Identification and prevalence of in vivo-induced genes in enterohaemorrhagic Escherichia coli

References

• Schmidt MA. LEEways: tales of EPEC, ATEC and EHEC. Cell Microbiol. 2010;12(11):1544–1552.
   PubMed Web of Science ®Google Scholar
• Hartland EL, Batchelor M, Delahay RM, et al. Binding of intimin from enteropathogenic Escherichia coli to Tir and to host cells. Mol Microbiol. 1999;32(1):151–158.
   PubMed Web of Science ®Google Scholar
• Ooka T, Seto K, Kawano K, et al. Clinical significance of Escherichia albertii. Emerg Infect Dis. 2012;18(3):488–492.
   PubMed Web of Science ®Google Scholar
• Phillips AD, Frankel G. Intimin-mediated tissue specificity in enteropathogenic Escherichia coli interaction with human intestinal organ cultures. J Infect Dis. 2000;181(4):1496–1500.
   PubMed Web of Science ®Google Scholar
• Zoja C, Buelli S, Morigi M. Shiga toxin-associated hemolytic uremic syndrome: pathophysiology of endothelial dysfunction. Pediatr Nephrol. 2010;25(11):2231–2240.
   PubMed Web of Science ®Google Scholar
• Melton-Celsa AR. Shiga Toxin (Stx) classification, structure, and function. Microbiol Spectr. 2014;2(4):EHEC-0024–2013.
   Google Scholar
• Siegler RL, Obrig TG, Pysher TJ, et al. Response to Shiga toxin 1 and 2 in a baboon model of hemolytic uremic syndrome. Pediatr Nephrol. 2003;18(2):92–96.
   PubMed Web of Science ®Google Scholar
• Bielaszewska M, Friedrich AW, Aldick T, et al. Shiga toxin activatable by intestinal mucus in Escherichia coli isolated from humans: predictor for a severe clinical outcome. Clin Infect Dis. 2006;43(9):1160–1167.
   PubMed Web of Science ®Google Scholar
• Karmali MA, Mascarenhas M, Shen S, et al. Association of genomic O island 122 of Escherichia coli EDL 933 with verocytotoxin-producing Escherichia coli seropathotypes that are linked to epidemic and/or serious disease. J Clin Microbiol. 2003;41(11):4930–4940.
   PubMed Web of Science ®Google Scholar
• Boerlin P, McEwen SA, Boerlin-Petzold F, et al. Associations between virulence factors of Shiga toxin-producing Escherichia coli and disease in humans. J Clin Microbiol. 1999;37(3):497–503.
   PubMed Web of Science ®Google Scholar
• Messens W, Bolton D, Frankel G, et al. Defining pathogenic verocytotoxin-producing Escherichia coli (VTEC) from cases of human infection in the European Union, 2007-2010. Epidemiol Infect. 2015;143(8):1652–1661.
   PubMed Web of Science ®Google Scholar
• McWilliams BD, Torres AG. Enterohemorrhagic Escherichia coli adhesins. Microbiol Spectr. 2014;2(3).
   Google Scholar
• Lim JY, Yoon J, Hovde CJ. A brief overview of Escherichia coli O157: h7and its plasmid O157. J Microbiol Biotechnol. 2010;20(1):5–14.
   PubMed Web of Science ®Google Scholar
• Perna NT, Plunkett G 3rd, Burland V, et al. Genome sequence of enterohaemorrhagic Escherichia coli O157:H7. Nature. 2001;409(6819):529–533.
   PubMed Web of Science ®Google Scholar
• Hayashi T, Makino K, Ohnishi M, et al. Complete genome sequence of enterohemorrhagic Escherichia coli O157: H7and genomic comparison with a laboratory strain K-12. DNA Res. 2001;8(1):11–22.
   PubMed Web of Science ®Google Scholar
• Datsenko KA, Wanner BL. One-step inactivation of chromosomal genes in Escherichia coli K-12 using PCR products. Proc Natl Acad Sci U S A. 2000;97(12):6640–6645.
   PubMed Web of Science ®Google Scholar
• Bertin Y, Chaucheyras-Durand F, Robbe-Masselot C, et al. Carbohydrate utilization by enterohaemorrhagic Escherichia coli O157: H7in bovine intestinal content. Environ Microbiol. 2013;15(2):610–622.
