The Duerkop Lab would like to thank the following funding sources
RESEARCH
The Duerkop lab studies mobile genetic elements (MGEs) in bacteria. These elements include bacteriophages (phages), plasmids, and insertion sequences. We are interested in questions pertaining to how MGEs influence the behavior of bacteria that interact with humans beneficially and during opportunistic infection. Our work centers on the study of multi-drug resistant enterococci and the microbiota.
Projects in the lab include: 1) The mechanisms underlying phage interactions with multidrug resistant enterococci; 2) Understanding how phage resistance in enterococci leads to antibiotic sensitivity; 3) Assessing mobilizable plasmids for antiphage defenses and deciphering phage-encoded counter-defenses; 4) Exploring phage transduction in the intestine and its impact on bacterial genome evolution and pathogenesis; 5) Studying bacterial insertion sequences and their contribution to bacterial genome diversity, selective evolution, and host adaptation; and 6) How enterococci colonize the intestine and interact with their mammalian hosts
PUBLICATIONS
2025
Zang Z, Duncan OK, Sabonis D, Shi Y, Miraj G, Fedorova I, Le S, Deng J, Zhu Y, Cai Y, Zhang C, Arya G, Duerkop BA, Liang H, Bondy-Denomy J, Ve T, Tamulaitiene G, Gerdt JP. Chemical inhibition of a bacterial immune system. bioRxiv. 2025. doi: https://doi.org/10.1101/2025.02.20.638879
2024
Bullen NP, Johnson CJ, Andersen SE, Arya G, Marotta SR, Lee Y-J, Weigele PR, Whitney JC, Duerkop BA. An enterococcal phage protein inhibits type IV restriction enzymes involved in antiphage defense. Nat Commun. 2024; 15(1):6955. doi: 10.1038/s41467-024-51346-1 View in PubMed
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Sheriff EK, Salvato F, Andersen SE, Chatterjee A, Kleiner M, Duerkop BA. Enterococcal quorum-controlled protease alters phage infection. FEMS Microbes. 2024; 5:xtae022. doi: 10.1093/femsmc/xtae022 View in PubMed
Maier JL, Gin C, Callahan B, Sheriff EK, Duerkop BA, Kleiner M. Pseudo-pac site sequences used by phage P22 in generalized transduction of Salmonella. PLoS Pathog. 2024; 20(6):e1012301. doi: 10.1371/journal.ppat.1012301. PMID: 38913753 View in PubMed
Kirsch JM, Hryckowian AJ, Duerkop BA. A metagenomics pipeline reveals insertion sequence-driven evolution of the microbiota. Cell Host Microbe. 2024; 32(5):739-754.e4. doi: 10.1016/j.chom.2024.03.005. PMID: 38565143 View in PubMed
Stellfox ME, Fernandes C, Shields RK, Haidar G, Hughes Kramer K, Dembinski E, Mangalea MR, Arya G, Canfield GS, Duerkop BA, Van Tyne D. Bacteriophage and antibiotic combination therapy for recurrent Enterococcus faecium bacteremia. mBio. 2024; e0339623. doi: 10.1128/mbio.03396-23. PMID: 38353560 View in PubMed
Sheriff EK, Andersen SE, Chatterjee A, Duerkop BA. Complete genome sequence of enterococcal phage G01. Microbial Resour Announc. 2024; e0121723. doi: 10.1128/mra.01217-23. PMID 38294211 View in PubMed
2023
​Kirsch JM, Ely S, Stellfox ME, Hullahalli K, Luong P, Palmer KL, Van Tyne D, Duerkop BA. Targeted IS-element sequencing uncovers transposition dynamics during selective pressure in enterococci. PLoS Pathog. 2023;19(6):e1011424. doi: 10.1371/journal.ppat.1011424. PMID: 37267422 View in PubMed
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Mangalea MR, Keift K, Duerkop BA, Anantharaman K. Assembly and annotation of viral metagenomes from short-read sequencing data. Methods Mol Biol. 2023;2649:317-337. doi: 10.1007/978-1-0716-3072-3_17 PMID: 37258871 View in PubMed
