Jonathan Budzik, MD, PhD

Title(s)Assistant Professor, Medicine
SchoolSchool of Medicine
Address513 Parnassus Avenue, HSE, #409
San Francisco CA 94143
Phone415-476-7147
PronounsHe/Him/His
ORCID ORCID Icon0000-0001-8025-7911 Additional info
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    Collapse Biography 
    Collapse education and training
    University of California, San Francisco, CA2020Diversity, Equity, and Inclusion Champion Training
    University of California, San Francisco, CA2017Pulmonary and Critical Care Medicine Fellowship
    University of California, San Francisco, CA2014Internal Medicine Residency
    University of Chicago, Chicago, ILMD2011Medicine
    University of Chicago, Chicago, ILPhD2009Microbiology

    Collapse Overview 
    Collapse overview
    My research is focused on the study of immune responses to pathogens including Mycobacterium tuberculosis. By understanding the mechanisms that enable pathogens to grow within our immune cells, we hope to enable the development of new therapies to treat infectious diseases.

    As a pulmonary and critical care physician, I provide patient care in the intensive care units, the adult cystic fibrosis clinic, and the bronchiectasis clinic. I am an Associate Director of the UCSF Adult Cystic Fibrosis program.

    Collapse ORNG Applications 
    Collapse Collaboration Interests

    Collapse Bibliographic 
    Collapse selected 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. to make corrections and additions.
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    Altmetrics Details PMC Citations indicate the number of times the publication was cited by articles in PubMed Central, and the Altmetric score represents citations in news articles and social media. (Note that publications are often cited in additional ways that are not shown here.) Fields are based on how the National Library of Medicine (NLM) classifies the publication's journal and might not represent the specific topic of the publication. Translation tags are based on the publication type and the MeSH terms NLM assigns to the publication. Some publications (especially newer ones and publications not in PubMed) might not yet be assigned Field or Translation tags.) Click a Field or Translation tag to filter the publications.
    1. Synthesis, structural characterization, and antimicrobial activity of Zn(cloxyquin)2: towards harnessing zinc intoxication and immune response restoration to combat Staphylococcus aureus and Mycobacterium tuberculosis. Dalton Trans. 2025 Jun 05. Mudarmah K, Abeydeera N, Chen G, Jogadi W, Krause JA, Budzik JM, Huang SD. PMID: 40470632.
      View in: PubMed   Mentions:
    2. Tax1bp1 enhances bacterial virulence and promotes inflammatory responses during Mycobacterium tuberculosis infection of alveolar macrophages. bioRxiv. 2024 Dec 16. Chin J, Abeydeera N, Repasy T, Rivera-Lugo R, Mitchell G, Nguyen VQ, Zheng W, Richards A, Swaney DL, Krogan NJ, Ernst JD, Cox JS, Budzik JM. PMID: 39763950; PMCID: PMC11702572.
      View in: PubMed   Mentions:
    3. Author Correction: Autophagy restricts Mycobacterium tuberculosis during acute infection in mice. Nat Microbiol. 2024 Jul; 9(7):1899. Golovkine GR, Roberts AW, Morrison HM, Rivera-Lugo R, McCall RM, Nilsson H, Garelis NE, Repasy T, Cronce M, Budzik J, Van Dis E, Popov LM, Mitchell G, Zalpuri R, Jorgens D, Cox JS. PMID: 38308100; PMCID: PMC11222042.
      View in: PubMed   Mentions:    Fields:    
    4. History of tuberculosis disease is associated with genetic regulatory variation in Peruvians. PLoS Genet. 2024 Jun; 20(6):e1011313. Nieto-Caballero VE, Reijneveld JF, Ruvalcaba A, Innocenzi G, Abeydeera N, Asgari S, Lopez K, Iwany SK, Luo Y, Nathan A, Fernandez-Salinas D, Chiñas M, Huang CC, Zhang Z, León SR, Calderon RI, Lecca L, Budzik JM, Murray M, Van Rhijn I, Raychaudhuri S, Moody DB, Suliman S, Gutierrez-Arcelus M. PMID: 38870230; PMCID: PMC11208071.
