image © Phage et al. Bacteriophage Ecology Group (BEG) News
Dedicated to the ecology and evolutionary biology of the parasites of unicellular organisms (UOPs)
© Stephen T. Abedon (editor)
contents | BEG News (012) | top of page
© Phage et al. April 1, 2002 issue (volume 12)

At this site you will find . . .

1. editorial this page
2. new BEG members this page
3. new links this page
4. new features this page
5. meetings this page
6. jobs this page
7. submissions (a.k.a., stuff to read) this page
8. letters this page
9. phage image this page
10. new publications (abstracts) this page
11. acknowledgements this page
12. Bacteriophage Ecology Group elsewhere
13. comments mail to

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Editorial

Editorials should be written on subjects relevant to The Bacteriophage Ecology Group as an organization, to BEG News (either the concept or a given issue of BEG News), or the science of Bacteriophage Ecology. While my assumption is that I will be writing the bulk of these editorials, I wish to encourage as many people as possible to seek to relieve me of this duty, as often as possible. Additionally, I welcome suggestions of topics that may be addressed. Please address all correspondences to abedon.1@osu.edu or to "Editorials," Bacteriophage Ecology Group News, care of Stephen T. Abedon, Department of Microbiology, The Ohio State University, 1680 University Dr., Mansfield, Ohio 44906. Please send all submissions as Microsoft Word documents, if possible (I'll let you know if I have trouble converting other document formats), and in English.

Shipping Phages

by Hans-Wolfgang Ackermann

It used to be that common, minor pathogens, such as Staphylococcus aureus and Pseudomonas aeruginosa, could be exchanged between scientists, by mail, without fuss, loss of time, permits, or shipment via expensive courier services. No longer. Today the exchange of these materials has become more and more difficult, and this indirectly affects phage research.

I became alerted to the problem because I am the curator of the Felix d'Herelle Reference Center for Bacterial Viruses (acronym HER), a small collection but, nevertheless, perhaps the largest collection of bacteriophages in the world. The collection houses some 450 bacteriophages and about as many bacterial hosts. The hosts include many Group 2 and a few Group 3 pathogens. Importation permits are not required for phages in the U.S. However, anybody who wants to acquire and propagate phages with hosts of risk groups 2 and 3 automatically needs a permit for the hosts from the CDC in Atlanta.

Transportation regulations have, in fact, sprung up everywhere on both national and international levels. These regulations, however, have nothing to do with legitimate concerns with germ warfare and the recent anthrax alert as they came into being in the 1980s. I believe, instead, that a monster has been created that seriously hampers research. The problem is not packaging regulations and not even paperwork or costs. I readily go along with restrictions on the circulation of Group 3 or 4 pathogens. The problem is that almost all microorganisms are classified as Group 2 and thus fall automatically under IATA (International Air Transport Association) Dangerous Goods Regulations and associated restrictions on the national level. I contend that much harm has been done to microbial research, that more is to come, and that these regulations are going to make our lives miserable.

The trend is to tighten regulations. In Canada, the Bureau for Laboratory Safety of the Health Ministry in Ottawa has produced extremely comprehensive lists of microorganisms that include Escherichia coli, Mycobacerium smegmatis, all members of the genus Lactococcus, all members of the genus Bifidobacterium and, on the fungal side, all members the genus Saccharomyces. Regulations of this type suggest that the Bureau must consider that the microorganisms producing cheese, bread, beer, and wine are dangerous. I surmise that few or no medical people have been involved in the relevant decisions. For example, of the approximately 12 members of the Bureau, none, except perhaps one person working in a medical school, seems to be a medical doctor. To my knowledge, microbiological societies have had little influence on regulations and the present situation has developed with minimal consultation of microbiologists. I am not impressed by the argument that some members of the normal flora are potentially and occasionally pathogenic. This relates to the current germ craze and has no rational basis.

Regulations and restrictions such as these have spawned a host of companies producing forms and packing material. Shipping companies and customs offices, at least in Canada, are required to control every shipment with a checklist of 50 items. Employees are literally going after every colon (with no pun intended) and, indeed, it happened to me that a shipment was nearly refused for a missing colon. Below are excerpts from messages that I received from New Zealand and Belgium, respectively:
As a Ph.D student, several years ago, I regularly sent and received all manner of (innocuous) plasmids and bacterial strains through the post in eppendorf tubes without any permission from anyone. Now I can only import specifically allowed material without sending a book chapter of irrelevant material and a wad of money to a committee of people who barely passed high school to decide whether or not importation is ok. Much of the problem in New Zealand is due to an over reaction by politicians and the green movement, a few years ago, to the "discovery" that scientists in New Zealand were doing recombinant DNA work.

It took the Belgian officials months to come to the following conclusion: "Hereby the Service of Biosafety and Biotechnology (SBB) confirms on the basis of the obtained information that phages D3, D3112, phiKZ, 7, 21, 68 (host: Pseudomonas aeruginosa), T4, T7, lambda (host: Escherichia coli) are neither genetically modified nor pathogens and are therefore not submitted to the Belgian regional decrees, in this case the decree of the Flemish region of 1 june 1995, on the contained use of genetically modified organisms and/or pathogens. Also the above mentioned phages cannot be considered as belonging to class 6.2 (infectious substances) or 9 (Miscellaneous Dangerous Substances and Articles, including genetically modified micro-organisms which are not dangerous for animals or humans, but which could modify animals, plants, microbiological substances and ecosystems in a way that does not occur naturally, and genetically modified organisms which are known or suspected to be dangerous to the environment), according to the UN recommendations on the transport of dangerous goods. Hence importation of these phages is not submitted to the conditions imposed by these regulations."
Can something be done? Perhaps if ASM makes representations at the CDC to exempt Group 2 microorganisms from import permits and Dangerous Goods declarations (not of the use of safe packaging material). If this cannot be done, then ASM should press for exemption of microorganisms of the normal flora and the environment, and of useful microbes. In turn, CDC must influence IATA to relax regulations on Group 2 pathogens. I would like to learn of your own experiences with respect to shipping phages, along with your suggestions.

Editorial Archive

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New BEG Members

The BEG members page can be found at www.phage.org/beg_members.htm. There are two ways of "joining" BEG. One, the "traditional" way, is to have your name listed on the web page and on the list server. The second, the "non-traditional" way, is to have your name only listed on the list server. The latter I refer to as "non-members" on that list. Members, e.g., individuals listed on the BEG members list page, should be limited to individuals who are actively involved in science (research, instruction, outreach, industry) and who can serve as a phage ecology resource to interested individuals. If you have an interest in phage ecology but no real expertise in the area, then you should join as a non-member. To join as a member, please contact BEG using the following link: abedon.1@osu.edu. Include:
  • your name
  • your e-mail address
  • your snail-mail address
  • the URL of your home page (if you have one)
  • a statement of whether or not you are the principal investigator
  • a statement of your research interests (or phage ecology interests)
  • a list of your phage ecology references, if any
Note that it is preferable that you include the full reference, including the abstract, if the reference is not already present in the BEG bibliography. Responsibility of members includes keeping the information listed on the BEG members page up to date including supplying on a reasonably timely basis the full references of your new phage ecology publications. Reprints can also be sent to The Bacteriophage Ecology Group, care of Stephen Abedon, Department of Microbiology, The Ohio State University, 1680 University Dr., Mansfield, Ohio 44906. To join BEG as a non-member, please contact BEG using the following link: abedon.1@osu.edu and minimally include your name and e-mail address.

Please welcome our newest members

name
(home page links)		 status e-mail address
Ido Golding --- igolding
@princeton.edu		 Lewis Thomas Fellow, Department of Molecular Biology, Princeton University, Princeton, New Jersey 08544
interests:I'm a postdoc research fellow, working on various aspects of lambda phage "life cycle". My PhD was in physics, so my previous excursions into biology have been mainly theoretical. A list of my publications can be found on my website. (contents | BEG members | top of page)
Esmail Samiwala PI samiwala
@wockhardtin.com		 Merind Limited (A Wockhardt Enterprise), Mulund Goregaon Link Road, Bhandup (w), Mumbai 400 078, INDIA
interests:We manufacture vitamin B12 which happens to be a fermentation process and highly prone to bacteriophage attacks. If the manufacturing site starts showing phage attacks, steps that need to be taken to counter the problem have to be studied in detail and implemented. (contents | BEG members | top of page)
Emma Stanley --- sbxecs
@nottingham.ac.uk		 Division of Food Microbiology, Sutton Bonnington Campus, University of Nottingham, Loughborough, Leicestershire, LE12 5RD
interests:Deveolping a detection assay for Mycobacterium paratuberculosis using bacteriophage amplification. (contents | BEG members | top of page)
James Taylor --- Jtaylor
@bio.warwick.ac.uk		 Dept. Of Biology, University of Warwick, Coventry, Warwickshire. CV4 7AL
interests:Ecology of Listeria monocytogenes bacteriophages. Use of Listeriaphage in the treatment of silage and milk products. (contents | BEG members | top of page)

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New Links

Links relevant to The Bacteriophage Ecology Group fall into a number of categories (e.g., see Bacteriophage Ecology Links at www.phage.org/beg_links.htm). Listed below are new links found on that page. If you know of a link that should be included on this page, or the whereabouts of a now-dead link, please let me know.
No Entry.

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New Features

In this section I highlight new or updated features of the BEG site. If you have any ideas of how either the BEG site or BEG News might be improved, please let me know.
No Entry.

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Meetings

The BEG Meetings link will continue. Reminders of upcoming meetings will be placed in this section of BEG News. If you know of any meetings that might be of interest to BEG members, or would like to recap a meeting that you've attended, then please send this information for posting to abedon.1@osu.edu or to "BEG Meetings," Bacteriophage Ecology Group News, care of Stephen T. Abedon, Department of Microbiology, The Ohio State University, 1680 University Dr., Mansfield, Ohio 44906.

Please send photos, etc. from meetings for inclusion in this section.

I'm not aware of anything new since the listing in BEG News issue 11.

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Jobs

Looking for job? Looking to fill a position? Please send advertisement and information to abedon.1@osu.edu or to "Jobs", Bacteriophage Ecology Group News, care of Stephen T. Abedon, Department of Microbiology, The Ohio State University, 1680 University Dr., Mansfield, Ohio 44906. Please send all information as text (e.g., as an e-mail) or as Microsoft Word documents, if possible (I'll let you know if I have trouble converting any other document formats), and in English. I will update this section as I receive material, regardless of what date this issue of BEG News goes live.

Click here for International Society for Microbial Ecology Employment Listings.

Click here for American Association for the Advancement of Science Employment Listings.

Click here for AAAS "Microbial Ecology" Search.

Click here for AAAS "Ecology and Microbiology" Search.

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Submissions

Submissions are non-editorial items describing or highlighting some aspect of bacteriophage ecology including news pieces, historical pieces, reviews, and write-ups of research. Peer review of submissions is possible and a desire for peer review should be indicated. Send all submissions to abedon.1@osu.edu or to "Submissions", Bacteriophage Ecology Group News, care of Stephen T. Abedon, Department of Microbiology, The Ohio State University, 1680 University Dr., Mansfield, Ohio 44906. Please send all submissions as Microsoft Word documents, if possible (I'll let you know if I have trouble converting any other document formats), and in English.

Rendering Phage Heads

by Steven McQuinn

The construction of T4 in 3D is an ongoing project. These first pictures, mostly of the phage T4 head, are high-polygon-count meshes modeled to approximate published, data-derived imagery. Researchers who are teasing out the fine details of T4 morphology, from the capsid head to the tail-fiber toes, will eventually publish more accurate meshes generated directly from their analyses. Nevertheless, there is some value in graphical interpretation, especially when showing functionality through animation. I am directing my efforts accordingly, eventually turning toward the creation of simplified low polygon meshes that can be used with interactive web3D formats such as Viewpoint.

