Science Update

It is now 9 months since the BUG project started and we are making good progress in several areas. Our major goal is to develop better diagnostics for detecting anthelmintic resistance in the field, but in order to identify the important genetic markers, we first need to generate the genomic resources. Since starting the project, considerable progress has been made by James Cotton and the team at the Wellcome Trust Sanger Institute (WTSI) in finishing the genome of Haemonchus contortus. This has involved intensive manual curation of the Illumina draft sequences and the use of PacBio long sequence reads to fill in gaps and join scaffolds. Optical mapping technology, which allows the construction of genome-wide restriction maps from strands of fluorescently labelled DNA, has also been used to guide long range assembly. Progress has been excellent and the aim of completing all six chromosomes and providing a reference quality genome is well in sight. Work is also underway on the sequencing and assembly of the draft Teladorsagia circumcincta genome. DNA samples for Illumina sequencing, PacBio and optical mapping have been prepared in Glasgow and sent to WTSI, where assembly of the genome has begun, guided by the most successful approaches for H. contortus.

Meanwhile, two genetic crosses between drug sensitive and drug resistant H. contortus isolates have been generated at the University of Edinburgh and Moredun Research Institute by Neil Sargison and Dave Bartley. The aim of this part of the project is to aid genome assembly and to identify regions of the genome involved in drug resistance. Preliminary analysis of the first (F1) generation is already yielding novel findings with respect to benzimidazole resistance and plans to undertake drug selection on the F3 generation of the crosses are in place. In Glasgow, we have been producing DNA libraries from individual F1 larvae for whole genome sequencing and the generation of a genetic linkage map. We are also optimizing a technique to sample large numbers of markers throughout the genome (Rad-Seq) for individual L3 larvae, which will be used to compare parasite populations harvested pre- and post- anthelmintic treatment on UK farms.

In Bristol, Eric Morgan and the team have been busy surveying farms for H. contortus infections with the aim of identifying appropriate premises for sampling this coming season. In Edinburgh, the sampling of local flocks for T. circumcinta has identified a number of farms for continuing surveillance and has provided field populations of L3 larvae to begin analysis. Meanwhile Cath Milne from SRUC held a well-attended focus group in the Scottish Borders to ascertain the opinion of farmers on worm control, a very important aspect of our project.

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Running to stand still

SagradaWhat is a picture of Barcelona’s La Sagrada Familia doing on the BUG blog? I recently joined a BBSRC funded workshop in Barcelona organised by Silvie Huijben (Institute for Global Health, Barcelona) and Paul Neve (Rothamsted Research Institute). The workshop was entitled ‘Running to stand still: evolution and management of drug and pesticide resistance in healthcare and agriculture’ and brought together a range of clinical, experimental and theoretical scientists all working on drug resistance in diverse systems, including malaria, bacteria, fungi, crop pests, mosquitoes, herbicides, cancer and, of course, helminths. Our aim was to discuss common principles and approaches to tackling drug resistance from a more evolutionary standpoint. It was a fantastic opportunity to explore the topic in a relaxed environment.

The meeting began with a number of overview talks that summarized the state of play in the different disciplines. The similarity in the questions we all ask was striking; however, as the meeting progressed it was clear that while the questions may be similar, the approaches that are possible are different. Some fields are much more advanced than others, but in many cases the data do not exist to establish directly whether a high dose or low dose of drug gives the best outcome for the patient/animal/crop or field. Similarly, while combination therapies are the ‘norm’ in some areas, for the helminths, the small range of drug classes available for use imposes limitations on this approach. For an experimental scientist, it was very interesting to listen to talks on theoretical approaches to drug resistance and it reinforced the importance of having mathematical modellers involved in our more experimental projects.

