Waging war on killer bacteria in a Carroll biology lab

Author: Malcolm McDowell Woods

Published Date: 1/22/2020

Categories: Biology F1RST Magazine Students


Not Just Another Phage

We’re running out of options in the fight against problem bacteria. Antibiotic overuse and misuse has triggered an explosion in antibiotic-resistant bacteria. The search for the next weapon is taking place in laboratories across the world—and here at Carroll University. Pioneer Scholar Kate Gentry and biology professor Christine Schneider are examining bacteriophages, parasitic viruses that infect and eventually kill host bacteria, to see if they hold any hope. 

Phage illustration
A bacteriophage, also known informally as a phage, is a virus that infects and replicates within bacteria and archaea. 

Picture yourself in a small boat afloat on an open, angry ocean. The waves are building and beginning to wash over the bow. And your boat is springing holes. Many holes.

We live in a sea of bacteria. Really, a world of bacteria. These microscopic, single-celled organisms are everywhere on our planet, in its soil, its water, even its air. In total, the mass of bacteria on Earth outweighs that of plants and animals. And they are even inside us. The cumulative bacteria in you or I may weigh as much as three pounds—about the weight of our brains. In fact, there are far more bacterial cells in your body than human cells, engaged in an intricate, symbiotic dance.

For most living things, and for us in particular, bacteria can be either good bacteria or bad bacteria.

The good bacteria in a very real sense help keep us alive, recycling nutrients, playing a vital role in the decomposition of organic matter and in removing toxins. Our own guts are host to millions of them—maybe 500 or more different types. These gut bacteria are critical to how we digest food and the amount and type of nutrients we gain from eating. Other bacteria are used in the production of fermented foods, such as yogurt, cheese and vinegars, among others.

As for bad bacteria, well, you probably know them as germs, though the truth is that bacteria aren’t inherently good or bad, just opportunists. Google “bacteria,” though, and you’ll be flooded with stories about flesh-eating bacteria, Legionnaires' disease and other deadly infections. Pathogenic bacteria are parasites responsible for a host of problems in the plant and animal kingdoms. They can cause blight and wilt in plants, affecting food crops, and deadly diseases in livestock. And they are a frightening adversary to human life, bringing with them disease, infection and even death. At times, a lot of death.

One of the most important advances in modern medicine was the development of effective antibiotics. These antimicrobial agents attack and stymie the growth of bacteria. While some types of antibacterial agents have been successfully employed for centuries, it was only in the last century, with the development of penicillin, that doctors had an effective and reproducible tool to fight infection. The discovery led to the creation of additional antibiotic medicines and other antibacterial agents, such as disinfectants and soaps. It was a miracle. A lifeboat.

The world finally had an effective way to fight off bad bacteria. Doctors and farmers and manufacturers went all in, and who could blame them? There were so many infections and illnesses to fight. The new arsenal of antibiotics was a potent tool that could neutralize many harmful bacteria. It must have seemed as though humankind had at last turned the corner in its struggle against pestilence, plague and general uncleanliness.

Alas, overuse brought about its own problem. A devastating problem.

Because those boom times in antibiotics accelerated natural selection among bacteria, triggering the evolution of drug-resistant bacteria and unleashing a rising tide of superbugs.

Kate Gentry and Dr
Kate Gentry and Dr
Kate Gentry conducting research in a laboratory
Kate Gentry conducting research in a laboratory

A Real Life Saver

This is not the first time Kate Genty has appeared in an issue of F1RST. In the spring, 2018, semester, near the end of her first year at the university, Gentry was one of two Carroll students to donate bone marrow through the Be the Match donor campaign. 

Read more


Pseudomonas aeruginosa is one such superbug. It’s ubiquitous in the natural world, seems to do quite well in man-made environments and, thanks to our interference, is rapidly selecting for multidrug-resistant strains. In fact, it’s an opportunistic little bug that’s been implicated in hospital-acquired infections and other serious illnesses, according to the Centers for Disease Control and Prevention (CDC). It can attack and infect the lungs of cystic fibrosis patients, in particular, spreading a biofilm across the surface of the lungs that impairs critical lung function. As its resistance to antibiotics grows, so does its danger. 

In a research lab in Carroll’s Michael and Mary Jaharis Laboratories building, the war against P. aeruginosa is being fought by biology professor Christine Schneider and Kate Gentry, one of her students. 

Specifically, they are hoping to bring new weapons to the fight. Bacteriophages, often simply referred to as phages, are viruses that infect and replicate within bacteria and archaea (a separate, single-celled organism). Their entire existence depends upon a steady supply of bacteria, so they’re found wherever bacteria live. However, unlike traditional antibiotics, which generally target a wide range of bacteria, destroying both good and bad bacteria, phages play favorites. 

