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

• Published in: Nature communications 2021-05, Vol.12 (1), p.2684-2684, Article 2684
• Main Authors: Hawkey, Jane, Paranagama, Kalani, Baker, Kate S., Bengtsson, Rebecca J., Weill, François-Xavier, Thomson, Nicholas R., Baker, Stephen, Cerdeira, Louise, Iqbal, Zamin, Hunt, Martin, Ingle, Danielle J., Dallman, Timothy J., Jenkins, Claire, Williamson, Deborah A., Holt, Kathryn E.
• Format: Article
• Language: English
• Subjects: 45/23; 631/114/1386; 631/181/757; 631/326/325/2482; 692/308/174; Anti-Bacterial Agents - pharmacology; Antimicrobial resistance; Australia; Azithromycin; Azithromycin - pharmacology; Ciprofloxacin; Ciprofloxacin - pharmacology; Cloning; Computer programs; Drug Resistance, Multiple, Bacterial - genetics; Dysentery; Dysentery, Bacillary - diagnosis; Dysentery, Bacillary - microbiology; England; Gene sequencing; Genetics, Population; Genome, Bacterial - genetics; Genomes; Genomics; Genomics - methods; Genotype; Genotypes; Genotyping; Geography; Global Health; Humanities and Social Sciences; Humans; Income; Microbial Sensitivity Tests - methods; multidisciplinary; Open source software; Outbreaks; Phylogeny; Polymorphism, Single Nucleotide; Population structure; Public health; Science; Science (multidisciplinary); Shigella sonnei; Shigella sonnei - classification; Shigella sonnei - genetics; Shigella sonnei - physiology; Shigellosis; Software; Source code; United States; Waterborne diseases; Whole Genome Sequencing
• ISSN: 2041-1723; 2041-1723
• DOI: 10.1038/s41467-021-22700-4

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. Whole genome sequencing is increasingly being adopted for Shigella sonnei outbreak investigation and surveillance, but there is no global classification standard. Here, the authors develop and validate a genomic framework implemented using open-source software, and demonstrate its application using surveillance data.