The poultry industry is under intense scrutiny right now when it comes to Salmonella control, but a new next generation sequencing technique called CRISPR-SeroSeq has developed a better way to stop the pathogen.

Overall, cases of Salmonella contamination in chicken decreased from 9% in 2016 to 6.57% in 2020, however, the number of people infected with Salmonella in the U.S. remained constant over the four-year period.

“Once we have Salmonella within our complex, it’s very easy for it to spread throughout our complex,” Nikki Shariat, Ph.D., assistant professor in the Department of Population Health, Poultry Diagnostic Research Center, University of Georgia College of Veterinary Medicine, said at the 2022 Poultry Tech Summit. 

“It will pass through the hatchery and from the hatchery, it can be disseminated out to multiple broiler farms. And from those broiler farms, we know that we can then find that Salmonella in the processing facility.”

During her research, Shariat discovered that the Salmonella serotypes commonly seen preharvest did not necessarily match with the serotypes seen after processing.

Specifically, S. Kentucky was found a lot by producers, whereas S. Infantis was the prevalent serotype at the processing plant.

Enter CRISPR-SeroSeq

These facts made Shariat realize that perhaps current microbiological techniques were only identifying the most common serotypes.


CRISPRs are native genomic regions naturally found within Salmonella. Even better, the CRISPR regions match very well in helping to identify Salmonella serotypes. CRISPR-SeroSeq, the next-generation sequencing technique developed in Shariat’s lab, can identify that a sample contains 95% S. Kentucky and 5% S. Infantis, for example.

In addition, research with CRISPR-SeroSeq identified that most samples test positive for two or more types of serotypes.

“This indicates that we need to think differently about how we’re identifying and controlling Salmonella,” Shariat said.

Deep serotyping techniques could help reduce Salmonella in several ways. It could improve the screening and selection for autogenous vaccines, ensure that the industry is collecting samples in the right way and at the correct time, more accurately target serotypes and anticipate which serotypes will become dominant next.

“These new technologies are improving what we know every day about Salmonella and about the ecology of this important pathogen in poultry," explained Shariat.

Attend the 2023 Poultry Tech Summit

The Poultry Tech Summit is the only event of its kind that connects researchers and entrepreneurs with poultry sector technology experts, financiers, venture capitalists and producers looking for new projects and investments to fund. Since its 2018 inception, this unique conference has facilitated and fast-tracked many pioneering ideas into adoption for the benefit of the poultry supply chain.

Details on the 2023 Poultry Tech Summit will be released in Spring 2023.