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TWiM #6 transcript

Here is a transcript of TWiM episode #6, "Antibacterial therapy with bacteriophage: Fact or fiction?". Thanks to Steve Stokowski for transcription.

The transcript is also available as a pdf file - click here to download.

Hosts: Vincent Racaniello, Cliff Mintz, Michael Schmidt, and Elio Schaechter

Aired 04 May 2011

Click to view this episode


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Vincent: This Week in Microbiology is brought to you by the American Society for Microbiology at


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This Week in Microbiology, episode number six. Recorded April 29th, 2011.


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Hi everybody, I am Vincent Racaniello and this is TWiM, the podcast that explores unseen life on earth.


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Joining me today from Princeton, New Jersey is Cliff Mintz.


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Cliff: Hello Vincent.


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Vincent: How are you Cliff?


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Cliff: I am fine.


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Vincent: How is Princeton, New Jersey? Is it treating you well?


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Cliff: It is treating me well. It is cloudy and just typical spring weather in New Jersey.


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Vincent: Yes, it is cloudy here.


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Let us see what the weather is down in South Carolina where Michael Schmidt would be. Welcome Michael.


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Michael: Thank you Vincent. We have spring again. We had summer for a few days and then all those horrific tornados came through and fortunately spring came back once the bad weather cleared out of the southeast.


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Vincent: You did not have tornados where you are did you?


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Michael: No, we were blessed. We had a number of warnings peppered through out the locality but fortunately we did not have any here in Charleston.


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Vincent: Okay, good to hear.


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Also joining us today for the first time, a new host of TWiM, from San Diego, California, Elio Schaechter. Welcome Elio.


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Elio: Well thank you. Nice to be on


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Vincent: Elio is from Small Things Considered, the wonderful blog where you can get Talmudic questions and answers to all other questions as well.


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How is the weather in San Diego, 72 and sunny?


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Elio: Well we have a wind chill factor of 75.


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Vincent: That is great. I love it.


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So Elio, your first time on TWiM, so now tell us a little bit about yourself.


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Elio: I spent most of my career at Tufts Medical School in Boston. And then I came to San Diego for very personal reasons my new wife. My late wife died and this was a childhood sweetheart that I knew and she was living in San Diego and I thought I would come here.


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Briefly let me tell you that I had, I want to share this, I had an epiphany when I came here. I spent most of my life either working on E Coli K12 or Salmonella Typhimurium LT2.


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Paying very little attention to the rest of the microbial world except here and there.


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When I came here I realized that by personality I was really much more drawn to environmental microbiology than I ever knew. So I discovered microbial ecology and environmental microbiology.


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Luckily in San Diego there is a whole bunch of young people, I call them young, who are terrific at this. So I got into it more and more and more.


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Now I figure the whole microbial world is for me to look at and enjoy. It is just a phenomenal experience. I mean it is something totally different that I had ever experienced in my life before.


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Vincent: I think we are beginning to appreciate more that than we ever did, what the ecology of microbes do for us, right?


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Because when I was a student we just thought they were bad basically. Now we realize that we can't....


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Elio: Or they were good model systems.


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Vincent: Model systems, that is right. And that now we realize we can not live without them.


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Elio: Exaclty.


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Vincent: So you were born in Milano.


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Elio: Yes, I was.


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Vincent: Part of my family was from Milano also. I was there many times.


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Elio: No wonder I like you.


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Vincent: I had part of my family from Milano, which is of course in the north and then the other part was from near Naples.


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So I use to visit both places. They could not be more different, of course. Culturally and all sorts of ways. Even the food is very different.


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Yes, that is where my family was partly from, there. So yes, that is a good connection.


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Well today, welcome to TWiM Elio, I hope you have fun because we always have fun here. We just talk about what we all love to do and that is talk about microbes.


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Today we have stories about bacteriophages essentially.


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We had some requests from listeners to talk first about using bacteriophages as therapy to take care of microbial infections.


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So that's what we are going to talk about first.


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There was a wonderful article in Microbe Magazine by Alexander Sulakvelidze. I don't know if I said that right.


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Michael: Everyone just calls him Sandro.


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Vincent: "Sandro."


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Michael: Because no one can pronounce his last name.


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Vincent: Oh, that's right, they have it hear in quotes, Alexander ("Sandro").


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Cliff: I am going to be interviewing Sandro on Tuesday for an article that I'm writing on antibiotic resistance and I want to include in the article about alternative therapies. I know that he is actively involved in phage therapies so I am talking to him.


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Vincent: I think he is an advisor to one of these companies.


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Cliff: He is actually either the Chief Scientific Officer or Co-Founder


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Vincent: Intralytix, right?


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There are a number of companies. One of these articles that we have here to look at.has a list of all the companies that are involved and it is pretty impressive.


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So this is a good thing to talk about. And it turns out, of course, that Michael Schmidt has actually done some of this.


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So let's start at the beginning. Let's start in 1915 when phages were first discovered by Twort and d'Herelle.


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I think d'Herelle actually wanted to use them for therapy to treat infections, right.


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Michael: That is absolutely correct.


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Vincent: And he did that for a long time. I think he started an institute in the Soviet Union which lasted many years, maybe still is there today.


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He was one of the initiators to try and do clinical applications to cure infections. I think he was interested in gastrinalintestinal infections of various sorts.


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Michael: That was one of their first success stories. They prepared a preparation and he along with some of his interns effectively did the phase one safety trials.


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They made the exlir a phage, they drank them and then they asked the question, "Were there any ill effects?", before they administered them to children in order to control the syptoms of dysentery.


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Dysentery is the inflammation of the intestinal area along with the accompanying syptoms of the constant urge to go to the bathroom, as well as the famous diarrheal activities.


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Vincent: Is dysentery bloody diarrhea?


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Michael: There is both flavors. You can have bloody diarrhea as well as non-bloody diarrhea and that is the salmonella story.


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Vincent: So in d'Herelle's case what were the microbes causing the dysentery, do we have any clue?


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Michael: I think it was probably salmonella though....


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Cliff: It was probably shigella dysenteriae.


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Michael: Yes, that's probably true. It was probably a shigella variant.


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Cliff: Just to step back. As a former flu microbiologist who is very much into distinquishing diarrhea symptoms,


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The classic diagnosis for shigellosis is bloody stool, which is very very common with that infection.


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With salmonella there can be a co- blood in the stool but it is not characteristic of the disease. Where as with shigellosis it is always present because the damage to the gastrointestinal mucosa with shigella infections is much more extensive as compared to salmonella. So you are getting blood as the result of the destruction intestinal mucosa as you go.


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Michael: To put it in context for today's world, each year the CDC estimates there are about 15,000 reported cases of dysentery but they guestimate based on their models that in the US alone there are about 450,000 case of dysentery.


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As we begin to expand our discussion here today about remedies for dysentery, albeit some of these things are self-limiting, but as we learned from our food poisoning episode, it really puts you on your back for a while.


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It would be nice if there was a therapeutic that could limit the symptoms. What we are going to talk about today, phage therapy, maybe an opportunity to limit the serverity of that disease course based on using a natural predator of the microbe causing the symptoms.


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Elio: Before we get into it, could I pipe in? A little bit about the history of who this guy Félix d'Herelle was because it is absolutely amazing. Can I do that?


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Vincent: You can do anything you would like.


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Elio: Well d'Herelle was a French-Canadian. As a young man his family moved back to France and he went to, lycée, high school there. Did not go to college.


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He was married then and went back to Canada and built a home laboratory. He did his own experiments and got some help from the Canadian government to figure out how to make maple syrup into schnapps. In other words, how to ferment maple syrup.


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He became a self-taught microbiologist.He got jobs in Guatemala, becuase of his skill in how to convert some natural products into a fermentable thing.


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Then Mexico. Then he went back to France and he worked for free at the Pasteur Institute. He was a volunteer at the Pasteur Institute.


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Then he went to Argentina where he again was working on... he fought locust plagues with some bacterium. I don't know what it was.


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Then he went back to France during W and orld War I and he made then, that's the story of the phage.


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He made something like 12 million doses of medication. All of that was allotted for the military at first.


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He wasn't done. He then went to Leiden in Belgium. He got a job there. And then went to Egypt, India, the United States, by which time he was offered a professorship at Yale, which he accepted for a short time.


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Then comes the Soviet Union where he went to Tbilisi, Georgia where he went to help found an institute which exists to this day.


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Then eventually he went back to France and did work in the Pasteur Institute, he got a paid position.


