Engineering viruses to kill deadly pathogens

Northwestern University researchers have successfully coaxed a deadly pathogen to destroy itself from the inside out.

Petri dishes with bacterial lawns, phage plaques.

The dark spots in the dishes mark areas where phage burst out of the bacteria, killing them. Photo credit: Cole Wilson

In the new study, researchers modified DNA from a bacteriophage or “phage,” a type of virus that infects and replicates inside of bacteria. Then, the research team put the DNA inside Pseudomonas aeruginosa (P. aeruginosa), a deadly bacterium that is also highly resistant to antibiotics. Once inside the bacterium, the DNA bypassed the pathogen’s defense mechanisms to assemble into virions, which sliced through the bacterium’s cell to kill it.

Building on a growing interest in “phage therapies,” the experimental work represents a critical step toward engineering designer viruses as new therapeutics to kill antibiotic-resistant bacteria. It also reveals vital information about the innerworkings of phages, a little-studied area of biology.

The study was published Jan. 31 in the journal Microbiology Spectrum.

“Antimicrobial resistance is sometimes referred to as the ‘silent pandemic,’” said Northwestern’s Erica Hartmann, who led the work. “The numbers of infections and deaths from infections are increasing worldwide. It’s a massive problem. Phage therapy has emerged as an untapped alternative to our reliance on using antimicrobials. But, in many ways, phages are microbiology’s ‘final frontier.’ We don’t know much about them. The more we can learn about how phage work, the more likely we can engineer more effective therapeutics. Our project is cutting-edge in that we are learning about phage biology in real time as we engineer them.”

An indoor microbiologist, Hartmann is an associate professor of civil and environmental engineering at Northwestern’s McCormick School of Engineering and a member of the Center for Synthetic Biology.

Desperate need for antibiotic alternatives

Associated with an increase in antimicrobial use, the rise of antibacterial resistance is an urgent and growing threat to the global population. According to the Centers for Disease Control and Prevention (CDC), nearly 3 million antimicrobial-resistant infections occur each year in the United States alone, with more than 35,000 people dying as a result.

The growing crisis has motivated researchers to look for alternatives to antibiotics, which are continually losing effectiveness. In recent years, researchers have started to explore phage therapies. But even though billions of phages exist, scientists know very little about them.

“For every bacterium that exists, there are dozens of phages,” Hartmann said. “So, there is an astronomically large number of phages on Earth, but we only understand a handful of them. We haven’t necessarily had the motivation to really study them. Now, the motivation is there, and we are increasing the number of tools we have to dedicate to their study.”

Treatment without side effects

To explore potential phage therapies, researchers either pinpoint or modify an existing virus to selectively target a bacterial infection without disrupting the rest of the body. Ideally, scientists one day could tailor a phage therapeutic to infect a specific bacterium and design “a la carte” therapeutics with precise traits and characteristics to treat individual infections.

“What’s powerful about phage is it can be very specific in the way that antibiotics are not,” Hartmann said. “If you take an antibiotic for a sinus infection, for example, it disrupts your entire gastrointestinal tract. A phage therapy can be designed to affect only the infection.”

While other researchers have investigated phages therapies, almost all of those studied have focused on using phages to infect Escherichia coli. Hartmann, however, decided to focus on P. aeruginosa, one of the five most deadly human pathogens. Particularly dangerous for people with compromised immune systems, P. aeruginosa is a leading cause of hospital infections, often infecting patients with burn or surgery wounds as well as lungs in people with cystic fibrosis.

“It is one of the highest priority, multi-drug resistant pathogens that many people are really concerned about,” Hartmann said. “It is extremely drug resistant, so there is an urgent need to develop alternative therapeutics for it.”

Mimicking infection, bypassing defenses

In the study, Hartmann and her team started with P. aeruginosa bacteria and purified DNA from several phages. Then, they used electroporation — a technique that delivers short, high-voltage pulses of electricity — to poke temporary holes in the bacteria’s outer cell. Through these holes, phage DNA entered the bacteria to mimic the process of infection.

In some cases, the bacteria recognized the DNA as a foreign object and shredded the DNA to protect itself. But after using synthetic biology to optimize the process, Hartmann’s team was able to knock out the bacteria’s antiviral self-defense mechanisms. In these cases, the DNA successfully carried information into the cell, resulting in virions that killed the bacteria.

“Where we were successful, you can see dark spots on the bacteria,” Hartmann said. “This is where the viruses burst out of the cells and killed all the bacteria.”

After this success, Hartmann’s team introduced DNA from two more phages that are naturally unable to infect their strain of P. aeruginosa. Yet again, the process worked.

