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John Metcalfe, MD, PhD, MPH

Title(s)Associate Professor, Medicine
SchoolSchool of Medicine
Phone415-596-9348
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    Collapse Biography 
    Collapse Education and Training
    University of California, BerkelyPh.D.2012Division of Epidemiology
    University of California, San FranciscoFellowship2009Pulmonary and Critical Care Medicine
    University of California, San FranciscoResidency 2006Internal Medicine
    Tufts University School of MedicineM.D.2003School of Medicine
    Tufts University School of MedicineMPH2003Chronic Complex Emergencies
    Humboldt State UniversityBS1998Molecular Biology
    Michigan State UniversityAB1995Sociology
    Collapse Awards and Honors
    University of California, Berkeley2008Chancellor's Fellow
    Robert Wood Johnson Foundation2010Harold Amos Scholar
    Doris Duke Charitable Foundation2015Clinical Scientist Development Award

    Collapse Overview 
    Collapse Overview
    John Z. Metcalfe, MD, PhD, MPH is an Associate Professor In Residence in the Division of Pulmonary and Critical Care Medicine at the University of California, San Francisco. A consultant in pulmonary medicine and an intensivist at the Zuckerberg San Francisco General Hospital, John has expertise in critical care and respiratory infectious diseases, with a particular interest in HIV-associated highly drug-resistant tuberculosis clinical management and translational research. He has specialized training in epidemiology, statistical prediction, diagnostic test evaluation, and randomized clinical trials; leads a Fogarty biomedical research training program (NIH D43) at the University of Zimbabwe; and is Chair of an AIDS Clinical Trials Group phase II/III adaptive RCT evaluating novel regimens for TB treatment shortening. He is also on the Editorial Board of PLoS Medicine, where he is Editor for Respiratory Medicine.

    Collapse Research 
    Collapse Research Activities and Funding
    Novel next-generation sequencing assay for monitoring multidrug resistant tuberculosis treatment in the setting of HIV infection
    NIH/NIAID R01AI131939Jan 19, 2018 - Dec 31, 2022
    Role: Principal Investigator
    Novel methods of pharmacologic monitoring for multidrug resistant tuberculosis treatment in the setting of HIV infection
    NIH/NIAID R01AI123024Jan 7, 2016 - Dec 31, 2020
    Role: Principal Investigator
    Training for Research Excellence and MeNtorship in Tuberculosis (TRENT)
    NIH/FIC D43TW009539Aug 1, 2013 - Mar 31, 2023
    Role: Co-Principal Investigator
    Improving Early Identification of Drug Resistant Tuberculosis in HIV Prevalent Se
    NIH/NIAID K23AI094251Mar 4, 2011 - Feb 29, 2016
    Role: Principal Investigator

    Collapse ORNG Applications 
    Collapse Global Health
    Collapse Websites
    Collapse Student Projects

    Collapse Bibliographic 
    Collapse Publications
    Publications listed below are automatically derived from MEDLINE/PubMed and other sources, which might result in incorrect or missing publications. Researchers can login to make corrections and additions, or contact us for help.
    List All   |   Timeline
    1. Timire C, Metcalfe JZ, Chirenda J, Scholten JN, Manyame-Murwira B, Ngwenya M, Matambo R, Charambira K, Mutunzi H, Kalisvaart N, Sandy C. Prevalence of drug-resistant tuberculosis in Zimbabwe: a health facility-based cross-sectional survey. Int J Infect Dis. 2019 Jul 26. PMID: 31357057.
      View in: PubMed
    2. Gerona R, Wen A, Aguilar D, Shum J, Reckers A, Bacchetti P, Gandhi M, Metcalfe J. Simultaneous analysis of 11 medications for drug resistant TB in small hair samples to quantify adherence and exposure using a validated LC-MS/MS panel. J Chromatogr B Analyt Technol Biomed Life Sci. 2019 Jul 23; 1125:121729. PMID: 31369929.
