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Publications


For a complete and updated publication list, click here.
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2025

  • Brzozowski, Robert S., Amelia K. Schmidt, Nicole L. Pershing, Annika Dankwardt, Dominick R. Faith, Alex C. Joyce, Andrew Maciver, William S. Henriques, Shelby E. Andersen, Blake Wiedenheft, Sherwood Casjens, Breck A. Duerkop, June L. Round, and Patrick R. Secor. “A Prophage-Encoded sRNA Limits Lytic Phage Infection of Adherent-Invasive E. coli.” bioRxiv, May 2025. https://doi.org/10.1101/2025.05.06.652453.
  • Burgener, Elizabeth B., Aditi Gupta, Kayo Nakano, Sophia L. Gibbs, Maya E. Sommers, Arya Khosravi, Michelle S. Bach, et al. “Pf Bacteriophage Is Associated with Decline in Lung Function in a Longitudinal Cohort of Patients with Cystic Fibrosis and Pseudomonas Airway Infection.” Journal of Cystic Fibrosis: Official Journal of the European Cystic Fibrosis Society 24, no. 2 (March 2025): 345–52. https://doi.org/10.1016/j.jcf.2024.09.018.
  • Fitzpatrick, Alexa D., Véronique L. Taylor, Pramalkumar H. Patel, Dominick R. Faith, Patrick R. Secor, and Karen L. Maxwell. “Phage Reprogramming of Pseudomonas Aeruginosa Amino Acid Metabolism Drives Efficient Phage Replication.” mBio 16, no. 3 (March 12, 2025): e0246624. https://doi.org/10.1128/mbio.02466-24.
  • Pourtois, Julie D., Naomi L. Haddock, Aditi Gupta, Arya Khosravi, Hunter Martinez, Amelia K. Schmidt, Prema S. Prakash, et al. “Pseudomonas Superinfection Drives Pf Phage Transmission within Airway Infections in Patients with Cystic Fibrosis.” bioRxiv: The Preprint Server for Biology, January 14, 2025, 2025.01.14.632786. https://doi.org/10.1101/2025.01.14.632786.

2024

  • Burgener, Elizabeth B., Pamela C. Cai, Michael J. Kratochvil, Laura S. Rojas-Hernandez, Nam Soo Joo, Aditi Gupta, Patrick R. Secor, et al. “The Lysogenic Filamentous Pseudomonas Bacteriophage Phage Pf Slows Mucociliary Transport.” PNAS Nexus 3, no. 9 (September 2024): pgae390. https://doi.org/10.1093/pnasnexus/pgae390.
  • Chen, Qingquan, Pam Cai, Tony Hong Wei Chang, Elizabeth Burgener, Michael J. Kratochvil, Aditi Gupta, Aviv Hargill, et al. “Pf Bacteriophages Hinder Sputum Antibiotic Diffusion via Electrostatic Binding.” Science Advances 10, no. 22 (May 31, 2024): eadl5576. https://doi.org/10.1126/sciadv.adl5576.
  • Copeland, Conner J., Jack W. Roddy, Amelia K. Schmidt, Patrick R. Secor, and Travis J. Wheeler. “VIBES: A Workflow for Annotating and Visualizing Viral Sequences Integrated into Bacterial Genomes.” NAR Genomics and Bioinformatics 6, no. 2 (June 2024): lqae030. https://doi.org/10.1093/nargab/lqae030.
  • Faith, Dominick R., Margie Kinnersley, Diane M. Brooks, Dan Drecktrah, Laura S. Hall, Eric Luo, Andrew Santiago-Frangos, Jenny Wachter, D. Scott Samuels, and Patrick R. Secor. “Characterization and Genomic Analysis of the Lyme Disease Spirochete Bacteriophage ϕBB-1.” PLoS Pathogens 20, no. 4 (April 2024): e1012122. https://doi.org/10.1371/journal.ppat.1012122.
  • Román-Cruz, Valery C., Shannon M. Miller, Roman A. Schoener, Chase Lukasiewicz, Amelia K. Schmidt, Blair L. DeBuysscher, David Burkhart, Patrick R. Secor, and Jay T. Evans. “Adjuvanted Vaccine Induces Functional Antibodies against Pseudomonas Aeruginosa Filamentous Bacteriophages.” Vaccines 12, no. 2 (January 24, 2024): 115. https://doi.org/10.3390/vaccines12020115.
  • Schmidt, Amelia K., Caleb M. Schwartzkopf, Julie D. Pourtois, Elizabeth B. Burgener, Dominick R. Faith, Alex Joyce, Tyrza Lamma, Geetha Kumar, Paul L. Bollyky, and Patrick R. Secor. “Targeted Deletion of Pf Prophages from Diverse Pseudomonas Aeruginosa Isolates Has Differential Impacts on Quorum Sensing and Virulence Traits.” Journal of Bacteriology 206, no. 5 (May 23, 2024): e0040223. https://doi.org/10.1128/jb.00402-23.
  • Schwartzkopf, Caleb M., Véronique L. Taylor, Marie-Christine Groleau, Dominick R. Faith, Amelia K. Schmidt, Tyrza L. Lamma, Diane M. Brooks, Eric Déziel, Karen L. Maxwell, and Patrick R. Secor. “Inhibition of PQS Signaling by the Pf Bacteriophage Protein PfsE Enhances Viral Replication in Pseudomonas Aeruginosa.” Molecular Microbiology 121, no. 1 (January 2024): 116–28. https://doi.org/10.1111/mmi.15202.

