Global diversity and antimicrobial resistance of typhoid fever pathogens: insights from 13,000SalmonellaTyphi genomes
Authors: Carey Megan E. , Dyson Zoe A. , Ingle Danielle J. , Amir Afreenish , Aworh Mabel K. , Chattaway Marie Anne , Chew Ka Lip , Crump John A. , Feasey Nicholas A. , Howden Benjamin P. , Keddy Karen H. , Maes Mailis , Parry Christopher M. , Puyvelde Sandra Van , Webb Hattie E. , Afolayan Ayorinde O. , Anandan Shalini , Andrews Jason R. , Ashton Philip M. , Basnyat Buddha , Bavdekar Ashish , Bogoch Isaac I. , Clemens John D. , da Silva Kesia E. , De Anuradha , de Ligt Joep , Diaz Guevara Paula Lucia , Dolecek Christiane , Dutta Shanta , Watkins Louise Francois , Garrett Denise O. , Godbole Gauri , Gordon Melita A. , Greenhill Andrew R. , Griffin Chelsey , Gupta Madhu , Hendricksen Rene , Heyderman Robert S. , Hooda Yogesh , Hormazabal Juan Carlos , Ikhimiukor Odion O. , Iqbal Junaid , Jacob Jobin J. , Jenkins Claire , Jinka Dasaratha Ramaiah , John Jacob , Kang Gagandeep , Kanteh Abdoulie , Kapil Arti , Karkey Abhilasha , Kariuki Samuel , Kingsley Robert A. , Koshy Roshine Mary , Lauer A. C. , Levine Myron M. , Lingegowda Ravikumar Kadahalli , Luby Stephen P. , Mackenzie Grant A. , Mashe Tapfumanei A. , Msefula Chisomo , Mutreja Ankur , Nagaraj Geetha , Nagaraj Savitha , Nair Satheesh , Naseri Take K. , Nimarota-Brown Susana , Njamkepo Elisabeth , Okeke Iruka N. , Perumal Sulochana Putli Bai , Pollard Andrew J. , Pragasam Agila Kumari , Qadri Firdausi , Qamar Farah N. , Rahman Sadia Isfat Ara , Rambocus Savitra D. , Rasko David A. , Ray Pallab , Robins-Browne Roy , Rongsen-Chandola Temsunaro , Rutanga Jean Pierre , Saha Samir K. , Saha Senjuti , Saigal Karnika , Sajib Mohammad Saiful Islam , Seidman Jessica C. , Shakya Jivan , Shamanna Varun , Shastri Jayanthi , Shrestha Rajeev , Sia Sonia , Sikorski Michael J. , Singh Ashita , Smith Anthony M. , Tagg Kaitlin A. , Tamrakar Dipesh , Tanmoy Arif Mohammad , Thomas Maria , Thomas Mathew S. , Thomsen Robert , Thomson Nicholas R. , Tupua Siaosi , Vaidya Krista , Valcanis Mary , Veeraraghavan Balaji , Weill François-Xavier , Wright Jackie , Dougan Gordon , Argimón Silvia , Keane Jacqueline A. , Aanensen David M. , Baker Stephen , Holt Kathryn E. ,   Global Typhoid Genomics Consortium Group Authorship
Published: December 2022

The Global Typhoid Genomics Consortium was established to bring together the typhoid research community to aggregate and analyseSalmonella entericaserovar Typhi (Typhi) genomic data to inform public health action. This analysis, which marks twenty-one years since the publication of the first Typhi genome, represents the largest Typhi genome sequence collection to date (n=13,000), and provides a detailed overview of global genotype and antimicrobial resistance (AMR) distribution and temporal trends, generated using open analysis platforms (GenoTyphi and Pathogenwatch). 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 potential of travel-associated data to provide informal “sentinel” surveillance for such locations. The data indicate ciprofloxacin non-susceptibility (>1 resistance determinant) is widespread across geographies and genotypes, with high-level 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. 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.