A study from researchers at the University of Georgia, published in Antimicrobial Agents and Chemotherapy, showed that 60 percent of cattle fecal samples contained multiple strains of salmonella that traditional testing methods missed. It also found that about one out of every 10 samples tested positive for Salmonella Reading, a drug-resistant serotype of Salmonella. 

The study highlights the importance of antimicrobial resistance (AMR) surveillance in diverse bacteria populations.

Technology developed by UGA researcher Nikki Shariat, an assistant professor of population health in the College of Veterinary Medicine in 2015, CRISPR-SeroSeq, enables researchers to analyze all the types of salmonella present in a given sample. Previously used methods only examined one or two colonies of bacteria, which left the potential to miss strains of salmonella.

Shariat’s technology identifies molecular signatures in Salmonella’s DNA in a specialized part called the CRISPR regions. This technology also helps researchers identify which strains of the bacteria are most abundant.

Salmonella Reading can cause severe illness in people. It has been the cause of several foodborne illness outbreaks in the past few years, including a 2019 outbreak in the U.S. linked to live turkeys and raw turkey products that resulted in 358 illnesses, 133 hospitalizations, and one death.

According to the study, Salmonella enterica can exist in food animals as multiserovar (multiple groups of closely related microorganism) populations, and different serovars can harbor diverse AMR profiles. Conventional Salmonella isolation assesses AMR only in the most abundant members of a multiserovar population, which typically reflects their relative abundance in the initial sample.

AMR in underlying serovars is an undetected reservoir that can readily be expanded upon antimicrobial use, according to the report. 

In the study, CRISPR-SeroSeq profiling demonstrated that 60 percent of cattle fecal samples harbored multiple serovars, including low levels of Salmonella Reading in 11 percent of samples, which were not found by culture-based Salmonella isolation testing.

The study’s findings have implications for treating sick food animals and the people who get infected by eating contaminated meat.

“This suggests that traditional tests have underestimated the amount of antibiotic-resistant bacteria in the past,” said Shariat. “We need to know the antimicrobial resistance profiles of the bacteria that are present in animals. That knowledge could make us change our choice of the type of antibiotic we use to treat ill animals. It can also help us selec the best antibiotic for people who get sick from eating contaminated meat.”