2023

  • Mattos, Camilla D. de, Dominick R. Faith, Artem A. Nemudryi, Amelia K. Schmidt, DeAnna C. Bublitz, Lauren Hammond, Margie A. Kinnersley, et al. “Polyamines and Linear DNA Mediate Bacterial Threat Assessment of Bacteriophage Infection.” Proceedings of the National Academy of Sciences of the United States of America 120, no. 9 (February 28, 2023): e2216430120. https://doi.org/10.1073/pnas.2216430120.
  • Rossem, M. T. van, S. Wilks, P. R. Secor, M. Kaczmarek, and G. D’Alessandro. “Homogenization Modelling of Antibiotic Diffusion and Adsorption in Viral Liquid Crystals.” Royal Society Open Science 10, no. 1 (January 2023): 221120. https://doi.org/10.1098/rsos.221120.
  • Sapiro, Anne L., Beth M. Hayes, Regan F. Volk, Jenny Y. Zhang, Diane M. Brooks, Calla Martyn, Atanas Radkov, et al. “Longitudinal Map of Transcriptome Changes in the Lyme Pathogen Borrelia Burgdorferi during Tick-Borne Transmission.” eLife 12 (July 14, 2023): RP86636. https://doi.org/10.7554/eLife.86636.
  • Schmidt, Amelia K., Dominick R. Faith, and Patrick R. Secor. “PICI Thieves: Molecular Piracy and Cooperation.” Cell Host & Microbe 31, no. 1 (January 11, 2023): 3–5. https://doi.org/10.1016/j.chom.2022.12.008.
  • Schwartzkopf, Caleb M., Autumn J. Robinson, Mary Ellenbecker, Dominick R. Faith, Amelia K. Schmidt, Diane M. Brooks, Lincoln Lewerke, Ekaterina Voronina, Ajai A. Dandekar, and Patrick R. Secor. “Tripartite Interactions between Filamentous Pf4 Bacteriophage, Pseudomonas Aeruginosa, and Bacterivorous Nematodes.” PLoS Pathogens 19, no. 2 (February 2023): e1010925. https://doi.org/10.1371/journal.ppat.1010925.
  • Wachter, Jenny, Britney Cheff, Chad Hillman, Valentina Carracoi, David W. Dorward, Craig Martens, Kent Barbian, et al. “Coupled Induction of Prophage and Virulence Factors during Tick Transmission of the Lyme Disease Spirochete.” Nature Communications 14, no. 1 (January 13, 2023): 198. https://doi.org/10.1038/s41467-023-35897-3.