In this way, phages are of great interest to researchers, noted Schneider. She and her students have been investigating phages for years, first attempting to learn more about their genetic makeup and now trying to establish just what makes them effective as bacteria killers.

Phage therapy itself isn’t new. It’s been employed as a medical treatment in eastern Europe since the middle of the twentieth century, championed by a research institute in Tbilisi, Georgia. Phage therapy has several benefits over traditional antibiotics: phages can target specific infections, are usually harmless to the host organism and are self-dosing—when the host bacteria die off, the phages are unable to continue replicating.

Schneider and her students have their sights on several phages that are known to target P. aeruginosa. “We focused on Pseudomonas aeruginosa because of the clinical problems it causes,” Schneider explained. “The CDC has labeled it one of their bugs of concern.”

Previous Carroll student Eric Graham ’16, who is now a medical student at Penn State, isolated several phages from raw sewage (phages are widely prevalent in bacteria-rich environments like sewage) and had their genomes sequenced in order to identify them. They discovered four phages that fell into the same family as ones already in use in phage therapy applications.

For biology major Gentry, that’s where the fun started. Last summer, Gentry was named a Pioneer Scholar, and engaged in a research project alongside Schneider, slicing up the phages’ genes and trying to determine which ones came loaded and which ones were blanks.

“We want to pick the phage apart and find genes that look promising to us,” said Gentry.

“We know only such a small piece of the phage world,” added Schneider. “We know they kill the bacteria but not clearly how that happens. Essentially, the phage hijacks the bacteria’s life processes and we are trying to tease out which genes help it do that.”

But how?

Step one was sequencing the phage’s genetic code. In her work, Gentry has moved on to the next stage, systematically reproducing individual phage genes to see if they can kill Escherichia coli. 

E. coli is another strain of bacteria. It normally resides in the guts of warm-blooded organisms. It’s camped in your intestinal tract right now and is mostly harmless, though it can contaminate food and cause food poisoning. “E. coli is the workhorse of any microbiology lab,” noted Schneider. It’s easy to manipulate and cheap to grow in a lab.

Abstract background
Pioneer Scholars

Undergraduate Research Program

 
The goal of the Pioneer Scholars Program is to provide undergraduate students in any discipline with an opportunity to engage in an intensive scholarly/creative project one-on-one with a faculty member. 
Learn More about the program

In her research, Gentry introduces constructs featuring specific genes from the phages into E. coli cells and then essentially flips a switch to turn the phage gene on. The goal is to have the bacteria die when she turns on the switch because that would imply the gene weaseled its way into the bacteria’s vital factories and shut them down. 

So far, none of the trials have resulted in the death of either E. coli or P. aeruginosa, but there are plenty more to go. So far, the killer genes have yet to be identified. And a casual observer might conclude that the research has been a failure.

Academic research serves more than one purpose, of course. Through scientific inquiry, humanity’s knowledge base is raised and we learn more about the world we inhabit, our place in it and the organisms and elements with which we share it. And research like the work being done here at Carroll may deliver real breakthroughs in our struggle to keep abreast of that rising tide of superbugs. In fact, the research being performed right now in that first-floor lab in Jaharis might just isolate that bacteria killer that renders P. aeruginosa harmless.

Or not. But either way, the research is a success. 

“We want to understand the process,” said Gentry. “Expanding our knowledge is the key. So far, nothing has worked. Obviously, in research you aren’t always going to find the results you are seeking, but finding out what doesn’t work is important, too.” All findings add to the knowledge base. 

And then there are the students at the center of the research. They gain advanced clinical research skills, develop working relationships with faculty, gain exposure to potential careers and see their self-confidence grow immeasurably.

In October, Gentry presented her findings at the North Central Branch meeting of the American Society for Microbiology, earning a third place for her presentation. It was a great opportunity for an undergraduate student. She may have a chance to share the research findings again during her spring semester in Spain. Then she’ll return to Carroll for her senior year. And to the lab. And to the search.

“I think that’s a really unique thing about Carroll,” Gentry noted. As she’s spoken with students from other colleges, she’s come to appreciate the level of dedication to undergraduate research shown by Carroll faculty. “Getting to work one-on-one with a faculty member doing important research is such a great opportunity. It was a huge time commitment for professor Schneider. She was here in the lab all summer. And I’m not just a lab hand, we actually collaborate on this.” 

By all accounts, it’s been a successful experiment. 

 

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