Research collaboration sheds new light on bacterial mechanisms of antibiotic resistance

Last fall, more than 100 people in 14 states got sick after eating at McDonald's. The Centers for Disease Control and Prevention traced the outbreak to raw onions on the quarter-pounder hamburger, which were contaminated with Escherichia coli, a plankton-like bacteria that thrives in the human gut, soil, livestock and drinking water.

Most of the 700-plus varieties of E. coli are harmless, but a handful of them can cause serious problems and require antibiotic treatment. Like many bacteria, E. coli have evolved means of resisting treatment, such as degrading the drug or armoring against it. Rates of antibiotic resistance are rising faster than researchers can develop new drugs, and the World Health Organization has categorized antibiotic resistance as a major global health threat.

Rather than trying to create a novel drug to fight the bacteria, UC Santa Cruz researcher Manel Camps is attempting to uncover the genetic origins of antibiotic resistance in bacteria. "The most effective mechanism of resistance for bacteria is to degrade the drug," said Camps. "But the bacteria must have a specific gene that does that,"—and they may take that gene from neighboring bacteria.

In collaboration with Rosa Rocha-Gracia at Benemerita Universidad Autonoma de Puebla in Puebla, Mexico, Camps and his colleagues are studying how pathogenic strains spread and share their resistance genes. The Camps lab is one of several at UC Santa Cruz conducting antibiotic resistance research.

Sharing is surviving

Antibiotic-resistant genes are typically found on bacterial plasmids—small circles of accessory DNA separate from the genome. Plasmids offer bacteria quick access to new genes, sort of like a booster pack.

In 2022, Camps and his colleagues, led by Benemerita Universidad Autonoma de Puebla graduate student Maria Balbuena Alonso, published a study in the journal Plasmid describing how antibiotic resistance genes jump between bacterial species in different environments via plasmid exchange. "Even though the bacterial strains that you find in food and in the clinic are different, their cargo is very similar," said Camps. "There's a subset of plasmids that seems to shuttle between environments."

The most common method for gene transfer is conjugation, where one bacterium extends a small tunnel to another nearby and threads a strand of DNA through it. The genes required for this transfer mechanism are often encoded on the plasmid. "Plasmids are known as selfish genetic elements," said Camps. "They don't really care how they stay in the population so long as they do." Plasmids multiply to guarantee their survival and in the process, spread antibiotic resistance.

Most genetic exchanges take place at the intersection of environments, such as in wastewater treatment plants, where many different bacterial strains intermingle. However, bacteria can also swap plasmids within the human body, meaning that a strain found in humans can pick up a gene from the environment and then propagate it in humans. Plasmids carrying resistance genes often co-host virulence genes, which can make bacteria more dangerous to humans by increasing their ability to spread and cause disease.

Acquiring a plasmid with both antibiotic resistance genes and virulence genes can make a harmless bacterium dangerous. Despite the survival benefits these plasmids provide the bacteria, they also suck energy from the host. When a plasmid is no longer serving its host, the bacteria will drop it to compete with more cells that don't carry plasmids and are more efficient.

Scientists still don't know exactly how this works, but it captured the attention of researchers in the Camps' lab as a potential therapeutic strategy. If the plasmid is lost, so too are the genes that confer drug resistance.

Christina Egami, a fourth-year Ph.D. student in the Camps lab, is working with undergraduate researchers to screen thousands of molecules that have already been cleared for use in humans. They are looking for a safe compound that causes bacteria to eject a plasmid or creates enough stress that the bacteria must kick it out to conserve energy. In either scenario, the antibiotic resistance genes don't get passed down to subsequent generations.

"If we have a way to get rid of these plasmids, or to promote loss, then that certainly is a way to mitigate the spread of resistance," Egami said.

Super plasmids

Plasmids with resistance to one or two antibiotics often acquire additional resistance genes. This phenomenon is called "genetic capitalism," said Camps. "Essentially, the winner keeps taking it all until you end up with a super plasmid with resistance against everything." If this plasmid spreads through the bacterial population, it can present as a complex infection that does not respond to treatment. Methicillin-resistant Staphylococcus aureus, or MRSA, is a classic example.

According to the CDC, drug-resistant infections killed 1.27 million people worldwide in 2019. The CDC also reported that the six most common types of resistant infections increased by 20% in the US during the COVID-19 pandemic, suggesting that even more deaths could be attributed to drug-resistant infections now.

Pathogenic E. coli are split into two categories based on the type of infection they can cause: intestinal pathogenic E. coli (InPEC) and extraintestinal pathogenic E. coli (ExPEC), which can cause urinary tract infections, bacterial meningitis and other severe illnesses. Most antibiotic-resistant E. coli infections worldwide are caused by a particular ExPEC subgroup that spreads through human-to-human contact.

In 2023, Camps and his colleagues in Puebla identified a strain of ExPEC E. coli in fresh spinach from a supermarket in Puebla, Mexico. Their findings suggested that the spinach was contaminated with a pathogen that could cause serious infection. "If you eat the spinach, not only will you get sick to your stomach, but that E. coli can go deeper and cause an infection in your urinary tract," said Gerardo Cortés-Cortés, co-author of the study published in Frontiers in Cellular and Infection Microbiology.

Researchers have isolated this strain from meat products, but had not found it in leafy greens before, added Cortés, a former postdoctoral fellow in the Camps lab. He doesn't know the cause, but speculates that the spinach field may have been irrigated with treated water from a wastewater treatment plant. If the sanitation process was lacking, E. coli could have contaminated the spinach. "Spinach leaves have small, microscopic holes that are just the perfect structure to protect E. coli," he said.

The discovery of high-risk E. coli in agricultural products represents a new aspect of Camp's genetic research. In the lab, researchers can control and manipulate the environment for experimental purposes, but it isn't always representative of nature. Now, "the first thing we do is check with our collaborators."

Applying a public health lens has enriched the significance of their findings. "We saw antibiotic resistance as an example of a new biochemical activity, but we were not looking at this as a public health problem until recently," said Camps. "This new dimension is boosting the potential impact of our research. We are also working to extend our studies to another microorganism of clinical relevance, Mycobacterium tuberculosis, which is the causative agent of tuberculosis, through exciting new collaborations."

Provided by University of California - Santa Cruz