2022

  • Bach, Michelle S., Christiaan R. de Vries, Arya Khosravi, Johanna M. Sweere, Medeea C. Popescu, Qingquan Chen, Sally Demirdjian, et al. “Filamentous Bacteriophage Delays Healing of Pseudomonas-Infected Wounds.” Cell Reports. Medicine 3, no. 6 (June 21, 2022): 100656. https://doi.org/10.1016/j.xcrm.2022.100656.
  • Faith, Dominick, Margie Kinnersley, Caleb M. Schwartzkopf, Camilla D. de Mattos, Amelia K. Schmidt, and Patrick R. Secor. “Complete Genome Sequence of the N4-like Pseudomonas Aeruginosa Bacteriophage vB_PaeP_CMS1.” Microbiology Resource Announcements 11, no. 7 (July 21, 2022): e0023922. https://doi.org/10.1128/mra.00239-22.
  • Rossem, Maria van, Sandra Wilks, Malgosia Kaczmarek, Patrick R. Secor, and Giampaolo D’Alessandro. “Modelling of Filamentous Phage-Induced Antibiotic Tolerance of P. Aeruginosa.” PloS One 17, no. 4 (2022): e0261482. https://doi.org/10.1371/journal.pone.0261482.
  • Schmidt, Amelia K., Alexa D. Fitzpatrick, Caleb M. Schwartzkopf, Dominick R. Faith, Laura K. Jennings, Alison Coluccio, Devin J. Hunt, et al. “A Filamentous Bacteriophage Protein Inhibits Type IV Pili To Prevent Superinfection of Pseudomonas Aeruginosa.” mBio 13, no. 1 (February 22, 2022): e0244121. https://doi.org/10.1128/mbio.02441-21.
  • Secor, Patrick R., Lia A. Michaels, DeAnna C. Bublitz, Laura K. Jennings, and Pradeep K. Singh. “The Depletion Mechanism Actuates Bacterial Aggregation by Exopolysaccharides and Determines Species Distribution & Composition in Bacterial Aggregates.” Frontiers in Cellular and Infection Microbiology 12 (2022): 869736. https://doi.org/10.3389/fcimb.2022.869736.

2021

  • Jennings, Laura K., Julia E. Dreifus, Courtney Reichhardt, Kelly M. Storek, Patrick R. Secor, Daniel J. Wozniak, Katherine B. Hisert, and Matthew R. Parsek. “Pseudomonas Aeruginosa Aggregates in Cystic Fibrosis Sputum Produce Exopolysaccharides That Likely Impede Current Therapies.” Cell Reports 34, no. 8 (February 23, 2021): 108782. https://doi.org/10.1016/j.celrep.2021.108782.
  • Kirsch, Joshua M., Robert S. Brzozowski, Dominick Faith, June L. Round, Patrick R. Secor, and Breck A. Duerkop. “Bacteriophage-Bacteria Interactions in the Gut: From Invertebrates to Mammals.” Annual Review of Virology 8, no. 1 (September 29, 2021): 95–113. https://doi.org/10.1146/annurev-virology-091919-101238.

2020

  • Burgener, Elizabeth B., Patrick R. Secor, Michael C. Tracy, Johanna M. Sweere, Elisabeth M. Bik, Carlos E. Milla, and Paul L. Bollyky. “Methods for Extraction and Detection of Pf Bacteriophage DNA from the Sputum of Patients with Cystic Fibrosis.” PHAGE (New Rochelle, N.Y.) 1, no. 2 (June 1, 2020): 100–108. https://doi.org/10.1089/phage.2020.0003.
  • Secor, Patrick R., Elizabeth B. Burgener, M. Kinnersley, Laura K. Jennings, Valery Roman-Cruz, Medeea Popescu, Jonas D. Van Belleghem, et al. “Pf Bacteriophage and Their Impact on Pseudomonas Virulence, Mammalian Immunity, and Chronic Infections.” Frontiers in Immunology 11 (2020): 244. https://doi.org/10.3389/fimmu.2020.00244.
  • Secor, Patrick R., and Ajai A. Dandekar. “More than Simple Parasites: The Sociobiology of Bacteriophages and Their Bacterial Hosts.” mBio 11, no. 2 (March 10, 2020): e00041-20. https://doi.org/10.1128/mBio.00041-20.
  • Sweere, Johanna M., Heather Ishak, Vivekananda Sunkari, Michelle S. Bach, Robert Manasherob, Koshika Yadava, Shannon M. Ruppert, et al. “The Immune Response to Chronic Pseudomonas Aeruginosa Wound Infection in Immunocompetent Mice.” Advances in Wound Care 9, no. 2 (February 1, 2020): 35–47. https://doi.org/10.1089/wound.2019.1039.

