Makoto M. Jones

Makoto M. Jones, MD, MS

Languages spoken: Japanese, English

Academic Information

Departments Primary - Internal Medicine

Divisions: Epidemiology

Board Certification

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

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

Education History

Undergraduate Brigham Young University
 BS
Professional Medical Saint Louis University School of Medicine
 MD
Residency University of Washington
 Resident
Fellowship University of Utah
 Fellow
Graduate Training University of Utah
 MS

Selected Publications

Journal Article

  1. 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.
  2. 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.
  3. Jones M, Samore MH, Carter M, Rubin M (2012). Long-term care facilities in Utah: a description of human and information technology resources applied to infection control practice. American journal of infection control, 40(5), 446-50.
  4. Taber P, Weir C, Butler JM, Graber CJ, Jones MM, Madaras-Kelly K, Zhang Y, Chou AF, Samore MH, Goetz MB, Glassman P (2021). Social dynamics of a population-level dashboard for antimicrobial stewardship: A qualitative analysis. American journal of infection control, 49(7), 862-867.
  5. Jones BE, Sauer B, Jones MM, Campo J, Damal K, He T, Ying J, Greene T, Goetz MB, Neuhauser MM, Hicks LA, Samore M (2015). Variation in Outpatient Antibiotic Prescribing for Acute Respiratory Infections in the Veteran Population: A Cross-sectional Study. Annals of internal medicine, 163(2), 73-80.
  6. Brown KA, Jones M, Daneman N, Adler FR, Stevens V, Nechodom KE, Goetz MB, Samore MH, Mayer (2016). Importation, Antibiotics, and Clostridium difficile Infection in Veteran Long-Term Care: A Multilevel Case-Control Study. Annals of internal medicine, 164(12), 787-94.
  7. Nelson RE, Stevens VW, Jones M, Khader K, Schweizer ML, Perencevich EN, Rubin MA, Samore M (2018). Attributable Cost and Length of Stay Associated with Nosocomial Gram-Negative Bacterial Cultures. Antimicrobial agents and chemotherapy, 62(11),
  8. Jones M, Ying J, Huttner B, Evans M, Maw M, Nielson C, Rubin MA, Greene T, Samore M (2014). Relationships between the importation, transmission, and nosocomial infections of methicillin-resistant Staphylococcus aureus: an observational study of 112 Veterans Affairs Medical Centers. Clinical infectious diseases, 58(1), 32-9.
  9. Jones BE, Jones MM, Huttner B, Stoddard G, Brown KA, Stevens VW, Greene T, Sauer B, Madaras-Kelly K, Rubin M, Goetz MB, Samore (2015). Trends in Antibiotic Use and Nosocomial Pathogens in Hospitalized Veterans With Pneumonia at 128 Medical Centers, 2006-2010. Clinical infectious diseases, 61(9), 1403-10.
  10. Goto M, O'Shea AMJ, Livorsi DJ, McDanel JS, Jones MM, Richardson KK, Beck BF, Alexander B, Evans ME, Roselle GA, Kralovic SM, Perencevich E (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. Clinical infectious diseases, 63(5), 642-650.
  11. Graber CJ, Jones MM, Goetz MB, Madaras-Kelly K, Zhang Y, Butler JM, Weir C, Chou AF, Youn SY, Samore MH, Glassman P (2020). Decreases in Antimicrobial Use Associated With Multihospital Implementation of Electronic Antimicrobial Stewardship Tools. Clinical infectious diseases, 71(5), 1168-1176.
  12. Stevens VW, Khader K, Echevarria K, Nelson RE, Zhang Y, Jones M, Timbrook TT, Samore MH, Rubin M (2020). Use of Oral Vancomycin for Clostridioides difficile Infection and the Risk of Vancomycin-Resistant Enterococci. Clinical infectious diseases, 71(3), 645-651.
  13. Nelson RE, Evans ME, Simbartl L, Jones M, Samore MH, Kralovic SM, Roselle GA, Rubin M (2019). Methicillin-resistant Staphylococcus aureus Colonization and Pre- and Post-hospital Discharge Infection Risk. Clinical infectious diseases, 68(4), 545-553.
  14. 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 D (2021). Optimal Urine Culture Diagnostic Stewardship Practice- Results from an Expert Modified-Delphi Procedure. Clinical infectious diseases,
