Typhi Mykrobe: fast and accurate lineage identification and antimicrobial resistance genotyping directly from sequence reads for the typhoid fever agent Salmonella Typhi
Typhi Mykrobe provides rapid and sensitive genotyping of Typhi genomes direct from Illumina and ONT reads, although lower accuracy was observed for R9 ONT data. It demonstrated accurate assignment of GenoTyphi lineage, detection of AMR determinants and prediction of corresponding AMR phenotypes, and identification of plasmid replicons.
Authors
- Jane Hawkey (ORCID: https://orcid.org/0000-0001-9661-5293)
- Benjamin P. Howden (ORCID: https://orcid.org/0000-0003-0237-1473)
- Paula Díaz (ORCID: https://orcid.org/0000-0002-8252-5622)
- Louise M. Judd (ORCID: https://orcid.org/0000-0003-3613-4839)
- Satheesh Nair (ORCID: https://orcid.org/0000-0002-7297-1485)
- Megan E. Carey (ORCID: https://orcid.org/0000-0002-7797-9080)
- Jobin John Jacob (ORCID: https://orcid.org/0009-0009-7745-192X)
- Sophie Octavia (ORCID: https://orcid.org/0000-0001-8506-9127)
- Justin Y. Kim (ORCID: https://orcid.org/0000-0003-0161-1236)
- Precious E. Osadebamwen (ORCID: https://orcid.org/0000-0002-4538-893X)
- Gabriel Temitope Sunmonu (ORCID: https://orcid.org/0000-0002-9667-2164)
- Sadia Rahman (ORCID: https://orcid.org/0000-0002-7983-087X)
- Jacqueline A. Keane (ORCID: https://orcid.org/0000-0003-0739-6848)
- Danielle J. Ingle (ORCID: https://orcid.org/0000-0003-0707-6537)
- John A. Crump (ORCID: https://orcid.org/0000-0002-4529-102X)
- Iruka N. Okeke (ORCID: https://orcid.org/0000-0002-1694-7587)
- Hidemasa Izumiya (ORCID: https://orcid.org/0000-0002-9797-7402)
- Assaf Rokney (ORCID: https://orcid.org/0000-0002-5210-0711)
- Philip Ashton (ORCID: https://orcid.org/0000-0002-1545-9661)
- Masatomo Morita (ORCID: https://orcid.org/0000-0002-2850-0053)
- Zoe A. Dyson (ORCID: https://orcid.org/0000-0002-8887-3492)
- Niyaz Ahmed (ORCID: https://orcid.org/0000-0001-6425-7583)
- Myron M. Levine (ORCID: https://orcid.org/0000-0002-5721-5040)
- Martin Hunt (ORCID: https://orcid.org/0000-0002-8060-4335)
- Ayorinde O. Afolayan (ORCID: https://orcid.org/0000-0003-1405-2365)
- Anthony M. Smith (ORCID: https://orcid.org/0000-0002-3637-7155)
- Arti Kapil (ORCID: https://orcid.org/0000-0001-7834-2754)
- Karen H. Keddy (ORCID: https://orcid.org/0000-0001-8640-2235)
- Saadia Andleeb (ORCID: https://orcid.org/0000-0002-0866-5993)
- Varun Shamanna (ORCID: https://orcid.org/0000-0003-2775-2280)
- Michael J. Sikorski (ORCID: https://orcid.org/0000-0002-3811-7285)
- Zamin Iqbal (ORCID: https://orcid.org/0000-0001-8466-7547)
- David A. Rasko (ORCID: https://orcid.org/0000-0002-7337-7154)
- Kathryn E. Holt (ORCID: https://orcid.org/0000-0003-3949-2471)
- Ryan R. Wick (ORCID: https://orcid.org/0000-0001-8349-0778)
- Isaac I. Bogoch (ORCID: https://orcid.org/0000-0003-1590-6748)
- Kaitlin A. Tagg (ORCID: https://orcid.org/0000-0001-5300-7984)
Institutions
- University of Maryland, Baltimore (US)
- Centers for Disease Control and Prevention (US)
- European Bioinformatics Institute (GB)
- University of Liverpool (GB)
- University of Freiburg (DE)
- The University of Melbourne (AU)
- Christian Medical College, Vellore (IN)
- University of Ibadan (NG)
- University of Toronto (CA)
- International Centre for Diarrhoeal Disease Research (BD)
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme (MW)
- Wellcome Sanger Institute (GB)
- Israel Ministry of Health (IL)
- John Radcliffe Hospital (GB)
- UNSW Sydney (AU)
- University of Hyderabad (IN)
- University of Oxford (GB)
- National Institute of Infectious Diseases (JP)
- London School of Hygiene & Tropical Medicine (GB)
- Cambridge School (PT)
- Peter Doherty Institute (AU)
- Public Health Agency (GB)
- Chelsea and Westminster Hospital (GB)
- Instituto Nacional de Salud (CO)
- National University of Medical Sciences (PK)
- National Institute for Communicable Diseases
- Institute of Medical Sciences (IN)
- University of Bath (GB)
- Monash University (AU)
- University of Pretoria (ZA)
- University of Otago (NZ)
Publication Details
- Journal
- Genome Medicine
- Published
- 2025-10-24
- DOI
- https://doi.org/10.1186/s13073-025-01551-4
- Primary Topic
- Salmonella and Campylobacter epidemiology
- Type
- article
- Field-Weighted Citation Impact
- 0.00
Funders
- U.S. Department of Health and Human Services
- Bill and Melinda Gates Foundation
- Wellcome Trust
- National Institute for Health Research Health Protection Research Unit
- National Institute for Health and Care Research
- Department of Health and Social Care
- University of Warwick
- University of Oxford
- Indian Council of Medical Research
- International Centre for Diarrhoeal Disease Research, Bangladesh
- National Institutes of Health
- Centers for Disease Control and Prevention
- National Health and Medical Research Council
- NIHR Oxford Biomedical Research Centre
- National Institute of Allergy and Infectious Diseases