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Resistance to change: AMR gene dynamics on a commercial pig farm with high antimicrobial usage.

Pollock J, Muwonge A, Hutchings MR, Mainda G, Bronsvoort BM, Gally DL, Corbishley A.

Sci Rep. 2020 Feb 3;10(1):1708. doi: 10.1038/s41598-020-58659-3.


A guide to machine learning for bacterial host attribution using genome sequence data.

Lupolova N, Lycett SJ, Gally DL.

Microb Genom. 2019 Dec;5(12). doi: 10.1099/mgen.0.000317.


Shiga toxin sub-type 2a increases the efficiency of Escherichia coli O157 transmission between animals and restricts epithelial regeneration in bovine enteroids.

Fitzgerald SF, Beckett AE, Palarea-Albaladejo J, McAteer S, Shaaban S, Morgan J, Ahmad NI, Young R, Mabbott NA, Morrison L, Bono JL, Gally DL, McNeilly TN.

PLoS Pathog. 2019 Oct 3;15(10):e1008003. doi: 10.1371/journal.ppat.1008003. eCollection 2019 Oct.


Changes in the Ileal, but Not Fecal, Microbiome in Response to Increased Dietary Protein Level and Enterotoxigenic Escherichia coli Exposure in Pigs.

Pollock J, Hutchings MR, Hutchings KEK, Gally DL, Houdijk JGM.

Appl Environ Microbiol. 2019 Sep 17;85(19). pii: e01252-19. doi: 10.1128/AEM.01252-19. Print 2019 Oct 1.


Whole Genome Sequence Analysis Reveals Lower Diversity and Frequency of Acquired Antimicrobial Resistance (AMR) Genes in E. coli From Dairy Herds Compared With Human Isolates From the Same Region of Central Zambia.

Mainda G, Lupolova N, Sikakwa L, Richardson E, Bessell PR, Malama SK, Kwenda G, Stevens MP, Bronsvoort BMD, Muma JB, Gally DL.

Front Microbiol. 2019 May 31;10:1114. doi: 10.3389/fmicb.2019.01114. eCollection 2019.


Transposon Insertion Sequencing Elucidates Novel Gene Involvement in Susceptibility and Resistance to Phages T4 and T7 in Escherichia coli O157.

Cowley LA, Low AS, Pickard D, Boinett CJ, Dallman TJ, Day M, Perry N, Gally DL, Parkhill J, Jenkins C, Cain AK.

mBio. 2018 Jul 24;9(4). pii: e00705-18. doi: 10.1128/mBio.00705-18.


Analysis of temporal fecal microbiota dynamics in weaner pigs with and without exposure to enterotoxigenic Escherichia coli1,2.

Pollock J, Gally DL, Glendinning L, Tiwari R, Hutchings MR, Houdijk JGM.

J Anim Sci. 2018 Sep 7;96(9):3777-3790. doi: 10.1093/jas/sky260.


Erratum: Patchy promiscuity: machine learning applied to predict the host specificity of Salmonella enterica and Escherichia coli.

Lupolova N, Dallman TJ, Holden NJ, Gally DL.

Microb Genom. 2018 Jun;4(6). doi: 10.1099/mgen.0.000193. Epub 2018 Jun 6. No abstract available.


Ribosome maturation by the endoribonuclease YbeY stabilizes a type 3 secretion system transcript required for virulence of enterohemorrhagic Escherichia coli.

McAteer SP, Sy BM, Wong JL, Tollervey D, Gally DL, Tree JJ.

J Biol Chem. 2018 Jun 8;293(23):9006-9016. doi: 10.1074/jbc.RA117.000300. Epub 2018 Apr 20.


An RNA-dependent mechanism for transient expression of bacterial translocation filaments.

Wang D, McAteer SP, Wawszczyk AB, Russell CD, Tahoun A, Elmi A, Cockroft SL, Tollervey D, Granneman S, Tree JJ, Gally DL.

Nucleic Acids Res. 2018 Apr 20;46(7):3366-3381. doi: 10.1093/nar/gky096.


Host species adaptation of TLR5 signalling and flagellin recognition.

Tahoun A, Jensen K, Corripio-Miyar Y, McAteer S, Smith DGE, McNeilly TN, Gally DL, Glass EJ.

