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The Duerkop Lab would like to thank the following funding sources 

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RESEARCH

The Duerkop lab studies mobile elements in bacteria including bacteriophages (phages), plasmids, and insertion sequences. We are interested in questions pertaining to how mobile elements interact with their bacterial hosts and how these interactions impact human health.

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 how phage transduction in the intestine promotes bacterial genome evolution and pathogenesis; and 5) Studying  bacterial insertion sequence elements and their contribution to strain level diversity, genome evolution, and host adaptation. 
 

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RESEARCH

PUBLICATIONS

2024

Sheriff EK, Salvato F, Andersen SE, Chatterjee A, Kleiner M, Duerkop BA. Enterococcal quorum-controlled protease alters phage infection. bioRxiv. 2024. doi: https://doi.org/10.1101/2024.05.10.593607 

 

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. bioRxiv. 2024. doi: https://doi.org/10.1101/2024.03.25.586692

 

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

Johnson CN, Bullen NP, Andersen SE, Arya G, Marotta SR, Whitney JC, Duerkop BA. Evolution of a small phage protein overcomes antiphage defense in Enterococcus faecalis. bioRxiv. doi: https://doi.org/10.1101/2023.11.16.567456

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

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

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 

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 faecalisMicrobiologyopen. 2022; 11(2):e1273. 

doi: 10.1002/mbo3.1273 PMID: 35478284 View in PubMed 

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

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

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

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

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

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

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

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

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 

View in PubMed

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

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  

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

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   

PUBLICATIONS
PEOPLE

PEOPLE

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Breck Duerkop (Associate Professor, Director - CU Anschutz Microbiology Graduate Program)

breck.duerkop@cuanschutz.edu

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. 

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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.   

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Susanne Meile (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.

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Josh Kirsch (PhD Student, Ruth L. Kirschstein NRSA Fellow - NIH)

Josh received a BS in Biochemistry from Western Washington University. Prior to starting graduate school he completed postbac training at the NIH - Rocky Mountain National Laboratories in Hamilton, MT. He joined the Biomedical Sciences Graduate Program in 2019. His projects focus on how mobile insertion sequence elements in E. faecalis and the microbiota contribute to genome evolution.    

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Emma Sheriff (PhD Student)

Emma attended the University of Alabama where she earned a BS in Biology with a minor in the Randall Research Scholars Program. She joined the Graduate Program in Microbiology at the University of Colorado School of Medicine in 2019. Using proteomic and genetic techniques, Emma's research explores how E. faecalis adapts to phage infection. 

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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.   

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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 2023, 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.   

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Nicole Messner (MS Student)

Nicole did her undergraduate studies at Virginia Tech where she earned a BS in Microbiology. She joined the BSBT Master's Program at the University of Colorado School of Medicine in 2022. 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.  

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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. 

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

Sara McBride (Lab Manager, 2017-2019)

Next position: Staff, Forest Rohwer and Anca Segall Labs, San Diego State University, San Diego, CA

Viviane Schink (Visiting MS Student, 2019)

Next position: Process Engineer at Elanco, Cuxhaven, Germany

Micah Keidan (Lab Manager, 2019-2020)

Next position: Staff, Vincent Young's Lab, University of Michigan, Ann Arbor, MI

Greg Canfield (Infectious Diseases Fellow, 2019-2021)

Next position: Infectious Diseases Fellow, Stanford University, Stanford, CA 

Anushila Chatterjee (Postdoctoral Fellow, 2017-2021)

Next position: STEM Research Project Developer, Vigyanshaala International, Delhi, India   

Mihnea "Mike" Mangalea (Postdoctoral Fellow, 2019-2021)

Next position: Bioinformatician, Centers for Disease Control, Atlanta, GA

Shannon Ely (MS Student, 2021-2022)

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

Jordan Lemus-Reyes (MS Student, 2023-2024)

Next position: Master's Internship, Jenna Guthmiller's lab, University of Colorado - Anschutz Medical Campus, Aurora, CO

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

Tel: 303-724-0940

Fax: 303-724-4226

breck.duerkop@cuanschutz.edu

CONTACT
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