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Colbert JF, Kirsch JM, Erzen CL, Langouët-Astrié CJ, Thompson GE, McMurtry SA, Kofonow JM, Robertson CE, Kovacs EJ, Sullivan RC, Hippensteel JA, Sawant NV, De Nisco NJ, McCollister BD, Schwartz RS, Horswill AR, Frank DN, Duerkop BA, Schmidt EP. Aging-associated augmentation of gut microbiome virulence capability drives sepsis severity. mBio. 2023; e0005223. doi: 10.1128/mbio.00052-23 PMID: 37102874 View in PubMed
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2022
Kunz Coyne AJ, Stamper K, Kebriaei R, Holger DJ, El Ghali A, Morrisette T, Biswas B, Wilson M, Deschenes MV, Canfield GS Duerkop BA, Arias CA, Rybak MJ. Phage cocktails with daptomycin and ampicillin eradicates biofilm-embedded multidrug-resistant Enterococcus faecium with preserved phage susceptibility. Antibiotics (Basel). 2022; 11(9):1175. doi: 10.3390/antibiotics11091175 View in PubMed
Johnson CN, Palacios Araya D, Schink V, Islam M, Mangalea MR, Decurtis EK, Ngo TV, Palmer KL, Duerkop BA. Genetically distant bacteriophages select for unique genomic changes in Enterococcus faecalis. Microbiologyopen. 2022; 11(2):e1273. ​
doi: 10.1002/mbo3.1273 PMID: 35478284 View in PubMed
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Lev K, Coyne AJK, Kebriaei R, Morrisette T, Stamper K, Holger DJ, Canfield GS, Duerkop BA, Arias CA, Rybak. Evaluation of bacteriophage-antibiotic combination therapy for biofilm-embedded MDR Enterococcus faecium. Antibiotics (Basel). 2022; 11(3):392. doi: 10.3390/antibiotics11030392 PMID: 35326855 View in PubMed
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Morrisette TM, Lev KL, Canfield GS, Duerkop BA, Kebriaei R, Stamper KC, Holger D, Lehman SM, Willcox S, Arias CA, Rybak MJ. Evaluation of bacteriophage cocktails alone and in combination with daptomycin against daptomycin-nonsusceptible Enterococcus faecium. Antimicrob Agents Chemother. 2022; 66(1):e0162321. doi: 10.1128/AAC.01623-21 PMID: 34723631 View in PubMed
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2021
Johnson CN, Sheriff EK, Duerkop BA, Chatterjee A. Let me upgrade you: Impact of mobile genetic elements on enterococcal adaptation and evolution. J Bacteriol. 2021; 203(21):e0017721. doi: 10.1128/JB.00177-21 PMID: 34370561 View in PubMed
Kirsch JM, Brzozowski RS, Faith D, Round JL, Secor PR, Duerkop BA. Bacteriophage-bacteria interactions in the gut - from invertebrates to mammals. Annu Rev Virol. 2021;8(1):95-113. doi: 10.1146/annurev-virology-091919-101238 PMID: 34255542 View in PubMed
Palacios Araya D, Palmer KL, Duerkop BA. 2021. CRISPR-based antimicrobials to obstruct antibiotic-resistant and pathogenic bacteria. PLoS Pathog. 2021;17(7):e1009672. doi: 10.1371/journal.ppat.1009672. PMID: 34237097 View in PubMed
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Mangalea MR, Paez-Espino D, Kieft KA, Chatterjee A, Seifert JA, Feser ML, Demoruelle MK, Chriswell ME, Sakatos A, Anantharaman K, Deane KD, Kuhn KA, Holers VM, Duerkop BA. Individuals at risk for rheumatoid arthritis harbor differential intestinal bacteriophage communities with distinct metabolic potential. Cell Host Microbe. 2021;29(5):726-739.e5 doi: 10.1016/j.chom.2021.03.020. PMID: 33957082 View in PubMed
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Canfield GS, Chatterjee A, Espinosa J, Mangalea MR, Sheriff EK, Keidan M, McBride SW, McCollister BD, Hang HC, Duerkop BA. Lytic bacteriophages facilitate antibiotic sensitization of Enterococcus faecium. Antimicrob Agents Chemother. 2021;65:e00143-21. doi: 10.1128/AAC.00143-21. PMID: 33649110 View in PubMed
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Chatterjee A, Willett JLE, Dunny GM, Duerkop BA. Phage infection and sub-lethal antibiotic exposure mediate Enterococcus faecalis type VII secretion system dependent inhibition of bystander bacteria. PLoS Genet. 2021;17(1):e1009204.
