow deserves broader recognition than he has received.