      View in: PubMed
    3. Pooran A, Theron G, Zijenah L, Chanda D, Clowes P, Mwenge L, Mutenherwa F, Lecesse P, Metcalfe J, Sohn H, Hoelscher M, Pym A, Peter J, Dowdy D, Dheda K. Point of care Xpert MTB/RIF versus smear microscopy for tuberculosis diagnosis in southern African primary care clinics: a multicentre economic evaluation. Lancet Glob Health. 2019 Jun; 7(6):e798-e807. PMID: 31097281.
      View in: PubMed
    4. de Vos M, Ley SD, Wiggins KB, Derendinger B, Dippenaar A, Grobbelaar M, Reuter A, Dolby T, Burns S, Schito M, Engelthaler DM, Metcalfe J, Theron G, van Rie A, Posey J, Warren R, Cox H. Bedaquiline Microheteroresistance after Cessation of Tuberculosis Treatment. N Engl J Med. 2019 05 30; 380(22):2178-2180. PMID: 31141643.
      View in: PubMed
    5. Metcalfe J, Bacchetti P, Gerona R, Esmail A, Dheda K, Gandhi M. Association of anti-tuberculosis drug concentrations in hair and treatment outcomes in MDR- and XDR-TB. ERJ Open Res. 2019 Apr; 5(2). PMID: 31041318.
      View in: PubMed
    6. Di Tanna GL, Khaki AR, Theron G, McCarthy K, Cox H, Mupfumi L, Trajman A, Zijenah LS, Mason P, Bandason T, Durovni B, Bara W, Hoelscher M, Clowes P, Mangu C, Chanda D, Pym A, Mwaba P, Cobelens F, Nicol MP, Dheda K, Churchyard G, Fielding K, Metcalfe JZ. Effect of Xpert MTB/RIF on clinical outcomes in routine care settings: individual patient data meta-analysis. Lancet Glob Health. 2019 Feb; 7(2):e191-e199. PMID: 30683238.
      View in: PubMed
    7. Chin AT, Rylance J, Makumbirofa S, Meffert S, Vu T, Clayton J, Mason P, Woodruff P, Metcalfe J. Chronic lung disease in adult recurrent tuberculosis survivors in Zimbabwe: a cohort study. Int J Tuberc Lung Dis. 2019 Feb 01; 23(2):203-211. PMID: 30808453.
      View in: PubMed
    8. Kühnert D, Coscolla M, Brites D, Stucki D, Metcalfe J, Fenner L, Gagneux S, Stadler T. Tuberculosis outbreak investigation using phylodynamic analysis. Epidemics. 2018 12; 25:47-53. PMID: 29880306.
      View in: PubMed
    9. Desai SR, Nair A, Rylance J, Mujuru H, Nathoo K, McHugh G, Majonga E, Metcalfe J, Kranzer K, Ferrand RA. Human Immunodeficiency Virus-Associated Chronic Lung Disease in Children and Adolescents in Zimbabwe: Chest Radiographic and High-Resolution Computed Tomographic Findings. Clin Infect Dis. 2018 Jan 06; 66(2):274-281. PMID: 29020237.
      View in: PubMed
    10. Metcalfe JZ, Streicher E, Theron G, Colman RE, Allender C, Lemmer D, Warren R, Engelthaler DM. Cryptic Microheteroresistance Explains Mycobacterium tuberculosis Phenotypic Resistance. Am J Respir Crit Care Med. 2017 11 01; 196(9):1191-1201. PMID: 28614668.
      View in: PubMed
    11. Metcalfe JZ, Streicher E, Theron G, Colman RE, Penaloza R, Allender C, Lemmer D, Warren RM, Engelthaler DM. Mycobacterium tuberculosis Subculture Results in Loss of Potentially Clinically Relevant Heteroresistance. Antimicrob Agents Chemother. 2017 11; 61(11). PMID: 28893776.
