Evergreen Phage 2019: Meeting Recap

Issue 44 | September 12, 2019
24 min read
Capsid and Tail

Image credit: Kema Malki

Hello phage people! It’s been about a month since Evergreen, and we’re ready with our wrap-up post. We’ve covered highlights, themes, and what really excited us about the conference!

Also in this issue: new insights into gut-phage interactions, how Intralytix’s multi-target phage cocktail works, a review on phages in dairy, a last chance to register for Phage Futures EU, and more!

What’s New

There are only 18 spots left at Phage Futures EU (Brussels Sept 25-26); if you’re on the fence or haven’t registered yet, best to decide and book soon! We’ll be there and would love to talk phages with you! Discount code PD10 will get you 10% off.

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How do bacteria in the gut interact with phages? In a new Cell Host & Microbe paper, Paola Soto-Perez and colleagues from UCSF show that Eggerthella lenta, a prevalent bacterial member of the human gut microbiota, uses CRISPR-Cas to target gut viral sequences (they built a human viral database to check!).

ResearchCRISPRGut microbiome

Upuli Dissanayake and colleagues at the University of Florida, along with the US phage company Intralytix, have published a paper showing an E. coli/Salmonella/Listeria-targeting phage cocktail reduces E. coli O157:H7 counts in mice without distorting their gut microbiota.

Phage TherapyResearchPhage cocktail

Where’s the field at with phage‐mediated control and detection of pathogens in the dairy context? Here’s a nice new review of the literature by Lisa O’Sullivan and colleagues from the Cork Institute of Technology, Ireland.

Phage BiocontrolDairy

If you’d like a hard copy of the special issue “Hurdles for Phage Therapy to Become A Reality”, a compilation of about 30 peer-reviewed articles published by the journal Viruses over the course of 2018 and 2019, you can order one here for about $100.

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Latest Jobs

Microbiologist / Molecular Biologist

Leonyte Biosystems, Berlin, Germany

Leonyte Biosystems is a fast-paced biotechnology start-up in Berlin, developing new in vitro diagnostics for detecting pathogens in food. We are looking to grow our team with a Microbiologist with strong experience in molecular biology to assist in the development of bacterial detection and identification tests for the food industry. The successful applicant will have experience in S2 bacterial culturing techniques, working with bacteriophage, general molecular biology techniques (e.g. real-time PCR, ELISA, cloning) as well as microscopy techniques (e.g. Gram-staining, DAPI staining, use of confocal fluorescence microscope). Previous experience within the food industry and in vitro diagnostics is a plus.

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Anyone can post a message to the phage community — and it could be anything from collaboration requests, post-doc searches, sequencing help — just ask!

September 12, 2019

Seeking research exchange opportunity

Fatma Abdelrahman

My name is Fatma Abdelrahman and I have BSc in Microbiology from the Faculty of Science, Zagazig University, Egypt. I’m currently a research assistant at the Center of Microbiology and Phage Therapy, Zewail City of Science and Technology, Egypt. My first paper about phage encapsulation is here.

I am looking forward to obtaining an internship or research visit in the fields of phage therapy, phage lysins, other phage-derived enzymes or related topics. I’m planning to pursue my master degree on these topics and I have chosen it to be my future research area.

If there are no fully funded research grants, there are several local institutions which can aid in providing adequate grants upon being accepted.

Please contact me at fabdelrahman@zewailcity.edu.eg

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September 12, 2019

Seeking postdoctoral research opportunity

Dr. Kübra Can

I am seeking a research position in phage therapy or moleculer phage studies. I hold a PhD from Istanbul University (Institute of Health Sciences, Medical Microbiology Department).

I have strong experience in clinical microbiology, bacteriophage therapy and animal disease models. I am interested in clinical microbiology and crosstalk between organs in mouse models. I am also eager to learn and implement new methods and NGS data analysis for future studies.

Please contact me at kubra.can@istanbul.edu.tr

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Evergreen Phage 2019: Meeting Recap

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Phage microbiologist and co-founder of Phage Directory
Co-founder
Phage Directory, Atlanta, GA, United States

Jessica Sacher is a co-founder of Phage Directory and has a Ph.D in Microbiology and Biotechnology from the University of Alberta.

