Super-resistant bacteria found in wild birds at a rehabilitation center on the coast of São Paulo state, Brazil

A vulture recently arrived at the Santos Municipal Orchid Garden and an owl living in captivity for ten years were colonized by antibiotic-resistant Escherichia coli.

By André Julião  |  Agência FAPESP – Researchers supported by FAPESP have found antibiotic-resistant bacterial clones in wild birds at a rehabilitation center. The identified Escherichia coli clones have been found in community- and hospital-acquired human infections worldwide, and they were present in the intestinal tracts of a vulture and an owl.

The impact of these strains on animals is unknown; however, in humans, they are known to cause infections in patients with weakened immune systems for which there are few effective treatment options. The study was published in the journal Veterinary Research Communications.

“Escherichia coli is a common bacterium in the intestinal tract of many animals, including humans. It becomes a problem when it enters the bloodstream or causes urinary tract or kidney infections, particularly when it affects people with compromised immune systems and in hospital settings. In these people, multidrug-resistant clones such as these often lead to death,” explains Fábio Sellera, a professor at the Metropolitan University of Santos (UNIMES) in the state of São Paulo, Brazil, and one of the study’s coordinators.

The study emphasizes the importance of establishing protocols for maintaining these rehabilitation centers and for releasing animals back into the wild.

“These facilities are very important for mitigating the effects of human activity on wildlife, but nowhere in the world are there evidence-based procedures for monitoring, preventing, and treating the colonization of rescued and reintroduced animals by antibiotic-resistant microorganisms,” the researcher warns.

Genomic analyses have shown that antibiotic resistance genes are located in mobile genetic elements that can transfer to other E. coli clones and bacteria of other species in the environment.

“As a result, even bacteria that have never had contact with antibiotics or polluted environments, which also select for this type of agent, can become resistant. That’s why there’s a need for continuous monitoring of the environment and potential hosts,” says Nilton Lincopan, a professor at the Biomedical Sciences Institute at the University of São Paulo (ICB-USP) and another coordinator of the study.

Lincopan is a researcher at the Antimicrobial Resistance Institute of São Paulo (ARIES), a Research, Innovation, and Dissemination Center (RIDC) supported by FAPESP.

He also coordinates One Health Brazilian Resistance (OneBR), a platform that gathers epidemiological, phenotypic, and genomic data on microorganisms classified by the World Health Organization (WHO) as “critical priority.”

This classification includes bacteria for which there are few therapeutic options and which require containment measures to prevent their spread. These bacteria are also a priority for the research and development of new antimicrobials (read more at agencia.fapesp.br/38759). 

The first authors of the study are three undergraduate research students: Bruna Garcia and Matheus Silva from UNIMES, who are supervised by Sellera; and Guilherme Paiva from ICB-USP, who is supervised by Lincopan and received a scholarship from FAPESP. 

Allies

The two colonized birds were at the Santos Municipal Orchid Garden rehabilitation center on the coast of São Paulo. A total of 49 wild animals (birds and mammals) at the facility had samples collected from their rectums or cloacas.

“Because they were rescued in a peri-urban area [a transition zone between urban and rural areas], these animals are more exposed to human impact and may come into contact with garbage, sewage, and pollution from surrounding cities. This can contribute to colonization by bacteria commonly found in human hospital environments,” Sellera points out.

The animals showed no clinical signs of infection, which supports the hypothesis that they lived with the pathogen without becoming ill. The vulture’s sample was collected as soon as it was admitted to the center, indicating that it arrived already colonized by the resistant clone. Due to multiple fractures, the animal had to be euthanized 24 hours after arrival.

The owl, on the other hand, has lived at the center for ten years after suffering a collision. Due to neurological sequelae, the animal cannot return to the wild. Upon admission, the bird was treated with antibiotics for suspected chlamydiosis. Shortly before the sample was collected for the study, it was given another antimicrobial after surgery. Therefore, it is unclear whether the owl arrived already colonized or acquired the bacteria at the center.

“Rehabilitation centers offer a valuable opportunity to monitor the presence of these agents in our fauna. Global mobilization and greater financial investment are needed to expand epidemiological surveillance and establish protocols for these centers in order to reduce the chances of transmission between animals or from humans to them,” Sellera says.

According to the researcher, testing could be carried out when animals are admitted, in addition to isolating colonized animals and attempting to decolonize those with medically important strains before reintroducing them into the wild.

One good example is the Costa Branca Cetacean Project, led by the State University of Rio Grande do Norte (UERN) in Brazil and headed by veterinarian Augusto Carlos da Bôaviagem Freire. In partnership with researchers from São Paulo, rescued animals, such as manatees, undergo pathogen testing.

Collection of manatee samples for testing of WHO critical priority antibiotic-resistant bacterial pathogens in the state of Rio Grande do Norte (photo: Augusto Carlos da Bôaviagem Freire/Costa Branca Cetacean Project-UERN)

Researchers in Rio Grande do Norte are trying to standardize decolonization methods using probiotics before returning the animals to their natural environment. Undergraduate research student Ana Clara Gales Landi and doctoral student Thais Martins Gonçalves, both from ICB-USP and supervised by Lincopan, are participating in this study with scholarships from FAPESP (25/03354-5 and 24/20180-8).

“The microorganisms that live in animals present in rehabilitation centers are a sample of what’s circulating in nature. Therefore, in addition to the fundamental work they do for wildlife, these places can be important allies in monitoring human pathogens,” says Lincopan.

The work was also supported by a scholarship from FAPESP awarded to João Pedro Rueda Furlan, who completed his postdoctoral studies at the Federal University of São Paulo’s School of Medicine (EPM-UNIFESP).

The article “High-risk Escherichia coli global clones ST10 and ST155 in wild raptors admitted to a rehabilitation center” can be read at link.springer.com/article/10.1007/s11259-025-10811-y.