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Makoto M. Jones

Makoto M. Jones, MD, MS

Languages spoken: English, Japanese

Academic Information

Departments Primary - Internal Medicine

Divisions: Epidemiology

Academic Office Information

Board Certification

  • American Board of Internal Medicine (Sub: Infectious Disease)
  • American Board of Preventive Medicine (Clinical Informatics)
  • National Board of Medical Examiners

Research Interests

  • Epidemiology/Nosocomial Infections
  • Mathematical Modeling
  • Infection Control
  • Antimicrobial Stewardship
  • Antibiotic-Resistant Pathogens
  • Medical Informatics
  • Health Services Research
  • Decision Support Systems, Clinical

My clinical interests lie primarily in the diagnosis and treatment of nosocomial pathogens and evidence-based prescription of antimicrobials.

Education History

Graduate Training University of Utah
University of Utah
Residency University of Washington
Saint Louis University School of Medicine
Undergraduate Brigham Young University

Selected Publications

Journal Article

  1. Rush E, Ozmen O, Kim M, Ortegon ER, Jones M, Park BH, Pizer S, Trafton J, Brenner LA, Ward M, Nebeker JR (2024). A framework for inferring and analyzing pharmacotherapy treatment patterns. BMC Med Inform Decis Mak, 24(1), 68. (Read full article)
  2. Livorsi DJ, Branch-Elliman W, Drekonja D, Echevarria KL, Fitzpatrick MA, Goetz MB, Graber CJ, Jones MM, Kelly AA, Madaras-Kelly K, Morgan DJ, Stevens VW, Suda K, Trautner BW, Ward MJ, Jump RLP (2024). Research agenda for antibiotic stewardship within the Veterans' Health Administration, 2024-2028. Infect Control Hosp Epidemiol, 1-7. (Read full article)
  3. Chapman AB, Peterson KS, Rutter E, Nevers M, Ying J, Classen D, Jones M, Samore M, Jones B (2024). A Linguistic Analysis Examining the Impact of COVID-19 on Pneumonia Diagnosis and Disease Models. Stud Health Technol Inform, 310, 1444-1445. (Read full article)
  4. Donnelly JP, Seelye SM, Kipnis P, McGrath BM, Iwashyna TJ, Pogue J, Jones M, Liu VX, Prescott HC (2025). Impact of Reducing Time-to-Antibiotics on Sepsis Mortality, Antibiotic Use, and Adverse Events. Ann Am Thorac Soc, 21(1), 94-101. (Read full article)
  5. Vivo A, Fitzpatrick MA, Suda KJ, Wilson GM, Jones MM, Evans ME, Evans CT (2023). Treatment effectiveness of antibiotic therapy in Veterans with multidrug-resistant Acinetobacter spp. bacteremia. Antimicrob Steward Healthc Epidemiol, 3(1), e230. (Read full article)
  6. Evans ME, Simbartl LA, McCauley BP, Flarida LK, Jones MM, Harris AD, Perencevich EN, Rubin MA, Hicks NR, Kralovic SM, Roselle GA (2023). Active Surveillance and Contact Precautions for Preventing Methicillin-Resistant Staphylococcus aureus Healthcare-Associated Infections during the COVID-19 Pandemic. Clin Infect Dis, 77(10), 1381-1386. (Read full article)
  7. Evans ME, Jones MM, Davis KW, Lane MT, Simbartl LA, McCauley BP, Gauldin N, Roselle GA (2022). Lack of correlation between standardized antimicrobial administration ratios (SAARs) and healthcare-facility-onset Clostridioides difficile infection rates in Veterans Affairs medical facilities. Infect Control Hosp Epidemiol, 44(6), 945-947. (Read full article)
  8. Hancock JA, Campbell S, Jones MM, Wang-Rodriguez J, VHA Microbiology SME Workgroup, Klutts JS (2023). Development and validation of a standardized blood culture contamination definition and metric dashboard for a large health care system. Am J Clin Pathol. (Read full article)
  9. Gamage SD, Evans ME, McCauley BP, Lipscomb KR, Flarida L, Jones MM, Baza M, Barraza J, Simbartl LA, Roselle GA (2022). Hospital coronavirus disease 2019 (COVID-19) public health reporting: Lessons from validation of an automated surveillance tool to facilitate data collection. Infect Control Hosp Epidemiol, 44(5), 802-804. (Read full article)
  10. Evans ME, Simbartl LA, Kralovic SM, Clifton M, DeRoos K, McCauley BP, Gauldin N, Flarida LK, Gamage SD, Jones MM, Roselle GA (2022). Healthcare-associated infections in Veterans Affairs acute-care and long-term healthcare facilities during the coronavirus disease 2019 (COVID-19) pandemic. Infect Control Hosp Epidemiol, 44(3), 420-426. (Read full article)