doi: 10.1371/journal.pgen.1009204. PMID: 33411815 View in PubMed
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Spencer BL, Chatterjee A, Duerkop BA, Baker CJ, Doran KS. Complete genome sequence of neonatal clinical group B streptococcal isolate CJB111. Microbiol Resour Announc. 2021;10(2):e01268-20. doi: 10.1128/MRA.01268-20. PMID:
33446593 View in PubMed
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2020
Kleiner M, Bushnell B, Sanderson KE, Hooper LV and Duerkop BA. Transductomics: sequencing based detection and analysis of transduced DNA in pure cultures and microbial communities. Microbiome. 2020;8(1):158.
doi: 10.1186/s40168-020-00935-5. PMID: 33190645 View in PubMed
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Alhajjar N, Chatterjee A, Spencer BL, Burcham LR, Willett JLE, Dunny GM, Duerkop BA, Doran KS. Genome-wide mutagenesis identifies factors involved in Enterococcus faecalis vaginal adherence and persistence. Infect Immun. 2020;88(10):e00270-20. doi: 10.1128/IAI.00270-20. PMID: 32778611 View in PubMed
Canfield GS and Duerkop BA. Molecular mechanisms of enterococcal-bacteriophage interactions and implications for human health. Curr Opin Microbiol. 2020;56:38-44. doi: 10.1016/j.mib.2020.06.003. PMID: 32652484 View in PubMed​
Morrisette T, Lev KL, Kebriaei R, Abdul-Mutakabbir J, Stamper KC, Morales S, Lehman SM, Canfield GS, Duerkop BA, Arias CA, Rybak MJ. Bacteriophage-antibiotic combinations for Enterococcus faecium with varying bacteriophage and daptomycin susceptibilities. Antimicrob Agents Chemother. 2020;64(9):e00993-20. doi: 10.1128/AAC.00993-20 PMID: 32571816 View in PubMed
Chatterjee A, Willett JLE, Nguyen UT, Monogue B, Palmer KL, Dunny GM, Duerkop BA. Parallel genomics uncover novel enterococcal-bacteriophage interactions. mBio. 2020;11:e03120-19. doi: 10.1128/mBio.03120-19. PMID: 32127456
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Mangalea MR and Duerkop BA. Fitness trade-offs resulting from bacteriophage resistance potentiate synergistic antibacterial strategies. Infect Immun. 2020;88(7). doi: 10.1128/IAI.00926-19. PMID: 32094257 View in PubMed
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2019
Johnson CN and Duerkop BA. Dyeing to connect. Nat Microbiol. 2019;4(12):2033-2034. doi: 10.1038/s41564-019-0616-1. PMID: 31754272. View in PubMed
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Rodrigues M, McBride SW, Hullahalli K, Palmer KL and Duerkop BA. Conjugative delivery of CRISPR-Cas9 for the selective depletion of antibiotic-resistant enterococci. Antimicrob Agents Chemother. 2019;63(11). doi: 10.1128/AAC.01454-19. PMID: 31527030. View in PubMed
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Price VJ, McBride SW, Hullahalli K, Chatterjee A, Duerkop BA, Palmer KL. Enterococcus faecalis CRISPR-Cas is a robust barrier to conjugative antibiotic resistance dissemination in the murine intestine. mSphere. 2019;4(4). doi: 10.1128/mSphere.00464-19. PMID: 31341074. View in PubMed
Chatterjee A, Johnson CN, Luong P, Hullahalli K, McBride SW, Schubert AM, Palmer KL, Carlson PE Jr and Duerkop BA. Bacteriophage resistance alters antibiotic-mediated intestinal expansion of enterococci. Infect Immun. 2019;87(6). doi: 10.1128/IAI.00085-19. PMID: 30936157. View in PubMed
Chatterjee A and Duerkop BA. Sugar and fatty acids Ack-celerate prophage induction. Cell Host Microbe. 2019;25(2):175-176. doi: 10.1016/j.chom.2019.01.012. PMID: 30763529. View in PubMed