Sci Rep. 2017 Dec 15;7(1):17677. doi: 10.1038/s41598-017-17935-5.


Patchy promiscuity: machine learning applied to predict the host specificity of Salmonella enterica and Escherichia coli.

Lupolova N, Dallman TJ, Holden NJ, Gally DL.

Microb Genom. 2017 Oct 3;3(10):e000135. doi: 10.1099/mgen.0.000135. eCollection 2017 Oct. Erratum in: Microb Genom. 2018 Jun;4(6):.


Evolutionary Context of Non-Sorbitol-Fermenting Shiga Toxin-Producing Escherichia coli O55:H7.

Schutz K, Cowley LA, Shaaban S, Carroll A, McNamara E, Gally DL, Godbole G, Jenkins C, Dallman TJ.

Emerg Infect Dis. 2017 Dec;23(12):1966-1973. doi: 10.3201/eid2312.170628.


Convergence of plasmid architectures drives emergence of multi-drug resistance in a clonally diverse Escherichia coli population from a veterinary clinical care setting.

Wagner S, Lupolova N, Gally DL, Argyle SA.

Vet Microbiol. 2017 Nov;211:6-14. doi: 10.1016/j.vetmic.2017.09.016. Epub 2017 Sep 22.


British Escherichia coli O157 in Cattle Study (BECS): to determine the prevalence of E. coli O157 in herds with cattle destined for the food chain.

Henry MK, Tongue SC, Evans J, Webster C, McKENDRICK IJ, Morgan M, Willett A, Reeves A, Humphry RW, Gally DL, Gunn GJ, Chase-Topping ME.

Epidemiol Infect. 2017 Nov;145(15):3168-3179. doi: 10.1017/S0950268817002151. Epub 2017 Sep 19.


Short-term evolution of Shiga toxin-producing Escherichia coli O157:H7 between two food-borne outbreaks.

Cowley LA, Dallman TJ, Fitzgerald S, Irvine N, Rooney PJ, McAteer SP, Day M, Perry NT, Bono JL, Jenkins C, Gally DL.

Microb Genom. 2016 Sep 8;2(9):e000084. doi: 10.1099/mgen.0.000084. eCollection 2016 Sep.


Evolution of a zoonotic pathogen: investigating prophage diversity in enterohaemorrhagic Escherichia coli O157 by long-read sequencing.

Shaaban S, Cowley LA, McAteer SP, Jenkins C, Dallman TJ, Bono JL, Gally DL.

Microb Genom. 2016 Dec 12;2(12):e000096. doi: 10.1099/mgen.0.000096. eCollection 2016 Dec.


Microbe Profile: Escherichia coli O157 : H7 - notorious relative of the microbiologist's workhorse.

Gally DL, Stevens MP.

Microbiology. 2017 Jan;163(1):1-3. doi: 10.1099/mic.0.000387.


Identification and Characterization of Novel Compounds Blocking Shiga Toxin Expression in Escherichia coli O157:H7.

Huerta-Uribe A, Marjenberg ZR, Yamaguchi N, Fitzgerald S, Connolly JP, Carpena N, Uvell H, Douce G, Elofsson M, Byron O, Marquez R, Gally DL, Roe AJ.

Front Microbiol. 2016 Nov 30;7:1930. eCollection 2016.


Small RNA interactome of pathogenic E. coli revealed through crosslinking of RNase E.

Waters SA, McAteer SP, Kudla G, Pang I, Deshpande NP, Amos TG, Leong KW, Wilkins MR, Strugnell R, Gally DL, Tollervey D, Tree JJ.

EMBO J. 2017 Feb 1;36(3):374-387. doi: 10.15252/embj.201694639. Epub 2016 Nov 11.


Alternate thermoregulation and functional binding of Escherichia coli type 1 fimbriae in environmental and animal isolates.

Marshall J, Rossez Y, Mainda G, Gally DL, Daniell TJ, Holden NJ.

FEMS Microbiol Lett. 2016 Nov;363(22). pii: fnw251. Epub 2016 Nov 2.


Support vector machine applied to predict the zoonotic potential of E. coli O157 cattle isolates.