  11. Graber CJ, Simon AR, Zhang Y, Goetz MB, Jones MM, Butler JM, Chou AF, Glassman PA (2022). Performance of infectious diseases specialists, hospitalists, and other internal medicine physicians in antimicrobial case-based scenarios: Potential impact of antimicrobial stewardship programs at 16 Veterans' Affairs medical centers. Infect Control Hosp Epidemiol, 44(3), 400-405. (Read full article)
  12. Chapman AB, Peterson KS, Rutter E, Nevers M, Zhang M, Ying J, Jones M, Classen D, Jones B (2022). Development and evaluation of an interoperable natural language processing system for identifying pneumonia across clinical settings of care and institutions. JAMIA Open, 5(4), ooac114. (Read full article)
  13. Jones BE, Ying J, Nevers MR, Alba PR, Patterson OV, Peterson KS, Rutter E, Christensen MA, Stern S, Jones MM, Gundlapalli A, Dean NC, Samore MC, Greene T (2022). Trends in Illness Severity, Hospitalization, and Mortality for Community-Onset Pneumonia at 118 US Veterans Affairs Medical Centers. J Gen Intern Med, 37(15), 3839-3847. (Read full article)
  14. Wilson GM, Fitzpatrick MA, Suda KJ, Smith BM, Gonzalez B, Jones M, Schweizer ML, Evans M, Evans CT (2022). Comparative effectiveness of antibiotic therapy for carbapenem-resistant Enterobacterales (CRE) bloodstream infections in hospitalized US veterans. JAC Antimicrob Resist, 4(5), dlac106. (Read full article)
  15. Smith JT, Manickam RN, Barreda F, Greene JD, Bhimarao M, Pogue J, Jones M, Myers L, Prescott HC, Liu VX (2022). Quantifying the breadth of antibiotic exposure in sepsis and suspected infection using spectrum scores. Medicine (Baltimore), 101(41), e30245. (Read full article)
  16. Rovelsky SA, Vu M, Barrett AK, Bukowski K, Wei X, Burk M, Jones M, Echevarria K, Suda KJ, Cunningham F, Madaras-Kelly KJ, UTI Management Improvement Group (2022). Outpatient treatment and clinical outcomes of bacteriuria in veterans: A retrospective cohort analysis. Antimicrob Steward Healthc Epidemiol, 2(1), e168. (Read full article)
  17. Widanagamaachchi W, Peterson K, Chapman A, Classen D, Jones M (2022). A flexible framework for visualizing and exploring patient misdiagnosis over time. J Biomed Inform, 134, 104178. (Read full article)
  18. Ramanathan S, Albarillo FS, Fitzpatrick MA, Suda KJ, Poggensee L, Vivo A, Evans ME, Jones M, Safdar N, Pfeiffer C, Smith B, Wilson G, Evans CT (2022). Infectious Disease Consults of Pseudomonas aeruginosa Bloodstream Infection and Impact on Health Outcomes. Open Forum Infect Dis, 9(9), ofac456. (Read full article)
  19. Fitzpatrick MA, Suda KJ, Poggensee L, Vivo A, Wilson G, Jones MM, Evans M, Safdar N, Evans CT (2022). Treatment of extensively-drug resistant (XDR) Acinetobacter and impact on clinical outcomes in U.S. veterans affairs (VA) medical centers. Am J Infect Control, 50(9), 1020-1025. (Read full article)
  20. Gawron AJ, Sultan S, Glorioso TJ, Califano S, Kralovic SM, Jones M, Kirsh S, Dominitz JA (2022). Pre-endoscopy coronavirus disease 2019 screening and severe acute respiratory syndrome coronavirus-2 nucleic acid amplification testing in the Veterans Affairs healthcare system: clinical practice patterns, outcomes, and relationship to procedure volume. Gastrointest Endosc, 96(3), 423-432.e7. (Read full article)
  21. Prescott HC, Seelye S, Wang XQ, Hogan CK, Smith JT, Kipnis P, Barreda F, Donnelly JP, Pogue JM, Iwashyna TJ, Jones MM, Liu VX (2022). Temporal Trends in Antimicrobial Prescribing During Hospitalization for Potential Infection and Sepsis. JAMA Intern Med, 182(8), 805-813. (Read full article)
  22. Fitzpatrick MA, Suda KJ, Ramanathan S, Wilson G, Poggensee L, Evans M, Jones MM, Pfeiffer CD, Klutts JS, Perencevich E, Rubin M, Evans CT, QUERI CARRIAGE Program (2022). Increased carbapenemase testing following implementation of national VA guidelines for carbapenem-resistant Enterobacterales (CRE). Antimicrob Steward Healthc Epidemiol, 2(1), e88. (Read full article)
  23. Kalvesmaki AF, Chapman AB, Peterson KS, Pugh MJ, Jones M, Gleason TC (2022). Analysis of a national response to a White House directive for ending veteran suicide. Health Serv Res, 57 Suppl 1(Suppl 1), 32-41. (Read full article)
  24. Vivo A, Fitzpatrick MA, Suda KJ, Jones MM, Perencevich EN, Rubin MA, Ramanathan S, Wilson GM, Evans ME, Evans CT (2022). Epidemiology and outcomes associated with carbapenem-resistant Acinetobacter baumannii and carbapenem-resistant Pseudomonas aeruginosa: a retrospective cohort study. BMC Infect Dis, 22(1), 491. (Read full article)
