Hello, I’m going to talk about Bacteriophages. More specifically, what they are, what they do, what they can do to help us and my experiences discovering my very own bacteriophage!
Let’s begin, well… what are bacteriophages? Take a look at (fig.1) the diagram to the left, they’re funny looking things, with a weird icosahedron (polygon with 20 faces) head, a long tail and some creepy legs, they look almost alien! Well the diagram doesn’t do them justice, here’s an actual picture of one (fig.2), under a very powerful microscope (an electron microscope) say ‘Hello’ to DirtMonster (real name) the phage I discovered, as you can see from the scale bar in the bottom right corner of the image, DirtMonster is very small, and from tail (bottom) to top, it is only 148 nm, which is 0.0000148 cm (1.48e-5 cm), super small huh!
So, now you have an idea on what they look like, what do they do? Well they kill bacterium, they are specialised viruses, one type of phage will kill one type of bacterium, like opposites in a way, an easy way to think about the relationship between bacteriophages and bacterium is a good vs. evil theme (though this is highly debatable if you’re a bacterium), bacteriophages are good and can only kill evil – the bacterium. Looking at (fig.3) their life cycle will show you how they reproduce! Lucky for us, Bacteriophages are simply unable to attack animal cells, plant cells, etc.
How good are bacteriophages at killing bacterium? To say they’re ‘good’ is an understatement, “It is estimated that phages kill and lyse between 15% and 40% of the ocean’s bacteria every day.” (fig.4) The deadliest thing on planet Earth, and better yet we’re not on the menu. What can bacteriophages to for us? According to the nature article (fig.5), “Phage therapy as a potential solution in the fight against AMR: obstacles and possible futures”, bacteriophages could have use not only in the medical fields as a substitute for antibiotics but “The potential applications go well beyond human health, being applicable also to biocontrol, animal health and the environment”, exciting stuff!
My experience discovering DirtMonster, has been amazing, as an undergraduate microbiologist student I could not have asked for a better first-hand experience with Bacteriophages. Throughout this semester, I have been able to learn and practice critical techniques that will aid in my future career as a microbiologist. A sense of contribution to scientific research even as an undergraduate was empowering and exciting, in addition to working with colleagues and with the lab technicians and lecturers. My time in the course allowed for a degree of independence with the support and guidance of lab technicians and lecturers. Using procedures and techniques in the Phage Hunt Lab Manual (fig.6), I was able to progress from searching for bacteriophages in the environment to viewing my bacteriophages under an electron microscope. I had a blast, and in the end, DirtMonster has found a new home.
Keen E. C. (2015). A century of phage research: bacteriophages and the shaping of modern biology. BioEssays : news and reviews in molecular, cellular and developmental biology, 37(1), 6–9. https://doi.org/10.1002/bies.201400152
The number of people in Europe who die annually from infections caused by prevalent bacteria that have developed antibiotic resistance is estimated at 25,000. According to Public Health England, key resistant bacteria like Escherichia coli (E. coli),Staphylococcus aureus, and Pseudomonas aeruginosa kill thousands of people yearly.
Antibiotic resistance is when the bacteria become resistant to antibiotics. That is where bacteriophages come in and saves the day. Bacteriophages can infect and kill bacteria, but unfortunately, bacteria can become resistant to phage too. Luckily there is a solution to both of these problems, and that solution is called synergy. This is not just any kind of synergy, but one between a virus and a medicine, and it is called phage – antibiotic synergy.
What are bacteriophages? Bacteriophages are the deadliest viruses on earth, and that’s because they are the most abundant entities on the planet. They only have bacteria as their hosts; hence they have been isolated everywhere bacteria exists. The advantage of using bacteriophages to fight infections comes from their specificity and ability to target just certain type of bacteria. This is very useful when we want to target unwanted bacteria and leave the beneficial ones alone.
So, what exactly is phage antibiotic synergy (PAS)? Synergy is defined as the interaction or cooperation of two agents to produce a combined effect greater than the sum of their separate effects.
Most simply, this is a trade-off. When bacteria become resistant to antibiotics, they need to give up phage resistance or vice-versa. This can be used to our advantage, and it is an important tool to fight antibiotic resistance. Numerous studies have shown that this kind of ‘cooperation’ has positive results, and PAS can be a great tool in fighting superbugs.
So that sounds all very well in theory, right, but are there any real-world examples of how this manifests? Let’s take a closer look.
Pharaoh and the Superbug.
The ancient mysteries of the Egyptian monarchs draw many adventurers to the land of Pharaoh each year, seeking to collect lifelong memories of awe and wonder. One US traveller collected more than just memories and a stash of photos. Tom acquired a superbug that was resistant to all known antibiotics while visiting Egypt with his wife Steffanie. While still in Egypt and well into their trip, Tom became very ill and had to be hospitalised. What was initially thought to be a “tummy bug” turned out to be a pancreatic infection with a bacteria called Acinetobacter. After being transported back to the US, Tom got into a septic shock and fell into a comma. Fighting for his life for months, in and out of the coma, Steffanie was told that Tom was going to die. So, being a scientist herself, Stephanie turned to research and looked for a way to save Tom’s life. That is when she discovered that bacteriophages can be the answer and went on a “phage hunt” to find suitable phage to treat Tom’s bacterial infection. After a cocktail of phage has been developed and approved by the Food and Drug Administration (FDA), Tom became the first person in America to be given a phage treatment intravenously. As a result, his condition improved almost immediately, and he woke up after months in a coma.
I Just Want to Breathe: Story of Page
Page is a 22-year-old who has the lung function of an elderly person. She was born with cystic fibrosis, a genetic disease that makes her very susceptible to severe lung infections. As a toddler, she was diagnosed with a bacterial infection. The bacterium attacking her lungs is called pseudomonas, or scientifically Pseudomonas aeruginosa, and it is naturally resistant to antibiotics and can cause serious disease. It is known to be associated with hospital-acquired infections, and in the lungs of people with cystic fibrosis can create a thick biofilm (or mucus), which makes it hard for these patients to breathe.