      View in: PubMed
    12. Metcalfe J, Gerona R, Wen A, Bacchetti P, Gandhi M. An LC-MS/MS-based method to analyze the anti-tuberculosis drug bedaquiline in hair. Int J Tuberc Lung Dis. 2017 09 01; 21(9):1069-1070. PMID: 28826458.
      View in: PubMed
    13. Chawana TD, Gandhi M, Nathoo K, Ngara B, Louie A, Horng H, Katzenstein D, Metcalfe J, Nhachi CFB. Defining a Cutoff for Atazanavir in Hair Samples Associated With Virological Failure Among Adolescents Failing Second-Line Antiretroviral Treatment. J Acquir Immune Defic Syndr. 2017 09 01; 76(1):55-59. PMID: 28520618.
      View in: PubMed
    14. O'Donnell MR, Padayatchi N, Metcalfe JZ. Elucidating the role of clofazimine for the treatment of tuberculosis. Int J Tuberc Lung Dis. 2016 12 01; 20(12):52-57. PMID: 28240574.
      View in: PubMed
    15. Rylance J, Mchugh G, Metcalfe J, Mujuru H, Nathoo K, Wilmore S, Rowland-Jones S, Majonga E, Kranzer K, Ferrand RA. Chronic lung disease in HIV-infected children established on antiretroviral therapy. AIDS. 2016 11 28; 30(18):2795-2803. PMID: 27662546.
      View in: PubMed
    16. Blount RJ, Tran MC, Everett CK, Cattamanchi A, Metcalfe JZ, Connor D, Miller CR, Grinsdale J, Higashi J, Nahid P. Tuberculosis progression rates in U.S. Immigrants following screening with interferon-gamma release assays. BMC Public Health. 2016 08 25; 16(1):875. PMID: 27558397; PMCID: PMC4997768.
    17. Moses MW, Zwerling A, Cattamanchi A, Denkinger CM, Banaei N, Kik SV, Metcalfe J, Pai M, Dowdy D. Serial testing for latent tuberculosis using QuantiFERON-TB Gold In-Tube: A Markov model. Sci Rep. 2016 07 29; 6:30781. PMID: 27469388.
      View in: PubMed
    18. Metcalfe JZ, Makumbirofa S, Makamure B, Sandy C, Bara W, Mason P, Hopewell PC. Xpert(®) MTB/RIF detection of rifampin resistance and time to treatment initiation in Harare, Zimbabwe. Int J Tuberc Lung Dis. 2016 07; 20(7):882-9. PMID: 27287639; PMCID: PMC4961684.
    19. Gerona R, Wen A, Koss C, Bacchetti P, Gandhi M, Metcalfe J. A multi-analyte panel for non-invasive pharmacokinetic monitoring of second-line anti-tuberculosis drugs. Int J Tuberc Lung Dis. 2016 07; 20(7):991-2. PMID: 27287660.
      View in: PubMed
    20. Gerona R, Wen A, Chin AT, Koss CA, Bacchetti P, Metcalfe J, Gandhi M. Quantifying Isoniazid Levels in Small Hair Samples: A Novel Method for Assessing Adherence during the Treatment of Latent and Active Tuberculosis. PLoS One. 2016; 11(5):e0155887. PMID: 27191185.
      View in: PubMed
    21. O'Donnell MR, Daftary A, Frick M, Hirsch-Moverman Y, Amico KR, Senthilingam M, Wolf A, Metcalfe JZ, Isaakidis P, Davis JL, Zelnick JR, Brust JC, Naidu N, Garretson M, Bangsberg DR, Padayatchi N, Friedland G. Re-inventing adherence: toward a patient-centered model of care for drug-resistant tuberculosis and HIV. Int J Tuberc Lung Dis. 2016 Apr; 20(4):430-4. PMID: 26970149; PMCID: PMC4863995.
