Phage Scientist – DuPont

DuPont Nutrition & Health is a USD 4.7 billion global business and one of the world’s largest producers of specialty food ingredients, developing and manufacturing solutions for the global food & beverage, nutrition and pharma market. With more than 8,500 employees, 50+ manufacturing sites and 20+ R&D centres across the world, N&H is on a mission to make food safer, more sustainable, better tasting and more nutritious.
N&H is part of DowDuPont, a globally listed company, which came to life following the merger of Dow Chemical and DuPont in 2017. DowDuPont has a turnover of approximately $62 billion, employs around 98,000 FTEs and is headquartered in Wilmington, USA.  The Upstream Culture Development group is part of the R&D Department of its Culture Development and Food Protection Division. The group is strongly involved in knowledge development and is responsible for selecting strains of microorganisms to be used in the design of starter cultures for dairy and other fermentation industries.

The group, which is based in France (86), is seeking a Phage Scientist

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Phage Directory (phage.directory): An origin story

When Twitter told me last week that my former next-door lab neighbour just mailed phages to a dying girl, I actually started believing that my research might mean something. Not eventually, but today.

I used to think phage researchers like me were meant to do plaque assays in a lab for a few decades, while “other people out there, in 50 years, maybe” would sift through the information I would eventually publish and use it to cure people of bacterial infections. I’d gotten comfortable with the idea of doing research for the sake of research. I’d become proud of my patience and my willingness to do science without needing it to help people. I thought this made me a good scientist.

My thinking started to change when I heard the story of Tom Patterson, the patient cured last year in San Diego of his A. baumannii infection following phage therapy. The part that really got to me was how his treatment was essentially crowd-sourced in an effort led by his wife, Steffanie Strathdee (@chngin_the_wrld).

Fast forward to a week and a half ago, when I noticed that Steffanie’s phage-sourcing efforts were back in full force. This time, she was working to save 25-year-old Mallory Smith from drug-resistant B. cepacia. This time, however, I was watching it in real time. She used hashtags and @mentions to ask researchers to send phages. She used caps lock to emphasize urgency.

I had a fleeting thought about texting my friend from Jon Dennis’ lab at the University of Alberta, because I knew they worked on B. cepacia. Instead, I thought, those hashtags aren’t for grad students like me or for labs like ours. Those messages are for companies that make lots and lots of phages using proprietary processes, for labs with ties to hospitals that work with patients, for government organizations like the US Navy and its phage library.

And then I saw Steffanie tweet a thank-you to @JonDennis8 for sending phages, and I realized that the kind of researcher she was trying to reach was me.

I shared all of this with my friend Jan Zheng, who specializes in how humans interact with computers. He designs ways of simplifying this experience. Upon seeing the Twitter trail and hearing about Mallory and Tom’s stories and the phage hunts associated with both, he excitedly proclaimed that he knew how we could simplify this experience too.

We spent the next several days creating Phage Directory (phage.directory), a website designed to help treat patients infected by drug-resistant pathogens with safe and effective doses of phages, on a last-resort, emergency basis through the FDA’s Emergency Investigational New Drug process.

Although phage therapy is not yet ready to be adopted by mainstream Western medicine, the FDA is ready for phage therapy on a case-by-case basis as long as antibiotics are tried first. To paraphrase what Scott Stibitz of the FDA said at the Evergreen Phage Meeting this year: those of us who have been repeating the trope that the FDA is an enemy of phage therapy should stop, because we’re wrong.

A major part of what Jan and I envision that this directory will do is to serve as a searchable resource and alert service to help patient advocates find phage researchers who are willing to send phages to a patient in need, on an individual, on-demand basis. We also hope to connect these researchers with those willing to test the host range of these phages on patient isolates and then to propagate and purify promising candidates prior to shipment to the patient.

Two days into building Phage Directory, we found out that Mallory had passed away. This heart wrenching news spurred us on, and we launched the site last Friday. We made a Twitter account and began reaching out to phage researchers and others who might be interested in the cause.

Now, a week after its launch, we have reached 100 followers on Twitter (mostly phage biologists) and have been talking to Steffanie about how a directory like this would optimally function. She put us in touch with Tobi Nagel of Phages for Global Health, who was excited to talk with us. Phages for Human Applications Group Europe (P.H.A.G.E.) has encouraged its members to sign up, and several of them have. Sylvain Moineau and the Félix d’Hérelle Center at Université Laval in Canada are also on board.

On Monday of this week, we found out that Mallory’s parents were thrilled to hear about Phage Directory, and want to help us help other patients in honour of their daughter. On Tuesday, the journalist at STAT News who wrote the original article detailing Steffanie’s efforts to find phages for Mallory interviewed Jan and me for his next story.

What began as an offhand comment that we should make “PhageBook” has become a very real and impassioned effort to identify the barriers to treating patients with phages, particularly in the West, and to systematically design ways to overcome these barriers. Especially at this stage, we are open to suggestions on how best to put together this resource.

In addition to its role as a phage researcher directory and virtual phage library, we envision Phage Directory becoming a resource for physicians and other patient advocates seeking to learn about the actions required to initiate phage therapy in a patient, the associated legal implications, and the particular phages and treatment strategies available.

We see it becoming a communication platform that facilitates and organizes secure exchanges between doctors and researchers, before, during and after phage treatment, e.g. which phages should be tried first or next? How does susceptibility to each phage and antibiotic evolve over the course of each treatment iteration?

We see it providing the public with an interactive lens into the world of phage therapy, where patients and families can identify and communicate with phage researchers and physicians willing to facilitate phage therapy.

We see it helping to build legitimacy and transparency into the process of phage therapy to help regulatory agencies gain confidence in its feasibility.

Overall, we see Phage Directory as an action-oriented tool that will break down barriers to phage therapy by providing a multi-stakeholder communication platform designed to simplify and streamline the process.

Since I’ve joined our remarkable phage community, I’ve become increasingly conscious of its deep commitment to bringing phage therapy to modern medicine. I hope that many of you will add yourselves to Phage Directory and that you’ll sign up for the alert service so you can be contacted in the event that a patient needs your phages.

