title: Identification of methicillin-resistant Staphylococcus aureus within the nation's Veterans Affairs medical centers using natural language processing.
abstract: BACKGROUND
  Accurate information is needed to direct healthcare systems' efforts to control methicillin-resistant Staphylococcus aureus (MRSA). Assembling complete and correct microbiology data is vital to understanding and addressing the multiple drug-resistant organisms in our hospitals.
  
  
  METHODS
  Herein, we describe a system that securely gathers microbiology data from the Department of Veterans Affairs (VA) network of databases. Using natural language processing methods, we applied an information extraction process to extract organisms and susceptibilities from the free-text data. We then validated the extraction against independently derived electronic data and expert annotation.
  
  
  RESULTS
  We estimate that the collected microbiology data are 98.5% complete and that methicillin-resistant Staphylococcus aureus was extracted accurately 99.7% of the time.
  
  
  CONCLUSIONS
  Applying natural language processing methods to microbiology records appears to be a promising way to extract accurate and useful nosocomial pathogen surveillance data. Both scientific inquiry and the data's reliability will be dependent on the surveillance system's capability to compare from multiple sources and circumvent systematic error. The dataset constructed and methods used for this investigation could contribute to a comprehensive infectious disease surveillance system or other pressing needs.
authors.affiliation: VA Salt Lake City Health Care System, Salt Lake City, UT, USA. makoto.jones@hsc.utah.edu
authors.forename: Makoto
authors.initials: M
authors.lastname: Jones
authors.forename: Scott L
authors.initials: SL
authors.lastname: DuVall
authors.forename: Joshua
authors.initials: J
authors.lastname: Spuhl
authors.forename: Matthew H
authors.initials: MH
authors.lastname: Samore
authors.forename: Christopher
authors.initials: C
authors.lastname: Nielson
authors.forename: Michael
authors.initials: M
authors.lastname: Rubin
mesh_terms: D000465:Algorithms; D015982:Bias; D006787:Hospitals, Veterans / Q000706:statistics & numerical data*; D006801:Humans; D016247:Information Storage and Retrieval / Q000379:methods* / Q000592:standards; D020407:Internet / Q000706:statistics & numerical data; D016347:Medical Records Systems, Computerized / Q000592:standards*; D055624:Methicillin-Resistant Staphylococcus aureus / Q000302:isolation & purification; D008828:Microbiological Techniques / Q000592:standards; D009323:Natural Language Processing; D011159:Population Surveillance / Q000379:methods; D011786:Quality Control; D012015:Reference Standards; D015203:Reproducibility of Results; D013203:Staphylococcal Infections / Q000453:epidemiology / Q000382:microbiology; D014481:United States; D014493:United States Department of Veterans Affairs