Using the Electronic Medical Record to Identify Community-Acquired Pneumonia: Toward a Replicable Automated Strategy

PLoS ONE

Volumn 8, Issue 8, 2013, Pages

  DeLisle, Sylvain ^a,b   Kim, Bernard ^a,b   Deepak, Janaki ^a,b   Siddiqui, Tariq ^a,b   Gundlapalli, Adi ^a,c   Samore, Matthew ^a,c   D'Avolio, Leonard ^a,d  

^a VETERANS AFFAIRS MEDICAL CENTER   (United States)

^b UNIVERSITY OF MARYLAND SCHOOL OF MEDICINE   (United States)

^c UNIVERSITY OF UTAH SCHOOL OF MEDICINE   (United States)

^d BRIGHAM AND WOMEN S HOSPITAL   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ADULT; AGED; ARTICLE; AUTOMATION; CHILL; CLASSIFIER; COMMUNITY ACQUIRED PNEUMONIA; COMPUTER PROGRAM; CONTROLLED STUDY; COUGHING; DYSPNEA; ELECTRONIC MEDICAL RECORD; FEMALE; FEVER; HOSPITAL ADMISSION; HUMAN; MACHINE LEARNING; MAJOR CLINICAL STUDY; MALE; NIGHT SWEAT; OUTPATIENT DEPARTMENT; PREDICTIVE VALUE; REFERENCE DATABASE; SENSITIVITY ANALYSIS; SPUTUM; THORAX PAIN; THORAX RADIOGRAPHY;

ADOLESCENT; ADULT; AGED; AGED, 80 AND OVER; ALGORITHMS; COMMUNITY-ACQUIRED INFECTIONS; ELECTRONIC HEALTH RECORDS; FEMALE; HUMANS; MALE; MIDDLE AGED; OUTPATIENTS; PNEUMONIA; REPRODUCIBILITY OF RESULTS; SOFTWARE; YOUNG ADULT;

EID: 84881522519     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0070944     Document Type: Article

References (47)