Finally, I hope that you’ll spread the word about this initiative so we can all take advantage of the momentum generated from Tom and Mallory’s recent public battles to put what we’ve collectively been writing and thinking about for years into a new kind of action.

d’Hérelle, F. (1918). Sur le rôle du microbe filtrant bactériophage dans la dysentérie bacillaire. Compt. rend. Acad. Sci. 167:970-972.

Stephen T. Abedon

Department of Microbiology – The Ohio State University

phage.org – phage-therapy.org – biologyaspoetry.org


 

I’ve been meaning to post machine-translated articles for some time now. Here is what you are seeing:

  • The posts are broken up by paragraphs with three sections per
  • The first section is the paragraph more or less retaining original page breaks (for easier reconciliation with the original document)
  • The second section is the paragraphs minus those page breaks
  • The third section, in bold, is the translation generated by Google with occasional help from a human being (e.g., moi)

Please feel free to make suggestions as to how to improve transcriptions and/or translations.

Oh, yes, and feel free to skip to the last “sentence” (actually, fragment), which, I think, is historically the most important point of the article.

BACTÉRIOLOGIE. – Sur le rôle du microbe filtrant bactériophage dans la

dysenterie bacillaire. Note de M. F. D’HÉRELLE, présentée par M. Roux.

 

BACTÉRIOLOGIE. – Sur le rôle du microbe filtrant bactériophage dans la dysenterie bacillaire. Note de M. F. D’HÉRELLE, présentée par M. Roux.

BACTERIOLOGY. – On the role of the filter microbe bacteriophage in bacillary dysentery. Note to Mr. F. D’HÉRELLE, by Mr Roux.

 

Dans une Note préliminaire (1) j’ai décrit un microbe filtrant trouvé

dans les déjections des convalèscents de dysenterie bacillaire. L’emploi

d’une technique moins imparfaite que celle dont je m’étais servi tout

d’abord (2) joint à l’examen systématique des selles de trente-quatre

malades, tous atteints de dysenterie à bacilles de Shiga, et dont plusieurs

ont pu être suivis journellement depuis le début de la maladie jusqu’à la fin

de la convalescence, m’ont permis d’etudier d’une manière plus complète

le mode d’action du microbe bactériophage et de préciser son rôle dans

l’évolution de la maladie.

 

Dans une Note préliminaire (1) j’ai décrit un microbe filtrant trouvé dans les déjections des convalèscents de dysenterie bacillaire. L’emploi d’une technique moins imparfaite que celle dont je m’étais servi tout d’abord (2) joint à l’examen systématique des selles de trente-quatre malades, tous atteints de dysenterie à bacilles de Shiga, et dont plusieurs ont pu être suivis journellement depuis le début de la maladie jusqu’à la fin de la convalescence, m’ont permis d’etudier d’une manière plus complète le mode d’action du microbe bactériophage et de préciser son rôle dans l’évolution de la maladie.

In a preliminary Note (1) I wrote [of] a filter[able] microbe found in excreta of dysentery bacillary [from] convalescents. The use of a technique less imperfect than the one I had used first (2) attached to the systematic examination of stools of thirty-four patients, all dysentery bacilli Shiga, and several of were followed daily from the beginning of the disease until the end of convalescence, allowed me to study in a more complete way the mode of action of the microbe bacteriophage and clarify its role in evolution of the disease.

 

(1) Comptes rendus, t. 165, 1917, p. 373.

(2) Comptes rendus de la Société de Biologie, séance du 7 décembre rg18.

 

Dans les cas de dysenterie bacillaire, même très graves, mais dans lesquels

l’état du patient s’améliore ‘rapidement, le microbe ,bactériophage

manifeste sa présence d’une· manière très active d’emblée, tant sur les cultures

du bacille isolé des déjections du patient que sur les souches du Shiga

du laboratoire, à partir du moment où les symptômes commencent à

s’amender. Le pouvoir bactériophage vis-à-vis du bacille dysentérique cesse

brusquement d’être décelable au début de la convalescence. A· partir de ce

moment, des examens répétés montrent également l’absence de bacilles

pathogènes.

 

Dans les cas de dysenterie bacillaire, même très graves, mais dans lesquels l’état du patient s’améliore ‘rapidement, le microbe ,bactériophage manifeste sa présence d’une manière très active d’emblée, tant sur les cultures du bacille isolé des déjections du patient que sur les souches du Shiga du laboratoire, à partir du moment où les symptômes commencent à s’amender. Le pouvoir bactériophage vis-à-vis du bacille dysentérique cesse brusquement d’être décelable au début de la convalescence. A partir de ce moment, des examens répétés montrent également l’absence de bacilles pathogènes.

In cases of bacillary dysentery, even very serious but in which the patient’s condition is improving quickly, the microbe, bacteriophage demonstrates its presence in a very active from the outset, both cultures of isolated bacillus excreta of the patient as the Shiga strains of laboratory, from the time symptoms begin to mend. Bacteriophage power vis-à-vis the dysentery bacillus suddenly ceases to be detectable in early convalescence. From that moment, repeated examinations also show the absence of pathogenic bacilli.

 

Dans les cas où la maladie se prolonge, le microbe bactériophage ne

manifeste qu’une action mille ou peu marquee, tant que l’état du patient

reste stationnaire. Si, dans quelques cas, l’action bactéricide est reiativement élevée sur les souches ayant subi de nombreux passages sur les

milieux de culture, par contre, elle est toujours inappréciable ou très faible

sur les cultures du bacille provenant du malade en observation. L’amélioration

se manifeste dès que l’action bactériophage devient énergique vis-à-vis de ce dernier.

 

Dans les cas où la maladie se prolonge, le microbe bactériophage ne manifeste qu’une action mille ou peu marquee, tant que l’état du patient reste stationnaire. Si, dans quelques cas, l’action bactéricide est relativement élevée sur les souches ayant subi de nombreux passages sur les milieux de culture, par contre, elle est toujours inappréciable ou très faible sur les cultures du bacille provenant du malade en observation. L’amélioration se manifeste dès que l’action bactériophage devient énergique vis-à-vis de ce dernier.

