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



Hawkey, Jane, Paranagama, Kalani, Baker, Kate S ORCID: 0000-0001-5850-1949, Bengtsson, Rebecca J, Weill, Francois-Xavier, Thomson, Nicholas R, Baker, Stephen, Cerdeira, Louise, Iqbal, Zamin, Hunt, Martin
et al (show 5 more authors) (2021) Global population structure and genotyping framework for genomic surveillance of the major dysentery pathogen, <i>Shigella sonnei</i>. NATURE COMMUNICATIONS, 12 (1). 2684-.

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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.

Item Type: Article
Uncontrolled Keywords: Humans, Shigella sonnei, Dysentery, Bacillary, Azithromycin, Ciprofloxacin, Anti-Bacterial Agents, Microbial Sensitivity Tests, Genetics, Population, Genomics, Phylogeny, Drug Resistance, Multiple, Bacterial, Genotype, Polymorphism, Single Nucleotide, Genome, Bacterial, Geography, United States, Australia, England, Global Health, Whole Genome Sequencing
Divisions: Faculty of Health and Life Sciences
Faculty of Health and Life Sciences > Institute of Infection, Veterinary and Ecological Sciences
Depositing User: Symplectic Admin
Date Deposited: 28 Jan 2022 11:49
Last Modified: 19 Oct 2023 09:10
DOI: 10.1038/s41467-021-22700-4
Related URLs:
URI: https://livrepository.liverpool.ac.uk/id/eprint/3147770