A six-year study in Boston has revealed that migrating rats are spreading leptospirosis, a life-threatening bacteria, throughout the city, with new genetic tools linking a human infection directly to rat carriers.
Researchers studied rodent behavior to understand the relationships between different populations and how their movements contribute to the spread of leptospirosis.
Urban rats are on the move, and they may be carrying more than just a nuisance.
According to a new six-year study led by Tufts
University, rats migrating through cities are spreading a harmful
bacteria that can cause a potentially life-threatening illness in humans. In a
breakthrough, researchers also developed a new method for testing rat kidneys
to better detect this hidden danger.
The disease, known as leptospirosis,
is caused by bacteria commonly found in rats. It spreads when infected rats
urinate into the environment, contaminating soil, puddles, or standing water.
Humans, pets, and wildlife can become infected by coming into contact with
these contaminated areas. Leptospirosis is found worldwide and is especially common
in tropical climates. However, with rising global temperatures, this disease
could become more widespread in cooler regions.
In Boston, researchers discovered that leptospirosis
continues to circulate in rat populations. As rats migrate across different
neighborhoods, they bring new bacterial strains with them. The study was led by
Dr. Marieke Rosenbaum, assistant professor at Tufts’ Cummings School of
Veterinary Medicine, in collaboration with scientists from Northern Arizona
University (NAU), the United States Department of Agriculture (USDA), and the
Centers for Disease Control and Prevention (CDC).
Adding urgency to the findings, genetic analysis
linked a 2018 human case of leptospirosis in Boston to local rats, strongly
suggesting they were the source of the infection.
The paper, published recently in the journal PLOS Neglected Tropical Diseases, is the latest
work conducted by Rosenbaum and collaborators as part of the Boston Urban Rat
Study, a research group investigating whether rats in Boston carry pathogens
that pose a risk to public health. For this study, she joined forces with the
City of Boston’s Inspectional Services Department and other groups throughout
the city to track rats from 2016 to 2022 and test rats for leptospirosis. She
and researchers then employed advanced molecular techniques to figure out
exactly what type of leptospirosis was present. The researchers analyzed DNA from 328 rat kidney
samples collected from 17 sites in Boston, and 59 rats representing 12 of 17
sites were positive for Leptospira bacteria.
A Breakthrough in Leptospirosis Testing
“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,”
says Rosenbaum. “It has specific requirements for temperature, pH, and
nutrients. 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.”
From there, the Northern Arizona University
collaborators at the Pathogen & Microbiome Institute (PMI) used targeted
DNA capture and amplification to pick out and enhance leptospirosis DNA in the
samples, which resulted in a lot of fine-scale genomic information about the
isolates.
“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 Dave Wagner, Ph.D., professor
of biological sciences and executive director of the PMI at NAU.
“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
says.
The researchers hope their findings will help guide
rat control and human leptospirosis mitigation efforts in urban settings.
On Human Cases
For this paper, Rosenbaum and the other authors
examined one human case of leptospirosis in collaboration with the CDC, which
had an isolate obtained from a patient in a Boston hospital that was reported
to the federal level. Researchers at Northern Arizona University used molecular
tools to get a genomic sequence, which they found to be nearly identical to a
sequence obtained in three different rats spanning multiple years from the same
location in Boston.
“It’s very strong evidence that the source of that
human case was a rat,” says Rosenbaum.
Rats are the most well-established source of
leptospirosis infection in humans. But not all cases get diagnosed or reported.
Some people may get infected, not develop any symptoms, and never know they
were infected. Others might develop a mild fever or other nonspecific symptoms
before their immune system clears the infection. However, a small percentage of
people will go on to develop a more serious case of the disease, which can
affect different organs and, ultimately, cause multi-organ failure and 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,” says Rosenbaum.
There are challenges to collecting data on
leptospirosis cases, as well. Few clinicians would think to test a patient for
leptospirosis without some knowledge that the person may have been exposed to
it. And even if they do test for it, sometimes positive results are not
reported to state or national systems that compile such data. In addition,
leptospirosis is responsive to antibiotics, so if a physician prescribes
antibiotics for a patient to treat a suspected infection, then the bacteria may
not get picked up by a test anyway, Rosenbaum explains.
On Rat Migration
“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,” says Rosenbaum. “It doesn’t look like they’re intermingling
with other populations a lot, and that’s contributing to a stable population
over time, but when they do disperse, they can take leptospirosis with them.
The actual genetic sequence of leptospirosis is also stable within a population
of rats over time. Rats in Boston Common have a strain of leptospirosis that
they maintain over the years in that location, and it’s different from the
strain we saw in another area that also was persisting over time.”
They found that a rat in Boston would have to travel
over 600 meters, or just over a 1/3 of a mile, to encounter another genetic
population of rats. They also found evidence that large, multi-lane roads
disrupted all connectivity between populations of rats on either side of the
road, and that rats used greenways and biological corridors for travel and
intermingling. Construction is another well-known disruptor of rat burrows that
forces rats to look for other places to persist, which can increase the spread
of the bacteria.
When it comes to pest control, Rosenbaum says an
important next step is to better understand how pest management interventions
impact rat migrations and their population structure, as well as how they
impact humans and the environment.
“Extermination is not realistic,” she says, “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.”
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