2018
Duerkop BA. Bacteriophages shift the focus of the mammalian microbiota. PLoS Pathog. 2018;14(10):e1007310. doi: 10.1371/journal.ppat.1007310. PMID: 30359456. View in PubMed
Duerkop BA, Kleiner M, Paez-Espino D, Zhu W, Bushnell B, Hassell B, Winter SE, Kyrpides NC and Hooper LV. Murine colitis reveals a disease-associated bacteriophage community. Nat Microbiol. 2018;3(9):1023-1031. doi: 10.1038/s41564-018-0210-y. PMID: 30038310. View in PubMed
Chatterjee A and Duerkop BA. Beyond Bacteria: Bacteriophage-eukaryotic host interactions reveal emerging paradigms of health and disease. Front Microbiol. 2018;9:1394. doi: 10.3389/fmicb.2018.01394. PMID: 29997604. View in PubMed
PEOPLE
Breck Duerkop (Associate Professor, Director - CU Anschutz Microbiology Graduate Program)
Breck received his BS in Biology from the University of Wisconsin-Milwaukee and a PhD in Microbiology from the University of Washington. He completed postdoctoral training at the University of Texas Southwestern Medical Center. Breck joined the faculty in the Department of Immunology and Microbiology at the University of Colorado School of Medicine in 2017.
Garima Arya (American Heart Association Postdoctoral Fellow)
Garima earned her BS from Mody Institute of Technology and Science, Lakshmangarh, Rajasthan, India, followed by a MS in Biotechnology from the Agricultural University, Hisar, Haryana, India. She obtained a PhD from the Indian Institute of Science Education and Research, Mohali, India. Garima's research focuses on E. faecium phage interactions and phage- antibiotic synergy.
Susanne Meile (EMBO Postdoctoral Fellow)
Susanne holds a BS degree in Biology, as well as a MS degree in Microbiology and Immunology, both earned at the Federal Institute of Technology Zurich (ETH Zurich), Switzerland. She obtained a PhD in Molecular- and Microbiology, followed by postdoctoral training at ETH Zurich. Her research topics center around the genetic engineering of bacteriophages and currently she explores how phages can shape microbial evolution within the gastrointestinal environment.
Shiomi Junker (Postdoctoral Fellow)
Shiomi graduated with a BS in Biotechnology from the State University of New York College of Environmental Science and Forestry. She then earned a PhD in Molecular Biology, Microbiology, and Biochemistry from Southern Illinois University. Her research focuses on the colonization of E. faecalis in the intestine, with a particular interest in how E. faecalis adapts spatially to the intestinal lumen and mucosal environments.
Shelby Andersen (PhD Student, NSF GRFP Recipient)
Shelby attended the University of Iowa where she earned her BS in Microbiology and certificate in Global Health Studies. She joined the Microbiology Graduate Program at the University of Colorado School of Medicine in 2021. Shelby's research focuses on the identification and characterization of anti-phage systems encoded on mobilizable plasmids.
Joanna Chau (PhD Student)
Joanna obtained her BS in Microbial Biology from the University of California - Berkeley. She joined the Microbiology Graduate Program at the University of Colorado School of Medicine in 2022, after completing postbac training at the NIH in Bethesda, MD. Joanna's research aims to understand the mechanisms that support enterococcal colonization of the intestine.