Lupolova N, Dallman TJ, Matthews L, Bono JL, Gally DL.

Proc Natl Acad Sci U S A. 2016 Oct 4;113(40):11312-11317. Epub 2016 Sep 19.


Identification of epitopes recognised by mucosal CD4(+) T-cell populations from cattle experimentally colonised with Escherichia coli O157:H7.

Corbishley A, Connelley TK, Wolfson EB, Ballingall K, Beckett AE, Gally DL, McNeilly TN.

Vet Res. 2016 Sep 2;47(1):90. doi: 10.1186/s13567-016-0374-5.


Phylogenomic approaches to determine the zoonotic potential of Shiga toxin-producing Escherichia coli (STEC) isolated from Zambian dairy cattle.

Mainda G, Lupolova N, Sikakwa L, Bessell PR, Muma JB, Hoyle DV, McAteer SP, Gibbs K, Williams NJ, Sheppard SK, La Ragione RM, Cordoni G, Argyle SA, Wagner S, Chase-Topping ME, Dallman TJ, Stevens MP, Bronsvoort BM, Gally DL.

Sci Rep. 2016 May 25;6:26589. doi: 10.1038/srep26589.


Correction: Elucidation of the RamA Regulon in Klebsiella pneumoniae Reveals a Role in LPS Regulation.

De Majumdar S, Yu J, Fookes M, McAteer SP, Llobet E, Spence SF, Monaghan A, Kissenpfennig A, Ingram RJ, Bengoechea J, Gally DL, Fanning S, Elborn JS, Schneiders T.

PLoS Pathog. 2016 May 11;12(5):e1005649. doi: 10.1371/journal.ppat.1005649. eCollection 2016 May.


Type III Secretion-Dependent Sensitivity of Escherichia coli O157 to Specific Ketolides.

Fernandez-Brando RJ, Yamaguchi N, Tahoun A, McAteer SP, Gillespie T, Wang D, Argyle SA, Palermo MS, Gally DL.

Antimicrob Agents Chemother. 2015 Nov 2;60(1):459-70. doi: 10.1128/AAC.02085-15. Print 2016 Jan.


Erratum: Prevalence and patterns of antimicrobial resistance among Escherichia coli isolated from Zambian dairy cattle across different production systems.

Mainda G, Bessell PR, Muma JB, McAteer SP, Chase-Topping ME, Gibbons J, Stevens MP, Gally DL, deC Bronsvoort BM.

Sci Rep. 2015 Sep 21;5:14162. doi: 10.1038/srep14162. No abstract available.


Applying phylogenomics to understand the emergence of Shiga-toxin-producing Escherichia coli O157:H7 strains causing severe human disease in the UK.

Dallman TJ, Ashton PM, Byrne L, Perry NT, Petrovska L, Ellis R, Allison L, Hanson M, Holmes A, Gunn GJ, Chase-Topping ME, Woolhouse MEJ, Grant KA, Gally DL, Wain J, Jenkins C.

Microb Genom. 2015 Sep 14;1(3):e000029. doi: 10.1099/mgen.0.000029. eCollection 2015 Sep.


Prevalence and patterns of antimicrobial resistance among Escherichia coli isolated from Zambian dairy cattle across different production systems.

Mainda G, Bessell PR, Muma JB, McAteer SP, Chase-Topping ME, Gibbons J, Stevens MP, Gally DL, deC Bronsvoort BM.

Sci Rep. 2015 Jul 27;5:12439. doi: 10.1038/srep12439. Erratum in: Sci Rep. 2015;5:14162. Bessell, Paul B [corrected to Bessell, Paul R].


Optimizing the Protection of Cattle against Escherichia coli O157:H7 Colonization through Immunization with Different Combinations of H7 Flagellin, Tir, Intimin-531 or EspA.

McNeilly TN, Mitchell MC, Corbishley A, Nath M, Simmonds H, McAteer SP, Mahajan A, Low JC, Smith DG, Huntley JF, Gally DL.

PLoS One. 2015 May 28;10(5):e0128391. doi: 10.1371/journal.pone.0128391. eCollection 2015.


Analysis of whole genome sequencing for the Escherichia coli O157:H7 typing phages.

Cowley LA, Beckett SJ, Chase-Topping M, Perry N, Dallman TJ, Gally DL, Jenkins C.

