John Metcalfe, MD, PhD, MPH

Professor In Residence
Medicine
+1 415 476-0735

I have a particular interest in clinical management of multidrug resistant tuberculosis (MDR-TB) in high HIV burden settings in Southern Africa. My research includes the development of non-invasive pharmacokinetic measures to enhance MDR-TB drug development and clinical trials. I am a member of the AIDS Clinical Trials Group TB Transformative Science Group, and have specialized training in epidemiology, statistical prediction, and diagnostic test evaluation. I am a specialty editor for respiratory diseases at PLoS Medicine.

Publications: 

Circularization of rv0678 for Genotypic Bedaquiline Resistance Testing of Mycobacterium tuberculosis.

Microbiology spectrum

Limberis JD, Nalyvayko A, Ernst JD, Metcalfe JZ

Alternative Methods for Therapeutic Drug Monitoring and Dose Adjustment of Tuberculosis Treatment in Clinical Settings: A Systematic Review.

Clinical pharmacokinetics

Rao PS, Modi N, Nguyen NT, Vu DH, Xie YL, Gandhi M, Gerona R, Metcalfe J, Heysell SK, Alffenaar JC

The 2021 WHO catalogue of Mycobacterium tuberculosis complex mutations associated with drug resistance: A genotypic analysis.

The Lancet. Microbe

Walker TM, Miotto P, K?ser CU, Fowler PW, Knaggs J, Iqbal Z, Hunt M, Chindelevitch L, Farhat M, Cirillo DM, Comas I, Posey J, Omar SV, Peto TE, Suresh A, Uplekar S, Laurent S, Colman RE, Nathanson CM, Zignol M, Walker AS, CRyPTIC Consortium, Seq&Treat Consortium, Crook DW, Ismail N, Rodwell TC

Frequent suboptimal thermocycler ramp rate usage negatively impacts GenoType MTBDRsl VER 2.0 performance for second-line drug resistant tuberculosis diagnosis.

The Journal of molecular diagnostics : JMD

Derendinger B, de Vos M, Pillay S, Venter R, Metcalfe J, Ghebrekristos Y, Minnies S, Dolby T, Beylis N, Warren R, Theron G

Comparative Performance of Genomic Methods for the Detection of Pyrazinamide Resistance and Heteroresistance in Mycobacterium tuberculosis.

Journal of clinical microbiology

Whitfield MG, Engelthaler DM, Allender C, Folkerts M, Heupink TH, Limberis J, Warren RM, Van Rie A, Metcalfe JZ

Catastrophic costs among tuberculosis-affected households in Zimbabwe: A national health facility-based survey.

Tropical medicine & international health : TM & IH

Timire C, Ngwenya M, Chirenda J, Metcalfe JZ, Kranzer K, Pedrazzoli D, Takarinda KC, Nguhiu P, Madzingaidzo G, Ndlovu K, Mapuranga T, Cornell M, Sandy C

Genetic variants and their association with phenotypic resistance to bedaquiline in Mycobacterium tuberculosis: a systematic review and individual isolate data analysis.

The Lancet Microbe

Nabila Ismail, Emmanuel Rivière, Jason Limberis, Stella Huo, John Z Metcalfe, Rob M Warren, Annelies Van Rie

Health care seeking patterns of rifampicin-resistant tuberculosis patients in Harare, Zimbabwe: A prospective cohort study.

PloS one

Tadokera R, Huo S, Theron G, Timire C, Manyau-Makumbirofa S, Metcalfe JZ

Xpert MTB/RIF-detected Rifampicin Resistance is a Sub-Optimal Surrogate for Multidrug Resistant Tuberculosis in Eastern Democratic Republic of the Congo: Diagnostic and Clinical Implications.

