Breck Duerkop, PhD

Publications

• Duerkop BA, Huo W, Bhardwaj P, Palmer KL, Hooper LV. Molecular Basis for Lytic Bacteriophage Resistance in Enterococci. MBio. 2016 Aug 30;7(4). PubMed PMID: 27578757
• Hughes ER, Winter MG, Duerkop BA, Spiga L, Furtado de Carvalho T, Zhu W, Gillis CC, Büttner L, Smoot MP, Behrendt CL, Cherry S, Santos RL, Hooper LV, Winter SE. Microbial Respiration and Formate Oxidation as Metabolic Signatures of Inflammation-Associated Dysbiosis. Cell Host Microbe. 2017 Feb 8;21(2):208-219. PubMed PMID: 28182951
• Zhu W, Winter MG, Byndloss MX, Spiga L, Duerkop BA, Hughes ER, Büttner L, de Lima Romão E, Behrendt CL, Lopez CA, Sifuentes-Dominguez L, Huff-Hardy K, Wilson RP, Gillis CC, Tükel Ç, Koh AY, Burstein E, Hooper LV, Bäumler AJ, Winter SE. Precision editing of the gut microbiota ameliorates colitis. Nature. 2018 Jan 11;553(7687):208-211. PubMed PMID: 29323293
• Duerkop BA, Kleiner M, Paez-Espino D, Zhu W4, Bushnell B, Hassell B, Winter SE, Kyrpides NC, Hooper LV. Murine colitis reveals a disease-associated bacteriophage community. Nat Microbiol. 2018 Sep;3(9):1023-1031.
• Zhu W, Winter MG, Byndloss MX, Spiga L, Duerkop BA, Hughes ER, Büttner L, de Lima Romão E, Behrendt CL, Lopez CA, Sifuentes-Dominguez L, Huff-Hardy K, Wilson RP, Gillis CC, Tükel Ç, Koh AY, Burstein E, Hooper LV, Bäumler AJ, Winter SE. Precision editing of the gut microbiota ameliorates colitis. Nature. 2018 Jan 11;553(7687):208-211
• Chatterjee A, Johnson CN, Luong P, Hullahalli K, McBride SW, Schubert AM, Palmer KL, Carlson PE Jr, Duerkop BA. Bacteriophage Resistance Alters Antibiotic-Mediated Intestinal Expansion of Enterococci. Infect Immun. 2019 Jun;87(6). PubMed PMID: 30936157
• 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 Jul 24;4(4). PubMed PMID: 31341074
• Chatterjee A, Duerkop BA. Beyond Bacteria: Bacteriophage-Eukaryotic Host Interactions Reveal Emerging Paradigms of Health and Disease. Front Microbiol. 2018 Jun 27;9:1394.
• Rodrigues M, McBride SW, Hullahalli K, Palmer KL, Duerkop BA. Conjugative Delivery of CRISPR-Cas9 for the Selective Depletion of Antibiotic-Resistant Enterococci. Antimicrob Agents Chemother. 2019 Nov;63(11). PubMed PMID: 31527030
• Duerkop BA. Bacteriophages shift the focus of the mammalian microbiota. PLoS Pathog. 2018 Oct 25;14(10):e1007310.