BMC Genomics. 2015 Apr 8;16:271. doi: 10.1186/s12864-015-1470-z.


Functional analysis of bovine TLR5 and association with IgA responses of cattle following systemic immunisation with H7 flagella.

Tahoun A, Jensen K, Corripio-Miyar Y, McAteer SP, Corbishley A, Mahajan A, Brown H, Frew D, Aumeunier A, Smith DG, McNeilly TN, Glass EJ, Gally DL.

Vet Res. 2015 Feb 19;46:9. doi: 10.1186/s13567-014-0135-2.


Elucidation of the RamA regulon in Klebsiella pneumoniae reveals a role in LPS regulation.

De Majumdar S, Yu J, Fookes M, McAteer SP, Llobet E, Finn S, Spence S, Monahan A, Monaghan A, Kissenpfennig A, Ingram RJ, Bengoechea J, Gally DL, Fanning S, Elborn JS, Schneiders T.

PLoS Pathog. 2015 Jan 29;11(1):e1004627. doi: 10.1371/journal.ppat.1004627. eCollection 2015 Jan. Erratum in: PLoS Pathog. 2015 Mar;11(3):e1004766. Monaghan, Avril [corrected to Monahan, Avril]. PLoS Pathog. 2016 May;12(5):e1005649.


Bacterial flagella: twist and stick, or dodge across the kingdoms.

Rossez Y, Wolfson EB, Holmes A, Gally DL, Holden NJ.

PLoS Pathog. 2015 Jan 15;11(1):e1004483. doi: 10.1371/journal.ppat.1004483. eCollection 2015 Jan. Review.


Strain-dependent cellular immune responses in cattle following Escherichia coli O157:H7 colonization.

Corbishley A, Ahmad NI, Hughes K, Hutchings MR, McAteer SP, Connelley TK, Brown H, Gally DL, McNeilly TN.

Infect Immun. 2014 Dec;82(12):5117-31. doi: 10.1128/IAI.02462-14. Epub 2014 Sep 29.


Identification of bacteriophage-encoded anti-sRNAs in pathogenic Escherichia coli.

Tree JJ, Granneman S, McAteer SP, Tollervey D, Gally DL.

Mol Cell. 2014 Jul 17;55(2):199-213. doi: 10.1016/j.molcel.2014.05.006. Epub 2014 Jun 5.


The metabolic enzyme AdhE controls the virulence of Escherichia coli O157:H7.

Beckham KS, Connolly JP, Ritchie JM, Wang D, Gawthorne JA, Tahoun A, Gally DL, Burgess K, Burchmore RJ, Smith BO, Beatson SA, Byron O, Wolfe AJ, Douce GR, Roe AJ.

Mol Microbiol. 2014 Jul;93(1):199-211. doi: 10.1111/mmi.12651. Epub 2014 Jun 9.


Multidrug-resistant Escherichia coli from canine urinary tract infections tend to have commensal phylotypes, lower prevalence of virulence determinants and ampC-replicons.

Wagner S, Gally DL, Argyle SA.

Vet Microbiol. 2014 Mar 14;169(3-4):171-8. doi: 10.1016/j.vetmic.2014.01.003. Epub 2014 Jan 13.


Bacteriophages as pathogens and immune modulators?

Lengeling A, Mahajan A, Gally DL.

mBio. 2013 Nov 12;4(6):e00868-13. doi: 10.1128/mBio.00868-13.


Flagella interact with ionic plant lipids to mediate adherence of pathogenic Escherichia coli to fresh produce plants.

Rossez Y, Holmes A, Wolfson EB, Gally DL, Mahajan A, Pedersen HL, Willats WG, Toth IK, Holden NJ.

Environ Microbiol. 2014 Jul;16(7):2181-95. doi: 10.1111/1462-2920.12315. Epub 2013 Nov 12.


Predicting the public health benefit of vaccinating cattle against Escherichia coli O157.

Matthews L, Reeve R, Gally DL, Low JC, Woolhouse ME, McAteer SP, Locking ME, Chase-Topping ME, Haydon DT, Allison LJ, Hanson MF, Gunn GJ, Reid SW.

