27th July 2008

Defining DNA Differences to Track and Tackle Typhoid

New-technology genome sequencing study reveals new genetic signatures


Evolution in <em>Salmonella Typhi</em>:<br /> Upper panel. Phylogenetic tree based on SNP data. Branch colours indicate lineages of <em>Typhi</em>; branch lengths are measured in number of SNPs. The central, small filled circle indicates the ancestral root and the dashed line represents the rest of the <em>Salmonella</em> lineage.<br /> Lower panel. Accumulation of gene-inactivating mutations in <em>Typhi</em> lineages. Points correspond to bifurcations in the tree above; y axis shows the total number of genes inactivated by deletion or nonsense mutation up to that bifurcation. Each line represents the accumulation of mutations in a particular isolate; different lineages of <em>Typhi</em> are coloured as above. LCA, last common ancestor.

For the first time, next-generation DNA sequencing technologies have been turned on typhoid fever - a disease that kills 600,000 people each year. The results will help to improve diagnosis, tracking of disease spread and could help to design new strategies for vaccination.

The study sets a new standard for analysing the evolution and spread of a disease-causing bacterium: it is the first study of multiple samples of any bacterial pathogen at this level of detail. It uncovers previously hidden genetic signatures of the evolution of individual lineages of Salmonella Typhi.

The team developed methods that are being used to type outbreaks, allowing researchers to identify individual organisms that are spreading in the population: using Google Earth, the outbreaks can be easily visualized. The team hope that these mapping data can be used to target vaccination campaigns more successfully with the aim of eradicating typhoid fever.

" Using the genomic biology of this study, we can now type Typhi, identify the strain that is causing infection, identify carriers and direct vaccination programmes most efficiently "

Kathryn Holt

Unlike most related Salmonella species, and in contrast to many other bacteria, Typhi is found only in humans and the genomes of all isolates are superficially extremely similar, hampering attempts to track infections or to type more prevalent variants. The detail of the new study transforms the ability of researchers to tackle Typhi.

"Modern genomic methods can be used to develop answers to diseases that have plagued humans for many years," explains Professor Gordon Dougan from the Wellcome Trust Sanger Institute and senior author on the study. "Genomes are a legacy of an organism's existence, indicating the paths it has taken and the route it is on. This analysis suggests we may have found Typhi's Achilles' heel: in adapting to an exclusively human lifestyle, it has become complacent, its genome is undergoing genetic decay and it's heading up an evolutionary dead end in humans."

"We believe that concerted vaccination programmes, combined with epidemiological studies aiming to track down and treat carriers, could be used to eradicate typhoid as a disease."

There are 17 million cases of Typhoid fever each year - although the World Health Organization cautions that this is a 'very conservative' estimate. Young people are most at risk: in Indonesia, nine out of ten cases occur in 3-19-year-olds.

"A key to survival of Salmonella Typhi is its ability to lie dormant in carriers, who show no symptoms but remain able to infect others," says Kathryn Holt, a PhD student at the Wellcome Trust Sanger Institute and first author on the study. "Our new tools will assist us in tracing the source of typhoid outbreaks, potentially even to infected carriers, allowing those individuals to be treated to prevent further spread of the disease."

"Using the genomic biology of this study, we can now type Typhi, identify the strain that is causing infection, identify carriers and direct vaccination programmes most efficiently. It is a remarkable step forward."

The study is a collaboration between researchers at the Wellcome Trust Sanger Institute, University College, Cork, Institut Pasteur in Paris and Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam. The team studied 19 isolates of Typhi from ten countries, using new sequencing methods that meant they could capture the rare signals of genetic variation in this stubborn genome. They produced more than 1.7 billion letters of genetic sequence and found evidence of fewer than 2000 mutation events, suggesting very little evolution since the emergence of Typhi at least 15,000 years ago.

Their analysis shows that the Typhi genome is decaying - as it becomes more closely allied to us, its human host, it is losing genes that are superfluous to life in the human body. More importantly, genes that contain instructions for the proteins on the surface of the bacterium - those most often attacked by our immune system defences - vary much less than do the equivalent genes in most other bacteria, suggesting that Typhi has a strategy to circumvent the selective pressures of our immune system.

"Both the genome and the proteins that make up the surface of Typhi - the targets for vaccines - show amazingly little variation," says Professor Julian Parkhill, Head of Pathogen Genomics. "We have been able to use novel technologies, developed for the analysis of human genome variation, to identify this variation: this would have been impossible a year ago. The technologies we have developed here could also be used in the battles against other disease-causing bacteria."

Notes to Editors

Publication details

Holt KE et al. (2008) High-throughput sequencing provides insights into genome variation and evolution in Salmonella Typhi. Nature Genetics, available online in advance of print publication on Sunday 27 June 2008 http://dx.doi.org/ 10.1038/ng.195


  • Typhoid fever kills 10-30% of untreated people. It has been controlled by vaccination and use of antibiotics: however, antibiotic resistance is an emerging problem, especially in south-east Asia.
  • Typhoid has claimed the lives of millions: among the more well known are Queen Victoria's husband, Albert, English author Arnold Bennett, Wilbur Wright of the Wright brothers and Leland Stanford, for whom the US university is named.
  • One of the best-known cases is that of Mary Mallon, a healthy carrier of typhoid, who worked for many years in the food industry in New York and is thought to have infected almost 50 people. She was eventually forcibly quarantined by authorities. http://en.wikipedia.org/wiki/Typhoid_fever & http://en.wikipedia.org/wiki/Mary_Mallon

Particpating Centres

  • The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, UK
  • Environmental Research Institute, University College Cork, Lee Road, Cork, Ireland
  • Max-Planck-Institut für Infektionsbiologie, Department of Molecular Biology, Charitéplatz 1, 10117, Berlin, Germany
  • Université Mixte de Recherche 6191 Centre National de la Recherche Scientifique - Commissariat à l'Énergie Atomique Aix-Marseille Université, Commissariat à l'Énergie Atomique Cadarache, 13108 Saint Paul lez Durance, France
  • Institut Pasteur, Laboratoire des Bactéries Pathogènes Entériques, 28 rue du docteur Roux, Paris, France
  • Oxford University Clinical Research Unit, Hospital for Tropical Diseases, 190 Ben Ham Tu, District 5, Ho Chi Minh City, Vietnam
  • Department of Veterinary Medicine, University of Cambridge, Madingley Road, Cambridge, UK

Funding and support

This work was supported by the Wellcome Trust. Additional support to individual researchers was provided by the Scientific Foundation Ireland. The work was also supported by the Sanger Institute core sequencing and informatics groups.


The Wellcome Trust Sanger Institute

The Wellcome Trust Sanger Institute, which receives the majority of its funding from the Wellcome Trust, was founded in 1992. The Institute is responsible for the completion of the sequence of approximately one-third of the human genome as well as genomes of model organisms and more than 90 pathogen genomes. In October 2006, new funding was awarded by the Wellcome Trust to exploit the wealth of genome data now available to answer important questions about health and disease.


The Wellcome Trust

The Wellcome Trust is a global charitable foundation dedicated to achieving extraordinary improvements in human and animal health. We support the brightest minds in biomedical research and the medical humanities. Our breadth of support includes public engagement, education and the application of research to improve health. We are independent of both political and commercial interests.


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