Jonathan E. Schmitz, Ph.D., M.D.

Assistant Professor

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Faculty Appointments
Assistant Professor of Pathology, Microbiology and Immunology Assistant Professor of Urology
M.D., Medicine, Cornell University, Ithaca, New YorkPh.D., Rockefeller University, New York, New YorkM.Phil., Biochemistry, University of Cambridge, Cambridge, United KingdomA.B., Chemistry, Princeton University, Princeton, New Jersey
Office Address
VUMC Molecular Infectious Diseases Lab
4519 The Vanderbilt Clinic
1301 Medical Center Drive
Nashville, TN 37232-5310
Research Description
As a Clinical Microbiologist and investigator of microbial pathogenesis, I am drawn to academic questions in which these two sub-disciplines of microbiology complement one another. In this context, the large majority of organisms that we isolate within the diagnostic laboratory would be considered ‘opportunistic pathogens’. Although these bacteria and fungi can elicit symptomatic infections under certain circumstances, they can also represent commensal species within the body — as part the normal human microbiome — or common environmental organisms to which we are routinely exposed. The factors that govern a microbe’s balance between harmful and benign are critical in elucidating infectious mechanisms and interpreting the significance of these organisms diagnostically. My primary research efforts and collaborations address these questions of opportunistic pathogenesis, with particular emphasis on how interactions between different organisms influence pathogenic behavior. It is important to recall that opportunistic pathogens do not encounter the human host in isolation, but against the background of numerous other organisms.

This work is part of my broader interest in the ‘personalization’ or microbial discovery, in which we can re-purpose the unique, patient-specific organisms that we isolate in the clinical laboratory to dissect questions of microbial physiology and host-interaction. Much like the human host, tremendous genotypic and phenotypic diversity exists within individual strains of these same microbial species, diversity that is not well accounted for by traditional experimental models of pathogenesis. By leveraging these derivatives of clinical care for the purpose of academic discovery, I hope to better align the goals of clinical diagnosis and basic investigation.
Clinical Description
I serve as the Medical Director of the VUMC Molecular Infectious Diseases Laboratory (MIDL). We are currently amidst a paradigm shift in the field of Clinical Microbiology, in which PCR and other nucleic acid techniques are complementing (or even replacing) traditional culture-based methods for diagnosing infections. At Vanderbilt, these assays — across bacterial, viral, fungal, and parasitic pathogens — are performed within MIDL, in support of the clinical mission of the Adult Hospital, Children's Hospital, and outpatient enterprise. In conjunction, I serve as an Attending on the Clinical Microbiology Service in the PMI Division of Laboratory Medicine. In this role, I provide consultative support (clinical interpretation and technical guidance) for testing that we conduct across the modalities of infectious-disease diagnostics (culture based, microscopy, molecular, and immunodiagnostic)
Research Keywords
Opportunistic pathogens; microbial pathogenesis; microbe-microbe interactions; personalized microbiology; urinary tract infections
Clinical Research Keywords
Clinical microbiology; molecular diagnostics
Crook J, Xu M, Slaughter JC, Willis J, Browning W, Estrada C, Gay J, Thomas G, Benton A, Quinn C, Schmitz J, Banerjee R. Impact of clinical guidance and rapid molecular pathogen detection on evaluation and outcomes of febrile or hypothermic infants. Infection control and hospital epidemiology [print-electronic]. 2020 Sep 9/3/2020; 1-7. PMID: 32880255, PII: S0899823X20003177, DOI: 10.1017/ice.2020.317, ISSN: 1559-6834.

Antoine-Reid T, Malone J, Maris AS, White-Abell J, Schmitz JE. Cross-Comparison of a Chemiluminescent Platform and a Commercial Receptor Binding Domain-Based ELISA Assay for Detecting SARS-CoV-2 IgG. The journal of applied laboratory medicine [print-electronic]. 2020 Aug 8/4/2020; PMID: 32750140, PMCID: PMC7454603, PII: 5880553, DOI: 10.1093/jalm/jfaa133, ISSN: 2576-9456.