  25. Eyre H, Chapman AB, Peterson KS, Shi J, Alba PR, Jones MM, Box TL, DuVall SL, Patterson OV (2022). Launching into clinical space with medspaCy: a new clinical text processing toolkit in Python. AMIA Annu Symp Proc, 2021, 438-447. (Read full article)
  26. Claeys KC, Trautner BW, Leekha S, Coffey KC, Crnich CJ, Diekema D, Fakih MG, Goetz MB, Gupta K, Jones MM, Leykum L, Liang SY, Pineles L, Pleiss A, Spivak ES, Suda KJ, Taylor J, Rhee C, Morgan DJ (2021). Optimal Urine Culture Diagnostic Stewardship Practice- Results from an Expert Modified-Delphi Procedure. Clin Infect Dis. (Read full article)
  27. Lynch KE, Viernes B, Gatsby E, DuVall SL, Jones BE, Box TL, Kreisler C, Jones M (2021). Positive Predictive Value of COVID-19 ICD-10 Diagnosis Codes Across Calendar Time and Clinical Setting. Clin Epidemiol, 13, 1011-1018. (Read full article)
  28. Wilson GM, Suda KJ, Fitzpatrick MA, Bartle B, Pfeiffer CD, Jones M, Rubin MA, Perencevich E, Evans M, Evans CT, QUERI CARRIAGE Program (2021). Risk Factors Associated With Carbapenemase-Producing Carbapenem-Resistant Enterobacteriaceae Positive Cultures in a Cohort of US Veterans. Clin Infect Dis, 73(8), 1370-1378. (Read full article)
  29. Chapman AB, Jones A, Kelley AT, Jones B, Gawron L, Montgomery AE, Byrne T, Suo Y, Cook J, Pettey W, Peterson K, Jones M, Nelson R (2021). ReHouSED: A novel measurement of Veteran housing stability using natural language processing. J Biomed Inform, 122, 103903. (Read full article)
  30. Wayne MT, Seelye S, Molling D, Wang XQ, Donnelly JP, Hogan CK, Jones MM, Iwashyna TJ, Liu VX, Prescott HC (2021). Temporal Trends and Hospital Variation in Time-to-Antibiotics Among Veterans Hospitalized With Sepsis. JAMA Netw Open, 4(9), e2123950. (Read full article)
  31. Wirth MS, Fitzpatrick MA, Suda KJ, Wilson GM, Ramanathan S, Evans ME, Jones MM, Pfeiffer CD, Evans CT (2020). Carbapenem-resistant Enterobacteriaceae epidemiology in Veterans' Affairs medical centers varies by facility characteristics. Infect Control Hosp Epidemiol, 42(7), 885-889. (Read full article)
  32. Taber P, Weir C, Butler JM, Graber CJ, Jones MM, Madaras-Kelly K, Zhang Y, Chou AF, Samore MH, Goetz MB, Glassman PA (2021). Social dynamics of a population-level dashboard for antimicrobial stewardship: A qualitative analysis. Am J Infect Control, 49(7), 862-867. (Read full article)
  33. Jones BE, Ying J, Nevers M, Alba PR, He T, Patterson OV, Jones MM, Stevens V, Shen J, Humpherys J, Peterson KS, Rutter ED, Gundlapalli AV, Weir CR, Dean NC, Fine MJ, Samore MC, Greene TH (2021). Computerized Mortality Prediction for Community-acquired Pneumonia at 117 Veterans Affairs Medical Centers. Ann Am Thorac Soc, 18(7), 1175-1184. (Read full article)
  34. Dieringer TD, Furukawa D, Graber CJ, Stevens VW, Jones MM, Rubin MA, Goetz MB (2020). Inpatient antibiotic utilization in the Veterans' Health Administration during the coronavirus disease 2019 (COVID-19) pandemic. Infect Control Hosp Epidemiol, 42(6), 751-753. (Read full article)
  35. Peterson KS, Lewis J, Patterson OV, Chapman AB, Denhalter DW, Lye PA, Stevens VW, Gamage SD, Roselle GA, Wallace KS, Jones M (2021). Automated Travel History Extraction From Clinical Notes for Informing the Detection of Emergent Infectious Disease Events: Algorithm Development and Validation. JMIR Public Health Surveill, 7(3), e26719. (Read full article)
  36. Khader K, Thomas A, Stevens V, Visnovsky L, Nevers M, Toth D, Keegan LT, Jones M, Rubin M, Samore MH (2021). Association Between Contact Precautions and Transmission of Methicillin-Resistant Staphylococcus aureus in Veterans Affairs Hospitals. JAMA Netw Open, 4(3), e210971. (Read full article)
  37. Nelson RE, Lautenbach E, Chang N, Jones M, Willson T, David M, Linkin D, Glick H, Doshi JA, Stevens VW (2020). Attributable Cost of Healthcare-Associated Methicillin-Resistant Staphylococcus aureus Infection in a Long-term Care Center. Clin Infect Dis, 72(Suppl 1), S27-S33. (Read full article)
  38. Nelson RE, Goto M, Samore MH, Jones M, Stevens VW, Evans ME, Schweizer ML, Perencevich EN, Rubin MA (2020). Expanding an Economic Evaluation of the Veterans Affairs (VA) Methicillin-resistant Staphylococcus aureus (MRSA) Prevention Initiative to Include Prevention of Infections From Other Pathogens. Clin Infect Dis, 72(Suppl 1), S50-S58. (Read full article)