Clinical infectious diseases : an official publication of the Infectious Diseases Society of America

Bisimwa BC, Nachega JB, Warren RM, Theron G, Metcalfe JZ, Shah M, Diacon AH, Sam-Agudu NA, Yotebieng M, Bulabula ANH, Katoto PDMC, Chirambiza JP, Nyota R, Birembano FM, Musafiri EM, Byadunia S, Bahizire E, Kaswa MK, Callens S, Kashongwe ZM

Diagnostic accuracy of a liquid chromatography-tandem mass spectrometry assay in small hair samples for rifampin-resistant tuberculosis drug concentrations in a routine care setting.

BMC infectious diseases

Metcalfe J, Bacchetti P, Esmail A, Reckers A, Aguilar D, Wen A, Huo S, Muyindike WR, Hahn JA, Dheda K, Gandhi M, Gerona R

Development and validation of a liquid chromatography-tandem mass spectrometry method for quantifying delamanid and its metabolite in small hair samples.

Journal of chromatography. B, Analytical technologies in the biomedical and life sciences

Reckers A, Huo S, Esmail A, Dheda K, Bacchetti P, Gandhi M, Metcalfe J, Gerona R

Treatment success, but living with the consequences of post-tuberculosis sequelae.

The international journal of tuberculosis and lung disease : the official journal of the International Union against Tuberculosis and Lung Disease

Tadyanemhandu C, Chirenda J, Garvey C, Metcalfe J

Validated LC-MS/MS Panel for Quantifying 11 Drug-Resistant TB Medications in Small Hair Samples.

Journal of visualized experiments : JoVE

Reckers A, Wen A, Aguilar D, Bacchetti P, Gandhi M, Metcalfe J, Gerona R

Presentation and outcome of suspected sepsis in a high-HIV burden, high antiretroviral coverage setting.

International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases

Chaka W, Berger C, Huo S, Robertson V, Tachiona C, Magwenzi M, Magombei T, Mpamhanga C, Katzenstein D, Metcalfe J

Correlation of Linezolid Hair Concentrations with Plasma Exposure in Patients with Drug-Resistant Tuberculosis.

Antimicrobial agents and chemotherapy

Wasserman S, Huo S, Ky K, Malig YN, Esmail A, Dheda K, Bacchetti P, Gerona R, Maartens G, Gandhi M, Metcalfe J

Minority Mycobacterium tuberculosis Genotypic Populations as an Indicator of Subsequent Phenotypic Resistance.

American journal of respiratory cell and molecular biology

Engelthaler DM, Streicher EM, Kelley EJ, Allender CJ, Wiggins K, Jimenez D, Lemmer D, Vittinghoff E, Theron G, Sirgel FA, Warren RM, Metcalfe JZ

More should be done now for patients with TB-associated chronic lung disease.

The international journal of tuberculosis and lung disease : the official journal of the International Union against Tuberculosis and Lung Disease

Tadyanemhandu C, Garvey C, Chin A, Metcalfe J

Prevalence of drug-resistant tuberculosis in Zimbabwe: A health facility-based cross-sectional survey.

International journal of infectious diseases : IJID : official publication of the International Society for Infectious Diseases

Timire C, Metcalfe JZ, Chirenda J, Scholten JN, Manyame-Murwira B, Ngwenya M, Matambo R, Charambira K, Mutunzi H, Kalisvaart N, Sandy C

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.

Journal of chromatography. B, Analytical technologies in the biomedical and life sciences

Gerona R, Wen A, Aguilar D, Shum J, Reckers A, Bacchetti P, Gandhi M, Metcalfe J

Point of care Xpert MTB/RIF versus smear microscopy for tuberculosis diagnosis in southern African primary care clinics: a multicentre economic evaluation.

The Lancet. Global health

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

Bedaquiline Microheteroresistance after Cessation of Tuberculosis Treatment.

The New England journal of medicine

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

Association of anti-tuberculosis drug concentrations in hair and treatment outcomes in MDR- and XDR-TB.

ERJ open research

Metcalfe J, Bacchetti P, Gerona R, Esmail A, Dheda K, Gandhi M

Chronic lung disease in adult recurrent tuberculosis survivors in Zimbabwe: a cohort study.

