Growing Lung Bacteria in Labs May Predict Antibiotics’ Effectiveness More Accurately

Antibiotic susceptibility tests that determine how people with lung infections will respond to antibiotics may work better if researchers grow the pathogenic bacteria in the lab along with other commensal bacteria found in the lungs, because it more accurately mimics their real environment, a recent study suggests.

The reason for this is that some infectious bacteria — such as Pseudomonas aeruginosa, which commonly trouble people with cystic fibrosis (CF) — are resistant to many antibiotics but rely on other bacterial species to survive. If antibiotics are able to eliminate the other bacteria, it is likely the pathogenic (harmful) one also will die.

The study reporting the findings, “Disruption of Cross-Feeding Inhibits Pathogen Growth in the Sputa of Patients with Cystic Fibrosis,” was published in the American Society for Microbiology‘s journal mSphere.

“CF is a genetic disease that leads to the build-up of mucus in the lungs and is very difficult to clear. In turn, any bacteria that colonize the airways are also difficult to clear, so this leaves any patient with CF prone to long-term chronic bacterial infections, a leading cause of patient mortality,” Ryan Hunter, PhD, assistant professor for the department of Microbiology and Immunology at the University of Minnesota, said in a university news story.

“As a result, one of the main treatments is aggressive antibiotic therapy. Current approaches have been somewhat effective, but there’s room for improvement,” Hunter said.

Currently, to determine the most effective antibiotic treatment for CF patients, a sample of the patient’s mucus is taken to the lab, where the disease-causing bacteria are isolated and tested against a range of antibiotics. But data is showing that these tests are not very accurate at predicting responses in the clinic, and some clinicians are no longer using them to guide treatment decisions.

A problem with the tests is that they fail to mimic the intricate environment seen in the lungs, from oxygen gradients to the presence of other bacterial species in the mucus, which often work as a community and rely on each other for nutrients.

“By culturing bacteria in a lab, you are taking it out of the environment it is used to growing in. It in no way reflects what is actually happening in the body. You are also taking it away from other bacteria it grows with,” Hunter said.

“We know that pathogens, like Pseudomonas, live in a very complex bacterial community, and just by targeting a single pathogen, you ignore the rest of the bacteria that it lives with in the lungs,” Hunter said.

P. aeruginosa is one such species that appears to work in cooperation with other bacteria. While it creates an anaerobic environment for the other bacteria to grow, the anaerobic bacteria produce nutrients from mucin (the main component of mucus) that P. aeruginosa would not be able to obtain on its own.

This means the bacteria species are dependent on each other to survive and that targeting the most susceptible one (the weakest link) could be enough to eliminate the entire bacterial community.

Hunter and colleagues wondered whether better mimicking the lung environment and the cooperation established among bacteria could help researchers make better predictions as to how effective an antibiotic would be in a clinical setting.

To find out, they took mucus samples from CF patients and tested multiple antibiotics against P. aeruginosa only (much like what is done in susceptibility tests), the anaerobic bacteria only, or the entire bacterial community.

Results demonstrated that some antibiotics, such as tobramycin and levofloxacin, were able to stop the growth of P. aeruginosa, but not of other species. Others, such as metronidazole, were effective against the anaerobic bacteria from most patients, but could not kill P. aeruginosa.

The team then found that antibiotics effective against at least one species were enough to dampen the growth of the entire bacterial community. This suggested that P. aeruginosa could be eliminated by antibiotics like metronidazole, for which they would not be vulnerable in susceptibility tests.

“In this paper, we showed that if we cultured all of the bacteria together under conditions in which they rely on one another and grow as a community, Pseudomonas aeruginosa, even if antibiotic-resistant, can be inhibited simply by reducing the growth of other bacteria that are present there,” Hunter said.

The findings are broadly applicable to other chronic bacterial infections in which the bacterial components work as a community, researchers believe.

“We use CF as our model system, but when it comes to the treatment of other chronic bacterial infections, such as sinus and gastrointestinal infections, this is applicable,” Hunter said.

“In theory, any bacterial community in which two or more members exchange metabolites, potentiate virulence, or rely on others for niche modification (e.g., oxygen consumption) could be targeted,” the researchers wrote.

The team now will further assess whether growing these bacterial communities in the lab more accurately predicts clinical responses in patients than standard susceptibility tests.