Abstract
BACKGROUND: Typhoid fever results from systemic infection with Salmonella enterica serovar Typhi (Typhi) and causes 10 million illnesses annually. Disease control relies on prevention (water, sanitation, and hygiene interventions or vaccination) and effective antimicrobial treatment. Antimicrobial-resistant (AMR) Typhi lineages have emerged and become established in many parts of the world. Knowledge of local pathogen populations informed by genomic surveillance, including of lineages (defined by the GenoTyphi scheme) and AMR determinants, is increasingly used to inform local treatment guidelines and to inform vaccination strategy. Current tools for genotyping Typhi require multiple read alignment or assembly steps and have not been validated for analysis of data generated with Oxford Nanopore Technologies (ONT) long-read sequencing devices. Here, we introduce Typhi Mykrobe, a command line software tool for rapid genotyping of Typhi lineages, AMR determinants, and plasmid replicons direct from sequencing reads. RESULTS: We validated Typhi Mykrobe lineage genotyping by comparison with the current standard read mapping-based approach and demonstrated 99.8% concordance across nearly 13,000 genomes sequenced with Illumina platforms. For the few isolates with discordant calls, we show that Typhi Mykrobe results are better supported by the evidence from raw sequence read data than the results generated using the mapping-based approach. We also demonstrate 99.9% concordance for detection of AMR determinants compared with the current standard assembly-based approach, with similar results for plasmid marker detection. Typhi Mykrobe predicts clinical resistance categorization (S/I/R) for eight drug classes, and we show strong agreement with phenotypic categorizations generated from reference laboratory minimum inhibitory concentration (MIC) data for n = 1572 Illumina-sequenced isolates (> 99% agreement within one doubling dilution). We show strong concordance (> 96% for genotype and > 98% for AMR and plasmid) between calls made from ONT reads and those made from Illumina reads for isolates sequenced on both platforms (n = 93 genomes). Typhi Mykrobe takes less than a minute per sample and is available at https://github.com/typhoidgenomics/genotyphi . CONCLUSIONS: 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.
| Original language | English |
|---|---|
| Article number | 130 |
| Number of pages | 1 |
| Journal | Genome Medicine |
| Volume | 17 |
| Issue number | 1 |
| Early online date | 24 Oct 2025 |
| DOIs | |
| Publication status | Published - 31 Dec 2025 |
Data Availability Statement
All code and instructions for genotyping isolates with GenoTyphi using Mykrobe is available in the GitHub repository at [https://github.com/typhoidgenomics/genotyphi]. The version reported in this paper is v2.1 (DOI: [https:/doi.org/10.5281/zenodo.13859721] ) The datasets and analysis code used in this article are available in a GitHub repository at [https://github.com/typhoidgenomics/TyphoidGenomicsConsortiumMykrobe]. The version reported in this paper is v1 (DOI = https:/doi.org/10.5281/zenodo.17117923).Acknowledgements
MAC and SN are affiliated to the National Institute for Health Research HealthProtection Research Unit (NIHR HPRU) in Genomics and Enabling Data at
University of Warwick in partnership with the UK Health Security Agency
(UKHSA). MAC and SN are based at UKHSA. MH is affiliated to the NIHR Health
Protection Research Unit in Healthcare Associated Infections and Antimicrobial
Resistance at Oxford University. The views expressed are those of the
author(s) and not necessarily those of the NIHR, the Department of Health and
Social Care or the UK Health Security Agency.
SIAR from the icddr,b is grateful to the Governments of Bangladesh, and
Canada for providing unrestricted support.
NA is grateful for support from ICMR India (IIRP-2023-2500).
KAT thanks the epidemiology and laboratory partners in state and local health
departments. The findings and conclusions in this report are those of the
authors and do not necessarily represent the official position of the Centers
for Disease Control and Prevention. Names of specific vendors, manufacturers,
or products are included for public health and informational purposes; inclusion
does not imply endorsement of the vendors, manufacturers, or products
by the Centers for Disease Control and Prevention or the US Department of
Health and Human Services.
AMS thanks all participants of the GERMS-SA Laboratory Surveillance Network,
South Africa, for submission of clinical isolates of Salmonella species to the
National Institute for Communicable Diseases; the surveillance network
includes laboratories belonging to the Department of Health (NHLS laboratories)
and laboratories that form part of the private sector. We thank all the lab
members involved in SEFI reference lab activities at CMC Vellore implicated in
culture maintenance and ONT data generation.
This work was supported by Monash eResearch capabilities, including the
high-performance computer M3 and Research Data Storage.
Global Typhoid Genomics Consortium Group Authorship.
Ali H. Abbas1,
Safina Abdul Razzak2,
Mabel K. Aworh3,
Stephen Baker4,
Buddha
Basnyat5,
Ka Lip Chew6,
Thomas C. Darton7,
Andrew R. Greenhill8,
Madhu
Gupta9,
Mochammad Hatta10,
Aamer Ikram11,
Dasaratha Ramaiah Jinka12,
A.
C. Lauer13,
Octavie Lunguya14,
Jaspreet Mahindroo15,
Tapfumanei Mashe16,
Elli
Mylona17,
Maria Pardos de la Gandara18,
Andrew J. Pollard19,
Saikt Rahman20,
Elrashdy M Redwan21,22,23,
Jean Pierre Rutanga24,
Jivan Shakya25,
Arif Tanmoy26,
Mathew S. Thomas27,
Sandra Van Puyvelde28,
Jacqueline M Wright29.