The international journal of tuberculosis and lung disease : the official journal of the International Union against Tuberculosis and Lung Disease

Chin AT, Rylance J, Makumbirofa S, Meffert S, Vu T, Clayton J, Mason P, Woodruff P, Metcalfe J

Effect of Xpert MTB/RIF on clinical outcomes in routine care settings: individual patient data meta-analysis.

The Lancet. Global health

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

Tuberculosis outbreak investigation using phylodynamic analysis.

Epidemics

Kühnert D, Coscolla M, Brites D, Stucki D, Metcalfe J, Fenner L, Gagneux S, Stadler T

Cryptic Microheteroresistance Explains Mycobacterium tuberculosis Phenotypic Resistance.

American journal of respiratory and critical care medicine

Metcalfe JZ, Streicher E, Theron G, Colman RE, Allender C, Lemmer D, Warren R, Engelthaler DM

Mycobacterium tuberculosis Subculture Results in Loss of Potentially Clinically Relevant Heteroresistance.

Antimicrobial agents and chemotherapy

Metcalfe JZ, Streicher E, Theron G, Colman RE, Penaloza R, Allender C, Lemmer D, Warren RM, Engelthaler DM

An LC-MS/MS-based method to analyze the anti-tuberculosis drug bedaquiline in hair.

The international journal of tuberculosis and lung disease : the official journal of the International Union against Tuberculosis and Lung Disease

Metcalfe J, Gerona R, Wen A, Bacchetti P, Gandhi M

Elucidating the role of clofazimine for the treatment of tuberculosis.

The international journal of tuberculosis and lung disease : the official journal of the International Union against Tuberculosis and Lung Disease

O'Donnell MR, Padayatchi N, Metcalfe JZ

Chronic lung disease in HIV-infected children established on antiretroviral therapy.

AIDS (London, England)

Rylance J, Mchugh G, Metcalfe J, Mujuru H, Nathoo K, Wilmore S, Rowland-Jones S, Majonga E, Kranzer K, Ferrand RA

Tuberculosis progression rates in U.S. Immigrants following screening with interferon-gamma release assays.

BMC public health

Blount RJ, Tran MC, Everett CK, Cattamanchi A, Metcalfe JZ, Connor D, Miller CR, Grinsdale J, Higashi J, Nahid P

Serial testing for latent tuberculosis using QuantiFERON-TB Gold In-Tube: A Markov model.

Scientific reports

Moses MW, Zwerling A, Cattamanchi A, Denkinger CM, Banaei N, Kik SV, Metcalfe J, Pai M, Dowdy D

A multi-analyte panel for non-invasive pharmacokinetic monitoring of second-line anti-tuberculosis drugs.

The international journal of tuberculosis and lung disease : the official journal of the International Union against Tuberculosis and Lung Disease

Gerona R, Wen A, Koss C, Bacchetti P, Gandhi M, Metcalfe J

Xpert(®) MTB/RIF detection of rifampin resistance and time to treatment initiation in Harare, Zimbabwe.

The international journal of tuberculosis and lung disease : the official journal of the International Union against Tuberculosis and Lung Disease

Metcalfe JZ, Makumbirofa S, Makamure B, Sandy C, Bara W, Mason P, Hopewell PC

G276(P) Chronic respiratory morbidity among HIV-infected children in Zimbabwe; a comparison of ART naïve and treated cohorts.

Archives of disease in childhood

S Rylance, J Rylance, G McHugh, H Mujuru, S Munyati, T Bandason, J Metcalfe, K Kranzer, R Ferrand

Re-inventing adherence: toward a patient-centered model of care for drug-resistant tuberculosis and HIV.

The international journal of tuberculosis and lung disease : the official journal of the International Union against Tuberculosis and Lung Disease

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

Moving Beyond Directly Observed Therapy for Tuberculosis.

