Current status of NGS in veterinary diagnostics and epidemiology

Question

[biotech]

I recently received an interesting offer to work as a microbiologist in an infectious disease diagnostics lab. Although I like diagnostics and outbreak management, I dream about using NGS combined with traditional techniques such as qPCR ELISA and culture/isolation.

I would like to know if there is any cost-effective protocol to do this, including reagents, speed, bioinformatics pipelines and databases.

The idea is to use NGS in veterinary diagnostics, to monitor pathogens in swine production.

Thanks

Answer 1

[Brian Bushnell]

Buying and operating MiSeq or Ion Proton should be really cheap compared to other widely available equipment like MRI machines, not to mention much less annoying to patients. And the computational resources for analysis would be a tiny fraction of the the cost of the sequencer; plus the software is generally free. I can't imagine that cost is a real issue here - it's more of a momentum and regulation thing. At least in the US, the way medical methods and devices are regulated make it impossible for a hospital to just buy a sequencer and start using it clinically on patients in an efficient manner.

[biotech]

Would be easier for veterinary diagnostics, more specifically swine production?

[Brian Bushnell]

I'm not at all an expert in this area, but for veterinary use in farm animals, it should be pretty straightforward - there are none of the concerns about data privacy, insurance reimbursement, proof of efficacy and decade-long clinical trials, etc.