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 - Global Typhoid Genomics Consortium Group Authorship
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 - Ligt, Joep de
AU - Guevara, Paula Lucia Diaz
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 - Qamar, Farah N.
AU - Hasan, Rumina
AU - Shakoor, Sadia
N1 - 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 - 10.7554/ELIFE.85867
DO - 10.7554/ELIFE.85867
M3 - Article
AN - SCOPUS:85175204073
SN - 2050-084X
VL - 12
JO - eLife
JF - eLife
M1 - e85867
ER -
