Metagenomics could fill the gaps in disease diagnostics

A Professor with the Western College of Veterinary Medicine says the use of metagenomics in the diagnosis of veterinary diseases offers the potential to fill gaps that exist in currently used diagnostic approaches.

23 July 2019, at 10:15am

Over the past 10 to 15 years we've seen a huge expansion in the application of molecular diagnostic techniques. Speaking to Farmscape, Dr Janet Hill, a Professor in the Department of Veterinary Microbiology with the University of Saskatchewan's Western College of Veterinary Medicine, says PCR-based assays have enabled the identification of pathogens by detecting their DNA but these tests are very targeted and can only detect what is specifically being tested for.

"Many people may be familiar with the idea of genomics or the study of the genome," explains Dr Hill, "We've had the human genome project and numerous animal genome projects that have resulted in determining the entire sequence of an organism's genome.

"Metagenomics takes us to another level which is, instead of studying the genome of one individual organism in isolation, we can instead study all of the genomes in a community of organisms.

"This is really important because a lot of the clinical specimens that we deal with, if you think about diagnostic specimens like a nasal swab or a faecal specimen, they actually contain not only some DNA from the host animal but also DNA from potentially thousands of microbes, so viruses and bacteria and even fungi and yeast as well.

"Metagenomics allows us to take that specimen, purify all of the DNA out of it and basically sequence all of it so what we get out of it is information about all of the different organisms that are present in that sample simultaneously.

Dr Hill says where metagenomics can really help is in those unusual circumstances where an explanation for an infectious disease can not be found using traditional methods. She says there have been examples of where new pathogens have been discovered through the application of metagenomic sequencing, such as the discovery of Porcine Circovirus 3 in 2015.