Derrick E. Fouts, PhD

Professor

Derrick Fouts is a Professor at the Rockville Campus. Dr. Fouts has extensive experience in viral and bacteriophage genomics, bacterial genomics, comparative genomics, and metagenomics of bacterial and viral communities.

Since joining Dr. Karen Nelson's group at TIGR/JCVI in 2001, Dr. Fouts has led several microbial sequencing projects, including animal, plant and human pathogens. Many of these projects were among the first to compare multiple strains. In addition to leading projects, Dr. Fouts has developed various software tools, including applications to perform multi-genome comparisons and heuristic software (Phage Finder) to identify prophage regions in bacterial genomes. He is currently leading the effort to sequence the human virome and reference viral and bacteriophage genomes as part of the NIH sponsored, Human Microbiome Project.

Dr. Fouts received his B.S. degree (1992) in Biology with honors from Indiana University, Bloomington, and his M.S. (1994) and PhD (1997) degrees in Microbiology from the University of Illinois Urbana/Champaign Department of Microbiology. In 1997, he began postdoctoral work in Dr. Alan Collmer's lab at Cornell University.

Publications

BMC infectious diseases. 2023-08-28; 23.1: 556.

Characteristics and genomic epidemiology of colistin-resistant Enterobacterales from farmers, swine, and hospitalized patients in Thailand, 2014-2017

Boonyasiri A, Brinkac LM, Jauneikaite E, White RC, Greco C, Seenama C, Tangkoskul T, Nguyen K, Fouts DE, Thamlikitkul V

PMID: 37641085

Journal of clinical microbiology. 2023-07-20; 61.7: e0019923.

Escherichia coli ST131 Associated with Increased Mortality in Bloodstream Infections from Urinary Tract Source

Brumwell A, Sutton G, Lantos PM, Hoffman K, Ruffin F, Brinkac L, Clarke TH, Adams MD, Fowler VG, Fouts DE, Thaden JT

PMID: 37338371

Hepatology (Baltimore, Md.). 2023-06-01; 77.6: 2073-2083.

Any alcohol use in NAFLD patients is associated with significant changes to the intestinal virome

Hsu CL, Lang S, Demir M, Fouts DE, Stärkel P, Schnabl B

PMID: 36631002

Hepatology communications. 2023-02-01; 7.2: e0029.

Malassezia restricta promotes alcohol-induced liver injury

Zeng S, Hartmann P, Park M, Duan Y, Lang S, Llorente C, Wang Y, Cabré N, Fouts DE, Bacher P, Jung WH, Stärkel P, Schnabl B

PMID: 36706195

Antibiotics (Basel, Switzerland). 2022-11-19; 11.11:

Design of a Bacteriophage Cocktail Active against Shigella Species and Testing of Its Therapeutic Potential in Galleria mellonella

Filippov AA, Su W, Sergueev KV, Kevorkian RT, Snesrud EC, Srijan A, He Y, Fouts DE, Lurchachaiwong W, McGann PT, Ellison DW, Swierczewski BE, Nikolich MP

PMID: 36421303

Hepatology communications. 2022-08-01; 6.8: 2058-2069.

Intestinal virome in patients with alcohol use disorder and after abstinence

Hsu CL, Zhang X, Jiang L, Lang S, Hartmann P, Pride D, Fouts DE, Stärkel P, Schnabl B

PMID: 35368152

JAC-antimicrobial resistance. 2022-06-01; 4.3: dlac040.

Clinical challenges treating Stenotrophomonas maltophilia infections: an update

Mojica MF, Humphries R, LiPuma JJ, Mathers AJ, Rao GG, Shelburne SA, Fouts DE, van Duin D, Bonomo RA

PMID: 35529051

Antimicrobial agents and chemotherapy. 2022-05-17; 66.5: e0179021.

Imipenem/Relebactam Resistance in Clinical Isolates of Extensively Drug Resistant Pseudomonas aeruginosa: Inhibitor-Resistant β-Lactamases and Their Increasing Importance

Hujer AM, Bethel CR, Taracila MA, Marshall SH, Rojas LJ, Winkler ML, Painter RE, Domitrovic TN, Watkins RR, Abdelhamed AM, D'Souza R, Mack AR, White RC, Clarke T, Fouts DE, Jacobs MR, Young K, Bonomo RA

PMID: 35435707

Journal of hepatology. 2022-04-01; 76.4: 788-799.