  15. Christensen MA, Nevers M, Ying J, Haroldsen C, Stevens V, Jones MM, Yarbrough PM, Goetz MB, Restrepo MI, Madaras-Kelly K, Samore MH, Jones B (2021). Simulated Adoption of 2019 Community-Acquired Pneumonia Guidelines Across 114 Veterans Affairs Medical Centers: Estimated Impact on Culturing and Antibiotic Selection in Hospitalized Patients. Clinical infectious diseases, 72(Suppl 1), S59-S67.
  16. 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. Clinical infectious diseases, 73(8), 1370-1378.
  17. Nelson RE, Goto M, Samore MH, Jones M, Stevens VW, Evans ME, Schweizer ML, Perencevich EN, Rubin M (2021). Expanding an Economic Evaluation of the Veterans Affairs (VA) Methicillin-resistant Staphylococcus aureus (MRSA) Prevention Initiative to Include Prevention of Infections From Other Pathogens. Clinical infectious diseases, 72(Suppl 1), S50-S58.
  18. Nelson RE, Lautenbach E, Chang N, Jones M, Willson T, David M, Linkin D, Glick H, Doshi JA, Stevens V (2021). Attributable Cost of Healthcare-Associated Methicillin-Resistant Staphylococcus aureus Infection in a Long-term Care Center. Clinical infectious diseases, 72(Suppl 1), S27-S33.
  19. Nelson RE, Stevens VW, Khader K, Jones M, Samore MH, Evans ME, Douglas Scott R 2nd, Slayton RB, Schweizer ML, Perencevich EL, Rubin M (2016). Economic Analysis of Veterans Affairs Initiative to Prevent Methicillin-Resistant Staphylococcus aureus Infections. American journal of preventive medicine, 50(5 Suppl 1), S58-S65.
  20. Nelson RE, Jones M, Liu CF, Samore MH, Evans ME, Stevens VW, Reese T, Rubin M (2018). The Impact of Healthcare-Associated Methicillin-Resistant Staphylococcus aureus Infections on Postdischarge Health Care Costs and Utilization across Multiple Health Care Systems. Health services research, 53 Suppl 3, 5419-5437.
  21. Huttner B, Jones M, Huttner A, Rubin M, Samore M (2013). Antibiotic prescription practices for pneumonia, skin and soft tissue infections and urinary tract infections throughout the US Veterans Affairs system. The Journal of antimicrobial chemotherapy, 68(10), 2393-9.
  22. Jones M, Huttner B, Leecaster M, Huttner A, Damal K, Tanner W, Nielson C, Rubin MA, Goetz MB, Madaras-Kelly K, Samore M (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. The Journal of antimicrobial chemotherapy, 69(12), 3401-8.
  23. Huttner B, Jones M, Madaras-Kelly K, Neuhauser MM, Rubin MA, Goetz MB, Samore M (2015). Initiation and termination of antibiotic regimens in Veterans Affairs hospitals. The Journal of antimicrobial chemotherapy, 70(2), 598-601.
  24. Madaras-Kelly K, Jones M, Remington R, Caplinger CM, Huttner B, Jones B, Samore (2016). Antimicrobial de-escalation of treatment for healthcare-associated pneumonia within the Veterans Healthcare Administration. The Journal of antimicrobial chemotherapy, 71(2), 539-46.
  25. Huttner B, Jones M, Rubin MA, Madaras-Kelly K, Nielson C, Goetz MB, Neuhauser MM, Samore M (2012). Double trouble: how big a problem is redundant anaerobic antibiotic coverage in Veterans Affairs medical centres?. The Journal of antimicrobial chemotherapy, 67(6), 1537-9.
  26. Chou AF, Graber CJ, Zhang Y, Jones M, Goetz MB, Madaras-Kelly K, Samore M, Glassman P (2018). Specifying an implementation framework for Veterans Affairs antimicrobial stewardship programmes: using a factor analysis approach. The Journal of antimicrobial chemotherapy, 73(9), 2559-2566.
  27. Huttner B, Jones M, Rubin MA, Madaras-Kelly K, Nielson C, Goetz MB, Neuhauser MM, Samore M (2012). Double trouble: how big a problem is redundant anaerobic antibiotic coverage in Veterans Affairs medical centres?. The Journal of antimicrobial chemotherapy, 67(6), 1537-9.
  28. Jones M, Huttner B, Madaras-Kelly K, Nechodom K, Nielson C, Bidwell Goetz M, Neuhauser MM, Samore MH, Rubin M (2012). Parenteral to oral conversion of fluoroquinolones: low-hanging fruit for antimicrobial stewardship programs?. Infection control and hospital epidemiology, 33(4), 362-7.
  29. Madaras-Kelly K, Jones M, Remington R, Hill N, Huttner B, Samore (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. Infection control and hospital epidemiology, 35(9), 1103-13.
