Journal article
Global diversity and antimicrobial resistance of typhoid fever pathogens: insights from a meta-analysis of 13,000 Salmonella Typhi genomes
- Abstract:
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Background:
The Global Typhoid Genomics Consortium was established to bring together the typhoid research community to aggregate and analyse Salmonella enterica serovar Typhi (Typhi) genomic data to inform public health action. This analysis, which marks 22 years since the publication of the first Typhi genome, represents the largest Typhi genome sequence collection to date (n=13,000).Methods:
This is a meta-analysis of global genotype and antimicrobial resistance (AMR) determinants extracted from previously sequenced genome data and analysed using consistent methods implemented in open analysis platforms GenoTyphi and Pathogenwatch.Results:
Compared with previous global snapshots, the data highlight that genotype 4.3.1 (H58) has not spread beyond Asia and Eastern/Southern Africa; in other regions, distinct genotypes dominate and have independently evolved AMR. Data gaps remain in many parts of the world, and we show the potential of travel-associated sequences to provide informal ‘sentinel’ surveillance for such locations. The data indicate that ciprofloxacin non-susceptibility (>1 resistance determinant) is widespread across geographies and genotypes, with high-level ciprofloxacin resistance (≥3 determinants) reaching 20% prevalence in South Asia. Extensively drug-resistant (XDR) typhoid has become dominant in Pakistan (70% in 2020) but has not yet become established elsewhere. Ceftriaxone resistance has emerged in eight non-XDR genotypes, including a ciprofloxacin-resistant lineage (4.3.1.2.1) in India. Azithromycin resistance mutations were detected at low prevalence in South Asia, including in two common ciprofloxacin-resistant genotypes.Conclusions:
The consortium’s aim is to encourage continued data sharing and collaboration to monitor the emergence and global spread of AMR Typhi, and to inform decision-making around the introduction of typhoid conjugate vaccines (TCVs) and other prevention and control strategies.
- Publication status:
- Published
- Peer review status:
- Peer reviewed
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(Preview, Version of record, pdf, 2.5MB, Terms of use)
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- Publisher copy:
- 10.7554/elife.85867
Authors
Contributors
+ Global Typhoid Genomics Consortium Group Authorship
- Division:
- MSD
- Department:
- NDM
- Sub department:
- Big Data Institute
- Role:
- Contributor
- Publisher:
- eLife Sciences Publications
- Journal:
- eLife More from this journal
- Volume:
- 12
- Article number:
- e85867
- Place of publication:
- England
- Publication date:
- 2023-09-12
- Acceptance date:
- 2023-08-02
- DOI:
- EISSN:
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2050-084X
- Pmid:
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37697804
- Language:
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English
- Pubs id:
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1525737
- Local pid:
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pubs:1525737
- Deposit date:
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2023-10-09
- ARK identifier:
Terms of use
- Copyright holder:
- Carey et al.
- Copyright date:
- 2023
- Rights statement:
- © Carey et al. This article is distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use and redistribution provided that the original author and source are credited.
- Notes:
- For the purpose of Open Access, the authors have applied a CC BY public copyright license to any Author Accepted Manuscript version arising from this submission.
- Licence:
- CC Attribution (CC BY)
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