   PubMed Web of Science ®Google Scholar
• Osorio CG, Crawford JA, Michalski J, et al. Second-generation recombination-based in vivo expression technology for large-scale screening for Vibrio cholerae genes induced during infection of the mouse small intestine. Infect Immun. 2005;73(2):972–980.
   PubMed Web of Science ®Google Scholar
• Crepin S, Harel J, Dozois CM. Chromosomal complementation using Tn7 transposon vectors in Enterobacteriaceae. Appl Environ Microbiol. 2012;78(17):6001–6008.
   PubMed Web of Science ®Google Scholar
• Karlyshev AV, Pallen MJ, Wren BW. Single-primer PCR procedure for rapid identification of transposon insertion sites. Biotechniques. 2000;28(6):1078,1080, 1082.
   PubMed Web of Science ®Google Scholar
• Criscuolo A, Brisse S. AlienTrimmer removes adapter oligonucleotides with high sensitivity in short-insert paired-end reads. Commentary on Turner (2014) Assessment of insert sizes and adapter content in FASTQ data from NexteraXT libraries. Front Genet. 2014;5:130.
   PubMed Web of Science ®Google Scholar
• Bankevich A, Nurk S, Antipov D, et al. SPAdes: a new genome assembly algorithm and its applications to single-cell sequencing. J Comput Biol. 2012;19(5):455–477.
   PubMed Web of Science ®Google Scholar
• Beghain J, Bridier-Nahmias A, Le Nagard H, et al. ClermonTyping: an easy-to-use and accurate in silico method for Escherichia genus strain phylotyping. Microb Genom. 2018;4(7).
   PubMed Web of Science ®Google Scholar
• Treangen TJ, Ondov BD, Koren S, et al. The Harvest suite for rapid core-genome alignment and visualization of thousands of intraspecific microbial genomes. Genome Biol. 2014;15(11):524.
   PubMed Web of Science ®Google Scholar
• Tamura K, Stecher G, Peterson D, et al. MEGA6: molecular Evolutionary Genetics Analysis version 6.0. Mol Biol Evol. 2013;30(12):2725–2729.
   PubMed Web of Science ®Google Scholar
• Letunic I, Bork P. Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees. Nucleic Acids Res. 2016;44(W1):W242–245.
   PubMed Web of Science ®Google Scholar
• Jones SA, Jorgensen M, Chowdhury FZ, et al. Glycogen and maltose utilization by Escherichia coli O157: h7in the mouse intestine. Infect Immun. 2008;76(6):2531–2540.
   PubMed Web of Science ®Google Scholar
• Torres AG, Payne SM. Haem iron-transport system in enterohaemorrhagic Escherichia coli O157:H7. Mol Microbiol. 1997;23(4):825–833.
   PubMed Web of Science ®Google Scholar
• Tatusov RL, Koonin EV, Lipman DJ. A genomic perspective on protein families. Science. 1997;278(5338):631–637.
   PubMed Web of Science ®Google Scholar
• Galperin MY, Makarova KS, Wolf YI, et al. Expanded microbial genome coverage and improved protein family annotation in the COG database. Nucleic Acids Res. 2015;43(Database issue):D261–269.
   PubMed Web of Science ®Google Scholar
• The European Union summary report on trends and sources of zoonoses, zoonotic agents and food-borne outbreaks in 2016. Efsa J. 2017;15(12):e05077.
   PubMed Web of Science ®Google Scholar
• Soysal N, Mariani-Kurkdjian P, Smail Y, et al. Enterohemorrhagic Escherichia coli hybrid pathotype O80: H2as a new therapeutic challenge. Emerg Infect Dis. 2016;22(9):1604–1612.
   PubMed Web of Science ®Google Scholar
• De Rauw K, Thiry D, Caljon B, et al. Characteristics of Shiga toxin producing- and enteropathogenic Escherichia coli of the emerging serotype O80: H2isolated from humans and diarrhoeic calves in Belgium. Clin Microbiol Infect. 2018;25(1):111.e5–111.e8.
