- Title
- Global diversity and antimicrobial resistance of typhoid fever pathogens : insights from a meta-analysis of 13,000 Salmonella Typhi genomes
- Creator
- Carey, Megan; Dyson, Zoe; Ingle, Danielle; Amir, Afreenish; Aworh, Mabel; Chattaway, Marie; Chew, Ka; Crump, John; Feasey, Nicholas; Howden, Benjamin; Keddy, Karen; Maes, Mailis; Parry, Christopher; Van Puyvelde, Sandra; Webb, Hattie; Afolayan, Ayorinde; Alexander, Anna; Anandan, Shalini; Andrews, Jason; Ashton, Philip; Basnyat, Buddha; Bavdekar, Ashish; Bogoch, Isaac; Clemens, John; da Silva, Kesia; De, Anuradha; de Ligt, Joep; Diaz Guevara, Paula; Dolecek, Christiane; Greenhill, Andrew
- Date
- 2023
- Type
- Text; Journal article
- Identifier
- http://researchonline.federation.edu.au/vital/access/HandleResolver/1959.17/197002
- Identifier
- vital:18775
- Identifier
-
https://doi.org/10.7554/ELIFE.85867
- Identifier
- ISSN:2050-084X (ISSN)
- Abstract
- 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 becomedominant 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. © Carey et al. **Please note that there are multiple authors for this article therefore only the name of the first 30 including Federation University Australia affiliate “Andrew Greenhill” is provided in this record**
- Publisher
- eLife Sciences Publications Ltd
- Relation
- eLife Vol. 12, no. (2023), p.
- Rights
- All metadata describing materials held in, or linked to, the repository is freely available under a CC0 licence
- Rights
- http://creativecommons.org/licenses/by/4.0/
- Rights
- Copyright © Carey et al
- Rights
- Open Access
- Full Text
- Reviewed
- Funder
- Department for Health and Social Care, the Department for International Development/Global Challenges Research Fund, the UK Medical Research Council, and the Wellcome Trust
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