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He was nominated for the Nobel Prize eight times but didn't quite make it. Anyhow, one hell of a character.


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Vincent: Interesting.


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Cliff: How long did he live?


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Elio: He died in 1949. He was born in 1873. So he was 72 [75] years old when he died.


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Cliff: He obviously wasn't eating enough yogurt when he was in Georgia.


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Elio: Well, he did okay, I mean 72 in those days was not so bad.


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Vincent: Well actually he lived through many trails of these phages according this review. Their first paper was in 1921 to treat skin infections and then there were a variety of tests at many companies, including that institute that he started in the Soviet Union.


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I guess that he was using lytic phages, right?


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Elio: Yes, sure, he didn't know. Temperate phages were not known until Lwoff discovered them sometime in the early thirties.


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Vincent: Okay, so that he got lucky that he got lytic phages initially. Those were the first ones he discovered, right?


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I guess that is because you can see them clearing the plates, right?


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Elio: Sure.


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Cliff: Do you think it is important to talk about lytic versus lysogeny so that people really understand what phages are because we keep on mentioning them but some listeners may not know.


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Vincent: Yes, go ahead.


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Cliff: I didn't do it. I just think it is a good idea.


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Michael: I can take a stab at it. I will use the same tact, I introduce this concept when i talk to the medical and dental students.


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The way I view lytic phages is the equivalent of a Pepsi worker going to a Coca-Cola plant and spinning the dials in the factory.


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The net consequence is the factory begins to produce Pepsi out of the Coca-Cola factory.


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All you need is the information coming in from the virus to effectively re-program the cell because, after all, the phage are nothing more than viruses that infect the baterial cell, converting the bacterial cell into a viral factory making more virus.


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The net consequence is that at the end of the shift, the Pepsi worker leaves with all the product and out they go, destorying the factory as they exit.


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In contrast, a lysogenic phage, or a temperate phage, is that Pepsi worker will actually don the uniform of the Coca-Cola worker and remain in the Coca-Cola factory, happy as can be, until such time as the factory no longer treats that Pepsi worker, in disquise now, well enough, so that now the Pepsi worker decides, "I have had enough working in the Coca-Cola factory, it is time for me to find greener pastures, maybe go over to Dr. Pepper."


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The net consequence is the Pepsi worker leaves the factory but no before he destroys the Coke factory.


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It is all about the viral genome being very sophisticated determining the nutritional status and the fittness of the host determing whether or not it would like to be lytic or whether or not it wants to remain.


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After all, the life of a virus is not easy. It has to find the host. In the dilute environment of the ocean or the environment in general, it is very challenging often to imagine, even though there is a large number of viruses out there, to actually locate an appropriate host that will be able to replicate your genome and not restrict you from fulfilling your programming.


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Vincent: I guess that is why there are so many phages, right? To really improve the chance that you are going to encounter a host.


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Michael: That is what is really remarkable about these genetic elements. They have been around for about three billion years.


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This is after all, probably the oldest mobile genetic element out there.


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I think they hang around to provide diversity to the microbial world.


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It is an easy and convenient way to move genetic information that provides general fitness to a population.


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It gives a whole new meaning to the word 'population' of the microbial world.


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Elio had a great piece a week or so ago on his blog about CRISPR sequences.


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Their role in the baterial genome and how they control the phage from effectively taking over a population.


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It really illustrates the wonder that the molecular biology of these really pretty sophisticated, albeit very small pieces of genetic information can have on facilitating profound behavioral modifications in a population because of expression of genes and all sorts of other wonderful things.


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Vincent: So the numbers here are amazing.


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Elio: Let me add something too. Can I add something too the CRISPR story?


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CRISPRs are, as many listeners may know and some may not, are sort of a trace in the genome of the bacterium left by a phage that was once involved in that bacterium.


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It is a sequence that tells you very specifically what phage you are at.


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You can use this to essentially do epidemiological studies to figure out what phages did what activities encountered.


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Now this has been used recently. In several labs people have studied frequency with which these changes occur.


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It is absolutely stunning. In Relman's lab, David Pride published a paper recently showing that in the mouth, the streptococcal of the mouth have a new CRISPR sequence practically everyday.


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It is as if they are attacked by a different phage everyday.


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It is simply amazing. This is a new concept in how we think about the bacterial world.


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It is not that bacteria get infected every so often... along comes a virus. This is not the case. It is something that  happens daily.


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Vincent: According to this paper, we shed ten to the ninth phages every day. Amazing.


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Elio: This is practically a paradigm shift. If not that, a shiftlet, as I call them.


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It really gives you a new perception of what the world of bacteria is like, what is it like to be a bacterium.


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It is not that being infected is a rare event. Consequently most of these infections are not likely to be lytic or are not even likely to be damaging to the bacteria.


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There are so many of it, that if they were, there would be no bacteria left.


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Michael: Elio raises a really good point about using phage as therapy.


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This requires you to have a cocktail of phage that will actually infect and kill the microbe that is causing the disease syndrome you are to treat.


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I think modern phage therapy will be the first practical application of personalized medicine.


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You will actually go to your physician, they will acquire a sample of the disease, and then will very quickly isolate a phage cocktail for which your infection is susceptible.


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It will really be personalized medicine. It is going to require a paradigm shift in how the FDA approves medications because personalized medicine will have to taylor it to your microbiome.


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So that you don't do any harm to your good bugs.


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The beauty of phage is that they are very specific.


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So you will very quickly have to isolate the infecting agent. Ask the question about CRISPR sequences to figure out if your phage cocktail on the shelf will be useful against your infection.


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Then, if it is not, go out and acquire a phage or modify it such that your phage on the shelf, that you are going to use as your therapy, will be effective.


00:21:13,990 --> 00:21:22,360

It is going to be create a whole new type of personalized medicine if phage therapy is going to come into wide spread use.


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Vincent: How long will that take to do all that?


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Michael: Well, it depends. That is what I think is so cool about these CRISPR sequences and how it is a give and take between the bacteria and the bacteria phage.


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There was one paper recently that came out on the isolation of the novel, I use to know it as actinobacillus, actinomycetemcomitans, which now is know referred to as aggregatibacter actinomycetemcomitans.


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They were isolating a novel bacteria phage capable of lysing this particular microbe that is involved in biofilms that cause periodontal disease.


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They reported the challenges that they had with getting a cocktail that could actually be generally applicable to going after things.


00:22:27,370 --> 00:22:29,370

I think it is really going to require some basic science to understand how quickly you can manipulate these phage in order to develop this cocktail


00:22:40,110 --> 00:23:00,200

Or, do what the folks at the Eliava Institute today in Tbilisi, George do. Is they just give you a poly-valent exilir of phage, hoping that the phage cocktail they provide to you will actually work on your particular infection.


00:23:00,300 --> 00:23:16,380

I think that is going to be the first wide-spread application of phage therapy is where you have this multi-phage complex that they are going to administer to after the particular offending agents.


00:23:16,480 --> 00:23:19,650

And in fact, that is how Eliava does it.


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Cliff: Vincent, can I interject something?


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Vincent: Of course.


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Cliff: Since you are the guy who cloned the first viral receptor, I think it is important to understand that the specificity of phages for a particular species or strains of bacteria is really based on their ability to find an appropriate receptor on the bacterium to enter the cell.


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If you do not have the appropriate phage receptor, the phage cannot attach to that receptor and then enter into the cell.


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Then what typically happens is that the phage carrying DNA or RNA will attach the recept and then the phage will compress itself, inject its DNA into the bacterial cell through the cell wall, through the receptor, and then the phage DNA will integrate, typically integrate with the bacterial chromosome.


00:24:20,850 --> 00:24:36,260

Then, as Michael eloquently stated before with the Pepsi and Coke analogy, if the phage is unhappy in the current environment, it may be shunted over to the lytic phase.


00:24:36,360 --> 00:24:44,120

But, if things are copacetic and life is good for awhile, then the phage enters into the lysogenic state.


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The other reason I bring up these receptors is that there are multiple phages that exist for the same species or strains of bacteria based on the different types of cellular receptors.


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One of the frequent events that occurs is that cells become resistant to phage re-infection for two reasons.


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If you take a bacterial population and you treat it with a phage preparation that you know is specific for that bacteria, there will emerge phase resistant mutants.


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There are two ways in which these so-called phage resistant mutants are generated.


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One is the loss of or mutation in the original receptor that the wild type phage would be able to not now bind to.


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The other is that once a bacterium is in the lysogenic state it confers an immunity property onto the bacterial cell that habors it that prevents re-infection by the same phage.