In 2014 Page’s pseudomonas became resistant to most antibiotics, and her condition became more and more difficult to treat. In 2017 she became very ill, and her lung function dropped to 44%, a dangerously low level. To make matters worse, Page also had a bad reaction to the antibiotics she was taking, and secondary infections in her gut as all her biome was cleared out. Realising they were running out of options, her father set out to do some independent research and convinced her doctor to give phage therapy a try. They got in touch with Dr Benjamin Chan from Yale University, who has an impressive collection of phage from all around the world. After analysing Page’s infection, Ben Chan was able to prepare a ‘cocktail’ of three bacteriophages in an attempt to eliminate the bacterium that was causing her infection. Even though initially her phage treatment appeared not to be working, it soon became evident that the bacteriophages were fighting the infection, and Page started to see some hope for a normal life. Even though the phage has not completely cleared the infection, they restored the antibiotic sensitivity of Pseudomonas aeruginosa. This was great news as antibiotics could be used again, and in combination with the phage therapy, Page’s lung capacity was back up to over 70%. Page gained her energy back and is able to do everyday things that otherwise she wouldn’t be able to do.
The Infected Aortic Graft.
The patient, in this case, has developed an infection around the transplanted graft following an aortic arch replacement surgery. Over the next 4 years, multiple other surgeries and antibiotics were unable to eliminate this infection. The patient in his late 70s was deemed too high of a risk for surgical replacement of his infected aortic graft and consented to alternative treatments over surgery.
The alternative for treating his infection was phage OMKO1. In previous research phage OMKO1 has shown to fight this type of infection by imposing pressure on bacteria to develop phage resistance, which in turn restored antibiotic resistance. Phage OMKO1 was administered to the infected site in combination with antibiotic ceftazidime. This combination has demonstrated synergy in previous studies (7). Despite some complications unrelated to the phage treatment, the patient fully recovered and cleared the infection. Even after the antibiotics were discontinued, the patient has not had a new infection even 18 months post-surgery. More about this case here: https://academic.oup.com/emph/article/2018/1/60/4923328 .
In conclusion, the phage antibiotic synergy can be our solution to antibiotic resistance, either by causing the bacteria to become more sensitive to phage or more sensitive to antibiotics. One great advantage of bacteriophages is their capability to evolve and find ways around the phage resistance developed by bacteria. After all, they have been involved in these feuds for billions of years!
Keen E. C. (2015). A century of phage research: bacteriophages and the shaping of modern biology. BioEssays : news and reviews in molecular, cellular and developmental biology, 37(1), 6–9. https://doi.org/10.1002/bies.201400152
Petar Knezevic, Sanja Curcin, Verica Aleksic, Milivoje Petrusic, Ljiljana Vlaski, Phage-antibiotic synergism: a possible approach to combatting Pseudomonas aeruginosa, Research in Microbiology, Volume 164, Issue 1, 2013, Pages 55-60, ISSN 0923-2508, https://doi.org/10.1016/j.resmic.2012.08.008.
Chan, B., Sistrom, M., Wertz, J. et al. Phage selection restores antibiotic sensitivity in MDR Pseudomonas aeruginosa. Sci Rep6, 26717 (2016). https://doi.org/10.1038/srep26717
Clara Torres-Barceló, Michael E. Hochberg, Evolutionary Rationale for Phages as Complements of Antibiotics, Trends in Microbiology, Volume 24, Issue 4, 2016, Pages 249-256, ISSN 0966-842X, https://doi.org/10.1016/j.tim.2015.12.011.
Benjamin K Chan, Paul E Turner, Samuel Kim, Hamid R Mojibian, John A Elefteriades, Deepak Narayan, Phage treatment of an aortic graft infected with Pseudomonas aeruginosa, Evolution, Medicine, and Public Health, Volume 2018, Issue 1, 2018, Pages 60–66, https://doi.org/10.1093/emph/eoy005
In 2016 Dr Margaret Chan the then director-general of the world health organization 2016 stated “the rise of antimicrobial resistance is a global crisis, recognised as one of the greatest health threats today… it is a slow-motion tsunami.”. One can wonder is there anything to stop this tsunami?
Penicillin was discovered and it seemed like humans finally found the superweapon they were always searching for. Little did they know, not only is it super but it has super side effects on the bacteria too. Bacteria have a protective layer surrounding their structure that eukaryotes (animal and plant cells) don’t have called peptidoglycan. This layer has the function to keep the shape and mediate the inflow and outflow of the cell. The strength of the peptidoglycan comes from its net-like structure mainly composed of peptide cross-linkages. These are formed from specific enzymes called transpeptidases. Penicillin mimics some components of transpeptidase which means it can bind to it irreversibly, causing it to be inhibited, ultimately preventing the enzyme from carrying out its cross-linking of peptidoglycan strands. Without these strands, there is no formation of peptidoglycan and the bacterial cell is susceptible to rupture and destruction of the cell due to a high intake of water into the cell otherwise called lysis ( Lobanovska & Pilla, 2017, pp. 135-14). Instead of bacteria just dying out one by one, humans were unknowingly creating a training zone where your average bacteria or fungi colony can turn into a resistant ‘superbug’ colony.