    22. Metcalfe JZ, O'Donnell MR, Bangsberg DR. Moving Beyond Directly Observed Therapy for Tuberculosis. PLoS Med. 2015 Sep; 12(9):e1001877. PMID: 26372602; PMCID: PMC4570797.
    23. Metcalfe JZ, Makumbirofa S, Makamure B, Mutetwa R, Peñaloza RA, Sandy C, Bara W, Mungofa S, Hopewell PC, Mason P. Suboptimal specificity of Xpert MTB/RIF among treatment-experienced patients. Eur Respir J. 2015 May; 45(5):1504-6. PMID: 25792637; PMCID: PMC4948946.
    24. Coscolla M, Barry PM, Oeltmann JE, Koshinsky H, Shaw T, Cilnis M, Posey J, Rose J, Weber T, Fofanov VY, Gagneux S, Kato-Maeda M, Metcalfe JZ. Genomic epidemiology of multidrug-resistant Mycobacterium tuberculosis during transcontinental spread. J Infect Dis. 2015 Jul 15; 212(2):302-10. PMID: 25601940; PMCID: PMC4490235.
    25. Metcalfe JZ, Vittinghoff E, Hopewell PC. Analysis of Green Light Committee implementation and acquisition of second-line drug resistance. Clin Infect Dis. 2015 Mar 15; 60(6):970. PMID: 25527651.
      View in: PubMed
    26. Kelly JD, Grace Lin SY, Barry PM, Keh C, Higashi J, Metcalfe JZ. Xpert MTB/RIF false detection of rifampin-resistant tuberculosis from prior infection. Am J Respir Crit Care Med. 2014 Dec 01; 190(11):1316-8. PMID: 25436783.
      View in: PubMed
    27. Tagmouti S, Slater M, Benedetti A, Kik SV, Banaei N, Cattamanchi A, Metcalfe J, Dowdy D, van Zyl Smit R, Dendukuri N, Pai M, Denkinger C. Reproducibility of interferon gamma (IFN-?) release Assays. A systematic review. Ann Am Thorac Soc. 2014 Oct; 11(8):1267-76. PMID: 25188809.
      View in: PubMed
    28. Metcalfe JZ, Mason P, Mungofa S, Sandy C, Hopewell PC. Empiric tuberculosis treatment in retreatment patients in high HIV/tuberculosis-burden settings. Lancet Infect Dis. 2014 Sep; 14(9):794-5. PMID: 25164190; PMCID: PMC4317243.
    29. Mupfumi L, Makamure B, Chirehwa M, Sagonda T, Zinyowera S, Mason P, Metcalfe JZ, Mutetwa R. Impact of Xpert MTB/RIF on Antiretroviral Therapy-Associated Tuberculosis and Mortality: A Pragmatic Randomized Controlled Trial. Open Forum Infect Dis. 2014 Mar; 1(1):ofu038. PMID: 25734106.
      View in: PubMed
    30. Davis JL, Kawamura LM, Chaisson LH, Grinsdale J, Benhammou J, Ho C, Babst A, Banouvong H, Metcalfe JZ, Pandori M, Hopewell PC, Cattamanchi A. Impact of GeneXpert MTB/RIF on patients and tuberculosis programs in a low-burden setting. a hypothetical trial. Am J Respir Crit Care Med. 2014 Jun 15; 189(12):1551-9. PMID: 24869625; PMCID: PMC4226012.
    31. Metcalfe JZ, Makumbirofa S, Makamure B, Sandy C, Bara W, Mungofa S, Hopewell PC, Mason P. Drug-resistant tuberculosis in high-risk groups, Zimbabwe. Emerg Infect Dis. 2014 Jan; 20(1):135-7. PMID: 24377879.
      View in: PubMed
    32. Pai M, Denkinger CM, Kik SV, Rangaka MX, Zwerling A, Oxlade O, Metcalfe JZ, Cattamanchi A, Dowdy DW, Dheda K, Banaei N. Gamma interferon release assays for detection of Mycobacterium tuberculosis infection. Clin Microbiol Rev. 2014 Jan; 27(1):3-20. PMID: 24396134.
