Nanopore sequencing could be the future of rapid diagnostics

Nanopore sequencing is a new technology that could be a more cost-effective, efficient approach to rapidly and accurately diagnose poultry respiratory diseases.

Chepko Danil Vitalevich | BigStockPhoto.com
Chepko Danil Vitalevich | BigStockPhoto.com

Nanopore sequencing is a new technology that could be a more cost-effective, efficient approach to rapidly and accurately diagnose poultry respiratory diseases.

“Nanopore sequencing is an exciting technology and it will continue to improve over the next few years, making it a viable contender for a new phase in rapid diagnostics,” explained Naola Ferguson-Noel, DCM, MAM, PhD, an associate professor at the Poultry Diagnostic & Research Center at the University of Georgia.

“Because of its small scale and potential for cost effective and very rapid sequencing, nanopore sequencing brings us significantly closer to modernizing our poultry diagnostic methods.”

Nanopore sequencing enables real-time analysis of long DNA or RNA fragments. The technology monitors changes to an electrical current as nucleic acids pass through a protein nanopore. (A protein nanopore measures less than 20 nm in diameter. For comparison, a sheet of paper is 100,000 nm thick.)

Challenges associated with diagnosis

“Poultry respiratory diseases are often complicated and multifactorial, resulting in redundant, expensive testing and extended turnaround times for a conclusive diagnosis,” Ferguson-Noel said. “Next generation sequencing techniques may be able to identify multiple respiratory pathogens quickly from a single sample, and also differentiate between vaccine and field strains as well as subtype when necessary.”

Next generation sequencing techniques, such as nanopore sequencing, are currently used in research labs but will hopefully soon be available for use in routine poultry diagnostics.

Simpler bioinformatic workflows

Ferguson-Noel recently led a research project, funded by the U.S. Poultry and Egg Association, that studied nanopore sequencing. The project compared nanopore sequencing with a broad sequencing technique that required an amplification step prior to nanopore sequencing.

“One of the biggest stumbling blocks we found in being able to transfer next generation sequencing technology to diagnostic labs is the bioinformatic analysis. Our goal was to create bioinformatic workflows that do not require advanced computer science knowledge as well as access to excessive computational power,” she said.

“If you can take DNA or RNA directly from a tracheal swab, sequence everything in that sample (broad sequencing), and reproducibly ensure sensitivity and specificity of testing in this manner, it would omit the need for an amplification step and shorten turnaround time to results.”

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