After the discovery of penicillin came the discovery of penicillinase (an enzyme with the ability to inactivate penicillin) from an E.coli strain. If that wasn’t alarming enough, only two years after this discovery came 4 Staphylococcus aureus strains that also were resistant to penicillin. It became so widespread that by the late 1960s, more than 80% of individuals who contracted S. aureus were penicillin-resistant. As this resistance continued to worsen doctors and researcher designed a new antibiotic called methicillin to tackle these effects. Methicillin was only slightly different to penicillin but proved to work… for a while. Like you would expect this was a temporary plaster to the long term effects. Specifically, what happened was a mutation occurred in the mecA gene and this gene is responsible for penicillin-binding proteins (PBP) which altered the form to PBP-2a. If the penicillin-binding proteins mutate or change then penicillin can no longer bind and be an inhibitor. Leading this form to have a reduced affinity for penicillin and methicillin giving resistance to the bacteria ( Lobanovska & Pilla, 2017, pp. 135-14). As more antibiotics were made to combat this threat, bacteria gained more resistances in contrast. If antibiotics cant win what can?!
Well, there are other alternative antibiotic therapies like metal with antimicrobial properties and African frogs. But one that is currently being used and I have a lot of confidence in is phage therapy. Phages are viruses for bacteria and due to their composition of nucleic acids and proteins they are low in toxicity. Not only that but unlike antibiotics which destroy good and bad bacteria when ingested phages are strain specific making it very unlikely that the phage will attack other useful bacteria in the body. The pros continue with their low environmental impact, versatility, single and low dose potential to name a few (Carrilo & Pilla, 2011, pp. 111-114).
The discovery and engineering of penicillin (original antibiotic) is no small feat and should be utilized in appropriate manners. It has helped save the lives of millions but with the rise of superbugs we have to look elsewhere for a new discovery. Its not a surprise that European countries see the benefits of phages and are joining in on the research with Georgia even opening a phage therapy center. We are and should continue making steps in the right direction by broadening our range of drug development.
Carrillo, L, C., & Abedon, T, S. (2011). Pros and cons phage therapy. Bacteriophage, 1(2), 111–114.
Lobanovska, M., & Pilla, G. (2017). Penicillin’s Discovery and Antibiotic Resistance: Lessons for the Future? THE JOURNAL OF BIOLOGY AND MEDICINE, 90(1), 135–14.
From the first moment I heard of the bacteria-killing viruses that hide in all aspects of the natural world, I was mesmerized. At the same time, I thought their name had a nice ring to it – ‘bacteriophages’. A tingle went through my brain, a faint recognition, and then I realized I knew exactly what I wanted to name whichever phage I found during this course. With this realization, I became prepared to throw myself at this course in a frenzy, determined to discover a phage worthy of receiving the perfect name.
Unfortunately, the first stage of phage discovery was also the stage in which I struggled the most. Simply finding a phage to begin with was proving to be more difficult a task than I had first envisioned, and after two failed rounds of isolating environmental samples I was feeling frustrated and defeated. Would I ever find a phage with which to bestow my blessing?
My savior came in the form of Heather Hendrickson, our lecturer and guide, who had graciously announced that the three enriched samples she had run earlier were available to be adopted. I quickly pounced on the offer and adopted the phage that had been isolated from soil surrounding a squash plant in the Massey University vegetable gardens. Time was of the essence. I needed to isolate, purify, amplify, extract DNA from, and characterize this phage quickly, lest another student steal this name out from under me.
Having conquered this first hurdle I marched on, confident that no further misfortunes would befall me in my quest for the perfect phage name.
The next step was to ensure that I was working with one specific phage, and so several rounds of serial dilutions, infections and platings were required. It was in the second round of purification that I encountered yet another barrier – my phage seemed to have disappeared. No more plaques appeared in any of my platings from this round, and I became fearful that a mistake on my part would be the nail in the perfect names’ coffin. Fortunately for me, however, several others were also experiencing this issue, and it was quickly resolved by adding Calcium Chloride to our bacteria cultures before infection. I breathed a silent sigh of relief when in the next round, there were plaques galore in all my platings. Determined as ever, and with another issue resolved and behind me, I continued.
The next stages passed without incident. I created webbed plates and successfully harvested a high titer lysate from them, to the tune of 8×10^10 pfu/ml. I also created more lysate for DNA extraction later on, at a slightly lower concentration.
This first lysate was brought to the University of Auckland for imaging by their electron microscope, at which point I discovered something wonderful.
My phage was unique.
Well, relatively unique anyway. Another student also had a similar phage, but other than us two, no potential cluster C phage had been discovered at Massey University in the history of the SEA-PHAGES programme. The cluster that a phage originates from cannot be accurately determined until its genome is sequenced, but judging from physical appearance, my phage appeared to be much more similar to those of cluster C than the others. This was wonderful news, as I now knew my phage was indeed worthy to accept my gift, and would carry its name proudly.
The next step was to run a restriction enzyme digest to characterize its genetic makeup, and then finally to archive it, at which point it would be sent to the University of Pittsburgh for storage. Unfortunately, I seemed to have accidentally managed to cut my uncut DNA in the restriction enzyme digest step. Oops. However, the show must go on and so I continued despite this blunder.
Lastly came archival of my phage, and for archival to be completed one other task must be finished first. The pinnacle of the project, the step that had been on my mind since the beginning.
Finally, the time had come.
I needed to name my phage.
I wanted to name the fruits of my labor after something greater than us all, to give it a name that reflects the countless hours of work I had put into the project. There was only one real choice, and that was to name it after my idol, a god among men, a divine being that graces us all simply by traversing the mortal plane.
However, upon reading rule #1 on the PhagesDB website my 12 week long quest came to a shocking conclusion. There, written at the top of the page, in bold font, were a set of words that brought me to my knees:
“Do not name your phage after Nicolas Cage.“
It was over. All the work I had put into this phage would be for naught. My phage would be unable to carry with it the blessing of sharing a name with the one true god. It would remain a simple phage, untouched by His infinite wisdom, doomed to exist without ever knowing the gentle warmth of Nicolas Cage.
Shattered, defeated, crushed, and with my hopes and dreams of birthing ‘Nicolas Phage’ into this world dashed against the rocks of despair, I turned my gaze elsewhere. Here, truly at rock bottom, I decided to persevere in the face of adversity, and discover a name as unique and rare as the phage it would be attributed to, just as our savior would have wished. For is it not in our darkest moments that we can truly see the light?