  39. Christensen MA, Nevers M, Ying J, Haroldsen C, Stevens V, Jones MM, Yarbrough PM, Goetz MB, Restrepo MI, Madaras-Kelly K, Samore MH, Jones BE (2020). Simulated Adoption of 2019 Community-Acquired Pneumonia Guidelines Across 114 Veterans Affairs Medical Centers: Estimated Impact on Culturing and Antibiotic Selection in Hospitalized Patients. Clin Infect Dis, 72(Suppl 1), S59-S67. (Read full article)
  40. Ramanathan S, Suda KJ, Fitzpatrick MA, Guihan M, Goedken CC, Safdar N, Evans M, Jones M, Pfeiffer CD, Perencevich EN, Rubin M, Evans CT, QUERI CARRIAGE Program (2020). A survey of infection control strategies for carbapenem-resistant Enterobacteriaceae in Department of Veterans' Affairs facilities. Infect Control Hosp Epidemiol, 43, 1-4. (Read full article)
  41. Graber CJ, Jones MM, Goetz MB, Madaras-Kelly K, Zhang Y, Butler JM, Weir C, Chou AF, Youn SY, Samore MH, Glassman PA (2019). Decreases in Antimicrobial Use Associated With Multihospital Implementation of Electronic Antimicrobial Stewardship Tools. Clin Infect Dis, 71(5), 1168-1176. (Read full article)
  42. Stevens VW, Khader K, Echevarria K, Nelson RE, Zhang Y, Jones M, Timbrook TT, Samore MH, Rubin MA (2019). Use of Oral Vancomycin for Clostridioides difficile Infection and the Risk of Vancomycin-Resistant Enterococci. Clin Infect Dis, 71(3), 645-651. (Read full article)
  43. Ramanathan S, Fitzpatrick MA, Suda KJ, Burns SP, Jones MM, LaVela SL, Evans CT (2019). Multidrug-resistant gram-negative organisms and association with 1-year mortality, readmission, and length of stay in Veterans with spinal cord injuries and disorders. Spinal Cord, 58(5), 596-608. (Read full article)
  44. Stevens VW, Shoemaker HE, Jones MM, Jones BE, Nelson RE, Khader K, Samore MH, Rubin MA (2020). Validation of the SHEA/IDSA severity criteria to predict poor outcomes among inpatients and outpatients with Clostridioides difficile infection. Infect Control Hosp Epidemiol, 41(5), 510-516. (Read full article)
  45. Jones BE, Ying J, Stevens V, Haroldsen C, He T, Nevers M, Christensen MA, Nelson RE, Stoddard GJ, Sauer BC, Yarbrough PM, Jones MM, Goetz MB, Greene T, Samore MH (2020). Empirical Anti-MRSA vs Standard Antibiotic Therapy and Risk of 30-Day Mortality in Patients Hospitalized for Pneumonia. JAMA Intern Med, 180(4), 552-560. (Read full article)
  46. Sutton JD, Carico R, Burk M, Jones MM, Wei X, Neuhauser MM, Goetz MB, Echevarria KL, Spivak ES, Cunningham FE, Skin and Soft Tissue Infection Medication Use Evaluation Group (2020). Inpatient Management of Uncomplicated Skin and Soft Tissue Infections in 34 Veterans Affairs Medical Centers: A Medication Use Evaluation. Open Forum Infect Dis, 7(1), ofz554. (Read full article)
  47. Bostwick AD, Jones BE, Paine R, Goetz MB, Samore M, Jones M (2019). Potential Impact of Hospital-acquired Pneumonia Guidelines on Empiric Antibiotics. An Evaluation of 113 Veterans Affairs Medical Centers. Ann Am Thorac Soc, 16(11), 1392-1398. (Read full article)
  48. Khader K, Thomas A, Jones M, Toth D, Stevens V, Samore MH, CDC Modeling Infectious Diseases in Healthcare Program MInD-Healthcare (2019). Variation and trends in transmission dynamics of Methicillin-resistant Staphylococcus aureus in veterans affairs hospitals and nursing homes. Epidemics, 28, 100347. (Read full article)
  49. Fitzpatrick MA, Suda KJ, Ramanathan S, Guihan M, Brown C, Safdar N, Evans M, Jones MM, Pfeiffer CD, Klutts JS, Icardi M, Perencevich E, Rubin M, Evans CT, QUERI CARRIAGE Program (2019). Laboratory practices for identification and reporting of carbapenem-resistant Enterobacteriaceae in Department of Veterans Affairs facilities. Infect Control Hosp Epidemiol, 40(4), 463-466. (Read full article)
  50. Bohan JG, Madaras-Kelly K, Pontefract B, Jones M, Neuhauser MM, Bidwell Goetz M, Burk M, Cunningham F, ARI Management Improvement Group (2019). Evaluation of uncomplicated acute respiratory tract infection management in veterans: A national utilization review. Infect Control Hosp Epidemiol, 40(4), 438-446. (Read full article)
  51. Jones M, Jernigan JA, Evans ME, Roselle GA, Hatfield KM, Samore MH (2019). Vital Signs: Trends in Staphylococcus aureus Infections in Veterans Affairs Medical Centers - United States, 2005-2017. MMWR Morb Mortal Wkly Rep, 68(9), 220-224. (Read full article)
  52. Nelson RE, Evans ME, Simbartl L, Jones M, Samore MH, Kralovic SM, Roselle GA, Rubin MA (2018). Methicillin-resistant Staphylococcus aureus Colonization and Pre- and Post-hospital Discharge Infection Risk. Clin Infect Dis, 68(4), 545-553. (Read full article)
