Global Typhoid Genomics Consortium

Coordinate sharing & release of typhoid genomics data to maximise its potential to inform public health

• The role of the consortium is to encourage and assist the deposition of raw genome data into public databases (ENA or SRA) and to coordinate downstream integration of the data for public health benefit. Members retain full control over their data and when they choose to make it public. 

• We use Typhi Pathogenwatch as the central analysis platform and database to generate inferred genotypes and AMR determinants from raw genomes, and to maintain a publicly available, continually updated interactive global phylogeny (described in this paper).

• We are developing the TyphiNET genomic surveillance dashboard to provide interactive global and national reports on AMR, and to indicate the underlying genetic drivers based on the Pathogenwatch database.

• We have established a standardised metadata template to facilitate harmonization of source information across aggregated Typhi data. 

Consortium Project: 21 Years of Typhoid Genomics

• In the twenty-one years since the first Salmonella Typhi genome was sequenced, both sequencing technology and the Typhi population have changed radically. Our aim is to provide an updated global snapshot of typhoid genome diversity and AMR, to introduce a mechanism for regular updates, and to facilitate use of genomic data to inform public health interventions. 

• All data contributors are included in the consortium, and many are contributing to analysis working groups. We aimed to involve every lab that has sequenced a Typhi genome, and to engage them in a collective effort to ensure that these data are translated for maximal public health impact. 

• The first paper has now been preprinted and is being assessed by eLife: "Global diversity and antimicrobial resistance of typhoid fever pathogens: insights from 13,000 Salmonella Typhi genomes". Read the preprint here on MedRxiv.

AMR prediction from typhoid genome data

• We will establish a working group to collate paired genome-phenotype data in order to benchmark and refine the existing AMR predictions, and to identify gaps in knowledge to prioritise further research.

• Consortium members contributing data will be expected to deposit both genome sequences and susceptibility phenotypes into NCBI's National Database of Antibiotic Resistant Organisms (NDARO) upon publication.

Coordinators: Kat Holt, Megan Carey, David Aanensen, Zoe Dyson and Stephen Baker. 

Steering Committee - a group of multidisciplinary international experts will oversee Consortium activities, chaired by Gordon Dougan:

• Buddha Basnyat (OUCRU, Nepal)

• Josefina Campos (Administración Nacional de Laboratorios e Institutos de Salud, Argentina)

• Marie Chattaway (Public Health England)

• Alan Christoffels (South African National Bioinformatics Institute, South Africa)

• Danielle Ingle (Microbiological Diagnostic Unit Public Health Laboratory, Australia)

• Sam Kariuki (Kenya Medical Research Institute, Kenya)

• Ana Lauer (US Centers for Disease Control and Prevention, USA)

• Chisomo Msefula (University of MalawiCollege of Medicine, Malawi)

• John Nash (Public Health Agency of Canada, Canada)

• Iruka Okeke (University of Ibadan, Nigeria)

• Firdausi Qadri (icddr,b, Bangladesh)

• Farah Qamar (Aga Khan University, Pakistan)

• Senjuti Saha (Child Health Research Foundation, Bangladesh)

• Sonia Sia (Research Institute for Tropical Medicine, Philippines)

• Balaji Veeraraghavan (Christian Medical College Vellore, India)

• Francois-Xavier Weill (Institut Pasteur, France)

Advisory Board: we will engage stakeholders from the global public health community, to identify ways to promote typhoid genomic surveillance and use of data for public health benefit.

• Adwoa Bentsi-Enchill (World Health Organization, Switzerland)

• Denise Garrett (Sabin Vaccine Institute, USA)

• Jacob John (Christian Medical College, Vellore, India)

• Elizabeth Klemm (Wellcome Trust, UK)

• Francisco Luquero (Gavi, the Vaccine Alliance, Switzerland)

• Jason Mwenda (World Health Organization AFRO, Republic of Congo)

• Kathy Neuzil (Center for Vaccine Development and Global Health, University of Maryland School of Medicine, USA)

• Carmem Pessoa-Silva (World Health Organization, Global Antimicrobial Resistance Surveillance System, Switzerland) 

• Pilar Ramon-Pardo (Pan American Health Organization)

• Jeff Stanaway (Institute for Health Metrics and Evaluation, USA)

• Duncan Steele (Bill & Melinda Gates Foundation, USA)

• Sofonias Tessema (Africa Pathogen Genome Initiative, Ethiopia)