Adams NM, Leelawong M, Benton A, Quinn C, Haselton FR, Schmitz JE. COVID-19 diagnostics for resource-limited settings: Evaluation of "unextracted" qRT-PCR. Journal of medical virology [print-electronic]. 2020 Jul 7/23/2020; PMID: 32779772, PMCID: PMC7405028, DOI: 10.1002/jmv.26328, ISSN: 1096-9071.

Harriott MM, Carnes SK, Stratton CW, Wright PW, Schmitz JE. The Brief Case: Mold Infection of an Indwelling Cranial Device-a Perplexing Combination of "Classic" Laboratory Findings [editorial]. J. Clin. Microbiol [electronic-print]. 2020 Apr 4/23/2020; 58(5): PMID: 32327542, PMCID: PMC7180266, PII: 58/5/e01116-19, DOI: 10.1128/JCM.01116-19, ISSN: 1098-660X.

Tang YW, Schmitz JE, Persing DH, Stratton CW. The Laboratory Diagnosis of COVID-19 Infection: Current Issues and Challenges. J. Clin. Microbiol [print-electronic]. 2020 Apr 4/3/2020; PMID: 32245835, PII: JCM.00512-20, DOI: 10.1128/JCM.00512-20, ISSN: 1098-660X.

Eskind CC, Shilts MH, Boone HH, Schmitz JE, Shaver CM, Satyanarayana G, Das SR. Acute Infection Disrupts the Respiratory Microbiome of Lung Transplant Recipients. J. Heart Lung Transplant [print-electronic]. 2020 Apr; 39(4S): S202. PMID: 32465061, PII: S1053-2498(20)30829-9, DOI: 10.1016/j.healun.2020.01.812, ISSN: 1557-3117.

Wright MF, Weiss VL, Lewis JS, Schmitz JE, Ely KA. Determination of high-risk HPV status of head and neck squamous cell carcinoma using the Roche cobas HPV test on cytologic specimens and acellular supernatant fluid. Cancer Cytopathol [print-electronic]. 2020 Mar 3/4/2020; PMID: 32129949, DOI: 10.1002/cncy.22258, ISSN: 1934-6638.

Colby JM, Wheeler FC, Petrie KA, Gould KL, Schmitz JE. Institutional Training Opportunities for PhD Students in Laboratory Medicine: An Unmet Career Development Need?. J Appl Lab Med. 2020 Mar 3/1/2020; 5(2): 412-6. PMID: 32445389, PII: 5762644, DOI: 10.1093/jalm/jfz028, ISSN: 2576-9456.

Juttukonda LJ, Katz S, Gillon J, Schmitz J, Banerjee R. Impact of a rapid blood culture diagnostic test in a children's hospital depends on Gram-positive vs. Gram-negative organism and day vs. night shift. J. Clin. Microbiol [print-electronic]. 2019 Dec 12/18/2019; PMID: 31852761, PII: JCM.01400-19, DOI: 10.1128/JCM.01400-19, ISSN: 1098-660X.

Eberly AR, Beebout CJ, Carmen Tong CM, Van Horn GT, Green HD, Fitzgerald MJ, De S, Apple EK, Schrimpe-Rutledge AC, Codreanu SG, Sherrod SD, McLean JA, Clayton DB, Stratton CW, Schmitz JE, Hadjifrangiskou M. Defining a Molecular Signature for Uropathogenic versus Urocolonizing Escherichia coli: The Status of the Field and New Clinical Opportunities. J. Mol. Biol [print-electronic]. 2019 Nov 11/30/2019; PMID: 31794727, PII: S0022-2836(19)30672-2, DOI: 10.1016/j.jmb.2019.11.008, ISSN: 1089-8638.

Harriott MM, Bhindi N, Kassis S, Summitt B, Perdikis G, Wormer BA, Rankin TM, Kaoutzanis C, Samaha M, Stratton C, Schmitz JE. Comparative Antimicrobial Activity of Commercial Wound Care Solutions on Bacterial and Fungal Biofilms. Ann Plast Surg. 2019 Oct; 83(4): 404-10. PMID: 31524733, PII: 00000637-201910000-00011, DOI: 10.1097/SAP.0000000000001996, ISSN: 1536-3708.