Click on the following 2D images to view in a separate window, which in newer browsers should be more-easily scaled to your monitor's resolution.

Below is a full-relief gif of T4's head on a transparent background.

This is a full-relief gif of T4's head on a transparent background.

Below is the T4 head, with tail attached. For more on the T4 tail, see this month's phage image.

This is the T4 head with tail attached.

Below is a close up of the head structure with various proteins labeled.

This is a close up of the head structure with various proteins labeled.

For a paper-cutout model of the T4 icosahedral head, click here (warning, PDF file is large: 1.6 megabytes). Below is an animated rendering of the paper-cutout model.

This is an animated rendering of the paper-cutout model of T4's icosahedral head.

References

  1. Baschong, W.C. et al. (1988). Head structure of bacteriophages T2 and T4. J. Ultrastruct. Res. 99:189-202.

  2. Mosig, G., Eiserling, F. (1988). In The Bacteriophages Plenum Press, New York 2:521.

  3. Olson, N. et al. (2001). The structure of isometric capsids of bacteriophage T4. Virology 279:385-391.

  4. Qu, C. The Icosahedral Server. mmtsb.scripps.edu/viper/chunxuqu/.

Submissions Archive

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Letters & Questions

Letters should consist of comments, short statements, or personal editorials. Send all letters to abedon.1@osu.edu or to "Letters", Bacteriophage Ecology Group News, care of Stephen T. Abedon, Department of Microbiology, The Ohio State University, 1680 University Dr., Mansfield, Ohio 44906. Please send all letters in English and all mailed or attached letters as Microsoft Word documents, if possible (I'll let you know if I have trouble converting any other document formats). In addition, to standard letters, BEG receives questions on a regular basis that may be addressed by BEG members. These questions are listed below. Anybody interested in answering these questions through BEG News, e-mail me at the following address: abedon.1@osu.edu. Alternatively, answer by clicking the authors name. Please note that these questions have not been edited for grammar, spelling, or clarity.
No Entry.

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Phage Images

Please send any phage images that you would like to present in this section to "Phage Images," The Bacteriophage Ecology Group, care of Stephen T. Abedon, Department of Microbiology, The Ohio State University, 1680 University Dr., Mansfield, Ohio 44906. Alternatively, you may scan the images yourself and send them as an attachment to abedon.1@osu.edu. Please save all scans in gif or jpg formats and preferably with an image size (in terms of width, height, and kbytes) that will readily fit on a standard web page. No copyrighted material without permission, please!

This is a modeled image of the T4 phage contractile tail sheath.

This is a modeled image of the T4 phage contractile tail sheath
copyright 2002, Steven McQuinn, smcquinn@hotmail.com or StevenMcQuinn@msn.com.

Phage Image Archive

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New Publications

New bacteriophage publications are listed below. Each quarter not-yet-listed publications from the previous two years will be presented along with their abstracts. The indicator "???" denotes, of course, that specific information is not yet in the BEG Bibliography. Please help in the compilation of the BEG Bibliography by supplying any updated information, correcting any mistakes, and, of course, sending the references to your bacteriophage ecology publications, as well as the references to any bacteriophage ecology publications that you know of but which are not yet in the bibliography (send to abedon.1@osu.edu or to "BEG Bibliography," Bacteriophage Ecology Group News, care of Stephen T. Abedon, Department of Microbiology, The Ohio State University, 1680 University Dr., Mansfield, Ohio 44906). Also, be sure to indicate any listed publications that you feel should not be presented in the BEG Bibliography. This list is also present with available abstracts at the end of BEG News.

  1. Steps toward mapping the human vasculature by phage display. Arap, W., Kolonin, M. G., Trepel, M., Lahdenranta, J., Cardo-Vila, M., Giordano, R. J., Mintz, P. J., Ardelt, P. U., Yao, V. J., Vidal, C. I., Chen, L., Flamm, A., Valtanen, H., Weavind, L. M., Hicks, M. E., Pollock, R. E., Botz, G. H., Bucana, C. D., Koivunen, E., Cahill, D., Troncoso, P., Baggerly, K. A., Pentz, R. D., Do, K. A., Logothetis, C. J., Pasqualini, R. (2002). Nature Medicine 8:121-127. [PRESS FOR ABSTRACT]

  2. Bacteriophage therapy rescues mice bacteremic from a clinical isolate of vancomycin-resistant Enterococcus faecium. Biswas, B., Adhya, S., Washart, P., Paul, B., Trostel, A. N., Powell, B., Carlton, R., Merril, C. R. (2002). Infection and Immunity 70:204-210. [PRESS FOR ABSTRACT]

  3. Phage genomics: Small is beautiful. Brussow, H., Hendrix, W. (2002). Cell 108:13-16. [PRESS FOR ABSTRACT]

  4. Evaluation of the international phage typing set and some experimental phages for typing of Listeria monocytogenes from poultry in Spain. Capita, R., Alonso-Calleja, C., Mereghetti, L., Moreno, B., del Camino, G. (2002). Journal of Applied Microbiology 92:90-96. [PRESS FOR ABSTRACT]

  5. A conductance method for the identification of Escherichia coli O157:H7 using bacteriophage AR1. Chang, T. C., Ding, H. C., Chen, S. (2002). Journal of Food Protection 65:12-17. [PRESS FOR ABSTRACT]

  6. Removal and inactivation of indicator bacteriophages in fresh waters. Duran, A. E., Muniesa, M., Mendez, X, Valero, F., Lucena, F., Jofre, J. (2002). Journal of Applied Microbiology 92:338-347. [PRESS FOR ABSTRACT]

  7. Enteric bacteriophages as potential fecal indicators in ground beef and poultry meat. Hsu, F. C., Shieh, Y. S. C., Sobsey, M. D. (2002). Journal of Food Protection 65:93-99. [PRESS FOR ABSTRACT]

  8. Identification and characterization of phage-resistance genes in temperate lactococcal bacteriophages. McGrath, S., Fitzgerald, G. F., van Sinderen, D. (2002). Molecular Microbiology 43:509-520. [PRESS FOR ABSTRACT]

  9. Bacteriophage therapy of infectious disease in aquaculture. Nakai, T., Park, S. C. (2002). Research in Microbiology 153:13-18. [PRESS FOR ABSTRACT]

  10. The nucleotide sequence of shiga toxin (Stx) 2e-encoding phage fP27 is not related to other Stx phage genomes, but the modular genetic structure is conserved. Recktenwald, J., Schmidt, H. (2002). Infection and Immunity 70:1896-1908. [PRESS FOR ABSTRACT]

  11. Expression of antisense RNA targeted against Streptococcus thermophilus bacteriophages. Sturino, J. M., Klaenhammer, T. R. (2002). Applied and Environmental Microbiology 68:588-596. [PRESS FOR ABSTRACT]

  12. Viruses stop antibiotic-resistant bacteria. Travis, J. (2002). Science News 161:???-??? [PRESS FOR ABSTRACT]

  13. Isolation and characterization of bacteriophages from fermenting sauerkraut. Yoon, S. S., Barrangou-Poueys, R., Breidt, F., Jr., Klaenhammer, T. R., Fleming, H. P. (2002). Applied and Environmental Microbiology 68:973-976. [PRESS FOR ABSTRACT]

  14. Validation of the use of gamma phage for identifying Bacillus anthracis. Abshire, T. G., Brown, J. E., Allan, C. M., Redus, S. L., Teska, J. D., Ezzell, J. W. (2001). Abstracts of the General Meeting of the American Society for Microbiology 101:176. [PRESS FOR ABSTRACT]

  15. Vibrio cholerae VPIPHI/CTXPHI/TCP: Interactions of phage-phage-bacterium. Ai, Y.-C., Meng, F. (2001). Weishengwu Xuebao 41:510-512. [no abstract]

  16. Isolation and characterisation of Campylobacter-specific bacteriophage from retail poultry. Atterbury, R., Connerton, P., Dodd, C., Rees, C., Connerton, I (2001). International Journal of Medical Microbiology 291:79-80. [no abstract]

  17. Persistence of viral pathogens and bacteriophages during sewage treatment: Lack of correlation with indicator bacteria. Baggi, F., Demarta, A., Peduzzi, R. (2001). Research in Microbiology 152:743-751. [PRESS FOR ABSTRACT]

  18. Luciferase reporter mycobacteriophages for detection, identification, and antibiotic susceptibility testing of Mycobacterium tuberculosis in Mexico. Banaiee, N., Bobadilla-del-Valle, M., Bardarov, S., Jr., Riska, P. F., Small, P. M., Ponce-de-Leon, A., Jacobs, W. R., Jr., Hatfull, G. F., Sifuentes-Osornio, J. (2001). Journal of Clinical Microbiology 39:3883-3888. [PRESS FOR ABSTRACT]

  19. Proteins PblA and PblB of Streptococcus mitis, which promote binding to human platelets, are encoded within a lysogenic bacteriophage. Bensing, B. A., Siboo, I. R., Sullam, P. M. (2001). Infection and Immunity 69:6186-6192. [PRESS FOR ABSTRACT]

  20. Bacteriophages transducing antibiotic resistance from a cluster of lysogenic strains of Pseudomonas aeruginosa isolated from patients. Blahova, J., Kralikova, K., Krcmery, V., Sr., Schafer, V (2001). Journal of Chemotherapy 13:331-333. [no abstract]

  21. Faecal bacteria and bacteriophage inactivation in a full-scale UV disinfection system used for wastewater reclamation. Bourrouet, A., Garcia, J., Mujeriego, R., Penuelas, G. (2001). Water Science and Technology 43:187-194. [PRESS FOR ABSTRACT]

  22. Collective action in an RNA virus. Brown, S. P. (2001). Journal of Evolutionary Biology 14:821-828. [PRESS FOR ABSTRACT]

  23. A general mechanism for viral resistance to suicide gene expression. Bull, J. J., Badgett, M. R., Molineux, I. J. (2001). Journal of Molecular Evolution 53:47-54. [PRESS FOR ABSTRACT]

  24. Water quality improvement of treated wastewater by intermittent soil percolation. Castillo, G., Mena, M. P., Dibarrart, F., Honeyman, G. (2001). Water Science and Technology 43:187-190. [PRESS FOR ABSTRACT]

  25. Rapid Identification of Escherichia coli O157:H7. Chang, T. C., Chen, S., Ding, H. C. (2001). Official Gazette of the United States Patent and Trademark Office Patents 1245:No. [PRESS FOR ABSTRACT]

  26. Bacteriophage T4 multiplication in a glucose-limited Escherichia coli biofilm. Corbin, B. D., McLean, R. J. C., Aron, G. M. (2001). Canadian Journal of Microbiology 47:680-684. [PRESS FOR ABSTRACT]

  27. Clinical and environmental isolates of Vibrio cholerae serogroup O141 carry the CTX phage and the genes encoding the toxin-coregulated pili. Dalsgaard, A., Serichantalergs, O., Forslund, A., Lin, W., Mekalanos, J., Mintz, E., Shimada, T., Wells, J. G. (2001). Journal of Clinical Microbiology 39:4086-4092. [PRESS FOR ABSTRACT]

  28. Comparative genomics of lactococcal phages: insight from the complete genome sequence of Lactococcus lactis phage BK5-T. Desiere, F., Mahanivong, C., Hillier, A. J., Chandry, P. S., Davidson, B. E., Brussow, H. (2001). Virology 283:240-252. [PRESS FOR ABSTRACT]

  29. Bacteriophages of Borrelia burgdorferi and other spirochetes. Eggers, Christian H., Casjens, Sherwood, Samuels, D. S., Saier, Milton H., Jr., Garcia-Lara, Jorge Eds (2001). JMMB Symposium Series. The spirochetes: Molecular and cellular biology. 35-44. [no abstract]

  30. Adsorption and survival of faecal coliforms, somatic coliphages and F-specific RNA phages in soil irrigated with wastewater. Gantzer, C., Gillerman, L., Kuznetsov, M., Oron, G. (2001). Water Science and Technology 43:117-124. [PRESS FOR ABSTRACT]