1 Department of Microbiology, Faculty of Veterinary Medicine, University
of Kufa, Kufa- Najaf Street, Najaf, Iraq2 Department of Paediatrics and Child
Health, Aga Khan University, P.O. Box 3500, National Stadium Rd, Karachi,
Sindh, Pakistan.3 North Carolina State University, 1060 William Moore Drive,
Raleigh, NC 27607, USA4 University of Cambridge, JCBC, Puddicome way,
Cambridge, CB2 0AW, United Kingdom5 OUCRU-Nepal, Jhamshikhel, Lalitpur,
Nepal6 National University Hospital, 5 Lower Kent Ridge Road, Singapore
119074, Republic of Singapore7 Clinical Infection Research Group, School of
Medicine and Population Health, University of Sheffield, Western Bank, Sheffield,
S10 2TN, United Kingdom8 Federation University Australia, Gippsland
Campus, Churchill, Victoria, Australia9 Postgraduate Institute of Medical
Education and Research, sector 12, Chandigarh. CMC Vellore, India10 Department
of Molecular Biology and Immunology, Faculty of Medicine, Hasanuddin
University, Makassar, 90245, Indonesia11 Fauji Foundation, Rawal Road,
Rawalpindi, Pakistan12 RDT Hospital, Bathalapalli, Srisathya Sai District, 515661,
India13 Centers for Disease Control and Prevention, Atlanta, United States
of America14 Department of Microbiology, Institut National de Recherche
Biomédicale, Kinshasa, Democratic Republic of the Congo15 MRC Centre for
Global Infectious Disease Analysis, School of Public Health, Imperial College
London, London, W12 0BZ, United Kingdom 16 World Health Organisation,
Zimbabwe17 Cambridge Institute of Therapeutic Immunology and Infectious
Disease (CITIID), University of Cambridge, Cambridge CB1 0AW, United
Kingdom18 Institut Pasteur, France19 Oxford Vaccine Group, Department of
Paediatrics, University of Oxford and the NIHR Oxford Biomedical Research
Centre, Oxford, UK20 RDT Hospital, Bathalapalli, Srisathya Sai District, 515661,
India21 Department of Biological Science, Faculty of Science, King Abdulaziz
University, Jeddah, Saudi Arabia22 Centre of Excellence in Bionanoscience
Research, King Abdulaziz University, Jeddah 21589, Saudi Arabia23 Therapeutic
and Protective Proteins Laboratory, Protein Research Department, Genetic
Engineering and Biotechnology Research Institute, City of Scientific Research
and Technological Applications, New Borg EL-Arab 21934, Alexandria, Egypt.24
University of Rwanda, KK 737 street, Kigali, B.P 3900, Rwanda25 Institute for
Research in Science and Technology, Sachal-2, Lalitpur, Nepal26 Child Health
Research Foundation, Dhaka, Bangladesh27 CMAI, ICMDA28 University of Antwerp,
Antwerp, Belgium29 Institute of Environmental Sciences and Research
27 Creyke Road, Christchurch, 8041, New Zealand.
Funding
DJI was supported by an Emerging Leadership Fellowship from the National Health and Medical Research Council (NHMRC) of Australia (GNT1195210). ZAD received funding from the European Union’s Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie (grant agreement No 845681). KEH received funding from the Wellcome Trust (grant 226432/Z/22/Z). INO was supported by Official Development Assistance (ODA) funding from the NIHR (grant number #16/136/111) and a Calestous Juma Science Leadership Fellowship from the BMGF (INV-036234). AMS is supported by the SEQAFRICA project, funded by the Department of Health and Social Care’s Fleming Fund using UK aid. MJS was supported by BMGF (INV-000049, OPP1161058) and National Institute of Allergy and Infectious Diseases (NIAID) of the National Institutes of Health (F30AI156973). JAC was supported by the Bill & Melinda Gates Foundation Typhoid Vaccine Acceleration Consortium (TyVAC, INV-030857). BPH was supported by a NHMRC Leadership Fellowship (GNT1196103). KAT and this work are supported by the Centers for Disease Control and Prevention. MML was supported by BMGF (OPP1194582, INV-000049, and INV-029806). MH was supported by the National Institute for Health Research (NIHR) Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at Oxford University in partnership with the UK Health Security Agency (UKHSA) (NIHR200915), and supported by the NIHR Biomedical Research Centre, Oxford. DAR is supported by the NIH (U19 AI110802-01, NIH T32AI162579). JJJ was supported by grants from Bill and Melinda Gates Foundation, USA (Investment ID INV-009497 OPP1159351) for the Project‚ National Surveillance System for Enteric Fever in India. RRW is supported by an ARC Discovery Early Career Researcher Award (DE250100677). JH was supported by an Emerging Leadership Fellowship from the NHMRC of Australia (GNT2034741).
Keywords
- Salmonella Typhi
- Antimicrobial resistance (AMR)
- Genotyping
- Lineage
- Pathogen sequencing
- Typhoid fever
- Whole genome sequencing (WGS)
ASJC Scopus subject areas
- Molecular Medicine
- Molecular Biology
- Genetics
- Genetics(clinical)
