How one resourceful team of scientists coordinated their attack on a chicken bug


Nobody here but us chickens: The broiler industry is by its very nature a hothouse for evolution of drug-resistant strains of parasites. The recent publication of genome sequences for all seven species of eimeria is expected to re-invigorate drug and vaccine development efforts. - Filepic

The lifeblood  of innovation.

Fundamental science is often overlooked, especially when the subject of your research is a parasite that makes chickens sick. Killer diseases like malaria and tuberculosis attract most of the funding, as they are serious threats and should be prioritised. But it is still important to make progress in other areas. Fundamental research is, after all, the lifeblood of the applied sciences – it’s what generates new leads for innovation to keep moving forward.

In 2002, three scientists got together and made it their mission to sequence the genome of Eimeria tenella – a type of Apicomplexan parasite which infects chickens, causing avian coccidiosis, a significant veterinary disease. They ended up with much more, publishing the genomes of seven species of eimeria.

Their labour is an example of how to get less high profile but no less important research done. It took resourcefulness, determination, and a lot of collaboration. One massive endeavour was divided into smaller, achievable goals, and overcame funding difficulties by piggybacking the research on other, better-funded projects. The effort was ad hoc, but showed that science does not have to be a slave to the global research agenda.

Prof Dr Wan Kiew Lian showing off a high-performance computer at the Malaysia Genome Institute which is used for number-crunching, processing the data from DNA sequencers elsewhere in the facility.
Prof Dr Wan Kiew Lian showing off a high-performance computer at the Malaysia Genome Institute which is used for number-crunching, processing the data from DNA sequencers elsewhere in the facility.

The in-betweeners

Avian coccidiosis isn’t much of a killer. A grand summary of the horrors of this disease would be that it causes chickens to bleed into their stools, lose weight and sometimes die. It’s not going to pull any major heartstrings, there are no hordes of dying innocents involved. But it does cost poultry farmers worldwide upwards of US$3bil (RM9.64bil) a year on control and prevention costs.

It’s important – global poultry production has tripled in the past 20 years. The world’s chicken flock consists of roughly 21 billion birds, providing an annual yield of about 1.1 trillion eggs and 90 million tonnes of meat. And demand is growing, tied to a rising middle class in Africa and Asia, with global consumption increasing at a rate of 2.5% a year.

It’s just not that important. It’s an in-betweener.

The threat is not imminent, because we currently use drugs to keep the parasite under control. Owing to the nature of high-intensity poultry farming, the broiler industry is by its very nature a hothouse for evolution of drug-resistant strains.

These drugs won’t last forever, and the question arises: why would anyone invest in developing new drugs if their product might soon end up obsolete?

The industry’s need

This was the situation three scientists were ruminating on one fine day in 2000. They were an Englishman named Martin Shirley, a Malaysian named Wan Kiew Lian, and a Brazilian named Arthur Gruber, who all study the parasites behind avian coccidiosis – eimeria – a single-celled group of organisms closely related to the more famous plasmodium, which causes malaria.

What could solve this inertia? Though drugs are still the most important method of parasite control, vaccines have become increasingly important.

A growing consumer movement opposed to drug-pumped chickens – in Europe especially – has also served to rally interest around vaccines; but the technologies for the development of current vaccines are already more than a decade old.

Nevertheless, molecular biology has in subsequent years progressed by leaps and bounds. The tools available to gain a better understanding of parasite biology are astounding, and can be applied to drug and vaccine development.

A major boon to the effort would be having a “blueprint” or genome to work with. A genome represents the complete set of code, or genes, needed to build an organism. It contains information and clues about important biochemical processes. Having access to this data vastly expands man’s biochemical playbook and can provide leads for drug and vaccine development.

Once a new genome is sequenced, scientists need only cross-reference the new code against matching sequences in a database. This gives us a way to identify sequences that code for actual genes, and even predict what those genes might do.