Capoor MN, Birkenmaier C, Wang JC, McDowell A, Ahmed FS, Brüggemann H, Coscia E, Davies DG, Ohrt-Nissen S, Raz A, Ruzicka F, Schmitz JE, Fischetti VA, Slaby O. A review of microscopy-based evidence for the association of Propionibacterium acnes biofilms in degenerative disc disease and other diseased human tissue. Eur Spine J [print-electronic]. 2019 Jul 7/29/2019; PMID: 31359216, PII: 10.1007/s00586-019-06086-y, DOI: 10.1007/s00586-019-06086-y, ISSN: 1432-0932.

Capoor MN, Lochman J, McDowell A, Schmitz JE, Solansky M, Zapletalova M, Alamin TF, Coscia MF, Garfin SR, Jancalek R, Ruzicka F, Shamie AN, Smrcka M, Wang JC, Birkenmaier C, Slaby O. Intervertebral disc penetration by antibiotics used prophylactically in spinal surgery: implications for the current standards and treatment of disc infections. Eur Spine J [print-electronic]. 2019 Apr; 28(4): 783-91. PMID: 30506486, PII: 10.1007/s00586-018-5838-z, DOI: 10.1007/s00586-018-5838-z, ISSN: 1432-0932.

Lines T, Greene M, Nesbitt WJ, Stratton CW, Schmitz JE. Enterococcus faecalis and Penicillin Susceptibility Testing: The Challenge of Multiple Methods and Agent-to-Agent Predictions. The Journal of Applied Laboratory Medicine. 2019 Jan; 3(4): 730-2. DOI: 10.1373/jalm.2018.027821.

Schmitz JE, Tang YW. The GenMark ePlex®: another weapon in the syndromic arsenal for infection diagnosis. Future Microbiol [print-electronic]. 2018 Dec; 13: 1697-708. PMID: 30547684, PMCID: PMC6439521, DOI: 10.2217/fmb-2018-0258, ISSN: 1746-0921.

Sefers S, Schmitz JE. Molecular Contamination and Amplification Product Inactivation - In: Advanced Techniques in Diagnostic Microbiology (Tang and Stratton, eds). Cham (Switzerland): Springer; 2018 Nov 11/10/2018.ISBN-13: 978-3-319-33899-6.. Available from:

Lawson SK, Chung D, Das S, Friesen J, Sefers S, Dunbar S, Schmitz JE. Analytical and Workflow Evaluation of the ARIES Sample-to-Result Molecular Assay for Clostridium difficile. Ann. Clin. Lab. Sci. 2018 Mar; 48(2): 168-76. PMID: 29678843, PII: 48/2/168, ISSN: 1550-8080.

Capoor MN, Ruzicka F, Sandhu G, Rollason J, Mavrommatis K, Ahmed FS, Schmitz JE, Raz A, Brüggemann H, Lambert PA, Fischetti VA, Slaby O. Importance of Propionibacterium acnes hemolytic activity in human intervertebral discs: A microbiological study. PLoS ONE. 2018; 13(11): e0208144. PMID: 30496247, PMCID: PMC6264842, PII: PONE-D-18-19770, DOI: 10.1371/journal.pone.0208144, ISSN: 1932-6203.

Juttukonda LJ, Berends ETM, Zackular JP, Moore JL, Stier MT, Zhang Y, Schmitz JE, Beavers WN, Wijers CD, Gilston BA, Kehl-Fie TE, Atkinson J, Washington MK, Peebles RS, Chazin WJ, Torres VJ, Caprioli RM, Skaar EP. Dietary Manganese Promotes Staphylococcal Infection of the Heart. Cell Host Microbe [print-electronic]. 2017 Oct 10/11/2017; 22(4): 531-542.e8. PMID: 28943329, PMCID: PMC5638708, PII: S1931-3128(17)30342-6, DOI: 10.1016/j.chom.2017.08.009, ISSN: 1934-6069.

