A very disruptive worm gets its comeuppance – we know who you are Spirometra erinaceieuropaei and your genome tells us what makes you tick.
You may have heard of the unfortunate Brit who discovered he had a tapeworm living in his brain. It took over four years for scientists to uncover what was wrong, and this took some exceptional detective work, all the while the worm was squirming across the man’s brain. The tapeworm, called a sparganum, has never before been seen in the UK. It is more common in South East Asia, where people can get infected either by eating raw frogs or reptiles, or using a balm made from raw frog meat directly on their eyes.
Here are two perspectives on the unusual discovery, the pathologist who first discovered the worm, and the scientist who helped to sequence the worm’s genome, which revealed a lot about how to treat this pesky invader, and some insights into its private life.
The Pathology Perspective - Dr. Andrew Dean
In 2008 the pathology department received the first sample of brain tissue from the neurosurgeon with the plaintive note “rather uncertain what this is – slowly enlarging over 6 months…? Tumour? TB? ”. We took a look at the small piece of brain down the microscope: it did not look normal. It was thankfully not a tumour but there were instead inflammatory signs. The brain was clearly responding to something, possibly some kind of infection. Frustratingly, tests for a wide range of micro-organisms including tuberculosis, bacteria and even fungi all proved negative.
A microscopic surprise…
Four years later the brain scans were still giving out unusual signals, and clinicians were still stumped. Even more perplexing than the negative tests, the anomaly appeared to have been making its way across the brain, even passing from one side to the other. Because of the patient’s ongoing symptoms it was decided that another tiny piece of brain should be removed for examination. And this time, something exceptional was seen down the microscope. In the brain tissue, clearly visible at around 1 cm long, was part of a worm! Apart from the fact that it was dead, the bit of worm was in good condition – obviously it had been alive until very recently. But what exactly was this worm?
In these situations, our first thought is to get an opinion from colleagues working in tropical-disease centres who are trained to recognize bizarre infections. Our second thought, more speculative but with prospect of a big scientific pay-off, was to seek a collaborator willing and able to analyse the organism’s DNA for a specific molecular fingerprint.
This first-thought rapidly paid off: digital images and copies of the microscope slides proved sufficient to recognize the worm as a “sparganum”, the larval-form of a type of tape-worm called Spirometra - never before seen in the UK. Physicians and surgeons could now dial up the appropriate treatment.
But what about the DNA angle? Who would be prepared to take it on? Would it confirm the diagnosis, or suggest a different species that looked very much the same? Would it hold the key to how the worm got there? Would there even be enough DNA to analyse?
We took to the internet and found a research-group led by Matt Berriman, who actively research the genomics of neglected parasitic diseases and were based only nine miles away, at the Wellcome Trust Sanger Institute. No, they hadn’t sequenced a sparganum (nobody ever had). Yes, they were happy to run with it if we could send some worm-DNA from the brain specimen. We selected the region of the microscope slide containing worm alone, scraped it off the glass, extracted the DNA, and sent it along…
The Parasite Genomes Perspective - Dr. Hayley Bennett
When Andrew Dean contacted us with news of this worm sample we were both surprised and excited from a scientific point-of-view. Our group had previously produced some very high quality genomes from the major disease-causing tapeworms worldwide, but had not sequenced any from this distantly related group of worms before. The collaboration proved fruitful for all of the team involved.
Our first priority was to sequence the DNA to confirm that this was indeed the species we expected. There is a more dangerous form of this worm that looks very similar and by examining the mitochondrial gene cox1: the “Barcode of life”, we were able to rule this possibility out and feed the good news back to the clinicians treating the patient. We also sequenced two more mitochondrial genes to try and determine the origin of the worm. We found that the worm contained sequences that were consistent with an origin of infection in China, but because of the current scarcity of molecular data collected from this parasite worldwide, we cannot say this for certain.
With the remaining tiny sample, only 40 billionths of a gram, we asked ourselves – could we also sequence the entire genome of Spirometra erinaceieuropaei using existing technology? We would typically begin a genome project by taking a hundred times that amount of DNA, prepared and stored very carefully, often from parasites that have been cultivated in the lab. Even though the sample had not been stored optimally with genome sequencing in mind, we decided that it would be worth a go. To make a sequencing “library” we took the DNA and chopped it into manageable size chunks, which were then read by the sequencing machine 100 letters at a time. Once this was done we used supercomputers to try and reassemble all of the letters using the overlaps between the pieces – a bit like a giant linear jigsaw puzzle. There were some spare pieces that remain unplaced, or assembled only in small sections, but we had some good chunks to take a look at and analyse.
Surprisingly, we found that the genome was huge for a flatworm, at 1.26 billion letters long, which is roughly a third of the size of the human genome. That’s a lot of information for what essentially looks like a small tube. We found lots of repetitive sequences filling up the gaps between genes and we think this accounts for some of its size.
To find out more about this worm we needed to look in depth at the genes that are present in its genome. First of all we looked at the genes targeted by the drug Albendazole, which is commonly used to treat tapeworm infections. We found that the sequence of genes in this worm indicate it is unlikely to be sensitive to this specific drug – important information for future cases. We also looked at genes that had previously been identified as good potential targets for drugs in other tapeworms, and found that many of them were also present and quite similar in Spirometra erinaceieuropaei. The genome will provide a continuing reference that can be consulted to see if treatments that are developed for the more common tapeworms can be repurposed for these very rare infections.
So what about the biology of the worm? Very little is known about Spirometra erinaceieuropaei, however we do know that it unusually requires at least three different hosts to fully complete its life cycle. To start, the free-swimming form hatches from an egg and infects a crustacean where it begins to develop. When the crustacean is then eaten by another host, such as a frog, the worm becomes a sparganum larva (the predominant form reported in human infections). When this larva is eaten by the final host, such as a cat or dog, it can turn into its adult form in the intestine and lay eggs. These eggs then end up in the feces, and then a lake to hatch and start the cycle again.
So how does this tapeworm differ from other species in terms of genes? How does the worm exist in the body tissue without being attacked by the immune system? Tapeworm larvae that go to mammalian body tissue usually encase themselves in their own protective wall, but this worm does not appear to do that.
We looked at what types of genes were particularly abundant in this worm, in comparison to the other tapeworms and found some possible explanations. For example, this worm oozes certain types of enzymes, which digest the building material of cells – possibly either helping the parasite invade its multitude of hosts by digesting tissue, or providing broken down nutrients to the worm. Some of these enzymes may also interfere with the normal immune system pathways. Genes for molecular motors which move around components of the cell were also present in abundance and it seems that these are particularly important to the worm – but we don’t know yet know why. We also found that fatty acid binding proteins found in other tapeworms were also found in Spirometra erinaceieuropaei, and these may allow the worm to scavenge essential nutrients from the host.
The genome provides us with a backbone reference for this worm, but further research could tell us how the worm uses this information at different stages of its complex life. By sequencing the genome of this worm and making comparisons to other tapeworms we can learn more and more about what is an important gene to a tapeworm and hopefully take steps towards effective treatments.