In cases where the disease is prolonged, the microbe bacteriophage manifesto that an action or a thousand little marquee as long as the patient remains stationary. If, in some cases, the bactericidal action is relatively high stem having undergone many passages on culture media, by cons, it is always invaluable and very low on the cultures of the bacillus from the observation sick. The improvement was evident as soon as the bacteriophage action becomes strong vis-à-vis the latter.

 

Dans les formes de longue durée et à rechutes, le pouvoir bactériophage

du microbe filtrant peut, à certains moments, être très énergique vis-à-vis

des bacilles de culture et variable d’un jour à l’autre, quoique toujours

relativement faible, vis-à-vis du bacille du malade. La guérison suit de près

le moment où l’action du microbe bactériophage se manifeste d’une manière

aussi intense pour l’une comme pour l’autre souche. Cette action persiste;

avec des fluctuations dans l’activité, aussi longtemps que le patient reste

porteur de germes. Ce dernier fait serait même de nature à faciliter le dépistage

des porteurs de germes, la mise en évidence du microbe bactériophage

étant plus simple et plus sûre que la recherche du bacille pathogène dans

les selles.

 

Dans les formes de longue durée et à rechutes, le pouvoir bactériophage du microbe filtrant peut, à certains moments, être très énergique vis-à-vis des bacilles de culture et variable d’un jour à l’autre, quoique toujours relativement faible, vis-à-vis du bacille du malade. La guérison suit de près le moment où l’action du microbe bactériophage se manifeste d’une manière aussi intense pour l’une comme pour l’autre souche. Cette action persiste; avec des fluctuations dans l’activité, aussi longtemps que le patient reste porteur de germes. Ce dernier fait serait même de nature à faciliter le dépistage des porteurs de germes, la mise en évidence du microbe bactériophage étant plus simple et plus sûre que la recherche du bacille pathogène dans les selles.

In the forms of long-term and relapsing, the bacteriophage of the filter microbe authority may, at times, be very aggressive vis-à-vis the bacilli culture and varies from one day to another, though still relatively low, vis-à-vis the bacillus of the patient. Healing closely when the action of the microbe bacteriophage manifests an intense way for the one as for the other strain. This action persists; with fluctuations in activity, as long as the patient remains buoyant germs. The latter would be able to facilitate the screening of carriers, the detection of the bacteriophage microbe is simpler and safer than the search for the pathogenic bacterium in the stool.

 

J’ai pu vérifier que , l’action du microbe bactériophage était prépondérante,

non pas seulement en ce qui touche à la disparition du bacille dysentérique

de l’intestin une fois la maladie déclarée, mais encore lors de son

éclosion. Au cours de la récente épidémie, j’ai eu l’occasion d’observer

plusieurs cas extrêmement bénins dans lesquels les symptômes se limitèrent

à quelques épreintes et à deux ou trois selles diarrhéiques: or, dans

tous ces cas, le microbe bactériophage fut, dès le début, présent et doué

d’un pouvoir antagoniste élevé. Malgré la bénignité de l’affection, il s’agissait

bien de dysenterie car, dans trois de ces cas, je pus isoler de la

première selle diarrhéique émise un bacille de Shiga typique.

 

J’ai pu vérifier que , l’action du microbe bactériophage était prépondérante, non pas seulement en ce qui touche à la disparition du bacille dysentérique de l’intestin une fois la maladie déclarée, mais encore lors de son éclosion. Au cours de la récente épidémie, j’ai eu l’occasion d’observer plusieurs cas extrêmement bénins dans lesquels les symptômes se limitèrent à quelques épreintes et à deux ou trois selles diarrhéiques: or, dans tous ces cas, le microbe bactériophage fut, dès le début, présent et doué d’un pouvoir antagoniste élevé. Malgré la bénignité de l’affection, il s’agissait bien de dysenterie car, dans trois de ces cas, je pus isoler de la première selle diarrhéique émise un bacille de Shiga typique.

I could verify that the action of the bacteriophage was dominant microbe, not only as it relates to the disappearance of dysentery bacillus bowel disease once declared, but during its outbreak. In the recent outbreak, I had the opportunity to observe several extremely mild cases in which symptoms were limited to a few tenesmus and two or three loose stools: gold, in all these cases, the microbe was bacteriophage, from the beginning, and now endowed with a high antagonistic power. Despite the mildness of the disease, it was good of dysentery because in three of these cases, I could isolate the first loose stool issued a typical Shiga bacillus.

 

Le microbe bactériophage préexiste dans l’intestin ou il vit narmalement

aux dépens du B. coli. Dans les selles normales, son pouvoir antagoniste

vis-à-vis de ce dernier bacille est toujours très faible; il peut devenir

considérable dans divers états morbides, dans certaines formes d’entérites

et de diarrhée banales, par exemple. La présence de bacilles dysentériques

dans l’intestin détermine en premier lieu une exaltation considérable de

la virulence du microbe bactériophage vis-à-vis du B. coli, puis, par une

accoutumance plus ou moins rapide, cette virulence s’exalte vis-à-vis du

bacille dysentérique; elle atteint d’emblée ou graduellement une puissance

considérable amenant la disparition rapide ou graduelle du bacille pathogène. Si la virulence du microbe bactériophage s’exalte d’emblée, les

bacilles dysentériques sont détruits dès le début de leur culture dans le

contenu intestinal, la maladie avorte avant tout symptôme ou se borne à

quelques troubles passagers. Si, pour une cause qui reste à déterminer, la

virulence du microbe bactériophage vis-à-vis du microbe pathogène ne se

manifeste pas d’emblée ou ne se manifeste que faiblement, une lutte s’établit

entre les deux organismes, les bacilles dysentériques se multiplient

dans le contenu intestinal, infiltrent la’ muqueuse, la maladie èclate et

l’état du patient enregistre ensuite fidèlement les fluctuations de la lutte.

