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Evolutionary pathways to antibiotic resistance are dependent upon environmental structure and bacterial lifestyle.

Santos-Lopez A, Marshall CW, Scribner MR, Snyder DJ, Cooper VS.

Elife. 2019 Sep 13;8. pii: e47612. doi: 10.7554/eLife.47612. [Epub ahead of print]


Evolution of Outbreak-Causing Carbapenem-Resistant Klebsiella pneumoniae ST258 at a Tertiary Care Hospital over 8 Years.

Marsh JW, Mustapha MM, Griffith MP, Evans DR, Ezeonwuka C, Pasculle AW, Shutt KA, Sundermann A, Ayres AM, Shields RK, Babiker A, Cooper VS, Van Tyne D, Harrison LH.

MBio. 2019 Sep 3;10(5). pii: e01945-19. doi: 10.1128/mBio.01945-19.


Environment changes epistasis to alter trade-offs along alternative evolutionary paths.

Hall AE, Karkare K, Cooper VS, Bank C, Cooper TF, Moore FB.

Evolution. 2019 Aug 16. doi: 10.1111/evo.13825. [Epub ahead of print]


Pseudomonas aeruginosa Interstrain Dynamics and Selection of Hyperbiofilm Mutants during a Chronic Infection.

Gloag ES, Marshall CW, Snyder D, Lewin GR, Harris JS, Santos-Lopez A, Chaney SB, Whiteley M, Cooper VS, Wozniak DJ.

MBio. 2019 Aug 13;10(4). pii: e01698-19. doi: 10.1128/mBio.01698-19.


Outbreak of Vancomycin-resistant Enterococcus faecium in Interventional Radiology: Detection Through Whole Genome Sequencing-Based Surveillance.

Sundermann AJ, Babiker A, Marsh JW, Shutt KA, Mustapha MM, Pasculle AW, Ezeonwuka C, Saul MI, Pacey MP, Van Tyne D, Ayres AM, Cooper VS, Snyder GM, Harrison LH.

Clin Infect Dis. 2019 Jul 16. pii: ciz666. doi: 10.1093/cid/ciz666. [Epub ahead of print]


A method of processing nasopharyngeal swabs to enable multiple testing.

Lopez SMC, Martin JM, Johnson M, Kurs-Lasky M, Horne WT, Marshall CW, Cooper VS, Williams JV, Shaikh N.

Pediatr Res. 2019 Jul 9. doi: 10.1038/s41390-019-0498-1. [Epub ahead of print]


Reduced ceftazidime and ertapenem susceptibility due to production of OXA-2 in Klebsiella pneumoniae ST258.

Iovleva A, Mettus RT, McElheny CL, Mustapha MM, Van Tyne D, Shields RK, Pasculle AW, Cooper VS, Doi Y.

J Antimicrob Chemother. 2019 Aug 1;74(8):2203-2208. doi: 10.1093/jac/dkz183.


Use of a cohorting-unit and systematic surveillance cultures to control a Klebsiella pneumoniae carbapenemase (KPC)-producing Enterobacteriaceae outbreak.

Reeme AE, Bowler SL, Buchan BW, Graham MB, Behrens E, Singh S, Hong JC, Arvan J, Hyke JW, Palen L, Savage S, Seliger H, Huerta S, Ledeboer NA, Kotay S, Mathers AJ, Cooper VS, Mustapha MM, Mettus RT, Doi Y, Munoz-Price LS.

Infect Control Hosp Epidemiol. 2019 Jul;40(7):767-773. doi: 10.1017/ice.2019.99. Epub 2019 May 14.


The use of Online Tools for Antimicrobial Resistance Prediction by Whole Genome Sequencing in MRSA and VRE.

Babiker A, Mustapha MM, Pacey MP, Shutt KA, Ezeonwuka CD, Ohm SL, Cooper VS, Marsh JW, Doi Y, Harrison LH.

J Glob Antimicrob Resist. 2019 Apr 18. pii: S2213-7165(19)30095-5. doi: 10.1016/j.jgar.2019.04.006. [Epub ahead of print]


NADH Dehydrogenases in Pseudomonas aeruginosa Growth and Virulence.

