Endemic bacteriophages: A cautionary tale for evaluation of bacteriophage therapy and other interventions for infection control in animals

Virology Journal

Volumn 9, Issue , 2012, Pages

  Kropinski, Andrew M ^a,b   Lingohr, Erika J ^a   Moyles, Dianne M ^b   Ojha, Shivani ^a   Mazzocco, Amanda ^a   She, Yi Min ^c   Bach, Susan J ^d   Rozema, Erica A ^e,f,g   Stanford, Kim ^f   McAllister, Tim A ^g   Johnson, Roger P ^a  

^a PUBLIC HEALTH AGENCY OF CANADA   (Canada)

^b UNIVERSITY OF GUELPH   (Canada)

^c HEALTH CANADA   (Canada)

^d AGRICULTURE AND AGRI FOOD CANADA   (Canada)

^e UNIVERSITY OF ALBERTA   (Canada)

^f ALBERTA AGRICULTURE AND RURAL DEVELOPMENT   (Canada)

^g LETHBRIDGE RESEARCH CENTRE   (Canada)

Author keywords

Bioinformatics; Electron microscopy; Escherichia coli O157:H7, VTEC; Genome; Morphology; Phage ecology; Phage therapy; Proteome

Indexed keywords

ARTICLE; BACTERIAL INFECTION; BACTERIAL STRAIN; BACTERIOPHAGE; CATTLE; COLONY FORMING UNIT; ESCHERICHIA COLI; GENOME ANALYSIS; HOST RANGE; NONHUMAN; NUCLEOTIDE SEQUENCE; PROTEIN ANALYSIS; SHEEP; ULTRASTRUCTURE;

ANIMALS; BIOLOGICAL THERAPY; CAPSID; CATTLE; CATTLE DISEASES; COLIPHAGES; ESCHERICHIA COLI INFECTIONS; ESCHERICHIA COLI O157; GENOME, VIRAL; MICROSCOPY, ELECTRON; MOLECULAR SEQUENCE DATA; SEQUENCE ANALYSIS, DNA; SHEEP; SHEEP DISEASES; SIPHOVIRIDAE; VIRAL PROTEINS;

ANIMALIA; BACTERIA (MICROORGANISMS); BOS; ENTEROBACTERIA PHAGE LAMBDA; ESCHERICHIA COLI; MYOVIRIDAE; OVIS ARIES; SIPHOVIRIDAE;

EID: 84866174761     PISSN: None     EISSN: 1743422X     Source Type: Journal    
DOI: 10.1186/1743-422X-9-207     Document Type: Article

References (60)