  31. Bacteriophages: Update on application as models for viruses in water. Grabow, W. O. K. (2001). Water SA (Pretoria) 27:251-268. [PRESS FOR ABSTRACT]

  32. Cheese making with bacteriophage resistant bacteria. Hicks, C. L. (2001). Official Gazette of the United States Patent and Trademark Office Patents 1251:No. [PRESS FOR ABSTRACT]

  33. Seasonal dynamics of viruses in an alpine lake: Importance of filamentous forms. Hofer, J. S., Sommaruga, R. (2001). Aquatic Microbial Ecology 26:1-11. [PRESS FOR ABSTRACT]

  34. Profiles of adaptation in two similar viruses. Holder, K. K., Bull, J. J. (2001). Genetics 159:1393-1404. [PRESS FOR ABSTRACT]

  35. Application of rapid detection for Mycobacterium tuberculosis with phage splitting assay. Hu, Z., Pang, M., Jin, A. (2001). Zhonghua Jiehe He Huxi Zazhi 24:611-613. [PRESS FOR ABSTRACT]

  36. Lytic and lysogenic infection of diverse Escherichia coli and Shigella strains with a verocytotoxigenic bacteriophage. James, C. E., Stanley, K. N., Allison, H. E., Flint, H. J., Stewart, C. S., Sharp, R. J., Saunders, J. R., McCarthy, A. J. (2001). Applied and Environmental Microbiology 67:4335-4337. [PRESS FOR ABSTRACT]

  37. Effects of disinfectants on Shiga-like toxin converting phage from enterohemorrhagic Escherichia coli O157 : H7. Kajiura, T, Tanaka, M., Wada, H., Ito, K., Koyama, Y., Kato, F. (2001). Journal of Health Science 47:203-207. [PRESS FOR ABSTRACT]

  38. Phage conversion of staphylococcal bi-component toxin. Kaneko, J. (2001). Nippon Nogeikagaku Kaishi 75:939-947. [no abstract]

  39. Behavior of restriction-modification systems as selfish mobile elements and their impact on genome evolution. Kobayashi, I (2001). Nucleic Acids Research 29:3742-3756. [PRESS FOR ABSTRACT]

  40. The bacteriophage lambda attachment site in wild strains of Escherichia coli. Kuhn, J., Campbell, A. (2001). Journal of Molecular Evolution 53:607-614. [PRESS FOR ABSTRACT]

  41. Vibrio detection by 6 species of bacteriophages of Vibrionaceae. Lin, Y., Chen, K., Ou, J. (2001). Zhonghua Weishengwuxue He Mianyixue Zazhi 21:108-110. [PRESS FOR ABSTRACT]

  42. The effects of seasonal variability and weather on microbial fecal pollution and enteric pathogens in a subtropical estuary. Lipp, E. K., Kurz, R., Vincent, R., Rodriguez-Palacios, C., Farrah, S. R., Rose, J. B. (2001). Estuaries 24:266-276. [PRESS FOR ABSTRACT]

  43. Isolation and characterisation of Campylobacter bacteriophage from free-range chicken farm. Loc-Carrillo, C. M., Connerton, P., Dodd, C., Rees, C., Connerton, I (2001). International Journal of Medical Microbiology 291:79. [no abstract]

  44. Production and release of Shiga toxin from Shigella dysenteriae 1. McDonough, M. A., Butterton, J. R. (2001). Abstracts of the General Meeting of the American Society for Microbiology 101:102. [PRESS FOR ABSTRACT]

  45. Novel in vivo use of a polyvalent Streptomyces phage to disinfest Streptomyces scabies-infected seed potatoes. McKenna, F., El-Tarabily, K. A., Hardy, G. E. S. T., Dell, B. (2001). Plant Pathology (Oxford) 50:666-675. [PRESS FOR ABSTRACT]

  46. Evidence for bacteriophages within gram-negative cocci: Obligate endoparasitic bacteria of Naegleria sp. Michel, R., Schmid, E. N., Gmeiner, G., Mueller, K. D., Hauroeder, B. (2001). Acta Protozoologica 40:229-232. [PRESS FOR ABSTRACT]

  47. Effects of bacteriophages on the population dynamics of four strains of pelagic marine bacteria. Middelboe, M., Hagstrom, A., Blackburn, N., Sinn, B., Fischer, U., Borch, N. H., Pinhassi, J., Simu, K., Lorenz, M. G. (2001). Microbial Ecology 42:395-406. [PRESS FOR ABSTRACT]

  48. Environmental bacteriophage-host interactions: Factors contribution to natural transduction. Miller, R. V. (2001). Antonie van Leeuwenhoek 79:141-147. [PRESS FOR ABSTRACT]

  49. Bacteriophage biology and Kenneth Schaffner's rendition of developmentalism. Morgan, G. J. (2001). Biology & Philosophy 16:85-92. [PRESS FOR ABSTRACT]

  50. A visualization method of filamentous phage infection and phage-derived proteins in Escherichia coli using biotinylated phages. Nakamura, M., Tsumoto, K., Ishimura, K., Kumagai, I (2001). Biochemical & Biophysical Research Communications 289:252-256. [PRESS FOR ABSTRACT]

  51. Presence of an inducible phage in an avian pathogenic Escherichia coli (APEC) strain. Nassar, A., Schouler, C., Dho-Moulin, M. (2001). Abstracts of the General Meeting of the American Society for Microbiology 101:114. [PRESS FOR ABSTRACT]

  52. DNA inversion in the tail fiber gene alters the host range specificity of carotovoricin Er, a phage-tail-like bacteriocin of phytopathogenic Erwinia carotovora subsp. carotovora Er. Nguyen, H. A., Tomita, T., Hirota, M., Kaneko, J., Hayashi, T., Kamio, Y. (2001). Journal of Bacteriology 183:6274-6281. [PRESS FOR ABSTRACT]

  53. Naturally occurring lactococcal plasmid pAH90 links bacteriophage resistance and mobility functions to a food-grade selectable marker. O'Sullivan, D., Ross, R. P., Twomey, D. P., Fitzgerald, G. F., Hill, C., Coffey, A. (2001). Applied and Environmental Microbiology 67:929-937. [PRESS FOR ABSTRACT]

  54. Filamentous bacteriophage stability in non-aqueous media. Olofsson, L., Ankarloo, J., Andersson, P. O., Nicholls, I. A. (2001). Chemistry & Biology (London) 8:661-671. [PRESS FOR ABSTRACT]

  55. [Stability of Lactococcus lactis phages treated with sodium hypochlorite and during storage]. Parada, J. L., de, Fabrizio SV (2001). Revista Argentina de Microbiologia 33:89-95. [PRESS FOR ABSTRACT]

  56. Removal of pathogenic and indicator microorganisms by a constructed wetland receiving untreated domestic wastewater. Quinonez-Diaz, M. de, Karpiscak, M. M., Ellman, E. D., Gerba, C. P. (2001). Journal of Environmental Science and Health Part A Toxic-Hazardous Substances & Environmental Engineering A36:1311-1320. [PRESS FOR ABSTRACT]

  57. Phage spread dynamics in clonal bacterial populations is depending on features of the founder cell. Ramirez, E., Carbonell, X, Villaverde, A. (2001). Microbiological Research 156:35-40. [PRESS FOR ABSTRACT]

  58. Gene transfer in bacterial biofilms. Roberts, AP., Mullany, P., Wilson, M., Doyle, R. J. (2001). Methods in Enzymology 60-65. [PRESS FOR ABSTRACT]

  59. Independent origins and horizontal transfer of bacterial symbionts of aphids. Sandstrom, J. P., Russell, J. A., White, J. P., Moran, N. A. (2001). Molecular Ecology 10:217-228. [PRESS FOR ABSTRACT]

  60. Shiga-toxin-converting bacteriophages. Schmidt, H. (2001). Research in Microbiology 152:687-695. [PRESS FOR ABSTRACT]

  61. Bacteriophages: A rich store of new antibiotics? Senior, K. (2001). Drug Discovery Today 6:865-866. [PRESS FOR ABSTRACT]

  62. Isolation of clones sensitive to bacteriophage lambda from the phage resistant Escherichia coli strain. Slavchenko, I. Y. (2001). Biopolimery i Kletka 17:160-165. [PRESS FOR ABSTRACT]

  63. The ability of acceptance of bacteriophages carried genes for verotoxin production by bacili of Enterobacteriaceae family. Sobieszczanska, B., Gryko, R. (2001). Medycyna Doswiadczalna i Mikrobiologia 53:269-276. [PRESS FOR ABSTRACT]

  64. Kinetics of T7 phage neutralization in the blood of normal and immunodeficient mice. Srivastava, A. S., Kaido, T. J., Carrier, E. (2001). Blood 98:407b. [PRESS FOR ABSTRACT]

  65. Persistence of two model enteric viruses (B40-8 and MS-2 bacteriophages) in water distribution pipe biofilms. Storey, M. V., Ashbolt, N. J. (2001). Water Science and Technology 43:133-138. [PRESS FOR ABSTRACT]

  66. Bacteriophages as therapeutic agents. Sulakvelidze, A., Morris, J. G. (2001). Annals of Medicine 33:507-509. [PRESS FOR ABSTRACT]

  67. Use of bioluminescent Salmonella for assessing the efficiency of constructed phage-based biosorbent. Sun, W., Brovko, L., Griffiths, M. (2001). Journal of Industrial Microbiology & Biotechnology 27:126-128. [PRESS FOR ABSTRACT]

  68. Bacteriophages, method for screening same and bactericidal compositions using same, and detection kits using same. Takahashi, S. (2001). Official Gazette of the United States Patent and Trademark Office Patents 1252:No. [PRESS FOR ABSTRACT]

  69. Association of the activatable Shiga toxin type 2 variant, Stx2d, with an inducible bacteriophage. Teel, L. D., Schmitt, C. K., Melton-Celsa, A. R., O'Brien, A. D. (2001). Abstracts of the General Meeting of the American Society for Microbiology 101:90-91. [PRESS FOR ABSTRACT]

  70. Evolution: Towards a genetical theory of adaptation. Travisano, M. (2001). Current Biology 11:R440-R442. [PRESS FOR ABSTRACT]

  71. The use of cadmium resistance on the phage-resistance plasmid pNP40 facilitates selection for its horizontal transfer to industrial dairy starter lactococci. Trotter, M., Mills, S., Ross, R. P., Fitzgerald, G. F., Coffey, A. (2001). Letters in Applied Microbiology 33:409-414. [PRESS FOR ABSTRACT]

  72. Investigation of expression of a phage encoded pertussis toxin operon in Bordetella avium lysogens. van Horne, S. J., Bjornsen, D., Carpentier, P., Temple, L. M. (2001). Abstracts of the General Meeting of the American Society for Microbiology 101:64-65. [PRESS FOR ABSTRACT]

  73. Phage therapy of Campylobacter jejuni colonization in broilers. Wagenaar, J. A., Van Bergen, M. A. P., Mueller, M. A., Monie, K., Carlton, R. M. (2001). International Journal of Medical Microbiology 291:92-93. [PRESS FOR ABSTRACT]

  74. Transducing phages of Actinomycetales. Westpheling, J., Burke, J. A. (2001). Official Gazette of the United States Patent and Trademark Office Patents 1247:No. [PRESS FOR ABSTRACT]

  75. Bacteriophage-based transgenic fish for mutation detection. Winn, R. N. (2001). Official Gazette of the United States Patent and Trademark Office Patents 1251:No. [PRESS FOR ABSTRACT]

  76. Efficient and predictable recovery of viruses from water by small scale ultrafiltration systems. Winona, L. J., Ommani, A. W., Olszewski, J., Nuzzo, J. B., Oshima, K. H. (2001). Canadian Journal of Microbiology 47:1033-1041. [PRESS FOR ABSTRACT]