 

Le microbe bactériophage préexiste dans l’intestin ou il vit narmalement aux dépens du B. coli. Dans les selles normales, son pouvoir antagoniste vis-à-vis de ce dernier bacille est toujours très faible; il peut devenir considérable dans divers états morbides, dans certaines formes d’entérites et de diarrhée banales, par exemple. La présence de bacilles dysentériques dans l’intestin détermine en premier lieu une exaltation considérable de la virulence du microbe bactériophage vis-à-vis du B. coli, puis, par une accoutumance plus ou moins rapide, cette virulence s’exalte vis-à-vis du bacille dysentérique; elle atteint d’emblée ou graduellement une puissance considérable amenant la disparition rapide ou graduelle du bacille pathogène. Si la virulence du microbe bactériophage s’exalte d’emblée, les bacilles dysentériques sont détruits dès le début de leur culture dans le contenu intestinal, la maladie avorte avant tout symptôme ou se borne à quelques troubles passagers. Si, pour une cause qui reste à déterminer, la virulence du microbe bactériophage vis-à-vis du microbe pathogène ne se manifeste pas d’emblée ou ne se manifeste que faiblement, une lutte s’établit entre les deux organismes, les bacilles dysentériques se multiplient dans le contenu intestinal, infiltrent la’ muqueuse, la maladie èclate et l’état du patient enregistre ensuite fidèlement les fluctuations de la lutte.

The microbe bacteriophage pre-exists in the intestine where it normally lives at the expense of B. coli. In normal stool, his antagonist power vis-à-vis the latter bacillus is still very low; it can become considerable in various disease states, in some forms of enteritis and diarrhea mundane, for example. The presence of dysentery bacilli in the intestine first determines considerable exaltation of the virulence of the microbe bacteriophage vis-à-vis the B. coli, and by a more or less rapid habituation, this virulence exalts vis-à -vis the dysentery bacillus; she reached immediately or gradually considerable power causing the rapid or gradual disappearance of pathogenic bacillus. If the virulence of the microbe bacteriophage exalts the outset, the dysentery bacilli are destroyed at the beginning of their culture in the intestinal contents, disease aborted before any symptoms or merely some temporary disturbance. If, for reasons yet to be determined, the virulence of the bacteriophage vis-à-vis the pathogen microbe does not manifest itself immediately or appears only faintly, a struggle takes place between the two organizations, dysentery bacilli multiply in the intestinal content, infiltrate the mucosal, the disease breaks out and the patient then records faithfully the fluctuations of the struggle.

 

En résumé, la pathogénie et la pathologie de la dysenterie pacillaire sont

dominées par deux facteurs agissant en sens contraire: le bacille dysentérique,

agent pathogène, et le microbe filtrant bactériophage, agent d’immunité.

 

En résumé, la pathogénie et la pathologie de la dysenterie pacillaire sont dominées par deux facteurs agissant en sens contraire: le bacille dysentérique, agent pathogène, et le microbe filtrant bactériophage, agent d’immunité.

In summary, the pathogenesis and pathology of dysentery pacillaire are dominated by two factors working in opposite directions: the dysentery bacillus, pathogen, and the filter microbe bacteriophage immunity agent.

 

Comme corollaire, l’expérimentation sur le lapin montre que les cultures

du microbe bactériophage jouissent d’un pouvoir préventif et curatif

dans la maladie expérimentale; d’autre part, le microbe bactériophage se

trouve invariablement présent dans l’intestin des malades dès que les symptômes s’amendent; il semble donc logique de proposer comme traitement

de la dysenterie bacillaire l’administration, dès l’apparition des premiers

symptômes, de cultures actives du microbe bactériophage.

 

Comme corollaire, l’expérimentation sur le lapin montre que les cultures du microbe bactériophage jouissent d’un pouvoir préventif et curatif dans la maladie expérimentale; d’autre part, le microbe bactériophage se trouve invariablement présent dans l’intestin des malades dès que les symptômes s’amendent; il semble donc logique de proposer comme traitement de la dysenterie bacillaire l’administration, dès l’apparition des premiers symptômes, de cultures actives du microbe bactériophage.

As a corollary, testing on rabbits showed that cultures of bacteriophage microbe enjoy a preventive and curative power in the experimental disease; secondly, the microbe bacteriophage is consistently present in the intestine of patients as soon as symptoms make amends; so it seems logical to propose as a treatment for shigellosis administration, from the onset of symptoms, active cultures of the microbe bacteriophage.

 

 

 

Archaeal Virus as Cat Toy

Stephen T. Abedon

Department of Microbiology – The Ohio State University

phage.org – phage-therapy.org – biologyaspoetry.org


 

This post is/was inspired by Stedman, K. M., M. DeYoung, M. Saha, M. B. Sherman, and M. C. Morais. 2015. Structural insights into the architecture of the hyperthermophilic fusellovirus SSV1. Virology 474:105-109. (ncbi.nlm.nih.gov/pubmed/25463608)

Turns out this spindle-shaped virus of Sulfolobus, potentially resembling “two fused fullerene cones”, is an almost perfect prolate spheroid, which (apparently) is the shape of a pig’s bladder, which in turn is the shape of the American football.

The virus itself, however, possesses a “hexameric tail”, which sort of looks like streamers emanating from one end of the “football”. And that, in turn, sure looks an awful lot like this, particularly were the tail trimmed:

http://www.entirelypets.com/jw-pet-cataction-football-streamers.html

“Art” imitates life belongs to cats!

For my renderings on this subject – archaeal virus as football – see:

https://www.facebook.com/pages/Bacteriophage-Ecology-Group/111721928901953

 

 

Virologica Sinica special issue on “Phages and Therapy”

Note: Open access to this special issue no longer appears to be available…

2015, Volume 30, Issue 1

EDITORIAL

Bacteriophages, revitalized after 100 years in the shadow of antibiotics [pubmed]
Hongping Wei
In this issue, readers will not only find that bacteriophage research is a booming field but also learn about the diverse applications currently being explored for bacteriophages. The biggest driving force behind these applications is the serious threat of bacterial antibiotic resistance that is emerging in the current era.