00:25:57,830 --> 00:26:02,880

I mean that, I believe that is kind of way it works.


00:26:02,980 --> 00:26:24,150

Elio: It is a little bit more complicated than that because the CRISPR sequences are highly specific for the phage that generated them and they are a defense mechanism by a complicated and not yet completely understood mechanism. They are the protective mechanism.


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It is like having been immunized against that one particular phage.


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On the other hand, they are so specific they do not work in case the phage is mutated again.


00:26:36,950 --> 00:26:40,480

So the phages overcome this by mutation.


00:26:40,580 --> 00:26:52,000

The point here, I think, is that..., there is a big question in my mind, how often does this matter in the real world?


00:26:52,100 --> 00:27:02,300

That is, in the experience that they had in Georgia, they should know how often they run into the problem of resistance, the bacteria becoming resistant to the phage.


00:27:02,400 --> 00:27:11,000

Because if this turns out to be a small problem then a cocktail of different phages might well work.


00:27:11,100 --> 00:27:22,270

On the other hand, if often you find that the bacteria are resistant to the phages then one has to do what Michael was talking about in the specialized, individualized preparations.


00:27:22,370 --> 00:28:02,300

Cliff: Right, and the other reason I brought up the resistance point was that one of the main concerns that everybody raises is the possibility of phage resistant mutants when you bring it into a clinical environment thereby necessitating a cocktail approach when, in fact, if you are going to put all your phage into one basket, you have got to know apriori the range of the bacteria that you can treat with this in the absence of doing real-time PCR in a physician room and then trying to figure out which mixture is going to work.


00:28:02,400 --> 00:28:08,750

There in lies the conundrum from the regulatory stand point that Michael was talking about.


00:28:08,850 --> 00:28:35,600

If you are going to have a wide range, like thousands of phage, for example, in a particular cocktail, it is going to be very difficult the way in which the regulatory system is setup in the United States and other highly regulated geographic regions to get a relevant cocktail approved for routine therapeutic use.


00:28:35,700 --> 00:28:45,400

Vincent: But there was a trial, a phase one in 2008, where they used a cocktail of eight phages. This was for leg ulcers so, I mean there is some precedence.


00:28:45,500 --> 00:29:13,110

Cliff: But what I am trying to say is, is that I believe personally, based on my knowledge of phage and the antibiotic world that I believe that phage therapy can be highly effective and should be used, in my opinion, for chronic baterial infections like wounds that will not heal, diabetic ulcers, even MRSA skin infections.


00:29:13,210 --> 00:29:26,660

It makes perfect sense when you are using it topically and in a chronic situation when you have an idea of what the bacteria are that are causing the problem so that you can effectively treat it.


00:29:26,760 --> 00:29:44,020

When you start talking about systemic utilization or even injecting phage subcutaneously and stuff becomes a lot less clear about how you are going to do it, what the regulatory issues or challenges are going to be for getting that kind of approval.


00:29:44,120 --> 00:29:55,350

Vincent: Well the message from Sandro's paper is that this 2008 trial has really paved the way for cocktails, that the FDA will eventually look at cocktails.


00:29:55,450 --> 00:30:15,220

Cliff: But what they will do is..., the way it works, the way drugs are approved is that typically, at least in the United States, FDA, the regulatory agency, does not want to approve a combination therapy unless everything is known about the individual components that make up the combination.


00:30:15,320 --> 00:30:29,290

So I suspect that with a cocktail of eight phages that have been either fairly well characterized or well characterized that makes perfect sense. Right, there are eight phages in there.


00:30:29,390 --> 00:30:38,640

I do not know what the mutation rate is. I do not know what the effectiveness is, a phase one trial is a safety trial to see whether or not people get sick.


00:30:38,740 --> 00:30:48,490

Whether or not therapeutically you are going to be able to.... I do not remember how it was administered, was it drunk, was it injected?


00:30:48,590 --> 00:30:50,060

Vincent: It is topical, just for leg ulcers.


00:30:50,160 --> 00:31:11,410

Cliff: It is topical. Right, I mean, so you know, and a phase one in that case was a small number of patients that was suffering from it and it was probably an institutional type trial, that is not an industrial strength trial, and it was probably done under experimental IND versus an official IND, investigation and drug application.


00:31:11,510 --> 00:31:29,700

So yes, I am not saying it should not be done. I am saying that in order to get buy in from people, physicians, and the powers that be, that you be very careful about the initial indications that you use it for.


00:31:29,800 --> 00:31:50,510

You know what I am saying? So rather than trying to hit the mother load and use it to treat sepsis, which is never going to happen, if you look at diabetic foot ulcers or difficult to heal wound infections, then you can take that cocktail of eight phages and probably get it approved.


00:31:50,610 --> 00:32:09,100

Elio: I think that Michael said something earlier in passing that for this to really work, not to just do it on a very limited basis, which is what you are talking about, but really expanding this to its full capacity, it does require a paradigm shift on the part of the FDA.


00:32:09,200 --> 00:32:35,400

In other words, it can not be done under these circumstances. However, it could be done if the FDA were ever to change its attitude toward or its procedure toward this particular approach, not every other drug in the world, but this particular approach and have sort of a generic liscense for the ability to construct individualized phage preparations.


00:32:35,500 --> 00:32:39,820

That is difficult to imagine, I am not saying this is going to happen tomorrow.


00:32:39,920 --> 00:32:51,720

Cliff: No, what I am saying is, from a basic research, from a fundamental stand point it is perfectly doable, feasible and I think somebody ought to do it.


00:32:51,820 --> 00:33:03,940

The problem is that from an economic and business perspective there is no way in which companies will do this on a mass scale because it is too expensive to do it this way.


00:33:04,040 --> 00:33:05,000

Now that said....


00:33:05,100 --> 00:33:24,820

Elio: I am not so sure. Now wait, wait a minute. I am not so sure. With modern technology it is possible to get a sample from a patient, figure out what bug is there, figure out if the virus you have on the shelf is adequate for it, and do it within 24 hours.


00:33:24,920 --> 00:33:26,110

Cliff: No but you are saying....


00:33:26,210 --> 00:33:35,350

Elio: There is an automatic way, if you did this not by hand, not the way we use to do it, but in a high through put way, it would not be that expensive and it would be very fast.


00:33:35,450 --> 00:33:36,870

I am just imagining things.


00:33:36,970 --> 00:33:47,260

Michael: This is the paradigm shift in personalized medicine. We are approaching..., and that is why I think this will be the first test case of personalized medicine.


00:33:47,360 --> 00:34:01,560

To begin to think about how do you regulate for safety personalized medicine because there have been a lot of folks out there looking at personalized medicine.


00:34:01,660 --> 00:34:38,670

This is a little bit off topic but we have all seen these micro-RNAs which, I consider micro-RNAs to be phage if you will, they just do not have the sophisticated delivery system of phage; and we have all gone to seminars where micro-RNAs have been used to control cancers and what not, so it would be interesting I think if I were to try to help the FDA think outside the box about personalized medicine and these controlling RNAs and how to begin the safety and efficacy.


00:34:38,770 --> 00:34:59,020

The beauty of phage is that they are specific. They are only going to affect one particular sub-species of bacteria based on whether or not they have particular immunity factors like CRISPR sequences and whether or not they have been lysogenized with a particular cohort of other phages.


00:34:59,120 --> 00:35:34,250

I think it would really think it would be important for them to think about something as simple and straight forward as treating a chronic skin ulcer in a very susceptible and at risk population, like a diabetic, going after a particular microbe using a mixed elixir of very specific phage going after a particular cohort of bacteria that are likely going to be responsible for that patient's ulcer.


00:35:34,350 --> 00:35:50,220

We saw it in one of the papers that Vincent had us take a look at, the controlled clinical trial of therapeutic bacterial phage preparations in chronic otitis media due to antibiotic resistance to monus aeruginosa.


00:35:50,320 --> 00:36:32,430

And thinking about delivery mechanism of at risk populations, you have the cystic fibrosis population that is extremely at risk for cystic fibrosis and phage, being that they are very small, you can understand how they could get into the biofilm associated with cf pseudomonas that is in the lung of this at risk and vulnerable population and this particular phage prep, in the case of a cf community, may have utility so that you do not have the use the nuclear weapons of those broad spectrum antibiotics to go after pseudomonas.


00:36:32,530 --> 00:36:47,510

As we all well know, pseudomonas aeruginosa is one of the most resistant microbes out there because it is an environmental organism that has been evolved to eat organics for a living.


