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Escherichia coli clonobiome: assessing the strains diversity in feces and urine by deep amplicon sequencing.

Shevchenko SG, Radey M, Tchesnokova V, Kisiela D, Sokurenko EV.

Appl Environ Microbiol. 2019 Sep 20. pii: AEM.01866-19. doi: 10.1128/AEM.01866-19. [Epub ahead of print]


Pandemic uropathogenic fluoroquinolone-resistant Escherichia coli have enhanced ability to persist in the gut and cause bacteriuria in healthy women.

Tchesnokova VL, Rechkina E, Chan D, Haile HG, Larson L, Ferrier K, Schroeder DW, Solyanik T, Shibuya S, Hansen K, Ralston JD, Riddell K, Scholes D, Sokurenko EV.

Clin Infect Dis. 2019 Jul 4. pii: ciz547. doi: 10.1093/cid/ciz547. [Epub ahead of print]


Pandemic fluoroquinolone resistant Escherichia coli clone ST1193 emerged via simultaneous homologous recombinations in 11 gene loci.

Tchesnokova V, Radey M, Chattopadhyay S, Larson L, Weaver JL, Kisiela D, Sokurenko EV.

Proc Natl Acad Sci U S A. 2019 Jul 16;116(29):14740-14748. doi: 10.1073/pnas.1903002116. Epub 2019 Jul 1.


Recombination-independent rapid convergent evolution of the gastric pathogen Helicobacter pylori.

Chattopadhyay S, Chi PB, Minin VN, Berg DE, Sokurenko EV.

BMC Genomics. 2018 Nov 21;19(1):835. doi: 10.1186/s12864-018-5231-7.


Rapid and Extensive Expansion in the United States of a New Multidrug-resistant Escherichia coli Clonal Group, Sequence Type 1193.

Tchesnokova VL, Rechkina E, Larson L, Ferrier K, Weaver JL, Schroeder DW, She R, Butler-Wu SM, Aguero-Rosenfeld ME, Zerr D, Fang FC, Ralston J, Riddell K, Scholes D, Weissman S, Parker K, Spellberg B, Johnson JR, Sokurenko EV.

Clin Infect Dis. 2019 Jan 7;68(2):334-337. doi: 10.1093/cid/ciy525.


The Uropathogenic Escherichia coli Subclone Sequence Type 131-H30 Is Responsible for Most Antibiotic Prescription Errors at an Urgent Care Clinic.

Tchesnokova V, Riddell K, Scholes D, Johnson JR, Sokurenko EV.

Clin Infect Dis. 2019 Feb 15;68(5):781-787. doi: 10.1093/cid/ciy523.


Epidemiology and Antimicrobial Resistance Characteristics of the Sequence Type 131-H30 Subclone Among Extraintestinal Escherichia coli Collected From US Children.

Miles-Jay A, Weissman SJ, Adler AL, Tchesnokova V, Sokurenko EV, Baseman JG, Zerr DM.

Clin Infect Dis. 2018 Jan 18;66(3):411-419. doi: 10.1093/cid/cix805.


Inactivation of Transcriptional Regulators during Within-Household Evolution of Escherichia coli.

Kisiela DI, Radey M, Paul S, Porter S, Polukhina K, Tchesnokova V, Shevchenko S, Chan D, Aziz M, Johnson TJ, Price LB, Johnson JR, Sokurenko EV.

J Bacteriol. 2017 Jun 13;199(13). pii: e00036-17. doi: 10.1128/JB.00036-17. Print 2017 Jul 1.


Bacterial clonal diagnostics as a tool for evidence-based empiric antibiotic selection.

Tchesnokova V, Avagyan H, Rechkina E, Chan D, Muradova M, Haile HG, Radey M, Weissman S, Riddell K, Scholes D, Johnson JR, Sokurenko EV.

PLoS One. 2017 Mar 28;12(3):e0174132. doi: 10.1371/journal.pone.0174132. eCollection 2017.


Clonal distribution and associated characteristics of Escherichia coli clinical and surveillance isolates from a military medical center.

Manges AR, Mende K, Murray CK, Johnston BD, Sokurenko EV, Tchesnokova V, Johnson JR.