Phage manufacturing in a cell

Not only did the phage kill the bacteria, the bacteria also ejected billions more phages. These phages can then be used to kill other bacteria, like those causing an infection.

Next, Hartmann plans to continue modifying phage DNA to optimize potential therapies. For now, her team is studying the phages expelled from the P. aeruginosa.

“This is an important piece in making phage therapies,” she said. “We can study our phage in order to decide which ones to develop and eventually mass produce them as a therapeutic.”

The study, “A synthetic biology approach to assemble and reboot clinically relevant Pseudomonas aeruginosa tailed phages,” was supported by the Walder Foundation, the National Science Foundation and the National Institutes of Health.

This story originally appeared on Northwestern Now.

Workshop on Microbiome Data Best Practices hosted by Jiaxian Shen, NMDC

Data don’t stand on their own! Dr. Jiaxian Shen from Hartmann Lab is hosting a workshop as part of the National Microbiome Data Collaborative (NMDC). The workshop, titled ‘Microbiome Data Best Practices: from Submission to Reuse,’ promises to be a useful guide for researchers wanting to ensure their data are valuable to others. Sign up here to attend!

Microbiome research thrives on the integration of data and metadata, individual studies and synthesized meta-analysis. The NMDC is an organization dedicated to creating integrated platforms and engaging research communities. As an NMDC ambassador, Jiaxian hosts workshops to promote our commitment of FAIR data principles and collaborative science.

Publication opportunity with Frontiers in Microbiomes!

Dr. Hartmann (editor) and Dr. Shuai (coordinator) from Hartmann Lab are organizing a Research Topic with Frontiers in Microbiomes titled Interactions Between Natural and Built Environment Microbiomes in a One Health Context.

This Research Topic aims to collect communications that may improve our understanding of the interactions between natural and built environment microbiomes from all aspects under the One Health framework. We welcome all submissions including original research papers, reviews, and methodologies under this theme. Sub-themes include, but are not limited to:

  • Mechanisms of antimicrobial resistance developed under the impact of anthropogenic chemicals in built environments
  • Microbial community diversity and metabolic characterizations in relation to the interactions between natural and built environments
  • Insights or novel frameworks for identifying monitoring, and quantitative risk assessments of emerging health risks from a One Health perspective
  • New perspectives on diverse interactions between human, animal, plant and built environment microbiomes
  • Computational approaches to monitor, classify and/or predict microbial growth and risks in our built environments
  • Impacts of climate change on the interactions between natural and built environment microbiomes

Consider submitting your work to this special article collection to get more exposure and make more impact! Feel free to contact members of the editorial board for more information (personalized deadline available upon request).

Abstract submission deadline: 24 June 2023

Manuscript submission deadline: 3 March 2024

Postdocs wanted!

The Hartmann lab is seeking multiple postdoctoral researchers! We have projects available in global dimensions of antimicrobial resistance, detection of respiratory pathogens on aircraft, and development of ecologically inspired molecular therapeutics for infection. Candidates are also encouraged to propose research topics of their own related to environmental chemistry and microbiomes.

Qualified candidates should have experience in at least some of the following:

  • Practical experience with shotgun or amplicon sequencing data
  • Knowledge and hands-on experience in molecular biology, microbiology, bacteriophages, and culture and genetic manipulation of bacteria and yeast
  • Have a combination of the following skills: design and use of CRISPR/Cas; DNA manipulation and analysis; PCR and plate-reader assay development
  • Practical experience with whole genome sequence data
  • Proficient in molecular biology techniques, including design and construction of genetic constructs using enzymatic (e.g. Gibson assembly) or yeast-based approaches
  • Ability to troubleshoot and optimize experimental protocols
  • Strong writing skills
  • Project management

To apply: Provide a CV with names and contact information for references to erica.hartmann@northwestern.edu. As always, include your favorite color for expedited consideration.

Northwestern University is an Equal Opportunity, Affirmative Action Employer of all protected classes, including veterans and individuals with disabilities. Women, racial and ethnic minorities, individuals with disabilities, and veterans are encouraged to apply. Hiring is contingent upon eligibility to work in the United States.

New tool RefDeduR out now!

Hartmann lab member Jiaxian Shen has been diving into systematic reviews and ran into issues deduplicating references after searching multiple databases. If you too have this problem, she now has an R package to help!

RefDeduR logo

RefDeduR performs string cleaning, exact matching, and fuzzy matching to make identifying and removing duplicates a streamlined, automated process. You can access it on GitHub and check out the preprint on bioRxiv!

Hartmann lab posters at AEESP!

