With a dearth of new classes of antibiotics in development, hospital infection control is crucial to prevent the rise of untreatable Gram-negative bacterial infections. Whole genome sequencing provides a level of resolution that far exceeds traditional typing methods. This high level resolution enables tracking the spread of pathogens within and between hospitals, thus identifying possible weaknesses in existing practices and points of intervention.
We aim to use genomic information to model outbreaks, monitor evolution of antibiotic resistance and develop risk assessment strategies. The NIH Clinical Center (CC) is a hospital that provides care for critically ill patients. As such, one ongoing concern is the possibility of hospital-acquired infections, particularly with multi-drug resistant (MDR) Gram-negative bacterial infections. Hospital-acquired infections result in 100,000 deaths per year, and represent a tremendous social cost to patients and their families. My laboratorys mission is to use genomic information to model clusters of bacterial infections and transmissions, monitor evolution of antibiotic resistance and develop risk assessment strategies. Klebsiella pneumoniae is a Gram-negative bacteria, which represents a major cause of nosocomial infections, primarily among immunocompromised patients. The emergence of strains resistant to carbapenems has left few treatment options, making infection containment critical. In 2011 the National Institutes of Health Clinical Center had a cluster of infections of carbapenem-resistant K. pneumoniae that affected 19 patients, 12 of who died. Whole-genome sequencing was performed on K. pneumoniae isolates to gain insight into why the outbreak progressed in spite of early implementation of infection control procedures. Integrated genomic and epidemiological analysis traced the outbreak to three independent transmissions from a single patient, who was discharged three weeks before the next case became clinically apparent. Additional genomic comparisons provided evidence for unexpected transmission routes, with subsequent mining of epidemiological data providing possible explanations for these transmissions. Our analysis demonstrates that integration of genomic and epidemiological data can yield actionable insights and facilitate the control of nosocomial transmission. Public health officials have raised concerns that plasmid transfer between Enterobacteriaceae species may spread resistance to carbapenems, an antibiotic class of last resort, thereby rendering common healthcare-associated infections nearly impossible to treat. We performed comprehensive surveillance and genomic sequencing to identify carbapenem-resistant Enterobacteriaceae in the NIH Clinical Center patient population and hospital environment in order to to articulate the diversity of carbapenemase-encoding plasmids and survey the mobility of and assess the mobility of these plasmids between bacterial species. We isolated a repertoire of carbapenemase-encoding Enterobacteriaceae, including multiple strains of Klebsiella pneumoniae, Klebsiella oxytoca, Escherichia coli, Enterobacter cloacae, Citrobacter freundii, and Pantoea species. Long-read genome sequencing with full end-to-end assembly revealed that these organisms carry the carbapenem-resistance genes on a wide array of plasmids. We continue to develop a national database of carbapenemase producing organisms. As well, within the NIH Clinical Center patient population we study genomic changes associated with long term carriage and the possibility of plasmid transfer between species or strains. With increasing rates of antibiotic resistance, bacterial infections have become more difficult to treat, elevating the importance of surveillance and prevention. Effective surveillance relies on the availability of rapid, cost-effective and informative typing methods to monitor bacterial isolates. PCR based typing assays are fast and inexpensive, but their utility is limited by the lack of targets which are capable of distinguishing between strains within a species. To identify highly informative PCR targets from the growing base of publicly available bacterial genome sequence, we developed a computer algorithm which uses existing genome sequences for isolates of a species of interest and identifies a set of genes whose patterns of presence or absence provides the best discrimination between strains in this species. A set of PCR primers targeting the identified genes is then designed, with each PCR product being of a different size to allow multiplexing. These target DNA regions and PCR primers can then be utilized to type bacterial isolates. Together with collaborators across the US government, we aim to produce reference genomes for hospital transmitted pathogens to enable research in this field. Our long-term goal is both to promote hospital infection control and to tailor drug strategies to minimize the acquisition of antibiotic resistance. Collaboration among physicians who have expertise in healthcare epidemiology, microbiologists who have expertise in diagnostics, and scientists who have expertise in genomics is critical to take advantage of emerging technologies and translate them into improved patient care.
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