  53. Nelson RE, Jones M, Liu CF, Samore MH, Evans ME, Stevens VW, Reese T, Rubin MA (2018). The Impact of Healthcare-Associated Methicillin-Resistant Staphylococcus aureus Infections on Postdischarge Health Care Costs and Utilization across Multiple Health Care Systems. Health Serv Res, 53 Suppl 3, 5419-5437. (Read full article)
  54. Nelson RE, Stevens VW, Jones M, Khader K, Schweizer ML, Perencevich EN, Rubin MA, Samore MH (2018). Attributable Cost and Length of Stay Associated with Nosocomial Gram-Negative Bacterial Cultures. Antimicrob Agents Chemother, 62(11). (Read full article)
  55. Chou AF, Graber CJ, Zhang Y, Jones M, Goetz MB, Madaras-Kelly K, Samore M, Glassman PA (2017). Specifying an implementation framework for Veterans Affairs antimicrobial stewardship programmes: using a factor analysis approach. J Antimicrob Chemother, 73(9), 2559-2566. (Read full article)
  56. Fitzpatrick MA, Suda KJ, Safdar N, Burns SP, Jones MM, Poggensee L, Ramanathan S, Evans CT (2017). Changes in bacterial epidemiology and antibiotic resistance among veterans with spinal cord injury/disorder over the past 9 years. J Spinal Cord Med, 41(2), 199-207. (Read full article)
  57. Jones M, Butler J, Graber CJ, Glassman P, Samore MH, Pollack LA, Weir C, Goetz MB (2016). Think twice: A cognitive perspective of an antibiotic timeout intervention to improve antibiotic use. J Biomed Inform, 71S, S22-S31. (Read full article)
  58. Leecaster MK, Weir CR, Drews FA, Hellewell JL, Bolton D, Jones MM, Nebeker JR (2016). Translation of Contextual Control Model to chronic disease management: A paradigm to guide design of cognitive support systems. J Biomed Inform, 71S, S60-S67. (Read full article)
  59. Kelly AA, Jones MM, Echevarria KL, Kralovic SM, Samore MH, Goetz MB, Madaras-Kelly KJ, Simbartl LA, Morreale AP, Neuhauser MM, Roselle GA (2017). A Report of the Efforts of the Veterans Health Administration National Antimicrobial Stewardship Initiative. Infect Control Hosp Epidemiol, 38(5), 513-520. (Read full article)
  60. Stevens VW, Nelson RE, Schwab-Daugherty EM, Khader K, Jones MM, Brown KA, Greene T, Croft LD, Neuhauser M, Glassman P, Goetz MB, Samore MH, Rubin MA (2017). Comparative Effectiveness of Vancomycin and Metronidazole for the Prevention of Recurrence and Death in Patients With Clostridium difficile Infection. JAMA Intern Med, 177(4), 546-553. (Read full article)
  61. Goto M, OShea AMJ, Livorsi DJ, McDanel JS, Jones MM, Richardson KK, Beck BF, Alexander B, Evans ME, Roselle GA, Kralovic SM, Perencevich EN (2016). The Effect of a Nationwide Infection Control Program Expansion on Hospital-Onset Gram-Negative Rod Bacteremia in 130 Veterans Health Administration Medical Centers: An Interrupted Time-Series Analysis. Clin Infect Dis, 63(5), 642-650. (Read full article)
  62. Fitzpatrick MA, Suda KJ, Safdar N, Goldstein B, Jones MM, Poggensee L, Ramanathan S, LeWan R, Evans CT (2016). Unique Risks and Clinical Outcomes Associated With Extended-Spectrum β-Lactamase Enterobacteriaceae in Veterans With Spinal Cord Injury or Disorder: A Case-Case-Control Study. Infect Control Hosp Epidemiol, 37(7), 768-76. (Read full article)
  63. Roosan D, Del Fiol G, Butler J, Livnat Y, Mayer J, Samore M, Jones M, Weir C (2016). Feasibility of Population Health Analytics and Data Visualization for Decision Support in the Infectious Diseases Domain: A pilot study. Appl Clin Inform, 7(2), 604-23. (Read full article)
  64. Brown KA, Jones M, Daneman N, Adler FR, Stevens V, Nechodom KE, Goetz MB, Samore MH, Mayer J (2016). Importation, Antibiotics, and Clostridium difficile Infection in Veteran Long-Term Care: A Multilevel Case-Control Study. Ann Intern Med, 164(12), 787-94. (Read full article)
  65. Chou AF, Graber CJ, Jones M, Zhang Y, Goetz MB, Madaras-Kelly K, Samore M, Kelly A, Glassman PA (2016). Characteristics of Antimicrobial Stewardship Programs at Veterans Affairs Hospitals: Results of a Nationwide Survey. Infect Control Hosp Epidemiol, 37(6), 647-54. (Read full article)
  66. Nelson RE, Stevens VW, Khader K, Jones M, Samore MH, Evans ME, Douglas Scott R 2nd, Slayton RB, Schweizer ML, Perencevich EL, Rubin MA (2016). Economic Analysis of Veterans Affairs Initiative to Prevent Methicillin-Resistant Staphylococcus aureus Infections. Am J Prev Med, 50(5 Suppl 1), S58-S65. (Read full article)