After long, grueling minutes of deliberation, sweat upon my brow and thoroughly proud of myself, I decided upon ‘Sasquash’ instead as it was a funny sounding pun on squash.
And thus, it was over. How far would ‘Sasquash’ go in this world? Would my phage of humble beginnings be the next life saving treatment to be administered to the ailing? For now, that remains unknown, but it is with hope and Nicolas Cage in my heart that I close the book on this chapter of phage hunting, and look to the horizon with vigor anew knowing that at the very least, I had brought one more phage into this world.
When you hear the words “Scientific Discovery” or “Medical Break Through” what do you think of. Is it a group of middle aged scientists wearing white lab coats in a sterile lab, staring fixedly into a test tube or a bunch of second year university students analysing dirt?
Okay so that might have been a bit of an over simplification, us Uni students also wear white lab coats and spend time in a sterile lab but we are analyzing dirt. “Well what kind of Medical Break Through can you find in dirt?” I hear you ask dear reader, all in good time.
It’s not the dirt itself we’re particularly interested in, it’s the microorganisms living inside it, specifically Bacteriophages. Bacteriophages are a group of viruses that infect, reproduce inside and kill bacterial cells. They are an incredibly ancient group of organisms potentially as old as bacteria. They were first discovered in 1915 by biologist Fredrick Twort who realized their potential to cure bacterial illness but further research was dropped when the first anti-biotics were discovered. They have since become of interest to scientists again now new strains of anti-biotic resistant bacteria have evolved.
I chose to do this course because it seemed like from what I could tell it was give me the hands on scientific experience I really wanted and chance to make novel discoveries about microscopic organisms no one else had ever seen before. The chance to feel like a real scientist
My phage hunt had very humble begging’s. My lab instructor, Dr Heather Hendrickson, had instructed the class to collect environmental samples from which we would attempt to find a phage. I was keen and eager to find a phage of my own so I started by collecting various samples, from stream water to moss. I collected samples from my university and neighborhood. It’s rather ironic that the one sample that showed evidence of phage was from my mother’s vegetable garden right in my backyard. Showing that the unknown can be found right outside your backdoor. This sample was called “D.C 1.4” the fourth of nine samples I collected.
Unfortunately for me and my class my home city of Auckland went into a Level three lockdown due to COVID-19, which basically meant we couldn’t go to our lab. The next couple stages of my phage hunt were done by Dr Hendrickson and our lab technician, Jarod so when I came back to the lab a week later I had a sample of phage I had to purify.
Purifying a Phage
The term purifying a phage may seem weird to you. How can you purify a virus? Well what “purifying a phage” means is that we try to get a sample with only one type of phage in it. To do this I did a process known as a serial dilution and plaque assay. This process involved me diluting my phage concentration to different concentrations and plating those concentrations. The aim being that as I diluted more and more I would have less phages in the sample and increase the likelihood that I only have one type of phage. I really struggled with this because my phage didn’t seem to be forming plaques. It was dishearting and made me question if I’d even be able to use this phage. I wasn’t the only person to have this problem however lots of people struggled to see plaques when purifying their phage. A hypothesis was formed by our lab instructor and technician that the problem was a low level a Calcium ions. Henceforth we added Calcium Chloride to our samples and I started to see more plaques forming. My phage hunt was saved!
Amping up the phage hunt
“Great, but what now?” the question I thought to myself. Well this is where I start the process of Amplification. Amplification in this context basically means to create a very concentrated solution of my phage called a ‘lysate’. Which I could then use in DNA analysis. To do this plate a concentration of phages that results in most of the plate being covered in plaques, this kind of plate is known as a webbed plate. This section became confusing for me. The concentration of my phage never seemed to be very inconsistent. Without any sort of reliable pattern I couldn’t predict what concentration I should plate in order to get a webbed plate. I persevered however and eventually achieved the required concentration of phage samples to move on.
The Electron Microscope
In order to visualize our phages we needed to use a Electron Microscope. “Cool but what makes it different from a regular microscope and why not just use a regular microscope?”. Well Phages are so small they are smaller that the lowest wave length of visible light. To help illustrate this I’ve included a screen shot from the website https://htwins.net/scale2/ created by Cary Huang.
Due to the phages incredibly small size we needed to use a microscope that didn’t use light to create it’s images but instead use electrons. This was hard to get my head around at first but seeing the electron microscope in person was very interesting but it doesn’t compare to being able to see and image of my phage. The experience was a kin to meeting a pen pal. Up to that point my phage had been purely abstract. Some incredibly small microorganism whose only evidence I had for it’s existence was the dead bacteria it left on my bacterial plates. But now I could see it visualize it put a “face” (or a phace) to my phage, weeks of work displayed clearly on a computer screen. Magical!
I had done it. I had discovered a phage. Which I affectionately named BellPepper due to the fact there is now a bell pepper plant growing in the garden where I collected by enviromental sample. This was such an amazing journey and I’ll value this experience for many years to come. I’ve realized that being a scientist isn’t just about making new and amazing discoveries but about making mistakes and adapting. In the end I did become a real scientist.
My recommendation for anyone given the option to do this course or something similar DO IT. I can not say enough how fun and interesting it was to be a part of this course.
References: Keen, Eric C. “A Century of Phage Research: Bacteriophages and the Shaping of Modern Biology.” BioEssays : News and Reviews in Molecular, Cellular and Developmental Biology, U.S. National Library of Medicine, Jan. 2015, http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4418462/.
Hello, my name is Samantha, and welcome to this blog. This blog is going to be about my journey in what we scientists (well aiming to become a scientist so I’m still in training) a Phage hunt.