After a strong showing at ASM this year, Hartmann lab members are back in action at AEESP in St Louis! Check out our posters:

Characterizing Antimicrobial Resistance in Staphylococcus spp. Isolated from the International Space Station
Presented by Olivia Barber
https://aeesp2022.exordo.com/programme/presentation/728

Meta-analysis of the Indoor Surface Microbiome
Presented by Jiaxian Shen
https://aeesp2022.exordo.com/programme/presentation/647

Understanding host-phage interactions of nitrite oxidizing bacteria in a nitritation reactor
Presented by Stefanie Huttelmaier
https://aeesp2022.exordo.com/programme/presentation/504

Also, check out this poster presented by Weitao Shuai, representing the Wells Lab
Harnessing power from the soil: long-term, stable power production from terrestrial microbial fuel cells integrated into green infrastructure
https://aeesp2022.exordo.com/programme/presentation/659

 

Check out tons of Hartmann lab work at ASM Microbe

Headed to ASM Microbe in DC this week? Join Prof. Erica Hartmann and PhD student Olivia Barber bright and early on Friday morning for a panel discussion on science advocacy.

And be sure to check out all of our posters and presentations:

Weitao Shuai
Session AES03 – Antimicrobial Resistance in the Environment 1
2443. Mitigation Of Antimicrobial Resistance During Onsite Greywater Treatment And Reuse
https://www.abstractsonline.com/pp8/#!/10522/presentation/4111

Olivia Barber
Session POM01 – Hard Surface Disinfectants: The Pathway to Development and Role in Targeted Hygiene Practices in Residential Homes
Does Periodic Disinfectant Exposure on Surfaces Induce Antimicrobial Resistance?
https://www.abstractsonline.com/pp8/#!/10522/presentation/1381

Jiaxian Shen
Session AES01-Microbiology of Engineered Environment
2374. Are We Ready For A Meta-analysis Of The Indoor Surface Microbiome?
https://www.abstractsonline.com/pp8/#!/10522/presentation/4236

Stefanie Huttelmaier
Session EEB01 – Species interactions and microbial community assembly
3195. Understanding Host-phage Interactions Of Nitrite Oxidizing Bacteria In A Nitritation Reactor
https://www.abstractsonline.com/pp8/#!/10522/presentation/4034

Jack Sumner
Session MBP10 New Microbiological Techniques
3947. Improving Sequencing Success In Bronchoalveolar Lavage Samples For Microbiome Study
https://www.abstractsonline.com/pp8/#!/10522/presentation/3857

Interdisciplinary research group developing roadmap to combat the rise of antibiotic-resistant bacteria

The development of modern antibiotics has played a profound role in our ability to treat a range of bacterial infections once considered life threatening. Yet as global access to antibiotics has steadily increased, so too has their overuse, resulting in a worrying rise in antibiotic-resistant bacteria.

In response, an interdisciplinary research group funded by the Northwestern Buffett Institute for Global Affairs was formed, drawing on the expertise of faculty members from Northwestern University’s Feinberg School of Medicine, McCormick School of Engineering and Weinberg College of Arts & Sciences, and in collaboration with experts from Northwestern Memorial Hospital, Lurie Children’s Hospital, the Argonne National Laboratory and Aga Khan University in Pakistan. The group is developing a roadmap to coordinate responses to antimicrobial resistance across academic, political, pharmaceutical and medical institutions.

The group, in partnership with the Center for Pathogen Genomics and Microbial Evolution at the Feinberg School of Medicine’s Institute for Global Health, recently received a grant from the Centers for Disease Control and Prevention to study antimicrobial resistance patterns and their associated clinical implications. The grant will provide the group with $500,000 annually for five years to support their research and will allow the group to build upon their collaboration with Aga Khan University.

In this Q&A, global working group leaders Erica Hartmann, assistant professor of civil and environmental engineering in the McCormick School of Engineering, and Mehreen Arshad, assistant professor of pediatrics (infectious diseases) in Northwestern Feinberg School of Medicine and attending physician in pediatric infectious diseases at Ann and Robert H. Lurie Children’s Hospital of Chicago, discuss the urgency of this problem and the solutions their group aims to develop.

What is the main issue you’re trying to tackle?
Arshad: Our work focuses on understanding antimicrobial resistance in different healthcare systems across the world. We are trying to better understand how these highly resistant bacteria spread across different communities and patient populations, and also understand what we can do to better treat and control their spread.

Hartmann: The problem that we are facing is that our arsenal of antibiotics is not expanding, and at the same time, pathogens are developing resistance to existing antibiotics. This means that diseases that we used to be able to treat very easily are becoming much more difficult to manage and even fatal. In 2019 alone, there were an estimated 5 million deaths attributed to some form of antimicrobial resistance worldwide, and that number is only expected to increase.

