Abstract
Original language | English |
---|---|
Article number | e85867 |
Journal | eLife |
Volume | 12 |
DOIs | |
Publication status | Published - 2023 |
Externally published | Yes |
Access to Document
Other files and links
Cite this
- APA
- Author
- BIBTEX
- Harvard
- Standard
- RIS
- Vancouver
}
In: eLife, Vol. 12, e85867, 2023.
Research output: Contribution to journal › Article › Academic › peer-review
TY - JOUR
T1 - Global diversity and antimicrobial resistance of typhoid fever pathogens
T2 - Insights from a meta-analysis of 13,000 Salmonella Typhi genomes
AU - Carey, Megan E.
AU - Dyson, Zoe A.
AU - Ingle, Danielle J.
AU - Amir, Afreenish
AU - Aworh, Mabel K.
AU - Chattaway, Marie Anne
AU - Chew, Ka Lip
AU - Crump, John A.
AU - Feasey, Nicholas A.
AU - Howden, Benjamin P.
AU - Keddy, Karen H.
AU - Maes, Mailis
AU - Parry, Christopher M.
AU - van Puyvelde, Sandra
AU - Webb, Hattie E.
AU - Afolayan, Ayorinde Oluwatobiloba
AU - Alexander, Anna P.
AU - Anandan, Shalini
AU - Andrews, Jason R.
AU - Ashton, Philip M.
AU - Basnyat, Buddha
AU - Bavdekar, Ashish
AU - Bogoch, Isaac I.
AU - Clemens, John D.
AU - da Silva, Kesia Esther
AU - de, Anuradha
AU - de Ligt, Joep
AU - Diaz Guevara, Paula Lucia
AU - Dolecek, Christiane
AU - Dutta, Shanta
AU - Ehlers, Marthie M.
AU - Watkins, Louise Francois
AU - Garrett, Denise O.
AU - Godbole, Gauri
AU - Gordon, Melita A.
AU - Greenhill, Andrew R.
AU - Griffin, Chelsey
AU - Gupta, Madhu
AU - Hendriksen, Rene S.
AU - Heyderman, Robert S.
AU - Hooda, Yogesh
AU - Hormazabal, Juan Carlos
AU - Ikhimiukor, Odion O.
AU - Iqbal, Junaid
AU - Jacob, Jobin John
AU - Jenkins, Claire
AU - Jinka, Dasaratha Ramaiah
AU - John, Jacob
AU - Kang, Gagandeep
AU - Kanteh, Abdoulie
AU - Kapil, Arti
AU - Karkey, Abhilasha
AU - Kariuki, Samuel
AU - Kingsley, Robert A.
AU - Koshy, Roshine Mary
AU - Lauer, A. C.
AU - Levine, Myron M.
AU - Lingegowda, Ravikumar Kadahalli
AU - Luby, Stephen P.
AU - Mackenzie, Grant Austin
AU - Mashe, Tapfumanei
AU - Msefula, Chisomo
AU - Mutreja, Ankur
AU - Nagaraj, Geetha
AU - Nagaraj, Savitha
AU - Nair, Satheesh
AU - Naseri, Take K.
AU - Nimarota-Brown, Susana
AU - Njamkepo, Elisabeth
AU - Okeke, Iruka N.
AU - Bai Perumal, Sulochana Putli
AU - Pollard, Andrew J.
AU - Pragasam, Agila Kumari
AU - Qadri, Firdausi
AU - Qamar, Farah N.
AU - Ara Rahman, Sadia Isfat
AU - Rambocus, Savitra Devi
AU - Rasko, David A.
AU - Ray, Pallab
AU - Robins-Browne, Roy
AU - Rongsen-Chandola, Temsunaro
AU - Rutanga, Jean Pierre
AU - Saha, Samir K.
AU - Saha, Senjuti
AU - Saiga, Karnika
AU - Islam Sajib, Mohammad Saiful
AU - Seidman, Jessica C.
AU - Shakya, Jivan
AU - Shamanna, Varun
AU - Shastri, Jayanthi
AU - Shrestha, Rajeev
AU - Sia, Sonia
AU - Sikorski, Michael J.
AU - Singh, Ashita
AU - Smith, Anthony M.
AU - Tagg, Kaitlin A.
AU - Tamrakar, Dipesh
AU - Tanmoy, Arif Mohammed
AU - Thomas, Maria
AU - Thomas, Mathew S.
AU - Thomsen, Robert
AU - Thomson, Nicholas R.
AU - Tupua, Siaosi
AU - Vaidya, Krista
AU - Valcanis, Mary
AU - Veeraraghavan, Balaji
AU - Weill, François-Xavier
AU - Wright, Jackie
AU - Dougan, Gordon
AU - Argimón, Silvia
AU - Keane, Jacqueline A.
AU - Aanensen, David M.
AU - Baker, Stephen
AU - Holt, Kathryn E.
N1 - Funding Information: Department for Health and Social Care, the Department for International Development/Global Challenges Research Fund, the UK Medical Research Council, and the Wellcome Trust Funding Information: 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. Funding: No specific funding was awarded for this meta-analysis. Coordinators were supported by fellowships from the European Union (ZAD received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreement No 845681), the Wellcome Trust (SB, Wellcome Trust Senior Fellowship), and the National Health and Medical Research Council (DJI is supported by an NHMRC Investigator Grant [GNT1195210]). Publisher Copyright: © Carey et al.
PY - 2023
Y1 - 2023
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=85175204073&partnerID=8YFLogxK
U2 - https://doi.org/10.7554/ELIFE.85867
DO - https://doi.org/10.7554/ELIFE.85867
M3 - Article
SN - 2050-084X
VL - 12
JO - eLife
JF - eLife
M1 - e85867
ER -