      View in: PubMed   Mentions:    Fields:    Translation:HumansCells
    5. Mycobacterium tuberculosis resides in lysosome-poor monocyte-derived lung cells during chronic infection. PLoS Pathog. 2024 May; 20(5):e1012205. Zheng W, Chang IC, Limberis J, Budzik JM, Zha BS, Howard Z, Chen L, Ernst JD. PMID: 38701094; PMCID: PMC11095722.
      View in: PubMed   Mentions: 10     Fields:    Translation:HumansAnimalsCells
    6. Mycobacterium tuberculosis resides in lysosome-poor monocyte-derived lung cells during chronic infection. Res Sq. 2023 Jun 15. Zheng W, Chang IC, Limberis J, Budzik J, Zha BS, Howard Z, Chen L, Ernst J. PMID: 37398178; PMCID: PMC10312915.
      View in: PubMed   Mentions:
    7. Mycobacterium tuberculosis resides in lysosome-poor monocyte-derived lung cells during chronic infection. bioRxiv. 2023 May 28. Zheng W, Chang IC, Limberis J, Budzik JM, Zha BS, Howard Z, Chen L, Ernst JD. PMID: 36711606; PMCID: PMC9882350.
      View in: PubMed   Mentions:
    8. Autophagy restricts Mycobacterium tuberculosis during acute infection in mice. Nat Microbiol. 2023 05; 8(5):819-832. Golovkine GR, Roberts AW, Morrison HM, Rivera-Lugo R, McCall RM, Nilsson H, Garelis NE, Repasy T, Cronce M, Budzik J, Van Dis E, Popov LM, Mitchell G, Zalpuri R, Jorgens D, Cox JS. PMID: 37037941; PMCID: PMC11027733.
      View in: PubMed   Mentions: 25     Fields:    Translation:AnimalsCells
    9. Ceragenins and Antimicrobial Peptides Kill Bacteria through Distinct Mechanisms. mBio. 2022 02 22; 13(1):e0272621. Mitchell G, Silvis MR, Talkington KC, Budzik JM, Dodd CE, Paluba JM, Oki EA, Trotta KL, Licht DJ, Jimenez-Morales D, Chou S, Savage PB, Gross CA, Marletta MA, Cox JS. PMID: 35073755; PMCID: PMC8787472.
      View in: PubMed   Mentions: 17     Fields:    Translation:Cells
    10. Efficient generation of isogenic primary human myeloid cells using CRISPR-Cas9 ribonucleoproteins. Cell Rep. 2021 05 11; 35(6):109105. Hiatt J, Cavero DA, McGregor MJ, Zheng W, Budzik JM, Roth TL, Haas KM, Wu D, Rathore U, Meyer-Franke A, Bouzidi MS, Shifrut E, Lee Y, Kumar VE, Dang EV, Gordon DE, Wojcechowskyj JA, Hultquist JF, Fontaine KA, Pillai SK, Cox JS, Ernst JD, Krogan NJ, Marson A. PMID: 33979618; PMCID: PMC8188731.
      View in: PubMed   Mentions: 27     Fields:    Translation:HumansAnimalsCells
    11. Antibiotic adverse reactions in adult cystic fibrosis patients. J Allergy Clin Immunol Pract. 2020 Nov - Dec; 8(10):3631-3633.e1. Anstey KM, Lee M, Dawson D, Jue V, Budzik JM, Yu M, Kleinhenz ME, Otani IM. PMID: 32673878.
      View in: PubMed   Mentions:    Fields:    Translation:Humans
    12. Dynamic post-translational modification profiling of Mycobacterium tuberculosis-infected primary macrophages. Elife. 2020 01 17; 9. Budzik JM, Swaney DL, Jimenez-Morales D, Johnson JR, Garelis NE, Repasy T, Roberts AW, Popov LM, Parry TJ, Pratt D, Ideker T, Krogan NJ, Cox JS. PMID: 31951200; PMCID: PMC7030789.
      View in: PubMed   Mentions: 28     Fields:    Translation:HumansAnimalsCells
    13. Pyrazinamide resistance, Mycobacterium tuberculosis lineage and treatment outcomes in San Francisco, California. PLoS One. 2014; 9(4):e95645. Budzik JM, Jarlsberg LG, Higashi J, Grinsdale J, Hopewell PC, Kato-Maeda M, Nahid P. PMID: 24759760; PMCID: PMC3997554.
      View in: PubMed   Mentions: 8     Fields:    Translation:HumansCells
    14. Isopeptide bonds of the major pilin protein BcpA influence pilus structure and bundle formation on the surface of Bacillus cereus. Mol Microbiol. 2012 Jul; 85(1):152-63. Hendrickx AP, Poor CB, Jureller JE, Budzik JM, He C, Schneewind O. PMID: 22624947; PMCID: PMC3538817.