Proc Natl Acad Sci U S A. 2013 Oct 1;110(40):16265-70. doi: 10.1073/pnas.1304978110. Epub 2013 Sep 16.


Salmonella transforms follicle-associated epithelial cells into M cells to promote intestinal invasion.

Tahoun A, Mahajan S, Paxton E, Malterer G, Donaldson DS, Wang D, Tan A, Gillespie TL, O'Shea M, Roe AJ, Shaw DJ, Gally DL, Lengeling A, Mabbott NA, Haas J, Mahajan A.

Cell Host Microbe. 2012 Nov 15;12(5):645-56. doi: 10.1016/j.chom.2012.10.009.


Lysogeny with Shiga toxin 2-encoding bacteriophages represses type III secretion in enterohemorrhagic Escherichia coli.

Xu X, McAteer SP, Tree JJ, Shaw DJ, Wolfson EB, Beatson SA, Roe AJ, Allison LJ, Chase-Topping ME, Mahajan A, Tozzoli R, Woolhouse ME, Morabito S, Gally DL.

PLoS Pathog. 2012;8(5):e1002672. doi: 10.1371/journal.ppat.1002672. Epub 2012 May 17.


Pathogenic potential to humans of bovine Escherichia coli O26, Scotland.

Chase-Topping ME, Rosser T, Allison LJ, Courcier E, Evans J, McKendrick IJ, Pearce MC, Handel I, Caprioli A, Karch H, Hanson MF, Pollock KG, Locking ME, Woolhouse ME, Matthews L, Low JC, Gally DL.

Emerg Infect Dis. 2012 Mar;18(3):439-48. doi: 10.3201/eid1803.111236.


Identification of a novel prophage regulator in Escherichia coli controlling the expression of type III secretion.

Flockhart AF, Tree JJ, Xu X, Karpiyevich M, McAteer SP, Rosenblum R, Shaw DJ, Low CJ, Best A, Gannon V, Laing C, Murphy KC, Leong JM, Schneiders T, La Ragione R, Gally DL.

Mol Microbiol. 2012 Jan;83(1):208-23. doi: 10.1111/j.1365-2958.2011.07927.x. Epub 2011 Dec 9.


Comparative analysis of EspF variants in inhibition of Escherichia coli phagocytosis by macrophages and inhibition of E. coli translocation through human- and bovine-derived M cells.

Tahoun A, Siszler G, Spears K, McAteer S, Tree J, Paxton E, Gillespie TL, Martinez-Argudo I, Jepson MA, Shaw DJ, Koegl M, Haas J, Gally DL, Mahajan A.

Infect Immun. 2011 Nov;79(11):4716-29. doi: 10.1128/IAI.00023-11. Epub 2011 Aug 29.


Insights into mucosal innate responses to Escherichia coli O157 : H7 colonization of cattle by mathematical modelling of excretion dynamics.

Tildesley MJ, Gally DL, McNeilly TN, Low JC, Mahajan A, Savill NJ.

J R Soc Interface. 2012 Mar 7;9(68):518-27. doi: 10.1098/rsif.2011.0293. Epub 2011 Aug 17.


Identification of bacterial target proteins for the salicylidene acylhydrazide class of virulence-blocking compounds.

Wang D, Zetterström CE, Gabrielsen M, Beckham KS, Tree JJ, Macdonald SE, Byron O, Mitchell TJ, Gally DL, Herzyk P, Mahajan A, Uvell H, Burchmore R, Smith BO, Elofsson M, Roe AJ.

J Biol Chem. 2011 Aug 26;286(34):29922-31. doi: 10.1074/jbc.M111.233858. Epub 2011 Jul 1.


Transcriptional regulators of the GAD acid stress island are carried by effector protein-encoding prophages and indirectly control type III secretion in enterohemorrhagic Escherichia coli O157:H7.

Tree JJ, Roe AJ, Flockhart A, McAteer SP, Xu X, Shaw D, Mahajan A, Beatson SA, Best A, Lotz S, Woodward MJ, La Ragione R, Murphy KC, Leong JM, Gally DL.

Mol Microbiol. 2011 Jun;80(5):1349-65. doi: 10.1111/j.1365-2958.2011.07650.x. Epub 2011 Apr 15.

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