  67. Nelson RE, Jones M, Leecaster M, Samore MH, Ray W, Huttner A, Huttner B, Khader K, Stevens VW, Gerding D, Schweizer ML, Rubin MA (2016). An Economic Analysis of Strategies to Control Clostridium Difficile Transmission and Infection Using an Agent-Based Simulation Model. PLoS One, 11(3), e0152248. (Read full article)
  68. Madaras-Kelly K, Jones M, Remington R, Caplinger CM, Huttner B, Jones B, Samore M (2016). Antimicrobial de-escalation of treatment for healthcare-associated pneumonia within the Veterans Healthcare Administration. J Antimicrob Chemother, 71(2), 539-46. (Read full article)
  69. Jones MM, Nelson RE, Rubin MA (2015). Cumulative Attributable Difference: An Infection Metric That Reflects a Value System. Infect Control Hosp Epidemiol, 36(12), 1385-7. (Read full article)
  70. Islam R, Weir CR, Jones M, Del Fiol G, Samore MH (2015). Understanding complex clinical reasoning in infectious diseases for improving clinical decision support design. BMC Med Inform Decis Mak, 15, 101. (Read full article)
  71. Jones BE, Jones MM, Huttner B, Stoddard G, Brown KA, Stevens VW, Greene T, Sauer B, Madaras-Kelly K, Rubin M, Goetz MB, Samore M (2015). Trends in Antibiotic Use and Nosocomial Pathogens in Hospitalized Veterans With Pneumonia at 128 Medical Centers, 2006-2010. Clin Infect Dis, 61(9), 1403-10. (Read full article)
  72. Nelson RE, Samore MH, Jones M, Greene T, Stevens VW, Liu CF, Graves N, Evans MF, Rubin MA (2015). Reducing Time-dependent Bias in Estimates of the Attributable Cost of Health Care-associated Methicillin-resistant Staphylococcus aureus Infections: A Comparison of Three Estimation Strategies. Med Care, 53(9), 827-34. (Read full article)
  73. Stevens VW, Khader K, Nelson RE, Jones M, Rubin MA, Brown KA, Evans ME, Greene T, Slade E, Samore MH (2015). Excess Length of Stay Attributable to Clostridium difficile Infection (CDI) in the Acute Care Setting: A Multistate Model. Infect Control Hosp Epidemiol, 36(9), 1024-30. (Read full article)
  74. Jones BE, Sauer B, Jones MM, Campo J, Damal K, He T, Ying J, Greene T, Goetz MB, Neuhauser MM, Hicks LA, Samore MH (2015). Variation in Outpatient Antibiotic Prescribing for Acute Respiratory Infections in the Veteran Population: A Cross-sectional Study. Ann Intern Med, 163(2), 73-80. (Read full article)
  75. Nelson RE, Jones M, Liu CF, Samore MH, Evans ME, Graves N, Lee B, Rubin MA (2015). The impact of healthcare-associated methicillin-resistant Staphylococcus aureus infections on post-discharge healthcare costs and utilization. Infect Control Hosp Epidemiol, 36(5), 534-42. (Read full article)
  76. Madaras-Kelly K, Jones M, Remington R, Caplinger C, Huttner B, Samore M (2015). Description and validation of a spectrum score method to measure antimicrobial de-escalation in healthcare associated pneumonia from electronic medical records data. BMC Infect Dis, 15, 197. (Read full article)
  77. Huttner B, Jones M, Madaras-Kelly K, Neuhauser MM, Rubin MA, Goetz MB, Samore MH (2015). Initiation and termination of antibiotic regimens in Veterans Affairs hospitals. J Antimicrob Chemother, 70(2), 598-601. (Read full article)
  78. Nelson RE, Stevens VW, Jones M, Samore MH, Rubin MA (2015). Health care-associated methicillin-resistant Staphylococcus aureus infections increases the risk of postdischarge mortality. Am J Infect Control, 43(1), 38-43. (Read full article)
  79. Jones M, Nielson C, Gupta K, Khader K, Evans M (2015). Collateral benefit of screening patients for methicillin-resistant Staphylococcus aureus at hospital admission: isolation of patients with multidrug-resistant gram-negative bacteria. Am J Infect Control, 43(1), 31-4. (Read full article)
  80. Patterson OV, Jones M, Yao Y, Viernes B, Alba PR, Iwashyna TJ, DuVall SL (2015). Extraction of Vital Signs from Clinical Notes. Stud Health Technol Inform, 216, 1035. (Read full article)
  81. Jones M, Huttner B, Leecaster M, Huttner A, Damal K, Tanner W, Nielson C, Rubin MA, Goetz MB, Madaras-Kelly K, Samore MH (2014). Does universal active MRSA surveillance influence anti-MRSA antibiotic use? A retrospective analysis of the treatment of patients admitted with suspicion of infection at Veterans Affairs Medical Centers between 2005 and 2010. J Antimicrob Chemother, 69(12), 3401-8. (Read full article)
