Germ Warfare

For millennia, infectious diseases have wreaked havoc among humans. We thought antibiotics were the ­answer. Now there is a new generation of superbugs posing a serious threat to public health by creating bacterial infections resistant to modern medicine. Despite our best efforts, they continue to mutate and outsmart our designer antibiotics. The York University Magazine spoke to two York ­professors who offered insight into their research on the war against superbugs and the power of bacterial nanomachines.

Microorganisms live on and within us and we normally benefit from this relationship; however, these bugs can turn on us and with deadly consequences. Biology Professor Dasantila Golemi-Kotra explains how humans inadvertently contributed to the evolution of superbugs and how we might be able to make them revert back to benign organisms.

THE MAGAZINE: Tell me about your research.

GOLEMI-KOTRA: My work is focused on antibiotic resistance and trying to understand how bacteria evolved to become resistant.

THE MAGAZINE: Bacterial resistance to antibiotics is relatively recent, isn’t it?

GOLEMI-KOTRA: Something we have realized is the way we – scientists – looked at antibiotic resistance was as a mechanism: bacteria evolved as a result of selection pressure exerted by the use of antibiotics in hospitals and so on. We came to understand later that bacteria (or microorganisms) have always been fighting against each other for survival and dominance of resources. But as a result of humans overusing antibiotics, this evolution has now been much faster than would otherwise be the case. It’s speeded up the evolutionary resistance process.

THE MAGAZINE: Even if we took away all the antibiotics tomorrow, would bacteria continue to evolve?

GOLEMI-KOTRA: Yes, and the reason is the number of bacteria. The numbers are huge and they populate pretty much every environment on Earth. So evolution would continue, but not at the rate it is at present due to human influence. In a natural setting, their evolution would be much, much slower.

Bacteria don’t just give up and die. They’re not passive.  They put up a fight and try to control the effect of the antibiotic

THE MAGAZINE: So bacterial evolution is tied into a need to dominate?

GOLEMI-KOTRA: Yes, they evolve in order to control the growth of other microorganisms. They either suppress for control or pretty much kill the other microorganisms. What research has shown us is that in any antibiotic we humans design – no matter how wonderful – resistance to that antibiotic will evolve. It’s not a matter of if; it’s only a matter of when. The rate at which resistance will emerge actually depends on how often we use an antibiotic. Hence, discovery of new antibiotics is not a long-term solution. It’s a necessary approach. We wouldn’t want to stop discovering effective antibiotics, but it’s not the way that will lead us to a permanent solution.

THE MAGAZINE: Is that what you are interested in – a more permanent solution, and perhaps using the same tactics bacteria use themselves?

GOLEMI-KOTRA: We realize now we don’t know much, in terms of the biology of killing [bacteria] by antibiotics. A lot of research was done in the early 2000s at the genome and protein levels to see what happens with the genes of bacteria when they are subjected to stress such as antibiotics. The amazing thing was that scientists discovered bacteria don’t just give up and die. They’re not passive. They put up a fight and try to control and manage the effect of the antibiotic.

It turns out the bacteria know exactly what they’re doing, and we want to understand how that response actually happens. If we could make bacteria unable to sense the antibiotic and respond to it, there would never be any need to evolve or mount a resistance. So if we can bypass its response system, we might be getting close to some answers.

THE MAGAZINE: Knowing what you know, how much do we have to worry about some bugs being totally resistant to antibiotics?

GOLEMI-KOTRA: There are a number of pathogens that are now totally resistant and they are called superbugs. There is no treatment. It’s especially risky for people with HIV or diabetes and for those who undergo transplant surgeries. The problem for these people is the immune system is already down, the body’s microflora affected, so outside microorganisms can take over very quickly.

Bacteria have sophisticated nanomachines (about 1/1000th the diameter of a human hair) to help them stick to various surfaces and exchange genetic material and molecules essential to their survival and spread. Faculty of Science Professor Gerald Audette explains how these nanomachines are created and how they enable infection and resistance to medical treatments. His research spans crystallography, bionanotechnology, nanomedicine and structural biochemistry.

THE MAGAZINE: Tell me how you came to focus on bacteria and their behaviour?

AUDETTE: I’m a structural biochemist by training. I like looking at big protein molecules in atomic detail using X-rays. When I was a postdoc, I got interested in therapeutic targets. It turned out that the bacteria Pseudomonas aeruginosa uses the type 4 pilus to stick to a bunch of things, including plastics, steel, dirt – and you and me. These fairly simple structures use a common structure to bind to cell receptors. And because they use a common structure and not a common sequence, they can vary the sequence and thereby avoid our body’s immune system. The systems that assemble these structures are what we call “bionanomachines,” and they really are little machines – they make protein fibres, use energy to do it and are extremely small. Our goal is to understand these systems better as a means of understanding infection and resistance.