   PubMed Web of Science ®Google Scholar
• Fabich AJ, Jones SA, Chowdhury FZ, et al. Comparison of carbon nutrition for pathogenic and commensal Escherichia coli strains in the mouse intestine. Infect Immun. 2008;76(3):1143–1152.
   PubMed Web of Science ®Google Scholar
• John M, Kudva IT, Griffin RW, et al. Use of in vivo-induced antigen technology for identification of Escherichia coli O157: H7proteins expressed during human infection. Infect Immun. 2005;73(5):2665–2679.
   PubMed Web of Science ®Google Scholar
• Le Bihan G, Jubelin G, Garneau P, et al. Transcriptome analysis of Escherichia coli O157: H7grown in vitro in the sterile-filtrated cecal content of human gut microbiota associated rats reveals an adaptive expression of metabolic and virulence genes. Microbes Infect. 2015;17(1):23–33.
   PubMed Web of Science ®Google Scholar
• Kerangart S, Cournoyer B, Loukiadis E. C-source metabolic profilings of foodborne Shiga-toxin producing E. coli match serogroup differentiations and highlight functional adaptations. Int J Food Microbiol. 2018;266:324–336.
   PubMed Web of Science ®Google Scholar
• Ferrandez A, Garcia JL, Diaz E. Genetic characterization and expression in heterologous hosts of the 3-(3-hydroxyphenyl)propionate catabolic pathway of Escherichia coli K-12. J Bacteriol. 1997;179(8):2573–2581.
   PubMed Web of Science ®Google Scholar
• Torres B, Porras G, Garcia JL, et al. Regulation of the mhp cluster responsible for 3-(3-hydroxyphenyl)propionic acid degradation in Escherichia coli. J Biol Chem. 2003;278(30):27575–27585.
   PubMed Web of Science ®Google Scholar
• Venter H, Mowla R, Ohene-Agyei T, et al. RND-type drug e ffl ux pumps from Gram-negative bacteria: molecular mechanism and inhibition. Front Microbiol. 2015;6:377.
   Web of Science ®Google Scholar
• Zhang Y, Xiao M, Horiyama T, et al. The multidrug efflux pump MdtEF protects against nitrosative damage during the anaerobic respiration in Escherichia coli. J Biol Chem. 2011;286(30):26576–26584.
   PubMed Web of Science ®Google Scholar
• Justino MC, Almeida CC, Goncalves VL, et al. Escherichia coli YtfE is a di-iron protein with an important function in assembly of iron-sulphur clusters. FEMS Microbiol Lett. 2006;257(2):278–284.
   PubMed Web of Science ®Google Scholar
• Hutchings MI, Mandhana N, Spiro S. The NorR protein of Escherichia coli activates expression of the flavorubredoxin gene norV in response to reactive nitrogen species. J Bacteriol. 2002;184(16):4640–4643.
   PubMed Web of Science ®Google Scholar
• Shimizu T, Tsutsuki H, Matsumoto A, et al. The nitric oxide reductase of enterohaemorrhagic Escherichia coli plays an important role for the survival within macrophages. Mol Microbiol. 2012;85(3):492–512.
   PubMed Web of Science ®Google Scholar
• Shimizu T, Hirai S, Yokoyama E, et al. An evolutionary analysis of nitric oxide reductase gene norV in enterohemorrhagic Escherichia coli O157. Infect Genet Evol. 2015;33:176–181.
   PubMed Web of Science ®Google Scholar
• Branchu P, Matrat S, Vareille M, et al. NsrR, GadE, and GadX interplay in repressing expression of the Escherichia coli O157: H7LEE pathogenicity island in response to nitric oxide. PLoS Pathog. 2014;10(1):e1003874.
   PubMed Web of Science ®Google Scholar
• Vareille M, de Sablet T, Hindre T, et al. Nitric oxide inhibits Shiga-toxin synthesis by enterohemorrhagic Escherichia coli. Proc Natl Acad Sci U S A. 2007;104(24):10199–10204.
   PubMed Web of Science ®Google Scholar
• Ichimura K, Shimizu T, Matsumoto A, et al. Nitric oxide-enhanced Shiga toxin production was regulated by Fur and RecA in enterohemorrhagic Escherichia coli O157. MicrobiologyOpen. 2017;6(4).
