­RETRA-Seq to inform antibiotic therapy of resistant bacteria

Background

Severe bacterial infections, characterized by their resistance to multiple antibiotics, are common in hospital-admitted patients and can lead to the development of severe infections, such as pneumonia or systemic septicemia, which are the leading cause of death in these patients. Ventilator-associated pneumonia (VAP) is one of the most common examples where patients admitted to the intensive care unit develop severe respiratory infections from bacteria that develop resistance to multiple antibiotics following an acute phase of infection.

The current treatment approach is to isolate the bacteria during the acute phase of infection and test their resistance to different antibiotics in cultures to determine the most effective antibiotic therapy to be used. However, there are multiple limitations of this approach, including the possibility of evaluating the wrong strain of bacteria due to culturing bias, and the poor understanding of the relationship between the development of bacterial resistance to antibiotics and the time of initial antibiotic therapy.

Technology Overview

To gain a better understanding of the mechanisms of bacterial resistance to antibiotics, Boston Children’s Hospital researchers invented a novel approach to investigate these changes at the molecular level. This approach involves multiple steps of sequencing bacterial genomes to identify the different strains of bacteria, as well as the genetic mutations that are responsible for the development of antibiotic resistance during different stages of infection. After performing extensive research on pseudomonas bacteria as the most common cause of VAP, the group concluded that utilizing this method of “resistance-targeted deep amplicon sequencing (RETRA-Seq)” together with the antibiotic cycling technique can provide an effective treatment.

Applications

1. Identification of the most effective antibiotics for treating severe infections, like ventilator-associated pneumonia.
2. Understanding the natural history of drug resistance in the bacteria that are responsible for life-threatening infections.
3. The ability to identify effective antibiotics to be used for bacteria that are difficult to culture in the lab.

Advantages

1. Unlike the current approach of culturing bacteria for antibiotic-resistance studies, this method provides more specific results, based on the molecular genetic changes for the specific strain of bacteria being studied.
2. The flexibility of the method means it can be applied to different bacteria and microorganisms.
3. The effectiveness of the resulting antibiotic-of-choice is more certain, preventing unnecessary time wasting and healthcare costs.
4. The data from conducting this novel method on multiple strains of bacteria can provide critical information for the development of more powerful antibiotic therapies.

Publications

• Chung, H., Merakou, C., Schaefers, M.M. et al. Rapid expansion and extinction of antibiotic resistance mutations during treatment of acute bacterial respiratory infections. Nat Commun 13, 1231 (2022).