• Chatterjee A, Duerkop BA. Sugar and Fatty Acids Ack-celerate Prophage Induction. Cell Host Microbe. 2019 Feb 13;25(2):175-176. PubMed PMID: 30763529
• Johnson CN, Duerkop BA. Dyeing to connect. Nat Microbiol. 2019 Dec;4(12):2033-2034. PubMed PMID: 31754272
• Mangalea MR, Duerkop BA. Fitness Trade-Offs Resulting from Bacteriophage Resistance Potentiate Synergistic Antibacterial Strategies. Infect Immun. 2020 Jun 22;88(7). PubMed PMID: 32094257
• Chatterjee A, Willett JLE, Nguyen UT, Monogue B, Palmer KL, Dunny GM, Duerkop BA. Parallel Genomics Uncover Novel Enterococcal-Bacteriophage Interactions. mBio. 2020 Mar 3;11(2). PubMed PMID: 32127456
• Morrisette T, Lev KL, Kebriaei R, Abdul-Mutakabbir JC, 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 Aug 20;64(9). PubMed PMID: 32571816
• Canfield GS, Duerkop BA. Molecular mechanisms of enterococcal-bacteriophage interactions and implications for human health. Curr Opin Microbiol. 2020 Aug;56:38-44. PubMed PMID: 32652484
• 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 Sep 18;88(10). PubMed PMID: 32778611
• Kleiner M, Bushnell B, Sanderson KE, Hooper LV, Duerkop BA. Transductomics: sequencing-based detection and analysis of transduced DNA in pure cultures and microbial communities. Microbiome. 2020 Nov 15;8(1):158. PubMed PMID: 33190645
• 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. In Press
• 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 Jan 14;10(2). PubMed PMID: 33446593
• 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 Jan;17(1):e1009204. PubMed PMID: 33411815
• 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 Mar 1. [Epub ahead of print] PubMed PMID: 33649110
• Morrisette T, 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 Jan 18;66(1):e0162321. PubMed PMID: 34723631
• Lev K, Kunz Coyne AJ, Kebriaei R, Morrisette T, Stamper K, Holger DJ, Canfield GS, Duerkop BA, Arias CA, Rybak MJ. Evaluation of Bacteriophage-Antibiotic Combination Therapy for Biofilm-Embedded MDR Enterococcus faecium . Antibiotics (Basel). 2022 Mar 15;11(3). PubMed PMID: 35326855
• Johnson CN, Palacios Araya D, Schink V, Islam M, Mangalea MR, Decurtis EK, Ngo TC, Palmer KL, Duerkop BA. Genetically distant bacteriophages select for unique genomic changes in Enterococcus faecalis. Microbiologyopen. 2022 Apr;11(2):e1273. PubMed PMID: 35478284
• Mangalea MR, Paez-Espino D, Kieft K, Chatterjee A, Chriswell ME, Seifert JA, Feser ML, Demoruelle MK, 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 May 12;29(5):726-739.e5. PubMed PMID: 33957082
• 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 Aug 30;11(9). PubMed PMID: 36139953
• 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. bioRxiv. 2022. doi: https://doi.org/10.1101/2022.08.24.505136
• Palacios Araya D, Palmer KL, Duerkop BA. CRISPR-based antimicrobials to obstruct antibiotic-resistant and pathogenic bacteria. PLoS Pathog. 2021 Jul;17(7):e1009672. PubMed PMID: 34237097
• 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 Sep 29;8(1):95-113. PubMed PMID: 34255542
• 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 Oct 12;203(21):e0017721. PubMed PMID: 34370561
• Morrisette T, 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. 2021 Nov 1;:AAC0162321. [Epub ahead of print] PubMed PMID: 34723631
• 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 Jun 27;14(3):e0005223. PubMed PMID: 37102874
• 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. PubMed PMID: 37258871
• 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 Jun;19(6):e1011424. PubMed PMID: 37267422
• Kirsch JM, Hryckowian AJ, Duerkop BA. Insertion sequence driven evolution of the microbiota revealed by a novel metagenomics pipeline. bioRxiv. 2023 Nov 10. PubMed PMID: 37873088
• 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. 2023 Dec 2. PubMed PMID: 38014348
• Sheriff EK, Andersen SE, Chatterjee A, Duerkop BA. Complete genome sequence of enterococcal phage G01. Microbiol Resour Announc. 2024 Mar 12;13(3):e0121723. PubMed PMID: 38294211
• 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 Mar 13;15(3):e0339623. PubMed PMID: 38353560
• Kirsch JM, Hryckowian AJ, Duerkop BA. A metagenomics pipeline reveals insertion sequence-driven evolution of the microbiota. Cell Host Microbe. 2024 May 8;32(5):739-754.e4. PubMed PMID: 38565143
• 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 Jun;20(6):e1012301. PubMed PMID: 38913753
• Bullen NP, Johnson CN, Andersen SE, Arya G, Marotta SR, Lee YJ, Weigele PR, Whitney JC, Duerkop BA. An enterococcal phage protein inhibits type IV restriction enzymes involved in antiphage defense. Nat Commun. 2024 Aug 13;15(1):6955. PubMed PMID: 39138193
• Sheriff EK, Salvato F, Andersen SE, Chatterjee A, Kleiner M, Duerkop BA. Enterococcal quorum-controlled protease alters phage infection. FEMS Microbes. 2024;5:xtae022. PubMed PMID: 39156124