PubMed · 5325218
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F I Apted. 1966. Cholera.. https://pubmed.ncbi.nlm.nih.gov/5325218/
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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.
In summary, MDR strains of S. typhi are both epidemic and endemic in many countries in Asia and MDR S. paratyphi A has recently emerged in Pakistan. Multiple clones may be present in a given area at any time. Fluoroquinolones and third generation cephalosporins have been used widely over the past decade to treat MDR strains. The clinical superiority of fluoroquinolones is now threatened by the rapid emergence of chromosomally mediated resistance and cephalosporin resistance is also being reported. Whether these problems can be overcome by the use of newer fluoroquinolones or cephalosporins remains to be seen. Meanwhile, furazolidone and azithromycin deserve further trials, and clinical and molecular surveillance of resistance patterns remains essential.
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