Typhi Mykrobe: fast and accurate lineage identification and antimicrobial resistance genotyping directly from sequence reads for the typhoid fever agent Salmonella Typhi

Author(s):

Danielle J. Ingle, Jane Hawkey, Martin Hunt, Zamin Iqbal, Jacqueline A. Keane, Ayorinde O. Afolayan, Niyaz Ahmed, Saadia Andleeb, Philip M. Ashton, Isaac I. Bogoch, Megan E. Carey, Marie Anne Chattaway, John A. Crump, Paula Diaz Guevara, Benjamin P. Howden, Hidemasa Izumiya, Jobin John Jacob, Louise M. Judd, Arti Kapil, Karen H. Keddy, Justin Y. Kim, Myron M. Levine, Masatomo Morita, Satheesh Nair, Sophie Octavia, Iruka N. Okeke, Precious E. Osadebamwen, Sadia Isfat Ara Rahman, Assaf Rokney, David A. Rasko, Varun Shamanna, Michael J. Sikorski, Anthony M. Smith, Gabriel T. Sunmonu, Kaitlin A. Tagg, Ryan R. Wick, Zoe A. Dyson, Kathryn E. Holt

Details:

Genome Medicine, Volume 17, Issue 1, 2025-12-01, Article number 130

Article Link: Click here

Affiliations:

• University of Oxford
• University of Melbourne
• Monash University
• UNSW Sydney
• University of Liverpool
• University of Toronto Faculty of Medicine
• Centers for Disease Control and Prevention
• University of Maryland School of Medicine
• University of Pretoria
• University of Otago
• London School of Hygiene & Tropical Medicine
• Universitätsklinikum Freiburg
• National University of Sciences and Technology
• Nuffield Department of Medicine
• University of Hyderabad
• National Institute of Infectious Diseases
• Christian Medical College, Vellore
• Wellcome Sanger Institute
• Chelsea and Westminster Hospital
• International Centre for Diarrhoeal Disease Research Bangladesh
• NIHR Oxford Biomedical Research Centre
• EMBL’s European Bioinformatics Institute
• Department of Microbiology & Immunology
• University of Maryland School of Dentistry
• Ministry of Health
• Department of Medicine
• Faculty of Health Sciences
• College of Medicine, University of Ibadan
• National Institute for Communicable Diseases
• UK Health Security Agency
• Malawi-Liverpool-Wellcome Trust Clinical Research Programme
• Center for Vaccine Development and Global Health (CVD)
• Instituto Nacional de Salud
• Milner Centre for Evolution
• Kempegowda Institute of Medical Sciences
• Microbiological Diagnostic Unit Public Health Laboratory
• Institute of Medical Sciences