bronchialveolar_lavage_microbiome. bronchialveolar_lavage_microbiome

The aim of the proposed project is to provide metagenomics sequencing data analysis valuable to the surveillance of the respiratory pathogens in critically ill patients with pneumonia on an intensive care unit, Addenbrookes hospital, in order to monitor changes in the respiratory microbiota of patients undergoing therapies and identify multidrugresistant strains that present a heightened health risk to patients. These data will provide important information to the development of strategies aimed at improving patient outcomes, reducing the development of antimicrobial resistance and facilitating infection control measures in hospital. Specifically, the proposed work will be a proof of principle study of one hundred patients. We will use metagenomics data to (1)define the molecular epidemiology of respiratory microbiota of one hundred critically ill patients diagnosed with pneumonia (2) track transmission of isolates within the intensive care unit and (3) determine the genotypes of pathogens associated with antimicrobial-resistant phenotypes. These data will build on analysis from DNA microarray technology developed at Addenbrooke’s Hospital. The Taqman array card screens for 96 common respiratory pathogens and will provide a rapid microbiological diagnosis for the patient, allowing implementation of a more targeted therapy. This is a project that will bring together expertise of the Principal Investigator at the Sanger Institute, with co- Investigators in Intensive Care, Respiratory and Clinical Microbiology departments based at Addenbrooke’s Hospital, Cambridge. The objectives will be achieved by a combination of expertise in metagenomics sequence analysis, pathogen genomics and molecular biology (Sanger Institute), as well as expertise in Intensive Care Medicine, Respiratory Medicine, Clinical Microbiology, Public Health and Infection Control (Addenbrooke’s Hospital, Cambridge). This data is part of a pre-publication release. For information on the proper use of pre-publication data shared by the Wellcome Trust Sanger Institute (including details of any publication moratoria), please see http://www.sanger.ac.uk/datasharing/