00:36:47,610 --> 00:37:16,680

So I think, as we begin to run out of the wonder antibiotics that we have been so fortunate to exploit for the last seventy years, we are going to have to begin to go back to the old stuff, the phage to go after these extremely recalcitrant infections that are in very vulnerable patient populations for which there is no good medication, right now.


00:37:16,780 --> 00:37:42,000

Vincent: It is also worth pointing out that treating humans who are ill is not the only application of bacteria phages. There are others. And some of them are already licensed. You know, taking care of food sanitation, treating the food with bacteria phages, environmental applications, even veterinary, preventing infections in chickens.


00:37:42,100 --> 00:37:47,510

Cliff: I agree that this is a PR problem to a large extent.


00:37:47,610 --> 00:37:52,020

Elio: No no, wait wait wait. It is not just PR, there is substance to this.


00:37:52,120 --> 00:38:16,210

Cliff: No no no, let me finish. It is a PR problem from the stand point that there are uses of these products that can be brought to the forward rather than be kept for animals or the food industry and where they could gain acceptance by the American public as well as physicians that may or may not use this.


00:38:16,310 --> 00:38:24,450

You can not say I am going to take a bacterial virus and use it as an anti-infectant because once you hear the word virus people are not going to want to use it.


00:38:24,550 --> 00:38:35,750

So it is a PR problem from the stand point of getting people attuned to the fact you can use these agents in a non-clinical way first to show that they are safe.


00:38:35,850 --> 00:38:40,590

Then move it forward for therapeutic purposes. That is what I was saying.


00:38:40,690 --> 00:39:02,030

I am taking a more commercial perspective on this, understanding that the Intralytix guys, that Sandra was one of the founders of that company, they started eight years ago trying to get their product approved as a disenfectant in food processing laboratories.


00:39:02,130 --> 00:39:14,340

It took them eight years. To me, that is a no brainer, right? It is like, what are you, kidding me? It is a great idea. It should have been commercialized and it should have been easy to get it approved.


00:39:14,440 --> 00:39:30,690

But, in order to get things approved, you need to demonstrate a whole lot of stuff regards to safety. Even though you and I both know, or everybody knows, that phage are not going to infect humans per se, it is not really that clear whether that is true or not.


00:39:30,790 --> 00:39:32,490

You know, you have to show it.


00:39:32,590 --> 00:39:34,890

Vincent: You have to show there are no side effects, essentially.


00:39:34,990 --> 00:39:52,370

Cliff: Show that there are no side effects and that there are no human sequences being brought to bear. I mean, my god, sprinkling phage on a laboratory counter, or using phage to ensure there is no salmonella in egg preparations or in cantalope, why would you not do it?


00:39:52,420 --> 00:40:06,170

I mean there is.... To me, as a scientist, there is absolutely no objections to it. I could eat phage, I eat phage everyday because I eat bacteria that are on fruits and stuff that I eat, right?


00:40:06,270 --> 00:40:07,570

So I am eating phage.


00:40:07,670 --> 00:40:11,910

Vincent: Yes, we all are. Apparently it is in our water as well.


00:40:12,010 --> 00:40:28,340

Cliff: If you sprinkle it on, an additional helping of phage on to a meat product to ensure people do not come down with shigellosis or ecoli infections or salmonella or whatever, people are going to..., you just can not do it. People do not know.


00:40:28,440 --> 00:40:34,560

Vincent: It is not that you can not do it, but people will freak out, just as they do for genetic modification of plants.


00:40:34,660 --> 00:40:57,390

Cliff: For example, we were talking about basilar astrogenesis and all the things with the toxin, why is it any different to incorporate the b thuringiensis toxin into plants themselves versus taking dried preparations of bacilus thuringiensis and using it as organic farming. Do you know what I mean?


00:40:57,490 --> 00:41:11,840

I mean, it is a total disconnect. People think, oh my god, a bacterial gene in a plant. But yet, you'll buy fruit from an organic farmer that has been using it for twenty years. Do you know what I mean, you are eating the same protein.


00:41:11,940 --> 00:41:19,550

I mean, that is what I was talking about. I agree, I am on everybodies side, I think phage therapy should have been developed twenty years ago.


00:41:19,650 --> 00:41:40,040

Michael: It is interesting in that the AMAs council on pharmacy and chemistry reported that phage therapy was ambiguous regarding as to its efficacy and they expanded their concerns regarding the lack of understanding of the nature of phage.


00:41:40,140 --> 00:42:11,420

That statement they made in 1934. Our understanding of phage has certainly expanded since 1934. And now our understanding of the human microbiome and the infections, and our understanding of molecular biology are now to a point where I think, as Elio introduced us earlier, we are going to have to have a paradigm shift in how we begin to think about these things.


00:42:11,520 --> 00:42:16,340

Cliff: But Michael, when you teach, do you still teach bacterial genetics to medical students?


00:42:16,440 --> 00:42:17,440

Michael: Yes, I still do.


00:42:17,540 --> 00:42:20,540

Cliff: How much time do you spend on phage?


00:42:20,640 --> 00:42:28,140

Michael: We spend less than twenty minutes. It is principally to introduce genetic circuitry to them.


00:42:28,240 --> 00:42:35,870

Cliff: And how much time when they take their clinical pharmacology courses, their ID course, do they spend on antibiotic therapies?


00:42:35,970 --> 00:42:39,200

Michael: Much much longer, orders of magnitude.


00:42:39,300 --> 00:42:58,200

Cliff: Right. So the point is, the fact is, and this is the reality base, I hate to be like the nay sayer here, but I am interjecting real life stuff into it and if you are training physicians who do not themselves understand what a bacteria phage is, they are not going to prescribe it because they do not understand it.


00:42:58,300 --> 00:43:17,530

So you are right, in order for there to be a paradigm shift away from antibiotics to phage we need to train physicians who are the ultimate prescribers of medications in this country and elsewhere to convince them and make them understand the need to understand bacterial phage and bacterial genetics.


00:43:17,630 --> 00:43:28,540

You can not expect somebody to prescribe a product just because it has been approved by the FDA, or some other regulatory agency, and use it unless they are comfortable and understand how it works.


00:43:28,640 --> 00:44:01,580

So that is what i am talking about. So if we want a paradigm shift, so what we need to do, we do not have to talk to people at FDA per se yet, you need to start telling it to the medical students you train and tell them this is why it is important, we are running out of anti-bacterials, phage represent a new frontier, I want you guys to know this stuff, here is how it works and you guys do not have to be afraid of it. And that is how you do a paradigm shift and how you get the FDA to budge because the people that are recommending approval of products are usually MD and PhDs or people who treat patients.


00:44:01,680 --> 00:44:11,810

So you can not expect, just because FDA approves a product to have physicians embrace it even though it has been blessed by a regulatory agency.


00:44:11,910 --> 00:44:19,440

It is kind of weird because, you know, twenty years ago I spent a lecture on bacterial genetics, not twenty minutes.


00:44:19,540 --> 00:44:32,860

Yes, our understanding of phages as scientists and PhDs has moved a lot in the last 70 years, but not the way it is being taught to the people where it makes the most difference to.


00:44:32,960 --> 00:44:42,220

So yes, you and I understand it really really well, but the people that actually are the players that need to be convinced, do not.


00:44:42,320 --> 00:45:04,230

Vincent: I am looking at There are two phage trials on-going. One is the leg ulcer, which is actually completed. And we talked about. And there is a second one which is recruiting. Again for non-healing, post operative wounds and various other infections. So there is not a lot.


00:45:04,330 --> 00:45:17,920

Even though there is a lot of publication now and a lot of talk, the actual in progress trials are few. There are a lot of companies working on these but I suspect there are some obstacles that still have to be overcome.


00:45:18,020 --> 00:45:41,870

Cliff: Vincent, back in 1994, maybe 95, 96, I met a CEO of a company that was trying to develop phage therapies for new antibiotics.


00:45:41,970 --> 00:45:52,000

Since that time I have met five or six other CEOs of companies trying to develop phage therapies as alternatives to conventional antibiotics.


00:45:52,100 --> 00:46:06,680

People have been trying to do this for many many years. The timing was probably not right. But I suspect with what is going on with the antibiotic resistance problem, now may be the time.


00:46:06,780 --> 00:46:17,990

In fact, I am even thinking about, after reading all these papers, now may be the time to go to the VC and say hey, let's start a phage company because this is going to work.


00:46:18,090 --> 00:46:22,000

Now is the right time, I think, to actually try and do it.


