Global population structure and genotyping framework for genomic surveillance of the major dysentery pathogen, Shigella sonnei

Jane Hawkey*, Kalani Paranagama, Kate S. Baker, Rebecca J. Bengtsson, François Xavier Weill, Nicholas R. Thomson, Stephen Baker, Louise Cerdeira, Zamin Iqbal, Martin Hunt, Danielle J. Ingle, Timothy J. Dallman, Claire Jenkins, Deborah A. Williamson, Kathryn E. Holt

*Corresponding author for this work

    Research output: Contribution to journalArticlepeer-review

    30 Citations (Scopus)

    Abstract

    Shigella sonnei is the most common agent of shigellosis in high-income countries, and causes a significant disease burden in low- and middle-income countries. Antimicrobial resistance is increasingly common in all settings. Whole genome sequencing (WGS) is increasingly utilised for S. sonnei outbreak investigation and surveillance, but comparison of data between studies and labs is challenging. Here, we present a genomic framework and genotyping scheme for S. sonnei to efficiently identify genotype and resistance determinants from WGS data. The scheme is implemented in the software package Mykrobe and tested on thousands of genomes. Applying this approach to analyse >4,000 S. sonnei isolates sequenced in public health labs in three countries identified several common genotypes associated with increased rates of ciprofloxacin resistance and azithromycin resistance, confirming intercontinental spread of highly-resistant S. sonnei clones and demonstrating the genomic framework can facilitate monitoring the spread of resistant clones, including those that have recently emerged, at local and global scales.

    Original languageEnglish
    Article number2684
    JournalNature Communications
    Volume12
    Issue number1
    DOIs
    Publication statusPublished - 1 Dec 2021

    Fingerprint

    Dive into the research topics of 'Global population structure and genotyping framework for genomic surveillance of the major dysentery pathogen, Shigella sonnei'. Together they form a unique fingerprint.

    Cite this