1. Peiris JS, Guan Y, Yuen KY, (2004) Severe acute respiratory syndrome. Nat Med 10: S88-97.
2. Inglesby TV, Dennis DT, Henderson DA, Bartlett JG, Ascher MS, et al. (2000) Plague as a biological weapon: medical and public health management. Working Group on Civilian Biodefense. JAMA 283: 2281-2290.
3. Dennis DT, Inglesby TV, Henderson DA, Bartlett JG, Ascher MS, et al. (2001) Tularemia as a biological weapon: medical and public health management. JAMA 285: 2763-2773.
4. Miller MA, Viboud C, Olson DR, Grais RF, Rabaa MA, et al. (2008) Prioritization of influenza pandemic vaccination to minimize years of life lost. J Inf Dis 198: 305-311.
5. Andreasen V, Viboud C, Simonsen L, (2008) Epidemiologic characterization of the 1918 influenza pandemic summer wave in Copenhagen: implications for pandemic control strategies. J Inf Dis 197: 270-278.
6. Viboud C, Grais RF, Lafont BA, Miller MA, Simonsen L, (2005) Multinational impact of the 1968 Hong Kong influenza pandemic: evidence for a smoldering pandemic. J Inf Dis 192: 233-248.
7. Lipsitch M, Hayden FG, Cowling BJ, Leung GM, (2009) How to maintain surveillance for novel influenza A H1N1 when there are too many cases to count. Lancet 374: 1209-1211.
8. Lipsitch M, Riley S, Cauchemez S, Ghani AC, Ferguson NM, (2009) Managing and reducing uncertainty in an emerging influenza pandemic. N Engl J Med 361: 112-115.
9. Thompson WW, Weintraub E, Dhankhar P, Cheng PY, Brammer L, et al. (2009) Estimates of US influenza-associated deaths made using four different methods. Influenza Other Respi Viruses 3: 37-49.
10. DeLisle S, South B, Anthony JA, Kalp E, Gundlapallli A, et al. (2010) Combining free text and structured electronic medical record entries to detect acute respiratory infections. PLoS ONE 5: e13377.
11. Savova G (2008) UIMA-based clinical information system. Language Resources and Evaluation Conference. Morocco.
12. Lafferty J, McCallum A, Pereira F (2001) Conditional random fields: probabilistic models for segmenting and labeling sequence data. International Conference on Machine Learning. San Francisco: Morgan Kaufman. 282-289.
13. D'Avolio LW, Nguyen TM, Farwell WR, Chen Y, Fitzmeyer F, et al. (2010) Evaluation of a generalizable approach to clinical information retrieval using the automated retrieval console (ARC). J Am Med Inform Assoc 17: 375-382.
14. D'Avolio LW, Nguyen TM, Goryachev S, Fiore LD, (2011) Automated concept-level information extraction to reduce the need for custom software and rules development. J Am Med Inform Assoc 18: 607-613.
15. Corley DE, Kirtland SH, Winterbauer RH, Hammar SP, Dail DH, et al. (1997) Reproducibility of the histologic diagnosis of pneumonia among a panel of four pathologists: analysis of a gold standard. Chest 112: 458-465.
16. Fine MJ, Auble TE, Yealy DM, Hanusa BH, Weissfeld LA, et al. (1997) A prediction rule to identify low-risk patients with community-acquired pneumonia. N Engl J Med 336: 243-250.
17. Niederman MS, Mandell LA, Anzueto A, Bass JB, Broughton WA, et al. (2001) Guidelines for the management of adults with community-acquired pneumonia. Diagnosis, assessment of severity, antimicrobial therapy, and prevention. Am J Respir Crit Care Med 163: 1730-1754.
18. Bartlett JG, Dowell SF, Mandell LA, File Jr TM, Musher DM, et al. (2000) Practice guidelines for the management of community-acquired pneumonia in adults. Infectious Diseases Society of America. Clin Infect Dis 31: 347-382.
19. Mandell LA, Wunderink RG, Anzueto A, Bartlett JG, Campbell GD, et al. (2007) Infectious Diseases Society of America/American Thoracic Society consensus guidelines on the management of community-acquired pneumonia in adults. Clin Infect Dis 44Suppl 2: S27-72.
20. Whittle J, Fine MJ, Joyce DZ, Lave JR, Young WW, et al. (1997) Community-acquired pneumonia: can it be defined with claims data? Am J Med Qual 12: 187-193.
21. Skull SA, Andrews RM, Byrnes GB, Campbell DA, Nolan TM, et al. (2008) ICD-10 codes are a valid tool for identification of pneumonia in hospitalized patients aged > or = 65 years. Epidemiol Infect 136: 232-240.
22. Yu O, Nelson JC, Bounds L, Jackson LA, (2011) Classification algorithms to improve the accuracy of identifying patients hospitalized with community-acquired pneumonia using administrative data. Epidemiol Infect 139: 1296-1306.
23. Marrie TJ, Durant H, Sealy E, (1987) Pneumonia-the quality of medical records data. Med Care 25: 20-24.