  30. Nelson RE, Jones M, Liu CF, Samore MH, Evans ME, Graves N, Lee B, Rubin M (2015). The impact of healthcare-associated methicillin-resistant Staphylococcus aureus infections on post-discharge healthcare costs and utilization. Infection control and hospital epidemiology, 36(5), 534-42.
  31. Stevens VW, Khader K, Nelson RE, Jones M, Rubin MA, Brown KA, Evans ME, Greene T, Slade E, Samore M (2015). Excess Length of Stay Attributable to Clostridium difficile Infection (CDI) in the Acute Care Setting: A Multistate Model. Infection control and hospital epidemiology, 36(9), 1024-30.
  32. Jones MM, Nelson RE, Rubin M (2015). Cumulative Attributable Difference: An Infection Metric That Reflects a Value System. Infection control and hospital epidemiology, 36(12), 1385-7.
  33. Chou AF, Graber CJ, Jones M, Zhang Y, Goetz MB, Madaras-Kelly K, Samore M, Kelly A, Glassman P (2016). Characteristics of Antimicrobial Stewardship Programs at Veterans Affairs Hospitals: Results of a Nationwide Survey. Infection control and hospital epidemiology, 37(6), 647-54.
  34. Fitzpatrick MA, Suda KJ, Safdar N, Goldstein B, Jones MM, Poggensee L, Ramanathan S, LeWan R, Evans C (2016). Unique Risks and Clinical Outcomes Associated With Extended-Spectrum ß-Lactamase Enterobacteriaceae in Veterans With Spinal Cord Injury or Disorder: A Case-Case-Control Study. Infection control and hospital epidemiology, 37(7), 768-76.
  35. Kelly AA, Jones MM, Echevarria KL, Kralovic SM, Samore MH, Goetz MB, Madaras-Kelly KJ, Simbartl LA, Morreale AP, Neuhauser MM, Roselle G (2017). A Report of the Efforts of the Veterans Health Administration National Antimicrobial Stewardship Initiative. Infection control and hospital epidemiology, 38(5), 513-520.
  36. Wirth MS, Fitzpatrick MA, Suda KJ, Wilson GM, Ramanathan S, Evans ME, Jones MM, Pfeiffer CD, Evans C (2021). Carbapenem-resistant Enterobacteriaceae epidemiology in Veterans' Affairs medical centers varies by facility characteristics. Infection control and hospital epidemiology, 42(7), 885-889.
  37. Dieringer TD, Furukawa D, Graber CJ, Stevens VW, Jones MM, Rubin MA, Goetz M (2021). Inpatient antibiotic utilization in the Veterans' Health Administration during the coronavirus disease 2019 (COVID-19) pandemic. Infection control and hospital epidemiology, 42(6), 751-753.
  38. Stevens VW, Shoemaker HE, Jones MM, Jones BE, Nelson RE, Khader K, Samore MH, Rubin M (2020). Validation of the SHEA/IDSA severity criteria to predict poor outcomes among inpatients and outpatients with Clostridioides difficile infection. Infection control and hospital epidemiology, 41(5), 510-516.
  39. 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. Infection control and hospital epidemiology, 43, 1-4.
  40. 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. Infection control and hospital epidemiology, 40(4), 438-446.
  41. 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. Infection control and hospital epidemiology, 40(4), 463-466.
  42. Nelson RE, Samore MH, Jones M, Greene T, Stevens VW, Liu CF, Graves N, Evans MF, Rubin M (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. Medical care, 53(9), 827-34.
  43. 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. Morbidity and mortality weekly report, 63(9), 194-200.
  44. Jones M, Jernigan JA, Evans ME, Roselle GA, Hatfield KM, Samore M (2019). Vital Signs: Trends in Staphylococcus aureus Infections in Veterans Affairs Medical Centers - United States, 2005-2017. MMWR. Morbidity and mortality weekly report, 68(9), 220-224.
  45. Fitzpatrick MA, Suda KJ, Safdar N, Burns SP, Jones MM, Poggensee L, Ramanathan S, Evans C (2018). Changes in bacterial epidemiology and antibiotic resistance among veterans with spinal cord injury/disorder over the past 9 years. The journal of spinal cord medicine, 41(2), 199-207.
  46. Ramanathan S, Fitzpatrick MA, Suda KJ, Burns SP, Jones MM, LaVela SL, Evans C (2020). 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.