For Phage Directory, she takes care of the science, writing, communications, and business aspects.

Who, what, where, when?

The meeting took place Aug 4-9, 2019 in Olympia, Washington at the Evergreen State College.

This year was the 23rd Evergreen conference (and it runs only once per two years), meaning it’s been around 46 years! Dr. Betty Kutter, professor emeritus at the Evergreen State College, has been the lead organizer since its establishment (read a recent in-depth interview with Betty here!).

The meeting covered almost everything you could think of when it comes to phage. Therapy, research, agriculture, bioinformatics, AI, you name it. There were 344 registered participants (about 100 more than last time!).

Present-day phage therapy: a multitude of approaches

The meeting started out with a session on human phage therapy: a bird’s eye view of the various ways human phage therapy is being done right now around the world.

Routine phage therapy at the Eliava Institute in Georgia

Mzia Kutateladze, the director of the Eliava Institute in Georgia, kicked off the session by telling us about how the Eliava treats cystic fibrosis patients with phages (they treat 20-30 CF patients with phages per month!).

Later in the week, Naomi Hoyle, a physician at the Eliava Phage Therapy Center told us about how her “two-month trip” to Georgia (as a student in Betty Kutter’s lab) became a 15-year trip, and about the collective clinical experience of the Eliava Institute when it comes to treating patients from all over with phages. Fun facts: they get around 2000 emails from patients per month, and they treated 400 patients with phages in 2018, and so far 300+ in 2019. Patients have come from 63 countries. Naomi made it clear that the Eliava intends to focus more on documenting the results of these treatments, and is open to participating in clinical trials.

Phage therapy through compounding pharmacies in Belgium

Bob Blasdel of Vesale Bioscience in Belgium gave a rundown of how compounding pharmacists in Belgium are now able to administer phages to patients. According to Belgium’s new “magistral" framework, the quality of each phage is certified by a Belgium-approved laboratory, and after that, physicians can prescribe these phages to patients. The phages are then prepared as active ingredients within preparations by pharmacists, and can then be given to patients.

Jean-Paul Pirnay, director of the Laboratory for Molecular and Cellular Technology at the Queen Astrid Military Hospital, later added to what we learned from Bob by telling us about the journey their team has been on as they’ve started treating more and more patients through the magistral framework. Of note, clinical trials are a priority for them too, since even though magistral phages are legal, insurance won’t reimburse patients unless trials are done.

Phage therapy as part of a clinical case series

Jon Iredell, an infectious disease physician at the Westmead Institute in Australia, told us about his team’s work with treating patients with sepsis and endocarditis with phage therapy using phages developed by Ampliphi (now Armata). Over the course of a 14-day treatment, they saw no adverse events, and saw a significant drop in bacterial load.

Compassionate use of phage therapy

Dwayne Roach, who recently started a phage lab at San Diego State University, told us about his lab’s work, with a focus on how they prepare phages for compassionate use cases as part of the Center for Innovative Phage Applications and Therapeutics (IPATH) at UCSD. He emphasized that academic labs preparing phages for human therapy comes with its challenges, but it’s the best option some patients have right now.

I got a chance to talk about how Mallory Smith’s compassionate use case got Phage Directory started, and how we now help doctors source phages for compassionate use cases (find a video of my talk here).

Regulation of compassionate therapy

We were also fortunate to have a regulatory perspective on compassionate phage therapy. Scott Stibitz of the US FDA told us about how the FDA sees phage therapy, and what they really want from phage developers. As he has emphasized before, the FDA is not the enemy of phage therapy, and they are actively working to regulate it safely and expeditiously.

A perspective from Pharma

Todd Black of Merck told us it’s a myth that pharma “will not try to make new antimicrobials”. Rather, they’ve all just been trying and failing. He emphasized that contrary to what people think, they don’t shy away from complicated solutions (he gave the Gardasil vaccine as an example), so using phages therapeutically is not out of the question for them. He pointed to gaps in the field of bacterial diagnostics that are currently making things hard (most “quick diagnostics” are insufficient, most antibiotic use is still empirical, and starting antibiotics and doing diagnostics afterward clouds the data and makes us miss what’s there).