24. Guevara RE, Butler JC, Marston BJ, Plouffe JF, File TM Jr, et al. (1999) Accuracy of ICD-9-CM codes in detecting community-acquired pneumococcal pneumonia for incidence and vaccine efficacy studies. Am J Epidemiol 149: 282-289.
25. Aronsky D, Haug PJ, Lagor C, Dean NC, (2005) Accuracy of administrative data for identifying patients with pneumonia. Am J Med Qual 20: 319-328.
26. van de Garde EM, Oosterheert JJ, Bonten M, Kaplan RC, Leufkens HG, (2007) International classification of diseases codes showed modest sensitivity for detecting community-acquired pneumonia. J Clin Epidemiol 60: 834-838.
27. Niederman MS, McCombs JS, Unger AN, Kumar A, Popovian R, (1998) The cost of treating community-acquired pneumonia. Clin Ther 20: 820-837.
28. Friedman C, Alderson PO, Austin JH, Cimino JJ, Johnson SB, (1994) A general natural-language text processor for clinical radiology. J Am Med Inform Assoc 1: 161-174.
29. Hripcsak G, Friedman C, Alderson PO, DuMouchel W, Johnson SB, et al. (1995) Unlocking clinical data from narrative reports: a study of natural language processing. Ann Intern Med 122: 681-688.
30. Hripcsak G, Austin JH, Alderson PO, Friedman C, (2002) Use of natural language processing to translate clinical information from a database of 889,921 chest radiographic reports. Radiology 224: 157-163.
31. Fiszman M, Chapman WW, Aronsky D, Evans RS, Haug PJ, (2000) Automatic detection of acute bacterial pneumonia from chest X-ray reports. J Am Med Inform Assoc 7: 593-604.
32. Chapman WW, Fizman M, Chapman BE, Haug PJ, (2001) A comparison of classification algorithms to automatically identify chest X-ray reports that support pneumonia. J Biomed Inform 34: 4-14.
33. Wilcox AB, Hripcsak G, (2003) The role of domain knowledge in automating medical text report classification. J Am Med Inform Assoc 10: 330-338.
34. Chapman WW, Haug PJ (1998) Bayesian modeling for linking causally related observations in chest X-ray reports. Proceedings./AMIA Annual Symposium AMIA Symposium: 587-591.
35. Lagor C, Aronsky D, Fiszman M, Haug PJ, (2001) Automatic identification of patients eligible for a pneumonia guideline: comparing the diagnostic accuracy of two decision support models. Stud Health Technol Inform 84: 493-497.
36. Hripcsak G, Knirsch C, Zhou L, Wilcox A, Melton GB, (2007) Using discordance to improve classification in narrative clinical databases: an application to community-acquired pneumonia. Comput Biol Med 37: 296-304.
37. Asatryan A, Benoit S, Ma H, English R, Elkin P, et al. (2011) Detection of pneumonia using free-text radiology reports in the BioSense system. Int J Med Inform 80: 67-73.
38. Haas JP, Mendonca EA, Ross B, Friedman C, Larson E, (2005) Use of computerized surveillance to detect nosocomial pneumonia in neonatal intensive care unit patients. Am J Infect Control 33: 439-443.
39. Mendonca EA, Haas J, Shagina L, Larson E, Friedman C, (2005) Extracting information on pneumonia in infants using natural language processing of radiology reports. J Biomed Inform 38: 314-321.
40. Aronsky D, Fiszman M, Chapman WW, Haug PJ (2001) Combining decision support methodologies to diagnose pneumonia. Proceedings/AMIA Annual Symposium AMIA Symposium: 12-16.
41. Nolt BR, Gonzales R, Maselli J, Aagaard E, Camargo CA Jr, et al. (2007) Vital-sign abnormalities as predictors of pneumonia in adults with acute cough illness. The American journal of emergency medicine 25: 631-636.
42. Melbye H, Straume B, Brox J, (1992) Laboratory tests for pneumonia in general practice: the diagnostic values depend on the duration of illness. Scand J Prim Health Care 10: 234-240.
43. Fine MJ, Stone RA, Singer DE, Coley CM, Marrie TJ, et al. (1999) Processes and outcomes of care for patients with community-acquired pneumonia: results from the Pneumonia Patient Outcomes Research Team (PORT) cohort study. Arch Intern Med 159: 970-980.
44. Begg CB, Greenes RA, (1983) Assessment of diagnostic tests when disease verification is subject to selection bias. Biometrics 39: 207-215.
45. Metlay JP, Fine MJ, (2003) Testing strategies in the initial management of patients with community-acquired pneumonia. Ann Intern Med 138: 109-118.
46. Syrjala H, Broas M, Suramo I, Ojala A, Lahde S, (1998) High-resolution computed tomography for the diagnosis of community-acquired pneumonia. Clin Infect Dis 27: 358-363.
47. Metlay JP, Schulz R, Li YH, Singer DE, Marrie TJ, et al. (1997) Influence of age on symptoms at presentation in patients with community-acquired pneumonia. Arch Intern Med 157: 1453-1459.