Learning More About Monitoring and Understanding Antibiotic Resistance with Dr. David Hooper

At the American Society for Microbiology (ASM) Microbe 2017 conference, David Hooper, MD, ASM Microbe Steering Committee Chair, Chief of Infection Control Unit at Massachusetts General Hospital sat down with Contagion

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and shared his research objectives.

What is the Primary Focus of Your Research?

The work in my laboratory involves understanding the fundamental mechanisms and epidemiology of bacterial resistance. We have been primarily focused on two areas over the past several years. One area of focus has been resistance due to efflux pumps, specifically, trying to understand the natural role of these efflux pumps. In some cases, the pumps are not there primarily for antibiotic resistance, but rather they function to help the bacteria survive in different environments.

For example, there is one case in which we think we understand the native function of an efflux pump known as Tet38. Originally, we discovered Tet38 because when it is over-expressed it confers tetracycline resistance. However, it turns out that when we studied animal models of Staphylococcus aureus-generated subcutaneous abscesses in mice, Tet38 and some other efflux pumps are selectively over-expressed in this environment (inside the mouse) relative to growth in the laboratory environment. Moreover, when we knock out Tet38, S. aureus do not survive as well.

And so, we inferred that these efflux pumps confer survival fitness. We observed that Tet38 also confers resistance to antibacterial skin fatty acids. S. aureus survives infamously well on skin, but if we knock out Tet38, S. aureus colonization is reduced 5-fold. We believe that resistance to endogenous antibiotic skin fatty acids may be part of the natural function of Tet38.

Does the Structure of These Anti-Bacterial Fatty Acids Resemble the Structure of Tetracycline?

No, these molecules are completely structurally different. Efflux pumps generally have broad chemical specificity, particularly amongst the gram-negative bacteria, but also S. aureus.

What is the Secondary Focus of Your Research?

Our other focus has been on plasmid-encoded fluoroquinolone resistance genes. Originally, the only resistance observed was believed to be due to chromosomal genes. All of the research was on non-transferrable chromosomal mutations; however, several years ago, George Jacoby, MD, first showed transferrable fluoroquinolone resistance while studying beta-lactamase-resistant gene transfer. It turned out to be an interesting family of plasmid genes termed ‘QNR’, for quinolone resistance. These are members of the pentapeptide repeat family that work in protein interactions. They bind to the gyrase due to a charge distribution that resembles DNA, but the pentapeptide repeat proteins do not inhibit the gyrase activity. Pentapeptide repeat proteins inhibit the ability of fluoroquinolone to inhibit the gyrase There is a worldwide distribution of QNR genes on plasmids.

We also had unexpected discoveries when studying QNR plasmid transfers. One isolate had a much higher level of fluoroquinolone resistance. We did random transposon mutagenesis and identified another set of gene mutations in the active site of a long-known kanamycin acetyltransferase-encoding gene. These mutations gave the enzyme the ability to inactivate fluoroquinolone.

It turned out to be an unexpected result, but it is a story that crystallized in my mind. If there is a mechanism out there and it is selectable, bugs will figure out a way to do it. In that regard, you have to give the bugs some respect.

The other epidemiology part of research as head of the infection control unit of the hospital involves tracking various resistant genes. Patients are indicated for these infections and then isolated.

What is an Example of Patients Needing to be Isolated?

Methicillin-resistant Staphylococcus aureus (MRSA) diagnosis is an indication for Centers for Disease Control and Prevention (CDC)-recommended isolation. This is because MRSA tends to hang out on skin. If you handle a MRSA-positive patient, then your skin can be colonized and potentially transmitted to the next patient.

In addition, we found similar results with vancomycin-resistant gonococcus. We performed mock physical exams on patients and analyzed what was transferred to the gloves and gowns. We found that two thirds of the time you could transfer organisms picked up on the gloves and gowns to an agar plate. Conversely, we found that using an alcohol cleanser eliminated the transfer of organisms from the patient to the gloves and gowns entirely.

What About the Current State and Trajectory of Multidrug-Resistant (MDR) Bacteria?

Fortunately, there are relatively low numbers of MDR bacteria in the United States, but the current data indicate that there has been some increase, particularly in gram-negative bacteria. One piece of good news is that MRSA rates have actually gone down. In hospital settings, we attribute this to more stronger focus on hand hygiene.

Are You Thinking About Microbiome Approaches to These Problems?

No, we are not really looking at this in the laboratory, but we do have a program for fecal transplants at the hospital and it does work. The real frontier in this field will be to the figure out the minimal cocktail of bugs needed so we will no longer need to do a fecal transfer; however, currently the big concern is to figure out if there is something out there that a donor has in his or her system that they could pass on to the patient. While they do screen donors, there is still a concern for adverse events. There is also some interesting suggestive data from animal models, which will be published, showing that fecal transplants in these models reduced antibiotic bacteria. Therefore, perhaps someday similar approaches can be used in the clinic. This supports the notion the perhaps some day we will be able to use microbiome based therapies to address issues of antibiotic resistance through competition.

It Seems Like the Whole Idea of Changing the Bacterial Ecosystem, Instead of Focusing on an Enzyme is Such a New Idea Historically Speaking. What Are Your Thoughts?

Yes, it is at such a new stage where we know so little that the theoretical potential is not yet limited by our experiential knowledge yet. And so, there is great excitement, but I am sure that there are some things that will not pan out. We just need to figure out the key components that drive dysbiosis.

Feature Image Source: Harvard Public Affairs & Communications [Stephanie Mitchell/Harvard Staff Photographer](http://news.harvard.edu/gazette/story/2013/09/when-bacteria-fight-back/)

W. Todd Penberthy, PhD is a medical writer with over 4 years of experience based in Orlando, Florida. Prior to that Todd was a professor directing biomedical research using zebrafish models of human disease with expertise in orthomolecular niacin-related science for 10 years.