This talk was a good reminder that there are a lot of myths going around about what pharmaceutical companies think, what they’re open to, and what their challenges are, and this seems especially true when it comes to antibiotics and phage therapy.

Back to the bench: research with phage therapy implications

The right phages for therapy

We heard several talks about cocktail design, phage formulation strategies, and using phages in animal models, especially from NIH, FDA and US Army and Navy researchers. Martha Clokie at the University of Leicester talked about the question of whether C. difficile phages need to have their integrases deleted before they can be used therapeutically, as they don’t seem to be active. Sebastien Lemire of Armata talked about how the fewer phages you have in a cocktail, the easier it is to produce them.

Understanding the cocktails that work

Betty Kutter raised the topic of better understanding how phage cocktails like Intestiphage, which have been used for nearly 100 years at the Eliava, and each contain hundreds of phages, work. Betty Kutter called for labs at undergraduate colleges to start taking on some of these experiments. She said, “Let’s stop saying ‘phage therapy is way too complex, it will never be approved here’ and start thinking about why this works so well in other places”.

Phages and the human body

It’s clear that one of the next main frontiers in phage research will be understanding how phages interact with human cells and the human immune system, and how they behave in the body (especially the gut).

Phages in the gut

Quentin Lamy-Besnier at the Institut Pasteur described the pros and cons between using conventional and axenic (germ-free) mice in phage/gut studies, and told us about a reservoir they identified in the mouse gut where phages can’t access their hosts. Siddharth Krishnamurthy (NIAID) told us about how phages contribute to mammalian intestinal immunity and influence rates of norovirus infection, and his work trying to get phage-free mice (feeding prophage-free bacteria to germ-free mice). Martha Clokie discussed how her lab has shown that C. difficile phages are more effective in the presence of human gut cells.

Phages and the immune system

The Bollyky lab at Stanford (Medeea Popescu and Paul Bollyky) talked about the immune responses, biology and even physics of filamentous P. aeruginosa phage Pf, a phage that actually helps its host cause disease in the lung by creating liquid crystals that promote biofilm formation. Dwayne Roach also told us about his lab’s research directions, which will focus on phage-host-immune interactions.

Phages in the healthcare environment

We heard from Rodney Donlan at the US Centers for Disease Control and Prevention (CDC), who described his lab’s work to develop a device to recapitulate and study healthcare-associated biofilms, and how he’s using it to study how phages impact water biofilms in hospital sinks.

Agriculture, food and water safety

Overview

We heard a lot about the opportunities and challenges when it comes to applying phages in agriculture. A great deal of work is being done to control pathogens of fish, crops, livestock, dairy, and other food. We heard about the diversity of phages available, strategies for studying how industry-relevant pathogens are infected by phages, and how to immobilize, formulate and apply them in context. The importance of testing in the field was raised, and manufacturing and distributing phages at scale was highlighted as one of the main challenges right now.

Phages in aquaculture

As one example, Jesca Nakavuma of Makerere University in Uganda discussed a fascinating international collaborative project she’s working on to minimize antibiotic use in animal production through actualizing phage application on the continent of Africa, starting with phages against tilapia pathogens. They’re planning to establish phage and host banks, to make phage cocktails, and ultimately establish their in vitro and on-farm performance. She discussed the importance of stakeholder acceptance in the process.

Engineering phages and phage proteins

Phage engineering was an interesting part of the conference. Phages and their most useful proteins are being engineered as therapeutics, microbiome-editors, vaccines, and better detectors of bacteria.

Detection

Eric Nelson of the University of Florida gave an interesting talk about how phages can prevent reliable detection of bacteria through standard methods, which is an important concept to consider, especially when tracking host numbers during phage therapy studies. Rob Edgar of the University of Pittsburgh presented another interesting angle on phage diagnostics: the use of photoacoustic flow cytometry to detect bacteria based on phage binding. Mariana Piuri of the University of Buenos Aires discussed her group’s exciting recent advances in TB detection by phages.

Useful phage proteins

Krystyna Dabrowska of the Polish Academy of Sciences told us about their safety studies with pneumococcal phage lysins, and Zuzanna Drulis-Kawa of the University of Wroclaw in Poland talked about the useful qualities of Klebsiella depolymerases and how they can be mixed and matched with different hosts to change phage specificity.