What drives this problem?
Arshad: The key driver of this problem that we’ve seen over the last decade or so seems to be the over-prescription and overuse of antibiotics, not just in the human population, but also in livestock and agriculture. We’ve seen a general rise in unrestricted access to antibiotics occurring in many countries around the world, including in the U.S.

Hartmann: One of the major challenges with fighting antimicrobial resistance is that we are not just dealing with one disease. There are many different pathogens that can develop antimicrobial resistance and many different types of resistance those pathogens can develop, which makes reporting very challenging. Often, you might not even know you have an antimicrobial infection until you try to take an antibiotic and it fails. It’s not something that we actively screen for on a global scale, which makes it difficult to understand the actual scope of the problem.

What is the interdisciplinary view your group brings to the table?
Hartmann: Antimicrobial resistance is obviously a medical issue of grave concern to doctors and patients, but it’s also a global phenomenon that requires a lot of modelling to understand how it transmits from person to person and region to region. It’s also a challenge from an evolutionary perspective because these are living organisms that are developing resistance through the process of evolution.

Arshad: Part of the challenge is as a global community we’ve been tackling this issue in bits and pieces. Within our group we have physicians, engineers, sociologists, social scientists, mathematicians and infection control experts. Working in silos will only get you so far, but we hope that by bringing all this expertise together, we are able to come up with more sustainable solutions to address the problem.

What possible solutions does your group hope to achieve?
Arshad: One major problem is that every institution gathers antimicrobial resistance-related data in a different way. This makes it extremely difficult to pull data from across different institutions or regions of the world. To address this, we’ve partnered with Aga Khan University in Pakistan with the hope to work together to develop shared basic metrics on measuring antimicrobial resistance, and by doing so, build a road map for standardizing some of the data collection and curation to make it more accessible.

Hartmann: Our vision is that doctors will eventually have access to information about what types of antimicrobial pathogens they need to be aware of and worried about, and at the same time, that policymakers will be aware of the types of threats people are facing and understand the types of policy actions they can take to respond.

This story was originally posted on Northwestern Now.

Undergrads – join us in the quest to understand antimicrobial textiles!

Are you an undergraduate student interested in research? The Hartmann lab is recruiting for summer 2022 to help with Prof. Hartmann’s NSF CAREER project on antimicrobial textiles. Projects (described below) are available in microbiology and bioinformatics. Hartmann lab undergraduates have accomplished great things, including being authors on research publications and presenting posters international conferences. Our alumni have gone on to PhD programs, medical school, and other great careers. If you’re interested in joining our fantastic group, get in touch!

Mia Tran in the lab

Hartmann lab alum Mia Tran measured metals in antimicrobial textiles. She is now a PhD student at Yale University.

Microbiology projects involve assessment of metal resistance in bacterial isolates. We have identified antimicrobials embedded in 5 textiles. Each textile contained a unique mixture of silver, copper, titanium, and zinc. We now need to characterize metal resistance in our bacteria for the study. For this project, the undergraduate student researcher will expose isolates in culture to varying concentrations of pure dissolved metals. By observing the sensitivity of these organisms to each individual metal in solution, we will establish a baseline for metal tolerance.

Bioinformatics projects involve exploration of metal resistance genes. To understand the mechanisms underlying metal resistance, or lack thereof, we will examine the genomes of the studied organisms for known genes related to metal resistance. For this project, the undergraduate student researcher will assemble and annotate whole genome sequences from our bacteria for the study. Annotated functions will be examined for metal resistance, antimicrobial resistance, mobile genetic elements, and other potential functions of interest. By identifying resistance genes, we will generate hypotheses regarding how bacteria survive exposure to antimicrobial textiles.

Hartmann lab wins at Political Capital

After participating in a workshop at ASM Microbe last year, PhD student Olivia Barber suggested that we all might want to learn more about science policy, advocacy, and how our work intersects with government. The American Society for Microbiology runs an educational gaming experience called Political Capital and was gracious enough to visit us over Zoom during our weekly lab meeting. With the ASM’s help, we split into teams and navigated our way through a frantic 4 week period leading up to a big vote on a bill to support microbiology research, fighting against an anti-spending group. Mistakes were made, lessons were learned, and in the end, one team prevailed!

Screenshot of a Zoom call

Science policy is a multi-faceted and complex process where scientists can participate both as individual constituents and subject matter experts. It was really fun to learn more about the process. Huge shoutout to Adam Katz, Lauren Gabel, and Allen Segal from ASM for teaching us about science policy and leading us through this game! To bring them into your group, email advocacy@asmusa.org.