PubMed · 14290446
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F A KINGERY. 1965-06-14. CHOLERA IMMUNIZATION.. https://pubmed.ncbi.nlm.nih.gov/14290446/
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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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We present here the beginnings of public health politics in Meiji Japan (1868-1912). Due to a two century isolation of Japan, public health concepts developed in the West from the end of the 18th century were foreign in premodern Japan. Due to its isolation, Japan was also relatively preserved from some acute infectious diseases such as cholera. In this paper, we investigate the role of cholera epidemics in the emergence of public health concepts in the peculiar context of Meiji Japan. We show that chronic diseases such as tuberculosis and leprosy were neglected for a long time and that the Meiji government set priority on acute infectious diseases that were considered as long as they disturbed public order. Nevertheless, some physicians and government officials considered issues of welfare and poverty. We also review some emerging concepts of social medicine. We try to show, that in Japan as well as in Western nations, public health politics were not exempt of contradictions and paradoxes and a permanent tension existed between coercitive policies and conceptions of welfare and rights to health.