  77. Influence of phage population on the phage-mediated bioluminescent adenylate kinase (AK) assay for detection of bacteria. Wu, Y., Brovko, L., Griffiths, M. W. (2001). Letters in Applied Microbiology 33:311-315. [PRESS FOR ABSTRACT]

  78. Dynamic bacterial and viral response to an algal bloom at subzero temperatures. Yager, P. L., Connelly, T. L., Mortazavi, B., Wommack, K. E., Bano, N., Bauer, J. E., Opsahl, S., Hollibaugh, J. T. (2001). Limnology and Oceanography 46:790-801. [PRESS FOR ABSTRACT]

  79. Role of ciliates, flagellates and bacteriophages on the mortality of marine bacteria and on dissolved-DNA concentration in laboratory experimental systems. Alonso, M. C., Rodriguez, V, Rodriguez, J., Borrego, J. J. (2000). Journal of Experimental Marine Biology and Ecology 244:239-252. [PRESS FOR ABSTRACT]

  80. Viruses in Trichomonas. Benchimol, M., Alderete, John F. (2000). XXVII Annual Meeting on Basic Research in Chagas Disease and the XVI Annual Meeting of Brazilian Society of Protozoology 95:62-63. [no abstract]

  81. Genome plasticity in Enterobacteriaceae. Brunder, W., Karch, H. (2000). International Journal of Medical Microbiology 290:153-165. [PRESS FOR ABSTRACT]

  82. The temperate nature of aquatic and soil bacteriophage. Cook, H. A., Gallucci, C. M., Hale, A. B. (2000). 76th Annual Meeting of the Pennsylvania Academy of Science 73:153. [no abstract]

  83. Pulsed-field gel electrophoresis analysis of virus assemblages present in a hypersaline environment. Diez, B., Anton, J., Guixa-Boixereu, N., Pedros-Alio, C., Rodriguez-Valera, F. (2000). International Microbiology 3:159-164. [PRESS FOR ABSTRACT]

  84. Compositions containing bacteriophages and methods of using bacteriophages to treat infections. Ghanbari, H. A., Averback, P. (2000). Official Gazette of the United States Patent and Trademark Office Patents 1238:No. [PRESS FOR ABSTRACT]

  85. A procedure for detection of coliphages in the drinking water. Kashkarova, G. P., Dorodnikov, A. I. (2000). Gigiena i Sanitariya 66-68. [no abstract]

  86. [Vibrio cholerae O139 bacteriophages]. Kudriakova, T. A., Makedonova, L. D., Kachkina, G. V., Saiamov, S. R. (2000). Zhurnal Mikrobiologii, Epidemiologii i Immunobiologii 28-30. [PRESS FOR ABSTRACT]

  87. Development and qualification of a novel virus removal filter for cell culture applications. Liu, S., Carroll, M., Iverson, R., Valera, C., Vennari, J., Turco, K., Piper, R., Kiss, R., utz, H. (2000). Biotechnology Progress 16:425-434. [PRESS FOR ABSTRACT]

  88. Bacteriophages active against Helicobacter pylori in UK sewage: Natural born killers? Morton, D., Bardhan, K. D. (2000). Gastroenterology 118:AGA. [no abstract]

  89. The presence of bacteriophages active against Helicobacter pylori in UK sewage: Natures eradicator? Morton, D., Bardhan, K. D. (2000). Gut 46:A69. [no abstract]

  90. Detection of bacterial pathogens by phage antibody display. Pai, N., Topping, K. P., Greenman, J., Paget, T. A. (2000). Disease Markers 16:99-100. [no abstract]

  91. Phage sensitivities of lactococci isolated from raw milk and whey. Sanlibaba, P., Akcelik, M. (2000). Turkish Journal of Biology 24:425-435. [PRESS FOR ABSTRACT]

  92. Studies on phage control of pustule disease in abalone Haliotis discus hannai. Tai-wu, L., Xiang, J., Liu, R. (2000). Journal of Shellfish Research 19:535. [no abstract]

  93. Elements of a theory for the mechanisms controlling abundance, diversity, and biogeochemical role of lytic bacterial viruses in aquatic systems. Thingstad, T. F. (2000). Limnology and Oceanography 45:1320-1328. [PRESS FOR ABSTRACT]

  94. Method and device for detecting bacteriophage using contrast-coloring and precipitable dyes. Wicks, J. H., Krejcarek, G. E., Williams, M. G. (2000). Official Gazette of the United States Patent and Trademark Office Patents 1236:No. [PRESS FOR ABSTRACT]

  95. Detection and occurrence of indicator organisms and pathogens. Baker, K. H., Herson, D. S. (1999). Water Environment Research 71:530-551. [no abstract]

  96. Distribution of the human faecal bacterium Bacteroides fragilis, its bacteriophages and their relationship to current sewage pollution indicators in bathing water. Bradley, G., Carter, J., Gaudie, D., King, C. (1999). 1998 Meeting of the Society for Applied Microbiology on Aquatic Microbiology 90S-100S. [no abstract]

  97. History of the discovery and study of brucellar bacteriophages. Lyapustina, L. V., Lyamkin, G. I., Taran, I. F. (1999). Zhurnal Mikrobiologii Epidemiologii i Immunobiologii 123-124. [no abstract]

  98. Enzyme for phage resistance. Moineau, S., Walker, S. A., Vedamuthu, E. R., Vandenbergh, P. A. (1999). Official Gazette of the United States Patent and Trademark Office Patents 1227:No. [PRESS FOR ABSTRACT]

  99. Method and test kits for detection of bacteriophage. Sanders, M. F. (1999). Official Gazette of the United States Patent and Trademark Office Patents 1223:NO. [no abstract]

  100. Effect of bacteriophages on TNF-alpha, IL-6 and IFN production by human peripheral blood cells (PBC). Weber-Dabrowska, B., Czarny, A., Mulczyk, M. (1999). Seventh Annual Conference of the International Cytokine Society 11:922. [no abstract]

  101. Method to detect bacteria. Wilson, S. M. (1999). Official Gazette of the United States Patent and Trademark Office Patents 1228. [PRESS FOR ABSTRACT]

  102. Bacteriophage of Chlamydia psittaci. Bavoil, P. M., Hsia, R. C. (1998). Official Gazette of the United States Patent and Trademark Office Patents 1209:2328. [no abstract]

  103. Method of selecting specific bacteriophages. Borrebaeck, C. A. K., Duenas, M. (1998). Official Gazette of the United States Patent and Trademark Office Patents 1206:2910. [no abstract]

  104. Bacteriophage-mediated gene transfer systems capable of transfecting eukaryotic cells. Chada, S., Dubensky, T. W., Jr. (1998). Official Gazette of the United States Patent and Trademark Office Patents 1209:459. [no abstract]

  105. Bacteriophage-triggered cell suicide systems and fermentation methods employing the same. Klaenhammer, T. R., Conkling, M. A., O'Sullivan, D., Djordjevic, G., Walker, S. A., Taylor, C. G. (1998). Official Gazette of the United States Patent and Trademark Office Patents 1213:1727. [no abstract]

  106. Bacteriophage genotypically modified to delay inactivations by the host defense system. Merril, C. R., Carlton, R. M., Adhya, S. L. (1998). Official Gazette of the United States Patent and Trademark Office Patents 1214:4125. [no abstract]

  107. Antibacterial therapy with bacteriophage genotypically modified to delay inactivation by the host defense system together with an antibiotic. Merril, C. R., Carlton, R. M., Adhya, S. L. (1998). Official Gazette of the United States Patent and Trademark Office Patents 1211:2866-2867. [no abstract]

  108. Phage-resistant streptococcus. Mollet, B., Pridmore, D., Zwahien, M. C. (1998). Official Gazette of the United States Patent and Trademark Office Patents 1211:2869. [no abstract]

  109. Nucleic acid sequence and plasmids comprising at least one phage resistence mechanism, bacteria containing them and their use. Prevots, F., Tolou, S., Daloyau, M. (1998). Official Gazette of the United States Patent and Trademark Office Patents 1206:2923. [no abstract]

  110. Genetically engineered reporter bacteria for the detection of bacteriophage. Rees, C. E. D., Rostas-Mulligan, K., Park, S. F., Denyer, S. P., Anderson, G. S., Stewart, B., Jassim, S. A. A. (1998). Official Gazette of the United States Patent and Trademark Office Patents 1208:410. [no abstract]

  111. Detection of listeria by means of recombinant bacteriophages. Scherer, S., Loessner, M. (1998). Official Gazette of the United States Patent and Trademark Office Patents 1215:2969. [no abstract]

  112. A theoretical approach to structuring mechanisms in the pelagic food web. Thingstad, T. F. (1998). Hydrobioligia 363:59-72. [PRESS FOR ABSTRACT]

contents | BEG News (012) | top of page

New Publications with Abstracts

For your convenience, a list of new publications without associated abstracts (but with links to abstracts) is found above. The list presented below is identical to the above list except that abstracts are included.

  1. Steps toward mapping the human vasculature by phage display. Arap, W., Kolonin, M. G., Trepel, M., Lahdenranta, J., Cardo-Vila, M., Giordano, R. J., Mintz, P. J., Ardelt, P. U., Yao, V. J., Vidal, C. I., Chen, L., Flamm, A., Valtanen, H., Weavind, L. M., Hicks, M. E., Pollock, R. E., Botz, G. H., Bucana, C. D., Koivunen, E., Cahill, D., Troncoso, P., Baggerly, K. A., Pentz, R. D., Do, K. A., Logothetis, C. J., Pasqualini, R. (2002). Nature Medicine 8:121-127. The molecular diversity of receptors in human blood vessels remains largely unexplored. We developed a selection method in which peptides that home to specific vascular beds are identified after administration of a peptide library. Here we report the first in vivo screening of a peptide library in a patient. We surveyed 47,160 motifs that localized to different organs. This large-scale screening indicates that the tissue distribution of circulating peptides is nonrandom. High-throughput analysis of the motifs revealed similarities to ligands for differentially expressed cell-surface proteins, and a candidate ligand-receptor pair was validated. These data represent a step toward the construction of a molecular map of human vasculature and may have broad implications for the development of targeted therapies

  2. Bacteriophage therapy rescues mice bacteremic from a clinical isolate of vancomycin-resistant Enterococcus faecium. Biswas, B., Adhya, S., Washart, P., Paul, B., Trostel, A. N., Powell, B., Carlton, R., Merril, C. R. (2002). Infection and Immunity 70:204-210. Colonization of the gastrointestinal tract with vancomycin-resistant Enterococcus faecium (VRE) has become endemic in many hospitals and nursing homes in the United States. Such colonization predisposes the individual to VRE bacteremia and/or endocarditis, and immunocompromised patients are at particular risk for these conditions. The emergence of antibiotic-resistant bacterial strains requires the exploration of alternative antibacterial therapies, which led our group to study the ability of bacterial viruses (bacteriophages, or phages) to rescue mice with VRE bacteremia. The phage strain used in this study has lytic activity against a wide range of clinical isolates of VRE. One of these VRE strains was used to induce bacteremia in mice by intraperitoneal (i.p.) injection of 109 CFU. The resulting bacteremia was fatal within 48 h. A single i.p. injection of 3 x 108 PFU of the phage strain, administered 45 min after the bacterial challenge, was sufficient to rescue 100% of the animals. Even when treatment was delayed to the point where all animals were moribund, approximately 50% of them were rescued by a single injection of this phage preparation. The ability of this phage to rescue bacteremic mice was demonstrated to be due to the functional capabilities of the phage and not to a nonspecific immune effect. The rescue of bacteremic mice could be effected only by phage strains able to grow in vitro on the bacterial host used to infect the animals, and when such strains are heat inactivated they lose their ability to rescue the infected mice