   PubMed Web of Science ®Google Scholar
• Camilli A, Mekalanos JJ. Use of recombinase gene fusions to identify Vibrio cholerae genes induced during infection. Mol Microbiol. 1995;18(4):671–683.
   PubMed Web of Science ®Google Scholar
• Fernandez De Henestrosa AR, Ogi T, Aoyagi S, et al. Identification of additional genes belonging to the LexA regulon in Escherichia coli. Mol Microbiol. 2000;35(6):1560–1572.
   PubMed Web of Science ®Google Scholar
• Kimmitt PT, Harwood CR, Barer MR. Toxin gene expression by shiga toxin-producing Escherichia coli: the role of antibiotics and the bacterial SOS response. Emerg Infect Dis. 2000;6(5):458–465.
   PubMed Web of Science ®Google Scholar
• Bogdan C. Nitric oxide synthase in innate and adaptive immunity: an update. Trends Immunol. 2015;36(3):161–178.
   PubMed Web of Science ®Google Scholar
• Rodionov DA, Vitreschak AG, Mironov AA, et al. Comparative genomics of the vitamin B12 metabolism and regulation in prokaryotes. J Biol Chem. 2003;278(42):41148–41159.
   PubMed Web of Science ®Google Scholar
• Motomura K, Hirota R, Ohnaka N, et al. Overproduction of YjbB reduces the level of polyphosphate in Escherichia coli: a hypothetical role of YjbB in phosphate export and polyphosphate accumulation. FEMS Microbiol Lett. 2011;320(1):25–32.
   PubMed Web of Science ®Google Scholar
• Chekabab SM, Jubelin G, Dozois CM, et al. PhoB activates Escherichia coli O157: H7virulence factors in response to inorganic phosphate limitation. PLoS One. 2014;9(4):e94285.
   PubMed Web of Science ®Google Scholar
• Cordonnier C, Le Bihan G, Emond-Rheault JG, et al. Vitamin B12 uptake by the gut commensal bacteria Bacteroides thetaiotaomicron limits the production of Shiga Toxin by enterohemorrhagic Escherichia coli. Toxins (Basel). 2016;8(1).
   PubMed Web of Science ®Google Scholar
• Hall BG, Xu L. Nucleotide sequence, function, activation, and evolution of the cryptic asc operon of Escherichia coli K12. Mol Biol Evol. 1992;9(4):688–706.
   PubMed Web of Science ®Google Scholar
• Ishida Y, Kori A, Ishihama A. Participation of regulator AscG of the beta-glucoside utilization operon in regulation of the propionate catabolism operon. J Bacteriol. 2009;191(19):6136–6144.
   PubMed Web of Science ®Google Scholar
• Belitsky BR, Sonenshein AL. GabR, a member of a novel protein family, regulates the utilization of gamma-aminobutyrate in Bacillus subtilis. Mol Microbiol. 2002;45(2):569–583.
   PubMed Web of Science ®Google Scholar
• Marches O, Wiles S, Dziva F, et al. Characterization of two non-locus of enterocyte effacement-encoded type III-translocated effectors, NleC and NleD, in attaching and effacing pathogens. Infect Immun. 2005;73(12):8411–8417.
   PubMed Web of Science ®Google Scholar
• Holmes A, Lindestam Arlehamn CS, Wang D, et al. Expression and regulation of the Escherichia coli O157: H7effector proteins NleH1 and NleH2. PLoS One. 2012;7(3):e33408.
   PubMed Web of Science ®Google Scholar
• Gao X, Wang X, Pham TH, et al. NleB, a bacterial effector with glycosyltransferase activity, targets GAPDH function to inhibit NF-kappaB activation. Cell Host Microbe. 2013;13(1):87–99.
   PubMed Web of Science ®Google Scholar
• Leo JC, Oberhettinger P, Schutz M, et al. The inverse autotransporter family: intimin, invasin and related proteins. Int J Med Microbiol. 2015;305(2):276–282.
   PubMed Web of Science ®Google Scholar
• Mortier-Barriere I, Velten M, Dupaigne P, et al. A key presynaptic role in transformation for a widespread bacterial protein: DprA conveys incoming ssDNA to RecA. Cell. 2007;130(5):824–836.
   PubMed Web of Science ®Google Scholar