The fecal mycobiome in non-alcoholic fatty liver disease

Demir M, Lang S, Hartmann P, Duan Y, Martin A, Miyamoto Y, Bondareva M, Zhang X, Wang Y, Kasper P, Bang C, Roderburg C, Tacke F, Steffen HM, Goeser T, Kruglov A, Eckmann L, Stärkel P, Fouts DE, Schnabl B

PMID: 34896404

Viruses. 2022-03-29; 14.4:

Identification and Characterization of vB_PreP_EPr2, a Lytic Bacteriophage of Pan-Drug Resistant Providencia rettgeri

Mencke JL, He Y, Filippov AA, Nikolich MP, Belew AT, Fouts DE, McGann PT, Swierczewski BE, Getnet D, Ellison DW, Margulieux KR

PMID: 35458437

Applied and environmental microbiology. 2022-02-08; 88.3: e0148621.

Cross-Genus "Boot-Up" of Synthetic Bacteriophage in Staphylococcus aureus by Using a New and Efficient DNA Transformation Method

Assad-Garcia N, D'Souza R, Buzzeo R, Tripathi A, Oldfield LM, Vashee S, Fouts DE

PMID: 34818102

Metabolites. 2022-01-05; 12.1:

Machine Learning Applied to Omics Datasets Predicts Mortality in Patients with Alcoholic Hepatitis

Gao B, Wu TC, Lang S, Jiang L, Duan Y, Fouts DE, Zhang X, Tu XM, Schnabl B

PMID: 35050163

Journal of hepatology. 2021-12-01; 75.6: 1465-1475.

Intestinal virome and therapeutic potential of bacteriophages in liver disease

Hsu C, Hsu CL, Duan Y, Fouts DE, Schnabl B

PMID: 34437908

Frontiers in physiology. 2021-07-19; 12.699253.

Dynamic Changes of the Fungal Microbiome in Alcohol Use Disorder

Hartmann P, Lang S, Zeng S, Duan Y, Zhang X, Wang Y, Bondareva M, Kruglov A, Fouts DE, Stärkel P, Schnabl B

PMID: 34349667

The Journal of antimicrobial chemotherapy. 2021-07-15; 76.8: 2017-2023.

Apramycin resistance in epidemic carbapenem-resistant Klebsiella pneumoniae ST258 strains

Hao M, Schuyler J, Zhang H, Shashkina E, Du H, Fouts DE, Satlin M, Kreiswirth BN, Chen L

PMID: 33942093

Cellular and molecular gastroenterology and hepatology. 2021-02-22; 12.1: 293-320.

Intestinal α1-2-Fucosylation Contributes to Obesity and Steatohepatitis in Mice

Zhou R, Llorente C, Cao J, Zaramela LS, Zeng S, Gao B, Li SZ, Welch RD, Huang FQ, Qi LW, Pan C, Huang Y, Zhou P, Beussen I, Zhang Y, Bryam G, Fiehn O, Wang L, Liu EH, Yu RT, Downes M, Evans RM, Goglin K, Fouts DE, Brenner DA, Bode L, Fan X, Zengler K, Schnabl B

PMID: 33631374

BMC infectious diseases. 2021-02-04; 21.1: 142.

Genomic and clinical characterisation of multidrug-resistant carbapenemase-producing ST231 and ST16 Klebsiella pneumoniae isolates colonising patients at Siriraj hospital, Bangkok, Thailand from 2015 to 2017

Boonyasiri A, Jauneikaite E, Brinkac LM, Greco C, Lerdlamyong K, Tangkoskul T, Nguyen K, Thamlikitkul V, Fouts DE

PMID: 33541274

Diagnostic microbiology and infectious disease. 2021-02-01; 99.2: 115242.

A comprehensive and contemporary "snapshot" of β-lactamases in carbapenem resistant Acinetobacter baumannii

Hujer AM, Hujer KM, Leonard DA, Powers RA, Wallar BJ, Mack AR, Taracila MA, Rather PN, Higgins PG, Prati F, Caselli E, Marshall SH, Clarke T, Greco C, Venepally P, Brinkac L, Kreiswirth BN, Fouts DE, Bonomo RA, Antibacterial Resistance Leadership Group (ARLG)

PMID: 33248392

Hepatology (Baltimore, Md.). 2020-12-01; 72.6: 2182-2196.