Torres A, Kasturiarachi N, DuPont M, Cooper VS, Bomberger J, Zemke A.

Front Microbiol. 2019 Feb 5;10:75. doi: 10.3389/fmicb.2019.00075. eCollection 2019.


Structural basis of DSF recognition by its receptor RpfR and its regulatory interaction with the DSF synthase RpfF.

Waldron EJ, Snyder D, Fernandez NL, Sileo E, Inoyama D, Freundlich JS, Waters CM, Cooper VS, Neiditch MB.

PLoS Biol. 2019 Feb 4;17(2):e3000123. doi: 10.1371/journal.pbio.3000123. eCollection 2019 Feb.


Improved Detection of Culprit Pathogens by Bacterial DNA Sequencing Affects Antibiotic Management Decisions in Severe Pneumonia.

Dunlap DG, Marshall CW, Fitch A, Rapport SF, Cooper VS, McVerry BJ, Morris A, Kitsios GD.

Am J Case Rep. 2018 Nov 26;19:1405-1409. doi: 10.12659/AJCR.912055.


Clostridioides difficile: a potential source of NpmA in the clinical environment.

Marsh JW, Pacey MP, Ezeonwuka C, Ohm SL, Snyder D, Cooper VS, Harrison LH, Doi Y, Mustapha MM.

J Antimicrob Chemother. 2019 Feb 1;74(2):521-523. doi: 10.1093/jac/dky420. No abstract available.


Parallel genetic adaptation across environments differing in mode of growth or resource availability.

Turner CB, Marshall CW, Cooper VS.

Evol Lett. 2018 Aug 4;2(4):355-367. doi: 10.1002/evl3.75. eCollection 2018 Aug.


Non-Uniform and Non-Random Binding of Nucleoprotein to Influenza A and B Viral RNA.

Le Sage V, Nanni AV, Bhagwat AR, Snyder DJ, Cooper VS, Lakdawala SS, Lee N.

Viruses. 2018 Sep 25;10(10). pii: E522. doi: 10.3390/v10100522.


Synonymous mutations make dramatic contributions to fitness when growth is limited by a weak-link enzyme.

Kristofich J, Morgenthaler AB, Kinney WR, Ebmeier CC, Snyder DJ, Old WM, Cooper VS, Copley SD.

PLoS Genet. 2018 Aug 27;14(8):e1007615. doi: 10.1371/journal.pgen.1007615. eCollection 2018 Aug.


Periodic Variation of Mutation Rates in Bacterial Genomes Associated with Replication Timing.

Dillon MM, Sung W, Lynch M, Cooper VS.

MBio. 2018 Aug 21;9(4). pii: e01371-18. doi: 10.1128/mBio.01371-18.


Phylogenomics of colistin-susceptible and resistant XDR Acinetobacter baumannii.

Mustapha MM, Li B, Pacey MP, Mettus RT, McElheny CL, Marshall CW, Ernst RK, Cooper VS, Doi Y.

J Antimicrob Chemother. 2018 Nov 1;73(11):2952-2959. doi: 10.1093/jac/dky290.


The OmpR Regulator of Burkholderia multivorans Controls Mucoid-to-Nonmucoid Transition and Other Cell Envelope Properties Associated with Persistence in the Cystic Fibrosis Lung.

Silva IN, Pessoa FD, Ramires MJ, Santos MR, Becker JD, Cooper VS, Moreira LM.

J Bacteriol. 2018 Aug 10;200(17). pii: e00216-18. doi: 10.1128/JB.00216-18. Print 2018 Sep 1.


Experimental Evolution as a High-Throughput Screen for Genetic Adaptations.

Cooper VS.

mSphere. 2018 May 9;3(3). pii: e00121-18. doi: 10.1128/mSphere.00121-18. eCollection 2018 May-Jun.


New Insights from Elucidating the Role of LMP1 in Nasopharyngeal Carcinoma.

Shair KHY, Reddy A, Cooper VS.

