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

Author

Listed:
  • Jane Hawkey

    (Monash University)

  • Kalani Paranagama

    (Monash University)

  • Kate S. Baker

    (University of Liverpool)

  • Rebecca J. Bengtsson

    (University of Liverpool)

  • François-Xavier Weill

    (Unité des bactéries pathogènes entériques)

  • Nicholas R. Thomson

    (Wellcome Genome Campus
    London School of Hygiene & Tropical Medicine)

  • Stephen Baker

    (University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus
    University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus)

  • Louise Cerdeira

    (Monash University)

  • Zamin Iqbal

    (European Molecular Biology Laboratory—European Bioinformatics Institute)

  • Martin Hunt

    (European Molecular Biology Laboratory—European Bioinformatics Institute
    University of Oxford)

  • Danielle J. Ingle

    (The University of Melbourne
    Australian National University)

  • Timothy J. Dallman

    (National Infection Service, Public Health England)

  • Claire Jenkins

    (National Infection Service, Public Health England)

  • Deborah A. Williamson

    (The University of Melbourne
    Royal Melbourne Hospital)

  • Kathryn E. Holt

    (Monash University
    London School of Hygiene & Tropical Medicine)

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.

Suggested Citation

  • 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 &, 2021. "Global population structure and genotyping framework for genomic surveillance of the major dysentery pathogen, Shigella sonnei," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
  • Handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-22700-4
    DOI: 10.1038/s41467-021-22700-4
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    Citations

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    Cited by:

    1. Shaofu Qiu & Kangkang Liu & Chaojie Yang & Ying Xiang & Kaiyuan Min & Kunpeng Zhu & Hongbo Liu & Xinying Du & Mingjuan Yang & Ligui Wang & Yong Sun & Haijian Zhou & Muti Mahe & Jiayong Zhao & Shijun L, 2022. "A Shigella sonnei clone with extensive drug resistance associated with waterborne outbreaks in China," Nature Communications, Nature, vol. 13(1), pages 1-13, December.
    2. Sophie Lefèvre & Elisabeth Njamkepo & Sarah Feldman & Corinne Ruckly & Isabelle Carle & Monique Lejay-Collin & Laëtitia Fabre & Iman Yassine & Lise Frézal & Maria Pardos de la Gandara & Arnaud Fontane, 2023. "Rapid emergence of extensively drug-resistant Shigella sonnei in France," Nature Communications, Nature, vol. 14(1), pages 1-10, December.
    3. George E. Stenhouse & Karen H. Keddy & Rebecca J. Bengtsson & Neil Hall & Anthony M. Smith & Juno Thomas & Miren Iturriza-Gómara & Kate S. Baker, 2023. "The genomic epidemiology of shigellosis in South Africa," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    4. Lewis C. E. Mason & David R. Greig & Lauren A. Cowley & Sally R. Partridge & Elena Martinez & Grace A. Blackwell & Charlotte E. Chong & P. Malaka Silva & Rebecca J. Bengtsson & Jenny L. Draper & Andre, 2023. "The evolution and international spread of extensively drug resistant Shigella sonnei," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    5. Iman Yassine & Sophie Lefèvre & Elisabeth E. Hansen & Corinne Ruckly & Isabelle Carle & Monique Lejay-Collin & Laëtitia Fabre & Rayane Rafei & Dominique Clermont & Maria Pardos Gandara & Fouad Dabbous, 2022. "Population structure analysis and laboratory monitoring of Shigella by core-genome multilocus sequence typing," Nature Communications, Nature, vol. 13(1), pages 1-14, December.

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