Intestinal Virome in Patients With Alcoholic Hepatitis

Jiang L, Lang S, Duan Y, Zhang X, Gao B, Chopyk J, Schwanemann LK, Ventura-Cots M, Bataller R, Bosques-Padilla F, Verna EC, Abraldes JG, Brown RS, Vargas V, Altamirano J, Caballería J, Shawcross DL, Ho SB, Louvet A, Lucey MR, Mathurin P, Garcia-Tsao G, Kisseleva T, Brenner DA, Tu XM, Stärkel P, Pride D, Fouts DE, Schnabl B

PMID: 32654263

Gut microbes. 2020-11-09; 12.1: 1785251.

Changes in the fecal bacterial microbiota associated with disease severity in alcoholic hepatitis patients

Lang S, Fairfied B, Gao B, Duan Y, Zhang X, Fouts DE, Schnabl B

PMID: 32684075

Gut microbes. 2020-11-09; 12.1: 1782157.

Intestinal permeability, microbial translocation, changes in duodenal and fecal microbiota, and their associations with alcoholic liver disease progression in humans

Maccioni L, Gao B, Leclercq S, Pirlot B, Horsmans Y, De Timary P, Leclercq I, Fouts D, Schnabl B, Stärkel P

PMID: 32588725

Gastroenterology. 2020-11-01; 159.5: 1839-1852.

Intestinal Virome Signature Associated With Severity of Nonalcoholic Fatty Liver Disease

Lang S, Demir M, Martin A, Jiang L, Zhang X, Duan Y, Gao B, Wisplinghoff H, Kasper P, Roderburg C, Tacke F, Steffen HM, Goeser T, Abraldes JG, Tu XM, Loomba R, Stärkel P, Pride D, Fouts DE, Schnabl B

PMID: 32652145

The Journal of antimicrobial chemotherapy. 2020-10-01; 75.10: 2760-2768.

AbGRI4, a novel antibiotic resistance island in multiply antibiotic-resistant Acinetobacter baumannii clinical isolates

Chan AP, Choi Y, Clarke TH, Brinkac LM, White RC, Jacobs MR, Bonomo RA, Adams MD, Fouts DE

PMID: 32681170

Journal of clinical microbiology. 2020-08-24; 58.9:

Newly Named Klebsiella aerogenes (formerly Enterobacter aerogenes) Is Associated with Poor Clinical Outcomes Relative to Other Enterobacter Species in Patients with Bloodstream Infection

Wesevich A, Sutton G, Ruffin F, Park LP, Fouts D, Fouts DE, Fowler VG, Thaden JT

PMID: 32493786

Clinical infectious diseases : an official publication of the Infectious Diseases Society of America. 2020-08-14; 71.4: 1095-1098.

Monitoring Ceftazidime-Avibactam and Aztreonam Concentrations in the Treatment of a Bloodstream Infection Caused by a Multidrug-Resistant Enterobacter sp. Carrying Both Klebsiella pneumoniae Carbapenemase-4 and New Delhi Metallo-β-Lactamase-1

Yasmin M, Fouts DE, Jacobs MR, Haydar H, Marshall SH, White R, D'Souza R, Lodise TP, Rhoads DD, Hujer AM, Rojas LJ, Hoyen C, Perez F, Edwards A, Bonomo RA

PMID: 31802119

Gut microbes. 2020-05-03; 11.3: 265-275.

Intestinal and hepatic microbiota changes associated with chronic ethanol administration in mice

Bluemel S, Wang L, Kuelbs C, Moncera K, Torralba M, Singh H, Fouts DE, Schnabl B

PMID: 30982395

Antimicrobial agents and chemotherapy. 2020-04-21; 64.5:

ARGONAUT II Study of the In Vitro Activity of Plazomicin against Carbapenemase-Producing Klebsiella pneumoniae

Jacobs MR, Good CE, Hujer AM, Abdelhamed AM, Rhoads DD, Hujer KM, Rudin SD, Domitrovic TN, Connolly LE, Krause KM, Patel R, Arias CA, Kreiswirth BN, Rojas LJ, D'Souza R, White RC, Brinkac LM, Nguyen K, Singh I, Fouts DE, van Duin D, Bonomo RA, Antibacterial Resistance Leadership Group

PMID: 32152078

Hepatology (Baltimore, Md.). 2020-02-01; 71.2: 522-538.