  47. Patterson OV, Jones M, Yao Y, Viernes B, Alba PR, Iwashyna TJ, DuVall S (2015). Extraction of Vital Signs from Clinical Notes. Studies in health technology and informatics, 216, 1035.
  48. South BR, Shen S, Jones M, Garvin J, Samore MH, Chapman WW, Gundlapalli A (2009). Developing a manually annotated clinical document corpus to identify phenotypic information for inflammatory bowel disease. BMC bioinformatics, 10 Suppl 9, S12.
  49. Madaras-Kelly K, Jones M, Remington R, Caplinger C, Huttner B, Samore (2015). Description and validation of a spectrum score method to measure antimicrobial de-escalation in healthcare associated pneumonia from electronic medical records data. BMC infectious diseases, 15, 197.
  50. Jones M, Butler J, Graber CJ, Glassman P, Samore MH, Pollack LA, Weir C, Goetz M (2017). Think twice: A cognitive perspective of an antibiotic timeout intervention to improve antibiotic use. Journal of biomedical informatics, 71S, S22-S31.
  51. Leecaster MK, Weir CR, Drews FA, Hellewell JL, Bolton D, Jones MM, Nebeker J (2017). Translation of Contextual Control Model to chronic disease management: A paradigm to guide design of cognitive support systems. Journal of biomedical informatics, 71S, S60-S67.
  52. 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 (2021). ReHouSED: A novel measurement of Veteran housing stability using natural language processing. Journal of biomedical informatics, 122, 103903.
  53. Jones M, DuVall SL, Spuhl J, Samore MH, Nielson C, Rubin (2012). Identification of methicillin-resistant Staphylococcus aureus within the nation's Veterans Affairs medical centers using natural language processing. BMC medical informatics and decision making, 12, 34.
  54. Islam R, Weir CR, Jones M, Del Fiol G, Samore M (2015). Understanding complex clinical reasoning in infectious diseases for improving clinical decision support design. BMC medical informatics and decision making, 15, 101.
  55. Jones MM, DuVall SL, Spuhl J, Samore MH, Nielson C, Rubin (2012). Extraction of Methicillin-Resistant Staphylococcus aureus Data from the Nation's Veterans Affairs Medical Centers. BMC medical informatics and decision making, 12, 34.
  56. Weir C, Drews FA, Butler J, Barrus RJ, Jones ML, Nebeker J (2013). Support for contextual control in primary care: a qualitative analysis. AMIA ... Annual Symposium proceedings. AMIA Symposium, 2013, 1463-71.
  57. Huttner B, Jones M, Rubin MA, Neuhauser MM, Gundlapalli A, Samore (2012). Drugs of last resort? The use of polymyxins and tigecycline at US Veterans Affairs medical centers, 2005-2010. PloS one, 7(5), e36649.
  58. Rubin MA, Jones M, Leecaster M, Khader K, Ray W, Huttner A, Huttner B, Toth D, Sablay T, Borotkanics RJ, Gerding DN, Samore M (2013). A simulation-based assessment of strategies to control Clostridium difficile transmission and infection. PloS one, 8(11), e80671.
  59. Nelson RE, Jones M, Leecaster M, Samore MH, Ray W, Huttner A, Huttner B, Khader K, Stevens VW, Gerding D, Schweizer ML, Rubin M (2016). An Economic Analysis of Strategies to Control Clostridium Difficile Transmission and Infection Using an Agent-Based Simulation Model. PloS one, 11(3), e0152248.
  60. 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.
  61. Lynch KE, Viernes B, Gatsby E, DuVall SL, Jones BE, Box TL, Kreisler C, Jones (2021). Positive Predictive Value of COVID-19 ICD-10 Diagnosis Codes Across Calendar Time and Clinical Setting. Clinical epidemiology, 13, 1011-1018.
  62. South BR, Shen S, Jones M, Garvin J, Samore MH, Chapman WW, Gundlapalli A (2009). Developing a manually annotated clinical document corpus to identify phenotypic information for inflammatory bowel disease. Summit on translational bioinformatics, 2009, 1-32.
  63. Roosan D, Del Fiol G, Butler J, Livnat Y, Mayer J, Samore M, Jones M, Weir (2016). Feasibility of Population Health Analytics and Data Visualization for Decision Support in the Infectious Diseases Domain: A pilot study. Applied clinical informatics, 7(2), 604-23.
