Targeted Metagenomic Analysis as a Clinical Tool for the Investigation of the Impact of Bundle of Interventions on the Burden of Resistance Genes Among Severely Ill Pediatric Patients

Background: Antimicrobial drug resistance is recognized as one of the most important global public health threats. There is an urgent need to reduce the spread of the multidrug-resistant bacteria (MDR-B) bacteria, particularly in clinically extremely vulnerable patients. The aim of this study was to investigate whether targeted gene amplification directly on clinical samples can be used as a rapid and effective tool for active surveillance of antimicrobial resistance in a Pediatric Intensive Care Unit (PICU). Methods: The study had three phases: 1) The Baseline phase performed prior to intervention, when first screening and sample collection was performed, 2) the Intervention phase, when a bundle of enhanced infection control measures (EICM) was applied, and 3) the Maintenance phase when enhanced infection control measures were combined with the implementation of the targeted molecular surveillance. The presence of four carbapenemases: blaKPC, blaOXA-48-like, blaVIM, and blaNDM as well as of blaTEM and blaSHV were evaluated by PCR after DNA isolation directly from stool samples. Results were compared to culture-based phenotypic analysis. Results and Conclusions: The applied EICM led to decreased colonization of blaKPC, blaVIM and blaTEM . Implementation of EICM has been shown that it may reduce the resistance burden in this clinical setting endemic to MDR-B. Direct implementation of a targeted and customized rapid molecular detection assay to clinical samples seems to be an effective clinical tool for the evaluation of antimicrobial stewardship measures.