Firstly let me introduce you to what a Phage actually is. These tiny little dudes are Bacteriophages. They range in size from 24 nm to 200nm, and that is what I set out to find (spoiler I did).
These bacteriophages were discovered in “1915, Bacteriophageswere first discovered in 1915 by William Twort, and in 1917 by Felix d’Herelle realized that they had the potential to kill bacteria”(Britanica,1998) These bacteriophages have been used ever since in a plethora of many different areas such as Phage therapy, or they can be added into an antibiotic and can be used to treat a bacterial infection.
The reason I went into this phage hunt or university paper is because I want to go into laboratory work on becoming a lab technician and I wanted to see if I actually liked doing that kind of work and I also wanted to experience life in a lab as with covid last year I missed out so I was determined to make that happen this year. But it is also a required paper for my degree so it worked out well in the end.
I started my phage hunt in my Grandfather’s worm bin and I was successful in my first round of environmental sample collecting. After I collected my sample I had to go on making it a liquid sample so that I could dilute and plate. But that was only the beginning of this journey.
I have found that I do not like serial dilutions, now a serial dilution is where you have as an example up to 10 microcentrifuge tubes of 90 ul of phage buffer – this is a mixture that the phage’s like to grow in – and then you put a full 10ul concentration of your sample into the first tube, then you go from one to the next
That is what I performed but up to 10. But what I didn’t realise is that I definitely bit off more than I could chew and wanted to plate not just once but twice. This meant that I had to perform serial dilution twice and plate 16 plates. And I had never done this before, and I ended up not actually diluting anything and just kept putting 10ul of my original sample into the new microcentrifuge tube and it didn’t work much to my disappointment. So, I had to do it all again, but I did it the correct way the second time and through that mistake, I have never done a serial dilution wrong again and I have a system that I do not deviate from.
To show you how I know I definitely failed at the dilutions.
This is a failed plate from my first round of dilutions.
But this is my plate from my next round of successful dilutions that I then picked my plaque from.
From here I purified the plague that I picked and have now named Gaga. Now you might be thinking oh Lady Gaga but you couldn’t be more wrong. Since I collected my sample from my Grandfather’s worm bin and nearly losing him last year I decided to name it after him and that was my nickname from him when I was young.
Anyway back to the sciency stuff, I had to go through 3 rounds of purification as even though I was using aseptic technic and being super carefully it seemed that I was still getting contamination on my plates, but after further inspection, we think it might have been a calcium chloride issue and once we started adding that my contamination left and I could/did continue in the process of getting my phage.
After that issue was fixed I was able to make webbed plates and collect my lysate, and from that lysate, I was able to do a full spot titer and was able to calculate my full plate titer. I repeated that process twice so that I could make sure that my lysate was at a high enough titer for DNA extraction and to be able to see my Phage in the Electron Microscope at Auckland University. I was able to calculate my titer and my highest was 4.33×10^10 pfu/ml.
Throughout this hunt, my phage morphology has stayed relatively the same (minus what they looked like before we had added the calcium chloride) they have stayed around the small/medium size and would always make gorgeous looking webbed plates.
Here are some examples:
One if not the most exciting parts of doing this paper was being able to go to Auckland University and experience an Electron microscope being used and being able to see my phage for the first time !!. I was very excited and I loved the whole experience.
So everyone meet Gaga !!
To end this blog, during this journey of being in a phage hunt, I was able to actually attend and learn in a lab because last year we went into lockdown due to covid and my labs were all cancelled. I can say that I am a lot more confident in the lab and can’t wait to become a lab technician. I was also able to attend the Phage SEA symposium mind you it was at 5 am but it was still an amazing experience and I would love to go to it again. This paper has been very eye-opening for me and I think it would be a great idea for anyone in the future that is looking for a career in science to do this or something similar as I have learned a lot and have enjoyed every bit (besides the dilutions but we don’t need to bring that up again).
Out with the old and in with the new. Antibiotics are no longer protecting us from certain bacterial diseases, but can engineered bacteriophages help instead?
The discovery of antibiotics changed modern medicine for all time. Just think about how amazing it is that the small molecules inside antibiotics can fight bacterial infections, by killing or inhibiting the growth of bacteria. However, over the years, researchers have noticed bacteria have become more resistant to antibiotics. That the bacteria in our bodies are evolving to the point where they are mutating and stopping antibiotics from working properly.
Isabelle Carnell-Holdaway was born with cystic fibrosis, a genetic disorder that develops sticky mucus inside of organs in the body. Due to this disorder, she is prone to harbour infectious diseases, as a result of respiratory and digestive problems. At 16 years old, Isabelle required a double lung transplant to remove the bacteria infecting her body, Mycobacterium abscessus. After the surgery, Isabelle had to take immunosuppressant drugs to prevent her body from rejecting the transplant lungs. Then the worst happened, the infection came back!
The re-growth of Mycobacterium abscessus caused the infection to form large black lesions on her skin and bacterial colonies in her liver, which prompted liver failure. Her doctors said that she had less than a 1% chance of surviving.
Enter bacteriophages! Now I know what everyone is thinking, a bacteria … what?
A bacteriophage, otherwise known as phages, are naturally occurring viruses that infect bacteria. Phages are an alternative option to antibiotics as they can efficiently kill bacteria without infecting or harming human cells.
These viruses attach to the bacterial host cell by recognising the cell receptor. The bacteriophage then injects their DNA inside the bacteria, taking over the cells replication mechanism and producing more phages. This process is known as the lytic cycle. During the lytic cycle, the bacterial cell will disintegrate, and newly reproduced bacteriophages will leave the host cell to infect other bacterial cells.
During bacterial infection, the bacteriophage can also undergo the lysogenic cycle. This pathway involves the bacteriophage DNA integrating into the bacterial host cells chromosome and becoming a prophage. Then after the bacteria host cell lyses, the prophage DNA replicates. Meaning even more phages!!