  3. Phage genomics: Small is beautiful. Brussow, H., Hendrix, W. (2002). Cell 108:13-16. The Age of Genomics dawned only gradually for bacteriophages. It was 1977 when the genome of phage phiX174 was published and 1983 when the "large" genome of phage lambda hit the streets. More recently, the pace has quickened, so that we now have over 100 complete phage genomes and can expect thousands in a very few years. These sequences have been marvelously informative for the biology of the individual phages, but with the advent of high volume sequencing technology, the real excitement for phage biology is that it is now possible to analyze the sequences together and thereby address-for the first time at whole genome resolution-a set of fundamental biological questions related to populations: What is the structure of the global phage population? What are its dynamics? How do phages evolve? This is Comparative Genomics with a capital "C"

  4. Evaluation of the international phage typing set and some experimental phages for typing of Listeria monocytogenes from poultry in Spain. Capita, R., Alonso-Calleja, C., Mereghetti, L., Moreno, B., del Camino, G. (2002). Journal of Applied Microbiology 92:90-96. Aims: The validity of the international phage set and 13 experimental phages for subtyping Listeria monocytogenes strains isolated from poultry in Spain was investigated. Methods and Results: Ninety-six L. monocytogenes strains (52 from serogroup 1/2 and 44 from serogroup 4) were phage-typed using the international phage set, 10 experimental phages for typing serogroup 1/2 strains (seven isolated in France: 1313, 9425, 1807, 351, 881, 717 and 586-, and three from Denmark: 5775, 12682 and 6223-) and three experimental phages isolated in France for typing serogroup 4 strains (2425 A, 4286 and 197). Percentages of serogroup 1/2, serogroup 4 and total phage-typeable strains were 57.7%, 52.3% and 55.2%, respectively. Important differences in the behaviour of the phages tested were found. The typeability rate, the specificity index and the percentage of strong reactions were greater in the phages of international set than in the experimental phages. The number of phage typeable strains and the number of phage types (42) were not modified by the use of experimental phages. Conclusions: The phage set used was not effective for typing L. monocytogenes strains from poultry in Spain, because a low typeability rate was found. Significance and Impact of the Study: Our results suggest the importance of the availability of new phages specific to a geographical area in order to improve the typeability of the system

  5. A conductance method for the identification of Escherichia coli O157:H7 using bacteriophage AR1. Chang, T. C., Ding, H. C., Chen, S. (2002). Journal of Food Protection 65:12-17. The feasibility of using a specific phage (AR1) in conjunction with a conductance method for the identification of Escherichia coli O157:H7 was evaluated. The multiplication of strains of E. coli O157:H7 was inhibited by AR1; therefore, a time point (detection time, DT) at which an accelerating change in conductance in the culture broth was not obtained. Bacterial strains were subcultured on sorbitol-MacConkey agar and incubated at 35°C for 24 h, and the ability of the bacteria to ferment sorbitol was recorded. An aliquot of 0.5 ml of the bacterial suspension (107 CFU/ml) and 0.5 ml of the phage suspension (108 PFU/ml) were added to the conductance tube of a Malthus analyzer containing 5 ml of culture broth. The tubes were incubated at 35°C, and conductance changes in the tubes were continuously monitored at 6-min intervals for 24 h by the instrument. A positive reaction was defined as an E. coli strain that could not utilize sorbitol and caused no conductance change (i.e., no DT) within an incubation period of 24 h. Of the 41 strains of E. coli O157:H7 tested, all produced positive reactions. When a total of 155 strains of non-O157:H7 E. coli were tested, 14 did not have a DT within 24 h. However, among these 14 strains, 13 were sorbitol fermenters, and the remaining one was a nonfermenter. Therefore, by definition, only one strain produced a false-positive reaction. The sensitivity and specificity of the present method were 100% (41 of 41) and 99.4% (154 of 155), respectively. The present method incorporating conductimetric measurement and phage AR1 for the identification of E. coli O157:H7 was simple and capable of automation

  6. Removal and inactivation of indicator bacteriophages in fresh waters. Duran, A. E., Muniesa, M., Mendez, X, Valero, F., Lucena, F., Jofre, J. (2002). Journal of Applied Microbiology 92:338-347. Aims: The removal and inactivation of faecal coliform (FC) bacteria, enterococci (ENT), sulphite-reducing clostridia (SRC), somatic coliphages, F-specific RNA bacteriophages and bacteriophages infecting Bacteroides fragilis in fresh waters. Methods and Results: Removal was studied in two areas of a river. The results showed different removal of each group of microbes. Faecal coliform bacteria were removed faster than any other, whereas SRC and bacteriophages infecting Bact. fragilis were the most persistent. Inactivation was measured by 'in situ' experiments, which showed significant differences in survival of the different groups of bacterial and bacteriophage indicators. The SRC and bacteriophages were more resistant than faecal coliforms and enterococci, with the exception of F-specific RNA bacteriophages in the summer. Inactivation experiments with pure cultures of bacteriophages confirmed that phage B40-8 of Bact. fragilis was the most resistant. Conclusions: Bacteria and bacteriophages show different resistance to natural inactivation. The use of phages allows information to be obtained in addition to that provided by bacterial indicators. Somatic coliphages and phages infecting Bact. fragilis might supply that indicator function. Significance and Impact of the Study: Confirmation was obtained that bacteriophages provided additional information to that provided by bacterial indicators to monitor the natural inactivation of viruses and/or pathogens

  7. Enteric bacteriophages as potential fecal indicators in ground beef and poultry meat. Hsu, F. C., Shieh, Y. S. C., Sobsey, M. D. (2002). Journal of Food Protection 65:93-99. Recovery efficiencies of enteric bacteriophages (F+ RNA coliphages, somatic coliphages, and Salmonella phages) as alternative fecal indicators were determined from ground beef and chicken breast meat using amino acid eluants (glycine and threonine) and a complex eluant (3% beef extract). Levels of F+ RNA coliphages (MS2, GA, Qbeta, FI, and SP), the somatic coliphage PHIX174, and three environmental isolates of Salmonella phages (isolated from raw sewage) were assayed using three respective hosts: Escherichia coli Famp, E. coli C, and Salmonella typhimurium. When 8% polyethylene glycol and 0.1 M NaCl were used to precipitate bacteriophages eluted with five different eluants, the highest recoveries of the three phage groups were with 0.5 M threonine and 0.25 M glycine-threonine. The average recoveries of F+ RNA coliphages, somatic coliphages, and the Salmonella phages from ground beef and chicken meat were 100, 69, and 65%, respectively, with threonine (0.5 M, pH 9.0) as the eluate. Of eight market food samples tested, F+ RNA coliphages were detected in five (63%) and somatic coliphages were detected in seven (88%). The overall detection sensitivity of the method was 3 PFU/100 g of ground beef or chicken meat. Levels of bacteriophages and bacterial indicators on chicken carcass surfaces were determined at identified critical control points at a poultry plant. Through the processing steps of evisceration, washing, and chilling, the levels of F+ RNA coliphages and fecal coliforms were reduced by 1.6 and 1.9 log10 PFU or CFU/100 g, respectively. F+ RNA coliphages and perhaps other enteric bacteriophages may be effective candidate indicators for monitoring the microbiological quality of meat, poultry, and perhaps other foods during processing. The bacteriophage concentration method developed provides a simple, rapid, and practical tool for the evaluation of fecal contamination levels in ground beef and processed chicken meat

  8. Identification and characterization of phage-resistance genes in temperate lactococcal bacteriophages. McGrath, S., Fitzgerald, G. F., van Sinderen, D. (2002). Molecular Microbiology 43:509-520. The sie2009 gene, which is situated between the genes encoding the repressor and integrase, on the lysogeny module of the temperate lactococcal bacteriophage Tuc2009, was shown to mediate a phage-resistance phenotype in Lactococcus lactis against a number of bacteriophages. The Sie2009 protein is associated with the cell membrane and its expression leaves phage adsorption, transfection and plasmid transformation unaffected, but interferes with plasmid transduction, as well as phage replication. These observations indicate that this resistance is as a result of DNA injection blocking, thus representing a novel superinfection exclusion system. A polymerase chain reaction (PCR)-based strategy was used to screen a number of lactococcal strains for the presence of other prophage-encoded phage-resistance systems. This screening resulted in the identification of two such systems, without homology to sie2009, which were shown to mediate a phage-resistance phenotype similar to that conferred by sie2009. To our knowledge, this is the first description of a phage-encoded superinfection exclusion/injection blocking mechanism in the genus Lactococcus

  9. Bacteriophage therapy of infectious disease in aquaculture. Nakai, T., Park, S. C. (2002). Research in Microbiology 153:13-18. Bacteriophages may be candidates as therapeutic agents in bacterial infections. Here we describe the protective effects of phages against experimentally induced bacterial infections of cultured fish and discuss the potential for phage therapy in aquaculture.

  10. The nucleotide sequence of shiga toxin (Stx) 2e-encoding phage fP27 is not related to other Stx phage genomes, but the modular genetic structure is conserved. Recktenwald, J., Schmidt, H. (2002). Infection and Immunity 70:1896-1908. In this study we determined the complete nucleotide sequence of Shiga toxin 2e-encoding bacteriophage fP27, isolated from the Shiga toxin-producing Escherichia coli patient isolate 2771/97. fP27 is integrated as a prophage in the chromosomal yecE gene. This integration generates identity segments of attL and attR sites with lengths of 11 nucleotides. The integrated prophage genome has a size of 42,575 bp. We identified 58 open reading frames (ORFs), each with a length of >150 nucleotides. The deduced proteins of 44 ORFs showed significant homologies to other proteins present in sequence databases, whereas 14 putative proteins did not. For 29 proteins, we could deduce a putative function. Most of these are related to the basic phage propagation cycle. The fP27 genome represents a mosaic composed of genetic elements which are obviously derived from related and unrelated phages. We identified five short linker sequences of 22 to 151 bp in the fP27 sequence which have also been detected in a couple of other lambdoid phages. These linkers are located between functional modules in the phage genome and are thought to play a role in genetic recombination. Although the overall DNA sequence of fP27 is not highly related to other known phages, the data obtained demonstrate a typical lambdoid genome structure.

  11. Expression of antisense RNA targeted against Streptococcus thermophilus bacteriophages. Sturino, J. M., Klaenhammer, T. R. (2002). Applied and Environmental Microbiology 68:588-596. Antisense RNA complementary to a putative helicase gene (hel3.1) of a cos-type Streptococcus thermophilus bacteriophage was used to impede the proliferation of a number of cos-type S. thermophilus bacteriophages and one pac-type bacteriophage. The putative helicase gene is a component of the Sfi21-type DNA replication module, which is found in a majority of the S. thermophilus bacteriophages of industrial importance. All bacteriophages that strongly hybridized a 689-bp internal hel3.1 probe were sensitive to the expression of antisense hel3.1 RNA. A 40 to 70% reduction in efficiency of plaquing (EOP) was consistently observed, with a concomitant decrease in plaque size relative to that of the S. thermophilus parental strain. When progeny were released, the burst size was reduced. Growth curves of S. thermophilus NCK1125, in the presence of variable levels of bacteriophage kappa3, showed that antisense hel3.1 conferred protection, even at a multiplicity of infection of approximately 1.0. When the hel3.1 antisense RNA cassette was expressed in cis from the kappa3-derived phage-encoded resistance (PER) plasmid pTRK690::ori3.1, the EOP for bacteriophages sensitive to PER and antisense targeting was reduced to between 10-7 and 10-8, beyond the resistance conferred by the PER element alone (less than 10-6). These results illustrate the first successful applications of antisense RNA and explosive delivery of antisense RNA to inhibit the proliferation of S. thermophilus bacteriophages

  12. Viruses stop antibiotic-resistant bacteria. Travis, J. (2002). Science News 161:???-??? Nearly a century ago, biologists discovered viruses that prey upon bacteria. When penicillin and other antibiotics emerged a few decades later, however, physicians largely abandoned their efforts to use these bacteriophages, or phages, to thwart infectious diseases. ¶ As more bacteria develop resistance to antibiotics, there's renewed interest in phages (SN: 6/3/00, p. 358). Scientists now report that these viruses can prevent mice from dying after being infected with an antibiotic-resistant bacterium.