1. Burden of acute gastrointestinal illness in Canada, 1999-2007: Interim summary of NSAGI activities. Thomas MK, Majowicz SE, Pollari F, Sockett PN, Canada Communicable Disease Report 2008 34 8 15 18800412
2. Estimated numbers of community cases of illness due to Salmonella, Campylobacter and verotoxigenic Escherichia coli: Pathogen-specific community rates. Thomas MK, Majowicz SE, Sockett PN, Fazil A, Pollari F, Doré K, Flint JA, Edge VL, Canadian Journal of Infectious Diseases & Medical Microbiology 2006 17 229 234 18159484 (Pubitemid 44519745)
3. Burden and cost of gastroenteritis in a Canadian community. Majowicz SE, McNab WB, Sockett P, Henson S, Doré K, Edge VL, Buffet MC, Fazil A, Read S, McEwwn S, Stacey D, Wilson JB, Journal of Food Protection 2006 69 651 659 16541699
4. Impact of food-borne disease from microbial pathogens, food types and pathogen-food combinations in Ontario. Ontario Ministry of Agriculture and Food and Rural Affairs (OMAFRA), OMAFRA Food Safety Science Unit Draft Report 4 2005 16
5. Bacteriophage control of foodborne bacteria.[erratum appears in J Food Prot. 2005 Jul; 68(7):1334]. Greer GG, Journal of Food Protection 2005 68 1102 1111 15895751
6. Bacteriophages as biocontrol agents in food. Hudson JA, Billington C, Carey-Smith G, Greening G, Journal of Food Protection 2005 68 426 437 15726992 (Pubitemid 40218154)
7. Phage for rapid detection and control of bacterial pathogens in food. Rees CD, Dodd CE, Advances in Applied Microbiology 2006 59 159 186 16829259 (Pubitemid 43996955)
8. Kutter E, Sulakvelidze A, Bacteriophages: Biology and Applications FL, USA: CRC Press, Boca Raton 2004
9. Campylobacter bacteriophages and bacteriophage therapy. Connerton PL, Timms AR, Connerton IF, Journal of Applied Microbiology 2011 111 255 265 10.1111/j.1365-2672.2011.05012.x 21447013
10. Salmonella in chicken: current and developing strategies to reduce contamination at farm level. Vandeplas S, Dubois DR, Beckers Y, Thonart P, Thewis A, Journal of Food Protection 2010 73 774 785 20377971
11. Bacteriophage biocontrol in animals and meat products. Atterbury RJ, Microbial Biotechnology 2009 2 601 612 10.1111/j.1751-7915.2009.00089.x 21255295
12. Bacteriophage for biocontrol of foodborne pathogens: calculations and considerations. Hagens S, Loessner MJ, Current Pharmaceutical Biotechnology 2010 11 58 68 10.2174/138920110790725429 20214608
13. Bacteriophages for prophylaxis and therapy in cattle, poultry and pigs. Johnson RP, Gyles CL, Huff WE, Ojha S, Huff GR, Rath NC, Donoghue AM, Animal Health Research Reviews 2008 9 201 215 10.1017/S1466252308001576 19102791
14. Food additives permitted for direct addition to food for human consumption; bacteriophage preparation. Department of Health and Human Services-Food and Drug Administration, The Federal Register 2006 71 47729 47732
15. Prevalence of Escherichia coli O157 and O157:H7-infecting bacteriophages in feedlot cattle feces. Oot RA, Raya RR, Callaway TR, Edrington TS, Kutter EM, Brabban AD, Letters in Applied Microbiology 2007 45 445 453 10.1111/j.1472-765X. 2007.02211.x 17897388 (Pubitemid 47493152)