Phage classification

More phage genomes than we know what to do with

Evelien Adriaenssens told us we’re approaching 1 million phage genomes if you count the uncultivated ones; around 25,000 are in GenBank.

The importance of taxonomy

Bright and early one morning, we had a talk on taxonomy by Evelien Adriaenssens, who has recently set up her own lab at the Quadram Institute in Norwich, UK, and is also on the ICTV committee for viral taxonomy. Her talk had us all laughing, “even though it was taxonomy” (sorry, taxonomists!). She discussed phage naming (there are no rules about what you can name your phage, but there are a lot of rules for official taxon names!). She used a dog analogy to explain that a phage does not equal a species… all dogs are of the species Canis lupus but they’re not all the same.

A new viral genus announced

On behalf of the ICTV, Evelien announced that a genus has been named after Betty Kutter: Kuttervirus!

Automating taxonomy

Ho Bin Jang of the Ohio State University gave a fascinating talk on how gene sharing networks between viral genomes can automate viral taxonomy. With vContact2, you can find taxonomic relationships between your favorite virus and all those that are published!

Phages in the wild

Communities and diversity

Kema Malki of the University of South Florida showed us beautiful viromics data she collected from springs of the Floridian Aquifer: she found distinct viral communities at different springs, and not a single genome shared by all springs. Andrew Millard of the University of Leicester gave a talk on the diversity of vibriophages and their propensity to carry antibiotic resistance genes. Julie Callanan from the University College Cork showed us just how many ssDNA phages she’s found so far.

Inefficient infections

Cristina Howard-Varona from Ohio State University had many of us reflecting on why we aren’t studying more inefficient phage infections, especially since most phage infections in the wild are inefficient.

A new technique for studying active viral communities

What if you could sequence the virome of just the active viruses in your sample? Gary Trubl from Lawrence Livermore National Lab told us about a new technique for phage ecology studies called stable isotope labeling, which involves labeling phages according to what they’re doing (dormant, deceased, new growth) with heavy water and C-13 plant material, and sequencing them separately.

Molecular studies

CRISPRs, anti-CRISPRs, and other means of phage defense

What’s a phage meeting without a session jam-packed with exciting new CRISPR-related findings? Joe Bondy-Denomy from the University of San Francisco told fascinating stories about a Listeria phage that causes lysogeny-specific Cas9 degradation to protect its prophage, and a Pseudomonas phage that hides its DNA from Cas9 by creating a nucleus-like structure. Mary Clare Rollins of Montana State University told us about her work into the mechanisms of anti-CRISPRs, which can interfere with any part of the CRISPR process (eg. they can mimic DNA and clog up the complex).

Sean Meaden of Exeter University told us about CRISPR spacer diversity, and about phage receptor mutations that lead to a loss of CRISPR spacers, and Tim Blower from Durham University talked about new BREX phage defense islands they’re characterizing.

Phage DNA modification: more common than you think

Phage DNA modification was one of the themes that came up several times. Peter Weigele at New England Biolabs talked about a wide array of modifications they’re finding in the DNA of phages. Clay Crippen of the University of Georgia talked about how Campylobacter phages, long known to make DNA that is refractory to genetic analysis, make A, C, T but not G. Maria Pajunen of the University of Helsinki discussed using RNA-seq to get the genome sequence of a Yersinia phage that was unsequenceable due to DNA modification.

Hands-on phage workshops

Workshops on phage genome annotation have become a pre-Evergreen staple for the last few years, but this year, participants were lucky enough to have three workshops to choose from!

Annotating phage genomes: Galaxy

Jason Gill of the Center for Phage Technology at Texas A&M taught a workshop on how to do phage annotation using the open source platform Galaxy. Galaxy is a way of using all the tools you’d normally use, like BLAST and SPAdes, without needing to use command line or manually track what you’ve done. Anyone can use the CPT’s instance of Galaxy; you can get a free account and access it from anywhere.