      View in: PubMed
    33. Millman AJ, Dowdy DW, Miller CR, Brownell R, Metcalfe JZ, Cattamanchi A, Davis JL. Rapid molecular testing for TB to guide respiratory isolation in the U.S.: a cost-benefit analysis. PLoS One. 2013; 8(11):e79669. PMID: 24278155; PMCID: PMC3835836.
    34. Prach LM, Pascopella L, Barry PM, Flood J, Porco TC, Hopewell PC, Metcalfe JZ. Rifampin monoresistant tuberculosis and HIV comorbidity in California, 1993-2008: a retrospective cohort study. AIDS. 2013 Oct 23; 27(16):2615-22. PMID: 23842135; PMCID: PMC4296030.
    35. Cattamanchi A, Walter ND, Metcalfe JZ, Davis JL. A transcriptional signature for active TB: have we found the needle in the haystack? PLoS Med. 2013 Oct; 10(10):e1001539. PMID: 24167454.
      View in: PubMed
    36. Gopal M, Padayatchi N, Metcalfe JZ, O'Donnell MR. Systematic review of clofazimine for the treatment of drug-resistant tuberculosis. Int J Tuberc Lung Dis. 2013 Aug; 17(8):1001-7. PMID: 23541151; PMCID: PMC4003893.
    37. Metcalfe JZ, Porco TC, Westenhouse J, Damesyn M, Facer M, Hill J, Xia Q, Watt JP, Hopewell PC, Flood J. Tuberculosis and HIV co-infection, California, USA, 1993–2008. Emerg Infect Dis. 2013 Mar; 19(3):400-6. PMID: 23745218; PMCID: PMC3648844.
    38. Makamure B, Mhaka J, Makumbirofa S, Mutetwa R, Mupfumi L, Mason P, Metcalfe JZ. Microscopic-observation drug-susceptibility assay for the diagnosis of drug-resistant tuberculosis in Harare, Zimbabwe. PLoS One. 2013; 8(2):e55872. PMID: 23409072.
      View in: PubMed
    39. Metcalfe JZ, Cattamanchi A, McCulloch CE, Lew JD, Ha NP, Graviss EA. Test variability of the QuantiFERON-TB gold in-tube assay in clinical practice. Am J Respir Crit Care Med. 2013 Jan 15; 187(2):206-11. PMID: 23103734.
      View in: PubMed
    40. Dantes R, Metcalfe J, Kim E, Kato-Maeda M, Hopewell PC, Kawamura M, Nahid P, Cattamanchi A. Impact of isoniazid resistance-conferring mutations on the clinical presentation of isoniazid monoresistant tuberculosis. PLoS One. 2012; 7(5):e37956. PMID: 22649569; PMCID: PMC3359338.
    41. Geng EH, Glidden DV, Bangsberg DR, Bwana MB, Musinguzi N, Nash D, Metcalfe JZ, Yiannoutsos CT, Martin JN, Petersen ML. A causal framework for understanding the effect of losses to follow-up on epidemiologic analyses in clinic-based cohorts: the case of HIV-infected patients on antiretroviral therapy in Africa. Am J Epidemiol. 2012 May 15; 175(10):1080-7. PMID: 22306557.
      View in: PubMed
    42. Metcalfe JZ, Everett CK, Steingart KR, Cattamanchi A, Huang L, Hopewell PC, Pai M. Interferon-? release assays for active pulmonary tuberculosis diagnosis in adults in low- and middle-income countries: systematic review and meta-analysis. J Infect Dis. 2011 Nov 15; 204 Suppl 4:S1120-9. PMID: 21996694; PMCID: PMC3192542.