  64. 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 M (2017). Comparative Effectiveness of Vancomycin and Metronidazole for the Prevention of Recurrence and Death in Patients With Clostridium difficile Infection. JAMA internal medicine, 177(4), 546-553.
  65. 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 M (2020). Empirical Anti-MRSA vs Standard Antibiotic Therapy and Risk of 30-Day Mortality in Patients Hospitalized for Pneumonia. JAMA internal medicine, 180(4), 552-560.
  66. Bostwick AD, Jones BE, Paine R, Goetz MB, Samore M, Jones (2019). Potential Impact of Hospital-acquired Pneumonia Guidelines on Empiric Antibiotics. An Evaluation of 113 Veterans Affairs Medical Centers. Annals of the American Thoracic Society, 16(11), 1392-1398.
  67. 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 T (2021). Computerized Mortality Prediction for Community-acquired Pneumonia at 117 Veterans Affairs Medical Centers. Annals of the American Thoracic Society, 18(7), 1175-1184.
  68. Nelson RE, Jones M, Rubin M (2012). Decolonization with Mupirocin and Subsequent Risk of Methicillin-Resistant Staphylococcus aureus Carriage in Veterans Affairs Hospitals. Infectious diseases and therapy, 1(1), 1.
  69. 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 infectious diseases, 7(1), ofz554.
  70. Peterson KS, Lewis J, Patterson OV, Chapman AB, Denhalter DW, Lye PA, Stevens VW, Gamage SD, Roselle GA, Wallace KS, Jones (2021). Automated Travel History Extraction From Clinical Notes for Informing the Detection of Emergent Infectious Disease Events: Algorithm Development and Validation. JMIR public health and surveillance, 7(3), e26719.
  71. Wayne MT, Seelye S, Molling D, Wang XQ, Donnelly JP, Hogan CK, Jones MM, Iwashyna TJ, Liu VX, Prescott H (2021). Temporal Trends and Hospital Variation in Time-to-Antibiotics Among Veterans Hospitalized With Sepsis. JAMA network open, 4(9), e2123950.
  72. Khader K, Thomas A, Stevens V, Visnovsky L, Nevers M, Toth D, Keegan LT, Jones M, Rubin M, Samore M (2021). Association Between Contact Precautions and Transmission of Methicillin-Resistant Staphylococcus aureus in Veterans Affairs Hospitals. JAMA network open, 4(3), e210971.
  73. Evans ME, Simbartl LA, McCauley BP, Flarida LK, Jones MM, Harris AD, Perencevich EN, Rubin MA, Hicks NR, Kralovic SM, Roselle G (2023). Active Surveillance and Contact Precautions for Preventing Methicillin-Resistant Staphylococcus aureus Healthcare-Associated Infections during the COVID-19 Pandemic. Clinical infectious diseases, 77(10), 1381-1386.
  74. Evans ME, Jones MM, Davis KW, Lane MT, Simbartl LA, McCauley BP, Gauldin N, Roselle G (2023). Lack of correlation between standardized antimicrobial administration ratios (SAARs) and healthcare-facility-onset Clostridioides difficile infection rates in Veterans Affairs medical facilities. Infection control and hospital epidemiology, 44(6), 945-947.
  75. Hancock JA, Campbell S, Jones MM, Wang-Rodriguez J, VHA Microbiology SME Workgroup, Klutts J (2023). Development and validation of a standardized blood culture contamination definition and metric dashboard for a large health care system. American journal of clinical pathology,
  76. Gamage SD, Evans ME, McCauley BP, Lipscomb KR, Flarida L, Jones MM, Baza M, Barraza J, Simbartl LA, Roselle G (2023). Hospital coronavirus disease 2019 (COVID-19) public health reporting: Lessons from validation of an automated surveillance tool to facilitate data collection. Infection control and hospital epidemiology, 44(5), 802-804.
  77. Graber CJ, Simon AR, Zhang Y, Goetz MB, Jones MM, Butler JM, Chou AF, Glassman P (2023). 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. Infection control and hospital epidemiology, 44(3), 400-405.
  78. Evans ME, Simbartl LA, Kralovic SM, Clifton M, DeRoos K, McCauley BP, Gauldin N, Flarida LK, Gamage SD, Jones MM, Roselle G (2023). Healthcare-associated infections in Veterans Affairs acute-care and long-term healthcare facilities during the coronavirus disease 2019 (COVID-19) pandemic. Infection control and hospital epidemiology, 44(3), 420-426.