16. Fecal prevalence of Escherichia coli O157, Salmonella, Listeria, and bacteriophage infecting E. coli O157:H7 in feedlot cattle in the Southern Plains region of the United States. Callaway TR, Edrington TS, Brabban AD, Keen JE, Anderson RC, Rossman ML, Engler MJ, Genovese KJ, Gwartney BL, Reagan JO, Poole TL, Harvey RB, Kutter EM, Nisbet DJ, Callaway TR, Edrington TS, Brabban AD, Keen JE, Anderson RC, Rossman ML, Engler MJ, Genovese KJ, Gwartney BL, Reagan JO, Poole TL, Harvey RB, Kutter EM, Nisbet DJ, Callaway TR, Edrington TS, Brabban AD, Keen JE, Anderson RC, Rossman ML, Engler MJ, Genovese KJ, Gwartney BL, Reagan JO, Poole TL, Harvey RB, Kutter EM, Nisbet DJ, Callaway TR, Edrington TS, Brabban AD, Keen JE, Anderson RC, Rossman ML, Engler MJ, Genovese KJ, Gwartney BL, Reagan JO, Poole TL, Harvey RB, Kutter EM, Nisbet DJ, Foodborne Pathogens & Disease 2006 3 234 244 10.1089/fpd.2006.3.234 23134566 (Pubitemid 44519322)
17. Bacteriophage isolated from feedlot cattle can reduce Escherichia coli O157:H7 populations in ruminant gastrointestinal tracts. Callaway TR, Edrington TS, Brabban AD, Anderson RC, Rossman ML, Engler MJ, Carr MA, Genovese KJ, Keen JE, Looper ML, Kutter EM, Nisbet DJ, Foodborne Pathog Dis 2008 5 183 191 10.1089/fpd.2007.0057 18407757 (Pubitemid 351545803)
18. Oral and rectal administration of bacteriophages for control of Escherichia coli O157:H7 in feedlot cattle. Rozema EA, Stephens TP, Bach SJ, Okine EK, Johnson RP, Stanford K, McAllister TA, Journal of Food Protection 2009 72 241 250 19350968
19. Enumeration of bacteriophages by double agar overlay plaque assay. Kropinski AM, Mazzocco A, Waddell TE, Lingohr E, Johnson RP, Methods in Molecular Biology 2009 501 69 76 10.1007/978-1-60327-164-6-7 19066811
20. Position paper: the creation of a rational scheme for the nomenclature of viruses of Bacteria and Archaea. Kropinski AM, Prangishvili D, Lavigne R, Environmental Microbiology 2009 11 2775 2777 10.1111/j.1462-2920.2009.01970.x 19519870
21. The T1-like bacteriophages. German GJ, Misra R, Kropinski AM, The Bacteriophages. Second edition New York, NY: Oxford University Press, Calendar RL, 2006 211 224
22. Blast 2 sequences-a new tool for comparing protein and nucleotide sequences. Tatusova TA, Madden TL, FEMS Microbiology Letters 1999 174 247 250 10.1111/j.1574-6968.1999.tb13575.x 10339815 (Pubitemid 29217013)
23. Low-usage codons and rare codons of Escherichia coli. Chen D, Texada DE, Gene Therapy and Molecular Biology 2006 10 1 12 (Pubitemid 351976172)
24. InBase: the Intein Database. Perler FB, Nucleic Acids Res 2002 30 383 384 10.1093/nar/30.1.383 11752343
25. Self-limiting nature of seasonal cholera epidemics: Role of host-mediated amplification of phage. Faruque SM, Islam MJ, Ahmad QS, Faruque AS, Sack DA, Nair GB, Mekalanos JJ, Proceedings of the National Academy of Sciences of the United States of America 2005 102 6119 6124 10.1073/pnas.0502069102 15829587 (Pubitemid 40594265)
26. Seasonal epidemics of cholera inversely correlate with the prevalence of environmental cholera phages. Faruque SM, Naser IB, Islam MJ, Faruque AS, Ghosh AN, Nair GB, Sack DA, Mekalanos JJ, Proceedings of the National Academy of Sciences of the United States of America 2005 102 1702 1707 10.1073/pnas. 0408992102 15653771 (Pubitemid 40209231)
27. Bacteriophages of plant pathogens. Okabe N, Goto M, Annual Review of Phytopathology 1963 1 397 418 10.1146/annurev.py.01.090163.002145
28. Prevalence and impact of bacteriophages on the presence of Escherichia coli O157:H7 in feedlot cattle and their environment. Niu YD, McAllister TA, Xu Y, Johnson RP, Stephens TP, Stanford K, Applied & Environmental Microbiology 2009 75 1271 1278 10.1128/AEM.02100-08 23139929
29. Characterization of four T1-like lytic bacteriophages that lyse Shigatoxin-producing Escherichia coli O157:H7. Niu YD, Stanford K, Ackermann H-W, McAllister TA, Canadian Journal of Microbiology 2012 58 923 927 10.1139/w2012-063 22691120
