PubMed · 1631838
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T Midtvedt. 1992-05-30. [Cholera].. https://pubmed.ncbi.nlm.nih.gov/1631838/
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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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Louisiana was struck by Hurricane Katrina on August 29, 2005, and by Hurricane Rita on September 24, 2005. The two hurricanes caused unprecedented damage from wind and storm surge to the Louisiana Gulf Coast region, and levee breaks resulted in flooding of large residential areas in and around New Orleans. With the flooding, an immediate public health concern was the potential for outbreaks of infectious diseases, including cholera. Nearly all Vibrio infections in the United States are caused by noncholeragenic Vibrio species (e.g., V. parahaemolyticus, V. vulnificus, and non-O1, non-O139 V. cholerae). Cases of cholera rarely occur in the United States, and cholera epidemics, such as those reported in certain developing countries, are unlikely, even with the extreme flooding caused by the two hurricanes. This report describes the investigation by the Louisiana Office of Public Health and CDC into two cases of toxigenic V. cholerae O1 infection in a Louisiana couple; the cases were attributed to consumption of undercooked or contaminated seafood. Although noncholeragenic Vibrio illnesses were reported in 22 residents of Louisiana and Mississippi after Hurricane Katrina, no epidemic of cholera was identified, and no evidence exists of increased risk to Gulf Coast residents.