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This chapter presents a method to process Clostridioides difficile whole genome next-generation sequencing (WGS) data for draft genome assembly, gene annotation, multilocus strain type identification (MLST), antimicrobial resistance (AMR), and generation of a relationship phylogeny. We use publicly available data to do a mock outbreak analysis to demonstrate how WGS can provide in-depth insight into these isolates.

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From FASTQ to Function to Phylogeny: In Silico Methods for Antimicrobial Resistance and Outbreak Investigation

  • 实验方案

  • 发表日期：

    2026年

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  • Mark D. Preston,
  • Tsz Ting Chow,
  • Richard A. Stabler

摘要

This chapter presents a method to process Clostridioides difficile whole genome next-generation sequencing (WGS) data for draft genome assembly, gene annotation, multilocus strain type identification (MLST), antimicrobial resistance (AMR), and generation of a relationship phylogeny. We use publicly available data to do a mock outbreak analysis to demonstrate how WGS can provide in-depth insight into these isolates.