30. Naturally resident and exogenously applied T4-like and T5-like bacteriophages can reduce Escherichia coli O157:H7 levels in sheep guts. Raya RR, Oot RA, Moore-Maley B, Wieland S, Callaway TR, Kutter EM, Brabban AD, Bacteriophage 2011 1 15 24 10.4161/bact.1.1.14175 21687531
31. Family Siphoviridae. Family S, Hendrix RW, Casjens SR, Lavigne R, Virus Taxonomy: Classification and Nomenclature of Viruses-Ninth Report of the International Committee on Taxonomy of Viruses New York: Elsevier Academic Press, King AMQ, Adams MJ, Carstens EB, Lefkowitz EJ, 2011
32. The genome of the novel phage Rtp, with a rosette-like tail tip, is homologous to the genome of phage T1. Wietzorrek A, Schwarz H, Herrmann C, Braun V, Journal of Bacteriology 2006 188 1419 1436 10.1128/JB.188.4.1419-1436.2006 16452425 (Pubitemid 43228675)
33. Genomic analysis of bacteriophage ESP2949-1, which is virulent for Cronobacter sakazakii. Lee YD, Kim JY, Park JH, Chang H, Archives of Virology 2011 157 199 202 22042210
34. CoreGenes: a computational tool for identifying and cataloging "core" genes in a set of small genomes. Zafar N, Mazumder R, Seto D, BMC Bioinformatics 2002 3 12 10.1186/1471-2105-3-12 11972896 (Pubitemid 38751192)
35. Comparative analysis of the widespread and conserved PB1-like viruses infecting Pseudomonas aeruginosa. Ceyssens PJ, Miroshnikov K, Mattheus W, Krylov V, Robben J, Noben JP, Vanderschraeghe S, Sykilinda N, Kropinski AM, Volckaert G, Mesyanzhinov V, Lavigne R, Environmental Microbiology 2009 11 2874 2883 10.1111/j.1462-2920.2009.02030.x 19678828
36. Phenotypic and genotypic variations within a single bacteriophage species. Ceyssens PJ, Glonti T, Kropinski NM, Lavigne R, Chanishvili N, Kulakov L, Lashkhi N, Tediashvili M, Merabishvili M, Virology Journal 2011 8:134 134
37. The HHpred interactive server for protein homology detection and structure prediction. Soding J, Biegert A, Lupas AN, Nucleic Acids Research 2005 33 244 W248 10.1093/nar/gki408 15980461 (Pubitemid 44529917)
38. Fast and accurate automatic structure prediction with HHpred. Hildebrand A, Remmert M, Biegert A, Soding J, Proteins 2009 77 Suppl 9 128 32 19626712
39. Protein structure prediction on the Web: a case study using the Phyre server. Kelley LA, Sternberg MJ, Nature Protocols 2009 4 363 371 19247286
40. The Universal Protein Resource (UniProt). Bairoch A, Apweiler R, Wu CH, Barker WC, Boeckmann B, Ferro S, Gasteiger E, Huang H, Lopez R, Magrane M, Martin MJ, Natale DA, O'Donovan C, Redaschi N, Yeh LS, Nucleic Acids Research 2005 33 154 D159 15608167
41. Reorganizing the protein space at the Universal Protein Resource (UniProt). UniProt Consortium, Nucleic Acids Research 2012 40 (Database issue) 71 D75 22102590
42. The protein interaction map of bacteriophage lambda. Rajagopala SV, Casjens S, Uetz P, BMC Microbiology 2011 11:213 213
43. Complementation by restricted phage T1. Christensen JR, Journal of Virology 1974 14 1411 1418 4610185
44. Structural basis of murein peptide specificity of a gamma-D-glutamyl-l- diamino acid endopeptidase. Xu Q, Sudek S, McMullan D, Miller MD, Geierstanger B, Jones DH, Krishna SS, Spraggon G, Bursalay B, Abdubek P, Acosta C, Ambing E, Astakhova T, Axelrod HL, Carlton D, Caruthers J, Chiu HJ, Clayton T, Deller MC, Duan L, Elias Y, Elsliger MA, Feuerhelm J, Grzechnik SK, Hale J, Han GW, Haugen J, Jaroszewski L, Jin KK, Klock HE, Knuth MW, Kozbial P, Kumar A, Marciano D, Morse AT, Nigoghossian E, Okach L, Oommachen S, Paulsen J, Reyes R, Rife CL, Trout CV, van den Bedem H, Weekes D, White A, Wolf G, Zubieta C, Hodgson KO, Wooley J, Deacon AM, Godzik A, Lesley SA, Wilson IA, Structure 2009 17 303 313 10.1016/j.str.2008.12.008 19217401