Eberly AR, Floyd KA, Beebout CJ, Colling SJ, Fitzgerald MJ, Stratton CW, Schmitz JE, Hadjifrangiskou M. Biofilm Formation by Uropathogenic Escherichia coli Is Favored under Oxygen Conditions That Mimic the Bladder Environment. Int J Mol Sci. 2017 Sep 9/30/2017; 18(10): PMID: 28973965, PMCID: PMC5666759, PII: ijms18102077, DOI: 10.3390/ijms18102077, ISSN: 1422-0067.

Guckes KR, Breland EJ, Zhang EW, Hanks SC, Gill NK, Algood HM, Schmitz JE, Stratton CW, Hadjifrangiskou M. Signaling by two-component system noncognate partners promotes intrinsic tolerance to polymyxin B in uropathogenic Escherichia coli. Sci Signal. 2017 Jan 1/10/2017; 10(461): PMID: 28074004, PII: 10/461/eaag1775, DOI: 10.1126/scisignal.aag1775, ISSN: 1937-9145.

Gilmer DB, Schmitz JE, Thandar M, Euler CW, Fischetti VA. The Phage Lysin PlySs2 Decolonizes Streptococcus suis from Murine Intranasal Mucosa. PLoS ONE. 2017; 12(1): e0169180. PMID: 28046082, PII: PONE-D-16-12740, DOI: 10.1371/journal.pone.0169180, ISSN: 1932-6203.

Capoor MN, Ruzicka F, Schmitz JE, James GA, Machackova T, Jancalek R, Smrcka M, Lipina R, Ahmed FS, Alamin TF, Anand N, Baird JC, Bhatia N, Demir-Deviren S, Eastlack RK, Fisher S, Garfin SR, Gogia JS, Gokaslan ZL, Kuo CC, Lee YP, Mavrommatis K, Michu E, Noskova H, Raz A, Sana J, Shamie AN, Stewart PS, Stonemetz JL, Wang JC, Witham TF, Coscia MF, Birkenmaier C, Fischetti VA, Slaby O. Propionibacterium acnes biofilm is present in intervertebral discs of patients undergoing microdiscectomy. PLoS ONE. 2017; 12(4): e0174518. PMID: 28369127, PMCID: PMC5378350, PII: PONE-D-17-02125, DOI: 10.1371/journal.pone.0174518, ISSN: 1932-6203.

Schmitz JE, Taniguchi T, Misawa N, Cover TL. Epithelial Coculture and l-Lactate Promote Growth of Helicobacter cinaedi under H2-Free Aerobic Conditions. Appl. Environ. Microbiol [electronic-print]. 2016 Nov 11/15/2016; 82(22): 6701-14. PMID: 27613684, PMCID: PMC5086564, PII: AEM.01943-16, DOI: 10.1128/AEM.01943-16, ISSN: 1098-5336.

Capoor MN, Ruzicka F, Machackova T, Jancalek R, Smrcka M, Schmitz JE, Hermanova M, Sana J, Michu E, Baird JC, Ahmed FS, Maca K, Lipina R, Alamin TF, Coscia MF, Stonemetz JL, Witham T, Ehrlich GD, Gokaslan ZL, Mavrommatis K, Birkenmaier C, Fischetti VA, Slaby O. Prevalence of Propionibacterium acnes in Intervertebral Discs of Patients Undergoing Lumbar Microdiscectomy: A Prospective Cross-Sectional Study. PLoS ONE. 2016; 11(8): e0161676. PMID: 27536784, PMCID: PMC4990245, PII: PONE-D-16-28739, DOI: 10.1371/journal.pone.0161676, ISSN: 1932-6203.

Schmitz JE and Stratton CW. Neisseria meningitidis - In: Molecular Medical Microbiology (Tang, et al., eds). New York (United States): Elsevier / Academic Press; 2015.ISBN-13: 978-0-12-397169-2.. Available from:

Hammer ND, Cassat JE, Noto MJ, Lojek LJ, Chadha AD, Schmitz JE, Creech CB, Skaar EP. Inter- and intraspecies metabolite exchange promotes virulence of antibiotic-resistant Staphylococcus aureus. Cell Host Microbe. 2014 Oct 10/8/2014; 16(4): 531-7. PMID: 25299336, PMCID: PMC4197139, PII: S1931-3128(14)00335-7, DOI: 10.1016/j.chom.2014.09.002, ISSN: 1934-6069.