00:46:22,100 --> 00:46:30,000

Vincent: Well, this one article written by Carl Teal, he says in the end, that one day physicians may have no choice but to use phage therapy, the antibiotics do not work.


00:46:30,100 --> 00:46:36,700

You know the companies are not making anti-macrobials anymore. A lot of them have shut down operations.


00:46:36,800 --> 00:46:43,660

Cliff: So I think all of us should now get our money together, take out our check books, and start a new phage company.


00:46:43,760 --> 00:46:44,760

Vincent: I don't have any money so....


00:46:44,860 --> 00:46:46,000

Cliff: That could well be.


00:46:46,100 --> 00:46:47,500

Vincent: That's what I would do.


00:46:47,600 --> 00:47:08,650

Elio: Also, I must say, I love to hear you talk that way in such an optimistic tone, but I do think the problems of getting there, from here to there, are formidable. They are really quite immense problems. I don't think it is going to be quite so fast for a whole lot of reasons.


00:47:08,750 --> 00:47:25,210

We haven't even touched on the fact that phages are wonderful antigens, they are particles that are taken up by the immune system and as people are trying to do, engineer them to be resistant to that. But that is not going to be an easy thing.


00:47:25,310 --> 00:47:39,420

I don't see it in quite such a glowing optimism. I think it is going to happen probably. It may well happen sooner than I know, but I think it is going to be a while. I am not quite so sanguine about it.


00:47:39,520 --> 00:47:50,510

Vincent: Let's mentioned some of the other problems, like Elio mentioned the antigenicity. How about when you lyse the bacteria they release endotoxin, right? That could be a problem.


00:47:50,610 --> 00:47:56,800

What about the effect on your microbiome if you take a cocktail, right?


00:47:56,900 --> 00:48:21,830

Michael: That is a good point. That is why the beauty of it is specificity. I think it is the push-pull. We have to begin to understand the inherent microbiome of the location that we are treating to ask the question of whether or not the phage elixir is going to do more harm than good.


00:48:21,930 --> 00:48:51,700

Cliff: I agree. But that is why, Vincent when you looked at, the actual indications, the clinical indications they were working on, those like diabetic foot ulcers or difficult to heal or non-healing wounds, that is where the need is really really still great and the unmet medical need there.


00:48:51,800 --> 00:48:58,400

Many people still lose their feet, toes, and other appendages because of diabetes and infections.


00:48:58,500 --> 00:49:10,050

So where there is a great need and the risk-benefit ratio is..., there is no question, you have to take the risk because there is no other alternative.


00:49:10,150 --> 00:49:20,510

That is where you start. You start there and demonstrate time and time again the chronic application of this mixture still works.


00:49:20,610 --> 00:49:36,050

Yes, there may be antibodies but over the course of a three or nine month treatment regimen, because of the multi-valency of the cocktail, this person's diabetic foot ulcer which didn't heal any other way, it worked.


00:49:36,150 --> 00:49:51,000

Then you will get enough public awareness where, okay it works here. We are not going to use it to treat sepsis, we are not definitely going to use it to try and treat a gram negative infection because of the endotoxin issue, right?


00:49:51,100 --> 00:49:57,190

We can use it for gram positive skin infections and difficult to heal wound infections.


00:49:57,290 --> 00:50:22,810

That is where you begin and that is where the paradigm shift begins. You take baby steps to introduce the concept and show its efficacy and safety. Then go down the pathway Michael and Elio were talking about to begin to address more serious systemic disease where the risks are a little bit higher because you are injecting it into the blood stream or you are drinking it or something like that.


00:50:22,910 --> 00:50:29,820

Michael: The papers that are out there today are following Cliff's recommendation.


00:50:29,920 --> 00:50:38,220

The paper on the ear infections with pseudomonas, I think was rather interesting.


00:50:38,320 --> 00:51:03,340

It teaches many lessons about how one needs to do viable counts and what one considers statistically significant, but at the end of the day, they treated a very small number of patients but four of the patients were actually,  by viable count, free of pseudomonas just by treating them with the phage cocktail.


00:51:03,440 --> 00:51:28,190

While the other patients in the experimental arm of the study, even though they reported a 56.9% reduction in the bacteria, there are not too many microbiologists out there who would consider 9.3 x 10 9 going down to 5.3 x 10 9 as being significant, even though that is 56%.


00:51:28,290 --> 00:51:55,170

I always measure whether or not it is there. It gives you a new sense of appreciation for the need for understanding how to do viable counts and how you have to begin to do some of these experiments where you really want to measure whether or not the microbe is present  and able to continue to come back.


00:51:55,270 --> 00:52:00,630

Because, the old adage, dead bacteria don't grow again is true.


00:52:00,730 --> 00:52:02,530

Cliff: I love that, that adage.


00:52:02,630 --> 00:52:07,980

Michael: Well, you know, that is the definition of cure.


00:52:08,080 --> 00:52:17,200

Cliff: I know, I am laughing with you because if it is 99.9999% effective there is still a hell of a lot of bacteria there, right?


00:52:17,300 --> 00:52:30,250

The funny thing is Michael that you bring up otitis media, I was just listening in my car, driving around wherever I was going, and they were talking about the antibiotic resistance stuff.


00:52:30,350 --> 00:52:45,680

Now, pediatric physicians are being trained that if someone comes in, a child comes in with an ear infection, you do not treat it with antibiotics unless you absolutely, without a doubt, there is no other choice.


00:52:45,780 --> 00:52:56,760

They do not want to use..., first of all, the effectiveness is relatively questionable, and why use antibiotics when you know it doesn't work that well.


00:52:56,860 --> 00:53:01,190

So otitis media for phage treatment would be an ideal....


00:53:01,290 --> 00:53:03,100

Vincent: Just drip it in the ear, right?


00:53:03,200 --> 00:53:13,770

Cliff: Just drip it in the ear and see if it works. If it works its great. If it doesn't, because the alternative of not giving the antibiotic is to let the infection ride itself out.


00:53:13,870 --> 00:53:31,140

There is another good example of an indication of it where a phage company, or somebody in the business, may want to look at that. Because, quite honestly, otitus media is a very large pediatric problem and it also can lead to more serious disease.


00:53:31,240 --> 00:53:37,740

That is why we have these vacines against the organism that cause otitis media, per se.


00:53:37,840 --> 00:53:47,140

So yes, I think that is another the people, as Michael said, are doing, they have thought about it and are working in the right areas.


00:53:47,240 --> 00:53:51,210

Michael: The rule of thumb is that you always go after low hanging fruit.


00:53:51,310 --> 00:53:54,450

Vincent: Yes, that is right.


00:53:54,550 --> 00:53:59,030

So should we wrap this up and move on to our second story now?


00:53:59,130 --> 00:54:06,760

Have we talked about this sufficiently for today? I am sure we will re-visit it as some results come forth in coming years.


00:54:06,860 --> 00:54:12,470

There is another paper we have which is a good segway from what we have been talking about right now.


00:54:12,570 --> 00:54:20,810

This was published in PLOS ONE, it is called Antibiotic Resistance Genes in the Bacteriaphage DNA Fraction of Environmental Samples.


00:54:20,910 --> 00:54:36,120

This is a rather straight forward study out of Barcelona where they collected river water and sewage and looked by amplification, by PCR for a couple of specific antibiotic resistance genes.


00:54:36,220 --> 00:54:51,250

Someone can tell me about these. They looked at two beta-lactamases and a mecA gene involved in MRSA resistance. So who can tell us what these blas and mecs are?


00:54:51,350 --> 00:54:57,350

Cliff: I can do that if you want me to? Take a stab.


00:54:57,450 --> 00:55:01,180

Vincent: You like that stab metaphor.


00:55:01,280 --> 00:55:07,190

Cliff: Yes, with the phage picking the plaques. Yes, I love that. I will take a stab at it.


00:55:07,290 --> 00:55:09,080

Michael: When in Rome.


00:55:09,180 --> 00:55:29,510

Cliff: So the bla gene encodes for an enzyme known as beta-lactamase, which is an enzyme that cleaves the beta-lactam ring of penicillin and cephalosporins, which are synthetic derivatives of penicillin.


00:55:29,610 --> 00:55:38,390

So the bacteria will produce the enzyme, it will cleave the beta-lactam ring or break it open and render the antibiotic ineffective.


00:55:38,490 --> 00:55:55,710

So if the bacterium is producing an enzyme that does that and it encounters penicillin outside of itself, because the beta-lactamase is secreted, it will inactivate any antibiotic that is out there and possibly some even if it makes it in.