  13. Isolation and characterization of bacteriophages from fermenting sauerkraut. Yoon, S. S., Barrangou-Poueys, R., Breidt, F., Jr., Klaenhammer, T. R., Fleming, H. P. (2002). Applied and Environmental Microbiology 68:973-976. This paper presents the first report of bacteriophage isolated from commercial vegetable fermentations. Nine phages were isolated from two 90-ton commercial sauerkraut fermentations. These phages were active against fermentation isolates and selected Leuconostoc mesenteroides and Lactobacillus plantarum strains, including a starter culture. Phages were characterized as members of the Siphoviridae and Myoviridae families. All Leuconostoc phages reported previously, primarily of dairy origin, belonged to the Siphoviridae family

  14. Validation of the use of gamma phage for identifying Bacillus anthracis. Abshire, T. G., Brown, J. E., Allan, C. M., Redus, S. L., Teska, J. D., Ezzell, J. W. (2001). Abstracts of the General Meeting of the American Society for Microbiology 101:176. In 1999, the CDC/APHL Laboratory Response Network to Bioterrorism selected gamma phage lysis of Bacillus anthracis as a specific method for identification of the bacterium. In the 1950s, Brown and Cherry originally isolated gamma phage and showed it to lyse specifically vegetative B. anthracis. That property has been used as the basis for an identification assay on culture plates at USAMRIID and elsewhere. We report here our results of a study to validate the assay for routine use. The primary intent of the assay is to test non-hemolytic, ground-glass-appearing bacterial colonies arising from culture of clinical or non-clinical samples on 5% sheep blood agar. Specifically, the assay was designed to demonstrate clear or partially clear circular zones of lysis on bacterial lawns at the site of gamma phage inoculation following incubation at 35+-2°C for 20 hours. The validation study tested the assay for specificity, precision, and ruggedness. When tested with 50 B. anthracis strains and 50 similar non-anthracis Bacillus species, whose identity was confirmed using whole-cell fatty acid analysis (MIDI, Inc., Newark DE), the analytical specificity was >95%. This value was intentionally low because our study design included two rare refractory B. anthracis strains as well as two rare susceptible non-anthracis strains, B. cereus ATCC 4342 and B. mycoides CDC 680. Repeatability, day-to-day precision, and analyst-to-analyst precision were superior. The assay is rugged to variations between phage lots, phage concentration, amounts of bacterial inoculum, and incubation times (as short as 8 h). The data show that the assay is satisfactory for routine use

  15. Vibrio cholerae VPIPHI/CTXPHI/TCP: Interactions of phage-phage-bacterium. Ai, Y.-C., Meng, F. (2001). Weishengwu Xuebao 41:510-512.

  16. Isolation and characterisation of Campylobacter-specific bacteriophage from retail poultry. Atterbury, R., Connerton, P., Dodd, C., Rees, C., Connerton, I (2001). International Journal of Medical Microbiology 291:79-80.

  17. Persistence of viral pathogens and bacteriophages during sewage treatment: Lack of correlation with indicator bacteria. Baggi, F., Demarta, A., Peduzzi, R. (2001). Research in Microbiology 152:743-751. The effects of different sewage treatments on the viral contamination in rivers which receive water from treatment plants without a final sand filtration step were investigated. They were all heavily contaminated with bacteriophages and human enteric viruses (detected by single step reverse transcription amplification followed by a nested polymerase chain reaction). Bacteriophages, but not faecal indicator organisms, were correlated with viral contamination

  18. Luciferase reporter mycobacteriophages for detection, identification, and antibiotic susceptibility testing of Mycobacterium tuberculosis in Mexico. Banaiee, N., Bobadilla-del-Valle, M., Bardarov, S., Jr., Riska, P. F., Small, P. M., Ponce-de-Leon, A., Jacobs, W. R., Jr., Hatfull, G. F., Sifuentes-Osornio, J. (2001). Journal of Clinical Microbiology 39:3883-3888. The utility of luciferase reporter mycobacteriophages (LRPs) for detection, identification, and antibiotic susceptibility testing of Mycobacterium tuberculosis was prospectively evaluated in a clinical microbiology laboratory in Mexico City, Mexico. Five hundred twenty-three consecutive sputum samples submitted to the laboratory during a 5-month period were included in this study. These specimens were cultivated in Middle-brook 7H9 (MADC), MGIT, and Lowenstein-Jensen (LJ) media. Of the 71 mycobacterial isolates recovered with any of the three media, 76% were detected with the LRPs, 97% were detected with the MGIT 960 method, and 90% were detected with LJ medium. When contaminated specimens were excluded from the analysis, the LRPs detected 92% (54 of 59) of the cultures. The median time to detection of bacteria was 7 days with both the LRPs and the MGIT 960 method. LRP detection of growth in the presence of p-nitro-alpha-acetylamino-beta-hydroxypropiophenone (NAP) was used for selective identification of M. tuberculosis complex (MTC) and compared to identification with BACTEC 460. Using the LRP NAP test, 47 (94%) out of 50 isolates were correctly identified as tuberculosis complex. The accuracy and speed of LRP antibiotic susceptibility testing with rifampin, streptomycin, isoniazid, and ethambutol were compared to those of the BACTEC 460 method, and discrepant results were checked by the conventional proportion method. In total, 50 MTC isolates were tested. The overall agreement between the LRP and BACTEC 460 results was 98.5%. The median LRP-based susceptibility turnaround time was 2 days (range, 2 to 4 days) compared to 10.5 days (range, 7 to 16 days) by the BACTEC 460 method. Phage resistance was not detected in any of the 243 MTC isolates tested. Mycobacteriophage-based approaches to tuberculosis diagnostics can be implemented in clinical laboratories with sensitivity, specificity, and rapidity that compare favorably with those of the MGIT 960 and BACTEC 460 methods. The phages currently provide the fastest phenotypic assay for susceptibility testing

  19. Proteins PblA and PblB of Streptococcus mitis, which promote binding to human platelets, are encoded within a lysogenic bacteriophage. Bensing, B. A., Siboo, I. R., Sullam, P. M. (2001). Infection and Immunity 69:6186-6192. The binding of platelets by bacteria is a proposed central mechanism in the pathogenesis of infective endocarditis. Platelet binding by Streptococcus mitis strain SF100 (an endocarditis isolate) was recently shown to be mediated in part by the surface proteins PblA and PblB. The genes encoding PblA and PblB are clustered with genes nearly identical to those of streptococcal phages r1t, 01205, and Dp-1, suggesting that pblA and pblB might reside within a prophage. To address this possibility, cultures of SF100 were exposed to either mitomycin C or UV light, both of which are known to induce the lytic cycle of many temperate phages. Both treatments caused a significant increase in the transcription of pblA. Treatment with mitomycin C or UV light also caused a substantial increase in the expression of PblA and PblB, as detected by Western blot analysis of proteins in the SF100 cell wall. By electron microscopy, phage particles were readily visible in the supernatants from induced cultures of SF100. The phage, designated SM1, had a double-stranded DNA genome of approximately 35 kb. Southern blot analysis of phage DNA indicated that pblA and pblB were contained within the SM1 genome. Furthermore, Western blot analysis of phage proteins revealed that both PblA and PblB were present in the phage particles. These findings indicate that PblA and PblB are encoded by a lysogenic bacteriophage, which could facilitate the dissemination of these potential virulence determinants to other bacterial pathogens

  20. Bacteriophages transducing antibiotic resistance from a cluster of lysogenic strains of Pseudomonas aeruginosa isolated from patients. Blahova, J., Kralikova, K., Krcmery, V., Sr., Schafer, V (2001). Journal of Chemotherapy 13:331-333.

  21. Faecal bacteria and bacteriophage inactivation in a full-scale UV disinfection system used for wastewater reclamation. Bourrouet, A., Garcia, J., Mujeriego, R., Penuelas, G. (2001). Water Science and Technology 43:187-194. A study was carried out to compare the inactivation of faecal bacteria and one type of bacteriophage in a full-scale UV disinfection system. The system is part of a water reclamation facility for effluent reuse in golf course and agricultural irrigation. Influent and effluent samples were taken over two sampling periods (three consecutive days in July and one day in August), with three different UV doses applied each day (ranging from 10 to 40 mWcntdots/cm2 and 20 to 80 mWcntdots/cm2 in July and August, respectively). Effluent samples were also taken from a chlorine disinfection channel (5 mg Cl2/L dose) operating in parallel to the UV system. Total coliforms (TC), faecal coliforms (FC), faecal streptoccoci (FS) and somatic coliphages (SC) were measured in each sample. F-specific RNA bacteriophages and bacteriophages of Bacteroides fragilis were also measured one day in July. The decay ratio observed for all the microorganisms was similar when UV doses applied were low (July), ranging from 1.15 to 1.25 log-units. This suggests that bacterial indicators may be suitable for virus inactivation control when low UV doses are applied; however, such low doses are inadequate to achieve effluent quality requirements for unrestricted irrigation. At higher UV doses (August), decay ratios for TC and FC were 3.1 and 2.8 log-units respectively, indicating that they were more susceptible to UV exposure than SC and FS, with decay ratios of 2.6 and 1.0 log-units, respectively. Nevertheless, these higher doses were also inadequate to achieve water quality requirements for unrestricted irrigation. The decay ratio of SC during chlorine disinfection was clearly lower than that of the other microorganisms. Bacteriophages of Bacteroides fragilis were more resistant to UV disinfection than SC and F-specific RNA. In fact, bacteriophages of Bacteroides fragilis were not affected during UV exposure. A UV dose ranging from 40 to 80 mWcntdots/cm2 marks the borderline beyond which inactivation rates of SC are clearly lower than those of bacterial indicators

  22. Collective action in an RNA virus. Brown, S. P. (2001). Journal of Evolutionary Biology 14:821-828. A recent empirical study by Turner and Chao on the evolution of competitive interactions among phage virus strains revealed that a strain grown at high rates of co-infection evolved towards lowered fitness relative to an ancestral strain. The authors went on to show that the fitness pay-off matrix between the evolved and ancestral strain conforms to the prisoners' dilemma. In this paper, I use Turner and Chao's data to parameterize a simple model of parasite collective action. The prisoners' dilemma is based on pairwise interactions of a discrete cooperate/defect nature. In contrast, the collective action model explicitly deals with individual-group interactions where the extent of cooperation is a continuous variable. I argue here that the 'collective action' modelling approach is more appropriate than the prisoners' dilemma for the biology of virus evolution, and hence better able to form a predictive framework for further work on related strains of virus, linking mixing ecology, cooperative phenotype and fitness. Furthermore, the collective action model is used to motivate discussion on the evolutionary ecology of viruses, with a focus on the 'levels of selection' debate and the evolution of virulence

  23. A general mechanism for viral resistance to suicide gene expression. Bull, J. J., Badgett, M. R., Molineux, I. J. (2001). Journal of Molecular Evolution 53:47-54. Bacteriophage T7 was challenged with either of two toxic genes expressed from plasmids. Each plasmid contained a different gene downstream of a T7 promoter; cells harboring each plasmid caused an infection by wild-type T7 to abort. T7 evolved resistance to both inhibitors by avoidance of the plasmid expression system rather than by blocking or bypassing the effects of the specific toxic gene product. Resistance was due to a combination of mutations in the T7 RNA polymerase and other genes expressed at the same time as the polymerase. Mutations mapped to sites that are unlikely to alter polymerase specificity for its cognate promoter but the basis for discrimination between phage and plasmid promoters in vivo was not resolved. A reporter assay indicated that, relative to wild-type phage, gene expression from the plasmid was diminished several-fold in cells infected by the evolved phages. A recombinant phage, derived from the original mutant but lacking a mutation in the gene for RNA polymerase, exhibited in-termediate activity in the reporter assay and intermediate resistance to the toxic gene cassettes. Alterations in both RNA polymerase and a second gene are thus responsible for resistance. These findings have broad evolutionary parallels to other systems in which viral inhibition is activated by viral regulatory signals such as defective-interfering particles, and they may have mechanistic parallels to the general phenomena of position effects and gene silencing.

