Methicillin-resistant Staphylococcus aureus (MRSA) is a major public health problem primarily related to receipt of health care. As part of the VHA MRSA Initiative, all hospitalized patients are expected to be screened for MRSA carriage upon admission to the hospital, transfer between hospital units and upon discharge from the hospital. Additionally, surveillance and preventive measures for MRSA is very time intensive and technological solutions are highly desirable.
The overall goal of this project is to create and validate informatics tools which utilize data mining techniques to identify individuals with MRSA, in order to support the implementation of evidence-based practices for preventing and reducing MRSA infections in the hospital setting.
This project will be focused around five specific aims.
Specific Aim 1: Develop, review and refine an ontology for clinically- and epidemiologically-relevant concepts to enable detection of MRSA for reporting purposes and gather requirements for developing a MRSA surveillance and reporting tool.
Specific Aim 2: Index MRSA-related Concepts in Clinical Narrative.
Specific Aim 3: Clinical Inference and Analysis of MRSA-Related Information contained in the medical record
Specific Aim 4: Develop and evaluate a prototype surveillance application that uses automatically processed VA electronic health record data
Translational Aim: Evaluate algorithms for making multi-type predictions based on heterogeneous data, using MRSA as a clinical domain.
In order to develop such a system, we analyzed workflow and sections of the EHR related to the surveillance process. An ontology including the signs and symptoms of various MRSA infections was specified using National Healthcare Safety Network (NHSN) surveillance criteria. Data needed to replicate the manual review workflow was obtained from a variety of sources including microbiology, vital signs, pharmacy, admission source, ICD codes, and demographic data. This established decision points within the overall algorithm for which specific data are needed. MRSA infections were sub-classified into five major types of infections (blood stream, lower respiratory, urinary tract, and skin and soft tissue), as well as whether or not the infection was associated with the presence of an invasive device and the epidemiologic source of infection (hospital-acquired, healthcare-associated community onset, or community associated).
We have extracted and annotated text data for Bloodstream infections and urinary tract infections (UTIs). We have refined the ontology we developed for MRSA and begun applying natural language processing (NLP) to these documents. We recently received approval and have created a national VA dataset of text and microbiologic data. We have also interviewed clinical infectious diseases and infection prevention specialists to identify important workflow and desired design features for the tool. We are currently using the algorithms, ontology and annotation guidelines, to refine the rules to discover MRSA concepts within documents, and make patient level inferences. This will involve using structured and NLP-annotated unstructured data on a given patient and tying these together to create rules that allow inferences about the nature of the infection or colonization.
Based on a review of NHSN guidelines, ten infection sub-classifications were found to be relevant to the research. The NLP pipeline was piloted with a document set from one of the medical centers. For this pilot, known infections based on each site's existing surveillance data were used as a reference standard for comparison. Based on the NLP pipeline and expert review, thirty terms or abbreviations consistently indicated the presence of a MRSA infection. In order to improve the accuracy in ruling out false positives, our results indicate that sectionalization, temporality, and parsing of VA templates will need to be further developed in order to accurately achieve the goals of our research.
In order to design a user interface for the surveillance too we are using the
Theoretic Framework- Promoting Action on Research Implementation in Health Services (PARiHS) Framework which assesses evidence, context and facilitation. We consider understanding workflow to be very important. In order to assess the context of future implementation and understand workflow, we interviewed key informants.
We have conducted 7 semi-structured interviews. Using a theoretical qualitative analysis, we have determined preliminary themes to inform our dashboard design. Some of the themes include: needing to evaluate clinical data to assess whether the clinical condition matches the surveillance definitions, accommodating a semi-structured workflow, providing a process by which a synthesis by the Infection Preventionist could be provided to the hospital epidemiologist, the need to aggregate multiple sources of data, among others.
MRSA is widely considered the most important antibiotic-resistant organism that causes healthcare associated infections.. Rates of resistance among these organisms have increased significantly over the last decade. In our previous work, we found overall point estimates for MRSA rates in U.S. (including VHA) hospitals to be 36% and increasing in all types of hospitals. Two-thirds of hospitals reported increasing MRSA rates, whereas only 4% reported decreasing rates, and 24% reported MRSA outbreaks within the previous year. Most hospitals (87%) reported having implemented measures to rapidly detect resistance, however, only half reported having either provided appropriate resources for antimicrobial resistance prevention (53%) or implemented antimicrobial use guidelines (60%). Current practices to prevent and control MRSA are widely shown to be inadequate. This project will promote more effective use of information technology to better inform decision making and implement processes to prevent and control MRSA.
The team is continuing to work further on the projects within this research study and will focus on completing Aim 4 in the time remaining.
