DUERKOP LAB

 

IMMUNOLOGY

&

MICROBIOLOGY

@ CU ANSCHUTZ

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The Duerkop Lab would like to thank the following funding sources 

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RESEARCH

The Duerkop lab studies bacterial viruses (bacteriophages or phages) and their interactions with their hosts. The long-term goal of the Duerkop lab is to understand how phages and other forms of mobile DNA contribute to host-microbe interactions in the intestine and their overall impact on human health.

Our lab seeks to: 1) Determine the mechanisms underlying phage interactions with multidrug resistant enterococci and how phages impact enterococcal colonization of the intestine; 2) Understand how native CRISPR-Cas systems function as barriers to nucleic acid acquisition in the intestine and how CRISPR-Cas contributes to the genetic diversity and ecology of the microbiota; 3) Explore the role phage communities play in maintaining a healthy intestinal microbiota and assess whether intestinal phages can shape the composition of the microbiota leading to chronic intestinal inflammation. 

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PROJECTS

PUBLICATIONS

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   

 
 

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 2016. 

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Garima Arya (Postdoctoral Fellow)

garima.arya@cuanschutz.edu

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

joshua.kirsch@cuanschutz.edu

Josh received a BS in Biochemistry from Western Washington University. He joined the Biomedical Sciences Graduate Program in 2019. His projects focus on how phage infection influences mobile elements in the E. faecalis genome and how the lung virome is shaped following stem cell transplantation in humans.     

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Emma Sheriff (PhD Student)

emma.sheriff@cuanschutz.edu

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. Emma's interests fall within the scope of phage-host interactions and their impact on T7SS gene regulation and antagonism.   

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Shelby Andersen (PhD Student)

shelby.andersen@cuanschutz.edu

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 2022. Shelby's research focuses on the identification and characterization of anti-phage systems encoded on mobilizable plasmids.   

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, 2017-2022)

Next position: Postdoc, Jason Rosch's Lab, St. Jude Children's Research Hospital, Memphis, TN

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