REVIEWS

Bacteriophage secondary infection [pubmed]
Stephen T Abedon
Phages are credited with having been first described in what we now, officially, are commemorating as the 100th. anniversary of their discovery. Those one-hundred years of phage history have not been lacking in excitement, controversy, and occasional convolution. One such complication is the concept of secondary infection, which can take on multiple forms with myriad consequences. The terms secondary infection and secondary adsorption, for example, can be used almost synonymously to describe virion interaction with already phage-infected bacteria, and which can result in what are described as superinfection exclusion or superinfection immunity. The phrase secondary infection also may be used equivalently to superinfection or coinfection, with each of these terms borrowed from medical microbiology, and can result in genetic exchange between phages, phage-on-phage parasitism, and various partial reductions in phage productivity that have been termed mutual exclusion, partial exclusion, or the depressor effect. Alternatively, and drawing from epidemiology, secondary infection has been used to describe phage population growth as that can occur during active phage therapy as well as upon phage contamination of industrial ferments. Here primary infections represent initial bacterial population exposure to phages while consequent phage replication can lead to additional, that is, secondary infections of what otherwise are not yet phage-infected bacteria. Here I explore the varying meanings and resultant ambiguity that has been associated with the term secondary infection. I suggest in particular that secondary infection, as distinctly different phenomena, can in multiple ways infl uence the success of phage-mediated biocontrol of bacteria, also known as, phage therapy.

Bacteriophage therapy against Enterobacteriaceae [pubmed]
Youqiang Xu, Yong Liu, Yang Liu, Jiangsen Pei, Su Yao, Chi Cheng
The Enterobacteriaceae are a class of gram-negative facultative anaerobic rods, which can cause a variety of diseases, such as bacteremia, septic arthritis, endocarditis, osteomyelitis, lower respiratory tract infections, skin and soft-tissue infections, urinary tract infections, intra-abdominal infections and ophthalmic infections, in humans, poultry, animals and fi sh. Disease caused by Enterobacteriaceae cause the deaths of millions of people every year, resulting in enormous economic loss. Drug treatment is a useful and effi cient way to control Enterobacteriaceae infections. However, with the abuse of antibiotics, drug resistance has been found in growing number of Enterobacteriaceae infections and, as such, there is an urgent need to find new methods of control. Bacteriophage therapy is an efficient alternative to antibiotics as it employs a different antibacterial mechanism. This paper summarizes the history of bacteriophage therapy, its bacterial lytic mechanisms, and the studies that have focused on Enterobacteriaceae and bacteriophage therapy.

Survival and proliferation of the lysogenic bacteriophage CTXΦ in Vibrio cholerae [pubmed]
Fenxia Fan, Biao Kan
The lysogenic phage CTXΦ of Vibrio cholerae can transfer the cholera toxin gene both horizontally (inter-strain) and vertically (cell proliferation). Due to its diversity in form and species, the complexity of regulatory mechanisms, and the important role of the infection mechanism in the production of new virulent strains of V. cholerae, the study of the lysogenic phage CTXΦ has attracted much attention. Based on the progress of current research, the genomic features and their arrangement, the host-dependent regulatory mechanisms of CTXΦ phage survival, proliferation and propagation were reviewed to further understand the phage’s role in the evolutionary and epidemiological mechanisms of V. cholerae.

Phage lytic enzymes: a history [pubmed]
David Trudil
There are many recent studies regarding the efficacy of bacteriophage-related lytic enzymes: the enzymes of ‘bacteria-eaters’ or viruses that infect bacteria. By degrading the cell wall of the targeted bacteria, these lytic enzymes have been shown to efficiently lyse Gram-positive bacteria without affecting normal fl ora and non-related bacteria. Recent studies have suggested approaches for lysing Gram-negative bacteria as well (Briersa Y, et al., 2014). These enzymes include: phage-lysozyme, endolysin, lysozyme, lysin, phage lysin, phage lytic enzymes, phageassociated enzymes, enzybiotics, muralysin, muramidase, virolysin and designations such as Ply, PAE and others. Bacteriophages are viruses that kill bacteria, do not contribute to antimicrobial resistance, are easy to develop, inexpensive to manufacture and safe for humans, animals and the environment. The current focus on lytic enzymes has been on their use as anti-infectives in humans and more recently in agricultural research models. The initial translational application of lytic enzymes, however, was not associated with treating or preventing a specifi c disease but rather as an extraction method to be incorporated in a rapid bacterial detection assay (Bernstein D, 1997).The current review traces the translational history of phage lytic enzymes-from their initial discovery in 1986 for the rapid detection of group A streptococcus in clinical specimens to evolving applications in the detection and prevention of disease in humans and in agriculture.

RESEARCH ARTICLES

Selection of phages and conditions for the safe phage therapy against Pseudomonas aeruginosa infections [pubmed]
Victor Krylov, Olga Shaburova, Elena Pleteneva, Sergey Krylov, Alla Kaplan, Maria Burkaltseva, Olga Polygach, Elena Chesnokova
The emergence of multidrug-resistant bacterial pathogens forced us to consider the phage therapy as one of the possible alternative approaches to treatment. The purpose of this paper is to consider the conditions for the safe, long-term use of phage therapy against various infections caused by Pseudomonas aeruginosa. We describe the selection of the most suitable phages, their most effective combinations and some approaches for the rapid recognition of phages unsuitable for use in therapy. The benefi ts and disadvantages of the various different approaches to the preparation of phage mixtures are considered, together with the specifi c conditions that are required for the safe application of phage therapy in general hospitals and the possibilities for the development of personalized phage therapy.

