Real-Time High Resolution Method for Genomic Surveillance of ESKAPE pathogens

PROJECT SUMMARY/ABSTRACT Antibiotic resistance is one of the most prominent public health threats. The burden of antibiotic resistance is drastically increasing. Infections caused by antibiotic resistant bacteria are a significant cause of morbidity and mortality especially in immunocompromised patients and elderly. Timely prevention and treatment of infections caused by antibiotic resistant pathogens are gaining urgency. Genomic surveillance of antibiotic resistant pathogens has emerged as an epidemiology tool to identify sources and track transmission routes of infections caused by antibiotic resistant pathogens for infection control and to evaluate antibiotic resistance for antibiotic stewardship. We believe that the adoption of routine use of such a genomic pathogen surveillance system in hospitals would be revolutionary in clinical medicine and help make hospitals safer places. However, the current genome-based surveillance methods do not have fast enough turnaround time and discriminatory power to serve as the effective and responsible translational methods of antibiotic resistant pathogens. To fill this gap, we will develop a surveillance system with the two real-time genomic applications for infection control and antibiotic stewardship focusing on ESKAPE, highly virulent and antibiotic resistant bacterial pathogens, Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species. The proposed study will be the first attempt allowing for real-time genomic surveillance which could be fully implemented and regularly used at hospitals. The proposed applications will allow early detection of transmission events and targeted interventions to prevent transmissions of antibiotic resistance infections and help in treatment of difficult infections supplementing antibiotic stewardship efforts, and cost reductions.