Biology of emergent Salmonella exposed
Researchers have characterised a new multi-drug resistant strain of Salmonella Typhimurium that is causing life-threatening disease in Africa.
This type of Salmonella bug normally causes diarrhoea and is rarely fatal. The new strain infects vulnerable children and adults in many regions of sub-Saharan Africa leading to death in up to one in four cases.
The new genome work, a collaboration between the Wellcome Trust Sanger Institute, the Malawi-Liverpool-Wellcome Trust Clinical Research Programme and the Kemri-Wellcome Trust Programme, shows how genetic changes transformed this infection into a new antibiotic-resistant form of the disease. The new strain, called ST313, appears to be better adapted to affect humans, is resistant to several commonly used antibiotics and may spread from person to person.
The severe effects of ST313 – invasive disease and high mortality rates – are seen predominantly in individuals with the immune compromising conditions, HIV, malaria, malnutrition or anaemia. Until today, it had been widely assumed that this wasn’t a new deadly form of the organism but, rather, that the existing diarrhoea-causing strain of the pathogen was taking advantage of the weakened immune system of patients with underlying health problems to cause a more severe disease.
Today’s results paint a truer picture.
“Multi-drug resistant forms of this deadly type of S. Typhimurium emerged only in the last decade. It seems to have evolved to acquire a unique armoury that allows it to efficiently infect vulnerable children and adults in some African regions. The results highlight the power of in-depth genome sequence analysis to challenge basic medical assumptions and distinguish closely related pathogens.
“This is a new form of pathogen.”
Dr Robert Kingsley from the Sanger Institute and lead author on the paper
The team studied approximately 50 samples of the bacterial DNA Extracted from blood samples of African patients with severe symptoms of infection and also suffering HIV, malaria, malnutrition or anaemia. They used these samples to produce a high-quality reference genome sequence. Based on this sequence, the team were able to look in fine detail at the genetic differences between ST313 and strains associated with milder disease symptoms across the globe.
“This work was entirely dependent on close collaboration that brings important samples collected over years together with genomic technology that can pick apart the important changes. This work is a great example of such cooperation: now we must build the capacity to expand this kind of research in affected countries.
Professor Rob Heyderman, Director of the Malawi-Liverpool-Wellcome Trust, Clinical Research Programme
“When we started looking in detail at our newly completed reference genome sequence, we saw the genetic signatures that suggested it may be adapting to humans. For example, this deadly strain has lost around one in 50 of the genes found in the ‘typical’ S. Typhimurium – a classic sign that it may be becoming more closely adapted to one host, in this case, humans.
“We also found similar patterns of genome degradation in ST313 compared S. Typhi – a bacterium which is known to be well adapted to its human host.”
Dr Robert Kingsley, Sanger Institute
Six out of 10 of the regions that showed degradation in the invasive ST313 are also degraded in S. Typhi, suggesting that the genomes have converged in their ability to thrive in the human host. This theory is bolstered by the finding that eroded areas of the genome tend to play important roles in the intimate interaction with cells of the human host.
The team’s findings suggest that ST313 may be spreading by a new method, not seen before in S. Typhimurium. This pathogen normally circulates among animals and is introduced to humans through food poisoning. It spends much of its time in the animal hosts. However, ST313 may be passing predominantly from person to person and so can adapt more rapidly to its human hosts: it doesn’t spend time acquiring mutations to help it thrive in the animal host, but on the contrary may be loosing them. This is likely to have helped seal its success and helped it to become the dominant strain among humans.
Multi-drug resistant ST313 has swept through humans in remarkable fashion: in an 18-month period beginning in 2002, it came to represent 95 per cent of S. Typhimurium isolates identified in Africa. However, antibiotic-sensitive versions of the same strain may have been evolving in regions of Africa for many decades.
“This new strain of S. Typhimurium has rapidly gained resistance to many of the commonly used antibiotics in the field. Our findings show that ST313 has acquired a block of genes that make it resistant to the common antibiotics. The genes jumped into ST313 on a mobile genetic element called a transposon, bringing with it additional genes that make the strain more deadly.
“Even when treated using drugs against which the bacterium has not gained resistance, the mortality rate remains staggeringly high, at 25 per cent.”
Dr Chisomo Msefula from the Malawi-Liverpool-Wellcome Trust Clinical Research Programme
The team hope that the new sequence will open the door for future studies of disease important to populations in Africa.
“There are more than 2500 different strains of Salmonella. The emergence and rise to dominance of ST313 in Africa is associated with uniquely susceptible host populations: we must be on our guard against the emergence of new pathogens in a rapidly changing world. This isn’t simply a story about HIV infection: There is little evidence that this type of disease is a problem in other areas of the world where HIV and malaria infection rates are high Such as southeast Asia.
“If we can understand what’s special about the types of Typhimurium that emerge and susceptible populations, we might be able to predict in future where new pathogens will emerge. We may also be able to design vaccines against those pathogens.”
Professor Gordon Dougan from the Sanger Institute and senior author on the paper
Two ST313 isolates in available databases come from outside Africa – one from India and one from the UK. Strikingly, both were from severe invasive disease. Invasive cases are very, very rare outside certain regions of Africa. The researchers don’t know whether the additional cases were from travellers to Africa or know the immune status of the patients.
Tracking the transmission pathways and the emergence of new strains can most effectively be done using new sequencing technologies to spot the tiny differences – single letter changes – in the genetic code. The completion of this new high-quality S. Typhimurium reference genome for the emergent ST313 strain opens the door for such investigations in the future.
More information
Funding
This work was supported by The Wellcome Trust and the Scientific Foundation of Ireland.
Participating Centres
- The Wellcome Trust Sanger Institute, Hinxton, Cambridge, CB10 1SA, United Kingdom
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, University of Malawi College of Medicine, Blantyre, Malawi
- Centre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya
- Department of Molecular Biology, Max-Planck Institute for Infection Biology, Berlin, Germany
- Kenya Medical Research Institute-Wellcome Trust Collaborative Project, Kilifi, Kenya
- Environmental Research Institute and Department of Microbiology, University College Cork, Cork, Ireland
- Department of Bacteriology, National University of Ireland, Galway, Ireland
- Medical Research Council Centre for Immune Regulation, Institute of Biomedical Research, The Medical School, University of Birmingham, Edgbaston, Birmingham, B15 2TT, United Kingdom
Publications:
Selected websites
The Malawi-Liverpool-Wellcome Trust Programme
The Malawi-Liverpool-Wellcome Trust Programme is a leading laboratory-based health research institution led by Malawian and international Scientists in partnership with the University of Malawi College of Medicine. MLW conducts internationally competitive research aimed at improving the health of people in Malawi and elsewhere in the Region. MLW hosts a comprehensive programme of professional development for the research leaders of the future.
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.