2019

  • Bollyky, Paul L., and Patrick R. Secor. “The Innate Sense of Bacteriophages.” Cell Host & Microbe 25, no. 2 (February 13, 2019): 177–79. https://doi.org/10.1016/j.chom.2019.01.020.
  • Burgener, Elizabeth B., Johanna M. Sweere, Michelle S. Bach, Patrick R. Secor, Naomi Haddock, Laura K. Jennings, Rasmus L. Marvig, et al. “Filamentous Bacteriophages Are Associated with Chronic Pseudomonas Lung Infections and Antibiotic Resistance in Cystic Fibrosis.” Science Translational Medicine 11, no. 488 (April 17, 2019): eaau9748. https://doi.org/10.1126/scitranslmed.aau9748.
  • Sweere, Johanna M., Jonas D. Van Belleghem, Heather Ishak, Michelle S. Bach, Medeea Popescu, Vivekananda Sunkari, Gernot Kaber, et al. “Bacteriophage Trigger Antiviral Immunity and Prevent Clearance of Bacterial Infection.” Science (New York, N.Y.) 363, no. 6434 (March 29, 2019): eaat9691. https://doi.org/10.1126/science.aat9691.

2018

  • Secor, Patrick R., Lia A. Michaels, Anina Ratjen, Laura K. Jennings, and Pradeep K. Singh. “Entropically Driven Aggregation of Bacteria by Host Polymers Promotes Antibiotic Tolerance in Pseudomonas Aeruginosa.” Proceedings of the National Academy of Sciences of the United States of America 115, no. 42 (October 16, 2018): 10780–85. https://doi.org/10.1073/pnas.1806005115.

2017

  • Jorth, Peter, Kathryn McLean, Anina Ratjen, Patrick R. Secor, Gilbert E. Bautista, Sumedha Ravishankar, Amir Rezayat, et al. “Evolved Aztreonam Resistance Is Multifactorial and Can Produce Hypervirulence in Pseudomonas Aeruginosa.” mBio 8, no. 5 (October 31, 2017): e00517-17. https://doi.org/10.1128/mBio.00517-17.
  • Nazik, Hasan, Lydia-Marie Joubert, Patrick R. Secor, Johanna M. Sweere, Paul L. Bollyky, Gabriele Sass, Lynette Cegelski, and David A. Stevens. “Pseudomonas Phage Inhibition of Candida Albicans.” Microbiology (Reading, England) 163, no. 11 (November 2017): 1568–77. https://doi.org/10.1099/mic.0.000539.
  • Secor, Patrick R., Lia A. Michaels, Kate S. Smigiel, Maryam G. Rohani, Laura K. Jennings, Katherine B. Hisert, Allison Arrigoni, et al. “Filamentous Bacteriophage Produced by Pseudomonas Aeruginosa Alters the Inflammatory Response and Promotes Noninvasive Infection In Vivo.” Infection and Immunity 85, no. 1 (January 2017): e00648-16. https://doi.org/10.1128/IAI.00648-16.
  • Secor, Patrick R., Gabriele Sass, Hasan Nazik, and David A. Stevens. “Effect of Acute Predation with Bacteriophage on Intermicrobial Aggression by Pseudomonas Aeruginosa.” PloS One 12, no. 6 (2017): e0179659. https://doi.org/10.1371/journal.pone.0179659.