Cancers (Basel). 2018 Mar 21;10(4). pii: E86. doi: 10.3390/cancers10040086. Review.


Genetic requirements for Staphylococcus aureus nitric oxide resistance and virulence.

Grosser MR, Paluscio E, Thurlow LR, Dillon MM, Cooper VS, Kawula TH, Richardson AR.

PLoS Pathog. 2018 Mar 19;14(3):e1006907. doi: 10.1371/journal.ppat.1006907. eCollection 2018 Mar.


Thrombospondin-1 protects against pathogen-induced lung injury by limiting extracellular matrix proteolysis.

Qu Y, Olonisakin T, Bain W, Zupetic J, Brown R, Hulver M, Xiong Z, Tejero J, Shanks RM, Bomberger JM, Cooper VS, Zegans ME, Ryu H, Han J, Pilewski J, Ray A, Cheng Z, Ray P, Lee JS.

JCI Insight. 2018 Feb 8;3(3). pii: 96914. doi: 10.1172/jci.insight.96914. eCollection 2018 Feb 8.


Frequency and Mechanisms of Spontaneous Fosfomycin Nonsusceptibility Observed upon Disk Diffusion Testing of Escherichia coli.

Lucas AE, Ito R, Mustapha MM, McElheny CL, Mettus RT, Bowler SL, Kantz SF, Pacey MP, Pasculle AW, Cooper VS, Doi Y.

J Clin Microbiol. 2017 Dec 26;56(1). pii: e01368-17. doi: 10.1128/JCM.01368-17. Print 2018 Jan.


High-Level Fosfomycin Resistance in Vancomycin-Resistant Enterococcus faecium.

Guo Y, Tomich AD, McElheny CL, Cooper VS, Tait-Kamradt A, Wang M, Hu F, Rice LB, Sluis-Cremer N, Doi Y.

Emerg Infect Dis. 2017 Nov;23(11):1902-1904. doi: 10.3201/eid2311.171130.


Ceftolozane-Tazobactam for the Treatment of Multidrug-Resistant Pseudomonas aeruginosa Infections: Clinical Effectiveness and Evolution of Resistance.

Haidar G, Philips NJ, Shields RK, Snyder D, Cheng S, Potoski BA, Doi Y, Hao B, Press EG, Cooper VS, Clancy CJ, Nguyen MH.

Clin Infect Dis. 2017 Jul 1;65(1):110-120. doi: 10.1093/cid/cix182.


Structural modification of LPS in colistin-resistant, KPC-producing Klebsiella pneumoniae.

Leung LM, Cooper VS, Rasko DA, Guo Q, Pacey MP, McElheny CL, Mettus RT, Yoon SH, Goodlett DR, Ernst RK, Doi Y.

J Antimicrob Chemother. 2017 Nov 1;72(11):3035-3042. doi: 10.1093/jac/dkx234.


Genome-wide analysis of influenza viral RNA and nucleoprotein association.

Lee N, Le Sage V, Nanni AV, Snyder DJ, Cooper VS, Lakdawala SS.

Nucleic Acids Res. 2017 Sep 6;45(15):8968-8977. doi: 10.1093/nar/gkx584.


Parallel Evolution of Two Clades of an Atlantic-Endemic Pathogenic Lineage of Vibrio parahaemolyticus by Independent Acquisition of Related Pathogenicity Islands.

Xu F, Gonzalez-Escalona N, Drees KP, Sebra RP, Cooper VS, Jones SH, Whistler CA.

Appl Environ Microbiol. 2017 Aug 31;83(18). pii: e01168-17. doi: 10.1128/AEM.01168-17. Print 2017 Sep 15.


Structure of O-Antigen and Hybrid Biosynthetic Locus in Burkholderia cenocepacia Clonal Variants Recovered from a Cystic Fibrosis Patient.

Hassan AA, Maldonado RF, Dos Santos SC, Di Lorenzo F, Silipo A, Coutinho CP, Cooper VS, Molinaro A, Valvano MA, Sá-Correia I.