PLoS medicine

Metcalfe JZ, O'Donnell MR, Bangsberg DR

Suboptimal specificity of Xpert MTB/RIF among treatment-experienced patients.

The European respiratory journal

Metcalfe JZ, Makumbirofa S, Makamure B, Mutetwa R, Peñaloza RA, Sandy C, Bara W, Mungofa S, Hopewell PC, Mason P

Genomic epidemiology of multidrug-resistant Mycobacterium tuberculosis during transcontinental spread.

The Journal of infectious diseases

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

Analysis of Green Light Committee implementation and acquisition of second-line drug resistance.

Clinical infectious diseases : an official publication of the Infectious Diseases Society of America

Metcalfe JZ, Vittinghoff E, Hopewell PC

Xpert MTB/RIF false detection of rifampin-resistant tuberculosis from prior infection.

American journal of respiratory and critical care medicine

Kelly JD, Grace Lin SY, Barry PM, Keh C, Higashi J, Metcalfe JZ

Reproducibility of interferon gamma (IFN-?) release Assays. A systematic review.

Annals of the American Thoracic Society

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

Empiric tuberculosis treatment in retreatment patients in high HIV/tuberculosis-burden settings.

The Lancet. Infectious diseases

Metcalfe JZ, Mason P, Mungofa S, Sandy C, Hopewell PC

Impact of Xpert MTB/RIF on Antiretroviral Therapy-Associated Tuberculosis and Mortality: A Pragmatic Randomized Controlled Trial.

Open forum infectious diseases

Mupfumi L, Makamure B, Chirehwa M, Sagonda T, Zinyowera S, Mason P, Metcalfe JZ, Mutetwa R

Impact of GeneXpert MTB/RIF on patients and tuberculosis programs in a low-burden setting. a hypothetical trial.

American journal of respiratory and critical care medicine

Davis JL, Kawamura LM, Chaisson LH, Grinsdale J, Benhammou J, Ho C, Babst A, Banouvong H, Metcalfe JZ, Pandori M, Hopewell PC, Cattamanchi A

Drug-resistant tuberculosis in high-risk groups, Zimbabwe.

Emerging infectious diseases

Metcalfe JZ, Makumbirofa S, Makamure B, Sandy C, Bara W, Mungofa S, Hopewell PC, Mason P

Gamma interferon release assays for detection of Mycobacterium tuberculosis infection.

Clinical microbiology reviews

Pai M, Denkinger CM, Kik SV, Rangaka MX, Zwerling A, Oxlade O, Metcalfe JZ, Cattamanchi A, Dowdy DW, Dheda K, Banaei N

Rapid molecular testing for TB to guide respiratory isolation in the U.S.: a cost-benefit analysis.

PloS one

Millman AJ, Dowdy DW, Miller CR, Brownell R, Metcalfe JZ, Cattamanchi A, Davis JL

Rifampin monoresistant tuberculosis and HIV comorbidity in California, 1993-2008: a retrospective cohort study.

AIDS (London, England)

Prach LM, Pascopella L, Barry PM, Flood J, Porco TC, Hopewell PC, Metcalfe JZ

A transcriptional signature for active TB: have we found the needle in the haystack?

PLoS medicine

Cattamanchi A, Walter ND, Metcalfe JZ, Davis JL

Systematic review of clofazimine for the treatment of drug-resistant tuberculosis.

The international journal of tuberculosis and lung disease : the official journal of the International Union against Tuberculosis and Lung Disease

Gopal M, Padayatchi N, Metcalfe JZ, O'Donnell MR

Tuberculosis and HIV co-infection, California, USA, 1993–2008.

Emerging infectious diseases

Metcalfe JZ, Porco TC, Westenhouse J, Damesyn M, Facer M, Hill J, Xia Q, Watt JP, Hopewell PC, Flood J

Microscopic-observation drug-susceptibility assay for the diagnosis of drug-resistant tuberculosis in Harare, Zimbabwe.

