Black fever beats drugs by adding just two DNA bases to its genome
In eLifetoday (22 March), Wellcome Trust Sanger Institute scientists show how the parasite responsible for the neglected tropical disease Black Fever (visceral leishmaniasis) can become immune to drug treatment. Studying the whole genomes of more than 200 samples of Leishmania donovani revealed that the addition of just two bases of DNA to a gene known as LdAQP1 stops the parasite from absorbing antimonial drugs.
While antimonials are no longer the first-line treatment for the disease, the discovery does show that whole-genome sequencing of L. donovani parasites could be used to study and track the emergence of resistance to frontline drugs – alerting health workers to potential hot spots of resistance.
Black Fever is the second most deadly parasitic disease after malaria, affecting nearly 300,000 people every year and killing up to 50,000. The parasite is mainly found in the Indian subcontinent, where up to 80 per cent of the disease occurs. To best understand how the parasite evolves and track the spread of drug resistance, researchers need a way to survey and monitor the parasite’s population structure. Unfortunately standard techniques to do this have proved fruitless because the strains of L. donovani parasite are so genetically similar.
“If you want to control visceral leishmaniasis, you need to understand what is going on at the geographic epicentre of the disease, and you need to be able to see changes at the level of individual DNA bases in the parasites’ genomes. Until now studies have been limited to looking at small regions of the parasite’s DNA or at what happens in the laboratory. To truly understand what is happening in the real world, we analysed the whole genomes of more than 200 samples from parasites captured in India, Nepal and Bangladesh over almost a decade.”
Dr James Cotton Senior author of the study from the Sanger Institute
Exploring the genetic landscape of L. donovani at such depth and breadth yielded new insights into the parasites’ ability to develop drug resistance, and its evolutionary history. In particular, the researchers found that the insertion of just two bases of DNA into the genome of approximately 35,000,000 bases helped the parasite to overcome antimonial drugs.
“We discovered that many of the parasites that were resistant to antimonial drug treatment had just two additional DNA bases in the gene LdAQP1, which produces an aquaglyceroporin protein. This insertion produces a scrambled version of this protein that can no longer move small molecules – including antimonials – across its cell membrane. These strains of L. donovani are likely to be resistant because they cannot take in the drugs.”
Dr Tim Downing One of the paper’s first authors from the Sanger Institute and National University of Ireland Galway
Black Fever – “kala azar” in Hindi – is second largest life-threatening parasitic disease after malaria. Spread through the bites of sandflies, the parasites enter the internal organs such as the liver, spleen and bone marrow, making them inflamed and swollen. The infection produces fever, weight loss, fatigue and anaemia and is fatal if left untreated.
“This study perfectly illustrates the relevance of collaboration between large sequencing centres like the Sanger Institute and clinicians and scientists involved in the battle against the most neglected diseases. Thanks to the acquired knowledge, it will be our turn now to beat Black Fever 2-0 by providing local health authorities with performance monitoring tools, and guiding research and development for new and more efficient anti-parasitic drugs.”
Professor Jean-Claude Dujardin of the Institute of Tropical Medicine Antwerp and the University of Antwerp, senior author of the study and leader of the consortium that ran the study
More information
Analysis of the genomes by the researchers revealed that the parasites responsible for the current epidemic first appeared in the Indian subcontinent in the 19th Century, matching the first historical records of Black Fever epidemics.
In addition, the current genetic diversity of the parasite traces back to the 1960s, around the time that the widespread use of DDT to eradicate malaria in India came to an end.
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Dr James Cotton
Dr Cotton’s research at the Sanger Institute is on evolutionary genomics of parasites, and particularly on parasites that cause neglected tropical diseases. This work covers a wide range of organisms from parasitic protozoa such as Leishmania to complex multicellular helminths, but they are united by a strong emphasis on either comparative or population genomic questions.
Berriman Group
The Berriman Group uses large-scale genome and transcriptome sequencing along with phenotyping to understand the biology of important parasites. We start with the production and analysis of high-quality reference genomes. The malaria parasite P. falciparum is the gold standard for this – we have curated its genome for more than a decade – but the approach is being extended to other more neglected parasites including schistosomes and whipworms.
L. donovani genome sequence research
Leishmania donovani is a protozoan parasite belonging to the Trypanosomatid group. As a major human tropical disease causing debilitating visceral and dermal leishmaniasis, examining genomic variation in strains infecting patients can illuminate the molecular mechanisms of its pathogenicity and resistance to drugs.
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