Diagn Microbiol Infect Dis. 2017 Apr;87(4):382-385. doi: 10.1016/j.diagmicrobio.2017.01.007. Epub 2017 Jan 20.


Escherichia coli Sequence Type 131 H30 Is the Main Driver of Emerging Extended-Spectrum-β-Lactamase-Producing E. coli at a Tertiary Care Center.

Johnson JR, Johnston B, Thuras P, Launer B, Sokurenko EV, Miller LG.

mSphere. 2016 Nov 23;1(6). pii: e00314-16. eCollection 2016 Nov-Dec.


SpyB, a Small Heme-Binding Protein, Affects the Composition of the Cell Wall in Streptococcus pyogenes.

Edgar RJ, Chen J, Kant S, Rechkina E, Rush JS, Forsberg LS, Jaehrig B, Azadi P, Tchesnokova V, Sokurenko EV, Zhu H, Korotkov KV, Pancholi V, Korotkova N.

Front Cell Infect Microbiol. 2016 Oct 13;6:126. eCollection 2016.


Household Clustering of Escherichia coli Sequence Type 131 Clinical and Fecal Isolates According to Whole Genome Sequence Analysis.

Johnson JR, Davis G, Clabots C, Johnston BD, Porter S, DebRoy C, Pomputius W, Ender PT, Cooperstock M, Slater BS, Banerjee R, Miller S, Kisiela D, Sokurenko EV, Aziz M, Price LB.

Open Forum Infect Dis. 2016 Jun 16;3(3):ofw129. eCollection 2016 Sep.


Uropathogenic Escherichia coli Metabolite-Dependent Quiescence and Persistence May Explain Antibiotic Tolerance during Urinary Tract Infection.

Leatham-Jensen MP, Mokszycki ME, Rowley DC, Deering R, Camberg JL, Sokurenko EV, Tchesnokova VL, Frimodt-Møller J, Krogfelt KA, Leth Nielsen K, Frimodt-Møller N, Sun G, Cohen PS.

mSphere. 2016 Jan 20;1(1). pii: e00055-15. doi: 10.1128/mSphere.00055-15. eCollection 2016 Jan-Feb.


A Novel 7-Single Nucleotide Polymorphism-Based Clonotyping Test Allows Rapid Prediction of Antimicrobial Susceptibility of Extraintestinal Escherichia coli Directly From Urine Specimens.

Tchesnokova V, Avagyan H, Billig M, Chattopadhyay S, Aprikian P, Chan D, Pseunova J, Rechkina E, Riddell K, Scholes D, Fang FC, Johnson JR, Sokurenko EV.

Open Forum Infect Dis. 2016 Jan 18;3(1):ofw002. doi: 10.1093/ofid/ofw002. eCollection 2016 Jan.


PanCoreGen - Profiling, detecting, annotating protein-coding genes in microbial genomes.

Paul S, Bhardwaj A, Bag SK, Sokurenko EV, Chattopadhyay S.

Genomics. 2015 Dec;106(6):367-72. doi: 10.1016/j.ygeno.2015.10.001. Epub 2015 Oct 9.


Greater ciprofloxacin tolerance as a possible selectable phenotype underlying the pandemic spread of the H30 subclone of Escherichia coli sequence type 131.

Johnson JR, Porter SB, Thuras P, Johnson TJ, Price LB, Tchesnokova V, Sokurenko EV.

Antimicrob Agents Chemother. 2015 Nov;59(11):7132-5. doi: 10.1128/AAC.01687-15. Epub 2015 Aug 31.


Erratum for Johnson et al., intensity and mechanisms of fluoroquinolone resistance within the H30 and H30Rx subclones of Escherichia coli sequence type 131 compared with other fluoroquinolone-resistant E. coli.

Johnson JR, Johnston B, Kuskowski MA, Sokurenko EV, Tchesnokova V.

Antimicrob Agents Chemother. 2015 Sep;59(9):5871. doi: 10.1128/AAC.01716-15. No abstract available.


Inactive conformation enhances binding function in physiological conditions.

Yakovenko O, Tchesnokova V, Sokurenko EV, Thomas WE.

Proc Natl Acad Sci U S A. 2015 Aug 11;112(32):9884-9. doi: 10.1073/pnas.1503160112. Epub 2015 Jul 27.


