Next Generation Sequencing Technology Delivers ‘Whole Picture’

‘We can catch everything’

Over the past 18 months, the Veterinary Diagnostic Laboratory has added two next generation sequencers and an outstanding faculty member—Dr. Leyi Wang—to generate and interpret results from them.

Both machines deliver whole-genome sequencing of bacteria and viruses and can rapidly identify multiple agents or novel pathogens in samples. The technology of genome sequencing has advanced tremendously in the past 20 years, and the costs have plummeted.

“The affordability of this technology will put much more robust diagnostics than were previously possible at the fingertips of veterinarians,” notes Dr. Wang.

Among the uses of genomic data are:

1. Outbreak tracebacks, in which the pathogen’s “family tree” can be mapped against a database of known genomes of a particular bacterium or virus, pinpointing the geographic locations of origin of the reference pathogens;
2. Identification of novel pathogens, i.e., ones that share little or no genomic structure with known pathogens;
3. Monitoring evolution of known pathogens using whole-genome sequencing. The information delivered with test results includes the virulence factor of the pathogen and, for bacteria, the pathogen’s antibiotic resistance profile;
4. Rapid identification of co-infections, when more than one pathogen is present. For example, this technology well fits for investigation of canine infectious respiratory disease complex caused by multiple etiologic agents.

“You can have the whole picture now,” he says. “It’s kind of like a net. We can catch everything inside of the sample. That’s the principle for all of next-generation genome sequencing.”

According to Dr. Wang, swine veterinarians have embraced this technology, given the importance of identifying the exact variant of viral diseases that may impact swine herds.

The technology also brings speed and accuracy to other veterinary practitioners.

“A veterinarian sent us a throat swab of a cat with a respiratory problem and asked us to do virus isolation for feline calicivirus and feline herpesvirus,” says Dr. Wang. “After we performed virus isolation and viewed it with the electron microscope, we were able to identify only calicivirus. But when I sequenced the sample, both calicivirus and herpesvirus were detected.”

As this case illustrates, the next generation sequencers work with much smaller quantities of sample and “catch everything”; with gene sequencing, results can be obtained without waiting for cultures to grow, and there’s no risk of overlooking a co-infection.

Pricing for next generation sequencing through the Veterinary Diagnostic Laboratory varies by target agent:

• Bacterial sequencing, $180;
• Viral sequencing, $275; and
• Metagenomic sequencing, $275.

Every assay includes bioinformatic analysis tailored to the needs of the client.

Specimens to be tested include cultured isolates, tissues, blood, feces, and body fluids.

For more information, contact the Veterinary Diagnostic Laboratory at (217) 333-1620 or vdloffice@vetmed.illinois.edu.