Intestinal Fungal Dysbiosis and Systemic Immune Response to Fungi in Patients With Alcoholic Hepatitis

Lang S, Duan Y, Liu J, Torralba MG, Kuelbs C, Ventura-Cots M, Abraldes JG, Bosques-Padilla F, Verna EC, Brown RS, Vargas V, Altamirano J, Caballería J, Shawcross D, Lucey MR, Louvet A, Mathurin P, Garcia-Tsao G, Ho SB, Tu XM, Bataller R, Stärkel P, Fouts DE, Schnabl B

PMID: 31228214

Alcoholism, clinical and experimental research. 2020-01-01; 44.1: 87-101.

A Novel Mouse Model of Acute-on-Chronic Cholestatic Alcoholic Liver Disease: A Systems Biology Comparison With Human Alcoholic Hepatitis

Furuya S, Argemi J, Uehara T, Katou Y, Fouts DE, Schnabl B, Dubuquoy L, Belorkar A, Vadigepalli R, Kono H, Bataller R, Rusyn I

PMID: 31710124

Nature. 2019-11-13; 575.7783: 505-511.

Bacteriophage targeting of gut bacterium attenuates alcoholic liver disease

Duan Y, Llorente C, Lang S, Brandl K, Chu H, Jiang L, White RC, Clarke TH, Nguyen K, Torralba M, Shao Y, Liu J, Hernandez-Morales A, Lessor L, Rahman IR, Miyamoto Y, Ly M, Gao B, Sun W, Kiesel R, Hutmacher F, Lee S, Ventura-Cots M, Bosques-Padilla F, Verna EC, Abraldes JG, Brown RS, Vargas V, Altamirano J, Caballería J, Shawcross DL, Ho SB, Louvet A, Lucey MR, Mathurin P, Garcia-Tsao G, Bataller R, Tu XM, Eckmann L, van der Donk WA, Young R, Lawley TD, Stärkel P, Pride D, Fouts DE, Schnabl B

PMID: 31723265

The Journal of infectious diseases. 2019-07-19; 220.4: 666-676.

Ceftazidime-Avibactam in Combination With Fosfomycin: A Novel Therapeutic Strategy Against Multidrug-Resistant Pseudomonas aeruginosa

Papp-Wallace KM, Zeiser ET, Becka SA, Park S, Wilson BM, Winkler ML, D'Souza R, Singh I, Sutton G, Fouts DE, Chen L, Kreiswirth BN, Ellis-Grosse EJ, Drusano GL, Perlin DS, Bonomo RA

PMID: 31099835

mBio. 2019-07-02; 10.4:

Population Structure, Molecular Epidemiology, and β-Lactamase Diversity among Stenotrophomonas maltophilia Isolates in the United States

Mojica MF, Rutter JD, Taracila M, Abriata LA, Fouts DE, Papp-Wallace KM, Walsh TJ, LiPuma JJ, Vila AJ, Bonomo RA

PMID: 31266860

BMC bioinformatics. 2019-01-07; 20.1: 8.

OMeta: an ontology-based, data-driven metadata tracking system

Singh I, Kuscuoglu M, Harkins DM, Sutton G, Fouts DE, Nelson KE

PMID: 30612540

Frontiers in cellular and infection microbiology. 2018-06-19; 8.193.

Genomic Comparison Among Global Isolates of L. interrogans Serovars Copenhageni and Icterohaemorrhagiae Identified Natural Genetic Variation Caused by an Indel

Santos LA, Adhikarla H, Yan X, Wang Z, Fouts DE, Vinetz JM, Alcantara LCJ, Hartskeerl RA, Goris MGA, Picardeau M, Reis MG, Townsend JP, Zhao H, Ko AI, Wunder EA

PMID: 29971217

Nature communications. 2017-10-16; 8.1: 837.