Gilmer DB, Schmitz JE, Euler CW, Fischetti VA. Novel bacteriophage lysin with broad lytic activity protects against mixed infection by Streptococcus pyogenes and methicillin-resistant Staphylococcus aureus. Antimicrob. Agents Chemother [print-electronic]. 2013 Jun; 57(6): 2743-50. PMID: 23571534, PMCID: PMC3716137, PII: AAC.02526-12, DOI: 10.1128/AAC.02526-12, ISSN: 1098-6596.

Pelzek AJ, Schuch R, Schmitz JE, Fischetti VA, et al. Isolation, Culture, and Characterization, of Bacteriophages. Current Protocols Essential Laboratory Techniques. 2013; 4(4): 1-31.

Pelzek AJ, Schuch R, Schmitz JE, Fischetti VA, et al. Isolation of Bacteriophages from Environmental Sources, and Creation of Functional Screening of Phage DNA Libraries. Current Protocols Essential Laboratory Techniques. 2013; 13(3): 1-35.

Pettit AC, Kropski JA, Castilho JL, Schmitz JE, Rauch CA, Mobley BC, Wang XJ, Spires SS, Pugh ME. The index case for the fungal meningitis outbreak in the United States. N. Engl. J. Med [print-electronic]. 2012 Nov 11/29/2012; 367(22): 2119-25. PMID: 23083311, DOI: 10.1056/NEJMoa1212292, ISSN: 1533-4406.

Schmitz JE, Ossiprandi MC, Rumah KR, Fischetti VA. Lytic enzyme discovery through multigenomic sequence analysis in Clostridium perfringens. Appl. Microbiol. Biotechnol [print-electronic]. 2011 Mar; 89(6): 1783-95. PMID: 21085950, PMCID: PMC3711215, DOI: 10.1007/s00253-010-2982-8, ISSN: 1432-0614.

Schmitz JE, Schuch R, Fischetti VA. Identifying active phage lysins through functional viral metagenomics. Appl. Environ. Microbiol [print-electronic]. 2010 Nov; 76(21): 7181-7. PMID: 20851985, PMCID: PMC2976241, PII: AEM.00732-10, DOI: 10.1128/AEM.00732-10, ISSN: 1098-5336.

Schmitz JE, Schuch R, Fischetti VA. Identifying Phage Lytic Enzymes: Past, Present, and Future - In: Enzybiotics (Villa and Veiga-Crespo, eds.). 1. Hoboken (United States): Wiley; 2010.

Schmitz JE, Daniel A, Collin M, Schuch R, Fischetti VA. Rapid DNA library construction for functional genomic and metagenomic screening. Appl. Environ. Microbiol [print-electronic]. 2008 Mar; 74(5): 1649-52. PMID: 18083885, PMCID: PMC2258639, PII: AEM.01864-07, DOI: 10.1128/AEM.01864-07, ISSN: 1098-5336.

Schmitz JE, Kettunen MI, Hu DE, Brindle KM. 1H MRS-visible lipids accumulate during apoptosis of lymphoma cells in vitro and in vivo. Magn Reson Med. 2005 Jul; 54(1): 43-50. PMID: 15968678, DOI: 10.1002/mrm.20529, ISSN: 0740-3194.

Du J, Stankiewicz MJ, Liu Y, Xi Q, Schmitz JE, Lekstrom-Himes JA, Ackerman SJ. Novel combinatorial interactions of GATA-1, PU.1, and C/EBPepsilon isoforms regulate transcription of the gene encoding eosinophil granule major basic protein. J. Biol. Chem [print-electronic]. 2002 Nov 11/8/2002; 277(45): 43481-94. PMID: 12202480, PII: M204777200, DOI: 10.1074/jbc.M204777200, ISSN: 0021-9258.

Schmitz, JE, Kansal, AR, and Torquato, S. A Cellular Automaton Model of Brain Tumor Treatment and Resistance. Journal of Theoretical Medicine. 2002; 4(4): 223-39.