Nicole Messner (PhD Student)
Nicole did her undergraduate studies at Virginia Tech where she earned a BS in Microbiology. She obtained her MS in Microbiology through the BSBT Master's Program at the University of Colorado School of Medicine in 2024. She joined the Microbiology Graduate Program at the University of Colorado School of Medicine in 2024. Nicole's research focuses on the genomic analysis of enterococcal phages and how phage-antibiotic combination therapy works against clinical isolates of MDR E. faecium.
Erika Desonie (MS Student)
Erika completed her undergraduate studies at University of South Florida - St. Petersburg campus where she earned a BS in Biology with a concentration in Biomedical Sciences. She joined the BSBT Master's Program at the University of Colorado School of Medicine in 2023. Erika's research focuses on the mechanism by which a natural product derivative increases phage infectivity.
Skye Patterson (Postbac, PIKE-PREP Research Scholar )
Skye did her undergraduate at the University of Texas at San Antonio, receiving a BA in Medical Humanities with a minor in Biology. She joined the Preparation in Interdisciplinary Knowledge to Excel - Postbaccalaureate Research Education Program (PIKE-PREP) at the University of Colorado School of Medicine in 2024. Skye's research focuses on phage DNA transduction of multidrug resistant bacteria and the microbiota. She is currently studying transduction within ESBL-producing Enterobacteriaceae.
Navtej Singh (Undergraduate Researcher)
Navtej is an undergraduate student at the University of Colorado Denver, where he is pursuing a BS in Biology. He joined the Duerkop Lab in 2024. Navtej works closely with Shelby Andersen on research focused on identifying and characterizing anti-phage defense systems.
Lab Alumni
Jason Hickman (Visiting Scientist, 2017)
Next position: Director of Animal Nutrition Research, Archer Daniels Midland (AMD), Decatur, IL
Phat Luong (MS Student, 2017-2018)
Next position: Medical School, Ross University, Barbados
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Sara McBride (Lab Manager, 2017-2019)
Next position: Staff, Forest Rohwer and Anca Segall Labs, San Diego State University, San Diego, CA
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Viviane Schink (Visiting MS Student, 2019)
Next position: Process Engineer at Elanco, Cuxhaven, Germany
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Micah Keidan (Lab Manager, 2019-2020)
Next position: Staff, Vincent Young's Lab, University of Michigan, Ann Arbor, MI
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Greg Canfield (Infectious Diseases Fellow, 2019-2021)
Next position: Infectious Diseases Fellow, Stanford University, Stanford, CA
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Anushila Chatterjee (Postdoctoral Fellow, 2017-2021)
Next position: STEM Research Project Developer, Vigyanshaala International, Delhi, India
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Mihnea "Mike" Mangalea (Postdoctoral Fellow, 2019-2021)
Next position: Bioinformatician, Centers for Disease Control, Atlanta, GA
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Shannon Ely (MS Student, 2021-2022)
Next position: Scientific Consultant, Boulder iQ, Boulder, CO
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Cydney Johnson (PhD Student, Ruth L. Kirschstein NRSA Fellow - NIH, 2017-2022)
Next position: Postdoc, Jason Rosch's Lab, St. Jude Children's Research Hospital, Memphis, TN
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Jordan Lemus-Reyes (MS Student, 2023-2024)
Next position: Master's Internship, Jenna Guthmiller's lab, University of Colorado - Anschutz Medical Campus, Aurora, CO
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Emma Sheriff (PhD Student, 2019-2024)
Next position: Postdoc, Ville Friman's Lab, University of Helsinki, Helsinki, Finland
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Joshua Kirsch (PhD Student, 2019-2024 - Postdoctoral Fellow, 2024-2025)
Next position: Fellow, Clinical Microbiology Fellowship Program, University of Washington, Seattle, WA
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CONTACT
The Duerkop Lab is located at the University of Colorado School of Medicine's Anschutz Medical Campus in Aurora, Colorado, 8 miles from downtown Denver and 20 miles from the foothills of the Rocky Mountains
12800 E. 19th Ave.
Research Complex I
P18-9402D
Aurora, CO, 80045
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Tel: 303-724-0940
Fax: 303-724-4226