45. Stability analysis of the bacteriophage fKMV lysin gp36C and its putative role during infection. Briers Y, Lavigne R, Plessers P, Hertveldt K, Hanssens I, Engelborghs Y, Volckaert G, Cellular & Molecular Life Sciences 2006 63 1899 1905 10.1007/s00018-006-6183-7 23139931
46. Tail-associated structural protein gp61 of Staphylococcus aureus phage fMR11 has bifunctional lytic activity. Rashel M, Uchiyama J, Takemura I, Hoshiba H, Ujihara T, Takatsuji H, Honke K, Matsuzaki S, FEMS Microbiology Letters 2008 284 9 16 10.1111/j.1574-6968.2008.01152.x 18462391 (Pubitemid 351776887)
47. The tail lysozyme complex of bacteriophage T4. Arisaka F, Kanamaru S, Leiman P, Rossmann MG, International Journal of Biochemistry & Cell Biology 2003 35 16 21 10.1016/S1357-2725(02)00098-5 20833257 (Pubitemid 35449169)
48. Rapid bacteriophage sedimentation in the presence of polyethylene glycol and its application to large-scale virus purification. Yamamoto KR, Alberts BM, Benzinger R, Lawhorne L, Treiber G, Virology 1970 40 734 744 10.1016/0042-6822(70)90218-7 4908735
49. Sambrook J, Russell DW, Molecular Cloning: A Laboratory Manual New York: Cold Spring Harbor Press 3 2001
50. Determination of bacteriophage genome size by pulsed-field gel electrophoresis. Lingohr E, Frost S, Johnson RP, Methods in Molecular Biology 2009 502 19 25 10.1007/978-1-60327-565-1-3 19082549
51. tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence. Lowe TM, Eddy SR, Nucleic Acids Research 1997 25 955 964 9023104 (Pubitemid 27298263)
52. ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences. Laslett D, Canback B, Nucleic Acids Research 2004 32 11 16 10.1093/nar/gkh152 14704338 (Pubitemid 38228599)
53. Pfam protein families database. Bateman A, Coin L, Durbin R, Finn RD, Hollich V, Griffiths-Jones S, Khanna A, Marshall M, Moxon S, Sonnhammer EL, Studholme DJ, Yeats C, Eddy SR, Nucleic Acids Research 2004 32 (Database issue) 138 D141 14681378
54. Sensen C. Menlo Park. Sonnhammer ELL, von Heijne G, Krogh A, Proceedings of the Sixth International Conference on Intelligent Systems for Molecular Biology CA: AAAI Press 1998 175 182
55. A combined transmembrane topology and signal peptide prediction method. Kall L, Krogh A, Sonnhammer EL, Journal of Molecular Biology 2004 338 1027 1036 10.1016/j.jmb.2004.03.016 15111065 (Pubitemid 38542831)
56. Prediction of transcription terminators in bacterial genomes. Ermolaeva MD, Khalak HG, White O, Smith HO, Salzberg SL, Journal of Molecular Biology 2000 301 27 33 10.1006/jmbi.2000.3836 10926490
57. PipMaker-a web server for aligning two genomic DNA sequences. Schwartz S, Zhang Z, Frazer KA, Smit A, Riemer C, Bouck J, Gibbs R, Hardison R, Miller W, Genome Research 2000 10 577 586 10.1101/gr.10.4.577 10779500 (Pubitemid 30259089)
58. Mauve: multiple alignment of conserved genomic sequence with rearrangements. Darling AC, Mau B, Blattner FR, Perna NT, Genome Research 2004 14 1394 1403 10.1101/gr.2289704 15231754 (Pubitemid 39029237)
59. Cleavage of structural proteins during the assembly of the head of bacteriophage T4. Laemmli UK, Nature 1970 227 680 685 10.1038/227680a0 5432063
60. The genome and proteome of the Kluyvera bacteriophage Kvp1-another member of the T7-like Autographivirinae. Lingohr EJ, Villegas A, She YM, Ceyssens PJ, Kropinski AM, Virology Journal 2008 5 122 10.1186/1743-422X-5-122 18937848