Annotating phage genomes: PATRIC

PATRIC is a free online platform that provides multi-omics data analysis tools for bacterial pathogens, and now also phages. The workshop was taught by Ramy Aziz (Cairo University), Maulik Shukla and Rebecca Wattam (PATRIC). PATRIC is more hands-off than Galaxy, which we learned has its pros and cons. The instructors emphasized the importance of good quality sequence metadata, as a lot of tools in PATRIC are based on metadata (the general message was: “tell us anything you can”, and “computer scientists are waiting for this clean metadata”). Ramy told us that if you know a gene came from a phage, just putting the word “phage” in your annotation can be hugely helpful to the next person.

Viromics

Evelien Adriaenssens and Alejandro Reyes Munoz of the Universidad de los Andes taught viromics, which was a fairly technical workshop that taught participants how to use Terminal and ssh to run genomics software.

(More on these workshops and platforms in future Capsid & Tail issues!)

Phages and artificial intelligence

There were two talks on phage-based AI at the conference, which is an exciting new angle that’s recently made it into the phage conversation. Shawna McCallin of the new phage AI startup Phages4A talked about using deep learning for phage-host assignment, and Thomas Sicheritz-Ponten of the University of Copenhagen talked about how to differentiate between phage and bacterial sequences according to features like GC content, length of genes, amino acid composition.

New places to publish phage data

Phage Insights

I gave a rundown of Phage Directory’s recently launched open access publishing platform for phage data: Phage Insights.

PHAGE

Martha Clokie, Editor-In-Chief of the new journal PHAGE: Therapy, Applications, and Research by publisher Mary Ann Liebert, announced the journal’s launch.

Student poster awards

The International Committee of Food Microbiology and Hygiene (ICFMH) gave three awards for oral poster presentations in the field of food science. Congratulations to the winners!

  • Amaru Djurhuus of the University of Copenhagen (1st; Phages for potato soft rot)
  • Tracey Peters of the University of Tennessee (2nd; coevolved Listeria phages)
  • Caitlin Carmody of Cornell University (3rd; magnetic T4 for E. coli detection)

Watch the talks! (Coming soon)

The Evergreen conference talks were videotaped, and while not yet ready, here’s the link to the YouTube channel where they’ll eventually be posted.

Tweeting at the Meeting

There were some truly excellent live-tweeters at the meeting that we want to spotlight! If you live-tweet at conferences, you know how hard it is to accurately capture a research talk while it’s happening, all while using the rest of your brain to listen to the presenter. We’re thankful for those who tweet at meetings because it helps those unable to be there in person experience some of the magic of a conference.

First, Tiffany Luong, a PhD student at SDSU, did incredible tweeting (and it was her first conference! Extremely impressed!). Plus, she wrote her own recap of the meeting here.

Hedieh Attai of IPATH/UCSD and Gary Trubl of Lawrence Livermore National Lab were excellent tweeters as well! Check out the collection of phage talks Gary shared after the meeting, which include talks by Heather Hendrickson, Matt Sullivan, Alexander Belcredi, Steffanie Strathdee and Karen Weynberg. Instead of Netflix tonight, you can watch these!

Lastly, we want to highlight Kema Malki of the University of South Florida, who not only tweeted about the science, but also created beautiful accompanying drawings (like the cover image of this week’s issue!).

If you want to see all the tweeting that was done at this meeting, search the hashtag #EvergreenPhage2019 and #Evergreen2019 on Twitter!

Dancing, night walks, and day hikes: the magic of Evergreen

I’ve written mostly about the incredible science that was presented at Evergreen this year, but the true treasure of this meeting is in the sense of community I always get from attending. This is in part because of the social events planned each night, the communal meals three times a day with everyone at the conference (there’s only one place to go for food at the college, so everyone’s always easy to find all week!). From DJ’d dance parties, nights out on the town at Jake’s, night walks to search for bioluminescent organisms in the Puget Sound, to the final day spent hiking at Mt. Rainier, the Evergreen phage meeting is magical each year.

Hiking Mt. Rainier is a staple of the Evergreen phage meeting
Hiking Mt. Rainier on the last day is a staple of the Evergreen phage meeting!

Betty and her volunteers
Betty Kutter and her team of volunteers (mostly undergraduate students in her lab at Evergreen), without whom the meeting wouldn’t have run! Image credit: Anna Dragos.

Cover image credits: Kema Malki

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