Growing resistance to our go-to antibiotics is one of the biggest threats the world faces. As common bacteria like Streptococcus and Salmonella become resistant to medications, what used to be easily treatable infections can now pose difficult challenges for vets and farmers alike.

New research from the University of Georgia claims that there may be more antimicrobial-resistant Salmonella in our food animals than scientists previously thought.

Using technology she developed, UGA researcher Nikki Shariat and Amy Siceloff, a first-year doctoral student in UGA’s Department of Microbiology, found that traditional culturing methods used to test livestock for problematic bacteria often miss drug-resistant strains of Salmonella. This finding has implications for treating sick food animals and the people who get infected by eating contaminated meat.

The study, published in Antimicrobial Agents and Chemotherapy, showed that 60 percent of cattle faecal samples contained multiple strains of Salmonella that traditional testing methods missed. More alarmingly, Shariat found that about one out of every 10 samples tested positive for a drug-resistant strain of Salmonella called Salmonella Reading. In addition to being antibiotic resistant, Salmonella Reading can cause severe illness in people.

A new technology emerges

Developed by Shariat in 2015, CRISPR-SeroSeq enables researchers to analyse all the types of Salmonella present in a given sample. Traditional methods only examine one or two colonies of bacteria, potentially missing some strains of Salmonella altogether. Shariat’s technology identifies molecular signatures in salmonella’s CRISPR regions, a specialised part of the bacteria’s DNA. It also helps researchers identify which strains of the bacteria are most abundant.

In the current study, Shariat and colleagues found multiple Salmonella strains in cattle faeces before the animals were treated with the antibiotic tetracycline. After treatment, several of the dominant Salmonella strains in the sample were wiped out, allowing Salmonella Reading to flourish.

Traditional culturing methods missed the antibiotic-resistant strain in the original samples. It was only once the antibiotic eliminated the more abundant strains that conventional methods were able to detect Salmonella Reading in the samples.

“This suggests that traditional tests have underestimated the amount of antibiotic-resistant bacteria in the past,” said Shariat, an assistant professor of population health in the College of Veterinary Medicine.

“We need to know the antimicrobial resistance profiles of the bacteria that are present in animals,” Shariat said. “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.”

Missing the mark

Shariat’s research claims that current surveillance efforts are likely underestimating the amount of antimicrobial resistance that exists.

According to the research team, agencies that track antimicrobial resistance, like the the US Food and Drug Administration (FDA), US Department of Agricutlure (USDA) and US Centers for Disease Control and Prevention (CDC), still rely on traditional sampling methods, which means they may be missing reservoirs of drug-resistant bacteria.

“The problem is you have hundreds of Salmonella colonies in a given sample, but you only pick one or two of them to test,” Shariat said. “It becomes a numbers game wher researchers only pick the most abundant ones, and this means that they underestimate the different types of Salmonella that are present.”

Shariat will hope that CRISPR-SeroSeq can help fill that knowledge gap, giving researchers a better idea of how much antibiotic resistant bacteria exists. This information could help livestock farmers reduce and control outbreaks and guide policy on how to fight back against a growing public health threat.