Genetically modified bacteria create protective shield against Salmonella attacks

The mammalian gut microbiome is teeming with a delicate balance of bacteria and the viruses that keep them in check, called bacteriophages, or phages. Each bacterial species usually has its own set of phage partners. 

When bad bacteria enter this ecosystem, there are typically no phages present, allowing them to cause mayhem. By the time the host is sick, it is too late for phages; they’ll simply reach a balance with the bad bacteria.

But what if the phages in the gut could prepare for the orally ingested pathogen and strike it down as it enters the gut, negating the need for a battle?

Associate Professor and Blackwood Junior Faculty Fellow Bryan Hsu and his team recently demonstrated that this prophylactic approach, using an engineered nonpathogenic E. coli bacterium, successfully protected mice from an oral Salmonella infection. Their work was published in Nature Microbiology.

The team believes this is a step toward an additional weapon against illnesses. 

Eventually, in the future, this could be used to treat other diseases. It’s not about replacing antibiotics but having one more option on the shelf to fight infections.” 

Rogerio A. Bataglioli, postdoctoral fellow, Department of Biological Sciences and lead author of the study

Bacteriophages, or phages, are viruses of bacteria and do not infect humans or animals. Hsu said phage therapy, the use of phages to treat bacterial infections, is particularly hard to make successful for treating intestinal pathogens. 

“It’s challenging, especially in the gut, because phages and bacteria tend to coexist for long periods of time,” said Hsu, an affiliate with Fralin Life Sciences Institute’s Center for Emerging, Zoonotic, Arthropod-borne Pathogens. 

This coexistence makes establishing the high phage-to-bacteria ratio needed to treat intestinal infections hard to achieve. 

“That’s extremely challenging to achieve in your gut,” Hsu said. “And then once you have a bacterial infection in your gut, a lot of times it’s just not even accessible to phages. It’s already hidden away in the mucosa or cells of your body; it’s not just free-flowing to where the phages would be able to access them.” 

To work around these impediments, the team engineered a nonpathogenic E. coli bacterium to carry a phage that only infects Salmonella. This ensures that when the phage is produced, it can specifically target the pathogen.

Usually, this type of Salmonella phage remains dormant in the Salmonella bacterial genome, but Hsu’s team made several genetic modifications so that it is carried by E. coli, and, once it is released into the gut, it automatically kills Salmonella in a process called lysis. This process rapidly increases the number of phages to fight the bacteria. The researchers coined this new type of phage-bacterial combination a “lytic phage-producing lysogen,” or “lyto-lysogen.”

Salmonella can typically detect phage DNA produced by non-Salmonella bacteria and prevent it from replicating. But in this case, the researchers were able to disguise the phage.

“We were able to trick the Salmonella bacteria into thinking the phage from E. coli was ‘not foreign’ by adding a Salmonella gene into the E. coli genome,” Bataglioli said. “A phage that comes from our E. coli can infect Salmonella, can propagate easily in Salmonella, lyse it, and then all the phages that are produced from Salmonella can just keep replicating.” 

This rapid reproduction eventually leads to the eradication of the infection from the gut. 

“What happens is that this good bacteria, the E. coli, produces all this antipathogen phage, and there is now a protective lining so that when Salmonella comes in, just after passing through the stomach and at its weakest point, it meets this high, killer density of phages,” Hsu said. 

The researchers say they targeted Salmonella due to its high global disease burden, as it can kill the elderly, children, and those with HIV; it has a high prevalence of antibiotic resistance; and it has been upgraded to a high-priority pathogen by the Centers for Disease Control and Prevention. They believe this work, however, has strong implications for other illnesses. 

“We’re starting off with Salmonella, but expanding, obviously, with the correct adaptations to target other diseases; other bacterial pathogens, would be an interesting route to explore,” Bataglioli said. 

“We have a framework in place that shows that we could potentially put other phages in there and target other bacteria,” Hsu said. 

Bataglioli plans to continue his bacteriophage research with the School of Chemical Engineering at the State University of Campinas in São Paulo, Brazil, in the fall.

Funding for this research was provided by the National Institute of General Medical Sciences of the National Institutes of Health. Bataglioli’s funding was supported by the Postdoctoral Fellowship in Drug Delivery from the PhRMA Foundation. 

Other researchers involved in this study include the following: 

• Hiba Baaziz, Ph.D., lab manager, biological sciences 

• David Da Silva Barreira, Ph.D., current postdoctoral researcher at the University of Wisconsin, Madison 

• Harsimran Kaur, Ph.D., presidential postdoctoral associate in biological sciences 

• Teresa Southard, associate professor at the Virginia-Maryland College of Veterinary Medicine