      View in: PubMed   Mentions: 6     Fields:    Translation:Cells
    15. Disseminated Nocardia farcinica: literature review and fatal outcome in an immunocompetent patient. Surg Infect (Larchmt). 2012 Jun; 13(3):163-70. Budzik JM, Hosseini M, Mackinnon AC, Taxy JB. PMID: 22612440; PMCID: PMC3375863.
      View in: PubMed   Mentions: 35     Fields:    Translation:Humans
    16. Two capsular polysaccharides enable Bacillus cereus G9241 to cause anthrax-like disease. Mol Microbiol. 2011 Apr; 80(2):455-70. Oh SY, Budzik JM, Garufi G, Schneewind O. PMID: 21371137; PMCID: PMC3538873.
      View in: PubMed   Mentions: 42     Fields:    Translation:AnimalsCells
    17. Architects at the bacterial surface - sortases and the assembly of pili with isopeptide bonds. Nat Rev Microbiol. 2011 Mar; 9(3):166-76. Hendrickx AP, Budzik JM, Oh SY, Schneewind O. PMID: 21326273.
      View in: PubMed   Mentions: 115     Fields:    Translation:Cells
    18. Intramolecular amide bonds stabilize pili on the surface of bacilli. Proc Natl Acad Sci U S A. 2009 Nov 24; 106(47):19992-7. Budzik JM, Poor CB, Faull KF, Whitelegge JP, He C, Schneewind O. PMID: 19903875; PMCID: PMC2785280.
      View in: PubMed   Mentions: 36     Fields:    Translation:Cells
    19. Sortase D forms the covalent bond that links BcpB to the tip of Bacillus cereus pili. J Biol Chem. 2009 May 08; 284(19):12989-97. Budzik JM, Oh SY, Schneewind O. PMID: 19269972; PMCID: PMC2676031.
      View in: PubMed   Mentions: 19     Fields:    Translation:Cells
    20. Capsule anchoring in Bacillus anthracis occurs by a transpeptidation reaction that is inhibited by capsidin. Mol Microbiol. 2009 Jan; 71(2):404-20. Richter S, Anderson VJ, Garufi G, Lu L, Budzik JM, Joachimiak A, He C, Schneewind O, Missiakas D. PMID: 19017271; PMCID: PMC2770442.
      View in: PubMed   Mentions: 31     Fields:    
    21. Cell wall anchor structure of BcpA pili in Bacillus anthracis. J Biol Chem. 2008 Dec 26; 283(52):36676-86. Budzik JM, Oh SY, Schneewind O. PMID: 18940793; PMCID: PMC2605976.
      View in: PubMed   Mentions: 26     Fields:    Translation:Cells
    22. Sortases make pili from three ingredients. Proc Natl Acad Sci U S A. 2008 Sep 16; 105(37):13703-4. Oh SY, Budzik JM, Schneewind O. PMID: 18784365; PMCID: PMC2544515.
      View in: PubMed   Mentions: 12     Fields:    Translation:Cells
    23. Amide bonds assemble pili on the surface of bacilli. Proc Natl Acad Sci U S A. 2008 Jul 22; 105(29):10215-20. Budzik JM, Marraffini LA, Souda P, Whitelegge JP, Faull KF, Schneewind O. PMID: 18621716; PMCID: PMC2481347.
      View in: PubMed   Mentions: 33     Fields:    Translation:Cells
    24. Assembly of pili on the surface of Bacillus cereus vegetative cells. Mol Microbiol. 2007 Oct; 66(2):495-510. Budzik JM, Marraffini LA, Schneewind O. PMID: 17897374.
      View in: PubMed   Mentions: 55     Fields:    Translation:Cells
    25. Pili prove pertinent to enterococcal endocarditis. J Clin Invest. 2006 Oct; 116(10):2582-4. Budzik JM, Schneewind O. PMID: 17016552; PMCID: PMC1578624.
      View in: PubMed   Mentions: 5     Fields:    Translation:HumansAnimalsCells
    26. Isolation and characterization of a generalized transducing phage for Pseudomonas aeruginosa strains PAO1 and PA14. J Bacteriol. 2004 May; 186(10):3270-3. Budzik JM, Rosche WA, Rietsch A, O'Toole GA. PMID: 15126493; PMCID: PMC400619.
      View in: PubMed   Mentions: 46     Fields:    Translation:Cells
    27. The role of bacterial biofilms in ocular infections. DNA Cell Biol. 2002 May-Jun; 21(5-6):415-20. Zegans ME, Becker HI, Budzik J, O'Toole G. PMID: 12167244.
      View in: PubMed   Mentions: 44     Fields:    Translation:HumansCells
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