For BUG, it was a useful experience to interact with such a diverse range of scientists and to think about the problem of anthelmintic resistance from a more evolutionary standpoint. Major questions remain like how to apply evolutionary principles to new drug design, what can we learn from scenarios where resistance has not evolved despite the use of a specific drug over an extended period of time? There are some good examples of this, e.g. Plasmodium vivax malaria and chloroquine in India, Candida albicans and amphotericin B. Other important topics discussed were the exploitation of fitness costs and the design of treatments using ‘evolutionary traps’. Several speakers highlighted the ecological impact of resistance; e.g. in anti-microbial resistance what is the effect on the microbiome of treatment, and, on a larger scale, the effect on the ecosystem? This is an important area in anthelmintic research where livestock frequently harbour multiple species with varying resistance profiles to any one drug. Application of novel approaches such as the ‘Nemabiome’ based on analysis of ITS-2 sequences or multiplexing PCR methods will help inform the outcome of differential responsiveness to drugs. Another area of interest that is often overlooked in discussions of drug resistance is the impact of the immune response; an effective immune response is often critical for removal of an infectious agent, how is that integrated with drug treatment and how does resistance impact the ability to clear infection? Is there a role for suboptimal vaccines in combination with drug therapy?

The meeting reinforced my view that while we know a lot about some aspects of anthelmintic resistance, there is still much to be learned and that there are overlaps with other fields that could be better exploited. Meetings such as this are incredibly valuable for breaking down the taxonomic partitioning that inevitably happen, where we each know a lot about our own areas, but not so much about other areas. On this basis, we are organising a ‘Resistance Day’ here in Glasgow, to bring together researchers working on drug resistance in helminths, protozoa, bacteria, fungi, viruses, and arthropods.

I will shortly leave for India where I will be attending another drug resistance discussion meeting in Bangalore and then off to Lucknow for a meeting at the Central Drug Research Institute on Current Trends in Drug Discovery and Research. Look out for more information!

New faces in the BUG Consortium

In August, we held the second BUG meeting in Liverpool to coincide with the World Association for the Advancement of Veterinary Parasitology (WAAVP) Conference 2015. In addition to being a very useful meeting scientifically, it was also a great opportunity to meet some of the newest members of the BUG Consortium in person. From Bristol, we met postdoctoral researcher Hannah Rose and technician Katie Bull, who are working with Eric Morgan in modelling climate-driven management of parasites and parasitic disease, and undertaking sampling of UK farm populations of Haemonchus contortus. Hannah gave us a very nice introduction to her modelling work and an update on the collection of field samples. It was also a chance to introduce Umer Chaudhry to the rest of the team, a postdoctoral researcher working with Neil Sargison at the Roslin Institute. Since joining us from Calgary, Umer has been applying molecular parasitology techniques to study two H. contortus genetic crosses and helping run anthelmintic resistance bioassays with Dave Bartley and Alison Morrison at the Moredun Research Institute (MRI). We were also given a fantastic insight into the technologies and expertise that underpin the manual curation of the H. contortus genome by Alan Tracey, a senior computer biologist in Matt Berriman’s group, who is working with James Cotton and the team at the Wellcome Trust Sanger Institute (WTSI).

In November, we spent an enjoyable day in Edinburgh at both the Roslin Institute and the MRI, discussing the work plans for the coming season and visiting the R(D)SVS sheep flock. Here we were joined by James and the most recent postdoctoral researcher to start on the project, Stephen Doyle. Steve is working with Matt and James at the WTSI and brings a wealth of helminth population genetics and genomics expertise from his previous post in Melbourne. So far, Steve has been honing his bioinformatics skills on the assembly of the Teladorsagia circumcinta genome and in the analysis of H. contortus whole genome amplified larval samples. This was also the first opportunity to introduce our new Glasgow-based PhD student Jennifer McIntyre to some of the members of BUG she’ll be working with most closely over the next few years. Jenni started her PhD in October 2015 funded by a BBSRC CASE award with KTN and AHDB and has been busy learning the tools of the trade: PCR and pyrosequencing. In the coming season she will begin her fieldwork with Neil, collecting farm samples for her studies on drug resistance in Teladorsagia circumcincta.