Front Microbiol. 2017 Jun 8;8:1027. doi: 10.3389/fmicb.2017.01027. eCollection 2017.


Host-selected mutations converging on a global regulator drive an adaptive leap towards symbiosis in bacteria.

Sabrina Pankey M, Foxall RL, Ster IM, Perry LA, Schuster BM, Donner RA, Coyle M, Cooper VS, Whistler CA.

Elife. 2017 Apr 27;6. pii: e24414. doi: 10.7554/eLife.24414.


Comparative genomics of Burkholderia multivorans, a ubiquitous pathogen with a highly conserved genomic structure.

Peeters C, Cooper VS, Hatcher PJ, Verheyde B, Carlier A, Vandamme P.

PLoS One. 2017 Apr 21;12(4):e0176191. doi: 10.1371/journal.pone.0176191. eCollection 2017.


RelA Mutant Enterococcus faecium with Multiantibiotic Tolerance Arising in an Immunocompromised Host.

Honsa ES, Cooper VS, Mhaissen MN, Frank M, Shaker J, Iverson A, Rubnitz J, Hayden RT, Lee RE, Rock CO, Tuomanen EI, Wolf J, Rosch JW.

MBio. 2017 Jan 3;8(1). pii: e02124-16. doi: 10.1128/mBio.02124-16.


Sequence Type 631 Vibrio parahaemolyticus, an Emerging Foodborne Pathogen in North America.

Xu F, Gonzalez-Escalona N, Haendiges J, Myers RA, Ferguson J, Stiles T, Hickey E, Moore M, Hickey JM, Schillaci C, Mank L, DeRosia-Banick K, Matluk N, Robbins A, Sebra RP, Cooper VS, Jones SH, Whistler CA.

J Clin Microbiol. 2017 Feb;55(2):645-648. doi: 10.1128/JCM.02162-16. Epub 2016 Dec 14. No abstract available.


Outbreak of Klebsiella pneumoniae Carbapenemase-Producing Citrobacter freundii at a Tertiary Acute Care Facility in Miami, Florida.

Jiménez A, Castro JG, Munoz-Price LS, de Pascale D, Shimose L, Mustapha MM, Spychala CN, Mettus RT, Cooper VS, Doi Y.

Infect Control Hosp Epidemiol. 2017 Mar;38(3):320-326. doi: 10.1017/ice.2016.273. Epub 2016 Dec 7.


Long-Term Evolution of Burkholderia multivorans during a Chronic Cystic Fibrosis Infection Reveals Shifting Forces of Selection.

Silva IN, Santos PM, Santos MR, Zlosnik JE, Speert DP, Buskirk SW, Bruger EL, Waters CM, Cooper VS, Moreira LM.

mSystems. 2016 May 24;1(3). pii: e00029-16. eCollection 2016 May-Jun.


Genome-Wide Biases in the Rate and Molecular Spectrum of Spontaneous Mutations in Vibrio cholerae and Vibrio fischeri.

Dillon MM, Sung W, Sebra R, Lynch M, Cooper VS.

Mol Biol Evol. 2017 Jan;34(1):93-109. doi: 10.1093/molbev/msw224. Epub 2016 Oct 15.


The Fitness Effects of Spontaneous Mutations Nearly Unseen by Selection in a Bacterium with Multiple Chromosomes.

Dillon MM, Cooper VS.

Genetics. 2016 Nov;204(3):1225-1238. doi: 10.1534/genetics.116.193060. Epub 2016 Sep 26.


Characterization of a Novel IncHI2 Plasmid Carrying Tandem Copies of blaCTX-M-2 in a fosA6-Harboring Escherichia coli Sequence Type 410 Strain.

Guo Q, Ding B, Jové T, Stoesser N, Cooper VS, Wang M, Doi Y.

Antimicrob Agents Chemother. 2016 Oct 21;60(11):6742-6747. doi: 10.1128/AAC.01173-16. Print 2016 Nov.


Phylogenomic Study of Burkholderia glathei-like Organisms, Proposal of 13 Novel Burkholderia Species and Emended Descriptions of Burkholderia sordidicola, Burkholderia zhejiangensis, and Burkholderia grimmiae.

