Study reveals new mechanism for rapid evolution of multi-drug resistant infections in patients

Newswise — A research study led by the University of Oxford provides a transformational new insight into how antimicrobial resistance (AMR) emerges in patients with bacterial infections. The findings, published today in the journal Nature Communications, could help develop more effective interventions to prevent AMR infections developing in vulnerable patients.

The study's results defy the conventional notion that individuals typically acquire a solitary genetic clone (or 'strain') of harmful bacteria when infected, and that resistance to antibiotic treatment evolves through the natural selection of new genetic mutations that arise during the infection. Instead, the findings propose that patients frequently experience co-infection by numerous clones of pathogens, wherein resistance emerges due to the selection of pre-existing resistant clones, as opposed to new mutations.

The scientists employed an innovative methodology to examine alterations in the genetic variability and antibiotic resistance of a specific bacterial species (Pseudomonas aeruginosa) obtained from patients prior to and following antibiotic therapy. The specimens were isolated from 35 patients in intensive care units (ICUs) across 12 European hospitals. Pseudomonas aeruginosa is an opportunistic pathogen responsible for significant hospital-acquired infections, particularly among immunocompromised and severely ill individuals, and is estimated to contribute to over 550,000 annual fatalities worldwide.

Upon admission to the ICU, each patient underwent screening for Pseudomonas aeruginosa, and subsequent samples were collected at regular intervals. The research team employed a blend of genomic analyses and antibiotic challenge tests to measure the extent of bacterial diversity and antibiotic resistance within each patient.

Around two-thirds of the patients participating in the study were found to be infected by a solitary strain of Pseudomonas. In some of these cases, antimicrobial resistance (AMR) developed as a result of the transmission of fresh resistant mutations that emerged during the infection, aligning with the established understanding of how resistance is acquired. However, intriguingly, the researchers made the surprising discovery that the remaining one-third of patients were actually infected by multiple strains of Pseudomonas.

Of paramount importance, when patients with mixed strain infections received antibiotic treatment, there was an approximately 20% higher escalation in resistance compared to patients with single strain infections. The rapid surge in resistance observed in patients with mixed strain infections was primarily attributed to the natural selection of pre-existing resistant strains that were already present at the initiation of antibiotic therapy. Although these strains typically constituted a minority of the initial pathogen population, their possession of antibiotic resistance genes conferred them a significant selective advantage in the presence of antibiotics.

Nevertheless, despite the accelerated emergence of antimicrobial resistance (AMR) in multi-strain infections, the study's findings indicate that such resistance may also be more prone to rapid decline under certain conditions. When samples from patients with single strain infections and those with mixed strain infections were cultured without the presence of antibiotics, the growth rate of AMR strains was comparatively slower in comparison to non-AMR strains. This observation supports the hypothesis that AMR genes entail fitness trade-offs, meaning they are negatively selected when antibiotics are absent. Notably, these trade-offs were more pronounced in mixed strain populations as opposed to single strain populations, suggesting that the presence of within-host diversity can contribute to the loss of resistance in the absence of antibiotic treatment.

Based on the research outcomes, the researchers propose that interventions focusing on curbing the transmission of bacteria among patients, such as enhanced sanitation practices and infection control measures, may prove to be more effective in combating antimicrobial resistance (AMR) compared to interventions aimed at preventing the emergence of new resistance mutations during infection, such as drugs that reduce bacterial mutation rates. This finding holds particular significance in settings characterized by a high infection rate, such as individuals with compromised immune systems. By prioritizing measures that limit bacterial spread, it is anticipated that the proliferation of AMR can be more effectively controlled.

Moreover, the findings indicate a need for a shift in clinical testing approaches, emphasizing the inclusion of pathogen strain diversity in infection assessments rather than relying on a limited number of pathogen isolates under the assumption of clonality. By capturing a broader representation of pathogen strains present in infections, more precise predictions can be made regarding the efficacy or failure of antibiotic treatments in individual patients. This approach draws parallels to the utilization of diversity measurements in cancer cell populations, which aid in predicting the success of chemotherapy. Therefore, incorporating a comprehensive understanding of pathogen strain diversity has the potential to enhance the accuracy of treatment predictions and improve patient outcomes.

Professor Craig Maclean, the lead researcher from the University of Oxford's Department of Biology, emphasized the crucial discovery of the study, stating, "The primary finding of this study is the rapid evolution of resistance in patients harboring diverse populations of Pseudomonas aeruginosa, driven by the selection of pre-existing resistant strains. The pace at which resistance develops in patients varies significantly among pathogens, and we speculate that the presence of extensive within-host diversity may account for why certain pathogens, like Pseudomonas, swiftly adapt to antibiotic treatment." The remark underscores the significance of within-host diversity and its influence on the adaptive capabilities of pathogens, shedding light on the rapid evolution of resistance observed in the study.

Additionally, Professor Craig Maclean emphasized the need for advancements in diagnostic methods for studying antibiotic resistance in patient samples. He stated, "The diagnostic methods employed for assessing antibiotic resistance in patient samples have undergone slow evolution over time, and our findings highlight the significance of developing new diagnostic approaches that facilitate the assessment of pathogen population diversity in patient samples." This remark underscores the call for innovative diagnostic techniques that can accurately capture the diversity of pathogen populations, enabling a more comprehensive understanding of antibiotic resistance dynamics in clinical settings.

The World Health Organization (WHO) has recognized antimicrobial resistance (AMR) as a critical global public health challenge, ranking it among the top 10 threats facing humanity. AMR arises when bacteria, viruses, fungi, and parasites become resistant to medicines, including antibiotics, rendering infections progressively more challenging or even untreatable. The rapid proliferation of multi-resistant pathogenic bacteria, which are resistant to all currently available antimicrobial drugs, is of particular concern. In 2019, AMR was associated with nearly 5 million deaths worldwide, underscoring the urgent need for effective strategies to combat this escalating threat.

Professor Willem van Schaik, the Director of the Institute of Microbiology and Infection at the University of Birmingham, who was not directly involved in the study, emphasized the implications of the findings. He stated, "This study provides strong evidence that clinical diagnostic protocols may need to be broadened to encompass multiple strains from a patient, in order to effectively capture the genetic diversity and potential for antibiotic resistance among strains colonizing critically ill patients." He further stressed the significance of continuous infection prevention measures aimed at mitigating the risk of hospital-acquired colonization and subsequent infection by opportunistic pathogens during patients' hospital stays. The comment highlights the importance of expanding diagnostic approaches and maintaining robust infection prevention efforts to address the challenges posed by antimicrobial resistance in clinical settings.

Professor Sharon Peacock, a renowned expert in Microbiology and Public Health at the University of Cambridge, who was not directly involved in the study, emphasized the significance of the findings in the context of ICU settings. She stated, "Multidrug-resistant infections, caused by various organisms such as Pseudomonas aeruginosa, pose a significant challenge in the management of patients in ICU settings globally." Professor Peacock further highlighted the study's contribution, stating that the findings provide additional evidence to underscore the critical importance of infection prevention and control measures in ICUs and hospitals at large. These measures are vital for reducing the risk of acquiring P. aeruginosa and other pathogenic organisms, thereby safeguarding patient well-being and addressing the challenges posed by multidrug-resistant infections.