Gastric acid suppression promotes alcoholic liver disease by inducing overgrowth of intestinal Enterococcus

Llorente C, Jepsen P, Inamine T, Wang L, Bluemel S, Wang HJ, Loomba R, Bajaj JS, Schubert ML, Sikaroodi M, Gillevet PM, Xu J, Kisseleva T, Ho SB, Depew J, Du X, Sørensen HT, Vilstrup H, Nelson KE, Brenner DA, Fouts DE, Schnabl B

PMID: 29038503

The Journal of clinical investigation. 2017-06-30; 127.7: 2829-2841.

Intestinal fungi contribute to development of alcoholic liver disease

Yang AM, Inamine T, Hochrath K, Chen P, Wang L, Llorente C, Bluemel S, Hartmann P, Xu J, Koyama Y, Kisseleva T, Torralba MG, Moncera K, Beeri K, Chen CS, Freese K, Hellerbrand C, Lee SM, Hoffman HM, Mehal WZ, Garcia-Tsao G, Mutlu EA, Keshavarzian A, Brown GD, Ho SB, Bataller R, Stärkel P, Fouts DE, Schnabl B

PMID: 28530644

Journal of neurovirology. 2017-04-01; 23.2: 171-185.

HSV-1 clinical isolates with unique in vivo and in vitro phenotypes and insight into genomic differences

Danaher RJ, Fouts DE, Chan AP, Choi Y, Depew J, McCorrison JM, Nelson KE, Wang C, Miller CS

PMID: 27739035

PLoS neglected tropical diseases. 2016-02-18; 10.2: e0004403.

What Makes a Bacterial Species Pathogenic?:Comparative Genomic Analysis of the Genus Leptospira

Fouts DE, Matthias MA, Adhikarla H, Adler B, Amorim-Santos L, Berg DE, Bulach D, Buschiazzo A, Chang YF, Galloway RL, Haake DA, Haft DH, Hartskeerl R, Ko AI, Levett PN, Matsunaga J, Mechaly AE, Monk JM, Nascimento AL, Nelson KE, Palsson B, Peacock SJ, Picardeau M, Ricaldi JN, Thaipandungpanit J, Wunder EA, Yang XF, Zhang JJ, Vinetz JM

PMID: 26890609

Cell host & microbe. 2016-02-10; 19.2: 227-39.

Intestinal REG3 Lectins Protect against Alcoholic Steatohepatitis by Reducing Mucosa-Associated Microbiota and Preventing Bacterial Translocation

Wang L, Fouts DE, Stärkel P, Hartmann P, Chen P, Llorente C, Depew J, Moncera K, Ho SB, Brenner DA, Hooper LV, Schnabl B

PMID: 26867181

Gastroenterology. 2015-01-01; 148.1: 203-214.e16.

Supplementation of saturated long-chain fatty acids maintains intestinal eubiosis and reduces ethanol-induced liver injury in mice

Chen P, Torralba M, Tan J, Embree M, Zengler K, Stärkel P, van Pijkeren JP, Depew J, Loomba R, Ho SB, Bajaj JS, Mutlu EA, Keshavarzian A, Tsukamoto H, Nelson KE, Fouts DE, Schnabl B

PMID: 25239591

Bacteriophage. 2012-07-01; 2.3: 190-199.

Next generation sequencing technologies and the changing landscape of phage genomics

Klumpp J, Fouts DE, Sozhamannan S

PMID: 23275870

Journal of hepatology. 2012-06-01; 56.6: 1283-92.

Bacterial translocation and changes in the intestinal microbiome in mouse models of liver disease

Fouts DE, Torralba M, Nelson KE, Brenner DA, Schnabl B

PMID: 22326468

PLoS genetics. 2008-07-25; 4.7: e1000141.

Complete genome sequence of the N2-fixing broad host range endophyte Klebsiella pneumoniae 342 and virulence predictions verified in mice

Fouts DE, Tyler HL, Deboy RT, Daugherty S, Ren Q, Badger JH, Durkin AS, Huot H, Shrivastava S, Kothari S, Dodson RJ, Mohamoud Y, Khouri H, Roesch LF, Krogfelt KA, Struve C, Triplett EW, Methé BA

PMID: 18654632

Journal of bacteriology. 2007-01-01; 189.1: 52-64.