Synonymous and nonsynonymous distances help untangle convergent evolution and recombination.

Chi PB, Chattopadhyay S, Lemey P, Sokurenko EV, Minin VN.

Stat Appl Genet Mol Biol. 2015 Aug;14(4):375-89. doi: 10.1515/sagmb-2014-0078.


Intensity and Mechanisms of Fluoroquinolone Resistance within the H30 and H30Rx Subclones of Escherichia coli Sequence Type 131 Compared with Other Fluoroquinolone-Resistant E. coli.

Johnson JR, Johnston B, Kuskowski MA, Sokurenko EV, Tchesnokova V.

Antimicrob Agents Chemother. 2015 Aug;59(8):4471-80. doi: 10.1128/AAC.00673-15. Epub 2015 May 18. Erratum in: Antimicrob Agents Chemother. 2015 Sep;59(9):5871.


Inhibition and Reversal of Microbial Attachment by an Antibody with Parasteric Activity against the FimH Adhesin of Uropathogenic E. coli.

Kisiela DI, Avagyan H, Friend D, Jalan A, Gupta S, Interlandi G, Liu Y, Tchesnokova V, Rodriguez VB, Sumida JP, Strong RK, Wu XR, Thomas WE, Sokurenko EV.

PLoS Pathog. 2015 May 14;11(5):e1004857. doi: 10.1371/journal.ppat.1004857. eCollection 2015 May.


Prevalence and persistence of Escherichia coli in the airways of cystic fibrosis patients - an unrecognized CF pathogen?

Barillova P, Tchesnokova V, Dübbers A, Küster P, Peters G, Dobrindt U, Sokurenko EV, Kahl BC.

Int J Med Microbiol. 2014 May;304(3-4):415-21. doi: 10.1016/j.ijmm.2014.02.008. Epub 2014 Feb 19.


The epidemic of extended-spectrum-β-lactamase-producing Escherichia coli ST131 is driven by a single highly pathogenic subclone, H30-Rx.

Price LB, Johnson JR, Aziz M, Clabots C, Johnston B, Tchesnokova V, Nordstrom L, Billig M, Chattopadhyay S, Stegger M, Andersen PS, Pearson T, Riddell K, Rogers P, Scholes D, Kahl B, Keim P, Sokurenko EV.

MBio. 2013 Dec 17;4(6):e00377-13. doi: 10.1128/mBio.00377-13.


Complete Genome Sequence of the Epidemic and Highly Virulent CTX-M-15-Producing H30-Rx Subclone of Escherichia coli ST131.

Andersen PS, Stegger M, Aziz M, Contente-Cuomo T, Gibbons HS, Keim P, Sokurenko EV, Johnson JR, Price LB.

Genome Announc. 2013 Dec 5;1(6). pii: e00988-13. doi: 10.1128/genomeA.00988-13.


Response to Giufre et al.

Johnson JR, Price LB, Sokurenko EV.

J Infect Dis. 2014 Feb 15;209(4):630-1. doi: 10.1093/infdis/jit582. Epub 2013 Nov 7. No abstract available.


Conformational inactivation induces immunogenicity of the receptor-binding pocket of a bacterial adhesin.

Kisiela DI, Rodriguez VB, Tchesnokova V, Avagyan H, Aprikian P, Liu Y, Wu XR, Thomas WE, Sokurenko EV.

Proc Natl Acad Sci U S A. 2013 Nov 19;110(47):19089-94. doi: 10.1073/pnas.1314395110. Epub 2013 Nov 4.


Structural and population characterization of MrkD, the adhesive subunit of type 3 fimbriae.

Stahlhut SG, Chattopadhyay S, Kisiela DI, Hvidtfeldt K, Clegg S, Struve C, Sokurenko EV, Krogfelt KA.

J Bacteriol. 2013 Dec;195(24):5602-13. doi: 10.1128/JB.00753-13. Epub 2013 Oct 11.


The clonal distribution and diversity of extraintestinal Escherichia coli isolates vary according to patient characteristics.

Banerjee R, Johnston B, Lohse C, Chattopadhyay S, Tchesnokova V, Sokurenko EV, Johnson JR.