  79. 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 (2022). Trends in Illness Severity, Hospitalization, and Mortality for Community-Onset Pneumonia at 118 US Veterans Affairs Medical Centers. Journal of general internal medicine, 37(15), 3839-3847.
  80. Fitzpatrick MA, Suda KJ, Poggensee L, Vivo A, Wilson G, Jones MM, Evans M, Safdar N, Evans C (2022). Treatment of extensively-drug resistant (XDR) Acinetobacter and impact on clinical outcomes in U.S. veterans affairs (VA) medical centers. American journal of infection control, 50(9), 1020-1025.
  81. Prescott HC, Seelye S, Wang XQ, Hogan CK, Smith JT, Kipnis P, Barreda F, Donnelly JP, Pogue JM, Iwashyna TJ, Jones MM, Liu V (2022). Temporal Trends in Antimicrobial Prescribing During Hospitalization for Potential Infection and Sepsis. JAMA internal medicine, 182(8), 805-813.
  82. 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 Progra (2022). Increased carbapenemase testing following implementation of national VA guidelines for carbapenem-resistant Enterobacterales (CRE). Antimicrobial stewardship & healthcare epidemiology, 2(1), e88.
  83. Vivo A, Fitzpatrick MA, Suda KJ, Jones MM, Perencevich EN, Rubin MA, Ramanathan S, Wilson GM, Evans ME, Evans C (2022). Epidemiology and outcomes associated with carbapenem-resistant Acinetobacter baumannii and carbapenem-resistant Pseudomonas aeruginosa: a retrospective cohort study. BMC infectious diseases, 22(1), 491.
  84. Eyre H, Chapman AB, Peterson KS, Shi J, Alba PR, Jones MM, Box TL, DuVall SL, Patterson O (2022). Launching into clinical space with medspaCy: a new clinical text processing toolkit in Python. AMIA ... Annual Symposium proceedings. AMIA Symposium, 2021, 438-447.
  85. Chapman AB, Peterson KS, Rutter E, Nevers M, Zhang M, Ying J, Jones M, Classen D, Jones (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.
  86. Wilson GM, Fitzpatrick MA, Suda KJ, Smith BM, Gonzalez B, Jones M, Schweizer ML, Evans M, Evans C (2022). Comparative effectiveness of antibiotic therapy for carbapenem-resistant Enterobacterales (CRE) bloodstream infections in hospitalized US veterans. JAC-antimicrobial resistance, 4(5), dlac106.
  87. Smith JT, Manickam RN, Barreda F, Greene JD, Bhimarao M, Pogue J, Jones M, Myers L, Prescott HC, Liu V (2022). Quantifying the breadth of antibiotic exposure in sepsis and suspected infection using spectrum scores. Medicine, 101(41), e30245.
  88. 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 Grou (2022). Outpatient treatment and clinical outcomes of bacteriuria in veterans: A retrospective cohort analysis. Antimicrobial stewardship & healthcare epidemiology, 2(1), e168.
  89. Widanagamaachchi W, Peterson K, Chapman A, Classen D, Jones (2022). A flexible framework for visualizing and exploring patient misdiagnosis over time. Journal of biomedical informatics, 134, 104178.
  90. 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 C (2022). Infectious Disease Consults of Pseudomonas aeruginosa Bloodstream Infection and Impact on Health Outcomes. Open forum infectious diseases, 9(9), ofac456.
  91. Gawron AJ, Sultan S, Glorioso TJ, Califano S, Kralovic SM, Jones M, Kirsh S, Dominitz J (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. Gastrointestinal endoscopy, 96(3), 423-432.e7.
  92. Kalvesmaki AF, Chapman AB, Peterson KS, Pugh MJ, Jones M, Gleason T (2022). Analysis of a national response to a White House directive for ending veteran suicide. Health services research, 57 Suppl 1(Suppl 1), 32-41.
  93. 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 RL (2024). Research agenda for antibiotic stewardship within the Veterans' Health Administration, 2024-2028. Infection control and hospital epidemiology, 1-7.
  94. Vivo A, Fitzpatrick MA, Suda KJ, Wilson GM, Jones MM, Evans ME, Evans C (2023). Treatment effectiveness of antibiotic therapy in Veterans with multidrug-resistant Acinetobacter spp. bacteremia. Antimicrobial stewardship & healthcare epidemiology, 3(1), e230.