00:55:55,810 --> 00:56:06,020

Vincent: So the penicillin like antibiotics and beta-lactamases, of all the antibiotics we have, like what fraction is that? Is that a majority?


00:56:06,120 --> 00:56:17,940

Cliff: They are the ones that are probably the safest and most efficacious, and the ones that physicians like to use the most when treating bacterial infections.


00:56:18,040 --> 00:56:20,040

Vincent: Of all sorts, of all different....


00:56:20,140 --> 00:56:30,430

Cliff: Of all sorts. They are like the frontline type antibiotics that physicians like to use because they are very effective and very very safe.


00:56:30,530 --> 00:56:41,940

Not surprisingly those are the antibiotics where we are seeing emerging and already emerged antibiotic resistance problems because they are so used.


00:56:42,040 --> 00:56:46,110

Vincent: So these two they picked because they are very prevalent, these two particular enzymes.


00:56:46,210 --> 00:57:03,720

Cliff: Let me just say that mecA is different than bla. I don't want to get too technical but in order for penicillian to be transported into the bacterial cell there are proteins in the bacterial cell wall known as penicillian binding proteins.


00:57:03,820 --> 00:57:15,930

So in order for penicillian to get in it needs to bind  first to the penicillian binding protein, of which in gram positive there are five, I believe, and then it gets transported.


00:57:16,030 --> 00:57:25,560

There are different penicillian binding proteins that are used for different species or different types or classes of beta-lactame antibiotics.


00:57:25,660 --> 00:57:38,640

The mec-2 gene seems to be very important in the transport of methicillin and related synthetic penicillians into a gram-positive cell.


00:57:38,740 --> 00:57:49,620

So mec-2 is known as the methicillin resistance gene, so MRSA that is what it confers, metha resistance, resistance to penicillin (MRSA -- Methicillin-resistant Staphylococcus aureus).


00:57:49,720 --> 00:58:12,400

Vincent: So they looked at three genes that encode, two beta-lactamases and one mecA, because they are just very common. And what they did is took this water and passed it through a 0.2 micron filter, where only the viruses will pass through, concentrated it. They treated it with DNase to get rid of all DNAs floating around like plasmids.


00:58:12,500 --> 00:58:18,740

What was left they presumed to be phages. They extract the DNA and then they look for these genes by PCR.


00:58:18,840 --> 00:58:24,650

Elio: Okay, what is new about this paper, the best I can tell, is that they found these genes in phages.


00:58:24,750 --> 00:58:25,250

Vincent: Right.


00:58:25,350 --> 00:58:35,290

Elio: People who have looked just at DNA in sediments and in waters have found plenty of these resistant genes, this is not a new thing.


00:58:35,390 --> 00:58:44,880

In general it is quite clear that the closer you are to people, the closer to polluting sources, the more likely you are to find these phages.


00:58:44,980 --> 00:58:54,190

In prestine waters they are rare. Sorry, these genes. In prestine waters they are rare. But they are common in contaminated waters.


00:58:54,290 --> 00:58:59,260

So what is new about this paper is the fact that they found them in phages.


00:58:59,360 --> 00:59:09,180

Not surprising in a way. I mean this is what you would expect from lysis and from phages being able to pick up the host DNA.


00:59:09,280 --> 00:59:18,770

So I am not so sure I know why..., this is an interesting paper but it does simply illustrate how wide spread this phenomenon is.


00:59:18,870 --> 00:59:27,420

Vincent: So do you think that these phages with the antibiotic resistance genes are simply coming from people because it is contamination of fecal material?


00:59:27,520 --> 00:59:31,150

Elio: Oh, it is almost certainly the case. People or animals certainly.


00:59:31,250 --> 00:59:38,040

Michael: Remember that the phage go through the generalized transducing aspect.


00:59:38,140 --> 00:59:57,420

A generalized transducing particle will pick up all host DNA or all plasma DNA and there is no viral DNA involved in it. It goes back to the Pepsi worker playing with the dials in the Coke factory, destroying it and everything gets packaged up and sent out.


00:59:57,520 --> 01:00:08,000

That frequency occurs once for every 10,000 phage that are produced per population effect.


01:00:08,100 --> 01:00:24,480

So it is not that surprising that they may be detecting generalized transducing phage or they actually may be detecting it in lysogens where it is a product of the specialized transduction due to aberrant excision.


01:00:24,580 --> 01:00:36,610

That occurs at a frequency between 10 to the 4 and 10 to the 5 depending upon the virus that you are looking at and how it is going about pulling it out.


01:00:36,710 --> 01:00:47,030

Since they were using PCR, specifically looking for the gene of the drug resistance, you don't know whether or not they had  generalized transducing fragments or not.


01:00:47,130 --> 01:00:54,110

Vincent: So they would like to think this is not from feces but they can't prove it.


01:00:54,210 --> 01:00:56,730

Cliff: Right, but yes.


01:00:56,830 --> 01:01:01,040

Vincent: But Elio says that in pristine waters you don't find these genes.


01:01:01,140 --> 01:01:16,750

Elio: Well I am not talking about this paper, I am talking about papers, for instance, somebody in San Diego at Point Loma University has been looking at this and he finds all kinds of antibiotic genes in dirty waters, like the Tijuana River estuary.


01:01:16,850 --> 01:01:21,520

But he goes to northern California to some fairly prestine sea waters and there is very little there.


01:01:21,620 --> 01:01:26,510

Vincent: Because I think their thesis is that these genes are in the environment and they are being mobilized by phages.


01:01:26,610 --> 01:01:41,010

Cliff: Yes, and I guess the data are still missing to verify that these are actually, can be transduced, as Michael is suggesting, in the environment.


01:01:41,110 --> 01:01:55,010

It would have been nicer if they would have been able to actually grow out a lot of phage and then extract DNA and do it the old fashion way and then figure out which phage it was coming from to see whether or not... whatever.


01:01:55,110 --> 01:02:18,940

There is a missing piece to it. But the important..., I guess for me the reason why I think what they found is important is that in the case of, you know, just as in a real life situation, what is going on with the New Dehli beta-lactamase gene that was identified six months ago, the one that's in India that we were talking about, Vincent.


01:02:19,040 --> 01:02:21,190

Vincent: So this is a brand new beta-lactamase, right?


01:02:21,290 --> 01:02:33,570

Cliff: It is a brand new beta-lactamase that has never been seen before that apparently is like the super beta-lactamase that will cleave every single cephalosporin known to humanity.


01:02:33,670 --> 01:02:55,260

The interesting thing is that I kind of didn't pay a lot of attention to it and since I have been putting together this article on antibiotic resistance I have been talking to people that work at companies that are in this space and apparently since the gene was first identified, it has been found everywhere in environmental sources in India.


01:02:55,360 --> 01:03:00,760

Everywhere. The water. Food. Everything that they have looked for, it's there.


01:03:00,860 --> 01:03:14,510

Which means that it's out. These are bacteria that are now carry because, these are gram-negatives, a gram-negative, I think it is klebsiella.


01:03:14,610 --> 01:03:21,340

These are things that can get into the human intestinal tract, carried by people. And they are now being transported everywhere.


01:03:21,440 --> 01:03:43,750

So the fact that you have fecal contamination, and these bacteria are in the environment now, suggest that if, in fact, generalized transduction can occur in nature, you can begin to see the amplification of this gene through different populations.


01:03:43,850 --> 01:03:59,930

And who knows what the possibilities are going to be if this gene is then transfered from Klebsiella into E Coli or into Pseudomonas and then, although E Coli phages can not infect Pseudomonas, right. And vica versa.


01:04:00,030 --> 01:04:18,920

But if the gene was now transfered from this Klebsiella to E Coli or whatever, you know have phages in Klebsiella and E Coli, that could also now begin to transduce it throughout those populations, if this in fact occurs.


01:04:19,020 --> 01:04:56,930

So for me, it was like more proof that we have to be, although we can teach it in bacterial genetics that transduction takes place and we can show it in the laboratory, the fact that they could find it in fecally contaminated water or streams or rivers, from a practical stand point means that it is now, one could argue that transduction or transfer of antibiotic genes could be another part of the amplification that takes place in a population of bacteria that are put under anti-microbial stress.


01:04:57,030 --> 01:05:06,220

Michael: Let's not forget the wonder of how these bacteria phage begin to interact with the host genome.


01:05:06,320 --> 01:05:10,550

They principally do it through insertion sequence elements.


01:05:10,650 --> 01:05:37,200

These insertion sequence elements are a good way of scanning the genome. So if you begin to think about this new genomics revolution that we are having, is to look for IS elements, and we already understand pathogenicity islands pretty well, where that is a large chunk of the host DNA that is foreign.