External Links for this Project
- Bravata DM, Ferguson J, Miech EJ, Agarwal R, McClain V, Austin C, Struve F, Foresman B, Li X, Wang Z, Williams LS, Dallas MI, Couch CD, Sico J, Fragoso C, Matthias MS, Chumbler N, Myers J, Burrus N, Dube A, French DD, Schmid AA, Concato J, Yaggi HK. Diagnosis and Treatment of Sleep Apnea in patients' homes: the rationale and methods of the "GoToSleep" randomized-controlled trial. Journal of clinical sleep medicine : JCSM : official publication of the American Academy of Sleep Medicine. 2012 Feb 15; 8(1):27-35. [view]
- Zillich AJ, Jaynes HA, Snyder ME, Harrison J, Hudmon KS, de Moor C, French DD. Evaluation of specialized medication packaging combined with medication therapy management: adherence, outcomes, and costs among Medicaid patients. Medical care. 2012 Jun 1; 50(6):485-93. [view]
- French DD, Margo CE. Factors associated with the utilization of cataract surgery for veterans dually enrolled in Medicare. Military medicine. 2012 Jun 1; 177(6):752-6. [view]
- Jones M, DuVall SL, Spuhl J, Samore MH, Nielson C, Rubin M. Identification of methicillin-resistant Staphylococcus aureus within the nation's Veterans Affairs medical centers using natural language processing. BMC medical informatics and decision making. 2012 Jul 11; 12(1):34. [view]
- Doebbeling BN, Zillich AJ. Risk for Non-adherence and Other Drug Therapy problems among ambulatory patients utilizing a safety-net health system. Pharmacotherapy. 2011 Oct 31; 31(10):419e. [view]
- French DD, Margo CE. Short-term mortality following cataract surgery: comparison of Veterans Health Administration and Medicare outcomes. Ophthalmic Epidemiology. 2012 Jun 1; 19(3):144-8. [view]
- Scotch M, Rabinowitz P, Brandt C. State-level zoonotic disease surveillance in the United States. Zoonoses and public health. 2011 Dec 1; 58(8):523-8. [view]
- Doebbeling BN. Crucial Opportunities for Addressing Hospital Acquired Infections (Invited Response to Commentary). [Letter to the Editor]. Forum. 2010 Jan 1; 5:3. [view]
- Zillich AJ, French DD. Evaluation of Specialized Medication Packaging combined with Medication therapy management: adherence, outcomes and costs among Medicaid patients. [Abstract]. Pharmacotherapy. 2011 Oct 31; 31(10):340e. [view]
- Rubin M, Garvin JH, Doebbeling B, Merchant M, Martinello RA, Mutalik P, Goldstein MK, Luther S, Samore M, South B, Gullans S. An Informatics Approach to Methicillin Resistant Staphylococcus Aureus Surveillance in the Department of Veterans Affairs. Poster session presented at: American Medical Informatics Association Annual Symposium; 2011 Oct 25; Washington, DC. [view]
- Doebbeling BN. Healthcare Associated Infections: Assessment Center Findings. Paper presented at: National Surgical Quality Improvement Program / Agency for Healthcare Research and Quality Meeting; 2010 Feb 22; Bethesda, MD. [view]
- Doebbeling BN. Ontology Development and Text Processing for MRSA Surveillance. Paper presented at: VA Consortium for Healthcare Informatics Research Steering Committee Meeting; 2010 Jun 22; Salt Lake City, UT. [view]
- Doebbeling BN. Perioperative Transitions in Care: Integrating Patient Flow, Information Flow and Clinical Workflow. Poster session presented at: American Medical Informatics Association Annual Symposium; 2011 Nov 16; Washington, DC. [view]
- Doebbeling BN. Programs to Reduce MRSA Infections. Paper presented at: University of Texas Southwestern Medical Center Healthcare Associated Infections Symposium; 2010 Aug 28; Dallas, TX. [view]
- Doebbeling BN. Redesign Strategies to Reduce MRSA: Community Collaboratives Using Positive Deciance and Lean. Paper presented at: Center for Disease Control Eliminating Hospital Acquired Infections Grantees Meeting; 2009 Oct 19; Atlanta, GA. [view]
- Doebbeling BN, Zillich AJ. Risk for non-adherence and other drug therapy problems among ambulatory patients utilizing a safety-net health-system. Poster session presented at: American College of Clinical Pharmacy Annual Meeting; 2011 Sep 12; Chicago, IL. [view]
- Doebbeling BN. Taking Transformational Change to Scale: Reducing MRSA and other Infections (Invited Panel on Tools and Strategies for Transformational Change). Paper presented at: Integrated Healthcare Association Pay-For-Performance Annual Summit; 2010 Mar 9; San Francisco, CA. [view]
- Doebbeling BN, Garvin JH, Martins SB, Rubin MA. Tools to Facilitate Shared Understanding for Natural Language Processing Design in a Distributed, Virtual Development Environment. Poster session presented at: American Medical Informatics Association Annual Symposium; 2010 Nov 16; Washington, DC. [view]
Health Systems, Infectious Diseases
Technology Development and Assessment, Research Infrastructure, Epidemiology
Acute illness, Infectious disease, Informatics