  82. Madaras-Kelly K, Jones M, Remington R, Hill N, Huttner B, Samore M (2014). Development of an antibiotic spectrum score based on veterans affairs culture and susceptibility data for the purpose of measuring antibiotic de-escalation: a modified Delphi approach. Infect Control Hosp Epidemiol, 35(9), 1103-13. (Read full article)
  83. Fridkin S, Baggs J, Fagan R, Magill S, Pollack LA, Malpiedi P, Slayton R, Khader K, Rubin MA, Jones M, Samore MH, Dumyati G, Dodds-Ashley E, Meek J, Yousey-Hindes K, Jernigan J, Shehab N, Herrera R, McDonald CL, Schneider A, Srinivasan A, Centers for Disease Control and Prevention CDC (2014). Vital signs: improving antibiotic use among hospitalized patients. MMWR Morb Mortal Wkly Rep, 63(9), 194-200. (Read full article)
  84. Jones M, Ying J, Huttner B, Evans M, Maw M, Nielson C, Rubin MA, Greene T, Samore MH (2014). Relationships between the importation, transmission, and nosocomial infections of methicillin-resistant Staphylococcus aureus: an observational study of 112 Veterans Affairs Medical Centers. Clin Infect Dis, 58(1), 32-9. (Read full article)
  85. Rubin MA, Jones M, Leecaster M, Khader K, Ray W, Huttner A, Huttner B, Toth D, Sablay T, Borotkanics RJ, Gerding DN, Samore MH (2013). A simulation-based assessment of strategies to control Clostridium difficile transmission and infection. PLoS One, 8(11), e80671. (Read full article)
  86. Huttner B, Jones M, Huttner A, Rubin M, Samore MH (2013). Antibiotic prescription practices for pneumonia, skin and soft tissue infections and urinary tract infections throughout the US Veterans Affairs system. J Antimicrob Chemother, 68(10), 2393-9. (Read full article)
  87. Weir C, Drews FA, Butler J, Barrus RJ, Jones ML, Nebeker JR (2013). Support for contextual control in primary care: a qualitative analysis. AMIA Annu Symp Proc, 2013, 1463-71. (Read full article)
  88. Nelson RE, Jones M, Rubin MA (2012). Decolonization with Mupirocin and Subsequent Risk of Methicillin-Resistant Staphylococcus aureus Carriage in Veterans Affairs Hospitals. Infect Dis Ther, 1(1), 1. (Read full article)
  89. Jones M, DuVall SL, Spuhl J, Samore MH, Nielson C, Rubin M (2012). Identification of methicillin-resistant Staphylococcus aureus within the nation's Veterans Affairs medical centers using natural language processing. BMC Med Inform Decis Mak, 12, 34. (Read full article)
  90. Jones M, Samore MH, Carter M, Rubin MA (2011). Long-term care facilities in Utah: a description of human and information technology resources applied to infection control practice. Am J Infect Control, 40(5), 446-50. (Read full article)
  91. Huttner B, Jones M, Rubin MA, Madaras-Kelly K, Nielson C, Goetz MB, Neuhauser MM, Samore MH (2012). Double trouble: how big a problem is redundant anaerobic antibiotic coverage in Veterans Affairs medical centres? J Antimicrob Chemother, 67(6), 1537-9. (Read full article)
  92. Huttner B, Jones M, Rubin MA, Madaras-Kelly K, Nielson C, Goetz MB, Neuhauser MM, Samore MH (2012). Double trouble: how big a problem is redundant anaerobic antibiotic coverage in Veterans Affairs medical centres? J Antimicrob Chemother, 67(6), 1537-9.
  93. Jones M, Huttner B, Madaras-Kelly K, Nechodom K, Nielson C, Bidwell Goetz M, Neuhauser MM, Samore MH, Rubin MA (2012). Parenteral to oral conversion of fluoroquinolones: low-hanging fruit for antimicrobial stewardship programs? Infect Control Hosp Epidemiol, 33(4), 362-7. (Read full article)
  94. Huttner B, Jones M, Rubin MA, Neuhauser MM, Gundlapalli A, Samore M (2012). Drugs of last resort? The use of polymyxins and tigecycline at US Veterans Affairs medical centers, 2005-2010. PLoS One, 7(5), e36649. (Read full article)
  95. Jones MM, DuVall SL, Spuhl J, Samore MH, Nielson C, Rubin M (2012). Extraction of Methicillin-Resistant Staphylococcus aureus Data from the Nation's Veterans Affairs Medical Centers. BMC Med Inform Decis Mak, 12, 34.
  96. South BR, Shen S, Jones M, Garvin J, Samore MH, Chapman WW, Gundlapalli AV (2009). Developing a manually annotated clinical document corpus to identify phenotypic information for inflammatory bowel disease. BMC Bioinformatics, 10 Suppl 9, S12. (Read full article)
  97. South BR, Shen S, Jones M, Garvin J, Samore MH, Chapman WW, Gundlapalli AV (2009). Developing a manually annotated clinical document corpus to identify phenotypic information for inflammatory bowel disease. Summit Transl Bioinform, 2009, 1-32. (Read full article)

