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Bacteriophages: Beacon of hope amidst the sea of superbugs

Urmi Bajpai

A call to collectively explore local phages, both as a means to develop and strengthen the culture of discovery-based science, and to collectively create repositories of local phages.

Undergraduate lab course in progress: "isolation of mycobacteriophages from soil/water samples"
Undergraduate lab course in progress: "isolation of mycobacteriophages from soil/water samples"   (Photo: Urmi Bajpai)

After the discovery of the magic drugs called antibiotics in the early 1940s and for  various other reasons that were not in the best interest of pharmaceutical companies, interest in bacteriophages as therapeutic agents against bacterial infections declined globally (but for in a few east European countries and the erstwhile Soviet Union). Now, several decades later, the euphoria is subsiding and we are witnessing the emergence of antibiotic-resistant bacteria as a serious threat. This scenario has stimulated interest in finding alternative strategies for fighting infections and the forgotten phages have the potential for a comeback. They are found in big numbers (ten for one bacterium), have huge genetic diversity, are extremely specific for their host, and safe for humans but are largely unexplored, waiting to be discovered in proportion to their abundance in nature and be of service. As of now, limited work is being done in India. Concerted effort is required to bring together research groups in the country to explore and tap the potential of local phages.

My first brush with the bacteriophages from natural resources happened in summer of 2012. It was at a ‘HHMI funded Phage Hunter Workshop’, organiszed primarily for school teachers by Graham Hatfull, a professor at the University of Pittsburgh, USA, which has served as an exemplary model for introducing research at school level. Anil Challa, then a postdoctoral fellow at the University of Wisconsin and now an instructor at the University of Alabama, had urged me to attend the same. I agreed but honestly wasn’t too inclined. Phages were in no way related to my research interests then, neither had I any plans to include them in my quest for finding new anti-mycobacterial drugs (through a CSIR-OSDD funded research project, we are trying to find novel drugs that target multiple enzymes involved in the synthesis of Muramic acid in M. tuberculosis).

We were asked by the organisers to bring along soil samples and I randomly collected them from New York and New Jersey, noted GPS location of the sites and headed to my first potential meeting with the phages.

Each of the participants was trained to test their soil samples for the presence of mycobacteriophages, using M. smegmatis Mc2155 as the host. It takes about two days for plaques to appear on the culture plate and so on the day 3, we were told by the very energetic instructor, Debbie, to observe the incubated plates for the presence of plaques, if any. And, to the dismay of all the participants but for the writer of this piece, no one found a phage (out of a total of about 60 samples) while there were three types of mycobacteriophages, as evident by different morphology of the plaques, spotted on my plates. Suddenly, a quiet lab atmosphere turned into a sort of jubilation and I was being addressed as the ‘girl who got phages’. Until now, I was just going through the motions, following instructions mechanically, but seeing those plaques and the TEM images of the purified phages, it was love at first sight (yes, they had to show up on my plates, I wouldn’t fall for images in text books or journals!) 

This experience was indeed impactful and spawned into various activities around phages in my own lab. After a period of lull and a few hiccups, in the following academic semester, ‘isolation of mycobacteriophages from soil/water samples’ was included in lab experiments for B.Sc. (Hons) Biomedical Science students. Furthermore, I conducted one winter project and two summer projects for ten students each, supported by the ELITE fellowship program of the college, which provides a stipend to students who take up summer projects. Here, another faculty member from the department also joined in. In the past couple of years, we have been able to isolate a good number of lytic mycobacteriophages and interestingly some of them have been found to infect pathogenic M. tuberculosis as well, which is usually the challenging part. The discovered phages are submitted by the students to a database on mycobacteriophages, maintained by the University of Pittsburgh. Currently, a team consisting of TATA-CSIR-OSDD fellows (TCOFs) and the undergraduate students are screening a large number of samples, annotating the genome of discovered phages, followed by purification, characterisation and assay of a few proteins. We are particularly interested in Endolysins, enzymes produced by bacteriophages in order to cleave the host’s cell wall, and in regulatory proteins and sequences from these local mycobacteriophages.

Engaging undergraduates (and school students) in such research activities is another encouraging example of crowdsourcing for building data and repositories. This approach is not only cost effective but also trains a large number of students in the process. The time and energy the students spend in carrying out lab classes and on random and often  redundant short-term projects could be channelized in creating resources with downstream applications. My proposition is: how about such simple experiments be included in various schools and colleges across the country? It would not only develop and strengthen the culture of discovery-based science, but gradually and collectively create repositories of local phages. This build-up exercise can yield useful findings given huge genetic diversity found in phages and their potential in offering solutions as anti-bacterials, in diagnosis of infectious organisms, in food industry, for treatment of waste-water and many more such applications. There are various research groups in the country who are already carrying out application based work on bacteriophages against Staphylococcus bacteria, enteric bacteria, biofilms of Pseudomonas, to name a few. The well known Ganga water project is another.

So, from someone who casually collected soil samples and half-heartedly participated in the workshop, here is a convert whose eyes are forever looking for a suitable spot to collect samples where phages could be found lurking, whatever the region, the landscape may be. All my acquaintances have been pestered at least once to get samples from their travels. I hope this enthusiasm gets infectious and eventually translates into strategies for managing infectious diseases caused by the superbugs in times to come. Though it’s still a long way to go, the phage community hopes that the momentum continues to build.

Acknowledgements:
I acknowledge the support received for this work from CSIR-OSDD grant, TATA-CSIR-OSDD fellowships and ELITE fellowships for the undergraduates, granted by Acharya Narendra Dev College.

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