Peeters C, Meier-Kolthoff JP, Verheyde B, De Brandt E, Cooper VS, Vandamme P.

Front Microbiol. 2016 Jun 8;7:877. doi: 10.3389/fmicb.2016.00877. eCollection 2016.


Evolution of the Insertion-Deletion Mutation Rate Across the Tree of Life.

Sung W, Ackerman MS, Dillon MM, Platt TG, Fuqua C, Cooper VS, Lynch M.

G3 (Bethesda). 2016 Aug 9;6(8):2583-91. doi: 10.1534/g3.116.030890.


Glutathione-S-transferase FosA6 of Klebsiella pneumoniae origin conferring fosfomycin resistance in ESBL-producing Escherichia coli.

Guo Q, Tomich AD, McElheny CL, Cooper VS, Stoesser N, Wang M, Sluis-Cremer N, Doi Y.

J Antimicrob Chemother. 2016 Sep;71(9):2460-5. doi: 10.1093/jac/dkw177. Epub 2016 Jun 3.


Environmental Conditions Associated with Elevated Vibrio parahaemolyticus Concentrations in Great Bay Estuary, New Hampshire.

Urquhart EA, Jones SH, Yu JW, Schuster BM, Marcinkiewicz AL, Whistler CA, Cooper VS.

PLoS One. 2016 May 4;11(5):e0155018. doi: 10.1371/journal.pone.0155018. eCollection 2016.


Benefit of transferred mutations is better predicted by the fitness of recipients than by their ecological or genetic relatedness.

Wang Y, Diaz Arenas C, Stoebel DM, Flynn K, Knapp E, Dillon MM, Wünsche A, Hatcher PJ, Moore FB, Cooper VS, Cooper TF.

Proc Natl Acad Sci U S A. 2016 May 3;113(18):5047-52. doi: 10.1073/pnas.1524988113. Epub 2016 Apr 18.


Laboratory Evolution of Microbial Interactions in Bacterial Biofilms.

Martin M, Hölscher T, Dragoš A, Cooper VS, Kovács ÁT.

J Bacteriol. 2016 Sep 9;198(19):2564-71. doi: 10.1128/JB.01018-15. Print 2016 Oct 1. Review.


Evolution of Ecological Diversity in Biofilms of Pseudomonas aeruginosa by Altered Cyclic Diguanylate Signaling.

Flynn KM, Dowell G, Johnson TM, Koestler BJ, Waters CM, Cooper VS.

J Bacteriol. 2016 Sep 9;198(19):2608-18. doi: 10.1128/JB.00048-16. Print 2016 Oct 1.


Diverse phenotypic and genetic responses to short-term selection in evolving Escherichia coli populations.

Dillon MM, Rouillard NP, Van Dam B, Gallet R, Cooper VS.

Evolution. 2016 Mar;70(3):586-99. doi: 10.1111/evo.12868. Epub 2016 Feb 12.


Genome sequence and comparative analysis of a putative entomopathogenic Serratia isolated from Caenorhabditis briggsae.

Abebe-Akele F, Tisa LS, Cooper VS, Hatcher PJ, Abebe E, Thomas WK.

BMC Genomics. 2015 Jul 18;16:531. doi: 10.1186/s12864-015-1697-8.


The Rate and Molecular Spectrum of Spontaneous Mutations in the GC-Rich Multichromosome Genome of Burkholderia cenocepacia.

Dillon MM, Sung W, Lynch M, Cooper VS.

Genetics. 2015 Jul;200(3):935-46. doi: 10.1534/genetics.115.176834. Epub 2015 May 12.


Genetic characterization of clinical and environmental Vibrio parahaemolyticus from the Northeast USA reveals emerging resident and non-indigenous pathogen lineages.

Xu F, Ilyas S, Hall JA, Jones SH, Cooper VS, Whistler CA.

Front Microbiol. 2015 Apr 7;6:272. doi: 10.3389/fmicb.2015.00272. eCollection 2015.

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