  95. Rush E, Ozmen O, Kim M, Ortegon ER, Jones M, Park BH, Pizer S, Trafton J, Brenner LA, Ward M, Nebeker J (2024). A framework for inferring and analyzing pharmacotherapy treatment patterns. BMC medical informatics and decision making, 24(1), 68.
  96. Chapman AB, Peterson KS, Rutter E, Nevers M, Ying J, Classen D, Jones M, Samore M, Jones (2024). A Linguistic Analysis Examining the Impact of COVID-19 on Pneumonia Diagnosis and Disease Models. Studies in health technology and informatics, 310, 1444-1445.
  97. Donnelly JP, Seelye SM, Kipnis P, McGrath BM, Iwashyna TJ, Pogue J, Jones M, Liu VX, Prescott H (2024). Impact of Reducing Time-to-Antibiotics on Sepsis Mortality, Antibiotic Use, and Adverse Events. Annals of the American Thoracic Society, 21(1), 94-101.
  98. Sawyer AM, Ray C, Klutts JS, Fitzpatrick M, Suda KJ, Hicks N, Evans M, Jones M, Pfeiffer CD, Evans CT, QUERI CARRIAGE Progra (2024). A cross-sectional survey of Department of Veterans Affairs laboratory practices for identification of carbapenem-resistant Acinetobacter baumannii and Pseudomonas aeruginosa. Antimicrobial stewardship & healthcare epidemiology, 4(1), e197.
  99. Jones BE, Chapman AB, Ying J, Rutter ED, Nevers MR, Baker A, Dean NC, Fix ML, Singh H, Cosby KS, Taber PA, Weir CD, Jones MM, Samore MH, Butler J (2024). Diagnostic Discordance, Uncertainty, and Treatment Ambiguity in Community-Acquired Pneumonia : A National Cohort Study of 115 U.S. Veterans Affairs Hospitals. Annals of internal medicine, 177(9), 1179-1189.
  100. Butler JM, Taft T, Taber P, Rutter E, Fix M, Baker A, Weir C, Nevers M, Classen D, Cosby K, Jones M, Chapman A, Jones B (2024). Pneumonia diagnosis performance in the emergency department: a mixed-methods study about clinicians' experiences and exploration of individual differences and response to diagnostic performance feedback. Journal of the American Medical Informatics Association, 31(7), 1503-1513.
  101. Peterson KS, Chapman AB, Widanagamaachchi W, Sutton J, Ochoa B, Jones BE, Stevens V, Classen DC, Jones M (2024). Automating detection of diagnostic error of infectious diseases using machine learning. PLOS digital health, 3(6), e0000528.
  102. Pfeiffer CD, Jones MM, Klutts JS, Francis QA, Flegal HM, Murray AO, Willson TM, Hicks NR, Evans CT, Evans M (2024). Development and implementation of a nationwide multidrug-resistant organism tracking and alert system for Veterans Affairs medical centers. Infection control and hospital epidemiology, 45(9), 1-6.
  103. Wilson GM, Fitzpatrick M, Suda KJ, Poggensee L, Jones M, Evans ME, Evans C (2024). Facility- and patient-level factors associated with implementation of contact precautions in hospitalized VA patients with positive CRE cultures. Antimicrobial stewardship & healthcare epidemiology, 4(1), e76.
  104. Ray C, Goedken C, Hughes AM, Wilson GM, Hicks NR, Fitzpatrick MA, Jones MM, Pfeiffer C, Klutts JS, Evans ME, Suda KJ, Evans C (2025). Standard vs. enhanced implementation strategies to increase adoption of a multidrug-resistant organism alert tool: a cluster randomized trial. Frontiers in health services, 5, 1566454.
  105. Duong KNC, Veettil SK, Nelson RE, Jones BE, Pavia AT, Nguyen DT, Jones MM, Samore MH, Zickmund SL, Galyean P, Chaiyakunapruk (2025). COVID-19 Vaccine Rollout Strategies in Utah from Local Health Departments' Perspectives: A Qualitative Analysis of Focus Group Discussions. Health equity, 9(1), 31-40.
  106. Morgan DJ, Goodman KE, Branch-Elliman W, Shenoy ES, Salinas JL, Jones M, Singh SP, Schrank GM, Pineles L, AlShanqeeti S, Harris AD, Klein (2025). Using generative AI for healthcare-associated infection surveillance. Clinical infectious diseases,
  107. Ozmen O, Rush E, Park BH, Jones M, Trafton J, Brenner L, Rupper RW, Ward M, Nebeker JR, Pizer S (2025). Combining Machine Learning and Comparative Effectiveness Methodology to Study Primary Care Pharmacotherapy Pathways for Veterans With Depression. Medical care, 63(6), 422-429.

