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Genomic surveillance for tracking typhoid fever and antimicrobial resistance

 A poster depiction of "Typhoid Mary" (1870-1938). This is an illustration that appeared in 1909 in The New York American
A poster depiction of "Typhoid Mary" (1870-1938). This is an illustration that appeared in 1909 in The New York American.

Typhoid fever is a systemic infection caused by the bacterium Salmonella enterica serovar Typhi (S. Typhi). Antimicrobials are the mainstay of typhoid disease control and effective antimicrobial therapy can reduce the rate of complications from 10–30% down to 1%. A new conjugate vaccine has recently been pre-qualified by the World Health Organization (WHO) and national immunisation programmes are currently being considered by many countries where the disease is endemic. However data on disease burden, pathogen populations and antimicrobial resistance (AMR) are scarce in most such settings. 

Where typhoid surveillance is undertaken, namely for routine surveillance of travel-related infections in high income countries and burden studies in low-income countries, whole genome sequencing (WGS) has been widely adopted as the primary method for characterisation of S Typhi isolates. WGS data can provide insights into pathogen diversity and transmission dynamics, as well as the emergence, dissemination and prevalence of AMR, much of which has relevance to understanding disease in settings other than those directly sampled (including regional trends, and country-of-acquisition for travel cases). However, the resulting data are not readily accessible to public health decision makers.  

In this seminar, Professor Kathryn Holt will give an overview of our current understanding of the emergence and spread of antimicrobial resistance (AMR) in typhoid pathogens globally. She will then introduce a new interactive dashboard (TyphiNET) that aims to provide a window into genome-derived surveillance information for non-genomics experts. The dashboard relies on critical infrastructure that is being developed alongside, including:

  1. a community-driven effort to publicly share S. Typhi sequence and source data in a manner that facilitates downstream aggregation for public health surveillance (the Global Typhoid Genomics Consortium);  
  2. the GenoTyphi genotyping scheme, which provides simple, stable, phylogenetically informative nomenclature to facilitate reporting and communication about pathogen variants; and  
  3. Typhi Pathogenwatch, a public genomic epidemiology platform that provides uniform identification of genotypes and AMR determinants from genome data (in addition to whole-genome-based clustering), which is then fed into the TyphiNET dashboard. 


Professor Kathryn Holt , Professor of Microbial Systems Genomics and Co-Director of the LSHTM AMR Centre

Kat is a computational biologist specialising in infectious disease genomics. She has a BA/BSc (Hons) majoring in Biochemistry, Applied Statistics and Philosophy (University of Western Australia); a Master of Epidemiology (University of Melbourne); and a PhD in Molecular Biology (University of Cambridge and Sanger Institute). Kat is currently Editor-in-Chief of the UK Microbiology Society journal Microbial Genomics and a Howard Hughes Medical Institute-Gates International Research Scholar. Kat’s research group uses computational genomics and sequencing, phylogenetics, spatiotemporal analysis and epidemiology to study evolution, transmission and antimicrobial resistance in bacterial pathogens including tropical diseases such as typhoid, dysentery, E. coli diarrhoea and tuberculosis; and healthcare-associated pathogens such as Klebsiella and Acinetobacter

Please note that the recording link will be listed on this page when available


Follow webinar link. Free and open to all. No registration required.