Rats are spreading a deadly disease across cities

Rats scurry through alleyways, tunnels, and parks. While these creatures are a common sight in city life, their movements may carry far more danger than many realize.

A newly published six-year study reveals how rat migrations within cities contribute to the spread of a serious bacterial infection called leptospirosis – a disease that can be fatal for both humans and animals.

In this study, scientists from Tufts University, along with researchers from Northern Arizona University, the United States Department of Agriculture (USDA), and the Centers for Disease Control and Prevention (CDC), worked together to track the spread of leptospirosis in Boston.

The team also introduced a new way to test rat kidneys for this disease-causing bacteria, a method that may change how future infections are traced.

What is leptospirosis?

Leptospirosis is caused by a bacterium that often thrives in rats. It’s spread primarily through rat urine, which contaminates soil, water, and other parts of the environment. From there, it can infect humans, dogs, and other animals.

While common in tropical areas, this disease is now appearing more in colder regions, likely due to the warming effects of climate change.

In Boston, the disease has been found in the city’s rat populations, with various strains moving between neighborhoods as rats migrate.

The research team was able to genetically link a 2018 human case of leptospirosis in Boston to infected rats in the same area, confirming a strong connection.

Tracking a hidden bacteria in rats

From 2016 to 2022, researchers worked with Boston’s Inspectional Services Department to trap and test rats from 17 different sites.

They collected and analyzed DNA from the kidneys of 328 rats. Out of those, 59 rats – covering 12 different sites – tested positive for the Leptospira bacteria. Culturing this bacterium is no easy task.

Marike Rosenbaum is an assistant professor in the Department of Infectious Disease and Global Health at Cummings School of Veterinary Medicine at Tufts University.

“The primary way to get a full genomic sequence of a virus or bacteria is to culture it, which was a challenge in this case because Leptospira is considered a fastidious organism. It has specific requirements for temperature, pH, and nutrients,” said Rosenbaum.

“But our USDA collaborators cultured the bacteria from not only fresh but also frozen rodent kidneys, which has never been reported in the literature before, to get isolates.”

Using the whole genome

Experts at Northern Arizona University’s Pathogen & Microbiome Institute used specialized DNA techniques to isolate and enhance the bacterial genetic material. This allowed researchers to gather a detailed view of how the bacteria spread and evolve.

“The new genetic and tools that we developed and used in this study are real game changers for leptospirosis research, as we can now use the power of the whole genome to look for relatedness among samples, something that just wasn’t possible before,” said Dr. Dave Wagner, executive director of the PMI at NAU.

Mapping the movement of disease

By combining genetic sequencing with information on rat migration, the team was able to see how leptospirosis travels through the city.

“Because we were able to do the culturing and the sequencing, we were able to look more closely at how the different strains of leptospirosis are related, which helps us understand how the bacteria are getting transmitted between rats and rat populations in the city,” Rosenbaum said.

This information could help shape better strategies for controlling rat populations and minimizing human exposure.

Threats to human health

The researchers also studied a single human case of leptospirosis in Boston, working with the CDC to analyze the bacterial strain. They compared it to those found in local rats.

The result was striking: the strain in the human was nearly identical to those found in three rats from the same area, even though those rats were collected in different years. “It’s very strong evidence that the source of that human case was a rat,” said Rosenbaum.

Not every case of leptospirosis is detected. Some people may have no symptoms at all. Others might feel slightly sick before recovering. However, a small number of infections lead to serious complications – including organ failure or even death.

“Human exposure to rats is not very common. But certain populations might be at higher risk, like unhoused people or people who engage in outdoor injection drug use, which are situations that lead to more direct contact with rats,” said Rosenbaum.

Diagnosing leptospirosis is tricky. Many doctors don’t think to test for it unless they suspect exposure. And even when they do, antibiotic treatment can eliminate the bacteria before it shows up on a test.

Positive results also aren’t always reported to public health databases, making it harder to track.

Understanding how rats travel

The research also uncovered how rats move throughout Boston. “Rats have a high degree of genetic structure, which means there are distinct rat populations throughout the city that are highly related to each other,” Rosenbaum explained.

These populations don’t mix often. But when rats do migrate – due to construction, habitat disruption, or environmental changes – they can carry bacteria with them. Each rat group tends to maintain its own unique strain of leptospirosis over time.

A rat in Boston typically needs to travel over 600 meters – more than a third of a mile – to encounter a genetically different group. Wide roads limit this movement, while green spaces and corridors make it easier for them to spread.

Eradicating rats isn’t the answer

The goal is not to eradicate rats entirely. That would be nearly impossible. Instead, scientists want to understand how different pest control methods affect rat migration and disease spread.

“Extermination is not realistic,” Rosenbaum said. “But I think better understanding of how the different pest control interventions are impacting rat migrations and transmission of pathogens amongst the rat population would be really helpful.”

By combining genetic science, city mapping, and public health, this study sheds new light on how a quiet pest in our cities can carry a very loud threat – one that deserves more attention.

The full study was published in the journal PLOS Neglected Tropical Diseases.

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