Bacteriophages used in treatments such as phage therapy usually undergo the lytic cycle, as they do not have integrated bacterial chromosomes.
Phage therapy refers to the use of bacteriophages to treat bacterial infections. Although not a well-known treatment nowadays, phages have become a beacon of interest in the past few years. Such as engineering bacteriophages to target and kill bacteria for overcoming antibiotic-resistant bacteria.
Bacteriophages alone cannot single-handedly kill all strains of a bacterial disease, as bacteria are becoming resistant to phages very quickly. The bacteria are evolving their structural features, such as the cell receptor, to prevent the attachment of the bacteriophage. Is that clever or what! However, to cure antibiotic-resistant bacterial infections, bacteriophages are being engineered to target and infect a wide spread of bacterial strains.
Everyone has heard of CRISPR, regardless of knowing anything about biology. But what is it? CRISPR is a bacterial immune system that stands for Clustered Regularly Interspaced Short Palindromic Repeats and assists in storing bacterial genetic information from viral infections. Bacteriophages at first are affected by this immune system but eventually evolve to develop anti-CRISPR proteins, which compensate the bacterial host cells CRISPR system.
Isabelle’s mother, Jo, was the one who came up with the idea to try phage therapy as an alternative option to antibiotics. Leading to contact with Professor Graham Hatfull at the Howard Hughes Medical Institute (HHMI) in the United States. Did you know that HHMI has the worlds most comprehensive collection of phages? And to think that my bacteriophage, Petit, will someday soon be a part of this collection as well is just mind-blowing! With around 15,000 vials of phage to work with, Prof. Hatfull had his hands full searching for the perfect combination of phage that could help Isabelle’s infection. Then success!! Three of the approximate 15,000 bacteriophages contributed towards making a phage cocktail, where two of the three phages required genetic engineering to be more effective.
A phage cocktail is when multiple bacteriophage types combined into a mixture can formulate a phage that possesses a target bacterial host cell. In this case, the three phages in the phage cocktail will be injected into Isabelle’s bloodstream twice a day and applied to the lesions on her skin, to kill Mycobacterium abscessus.
So what happened to Isabelle? Did the phage cocktail treatment work? Yes, it did!
According to James Gallagher (2019), Jo told BBC News that “when we left hospital, she looked like a skeleton with skin on, she was so poorly. It was incredible the effect the phage had on her. She’s got back her own life, the life of a 17-year-old girl.”
Isabelle’s bacterial infection is under control but not fully healed. From the two daily infusions of the phage cocktail, her lesions, wounds and liver problems have started to heal. Further research is underway to discover the fourth bacteriophage to the phage cocktail, which will hopefully help cure Isabelle completely.
Chan, Benjamin K, et al. (2013). “Phage Cocktails and the Future of Phage Therapy.” Future Microbiology, 8(6), 769–783.
It all started when I enrolled in a compulsory paper for my degree, Bacteriophage Discovery and Genomics. I was excited! The course sounded interesting and fun but besides that, I did not know what I was getting myself into. Little did I know I would become a mother to a phage. Now I do not have much experience as a mother, but my maternal instincts kicked in as soon as I met my phage. It was the cutest phage of them all in my eyes. Let me take you on my journey of phage hunt so far.
As a parent, I had to do some research first as to what bacteriophages were and what bacteriophages could do. I wanted to know all the potential that a phage held. Bacteriophages destroy bacteria, they are a virus that can kill bacteria (Squires, 2018). How can they be used? Phage therapy. This is where a bacteriophage is used to attack a bacterial infection. As antibiotic-resistant bacteria increase, it is important to find different ways to combat bacteria. Phage therapy can be used for humans and animals. There have been developments in phage treatments of P. aeruginosa (bacterial infection) for dogs, where a commercial veterinary product was made available in Europe for use due to a few successful studies performed on dogs with P. aeruginosa-associated otitis externa (Squires, 2018). How awesome is that? Phage therapy is by no means new, (it was first used 102 years ago!) but between 1960-2000 a few centres in Poland and Georgia used it and the Soviet Union was the only country that manufactured bacteriophage products industrially (Vlassov et al, 2020).
This video is another example of how awesome and the potential of phage therapy can be where it saved this man’s life!
After research, it was now time to find a phage, can’t be hard right? Spoiler alert, I was wrong. In my first round of collection and isolation I collected from dirt, soil, a stream where ducks live, algae filled stream and dirty vase water. This was all interrupted by a change in alert levels that put us into lockdown. I waited impatiently to see if I had found any phages for a week until the alert levels went down, and I came back to no plaques so no phages. Disappointed? Yes. Frustrated? Yes. More motivated? Yes. The second round of collection and isolation I was now wiser and this time I was determined to find a phage. Compost bins seemed to work for previous students, so I went to my sister’s and collected two samples from the compost bin, one from the top and one from the bottom. Drum roll, please….. I FOUND PHAGES from both samples!!
Choosing which plaque to pick was a struggle as you can see from my multiple circles, it was like choosing what to watch on Netflix. Eventually, KL 14.1 and KL 15.1 became the chosen ones, because of their size, shape, and location. I picked these plaques with wobbly hands (pro tip: eat enough before a lab) and serial diluted them for my first round of purification.
Serial dilutions at first were slightly tricky, making sure the volume on the pipette was correct, and aseptic technique was being followed felt very foreign due to all my labs being online last year. However, by my third round of purification thankfully I was much more confident. After the first round of purification and the second round of purification had been done, the plates from the second round came back with…nothing. NOTHING! Deep breaths, my child disappeared. This felt weird as I plated a directly picked plaque so why were there no plaques? A few classmates had this issue as well, so it was determined that the issue could have been the calcium chloride. I did the purification process again where I was successful and my child appeared, and once more of purification.