2016

  • Penner, Jack C., Jose A. G. Ferreira, Patrick R. Secor, Johanna M. Sweere, Maria K. Birukova, Lydia-Marie Joubert, Janus A. J. Haagensen, et al. “Pf4 Bacteriophage Produced by Pseudomonas Aeruginosa Inhibits Aspergillus Fumigatus Metabolism via Iron Sequestration.” Microbiology (Reading, England) 162, no. 9 (September 2016): 1583–94. https://doi.org/10.1099/mic.0.000344.

2015

  • Jennings, Laura K., Kelly M. Storek, Hannah E. Ledvina, Charlène Coulon, Lindsey S. Marmont, Irina Sadovskaya, Patrick R. Secor, et al. “Pel Is a Cationic Exopolysaccharide That Cross-Links Extracellular DNA in the Pseudomonas Aeruginosa Biofilm Matrix.” Proceedings of the National Academy of Sciences of the United States of America 112, no. 36 (September 8, 2015): 11353–58. https://doi.org/10.1073/pnas.1503058112.
  • Secor, Patrick R., Laura K. Jennings, Lia A. Michaels, Johanna M. Sweere, Pradeep K. Singh, William C. Parks, and Paul L. Bollyky. “Biofilm Assembly Becomes Crystal Clear – Filamentous Bacteriophage Organize the Pseudomonas Aeruginosa Biofilm Matrix into a Liquid Crystal.” Microbial Cell (Graz, Austria) 3, no. 1 (December 31, 2015): 49–52. https://doi.org/10.15698/mic2016.01.475.
  • Secor, Patrick R., Johanna M. Sweere, Lia A. Michaels, Andrey V. Malkovskiy, Daniel Lazzareschi, Ethan Katznelson, Jayakumar Rajadas, et al. “Filamentous Bacteriophage Promote Biofilm Assembly and Function.” Cell Host & Microbe 18, no. 5 (November 11, 2015): 549–59. https://doi.org/10.1016/j.chom.2015.10.013.

2012

  • Secor, Patrick R., Laura K. Jennings, Garth A. James, Kelly R. Kirker, Elinor Delancey Pulcini, Kate McInnerney, Robin Gerlach, et al. “Phevalin (Aureusimine B) Production by Staphylococcus Aureus Biofilm and Impacts on Human Keratinocyte Gene Expression.” PloS One 7, no. 7 (2012): e40973. https://doi.org/10.1371/journal.pone.0040973.

2011

  • Secor, Patrick R., Garth A. James, Philip Fleckman, John E. Olerud, Kate McInnerney, and Philip S. Stewart. “Staphylococcus Aureus Biofilm and Planktonic Cultures Differentially Impact Gene Expression, Mapk Phosphorylation, and Cytokine Production in Human Keratinocytes.” BMC Microbiology 11 (June 21, 2011): 143. https://doi.org/10.1186/1471-2180-11-143.

2009

  • Kirker, Kelly R., Patrick R. Secor, Garth A. James, Philip Fleckman, John E. Olerud, and Philip S. Stewart. “Loss of Viability and Induction of Apoptosis in Human Keratinocytes Exposed to Staphylococcus Aureus Biofilms in Vitro.” Wound Repair and Regeneration: Official Publication of the Wound Healing Society [and] the European Tissue Repair Society 17, no. 5 (2009): 690–99. https://doi.org/10.1111/j.1524-475X.2009.00523.x.

2008

  • Dowd, Scot E., Yan Sun, Patrick R. Secor, Daniel D. Rhoads, Benjamin M. Wolcott, Garth A. James, and Randall D. Wolcott. “Survey of Bacterial Diversity in Chronic Wounds Using Pyrosequencing, DGGE, and Full Ribosome Shotgun Sequencing.” BMC Microbiology 8 (March 6, 2008): 43. https://doi.org/10.1186/1471-2180-8-43.