Molecular dissection of phage lysin PlySs2: integrity of the catalytic and cell wall binding domains is essential for its broad lytic activity [pubmed]
Yanling Huang, Hang Yang, Junping Yu, Hongping Wei
The novel phage lysin PlySs2, is reported to be highly active against various bacteria, including staphylococci, streptococci and Listeria. However, the molecular mechanisms underlying its broad lytic spectrum remain to be established. In the present study, the lytic activity of the catalytic domain (CD, PlySc) and binding specificity of the cell wall binding domain (CBD, PlySb) of PlySs2 were examined. Our results showed that PlySc alone maintains very limited lytic activity. Enhanced green fluorescent protein (EGFP)-fused PlySb displayed high binding affinity to the streptococcal strains tested, including S. suis, S. dysgalactiae, and S. agalactiae, but not staphylococci, supporting its utility as a good CBD donor for streptococcal-targeted lysin engineering. EGFP-fused intact PlySs2 similarly displayed high affinity for streptococci, but not staphylococci. Notably, four truncated PlySb fragments showed no binding capacity. These fi ndings collectively indicate that integrity of the PlySc and PlySb domains is an essential determinant of the broad lytic activity of PlySs2.

Isolation and characterization of glacier VMY22, a novel lytic cold-active bacteriophage of Bacillus cereus [pubmed]
Xiuling Ji, Chunjing Zhang, Yuan Fang, Qi Zhang, Lianbing Lin, Bing Tang, Yunlin Wei
As a unique ecological system with low temperature and low nutrient levels, glaciers are considered a “living fossil” for the research of evolution. In this work, a lytic cold-active bacteriophage designated VMY22 against Bacillus cereus MYB41-22 was isolated from Mingyong Glacier in China, and its characteristics were studied. Electron microscopy revealed that VMY22 has an icosahedral head (59.2 nm in length, 31.9 nm in width) and a tail (43.2 nm in length). Bacteriophage VMY22 was classifi ed as a Podoviridae with an approximate genome size of 18 to 20 kb. A one-step growth curve revealed that the latent and the burst periods were 70 and 70 min, respectively, with an average burst size of 78 bacteriophage particles per infected cell. The pH and thermal stability of bacteriophage VMY22 were also investigated. The maximum stability of the bacteriophage was observed to be at pH 8.0 and it was comparatively stable at pH 5.0-9.0. As VMY22 is a cold-active bacteriophage with low production temperature, its characterization and the relationship between MYB41-22 and Bacillus cereus bacteriophage deserve further study.

LETTERS

Variation of resistance and infectivity between Pseudomonas fluorescens SBW25 and bacteriophage Ф2 and its therapeutic implications [pubmed]
Hanchen Chen, Guohua Chen
Studies of the coevolutionary dynamics between Pseudomonas fluorescens SBW25 and bacteriophage Ф can explore host resistance and parasite infectivity with applications in the ecological and therapeutic fields.Coevolutionary dynamics determine the efficacy of phage-based therapy. In the study described here, bacterial resistance and phage infectivity fluctuated with culturetime, perhaps resulting from random mutation and temporaladaptation, which reminds us of the necessity toconsider evolutionary mechanisms when applying phageto treat bacterial infections.

A novel transposable Mu-like prophage in Bacillus alcalophilus CGMCC 1.3604 (ATCC 27647) [pubmed]
Junjie Yang, Yimeng Kong, Xuan Li, Sheng Yang
In this letter, we provide evidence for the first transposable prophage BalMu-1 in Bacilli. The transposable prophage (BalMu-1, Genbank No. KP063902 and KP063903) was identified in Bacillus alcalophilus CGMCC 1.3604(ATCC 27647) through high throughput genome sequencing and PCR-dideoxy chain-termination(Sanger) sequencing.

Isolation and characterization of a lytic bacteriophage φKp-lyy15 of Klebsiella pneumoniae [pubmed]
Yinyin Lu, Hongyan Shi, Zhe Zhang, Fang Han, Jinghua Li, Yanbo Sun
In conclusion, the lytic bacteriophage φKp-lyy belonging to the Siphoviridae family specific for K. pneumonia was isolated and characterized. φKp-lyy displayed a short latent period, stability to a wide pH rang, high thermal resistance, and lytic activity toward a relatively broad range of K. pneumonia isolates. Thus, phage φKplyy should be considered as a candidate for inclusion in phage cocktails to control K. pneumoniae-associated nosocomial infections.

Expression and purification of recombinant lyase gp17 from the LSB-1 phage in Escherichia coli [pubmed]
Taiwu Wang, Hui Lin, Lu Zhang, Guorong Huang, Long Wu, Lei Yu, Hongyan Xiong
In this study, we successfully expressed and purified the recombinant gp17 protein from the LSB-1 phage and also confirmed its bacteriostatic effect. Assays also showed that the recombinant enzyme was soluble and had signifi cant lyase effects on the host bacterium, EIEC8401. A preliminary study demonstrated that the enzyme did not have inhibitory effects on other strains (unpublished data), which might indicate that the exclusive antibacterial effect of gp17 on EIEC8401 could have a special significance in practical application in bacterial therapy.

T4-like coliphage φKAZ14 virulent to pathogenic and extended spectrum β-lactamase-producing Escherichia coli of poultry origin [pubmed]
Kaikabo Adamu Ahmad, Abdulkarim Sabo Mohanmmed, Faridah Abas, Sieo Chin Chin
The aim of the present study was to isolate bacteriophages for the pre-harvest biocontrol of APEC 01 and ESBL-producing E. coli in chicken, in order to mitigate the risk of these pathogens to the food chain. Isolation and characterization of the T4-like coliphage KAZ14, lytic to APEC 01 and ESBL-producing E. coli, is reported and discussed.

Isolation and complete genome sequence of a novel virulent mycobacteriophage, CASbig [pubmed]
Tieshan Teng, Junping Yu, Hang Yang, Hongping Wei
In this study, we report the isolation and the complete genome of a novel mycobacteriophage, CASbig, which has an icosahedral head (diameter 50 ± 2 nm) and a long, non-contractile tail (length 160 ± 5 nm) with transverse striations, ending in a small knob. The length of the tail includes the middle of the baseplate, and the head measurements were taken between opposite apices. These characteristics indicate that the phage belongs to the family Siphoviridae morphotypes.