Bacteria assemble these nanomachines that they then use for any number of cool applications like, as I said, sticking to us or other surfaces, but also getting molecules in and out of cells. And those machines play a definite role in infection. Some of them look like a needle, and bacteria use them to punch holes in cells. These systems are known as secretion systems, and I and my research colleagues are interested in two different types for two different reasons.

To figure out what’s going on, you’ve got to solve the puzzle. And to solve the puzzle, you’ve got to put all the bits together

The first system involves transferring DNA between bacteria. Bacteria can use these special protein-based nanomachines to assemble protein “bridges” (tubes of protein) to move a mobile bit of DNA from one cell to another. By determining the 3D structure of the proteins that make this system up, and how they interact at the molecular level to make up the functional secretion system, we can figure out how it works and also get ideas about how to possibly render it inactive – or less active. That could help make the current arsenal of antibiotics more useful, in the sense that it could take bacteria longer to develop resistance to those antibiotics.

The second system is a structure known as a pilus. Think of it as a grappling hook. We found a version of the pilin (the pilus is thousands of copies of the pilin) that can assemble pilus-like structures without the bacterial system being involved. We’re interested in understanding how this happens. It’s another way bacteria use a large number of different methods to get molecules across their fences – whether to inject something into you, me or somebody else; to stick to surfaces; aid infection; or transfer DNA from one cell to another.

THE MAGAZINE: So the challenge is to look at the myriad variations in these nanomachines?

AUDETTE: Yes, and how they’re put together. To figure out what’s going on, you’ve got to solve the puzzle. And to solve the puzzle, you’ve got to put all the bits together. This is at the atomic level: Here’s atom No. 1 and it’s connected to atom No. 2, and so on. We use X-ray crystallography. We generate tiny crystals of the proteins we are studying and place them in an X-ray diffractometer. We then determine the structure of the protein within the crystal by analyzing the diffraction pattern, which looks like a series of spots that are produced when a beam of X-rays interacts with the crystal.

THE MAGAZINE: We often talk about viruses and bacteria in the same breath, but are they two distinctly different things?

AUDETTE: They are two different things. There are viruses that infect bacteria, but not the other way around.

THE MAGAZINE: Can you outline how they differ?

AUDETTE: Bacteria are living things. Given the right set of nutrients and proper temperature, they will grow all on their own. If you think of a bacteria most people are familiar with, such as E. coli, and you put it in a medium and give it some air and grow it at 37 C, each cell will become two cells quickly; in fact, it will double every 20 minutes. Our human cells also grow over time, but bacteria are very good at growing very fast – so fast they can overwhelm their host.

THE MAGAZINE: So viruses are not living?

AUDETTE: No. They cannot grow or divide on their own, so they aren’t considered “alive” in the way you and I think of the term. They’ve got to usurp our cells or bacterial cells. So a bacterial infecting virus will land on the bacteria and get its DNA in there, and once in, it codes for all it needs to make more of itself, but it can’t do it all on its own – it has to have the host. Viruses need something to stay alive and replicate, somewhere that will provide them with the machinery to survive and make more of themselves.

THE MAGAZINE: Is it fair to use words like “bad” or “good” when it comes to bacteria?

AUDETTE: Some bacteria are bad, some aren’t. E. coli, for instance, is fairly benign for the most part. But Walkerton had a somewhat bad strain of E. coli (strain O157:H7) contaminate its water – it was a case of a good bacteria gone bad. Or if you think of hamburger fever, often a result of undercooked hamburgers, where you’ve got a bacteria (again, E. coli O157:H7) coming in and saying, “Great, I’ve got a nice warm environment to flourish in!” Another is Helicobacter pylori; it’s in many of our stomachs in small amounts as part of the normal bacterial population (often called the “normal flora” and, more properly, “microbiota”). If you get a bit of an ulcer and the lining of your stomach gets weakened, it can colonize that and cause gastroenteritis and if not treated can result in gastric cancer. But if there’s no problem, it just hangs out and does what it does. About 80 per cent of humans have it in their stomachs and never know it’s there. It helps us digest things, but like anything it’s opportunistic. Bacteria all have their preferred living environments and they’re also competing against one another for ascendancy.

THE MAGAZINE: Has our cleanliness-obsessed culture worked against us when it comes to living in harmony with germs?

AUDETTE: I think in a way it has. I’m all for cleanliness, but I don’t advocate going overboard. The challenge comes because our bodies are designed to be protective, so we get colds and sniffles and get dirty. But this can help strengthen our innate immune system, which is always on, and our adaptive immune system, which gets exposed to things in our environment – in the soil or air or water – and learns to fight them off. Some people worry that because we are obsessed with not being exposed to microbes or bacteria, we have adapted to a state of continual cleanliness, which is a construct of our modern world. The worry is that when a bigger germ threat comes along we’ll be less able to handle it, which means we need to understand how bacteria use the tools they have to aid in infection and resistance.