  24. Water quality improvement of treated wastewater by intermittent soil percolation. Castillo, G., Mena, M. P., Dibarrart, F., Honeyman, G. (2001). Water Science and Technology 43:187-190. Our research aimed to evaluate intermittent soil infiltration of treated sewage for reuse in the north of Chile. Aerated lagoon effluent was infiltrated in columns packed with native soils (sandy-lime, lime-gravel and limey-sand). Columns were operated for more than a year under different cycles of filling and drying, depths and load pressures depending on soil characteristics. The efficiency of the system was determined through influent-effluent microbiological indicators level (faecal coliforms, E. coli, Salmonella spp, MS2 phage, and protozoan cysts), physicochemical characterisation (TOC, COD, BOD, nitrogen), and hydraulic flow measurement. Results showed: (a) high reduction of enteric bacteria (5-7 log10), some inactivation of phage (2-4 log10) and complete removal of intestinal cyst; (b) stable removal of organic matter (80-90% reduction of TOC, COD, BOD); and (c) partial ammonia reduction through adsorption and nitrification with denitrification mainly occurring in sandy soil. Preliminary data from pilot plant working in the field showed better results that those obtained in the laboratory especially removal of microbiological indicators. Microbiological quality of effluent met Class A regulations for agricultural reuse (WHO, 1989) and the system looks like an attractive alternative to cope with water shortage in the region

  25. Rapid Identification of Escherichia coli O157:H7. Chang, T. C., Chen, S., Ding, H. C. (2001). Official Gazette of the United States Patent and Trademark Office Patents 1245:No. A method of determining whether a test microorganism is a known microorganism, involving use of an agent that specifically affects the growth of the known microorganism. The invention also features a method of identifying E. coli O157:H7 that are based on the following criteria: a test microorganism is E. coli O157:H7 if the microorganism is (i) E. coli, (ii) incapable of fermenting sorbitol, and (iii) susceptible to infection by AR1 phage

  26. Bacteriophage T4 multiplication in a glucose-limited Escherichia coli biofilm. Corbin, B. D., McLean, R. J. C., Aron, G. M. (2001). Canadian Journal of Microbiology 47:680-684. An Escherichia coli K-12 biofilm was grown at a dilution rate of 0.028 h-1 for 48 h in a glucose-limited chemostat coupled to a modified Robbins' device to determine its susceptibility to infection by bacteriophage T4. Bacteriophage T4 at a multiplicity of infection (MOI) of 10 caused a log reduction in biofilm density (expressed as colony forming units (CFU) per cm2) at 90 min postinfection. After 6 h, a net decrease and equilibrium in viral titer was seen. When biofilms were exposed to T4 phage at a MOI of 100, viral titer doubled after 90 min. After 6 h, viral titers (expressed as plaque forming units (PFU) per cm2) stabilized at levels approximately one order of magnitude higher than seen at a MOI of 10. Scanning confocal laser microscopy images also indicated disruption of biofilm morphology following T4 infection with the effects being more pronounced at a MOI of 100 than at a MOI of 10. These results imply that biofilms under carbon limitation can act as natural reservoirs for bacteriophage and that bacteriophage can have some influence on biofilm morphology

  27. Clinical and environmental isolates of Vibrio cholerae serogroup O141 carry the CTX phage and the genes encoding the toxin-coregulated pili. Dalsgaard, A., Serichantalergs, O., Forslund, A., Lin, W., Mekalanos, J., Mintz, E., Shimada, T., Wells, J. G. (2001). Journal of Clinical Microbiology 39:4086-4092. We report sporadic cases of a severe gastroenteritis associated with Vibrio cholerae serogroup O141. Like O1 and O139 serogroup strains of V. cholerae isolated from cholera cases, the O141 clinical isolates carry DNA sequences that hybridize to cholera toxin (CT) gene probes. The CT genes of O1 and O139 strains are carried by a filamentous bacteriophage (termed CTX phage) which is known to use toxin-coregulated pili (TCP) as its receptor. In an effort to understand the mechanism of emergence of toxigenic O141 V. cholerae, we probed a collection of O141 clinical and environmental isolates for genes involved in TCP production, toxigenicity, virulence regulation, and other phylogenetic markers. The collection included strains isolated between 1964 and 1995 from diverse geographical locations, including eight countries and five U.S. states. Information collected about the clinical and environmental sources of these isolates suggests that they had no epidemiological association. All clinical O141 isolates hybridized to probes specific for genes encoding CT (ctx), zonula occludens toxin (zot), repetitive sequence 1 (RS1), RTX toxin (rtxA), the major subunit of TCP (tcpA), and the essential regulatory gene that controls expression of both CT and TCP (toxR). In contrast, all but one of the nonclinical O141 isolates were negative for ctx, zot, RS1, and tcpA, although these strains were positive for rtxA and toxR. The one toxigenic environmental O141 isolate was also positive for tcpA. Ribotyping and CT typing showed that the O141 clinical isolates were indistinguishable or closely related, while a toxigenic water isolate from Louisiana showed a distantly related ribotype. Nonclinical O141 isolates displayed a variety of unrelated ribotypes. These data support a model for emergence of toxigenic O141 that involves acquisition of the CTX phage sometime after these strains had acquired the pathogenicity island encoding TCP. The clonal nature of toxigenic O141 strains isolated from diverse geographical locations suggests that the emergence is a rare event but that once it occurs, toxigenic O141 strains are capable of regional and perhaps even global dissemination. This study stresses the importance of monitoring V. cholerae non-O1, non-O139 serogroup strains for their virulence gene content as a means of assessing their epidemic potential

  28. Comparative genomics of lactococcal phages: insight from the complete genome sequence of Lactococcus lactis phage BK5-T. Desiere, F., Mahanivong, C., Hillier, A. J., Chandry, P. S., Davidson, B. E., Brussow, H. (2001). Virology 283:240-252. Lactococcus lactis phage BK5-T and Streptococcus thermophilus phage Sfi21, two cos-site temperate Siphoviridae with 40-kb genomes, share an identical genome organization, sequence similarity at the amino acid level over about half of their genomes, and nucleotide sequence identity of 60% over the DNA packaging and head morphogenesis modules. Siphoviridae with similarly organized genomes and substantial protein sequence similarity were identified in several genera of low-GC-content Gram-positive bacteria. These phages demonstrated a gradient of relatedness ranging from nucleotide sequence similarity to protein sequence similarity to gene map similarity over the DNA packaging and head morphogenesis modules. Interestingly, the degree of relatedness was correlated with the evolutionary distance separating their bacterial hosts. These observations suggest elements of vertical evolution in phages. The structural genes from BK5-T shared no sequence relationships with corresponding genes/proteins from lactococcal phages belonging to distinct lactococcal phage species, including phage sk1 (phage species 936) that showed a closely related gene map. Despite a clearly distinct genome organization, lactococcal phages sk1 and c2 showed nine sequence-related proteins. Over the early gene cluster phage BK5-T shared nine regions of high nucleotide sequence similarity, covering at most two adjacent genes, with lactococcal phage r1t (phage species P335). Over the structural genes, the closest relatives of phage r1t were not lactococcal phages belonging to other phage species, but Siphoviridae from Mycobacteria (high-GC-content Gram-positive bacteria). Evidence for recent horizontal gene transfer between distinct phage species was obtained for dairy phages, but these transfers were limited to phages infecting the same bacterial host species.

  29. Bacteriophages of Borrelia burgdorferi and other spirochetes. Eggers, Christian H., Casjens, Sherwood, Samuels, D. S., Saier, Milton H., Jr., Garcia-Lara, Jorge Eds (2001). JMMB Symposium Series. The spirochetes: Molecular and cellular biology. 35-44.

  30. Adsorption and survival of faecal coliforms, somatic coliphages and F-specific RNA phages in soil irrigated with wastewater. Gantzer, C., Gillerman, L., Kuznetsov, M., Oron, G. (2001). Water Science and Technology 43:117-124. This study was carried out to compare the adsorption and survival of faecal coliforms, somatic coliphages and F-specific RNA phages in soil irrigated with wastewater. Adsorption isotherms showed that 3-10X more faecal coliforms than somatic coliphages were adsorbed from wastewater onto soil. The adsorption behavior of F-specific RNA phages was intermediate between those of these two microorganisms. In wastewater, the inactivation factor of somatic coliphages at 8-22°C was 5-7 lower than those of faecal coliforms. F-specific RNA phages have a decrease close to faecal coliforms. In soil, at temperatures of 8-22°C and at moistures of 15-35%, somatic coliphages survived longer than the two other microorganisms. These results seemed to be confirmed by the soil column experiments. The rate of inactivation of all microorganisms was lower in soil than in wastewater and depended extensively on soil temperature and moisture content. Survival was optimal at low temperature (8°C) and low moisture content (15%). Thus, somatic coliphages seemed to be a better indicator of faecal contamination than faecal coliforms under our experimental conditions and based only on the two criteria tested (survival and adsorption). Somatic coliphages were able to contaminate the soil over greater distances and survive better in both wastewater and soil than faecal coliforms. These results need to be confirmed by studies on several soil columns using different kinds of soil and different kinds of wastewater

  31. Bacteriophages: Update on application as models for viruses in water. Grabow, W. O. K. (2001). Water SA (Pretoria) 27:251-268. Phages are valuable models or surrogates for enteric viruses because they share many fundamental properties and features. Among these are structure, composition, morphology, size and site of replication. Even though they use different host cells, coliphages and Bacteroides fragilis phages predominantly replicate in the gastro-intestinal tract of humans and warm-blooded animals where enteric viruses also replicate. A major advantage of phages is that, compared to viruses, they are detectable by simple, inexpensive and rapid techniques. In view of these features, phages are particularly useful as models to assess the behaviour and survival of enteric viruses in the environment, and as surrogates to assess the resistance of human viruses to water treatment and disinfection processes. Since there is no direct correlation between numbers of phages and viruses, phages cannot to a meaningful extent be used to indicate numbers of viruses in polluted water. The presence of phages typically associated with human and animal excreta indicates the potential presence of enteric viruses. However, the absence of these phages from water environments is generally a meaningful indication of the absence of enteric viruses. This is because phages such as somatic coliphages, F-RNA coliphages and B. fragilis phages generally outnumber enteric viruses in water environments, and they are at least as resistant to unfavourable conditions including those in water treatment and disinfection processes. However, using highly sensitive molecular techniques viruses have been detected in drinking water supplies which yielded negative results in conventional tests for phages. Initially, data on phages were rather confusing because a wide variety of techniques was used. However, techniques for the detection of phages are being standardised internationally. This applies in particular to somatic and F-RNA coliphages, and B. fragilis phages, which are most commonly used in water quality assessment. Reliable and practical techniques now available include direct quantitative plaque assays on samples of water up to 100 ml, and qualitative tests on 500 ml or more using highly sensitive enrichment procedures

  32. Cheese making with bacteriophage resistant bacteria. Hicks, C. L. (2001). Official Gazette of the United States Patent and Trademark Office Patents 1251:No. A method is provided for reducing or preventing bacteriophage attack on bacteria used in a cheese making process. The method includes (a) treating a blocker peptide precursor with a protease enzyme that hydrolyzes the precursor to produce blocker peptides; (b) collecting the blocker peptides so produced; (c) formulating a starter media with the blocker peptides; (d) growing bulk cultures of cheese making bacteria in the inoculated starter media; and (e) adding bacteria grown in the inoculated starter media to a fermentation medium for producing cheese. The present invention also includes a method of making cheese and cheese produced by the method