INSIGHT

Experience of the Eliava Institute in bacteriophage therapy [pubmed]
Mzia Kutateladze
The rapid propagation of multidrug resistant bacterial strains is leading to renewed interest in bacteriophage therapy. With challenges in the treatment of bacterial infections, it is essential for people worldwide to understand how alternative approaches, such as bacteriophages, could be used to combat antibiotic resistant bacteria. The Eliava Institute of Bacteriophages, Microbiology and Virology (Tbilisi, Georgia) is arguably the most famous institution in the world focused on the isolation, study, and selection of phages active against a variety of bacterial pathogens.

Phages vs. Potato Soft Rot

Stephen T. Abedon

Department of Microbiology – The Ohio State University

phage.org – phage-therapy.org – biologyaspoetry.org


 

Here’s an interesting news item, from only a couple of years back (April 4, 2013): “Taking a greener approach to managing potato spoilage”

http://www.farmersguardian.com/home/arable/arable-news/taking-a-greener-approach-to-managing-potato-spoilage/54554.article

Here are some quotes:

The innovative, eco-friendly product is called Biolyse and works by using naturally-occurring bacteriophage

APS chief executive Dr Alison Blackwell says now the product is proven to work on a large scale in potatoes, there is potential for it to be rolled out to other areas within the food processing industry.

Dundee-based APS has been developing bacteriophage since 2004.

Three years ago, APS received a Scottish Enterprise Research and Development grant and was then able to work closely with a team from Branston’s Abernethy site in Perthshire, Scotland, to identify the bacteria causing rots and develop a suitable bacteriophage.

Biolyse was launched in the Abernethy factory in November 2011 and rolled out across Branston’s other two sites in Lincolnshire and Somerset in 2012. The product is also used by QV Foods and Albert Bartlett.

There is a consistent five to tenfold reduction in rots pre and post bacteriophage treatment.

Installing the application equipment for Biolyse cost about £10,000 and was fairly simple, according to Kevin Imrie, site manager at Abernethy.

Anybody have any idea how this product currently is doing?

Here is APS Biocontrol’s web site: http://www.advancedpestsolutions.co.uk/

Further reading:

T4-related bacteriophage LIMEstone isolates for the control of soft rot on potato caused by ‘Dickeya solani’

Phage-Mediated Biocontrol of Plant Pathogens (2001 to “current”)

Phage therapy for plant disease control

Bacteriophage Ecology and Plants

 

E. coli, CRISPR, Biases in Our Understanding of Phage Ecology, and Possible Implications for Phage Therapy

Stephen T. Abedon

Department of Microbiology – The Ohio State University

phage.org – phage-therapy.org – biologyaspoetry.org


 

We’re all biased by what we know best and the link below discusses why, historically as well as microbiologically, we all “grew up” with the notion that envelope mutations are the primary means by which phage resistance evolves in bacteria. So thank you E. coli (I state with sarcasm):

http://schaechter.asmblog.org/schaechter/2014/11/why-crispr-doesnt-work-in-.html

What, I ask, are the implications for phage therapy of resistance mechanisms to specific phages that are essentially cost free and, at least arguably, Lamarckian as well, i.e., as due to CRISPR? For well-trained phage-therapy teams, I suspect not much. This is because, whether employing cocktails or monophages, the intention generally will be to hit bacterial targets hard and with whatever it takes to clear the infection, such as to switching phages during monophage therapy if resistance is noted.

But for monophages in the hands of less well-trained individuals, e.g., over-the-counter phage formulations or in the hands of poorly trained or regulated clinicians, the potential for development and then transmission of fully fit pathogens that nonetheless are fully resistant to a specific monophage could be fairly high. Importantly, and as relevant to the cited E. coi-CRISPR story, this issue may be more relevant for some pathogens, i.e., those with intact CRISPR systems, than it is for others.

So perhaps we can add inhibition of the potential for therapy-induced evolution of phage resistance among pathogens – as could then be transmitted across affected human communities – as an additional advantage of  prêt-à-porter (phage cocktails) versus sur-mesure (monophage therapy), while still retaining an argument for sur-mesure particularly among highly experienced phage therapists.

As we note in Chan and Abedon (2012), I nevertheless don’t buy arguments that spontaneously occurring phage host range mutations can be counted on in situ to counter bacterial evolution to phage resistance whether in the context of phage cocktails or instead monotherapy. From p. 19 of that publication:

A further consideration is that just as cocktails of phages may be thwarted in their ability to target low densities of phage-resistant bacteria, particularly given active treatment, these concerns should be even greater if one is relying on in situ phage evolution to supply resistance-countering phages… The reason for this is that the necessary host-range mutant phage types will be present in even lower densities than the phages explicitly found in cocktails. These same concerns may also be seen even in the absence of spatial structure so long as those phages within a cocktail that are amplified in situ, that is, in the course of active treatment, are not the same phages to which bacterial phage-resistant mutants are sensitive… Active therapy even with phage cocktails thus may be inherently incompatible with early interference with the evolution of bacterial resistance to phages.

 

Phage cocktails nevertheless should be better suited than monophages for dealing with evolving bacterial resistance to phages simply because cocktails inherently possess greater total numbers of phage particles that display divergent host ranges. On the other hand, the generation of cocktails of phages that display divergent host ranges – but where those phages nevertheless have been derived from a common genetic “platform” – might be expected to perform little better than monophages in the face of CRISPR-mediated phage resistance in target bacteria.

Further (Phage Therapy) Reading:

Chan, B. K., S. T. Abedon, and C. Loc-Carrillo. 2013. Phage cocktails and the future of phage therapy. Future.Microbiol. 8:769-783. [PubMed]

Chan, B. K. and S. T. Abedon. 2012. Phage therapy pharmacology: phage cocktails. Adv.Appl.Microbiol.  78:1-23. [PubMed]

Pirnay, J. P., V. D. De, G. Verbeken, M. Merabishvili, N. Chanishvili, M. Vaneechoutte, M. Zizi, G. Laire, R. Lavigne, I. Huys, G. Van den Mooter, A. Buckling, L. Debarbieux, F. Pouillot, J. Azeredo, E. Kutter, A. Dublanchet, A. Gorski, and R. Adamia. 2011. The phage therapy paradigm: prêt-à-porter or sur-mesure? Pharm.Res 28:934-937. [PubMed]

Importance of Specificity

Stephen T. Abedon

Department of Microbiology – The Ohio State University

phage.org – phage-therapy.org – biologyaspoetry.org


 

This article is not yet fully out but certainly is intriguing: http://www.cell.com/cell/abstract/S0092-8674(15)00003-3

The title is “Disease-Specific Alterations in the Enteric Virome in Inflammatory Bowel Disease” by Norman et al.

