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

Assistant Professor

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Faculty Appointments
Assistant Professor of Pathology, Microbiology and Immunology
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
4514 TVC
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. This diagnostic testing at Vanderbilt—across bacterial, viral, fungal, and parasitic pathogens—occurs within MIDL, in support of the clinical mission of the Adult Hospital, Children's Hospital, and outpatient enterprise.
Research Keywords
Opportunistic pathogens, microbe-microbe interactions, personalized microbiology
Clinical Research Keywords
Clinical microbiology, molecular diagnostics
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.

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.

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.

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, 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. 2002.