Antimicrobial Resistance Emerges More Quickly in Mixed Strain Bacterial Infections

Pseudomonas aeruginosa is a bacterial pathogen that can be highly resistant to antibiotics.

A new study challenges the long-standing belief that people are generally infected by a single genetic strain of bacterial pathogen, and that resistance to antibiotic treatment evolves because of natural selection for new genetic mutations that occur during the infection. However, the findings of a new study published today in Nature Communications suggest that patients are commonly coinfected by multiple or diverse pathogen clones, with resistance emerging as a result of selection for preexisting resistant clones, rather than new mutations.

“The key finding of this study is that resistance evolves rapidly in patients colonized by diverse Pseudomonas aeruginosa populations due to selection for preexisting resistant strains,” senior study author Craig Maclean, PhD, professor, University of Oxford’s Department of Biology, said in a statement. “The rate at which resistance evolves in patients varies widely across pathogens, and we speculate that high levels of within-host diversity may explain why some pathogens, such as Pseudomonas, rapidly adapt to antibiotic treatment.”

Using a novel approach, Maclean and his coinvestigators examined genetic diversity and antibiotic resistance of Pseudomonas by collecting from patients before and after antibiotic treatment. They took samples from 35 intensive care unit (ICU) patients in 12 European hospitals.

The investigators used a combination of genomic analyses and antibiotic challenge tests to quantify within-patient bacterial diversity and antibiotic resistance.

Mixed Strain Pathogens and AMR
Approximately 2/3 of the patients in the study were infected by a single Pseudomonas strain. AMR evolved in some of these patients due to the spread of new resistance mutations that occurred during infection, supporting the conventional model of resistance acquisition. However, the remaining third of patients were infected by multiple strains of Pseudomonas.

AMR increased by about 20% more when patients with mixed strain infections were treated with antibiotics, compared to patients with single strain infections. The rapid increase in resistance in patients with mixed strain infections was driven by natural selection for preexisting resistant strains that were already present at the onset of antibiotic treatment.

These strains usually made up a minority of the pathogen population that was present at the start of antibiotic treatment, but the antibiotic resistance genes that they carried gave them a strong selective advantage under antibiotic treatment.

Although AMR emerged more quickly in multi-strain infections, the findings also suggest it may be lost more rapidly in these conditions. When samples from single strain and mixed strain patients were cultured in the absence of antibiotics, the AMR strains grew more slowly compared with non-AMR strains. This supports the hypothesis that AMR genes carry fitness trade-offs, such that they are selected against when no antibiotics are present. These trade-offs were stronger in mixed strain populations than in single strain populations, suggesting that within-host diversity can also drive the loss of resistance in the absence of antibiotic treatment.

According to the researchers, the findings suggest that interventions aimed at limiting the spread of bacteria between patients (such as improved sanitation and infection control measures) may be a more effective intervention to combat AMR than interventions that aim to prevent new resistance mutations arising during infection, such as drugs that decrease the bacterial mutation rate. This is likely to be especially important in settings where the infection rate is high, such as patients with compromised immunity.

In terms of important takeaways, further diagnostic testing may need to be utilized to further understand single and multiple strain identifications and identify potential AMR.

“Our findings suggest that measuring the diversity of pathogen populations might make it possible to more accurately predict the likelihood of treatment failure at the level of individual patients, in the same way that measurements of diversity in cancer cell populations have been informative for predicting the success of chemotherapy,” the investigators wrote.

"This study strongly suggests that clinical diagnostic procedures may need to be expanded to include more than one strain from a patient, to accurately capture the genetic diversity and antibiotic resistance potential of strains that colonize critically ill patients,” Professor Willem van Schaik, PhD, MSc, director of the Institute of Microbiology and Infection at the University of Birmingham, said. He was not directly involved with the study. “It also highlights the importance of ongoing infection prevention efforts that aim to reduce the risk of hospitalized patients being colonized, and subsequently infected, by opportunistic pathogens during their hospital stay.”