01:05:37,300 --> 01:05:59,850

It is thought that this DNA had gotten into the host by virtue of the fact by being brought in by phage and then undergoing insertion via these insertion elements or, in some cases, they actually they target a not frequently used tRNA gene.


01:05:59,950 --> 01:06:17,970

It inserts itself at the tRNA gene and you have these pathogenicity islands where you can actually have approximately 200 kb of DNA going into some microbes that confer virulence to those microbes.


01:06:18,070 --> 01:06:30,160

So it is not all that surprising to think about phage that may be passengers of these pathogenicity islands that can get in and out.


01:06:30,260 --> 01:06:51,190

We have to remember once DNA gets into the cell, as long as it is tagged with the appropriate restriction modification signatures, it can be pretty promiscuous, especially if it gets attacked by a phage and you end up with a generalized transducing particle.


01:06:51,290 --> 01:06:56,210

Then that DNA gets inserted into the appropriate susceptible host.


01:06:56,310 --> 01:07:16,640

I think this paper is really very facinating because it is illustrating, to those folks who have not have the benefit of bacterial genetics course from the olden days when you use to map with transducing particles. Now I am going to show how old I am.


01:07:16,740 --> 01:07:30,100

The transducing particle mapping problems where the gold standard of every qualifying exam.  You got sent to the board and you were told to map a gene based on a frequency table.


01:07:30,200 --> 01:07:43,550

Talking about breaking out in flop sweat. That was the nightmare of a lot of graduate students back in the eighties and early nineties until the molecular biologists killed it.


01:07:43,650 --> 01:07:58,280

Cliff: I'll take it even further Michael. Try the nineteen seventies when I was taking my microbial genetics and we had a take home problem to figure out where the gene was located in the bacterium based on transduction frequencies.


01:07:58,380 --> 01:08:15,440

Vincent: Let me ask, tell me if this senario is correct. Let's say these phage carrying these antibiotic resistance genes did not originate from humans but, my understanding is that all antibiotic resistance genes come from the enviroment, right.


01:08:15,540 --> 01:08:31,290

So that these phages have picked up these genes from some bacteria in the environment. So that if that's correct then. The scenario is that these phages could make there way into humans then at some point and that could be an issue. Is that what the whole point is of this?


01:08:31,390 --> 01:08:38,800

Cliff: No, the point is to show that phage, at least from the way I see it, is that there has been this ....


01:08:38,900 --> 01:08:46,370

How is antibiotic resistance amplified in a bacterial population that is under antibacterial stress.


01:08:46,470 --> 01:09:02,080

The assumption is that there is mobile genetic elements, there is blasmids and stuff and people have largely discounted a role, per se, for phages carrying, as Michael pointed out, generalized transducing particles.


01:09:02,180 --> 01:09:11,780

For me, it is just another example of, perhaps, how rapidly this thing can happen if phage get involved.


01:09:11,880 --> 01:09:17,610

Because they haven't found phage before, basically, right. They haven't found it very often. That is bsically it right.


01:09:17,710 --> 01:09:28,000

Well, what I am saying is that no one has looked for  antibiotic resistance genes, has identified genes in phage DNA in the environment.


01:09:28,100 --> 01:09:40,180

My story is that we know that E Coli phages only infect E Coli, at least that is the dogma. Same thing with staph and staph, Klebsiella.


01:09:40,280 --> 01:09:51,570

But klebsiella can mate or through transformation conjugation, whatever, transfer an antibiotic resistance gene, say, to E Coli.


01:09:51,670 --> 01:09:59,110

So klebsiella is where this New Delhi beta-lactemase that has been identified gets transfered to E Coli.


01:09:59,210 --> 01:10:09,590

E Coli then has phages that pick it up and transfer it to other E Colis. E Colis are normal inhabitants of our intestinal tract.


01:10:09,690 --> 01:10:28,450

People eat..., somehow take these E Coli, they inhabit the intestinal tract. These people now travel all over the world and they are carrying these antibiotic resistance genes in their intestinal tracts. It gets deposited to the sewage system in Brazil, Vietnam, the United States, whatever.


01:10:28,550 --> 01:10:32,690

Now we have the same thing that could happen everywhere.


01:10:32,790 --> 01:10:43,900

The point I was trying to make was, when I first heard of about the New Dehli thing, I said it is only India, they are making a big deal about it. Right now I think it has been identified in every single continent.


01:10:44,000 --> 01:10:49,740

It was discovered six months ago, or maybe a year ago, before it was published. It is now everywhere.


01:10:49,840 --> 01:11:02,060

Infectious disease physicians are freaking out, becasue as I mentioned previously, it is these beta-lactane like antibiotics they like to use.


01:11:02,160 --> 01:11:16,420

If they are no longer effective against gram negatives, the next thing they are going to have to use are the next generation, like amino glycosides, which are very toxic. Or some other more toxic antibiotics which then create additional problems.


01:11:16,520 --> 01:11:31,710

So they are shaky because gram-positive bacteria are relatively, you know MRSA gets all the ink, but they are treatable. We have a whole variety of antibiotics that can be used if we chose to use them.


01:11:31,810 --> 01:11:45,440

It is the gram-negative bacteria, like the klebsiellas, the pseudomonases, the e colis, the salmonellas, the actinobactors, those are the places where there are no good, safe antibiotics at work any more.


01:11:45,540 --> 01:11:53,840

You can not use beta-lactives and cephalosporins really much against gram-negative infections anymore because they are all resistant.


01:11:53,940 --> 01:12:01,880

Vincent: Alright, I think we should move on to the final part of this program.


01:12:01,980 --> 01:12:02,950

Cliff: It is a long episode. Sorry.


01:12:03,050 --> 01:12:04,320

Vincent: Hey, it's okay, it's not a problem. People don't have to listen to the whole thing.


01:12:04,420 --> 01:12:17,660

Now let's just do a few emails from our listeners. The first is from Don who writes, I was intrigued by the comments on the antimacrobial effects of copper having used silver suchers in contaminated cases in the sixties.


01:12:17,760 --> 01:12:30,090

It struck me that an easy and cheap test would be to copper plate, which uses very little, the door, faucet, and toilet handles in an ICU and see if the hospital acquired infections changed.


01:12:30,190 --> 01:12:39,360

This is fairly low tech requiring a screw driver, an auto battery, and some copper sulphate root killer, or it could be done by many firms who do it commercially.


01:12:39,460 --> 01:12:41,610

Thanks for the really good podcast.


01:12:41,710 --> 01:12:43,710

What do you think Michael?


01:12:43,810 --> 01:12:55,720

Michael: I think I am going to be publishing the clinical trial that we have been doing at three hospitals. I will answer that question once we enroll a few more patients.


01:12:55,820 --> 01:12:59,490

But not to let the cat out of the bag.


01:12:59,590 --> 01:13:03,600

Vincent: Yes, we will know from you. When you publish it, we will talk about it.


01:13:03,700 --> 01:13:05,800

But he is on the right track, I presume.


01:13:05,900 --> 01:13:22,520

Michael: Yes, he is on the right track and, as you know, there was that very famous case where they incorporated silver wire into the sewing cuff of heart valves, artificial heart valves, or pig valves, I think, one of the two.


01:13:22,620 --> 01:13:31,390

This was an issue where the sewing cuff was actually contaminated with a biofilm.


01:13:31,490 --> 01:13:41,800

Again it goes back and illustrates the importance of being able to assess whether or not there is an infectious microbe associated with a particular material.


01:13:41,900 --> 01:13:59,460

They assayed it. They answered the question in the negative, that there was no infectious agent associated with the sewing cuff. And then they established there was actually a biofilm growing on the silver wire that was used in the sewing cuff.


01:13:59,560 --> 01:14:03,510

And they had to recall all those heart valves that were inplanted in the patients.


01:14:03,610 --> 01:14:15,420

You know that thing that we first learned in our micro class, how to do a viable count and how do you ask if there is a viable bacterium present?


01:14:15,520 --> 01:14:24,930

It is seemingly pretty low tech, but in clinical microbiology it is really pretty important, especially if you are going to get a heart valve.


01:14:25,030 --> 01:14:59,270

Vincent: Alright, our next one is from Zowawih. Hi, I am a big fan of your great education/entertaining programs. I would like to suggest Vincent to invite experts in antimicrobial resistant bacteria in his newly launched TWiM program. This problem is very serious and thus the WHO themed their day with the antibiotic resistance issue. Likewise the CDC chose a week on September last year to address the devastating health related issue. Inviting experts and pioneers in this field will highlight and explain queries.