I collected lysates from webbed plates and performed a spot titer and full plate titer. Collecting lysates and full plate titers were repeated three more times to ensure that I had enough to extract DNA from my phage, my highest titer was 3.2 x 10^10 pfu/ml. Below are a few images of my process of spot titer, full plate titers and making webbed plates. Look at how big my morphologies are!
One of the most exciting parts about this whole phage journey was being able to see my phage at the University of Auckland under the Electron Microscope. I felt relief when I saw my phage for the first time and of course love. After weeks of working with liquids, it was amazing to be able to see what that liquid looked like. I imagine this is how it feels to see your child for the first time. It measured in at 137.42 nm on average for tail length and 63.57 nm on average for capsid diameter. Isn’t my phage adorable?!
At this point, I felt like KL14.1 deserved a better name and seeing them made me feel even more connected. Hulk, the big green angry avenger felt fitting to my phage but sadly it was taken, Bruce or Banner, the human behind the big green angry avenger also taken. Time to call a friend, here are a few suggestions I got: Darth Phageus The Wise, Doctor Phage, Agent P, Phagent P, Grogu and I came up with an additional name Darth Phader (sadly it was taken). From there it was time to channel my phage’s energy and see what name fit them the most. Everyone meet Grogu (aka Baby Yoda), it felt fitting as my phage is adorable and strong. Grogu is going to defeat all Mycobacterium smegmatis that exists, I have high expectations for my children.
During this phage journey, I was able to attend the SEAPHAGES symposium, this was an amazing experience. It made this journey feel like it was a part of a wider project, where I could see what other students had done with their phage as well as attend talks given by the SEA researchers. It was my first time attending a science conference and it was great to be surrounded by people who were so passionate about their project.
Although I am not at the end of my phage hunt journey just yet (almost!), it has been both challenging and rewarding. It has made me appreciate the time and effort that goes into research and allowed me the opportunity to gain confidence in the lab. Most importantly the love you can feel for such a small thing and the amount of care needed with bacteriophages. It will be a bittersweet moment when I have to send my child off to college (college being Pittsburgh, USA). To finish off I present you with a tweet that represented how I felt with caring for my child, Grogu.
Imagine suffering a slow death at the hands of… a gruesome blob of slime. You may not believe it now, but it’s highly likely a conglomerate of bacteria is residing unapologetically inside the lovely and warm home it likes to call… YOU.
So what are these mysterious sci-fi like creatures? They are simply called biofilms. The most un-monstrous name ever. Well that’s probably because they aren’t all bad. Some of them hang around to help you out, like the healthy bacteria in your gut for example.
But I’m here to warn you of the pathogenic kind that wad together to attack!
They say strength is best in numbers and that is exactly how these bitty blobs love to manifest. Whilst trying to make your life miserable, they enjoy dabbling in the art of rallying themselves together in order to take on your one and only innate defence; your immune system.
To put it more scientifically, biofilms are populations of bacteria that cohere and attach onto a solid surface often surrounded by a gel like coat. This coat provides the essentials such as nutrition, protection, transportation, and enzyme activity facilitation (Flemming et al 2007).
Ever heard of dental plaque? Ah yes, the pesky culprit to bad breath. Well yes, that’s a biofilm. Better keep those pearly whites clean or it will be you versus gum disease!
So how do biofilms find their way into the comfort of your body in the first place?
Contaminated equipment found in places such as hospitals or the commercial food industry can house the founding populations of pathogenic bacteria. If they manage to creep their way into your body through the likes of ingestion, medical implantations and of course in simpler ways like when we forget to wash our grubby hands, they will aggregate and ta da! A biofilm is formed. (Szafránski et al 2017).
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As with any shadowy gang looming in a dark alleyway, biofilms can be one of the most feared sources of contamination as they put up a tough front and will probably win in a fight! In other words, they can be extremely difficult to eradicate and can result in serious infection.
Now, you may be pondering the simple answer to combatting these bacterial baddies; antibiotics, right? Well, not really. Due to the slow growing nature of biofilm bacterial cells, there is a reduction in antibiotic penetration.
Antibiotics work best during cell division as crucial pathways are interrupted. Therefore, as these cells do not divide as often, the effect of antibiotics can be reduced and can often lead to antibiotic resistance, and that’s a big problem! (Szafránski et al 2017).
What if I were to tell you of a more “au naturel” approach to abolishing these nasty biofilms? Don’t worry, I’m not going to tell you to buy some crystals, sit under the moon and manifest the total obliteration of biofilms from the universe. The answer lies in microbiology, and the cure could even be found in your own backyard.
Bacteriophages, often simply known as phages, can be found in bacterially rich hot spots such as your very own garden.
These tiny viruses are considered non-living as without the help of their bacterial hosts they would be simply well… non-existent.
After injecting their DNA into bacterial host cells, they are then able to hijack the cells programming in order to replicate hundreds of copies of themselves. Eventually, there is only one way to break free… that is to burst open the bacterial cell with no remorse killing it in the process. These phage babies then move on to rapidly infect neighbouring cells and given enough time, you can say bye- bye biofilms!
Another great thing about phage therapy as opposed to antibiotics, is that phages choose their victims very discriminately which means that when used for therapy in the human body, our “healthy” bacteria is not disrupted. (Szafránski et al 2017).
However, this can be seen as a downfall to phage therapy as there is no “one hit wonder” solution to the eradication of all biofilms.
Different phages are needed to target an array of bacterial infections. However, new studies are experimenting with “mixing” different phages together in order to broaden host range (Chan et al, 2015). A cocktail of phages? That sounds great in a world of microbiology, but I think I’d rather stick to strawberry margaritas.
Watch: A video on how bacteriophages are being extensively used in the Soviet Union.
As if these mighty viral machines aren’t terrifying enough, they can be genetically engineered to partake in more murderous mischief by secreting special enzymes such as “dispersin B” that target to efficiently penetrate the protective coat and weaken the biofilm’s structural integrity (Lu and Collins, 2007).