    43. Brust JC, O'Donnell MR, Metcalfe JZ. TB/HIV: an orphan disease? Am J Respir Crit Care Med. 2011 Jun 01; 183(11):1441-2. PMID: 21642250.
      View in: PubMed
    44. Cattamanchi A, Smith R, Steingart KR, Metcalfe JZ, Date A, Coleman C, Marston BJ, Huang L, Hopewell PC, Pai M. Interferon-gamma release assays for the diagnosis of latent tuberculosis infection in HIV-infected individuals: a systematic review and meta-analysis. J Acquir Immune Defic Syndr. 2011 Mar 01; 56(3):230-8. PMID: 21239993.
      View in: PubMed
    45. Kato-Maeda M, Metcalfe JZ, Flores L. Genotyping of Mycobacterium tuberculosis: application in epidemiologic studies. Future Microbiol. 2011 Feb; 6(2):203-16. PMID: 21366420; PMCID: PMC4296029.
    46. Metcalfe JZ, Kim EY, Lin SY, Cattamanchi A, Oh P, Flood J, Hopewell PC, Kato-Maeda M. Determinants of multidrug-resistant tuberculosis clusters, California, USA, 2004-2007. Emerg Infect Dis. 2010 Sep; 16(9):1403-9. PMID: 20735924; PMCID: PMC3294976.
    47. Davis JL, Worodria W, Kisembo H, Metcalfe JZ, Cattamanchi A, Kawooya M, Kyeyune R, den Boon S, Powell K, Okello R, Yoo S, Huang L. Clinical and radiographic factors do not accurately diagnose smear-negative tuberculosis in HIV-infected inpatients in Uganda: a cross-sectional study. PLoS One. 2010 Mar 26; 5(3):e9859. PMID: 20361038; PMCID: PMC2845634.
    48. Metcalfe JZ, Cattamanchi A, Vittinghoff E, Ho C, Grinsdale J, Hopewell PC, Kawamura LM, Nahid P. Evaluation of quantitative IFN-gamma response for risk stratification of active tuberculosis suspects. Am J Respir Crit Care Med. 2010 Jan 01; 181(1):87-93. PMID: 19797760.
      View in: PubMed
    49. Cattamanchi A, Dantes RB, Metcalfe JZ, Jarlsberg LG, Grinsdale J, Kawamura LM, Osmond D, Hopewell PC, Nahid P. Clinical characteristics and treatment outcomes of patients with isoniazid-monoresistant tuberculosis. Clin Infect Dis. 2009 Jan 15; 48(2):179-85. PMID: 19086909; PMCID: PMC2756509.
    50. Gouveia EL, Metcalfe J, de Carvalho AL, Aires TS, Villasboas-Bisneto JC, Queirroz A, Santos AC, Salgado K, Reis MG, Ko AI. Leptospirosis-associated severe pulmonary hemorrhagic syndrome, Salvador, Brazil. Emerg Infect Dis. 2008 Mar; 14(3):505-8. PMID: 18325275; PMCID: PMC2570821.
    51. Roshanravan B, Kari E, Gilman RH, Cabrera L, Lee E, Metcalfe J, Calderon M, Lescano AG, Montenegro SH, Calampa C, Vinetz JM. Endemic malaria in the Peruvian Amazon region of Iquitos. Am J Trop Med Hyg. 2003 Jul; 69(1):45-52. PMID: 12932096.
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    52. Stephanie Margaret Selike Wilmore, MRCP, MSc; Katharina Kranzer; Alan Williams; Beauty Makamure; Agness Nhdiza; Justin Mayini; Tsitsi Bandason; John Metcalfe; Mark Nicol; Indran Balakrishnan; Matthew Ellington; Neil Woodford; Susan Hopkins; Tim D McHugh; Rashida Ferrand. .Carriage of Extended-Spectrum Beta-Lactamase-producing Enterobacteriaceae in HIV-infected children in Zimbabwe. Accepted, Journal of Medical Microbiology.