01:14:59,370 --> 01:15:06,160

Well, we plan to do that. We will get a program together on antibiotic resistance in the future.


01:15:06,260 --> 01:15:16,420

Next one is from Chris who writes, I recall hearing about a bacterial contamination of cantaloupe years ago, which is when I started to wash them in soapy water before slicing.


01:15:16,520 --> 01:15:47,120

Of course, I try to follow the rules. We actually cut meat products on the counter between the stove and sink, and the rest on the kitchen island to prevent cross contamination. Often I will prep for cooking by cutting the veggies on a dishwasher proof cutting board on the island, put them in bowls and set aside. Then move the cutting board to the counter, cut the meat and either put it in the bowl or the pan. Then put the cutting board in the dishwasher, set the knife to be hand washed next o the sink. Then cooking is quicker because I have everything ready, using a food safe place.


01:15:47,220 --> 01:16:04,860

The other day I was watching an old cooking show with Julia Child. I just about gagged when I saw the other chef she was working with put an herb stuffing between the breast and skin, and then reach over to pick up salt from a bowl with his fingers without washing his hands or using a spoon!


01:16:04,960 --> 01:16:25,940

I have a TWiM idea from watching cooking shows, especially one that showed all of the varieties of salt: pink salt, which gets its color from an extremophile bacteria (a tidbit I want to share at the local upscale kitchen store when I get a chance!). Oh, cool, just checking the halophile wiki, I learned they are essential for some fermented foods like soy sauce, sauerkraut, anchovies, etc.


01:16:26,040 --> 01:16:28,040

There is a halophile wiki huh?


01:16:28,140 --> 01:16:29,220

Cliff: I think there is a wiki for everything.


01:16:29,320 --> 01:16:30,600

Vincent: Amazing.


01:16:30,700 --> 01:16:41,270

Alright, let's do one more. From Frank, First:  Thanks for making a career of TWI-Podcasts!  A great service and an entertaining and educational format.


01:16:41,370 --> 01:17:21,840

In TWIM #1 you reviewed the antibacterial properties of copper and it’s potential for control of MRSA compared to other methods being pursued.  While the science of antibiotic mechanisms is fascinating, we may be blinded by the technology instead of understanding the logic of the problem.  The references below are a few of the many showing (not surprisingly) that the people who spend their days around hospitals are the reservoirs for MRSA.  Anywhere from 6% to 21% of healthcare workers (in this case anyone working in a hospital) have been shown to carry MRSA in their nares. This is higher than the rate in incoming patients. Remove the reservoirs and control is much easier!


01:17:21,940 --> 01:17:52,050

While we are great at technical solutions, we are close to powerless at social, particularly politically social solutions.  It would seem that a major reduction could be achieved through regular testing of healthcare workers to identify carriers, their removal from patient care, treatment with mupirocin topically and return to patient care.  Hospitals object to the cost of testing although as carriage rates decrease so would costs.  Unions object to the potential unpaid removal from work during treatment as well as the treatment cost.


01:17:52,150 --> 01:18:12,190

Doctors generally refuse to be tested, even for hepatitis or HIV. Despite the enormous monetary cost of MRSA to hospitals and to our overall healthcare system, plus the unnecessary deaths, our society insists that “magic bullet” pharmaceuticals and antibacterial hardware are the only way to solve this problem. Pogo had it right about “the enemy”.


01:18:12,290 --> 01:18:22,140

Thanks again for the education and entertainment.  Vincent and your TWIV, TWIP, TWIM teams are an exceptionally bright spot in scientific education!


01:18:22,240 --> 01:18:25,350

Well there you go gentlemen, you are a bright spot.


01:18:25,450 --> 01:18:27,610

Cliff: I sound like a sun spot?


01:18:27,710 --> 01:18:28,410

Michael: Thank you Frank.


01:18:28,510 --> 01:18:42,200

Vincent: You know, I am think that maybe we should, I read in one of those phage papers they proposed to put phages in the noses of health care workers to reduce the amount of..., or maybe it was patients before they come into the hospital to reduce infections.


01:18:42,300 --> 01:18:48,340

Cliff: You know Vince Vecchietti, I am thinking like seven or eight years ago, identified a protein.


01:18:48,440 --> 01:18:49,680

Vincent: He had a lysis right?


01:18:49,780 --> 01:19:01,710

Cliff: That was his idea..., to develop a nasal treatment to remove or reduce the carrying of MSRAs.


01:19:01,810 --> 01:19:05,040

It was from a staphylococcal phage.


01:19:05,140 --> 01:19:09,790

I lost track of what happened and I haven't read any about the approach.


01:19:09,890 --> 01:19:11,890

Vincent: He has a company you know. He's trying to push it forward.


01:19:11,990 --> 01:19:18,460

Cliff: So he is still trying to do that stuff. Yes, because that was a brilliant idea and I am sure now would be a good time for lysis.


01:19:18,560 --> 01:19:22,450

Vincent: It is sort of like taking the phage one step further. You get the protein that does the lysis.


01:19:22,550 --> 01:19:25,550

Cliff: Then you have to worry about the protein.


01:19:25,650 --> 01:19:27,500

Vincent: I think it is just for topical applications.


01:19:27,600 --> 01:19:43,060

Cliff: I mean it makes sense. There are lots of hospitals that are doing what Frank suggests. They are doing it in screening and they are doing it fairly rigorously.


01:19:43,160 --> 01:19:57,290

The data, I heard again a report on NPR, the data from a hospital that is really focused on infection control versus one that is not, it is not so clear whether it really works, all that stuff.


01:19:57,390 --> 01:20:10,280

So it is still up in the air. But Frank is absolutely right, if you could identify the people that are carrying it and practice appropriate infection control, then you will, by definition, reduce the incidents.


01:20:10,380 --> 01:20:12,650

It is always about money Vincent.


01:20:12,750 --> 01:20:14,200

Vincent: Oh yes.


01:20:14,300 --> 01:20:23,660

Alright, that will do it for another TWiM. You can find us on iTunes, at the Zune Marketplace, and at


01:20:23,760 --> 01:20:32,890

There is also a wonderful app for your iPhone or Android device which you can use to stream the device.  It is at


01:20:32,990 --> 01:20:40,180

If you like TWiM tell your friends about it. And tell them to write a review on iTunes to help bring us to the top of the list there.


01:20:40,280 --> 01:20:51,570

Send us your questions to TWiM at or go over to and there is a place where you can leave a comment there as well.


01:20:51,670 --> 01:20:54,710

Elio Schaechter thank you for joining us today.


01:20:54,810 --> 01:20:56,810

Elio: My pleasure, this was a lot of fun.


01:20:56,910 --> 01:21:00,990

Vincent: Good, I am glad you liked it and you'll be back with us again soon. That's great.


01:21:01,090 --> 01:21:04,810

Elio is at Small Things Considered.


01:21:04,910 --> 01:21:06,510

You have fun doing that, right?


01:21:06,610 --> 01:21:08,080

Elio: Oh, do I ever.


01:21:08,180 --> 01:21:12,890

Vincent: Great. You told me once it loosened you up to blog, right?


01:21:12,990 --> 01:21:14,990

Elio: Absolutely.


01:21:15,090 --> 01:21:18,560

Vincent: Michael Schmidt, thank you.


01:21:18,660 --> 01:21:20,510

Michael: You are welcome Vincent. It was fun again today.


01:21:20,610 --> 01:21:23,720

Vincent: Always fun. No shortage of fun stories to talk about.


01:21:23,820 --> 01:21:27,330

Michael is at the Medical University of South Carolina.


01:21:27,430 --> 01:21:28,940

Thanks you Cliff Mintz.


01:21:29,040 --> 01:21:32,310

Cliff: You are welcome Vincent. It was a pleasure as always.


01:21:32,410 --> 01:21:35,410

Vincent: Cliff is at


01:21:35,510 --> 01:21:41,330

I am Vincent Racaniello. You can find me at


01:21:41,430 --> 01:21:54,830

I would like to thank the American Society of Microbiology for supporting TWiM, Communications Director Barbara Hyde, and Chris Condayan and Ray Ortega for the behind the scenes technical help.


01:21:54,930 --> 01:22:05,000

Thanks for listening everyone. We will see you next time on This Week in Microbiology.

Steve Stokowski made this caption file using a YouTube Machine Translation and the online captioning tool Subtitle-Horse.


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