Guerilla science

“Let’s do it,” was how the conversation went among Shirley, Wan and Gruber.

As in all passion-infused topics, it’s easy to get carried away. The three parted with firm ambitions to form an “Eimeria Genome Consortium”. The goal was to eventually compile an annotated whole genome sequence for Eimeria tenella – the most pathogenic of the seven species known to infect poultry. They would split the work, finding their own funding from their respective countries.

Shirley, one of the world’s foremost experts on avian coccidiosis (who was at the time a professor at the Britain-based Institute for Animal Health), got the biggest task: to sequence all 55 million base pairs of DNA contained in all 14 chromosomes that make up the parasite’s genome.

Dr Wan, a professor from the School of Biosciences and Biotechnology at Universiti Kebangsaan Malaysia (UKM), would conduct a more detailed analysis of specific chromosomes.

And Gruber, an associate professor based at the University of Sao Paolo in Brazil, would find out which bits of the genome were important by looking at gene expression at various stages of the parasite’s life cycle.

Cross-border collaboration

For Wan, the challenge was funding, but he was in luck – the Malaysia Genome Institute had just acquired some new sequencing machines. These US-developed sequencers usually require some readjustments related to operating them in new environments.

Wan was made sequence coordinator, his first task being to devise a set of optimal protocols for operating the machine. Needing samples to run through the machine, Wan used this golden opportunity to sequence Eimeria tenella, chromosomes 1 and 2.

Elsewhere, work on the whole genome was slow going.

Shirley was operating off a grant from Britain’s Biotechnology and Biological Sciences Research Council, and collaborating with people at the world-famous Wellcome Trust Sanger Institute, just outside of Cambridge. They had a lot of firepower – maybe 100 state-of-the-art sequencing machines – but a lot of work besides eimeria goes on at Sanger, and the parasite was often left on the back burner.

Nervous presentation

Wan’s was the first group to get some results. Their findings revealed something extremely unusual: a unique banding pattern in the DNA. No one had seen anything like it in any organism before.

“Repeats in the (genetic) code are fairly common, but usually scattered throughout the entire genome. In Eimeria tenella, however, we found a distinct banded pattern (of regions with frequent repeats and regions free of repeats),” Wan says.

Wan and his Masters students working on the project travelled to England to brief Shirley and the team at Sanger. They were greeted with caution, and a flurry of questions. Maybe the assembly was not done right?

“It was daunting,” Wan says. “For these guys, sequencing work is their bread and butter. They had seen so many genomes, and this was our first.”

Wan handed over their data so it could be checked. Caution turned into surprise and excitement. The results sparked curiosity, and generated enough buzz to get the main genome sequencing work back on track.

Results!

A string of papers followed their first briefing in 2007. More institutions and scientists across the globe got involved, making the eimeria genome quest a truly collaborative effort. In 2014, the final paper was published – the genome for all seven eimeria species – in the international peer-reviewed journal Genome Research.

A decade ago, Wan thought he would make a career out of this work, finishing the sequencing on the seventh eimeria species in time for retirement. But science bulldozed its way ahead of schedule.

Sitting in an office at the Malaysia Genome Institute in Bangi, Selangor, Wan looks relieved even though the work is not over. At 47, he has at least a decade before retirement. Now that there are seven eimeria genomes to work with, he’s definitely got enough research material and is applying for funds to work on a vaccine that caters to the Malaysian poultry industry specifically.

Wan learnt two things from the experience: first, it can take years for seeds planted to bear fruit; and second, you don’t work alone – you collaborate, especially if you are aiming to get published in a good journal.

“Instead of doing it yourself, it makes sense to leverage off each other. That way you gain new skills, learn and produce better quality work. Some of my Masters students ended up being supervised by world-class professors from Cambridge in the course of these projects.”

Science is, fundamentally, a concerted human effort to understand the world a little better, day by day. That seven little chicken parasites got their genomes sequenced is a testament to the varied and resourceful ways the most committed of scientists go about this.

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