Review

  1. Duong KNC, Nguyen DT, Kategeaw W, Liang X, Khaing W, Visnovsky LD, Veettil SK, McFarland MM, Nelson RE, Jones BE, Pavia AT, Coates E, Khader K, Love J, Vega Yon GG, Zhang Y, Willson T, Dorsan E, Toth DJA, Jones MM, Samore MH, Chaiyakunapruk (2024). Incorporating social determinants of health into transmission modeling of COVID-19 vaccine in the US: a scoping review. Lancet regional health. Americas, 35, 100806.

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?. Spring2009,

Editorial

  1. Jones BE, Jones M (2020). Pneumonia and Electronic Health Records-A Window Into Disease, A Mirror of Our Behavior, or Just Another Streetlight?. Clinical infectious diseases, 71(7), 1613-1615.
  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 M (2015). Taking an Antibiotic Time-out: Utilization and Usability of a Self-Stewardship Time-out Program for Renewal of Vancomycin and Piperacillin-Tazobactam. Hospital pharmacy, 50(11), 1011-24.

Letter

  1. Graber CJ, Madaras-Kelly K, Jones MM, Neuhauser MM, Goetz M (2013). Unnecessary antimicrobial use in the context of Clostridium difficile infection: a call to arms for the Veterans Affairs Antimicrobial Stewardship Task Force. Infection control and hospital epidemiology, 34(6), 651-3.

Abstract

  1. Jones MM, Samore MH, Jernigan JA, O'Connor-Wright S, Nechodom P, Rubin (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.
  2. Shen S, South BR, Jones MM, Garvin JH, Samore MH, Chapman WW, Gundlapalli A (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.
  3. Jones MM, Samore MH, Nechodom P, Rubin M (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.
  4. Jones MM, Samore MH, Nechodom P, Rubin M (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.
  5. Jones, M, Leecaster, M, Ford, L, Spuhl, J, Howell, J, Nechodom, P, Samore, M, Rubin, (2010). Bias Over Time When Human Reviewers Diagnose Healthcare-Associated Infection (HAI) Due to Methicillin-resistant Staphylococcus aureus (MRSA).
  6. Jones, M., Huttner, B., Mayer, J., Rubin, M., Madaras-Kelly, M., Samore, M (2011). Variation of Inpatient Antibiotic Use in Acute Care Facilities of the Veterans Health Administration between 2005 and 2009.
  7. Jones, M., Ying, J.,Greene, T., Leecaster, M., Huttner, B., Mayer, J., Rubin, M., Samore, M (2011). Analysis of MRSA Transmission Dynamics in the Veterans Affairs System.
  8. Jones, M, Rubin, M, Greene, T, Leecaster, M, Spuhl, J, Nielson, C, Evans, M, Jain, R, Samore, (2011). Comparing the Performance of Clinical History of MRSA vs. Active Surveillance at Individual and Hospital Ward Levels.
  9. Jones M, Huttner B, Nechodom K, Nielson C, Rubin M, Samore (2012). Rapid Turnaround Time and Improved Adoption of PCR for Admission Methicillin-Resistant Staphylococcus aureus Screening at Veterans Affairs Hospitals.
  10. Jones M, Huttner B, Huttner A, Nielson C, Samore M, Rubin M (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.

Other

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

Report

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