The genomic epidemiology of shigellosis in South Africa
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 e...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English |
| Published: |
Nature Portfolio
2023-11-01
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| Series: | Nature Communications |
| Online Access: | https://doi.org/10.1038/s41467-023-43345-5 |
| _version_ | 1797452115322339328 |
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| author | George E. Stenhouse Karen H. Keddy Rebecca J. Bengtsson Neil Hall Anthony M. Smith Juno Thomas Miren Iturriza-Gómara Kate S. Baker |
| author_facet | George E. Stenhouse Karen H. Keddy Rebecca J. Bengtsson Neil Hall Anthony M. Smith Juno Thomas Miren Iturriza-Gómara Kate S. Baker |
| author_sort | George E. Stenhouse |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-09T15:04:07Z |
| format | Article |
| id | doaj.art-8a1c9927a4c8493ba55330c04e7144f1 |
| institution | Directory Open Access Journal |
| issn | 2041-1723 |
| language | English |
| last_indexed | 2024-03-09T15:04:07Z |
| publishDate | 2023-11-01 |
| publisher | Nature Portfolio |
| record_format | Article |
| series | Nature Communications |
| spelling | doaj.art-8a1c9927a4c8493ba55330c04e7144f12023-11-26T13:46:10ZengNature PortfolioNature Communications2041-17232023-11-0114111410.1038/s41467-023-43345-5The genomic epidemiology of shigellosis in South AfricaGeorge E. Stenhouse0Karen H. Keddy1Rebecca J. Bengtsson2Neil Hall3Anthony M. Smith4Juno Thomas5Miren Iturriza-Gómara6Kate S. Baker7Clinical Infection, Microbiology, and Immunology, University of Liverpool2Independent ConsultantClinical Infection, Microbiology, and Immunology, University of LiverpoolEarlham Institute, Norwich Research ParkCentre for Enteric Diseases, National Institute for Communicable Diseases (NICD), Division of the National Health Laboratory Service (NHLS)Centre for Enteric Diseases, National Institute for Communicable Diseases (NICD), Division of the National Health Laboratory Service (NHLS)Clinical Infection, Microbiology, and Immunology, University of LiverpoolClinical Infection, Microbiology, and Immunology, University of LiverpoolAbstract 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.https://doi.org/10.1038/s41467-023-43345-5 |
| spellingShingle | George E. Stenhouse Karen H. Keddy Rebecca J. Bengtsson Neil Hall Anthony M. Smith Juno Thomas Miren Iturriza-Gómara Kate S. Baker The genomic epidemiology of shigellosis in South Africa Nature Communications |
| title | The genomic epidemiology of shigellosis in South Africa |
| title_full | The genomic epidemiology of shigellosis in South Africa |
| title_fullStr | The genomic epidemiology of shigellosis in South Africa |
| title_full_unstemmed | The genomic epidemiology of shigellosis in South Africa |
| title_short | The genomic epidemiology of shigellosis in South Africa |
| title_sort | genomic epidemiology of shigellosis in south africa |
| url | https://doi.org/10.1038/s41467-023-43345-5 |
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