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The genomic epidemiology of shigellosis in South Africa

Author

Listed:
  • George E. Stenhouse

    (University of Liverpool)

  • Karen H. Keddy

    (2Independent Consultant)

  • Rebecca J. Bengtsson

    (University of Liverpool)

  • Neil Hall

    (Norwich Research Park)

  • Anthony M. Smith

    (National Institute for Communicable Diseases (NICD), Division of the National Health Laboratory Service (NHLS)
    University of Pretoria)

  • Juno Thomas

    (National Institute for Communicable Diseases (NICD), Division of the National Health Laboratory Service (NHLS))

  • Miren Iturriza-Gómara

    (University of Liverpool)

  • Kate S. Baker

    (University of Liverpool
    University of Cambridge)

Abstract

Shigellosis, a leading cause of diarrhoeal mortality and morbidity globally, predominantly affects children under five years of age living in low- and middle-income countries. While whole genome sequence analysis (WGSA) has been effectively used to further our understanding of shigellosis epidemiology, antimicrobial resistance, and transmission, it has been under-utilised in sub-Saharan Africa. In this study, we applied WGSA to large sub-sample of surveillance isolates from South Africa, collected from 2011 to 2015, focussing on Shigella flexneri 2a and Shigella sonnei. We find each serotype is epidemiologically distinct. The four identified S. flexneri 2a clusters having distinct geographical distributions, and antimicrobial resistance (AMR) and virulence profiles, while the four sub-Clades of S. sonnei varied in virulence plasmid retention. Our results support serotype specific lifestyles as a driver for epidemiological differences, show AMR is not required for epidemiological success in S. flexneri, and that the HIV epidemic may have promoted Shigella population expansion.

Suggested Citation

  • 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.
    • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-43345-5
    DOI: 10.1038/s41467-023-43345-5
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    References listed on IDEAS

    as
    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. 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.
    3. Kate S. Baker & Timothy J. Dallman & Nigel Field & Tristan Childs & Holly Mitchell & Martin Day & François-Xavier Weill & Sophie Lefèvre & Mathieu Tourdjman & Gwenda Hughes & Claire Jenkins & Nicholas, 2018. "Horizontal antimicrobial resistance transfer drives epidemics of multiple Shigella species," Nature Communications, Nature, vol. 9(1), pages 1-10, December.
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