Antimicrob Agents Chemother. 2013 Dec;57(12):5912-7. doi: 10.1128/AAC.01065-13. Epub 2013 Sep 16.


Escherichia coli sequence type 131 (ST131) subclone H30 as an emergent multidrug-resistant pathogen among US veterans.

Colpan A, Johnston B, Porter S, Clabots C, Anway R, Thao L, Kuskowski MA, Tchesnokova V, Sokurenko EV, Johnson JR; VICTORY (Veterans Influence of Clonal Types on Resistance: Year 2011) Investigators.

Clin Infect Dis. 2013 Nov;57(9):1256-65. doi: 10.1093/cid/cit503. Epub 2013 Aug 6.


Predictive diagnostics for Escherichia coli infections based on the clonal association of antimicrobial resistance and clinical outcome.

Tchesnokova V, Billig M, Chattopadhyay S, Linardopoulou E, Aprikian P, Roberts PL, Skrivankova V, Johnston B, Gileva A, Igusheva I, Toland A, Riddell K, Rogers P, Qin X, Butler-Wu S, Cookson BT, Fang FC, Kahl B, Price LB, Weissman SJ, Limaye A, Scholes D, Johnson JR, Sokurenko EV.

J Clin Microbiol. 2013 Sep;51(9):2991-9. doi: 10.1128/JCM.00984-13. Epub 2013 Jul 10.


Allosteric coupling in the bacterial adhesive protein FimH.

Rodriguez VB, Kidd BA, Interlandi G, Tchesnokova V, Sokurenko EV, Thomas WE.

J Biol Chem. 2013 Aug 16;288(33):24128-39. doi: 10.1074/jbc.M113.461376. Epub 2013 Jul 2.


rbrothers: R Package for Bayesian Multiple Change-Point Recombination Detection.

Irvahn J, Chattopadhyay S, Sokurenko EV, Minin VN.

Evol Bioinform Online. 2013 Jun 12;9:235-8. doi: 10.4137/EBO.S11945. Print 2013.


Microbial variome database: point mutations, adaptive or not, in bacterial core genomes.

Chattopadhyay S, Taub F, Paul S, Weissman SJ, Sokurenko EV.

Mol Biol Evol. 2013 Jun;30(6):1465-70. doi: 10.1093/molbev/mst048. Epub 2013 Mar 14.


Tracking recent adaptive evolution in microbial species using TimeZone.

Chattopadhyay S, Paul S, Dykhuizen DE, Sokurenko EV.

Nat Protoc. 2013 Apr;8(4):652-65. doi: 10.1038/nprot.2013.031. Epub 2013 Mar 7.


Evolutionary analysis points to divergent physiological roles of type 1 fimbriae in Salmonella and Escherichia coli.

Kisiela DI, Chattopadhyay S, Tchesnokova V, Paul S, Weissman SJ, Medenica I, Clegg S, Sokurenko EV.

MBio. 2013 Mar 5;4(2). pii: e00625-12. doi: 10.1128/mBio.00625-12.


Abrupt emergence of a single dominant multidrug-resistant strain of Escherichia coli.

Johnson JR, Tchesnokova V, Johnston B, Clabots C, Roberts PL, Billig M, Riddell K, Rogers P, Qin X, Butler-Wu S, Price LB, Aziz M, Nicolas-Chanoine MH, Debroy C, Robicsek A, Hansen G, Urban C, Platell J, Trott DJ, Zhanel G, Weissman SJ, Cookson BT, Fang FC, Limaye AP, Scholes D, Chattopadhyay S, Hooper DC, Sokurenko EV.

J Infect Dis. 2013 Mar 15;207(6):919-28. doi: 10.1093/infdis/jis933. Epub 2013 Jan 3.


Role of homologous recombination in adaptive diversification of extraintestinal Escherichia coli.

Paul S, Linardopoulou EV, Billig M, Tchesnokova V, Price LB, Johnson JR, Chattopadhyay S, Sokurenko EV.

J Bacteriol. 2013 Jan;195(2):231-42. doi: 10.1128/JB.01524-12. Epub 2012 Nov 2.


Convergent molecular evolution of genomic cores in Salmonella enterica and Escherichia coli.