The basic premise is that phages may very well be knocking out beneficial bacteria, in the gut, resulting in disease.

Here is a synopsis: https://www.sciencenews.org/article/when-bacteria-killing-viruses-take-over-it%E2%80%99s-bad-news-gut

To me what’s particularly interesting about this study, what little currently can be easily accessed, is that it actually can be viewed as an argument for the benefits of phage specificity in the guise of phage-mediated biocontrol of bacteria, i.e., phage therapy as applied clinically.

Specifically (if you will pardon the pun), when phages are employed in phage therapy, there is at best an only low potential that beneficial bacteria will be directly affected because phage host ranges tend to be quite narrow, typically at best spanning a single bacterial species and potentially some members of closely related genera. This contrasts with the typical antibiotic, which can be much less discriminatory in its impact on normal microflora, potentially resulting in bacterial superinfections.

Indeed, some antibiotics even can induce prophages, resulting in antibiotics potentially giving rise to excessive phage numbers that can impact beneficial bacteria. It is even possible for antibiotics to have an indirect impact by killing off certain bacteria that might then allow an overgrowth of beneficial bacteria which in turn could result in an achievement of so-called “winner” densities. Excessively high densities of specific bacterial types may then be followed by phage-induced reductions in the presence of these beneficial bacteria to below those levels present prior to antibiotic exposure (and then potentially overgrowth of harmful bacteria).

Sure these scenarios are complex and the latter certainly speculative. But the bottom line nonetheless is this: Some phages are bad – and we know this already since many phages carry bacterial virulence factor genes – but not all phages are bad, and those phages that are good in many or most instances probably give rise to somewhat less negative impact on the body than the majority of antibiotics.

Celebrate the diversity of phages, and their specificity!

Phage-Mediated Biocontrol of Plant Pathogens (2001 to “current”)

Stephen T. Abedon

Department of Microbiology – The Ohio State University

phage.org – phage-therapy.org – biologyaspoetry.org


 

I gave the opening talk at the 2nd International Symposium, “New Stages of Phage Biocontrol of Plant Diseases”, held September 18, 2014, at Hiroshima University, Japan. Though my talk was at best peripheral to the emphasis of the symposium, i.e., watch here, I did strive to get into the spirit of things by tracking down references to phage-mediated biocontrol of plant pathogens. Clearly I did not succeed in finding every last one of these references, but nevertheless I probably IDed the ones that “everybody” in the field knows about, and maybe perhaps then some. I’ve sorted these by year plus have indicated the target pathogen as well as the disease that is caused by that pathogen. Where possible I’ve provided a link to the article, though note that I’m providing no promises regarding your potential to find all of these articles online for free! Shown only are experimental articles, and note that I have not confirmed the validity of many of these. So if you know better, or can otherwise help by adding to this list, please let me know!

Here are those papers published in the Twenty-First Century (2001 and newer) up to at least the date of my talk:

Continue reading

Going Bottomless in the Plaque World

Stephen T. Abedon

Department of Microbiology – The Ohio State University

phage.org – phage-therapy.org – biologyaspoetry.org


 

Bottom agar = Hard agar = Solid media

Top agar = Soft agar = Sloppy agar = Semi-Solid media.

I’m embarrassed to say that I’ve had this article in my reference database since August of 2007: Rizvi, S., Mora, P.T. (1963). Bacteriophage plaque-count assay and confluent lysis on plates without bottom agar layer. Nature 200:1324-1325. It is only today, however, and apparently as a form of avoidance behavior (there’s a talk I’m supposed to be working on), that I’ve obtained the reprint and set out to read it.

Their second sentence reads, “Having spent considerable time on preparation of ‘bottom’ agar plates for the agar layer assay by the plaque count method and for high-titre bacteriophage stock preparation on a large number of plates by the confluent lysis method…” And thus they are off striving to do something about this by investigating “…the possibility of saving time by using plates without ‘bottom’ agar for assay and stock preparation.”

The media they used for their ‘bottomless’ agar consisted of the following:

  • 10 g Difco bacto-casamino-acids (acid hydrolysed casein)
  • 15 g Difco bacto-nutrient broth
  • 10 g Sucrose
  • 1g Dextrose
  • 5g Crystalline magnesium sulphate
  • 5 g Sodium chloride
  • 8g Agar

Efficiencies of plating in testing phages T1 through T7 they found to be essentially 100% for T1, T3, and T7, and basically 50% for the rest. To the extent that my interpretation of the ‘smudges’ provided in Nature’s PDF can be trusted, the per plate yields for confluent lysis phage preps were more or less the same with versus without bottom agar. Consistently for the latter they note: “The yields obtained on plates without ‘bottom’ agar were slightly better than the yields obtained on plates with ‘bottom’ agar.”

They also note that, “Confluent lysis can be adapted for large-scale bacteriophage production by carrying it out on large stainless steel trays.”

Historical Referencing:

These authors also cite four, mostly Mark Adams-dominated publications for plaque count method (first three) and confluent lysis stock preparation (last). These are:

(1) Gratia, A. (1936). Des relations numeriques entre bactéries lysogenes et particules de bacteriophage. Ann. Inst. Pasteur, 57:652-676.

(2) Adams, M. H. (1950). Methods of Study of Bacterial Viruses. (Methods in Medical Research, 2:1) The Year Book Publishers, Inc., Chicago.

(3) Adams, M. H. (1959). Bacteriophages. Interscience Publishers, Inc., New York.

(4) Swanstrom, M., and Adams, M. H. (1951). Agar layer method for production of high titer stocks. Proc. Soc. Exp. Biol. and Med. 78:372-375.