PloS one

Makamure B, Mhaka J, Makumbirofa S, Mutetwa R, Mupfumi L, Mason P, Metcalfe JZ

Test variability of the QuantiFERON-TB gold in-tube assay in clinical practice.

American journal of respiratory and critical care medicine

Metcalfe JZ, Cattamanchi A, McCulloch CE, Lew JD, Ha NP, Graviss EA

Impact of isoniazid resistance-conferring mutations on the clinical presentation of isoniazid monoresistant tuberculosis.

PloS one

Dantes R, Metcalfe J, Kim E, Kato-Maeda M, Hopewell PC, Kawamura M, Nahid P, Cattamanchi A

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.

American journal of epidemiology

Geng EH, Glidden DV, Bangsberg DR, Bwana MB, Musinguzi N, Nash D, Metcalfe JZ, Yiannoutsos CT, Martin JN, Petersen ML

Interferon-? release assays for active pulmonary tuberculosis diagnosis in adults in low- and middle-income countries: systematic review and meta-analysis.

The Journal of infectious diseases

Metcalfe JZ, Everett CK, Steingart KR, Cattamanchi A, Huang L, Hopewell PC, Pai M

TB/HIV: an orphan disease?

American journal of respiratory and critical care medicine

Brust JC, O'Donnell MR, Metcalfe JZ

Interferon-gamma release assays for the diagnosis of latent tuberculosis infection in HIV-infected individuals: a systematic review and meta-analysis.

Journal of acquired immune deficiency syndromes (1999)

Cattamanchi A, Smith R, Steingart KR, Metcalfe JZ, Date A, Coleman C, Marston BJ, Huang L, Hopewell PC, Pai M

Genotyping of Mycobacterium tuberculosis: application in epidemiologic studies.

Future microbiology

Kato-Maeda M, Metcalfe JZ, Flores L

Determinants of multidrug-resistant tuberculosis clusters, California, USA, 2004-2007.

Emerging infectious diseases

Metcalfe JZ, Kim EY, Lin SY, Cattamanchi A, Oh P, Flood J, Hopewell PC, Kato-Maeda M

Evolution of tuberculosis/HIV co-infection in California during the HAART Era, 1996-2007.

Retrovirology

John Metcalfe, Matt Facer, Mark Damesyn, Qiang Xia, James Watt, Julia Hill, Philip Hopewell, Janice Westenhouse, Jennifer Flood

Clinical and radiographic factors do not accurately diagnose smear-negative tuberculosis in HIV-infected inpatients in Uganda: a cross-sectional study.

PloS one

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

Evaluation of quantitative IFN-gamma response for risk stratification of active tuberculosis suspects.

American journal of respiratory and critical care medicine

Metcalfe JZ, Cattamanchi A, Vittinghoff E, Ho C, Grinsdale J, Hopewell PC, Kawamura LM, Nahid P

Clinical characteristics and treatment outcomes of patients with isoniazid-monoresistant tuberculosis.

Clinical infectious diseases : an official publication of the Infectious Diseases Society of America

Cattamanchi A, Dantes RB, Metcalfe JZ, Jarlsberg LG, Grinsdale J, Kawamura LM, Osmond D, Hopewell PC, Nahid P

Leptospirosis-associated severe pulmonary hemorrhagic syndrome, Salvador, Brazil.

Emerging infectious diseases

Gouveia EL, Metcalfe J, de Carvalho AL, Aires TS, Villasboas-Bisneto JC, Queirroz A, Santos AC, Salgado K, Reis MG, Ko AI

Endemic malaria in the Peruvian Amazon region of Iquitos.

The American journal of tropical medicine and hygiene

Roshanravan B, Kari E, Gilman RH, Cabrera L, Lee E, Metcalfe J, Calderon M, Lescano AG, Montenegro SH, Calampa C, Vinetz JM

Carriage of Extended-Spectrum Beta-Lactamase-producing Enterobacteriaceae in HIV-infected children in Zimbabwe

Accepted, Journal of Medical Microbiology.

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.