  33. Seasonal dynamics of viruses in an alpine lake: Importance of filamentous forms. Hofer, J. S., Sommaruga, R. (2001). Aquatic Microbial Ecology 26:1-11. Viruses are an important component of the planktonic food web in freshwater and marine systems, but most studies have been done in the ocean and in lowland lakes. In this work, the seasonal dynamics and structure of the virioplankton as well as their impact on bacteria during a day/night cycle were studied in an alpine lake located 2417 m above sea level. The abundance of virus-like particles (VLP) was determined at 5 discrete depths (0.5 to 8 m) by direct counts with a TEM in samples collected from May to November 1998 at weekly to bi-weekly intervals. Viruses reached the highest abundances under ice (4.6 X 106 VLP ml-1) with a second maximum in autumn. After ice-break, the VLP abundance decreased to undetectable values (<2 X 104 VLP ml-1) probably because of the negative effect of solar radiation that was negatively correlated with the viral abundance in the upper 2 m of the water column (Spearman rank correlation, rs = -0.773, p < 0.01). The virioplankton was morphologically diverse, consisting of forms commonly found in other aquatic systems, but unlike other studies, we found filamentous VLP (FVLP) 450 to 730 nm long that attained abundances of up to 1.3 X 106 ml-1 and accounted for 7 to 100% of the total viral abundance. These FVLP were found occasionally inside filamentous heterotrophic bacteria (> 10 mum) and their respective abundances were positively correlated (rs = 0.728, p < 0.01). The absence of these conspicuous forms in other aquatic ecosystems suggests that FVLP are well adapted to the harsh environmental conditions or are specific to bacterial hosts found in alpine lakes. Finally, between 5 and 28% of the newly produced bacteria were killed by non-filamentous viruses, which therefore are a modest cause of bacterial mortality in this lake

  34. Profiles of adaptation in two similar viruses. Holder, K. K., Bull, J. J. (2001). Genetics 159:1393-1404. The related bacteriophages variant phiX174 and G4 were adapted to the inhibitory temperature of 44° and monitored for nucleotide changes throughout the genome. Phage were evolved by serial transfer at low multiplicity of infection on rapidly dividing bacteria to select genotypes with the fastest rates of reproduction. Both phage showed overall greater fitness effects per substitution during the early stages of adaptation. The fitness of variant phiX174 improved from -0.7 to 5.6 doublings of phage concentration per generation. Five missense mutations were observed. The earliest two mutations accounted for 85% of the ultimate fitness gain. In contrast, G4 required adaptation to the intermediate temperature of 41.5degree before it could be maintained at 44°. Its fitness at 44° increased from -2.7 to 3.2, nearly the same net gain as in variant phiX174, but with three times the opportunity for adaptation. Seventeen mutations were observed in G4: 14 missense, 2 silent, and 1 intergenic. The first 3 missense substitutions accounted for over half the ultimate fitness increase. Although the expected pattern of periodic selective sweeps was the most common one for both phage, some mutations were lost after becoming frequent, and long-term polymorphism was observed. This study provides the greatest detail yet in combining fitness profiles with the underlying pattern of genetic changes, and the results support recent theories on the range of fitness effects of substitutions fixed during adaptation

  35. Application of rapid detection for Mycobacterium tuberculosis with phage splitting assay. Hu, Z., Pang, M., Jin, A. (2001). Zhonghua Jiehe He Huxi Zazhi 24:611-613. Objective: To study the significance of rapid identification for Mycobacterium tuberculosis with phage splitting assay. Methods: Strains of Mycobacterium tuberculosis, non-tuberculosis mycobacterium, non-mycobacterium and samples of sputum with pulmonary tuberculosis were rapidly detected by phage spot technique. Results: The strains of Mycobacterium tuberculosis H37Rv, bovis and africanum were all positive. The results of 10 strains of non-tuberculosis mycobacterium and 7 strains of non-mycobacterium were negative. All of 30 clinical isolates from the patients of the pulmonary tuberculosis were positive. 19 of 20 sputum specimen of pulmonary tuberculosis, which were all positive detected by smear and culture, were positive. There were 15 specimen positive in 21 sputum with negative tested by smear and positive by culture. Besides, 5 of 19 sputum specimen with negative by smear and culture were positive detected by this method. Conclusion: The phage splitting assay can be used for rapid identification of Mycobacterium tuberculosis, which possesses high specificity and sensitivity for detection of Mycobacterium tuberculosis in sputum specimen

  36. Lytic and lysogenic infection of diverse Escherichia coli and Shigella strains with a verocytotoxigenic bacteriophage. James, C. E., Stanley, K. N., Allison, H. E., Flint, H. J., Stewart, C. S., Sharp, R. J., Saunders, J. R., McCarthy, A. J. (2001). Applied and Environmental Microbiology 67:4335-4337. A verocytotoxigenic bacteriophage isolated from a strain of enterohemorrhagic Escherichia coli O157, into which a kanamycin resistance gene (aph3) had been inserted to inactivate the verocytotoxin gene (vt2), was used to infect Enterobacteriaceae strains. A number of Shigella and E. coli strains were susceptible to lysogenic infection, and a smooth E. coli isolate (O107) was also susceptible to lytic infection. The lysogenized strains included different smooth E. coli serotypes of both human and animal origin, indicating that this bacteriophage has a substantial capacity to disseminate verocytotoxin genes. A novel indirect plaque assay utilizing an E. coli recA441 mutant in which phage-infected cells can enter only the lytic cycle, enabling detection of all infective phage, was developed

  37. Effects of disinfectants on Shiga-like toxin converting phage from enterohemorrhagic Escherichia coli O157 : H7. Kajiura, T, Tanaka, M., Wada, H., Ito, K., Koyama, Y., Kato, F. (2001). Journal of Health Science 47:203-207. Inactivation of free phage carrying slt2 from enterohemorrhagic Escherichia coli (E. coli) O157 : H7 by four kinds of common disinfectants in Japan was examined under conditions with (dirty) and without (clean) interfering substance. Ethanol (EtOH) inactivated the phage within one minute under both conditions. The effect of sodium hypochlorite (NaOCl) on this phage decreased under the dirty condition, but was potentiated by increasing the concentration and contact time to the degree that could be sufficient for practical use. Use of benzalkonium chloride (BAC) at a high concentration: 0.2%, would be effective. Alkyldiaminoethylglycine hydrochloride (DAG) was not effective on this phage

  38. Phage conversion of staphylococcal bi-component toxin. Kaneko, J. (2001). Nippon Nogeikagaku Kaishi 75:939-947.

  39. Behavior of restriction-modification systems as selfish mobile elements and their impact on genome evolution. Kobayashi, I (2001). Nucleic Acids Research 29:3742-3756. Restriction-modification (RM) systems are composed of genes that encode a restriction enzyme and a modification methylase. RM systems sometimes behave as discrete units of life, like viruses and transposons. RM complexes attack invading DNA that has not been properly modified and thus may serve as a tool of defense for bacterial cells. However, any threat to their maintenance, such as a challenge by a competing genetic element (an incompatible plasmid or an allelic homologous stretch of DNA, for example) can lead to cell death through restriction breakage in the genome. This post-segregational or post-disturbance cell killing may provide the RM complexes (and any DNA linked with them) with a competitive advantage. There is evidence that they have undergone extensive horizontal transfer between genomes, as inferred from their sequence homology, codon usage bias and GC content difference. They are often linked with mobile genetic elements such as plasmids, viruses, transposons and integrons. The comparison of closely related bacterial genomes also suggests that, at times, RM genes themselves behave as mobile elements and cause genome rearrangements. Indeed some bacterial genomes that survived post-disturbance attack by an RM gene complex in the laboratory have experienced genome rearrangements. The avoidance of some restriction sites by bacterial genomes may result from selection by past restriction attacks. Both bacteriophages and bacteria also appear to use homologous recombination to cope with the selfish behavior of RM systems. RM systems compete with each other in several ways. One is competition for recognition sequences in post-segregational killing. Another is super-infection exclusion, that is, the killing of the cell carrying an RM system when it is infected with another RM system of the same regulatory specificity but of a different sequence specificity. The capacity of RM systems to act as selfish, mobile genetic elements may underlie the structure and function of RM enzymes

  40. The bacteriophage lambda attachment site in wild strains of Escherichia coli. Kuhn, J., Campbell, A. (2001). Journal of Molecular Evolution 53:607-614. The attachment site (attlambda) of bacteriophage lambda was examined in wild strains of Escherichia coli. Although the att region is non-coding, the DNA sequence was invariant in the 13 strains examined. Two other non-coding regions showed nine changes, all associated with a single strain. In four of 33 strains, sequences were inserted in or near the attlambda site and in two of these the insert was related to lambda. Among strains that can be lysogenized by lambda, integration was via the attlambda site in all cases. Some resistant strains can be lysogenized, and these have been termed "lenient". Most of these fail to give normal phage yield after induction. In some cases rare lysogens have been formed in cells that belong to a mutant sub-population

  41. Vibrio detection by 6 species of bacteriophages of Vibrionaceae. Lin, Y., Chen, K., Ou, J. (2001). Zhonghua Weishengwuxue He Mianyixue Zazhi 21:108-110. Objective: To predigest the detection procedure of 6 species of pathogenic bacteria of Vibrionaceae. Methods: Six species of specific bacteriophages were isolated and filtered to identify and type corresponding pathogenic bacteria. Results: 440 strains of bacteriophages, among which 54 strains were selected to form the typing bacteriophage groups, were isolated from 1400 environmental specimens. The typing bacteriophage groups could identify and type 80%-90% of bacteria in laboratory or those from environment. Conclusion: The application of specific bacteriophages to identify the corresponding pathogenic bacteria is fast, economic and easy to operate, so bacteriophage typing is an effective method in epidemiology investigation

  42. The effects of seasonal variability and weather on microbial fecal pollution and enteric pathogens in a subtropical estuary. Lipp, E. K., Kurz, R., Vincent, R., Rodriguez-Palacios, C., Farrah, S. R., Rose, J. B. (2001). Estuaries 24:266-276. The Charlotte Harbor estuary in southwest Florida was sampled monthly for one year at twelve stations, in the lower reaches of the Myakka and Peace Rivers. The objectives of the study were to address the distribution and seasonal changes in microbial indicators and human pathogen levels in Charlotte Harbor shellfish and recreational waters, and to determine those factors that may be important in the transport and survival of pathogens. Monthly water samples and quarterly sediment samples were analyzed for fecal coliform bacteria, enterococci, Clostridium perfringens, and coliphage. Quarterly samples also were analyzed for the enteric human pathogens, Cryptosporidium spp., Giardia spp., and enteroviruses. Fecal indicator organisms were generally concentrated in areas of low salinity and high densities of septic systems; however, pollution became widespread during wet weather in the late fall and winter of 1997-1998, coincident with a strong El Nino event. Between December 1997 and February 1998, enteroviruses were detected at 75% of the sampling stations; none were detected in other months. Enteric protozoa were detected infrequently and were not related to seasonal influences. Fecal indicators and enteroviruses were each significantly associated with rainfall, streamflow, and temperature. Regression models suggest that temperature and rainfall can predict the occurrence of enteroviruses in 93.7% of the cases. Based on findings in this watershed, factors such as variability in precipitation, streamflow, and temperature show promise in modeling and forecasting periods of poor coastal water quality

  43. Isolation and characterisation of Campylobacter bacteriophage from free-range chicken farm. Loc-Carrillo, C. M., Connerton, P., Dodd, C., Rees, C., Connerton, I (2001). International Journal of Medical Microbiology 291:79.

  44. Production and release of Shiga toxin from Shigella dysenteriae 1. McDonough, M. A., Butterton, J. R. (2001). Abstra