Chattopadhyay S, Paul S, Kisiela DI, Linardopoulou EV, Sokurenko EV.

J Bacteriol. 2012 Sep;194(18):5002-11. doi: 10.1128/JB.00552-12. Epub 2012 Jul 13.


Footprint of positive selection in Treponema pallidum subsp. pallidum genome sequences suggests adaptive microevolution of the syphilis pathogen.

Giacani L, Chattopadhyay S, Centurion-Lara A, Jeffrey BM, Le HT, Molini BJ, Lukehart SA, Sokurenko EV, Rockey DD.

PLoS Negl Trop Dis. 2012;6(6):e1698. doi: 10.1371/journal.pntd.0001698. Epub 2012 Jun 12.


Evolution of Salmonella enterica virulence via point mutations in the fimbrial adhesin.

Kisiela DI, Chattopadhyay S, Libby SJ, Karlinsey JE, Fang FC, Tchesnokova V, Kramer JJ, Beskhlebnaya V, Samadpour M, Grzymajlo K, Ugorski M, Lankau EW, Mackie RI, Clegg S, Sokurenko EV.

PLoS Pathog. 2012;8(6):e1002733. doi: 10.1371/journal.ppat.1002733. Epub 2012 Jun 7.


Adaptive evolution of class 5 fimbrial genes in enterotoxigenic Escherichia coli and its functional consequences.

Chattopadhyay S, Tchesnokova V, McVeigh A, Kisiela DI, Dori K, Navarro A, Sokurenko EV, Savarino SJ.

J Biol Chem. 2012 Feb 24;287(9):6150-8. doi: 10.1074/jbc.M111.303735. Epub 2012 Jan 3.


The two-pathway model of the biological catch-bond as a limit of the allosteric model.

Pereverzev YV, Prezhdo E, Sokurenko EV.

Biophys J. 2011 Oct 19;101(8):2026-36. doi: 10.1016/j.bpj.2011.09.005.


Single nucleotide polypmorphisms of fimH associated with adherence and biofilm formation by serovars of Salmonella enterica.

Dwyer BE, Newton KL, Kisiela D, Sokurenko EV, Clegg S.

Microbiology. 2011 Nov;157(Pt 11):3162-71. doi: 10.1099/mic.0.051425-0. Epub 2011 Aug 18.


Allosteric catch bond properties of the FimH adhesin from Salmonella enterica serovar Typhimurium.

Kisiela DI, Kramer JJ, Tchesnokova V, Aprikian P, Yarov-Yarovoy V, Clegg S, Sokurenko EV.

J Biol Chem. 2011 Nov 4;286(44):38136-47. doi: 10.1074/jbc.M111.237511. Epub 2011 Jul 27.


The bacterial fimbrial tip acts as a mechanical force sensor.

Aprikian P, Interlandi G, Kidd BA, Le Trong I, Tchesnokova V, Yakovenko O, Whitfield MJ, Bullitt E, Stenkamp RE, Thomas WE, Sokurenko EV.

PLoS Biol. 2011 May;9(5):e1000617. doi: 10.1371/journal.pbio.1000617. Epub 2011 May 10.


Regulation of catch binding by allosteric transitions.

Pereverzev YV, Prezhdo OV, Sokurenko EV.

J Phys Chem B. 2010 Sep 16;114(36):11866-74. doi: 10.1021/jp1031459.


Donor strand exchange and conformational changes during E. coli fimbrial formation.

Le Trong I, Aprikian P, Kidd BA, Thomas WE, Sokurenko EV, Stenkamp RE.

J Struct Biol. 2010 Dec;172(3):380-8. doi: 10.1016/j.jsb.2010.06.002. Epub 2010 Jun 4.


Structural basis for mechanical force regulation of the adhesin FimH via finger trap-like beta sheet twisting.

Le Trong I, Aprikian P, Kidd BA, Forero-Shelton M, Tchesnokova V, Rajagopal P, Rodriguez V, Interlandi G, Klevit R, Vogel V, Stenkamp RE, Sokurenko EV, Thomas WE.

Cell. 2010 May 14;141(4):645-55. doi: 10.1016/j.cell.2010.03.038.

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