Conference Proceedings

  1. South BR, Shen S, Jones M, Garvin J, Samore MH, Chapman WW Gundlapalli AV (2009). Applying Annotation Methods to Large Repositories of Electronic Clinical Documents to extract Phenotypic Information: Where Should We Start the Search? American Medical Informatics Association – Second Annual Summit on Translational Bioinformatics, San Francisco, Spring2009.


  1. Jones BE, Jones MM (2019). Pneumonia and Electronic Health Records-A Window Into Disease, A Mirror of Our Behavior, or Just Another Streetlight? Clin Infect Dis, 71(7), 1613-1615. (Read full article)
  2. Graber CJ, Jones MM, Glassman PA, Weir C, Butler J, Nechodom K, Kay CL, Furman AE, Tran TT, Foltz C, Pollack LA, Samore MH, Goetz MB (2015). Taking an Antibiotic Time-out: Utilization and Usability of a Self-Stewardship Time-out Program for Renewal of Vancomycin and Piperacillin-Tazobactam. Hosp Pharm, 50(11), 1011-24. (Read full article)


  1. Graber CJ, Madaras-Kelly K, Jones MM, Neuhauser MM, Goetz MB (2013). Unnecessary antimicrobial use in the context of Clostridium difficile infection: a call to arms for the Veterans Affairs Antimicrobial Stewardship Task Force. [Letter to the editor]. Infect Control Hosp Epidemiol, 34(6), 651-3. (Read full article)


  1. Jones M, Huttner B, Nechodom K, Nielson C, Rubin M, Samore M (10/20/2012). Rapid Turnaround Time and Improved Adoption of PCR for Admission Methicillin-Resistant Staphylococcus aureus Screening at Veterans Affairs Hospitals [Abstract]. ID Week 2012.
  2. Jones M, Huttner B, Huttner A, Nielson C, Samore M, Rubin MA (10/19/2012). Can Active Methicillin-Resistant Staphylococcus aureus Surveillance Increase Vancomycin Use? A Retrospective Analysis of Antibiotic Use and Microbiology Data from 129 Veterans Affairs Hospitals between 2005 and 2010 [Abstract]. IDWeek 2012.
  3. Jones, M, Rubin, M, Greene, T, Leecaster, M, Spuhl, J, Nielson, C, Evans, M, Jain, R, Samore, M (10/2011). Comparing the Performance of Clinical History of MRSA vs. Active Surveillance at Individual and Hospital Ward Levels [Abstract]. Infectious Disease Society of America Conference, Vancouver, British Columbia, Canada.
  4. Jones, M, Huttner, B, Mayer, J, Rubin, M, Madaras-Kelly, M, Samore, M (04/2011). Variation of Inpatient Antibiotic Use in Acute Care Facilities of the Veterans Health Administration between 2005 and 2009. [Abstract]. Annual Scientific Meeting of The Society for Healthcare Epidemiology of America.
  5. Jones, M, Ying, J, Greene, T, Leecaster, M, Huttner, B, Mayer, J, Rubin, M, Samore, M (04/2011). Analysis of MRSA Transmission Dynamics in the Veterans Affairs System [Abstract]. Annual Scientific Meeting of The Society for Healthcare Epidemiology of America.
  6. Jones, M, Leecaster, M, Ford, L, Spuhl, J, Howell, J, Nechodom, P, Samore, M, Rubin, M (10/2010). Bias Over Time When Human Reviewers Diagnose Healthcare-Associated Infection (HAI) Due to Methicillin-resistant Staphylococcus aureus (MRSA) [Abstract].
  7. Jones MM, Samore MH, Nechodom P, Rubin MA (2010). Comparison of Automated and Manual Methods of Estimating Methicillin-Resistant Staphylococcus aureus (MRSA) Healthcare-Associated Infection (HAI) Rates. SHEA. Atlanta. Accepted as a poster. [Abstract].
  8. Shen S, South BR, Jones MM, Garvin JH, Samore MH, Chapman WW, Gundlapalli AV (2009). Using Open Source Tools to Build an Annotated Corpora for Inflammatory Bowel Disease. AMIA. Orlando, FA. Accepted and presented as a poster by Shuying Shen. [Abstract].
  9. Jones MM, Samore MH, Nechodom P, Rubin MA (2009). Surveillance for hospital-acquired VRE and MRPA infections using electronic algorithms. Infectious Disease Society of America. Philadelphia, Pennsylvania. Accepted as a poster. Received IDSA fellow’s travel grant. [Abstract].
  10. Jones MM, Samore MH, Jernigan JA, OConnor-Wright S, Nechodom P, Rubin M (2008). Surveillance for hospital-acquired methicillin-resistant Staphylococcus aureus(MRSA) infections using electronic algorithms. SHEA. San Diego. Accepted and oral presentation delivered by Makoto Jones 3/21/09. [Abstract]. Society for Healthcare Epidemiology of America Conference.


  1. Duong KNC, Le LM, Veettil SK, Saidoung P, Wannaadisai W, Nelson RE, Friedrichs M, Jones BE, Pavia AT, Jones MM, Samore MH, Chaiyakunapruk N (2023). Disparities in COVID-19 related outcomes in the United States by race and ethnicity pre-vaccination era: an umbrella review of meta-analyses. Front Public Health (11, p. 1206988). Switzerland. (Read full article)


  1. Rubin MA, Jones M, Huntington JL, Durfee MJ, Moore SL, Lloyd JF, Nielson C, Gilmartin H, Evans RS, Biffl WL, Savitz LA, Price CS (June 2014). Advances in the Prevention and Control of HAIs: Screening for Surgical Site Infections by Applying Classification Trees to Electronic Data.. Rockville, MD.: Agency for Healthcare Research and Quality.