We are truly living in an exciting time. The treatment of biofilm infections through the use of phage is starting to come into light.
With an exponentially growing global population, the risk of antibiotic resistance runs a little too close for comfort. With a little more research and a lot more trust from people like you and I, we could see a breakthrough in treatments and more lives spared. Is this a good thing? Or are us humans getting too smart for our own good?
Either way, these mighty viruses are things we should never fear! They could just be the superhero that we have long been looking for. What’s more? They might just be hanging out in your garden that you finally got around to planting in lockdown.
The hunt begins!
Szafránski, S.P., Winkle, A., & Stiesch, M. (2017). The use of bacteriophages to biocontrol oral biofilms. Journal of Biotechnology, 250, 29-44. (this journal does not use issue numbers).
Flemming H.C., Neu, T.R., & Wozniak, D.J. (2007). The EPS matrix: The house of biofilm cells. Journal of Bacteriology, 22(189) 7945-7947.
Chan, B.K., Abedon, S.T., & Loc-Carrillo, C. (2013). Phage cocktails and the future of phage therapy. Future Microbiology, 8(6). (Page numbers not specified) .
Lu, T.K., & Collins, J.J. (2007). Dispersing biofilms with engineered enzymatic bacteriophage. Proceedings of the National Academy of Sciences, 104(27), 11197-11202.
All thanks to Covid-19, the virus community has been discriminated against since the start of 2020, but just like people, there are good ones out there, so let me explain…
A bacteriophage or phage for short (bacterio – related to bacteria and phage – eater), is a virus that targets bacteria cells and utilises their tools to replicate their own DNA, resulting in more phage’s (Srisuknimit, 2018). Bacteriophages aren’t considered living organisms and without bacteria, they would simply go extinct.
Bacteriophages either have a lytic or lysogenic cycle they use to infect bacteria hosts. Lytic phage’s use bacteria tools within the cytoplasm (cell body) to replicate their DNA, and after successful production of more phage’s, they cause the host cell to explode which set phage’s free into the environment. Lysogenic bacteriophages are more cunning; when they insert their DNA into the host, it will be incorporated into the hosts genome creating a prophage, therefore when the bacteria procreate they take with them the virus DNA (Urry et al., 2017), which in turn produces a larger quantity of phage’s.
The pictures below illustrate these two processes.
If you are still confused as to what bacteriophages even are, here is a great animated video that illustrates them further.
Now… how would you feel if your doctor prescribed you a bacteriophage virus to treat an infection? I know it sounds a bit daunting considering the times but it also could be the future for certain medical treatments. The lytic mechanism was put to good use firstly by d’Herelle, a French microbiologist, who successfully used a phage to treat a bacterial infection in the stomach (dysentery) in 1919 (Sulakvelidze et al., 2001). At this time, there was little information on what they were or how they even worked. With the knowledge we have today, phage therapy is slowly being used to treat a range of illnesses, along with potentially combatting the antibiotic resistance issue we face.
The development of antibiotics was revolutionary in treating bacterial infections, but with the unstoppable process of mutations, bacteria have become resistant, forcing us to discover and use alternative treatments. If you aren’t sure exactly what antibiotics are, it is a manufactured chemical that is kills non-specific bacteria when ingested (Srisuknimit, 2018). The downside to antibiotics being non-specific is that they not only kill bacteria that are responsible for causing infection, but also those that aid in helping our cells with various metabolic processes (Loc-Carrillo and Abedon, 2011). On the other hand, bacteriophages are specific with their hosts, killing only targeted bacteria.
Replacing antibiotics with phage’s is one thing, but these little non-living bacteria eating, alien like “things” can do so much more. Starting with a very relevant topic; scientists have found they could be a vehicle for administering a vaccine, along with detecting low numbers pathogenic bacteria (Clark and March, 2006), which determines whether the infection will resist certain antibiotics or not. Phages aren’t only proving their superiority to us, but due to the fact phages are a creation of nature and not manufactured in a lab like antibiotics, the environment should be on-board of the switch too (Loc-Carrillo and Abedon, 2011).
Like I mentioned earlier, phage therapy was performed a long time ago, in fact even before antibiotics were created; but the reason why it hasn’t become a common practice is due to a variety of reasons. The fact that bacteriophages are complex components of nature, sourcing and purifying a particular phage is difficult (Srisuknimit, 2018). Considering there are approximately 1031 phage particles in the world (Hatfull, 2015), it can be a process in itself finding one, (as we are all aware of, taking Bacteriophage Discovery at Massey University). Determining what bacteria is causing the infection in the first place and then localising a phage that is specific to that bacteria is a lengthy and complicated process (Srisuknimit, 2018).
Features of bacteriophages have sparked scientists interest for many years in the medical field, by curing bacterial infections but with new technology and increased knowledge, the use of phages will be more than just a replacement for antibiotics. Is it too much to expect from society to accept this new concept of using a virus to help treat illnesses? Especially after suffering tremendously for the last year and half, or is this bacteriophages real time to shine and prove that good viruses do exist!
Would you be willing to voluntarily ingest a virus in hope to treat an illness?
Clark, J. R., & March, J. B. (2006). Bacteriophages and biotechnology: vaccines, gene therapy and antibacterials. Trends in biotechnology, 24(5), 212-218.
Hatfull, G. F. (2015). Dark matter of the biosphere: the amazing world of bacteriophage diversity. Journal of virology, 89(16), 8107-8110.
Sulakvelidze, A., Alavidze, Z., & Morris, J. G. (2001). Bacteriophage therapy. Antimicrobial agents and chemotherapy, 45(3), 649-659.
Urry, L. A., Meyers, N., Cain, M., Wasserman, S., Minorksy, P., & Reece, J. (2017). Campbell biology : Australian and New Zealand edition ebook. ProQuest Ebook Central https://ebookcentral.proquest.com