Staff highlights: Whole genome sequencing (WGS) at AHL
Animal Health Laboratory, University of Guelph, Guelph, ON
AHL Newsletter 2021;25(2):6.
Whole genome sequencing (WGS), also called next generation sequencing (NGS), is a very powerful technology that provides a large amount of sequencing data cost-effectively and in a relatively short period of time. It is also known as massively parallel sequencing because sequencing of multiple samples can be done at the same time.
There are numerous clinical applications of WGS. WGS can be used for identification and characterization of novel pathogens (i.e., bacteria, viruses, parasites) in clinical samples, metagenomics, strain typing, susceptibility prediction, and virulence factor determination, among other applications.
In 2019, AHL became the only Canadian core lab for the Federal Drug Administration (FDA) Veterinary Laboratory Investigation and Response Network (Vet-LIRN) that performs whole genome sequencing of Escherichia coli, Staphylococcus pseudintermedius, and Salmonella spp. and deposits sequence data at the National Center for Biotechnology Information (NCBI). To date, more than 300 bacterial isolates have been sequenced in support of the Vet-LIRN program which monitors antimicrobial resistance trends in bacteria isolated predominantly from dogs. This trend will continue in upcoming years with an estimated 300 bacterial isolates being sequenced annually.
In addition to the Vet-LIRN project, AHL has been doing WGS of other clinical bacterial isolates (i.e., pure culture) to gather additional information. For the Ontario Animal Health Network (OAHN) swine network, AHL performed WGS of Erysipelothrix rhusiopathiae isolates from Ontario. Based on WGS data, we were able to determine antimicrobial resistance determinants and virulence factors. Moreover, this work showed that there are 8 different multilocus sequence types (MLST) present among Ontario isolates. Only one belonged to the previously described sequence type (ST), whereas seven STs were not previously known (1).
To establish the origin of same Salmonella serotypes, AHL did WGS of 30 Salmonella isolates as well. Based on whole genome MLST data, it was possible to determine which isolates originated from the same source and which did not, a valuable tool in tracing outbreaks. AHL used WGS to detect virulence factors and to determine the O and H types of E. coli isolated from poultry. WGS was also instrumental in confirming that Streptococcus equi subsp. zooepidemicus isolated from a recent swine case belonged to the more virulent ST194 strain known to cause disease outbreaks and mortalities in swine operations in Manitoba and the USA (2).
Additional characterization of isolates may also have significant clinical application when it comes to vaccine production, as was shown in one of our cases. When vaccine isolates were compared to clinical isolates it was shown that they belong to different MLST types, explaining the clinical outbreaks of disease despite routine vaccination.
These are just a few examples of the utility of WGS in clinical applications. At present, AHL offers WGS of bacterial isolates to obtain relatedness and virulence information, as specified above. We are also working to expand WGS to include the detection of bacterial and viral pathogens directly from clinical samples. AHL
1. Slavić D, et al. Investigation of the increase of swine erysipelas in Ontario (OAHN 009115). AHL Newsletter 2020:24(3):8
2. DeLay J, et al. Strepcococcus equi subsp. zooepidemicus septicemia: First confirmed case in Ontario swine. AHL Newsletter 2021; 25(1):11.