Prospecting for pathogens in museum vaults

Bats, rodents, birds, deer and other preserved museum specimens could hold clues about the next pandemic-causing pathogen. Rather than waiting for the next pandemic to take the world by surprise, researchers at Texas Biomed are developing genetic-based tools to investigate collections and see what might be lurking.

“Forever, we’ve been talking about how museums are a good repository for pathogen information, but the challenge has been how to go about getting that in a reasonable way,” says Roy “Neal” Platt II, Ph.D., a Staff Scientist in the lab of Professor Tim Anderson, Ph.D.

Museum specimens have been collected for hundreds of years and are catalogued with locations and dates. Small animals are often dried, but can also be frozen or chemically preserved whole, with tiny tissue samples extracted and frozen separately. This vast archive of biodiversity can tell scientists about the animals as well as the bacteria, viruses and parasites they carried. While not all pose a threat to people, more than 60 percent of pathogens that infect people are zoonotic – they start in animals and jump.

“If you really want to study zoonotic pathogens, museums are a very good place to start,” says Egie Enabulele, Ph.D., a postdoctoral researcher in Dr. Anderson’s lab.

Sequencing the DNA of museum specimens reveals which animals are natural hosts or carriers of which pathogens and may help scientists discover new species of infectious organisms. The “where and when” the specimens were collected matters, too. Scientists can combine all these data points to gain a better picture of how widespread pathogens are, where they have been circulating and how that has changed over time, especially related to climate and habitat changes.

Specific changes can provide insight about how pathogens evolve and the potential for spread in people. With specimens collected more recently, within the last 30 years or so, findings can be extrapolated to current wildlife populations and inform wildlife management and public health strategies.

However, looking through museums for any and all potential pathogen threats poses an almost insurmountable challenge, requiring a monumental amount of time, money and tissue samples. Advancements in genetic sequencing in recent years are bringing costs down, and now, Dr. Platt and Dr. Enabulele have developed a clever solution to address the other challenges: a genetic tool designed to extract a wide range of pathogen DNA from a tiny tissue sample.

Instead of looking for one specific bug at a time – think of an at-home COVID-19 test which is designed to detect only SARS-CoV-2 – they designed a test that could detect broad groups of bacteria, fungi and parasites at the same time.

“This was our attempt to try to go about getting that information in a relatively cheap, efficient way,” says Dr. Platt.

HOW IT WORKS

Dr. Platt identified short snippets of DNA sequences shared amongst major groups of mammalian parasites, including bacteria, fungi, helminths (parasitic worms) and protozoans (single-celled parasites, such as malaria). Based on those sequences, he designed DNA-based probes for each of those pathogen groups and then combined them into one “assay,” or test. When one of the 80,000 probes matches a similar sequence in a sample, it binds to it. Those matches are extracted from the rest of the sample and then genetically sequenced.

A key issue they had to address: how do you detect additional pathogens you don’t even know exist?

The probes are designed with flexibility in mind, binding to DNA sequences that are up to 12 percent “off-target” or different, which could be variations of pathogens not discovered before.

This entire process would be very difficult to do with traditional PCR genetic sequencing, which works best with identifying DNA or RNA sequences that are an exact match.

“You’d have to have 1,600 PCR reactions to do what we’re able to do in a single tube,” Dr. Platt says.

A SPEC OF TISSUE

Dr. Platt and Dr. Enabulele worked with collaborators at several museums, including those at Texas Tech University, the University of Michigan, Chicago State University and the Field Museum of Natural History in Chicago, to gather a wide range of mammal tissue to analyze for pathogen DNA and demonstrate the versatility of the test.

The amount of tissue that museums send for this type of work is tiny – literally, the size of a grain of rice, a pen tip or a broken piece of mechanical pencil lead. And yet, that is all Dr. Enabulele needs to begin processing samples in the lab, making this approach relatively noninvasive to extract valuable information from preserved specimens. A key concern with museum samples is how well DNA is preserved. The probes in this test are very short genetic sequences, so even if DNA has degraded into small fragments, the test still works.

“No matter how old the samples are, we can still fish something out,” says Dr. Enabulele.

When they ran their tests, the team made a few unexpected discoveries around a bacteria called Bartonella, which can cause rare diseases, including cat-scratch disease. It is transmitted from pets to people via lice, causing rash, swollen lymph nodes and fever, but usually resolves on its own.

The researchers found the bacteria was widespread, showing up in 36 of 38 specimens tested, including rodents, bats, porcupines, armadillos and deer. They detected several Bartonella species that were not included in the assay, but are known to science, thanks to the flexibility of the test. They also detected a Bartonella species in a museum sample collected in 2009, which was surprising because that species was “discovered” in 2018.

“What we’ll be calling new to science today is already in the museum hiding somewhere,” Dr. Enabulele says.

BEFORE THE PANDEMIC

Dr. Platt and Dr. Enabulele have been working on the project since 2019. It originally began with an interest to search for parasitic worms called schistosomes in museum samples. But Dr. Anderson asked them: “Why stop there? Why not find out what else those animals were infected with?” They broadened their scope and won a Texas Biomedical Forum pilot grant at the end of 2019 to begin the work, just before the COVID-19 pandemic hit.

“The pandemic underscores just how critical this type of work is,” Dr. Anderson says. “It is important to know what pathogens are all around us to determine which could be the next big thing.”

Rather than a mad dash to figure out where a disease comes from every time a new one emerges, it would be helpful to have an established baseline of what’s out there and which animals are natural hosts. This information could empower public health officials – working with collaborators across disciplines like wildlife biology, environmental science and biomedical research in a “One Health” approach – to stay ahead of potential problems before they spread.

“COVID really showed us that this reactionary approach doesn’t work well,” says Cody Thompson, Ph.D., Mammal Collections Manager and Associate Research Scientist at the University of Michigan Museum of Zoology, who collaborated on the project. “We need to be better at forecasting and understanding how things are changing in the environment around us. Museums, as the global archive of flora and fauna, can help provide a deep history of how pathogens have moved around the planet.”

The team published their research about the pathogen DNA test in the journal Emerging Infectious Diseases. In the future, the researchers would like to work with collaborators to make the test even more efficient and sensitive.

“It is easy to imagine this being scaled up and then once you have the data, the sky’s the limit,” Dr. Platt says.