Disease and treatment

Discovery: antibiotic-resistant bacteria can hide for years

Research on antibiotic-resistant bacteria has intensified to determine how they survive exposure to antibiotics. Antibiotic-resistant infections frequently return with increasing and deadly strength among patients with chronic bacterial infections. Now a Danish research group has shown that bacteria develop antimicrobial resistance much earlier than previously assumed. This new knowledge may be important for helping people with cystic fibrosis and chronic obstructive pulmonary disease.

Mucus with the consistency of chewing gum: one of the nightmares people with cystic fibrosis deal with daily. A genetic mutation results in a defect in the cells’ chloride channels, which drain the mucus in the lungs of these patients. This makes the mucus a paradise for microorganisms, and for people with cystic fibrosis elimination of bacteria such as Pseudomonas aeruginosa is virtually impossible. These bacteria propagate in the mucus and stimulate the immune system causing recurring inflammatory states. Over time, the bacteria also become resistant to almost all known antibiotics.

“When the antibiotics used no longer cure people, this constantly threatens life. Unfortunately, existing culture methods do not enable us to identify the resistant bacteria as early as we should. Our results show that antimicrobial resistance occurs early in the course of the infection, and the standard method of treating people may even help to give the antibiotic-resistant bacteria a better chance of surviving,“ explains a main author of the study, Helle Krogh Johansen, Consultant at Rigshospitalet and Professor at the Department of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen.

Small changes create major differences

The researchers discovered the remarkable results by sequencing the genomes of Pseudomonas aeruginosa strains from 34 people with cystic fibrosis. The most frequent bacterial mutation was in the mexZ gene, which regulates a pump that influences the bacteria’s sensitivity to the antibiotics most used to treat people with cystic fibrosis. A mutation in the mexZ gene eliminates the regulation of the pump and therefore allows the relevant antibiotics to be pumped out of the bacteria.

“The surprising thing, however, was that examining mexZ mutants for antibiotic resistance using the conventional culture method could not detect resistance to the relevant antibiotic. We therefore continued treatment, thinking that it was effective and that there were no antibiotic-resistant bacteria. The problem was that there were some.”

The study showed that antimicrobial resistance occurs earlier than expected and that traditional microbiological culturing methods are not sensitive enough to register this. Initially, this made no sense to the researchers. However, they got important answers when they carried out fitness experiments, in which antibiotic-resistant bacteria compete with the original bacteria in the presence of antibiotics.

“The experiments showed that mexZ mutations resulted in very small increases in antibiotic resistance, which cannot be detected clinically. However, these small increases are sufficient for mexZ mutant bacteria to rapidly outcompete the normal bacteria in the presence of antibiotics, without this being detected clinically. Further, new mutations also emerge over time resulting in the generation of highly resistant bacteria”.

Bones, urinary tract and lungs

These new experiments have some obvious consequences for how people with cystic fibrosis are diagnosed and treated. Today, they attend monthly health check-ups that include examining sputum samples from their airways to see whether they have bacteria that require treatment.

“People are given antibiotics if pathogenic bacteria are present in their sputum. The new results show that we need to develop a new, more sensitive test to detect whether bacteria are already beginning to develop antimicrobial resistance. In addition, this may also be important for antibiotic treatment. People may need to be treated with higher doses or with other antibiotics to kill the bacteria – instead of risking continued survival and development of high resistance.”

Although the discovery has the greatest implications for people with cystic fibrosis, the researchers definitely believe that this may prove to be even more useful for other chronic infections in bones, the urinary tract and the lungs such as chronic obstructive pulmonary disease.

“If microbiology laboratories continue to assess antibiotic resistance based on the current guidelines, these mutations that result in low-level antibiotic resistance will be overlooked, and this will greatly influence the effectiveness of antibiotic treatment. In the long term, introducing molecular biological examinations to assist the standard culture methods can improve the detection of bacteria and thus also improve antibiotic treatment.”

Mutations causing low level antibiotic resistance ensure bacterial survival in antibiotic-treated hosts” by Jakob Frimodt-Møller, Elio Rossi, Janus A.J. Haagensen, Marilena Falcone, Søren Molin and Helle Krogh Johansen has been published in Scientific Reports. In 2015, the Novo Nordisk Foundation awarded a grant to Helle Krogh Johansen for the project Bacterial Biofilm Infections – Fact or Fiction. Several of the other authors are affiliated with the Novo Nordisk Foundation Center for Biosustainability at the Technical University of Denmark.

Helle Krogh Johansen
Dr. med., Chief Physician
The research area is (shared research between RH and DTU) bacterial airway infections in patients with cystic fibrosis (CF). Most CF patients have bacteria in their lungs from early childhood until they die prematurely. The bacterial lung infections in CF patients, is an excellent model to study infectious disease for which antibiotic treatment is challenged by frequent lack of success. Equally important is that modern human life-style, as well as increases in the average population life span, will create problems with long-term bacterial infections that are difficult or impossible to treat. Moreover, the rising global problem of antibiotic resistance threatens to become the biggest health risk within the next 20-30 years. Our research is directly addressing the problem of antibiotic resistance.