Complete sequence analysis of novel plasmids from emetic and periodontal Bacillus cereus isolates reveals a common evolutionary history among the B. cereus-group plasmids, including Bacillus anthracis pXO1

Rasko DA, Rosovitz MJ, Økstad OA, Fouts DE, Jiang L, Cer RZ, Kolstø AB, Gill SR, Ravel J

PMID: 17041058

Nucleic acids research. 2006-10-24; 34.20: 5839-51.

Phage_Finder: automated identification and classification of prophage regions in complete bacterial genome sequences

Fouts DE

PMID: 17062630

Journal of bacteriology. 2006-05-01; 188.9: 3402-8.

Sequencing Bacillus anthracis typing phages gamma and cherry reveals a common ancestry

Fouts DE, Rasko DA, Cer RZ, Jiang L, Fedorova NB, Shvartsbeyn A, Vamathevan JJ, Tallon L, Althoff R, Arbogast TS, Fadrosh DW, Read TD, Gill SR

PMID: 16621835

Journal of bacteriology. 2005-04-01; 187.7: 2426-38.

Insights on evolution of virulence and resistance from the complete genome analysis of an early methicillin-resistant Staphylococcus aureus strain and a biofilm-producing methicillin-resistant Staphylococcus epidermidis strain

Gill SR, Fouts DE, Archer GL, Mongodin EF, Deboy RT, Ravel J, Paulsen IT, Kolonay JF, Brinkac L, Beanan M, Dodson RJ, Daugherty SC, Madupu R, Angiuoli SV, Durkin AS, Haft DH, Vamathevan J, Khouri H, Utterback T, Lee C, Dimitrov G, Jiang L, Qin H, Weidman J, Tran K, Kang K, Hance IR, Nelson KE, Fraser CM

PMID: 15774886

PLoS biology. 2005-01-01; 3.1: e15.

Major structural differences and novel potential virulence mechanisms from the genomes of multiple campylobacter species

Fouts DE, Mongodin EF, Mandrell RE, Miller WG, Rasko DA, Ravel J, Brinkac LM, Deboy RT, Parker CT, Daugherty SC, Dodson RJ, Durkin AS, Madupu R, Sullivan SA, Shetty JU, Ayodeji MA, Shvartsbeyn A, Schatz MC, Badger JH, Fraser CM, Nelson KE

PMID: 15660156

Science (New York, N.Y.). 2004-04-02; 304.5667: 66-74.

Environmental genome shotgun sequencing of the Sargasso Sea

Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu D, Paulsen I, Nelson KE, Nelson W, Fouts DE, Levy S, Knap AH, Lomas MW, Nealson K, White O, Peterson J, Hoffman J, Parsons R, Baden-Tillson H, Pfannkoch C, Rogers YH, Smith HO

PMID: 15001713

Journal of bacteriology. 2003-09-01; 185.18: 5591-601.

Complete genome sequence of the oral pathogenic Bacterium porphyromonas gingivalis strain W83

Nelson KE, Fleischmann RD, Deboy RT, Paulsen IT, Fouts DE, Eisen JA, Daugherty SC, Dodson RJ, Durkin AS, Gwinn M, Haft DH, Kolonay JF, Nelson WC, Mason T, Tallon L, Gray J, Granger D, Tettelin H, Dong H, Galvin JL, Duncan MJ, Dewhirst FE, Fraser CM

PMID: 12949112

Molecular plant-microbe interactions : MPMI. 2003-01-01; 16.1: 43-52.

A pseudomonas syringae pv. tomato DC3000 Hrp (Type III secretion) deletion mutant expressing the Hrp system of bean pathogen P. syringae pv. syringae 61 retains normal host specificity for tomato

Fouts DE, Badel JL, Ramos AR, Rapp RA, Collmer A

PMID: 12580281

Proceedings of the National Academy of Sciences of the United States of America. 2002-02-19; 99.4: 2275-80.

Genomewide identification of Pseudomonas syringae pv. tomato DC3000 promoters controlled by the HrpL alternative sigma factor

Fouts DE, Abramovitch RB, Alfano JR, Baldo AM, Buell CR, Cartinhour S, Chatterjee AK, D'Ascenzo M, Gwinn ML, Lazarowitz SG, Lin NC, Martin GB, Rehm AH, Schneider DJ, van Dijk K, Tang X, Collmer A

PMID: 11854524