Red-naped ibises carry antibiotic-resistant bacteria, study finds

A new study of red-naped ibises in Udaipur found diverse bacteria in their faeces, including multidrug-resistant strains.
It finds that ibises can carry antibiotic-resistant bacteria, but does not establish transmission to humans or livestock; researchers say further genomic and cross-species studies are needed.
The findings suggest that the birds may acquire environmental bacteria while foraging in soil and wetlands.

Antibiotic resistance is not confined to people alone. Wildlife can also encounter and carry resistant bacteria, with birds picking them up from contaminated water, food, waste and other human-associated environments. As they move between habitats, they may spread these bacteria through their faeces, making them useful candidates in tracking the movement of antibiotic resistance in the environment. A new study of red-naped ibises in Udaipur, Rajasthan, has now found diverse bacteria in their faeces, including multidrug-resistant strains.

The red-naped ibis is a common, resident, non-migratory wading bird that occurs across a range of habitats in and around Udaipur. It is also an opportunistic omnivore, consuming insects, amphibians, reptiles, small fish, livestock carcasses and occasionally plant material. The ibises have also been observed foraging at garbage disposal sites and on carrion.

“It was not simply a matter of choosing a common and easily observable bird,” elaborates Vijay Kumar Koli, an assistant professor and in-charge head of the Wildlife Research Laboratory at Mohanlal Sukhadia University, Udaipur, and a co-author of the study. “Its year-round presence, broad habitat use, feeding behaviour and frequent contact with human-influenced environments make it a useful species for investigating how environmental bacteria and antibiotic resistance may circulate at the wildlife-human-environment interface.”

Nesting trees of the red-naped ibis in Udaipur, Rajasthan. The bird is a common non-migratory wader that is found across the city. Image by Kanishka Mehta.

Sampling the ibises

The researchers collected 45 faecal samples between July 2022 and June 2023, with 15 samples collected during each of three seasons — summer, monsoon and winter. Samples came from roosting and nesting sites in different habitats across Udaipur city and, occasionally, from birds observed foraging on the ground.

“One practical challenge was obtaining fresh faecal samples from free-ranging birds without disturbing them. We did not capture or handle the ibises. Instead, when an ibis was encountered, it was observed from a distance of more than 15 metres until it defecated. The fresh faecal material was collected immediately after the bird left the site using a sterile swab in saline solution,” says Namita Ashish Singh, of the Applied Microbiology and Food Safety Laboratory at Mohanlal Sukhadia University and another co-author of the study.

The scientific work to analyse antibiotic-resistant bacteria involved several steps. The researchers first isolated coliforms – a group of bacteria commonly found in the digestive tracts and wastes of animals, including humans– and examined their physical and biochemical characteristics. They then used DNA sequencing to identify the bacteria. In total, they identified 60 bacterial isolates representing eight genera.

Testing the antibiotic susceptibility presented another important challenge because resistance needed to be interpreted carefully. “We tested 30 representative isolates against antibiotics from multiple classes using the Kirby-Bauer disk diffusion method (a standard laboratory test for antibiotic susceptibility) and interpreted the results using established clinical breakpoints. We excluded antibiotics to which these bacteria are known to have intrinsic resistance when defining multidrug resistance,” explains Singh.

The researchers also used statistical tests to compare the bacteria found in summer, monsoon and winter. They looked at the diversity of bacteria, the amount of coliform bacteria, and how often different bacterial groups occurred in each season.

Researchers analysed 45 faecal samples collected over a year during each season from roosting and nesting sites in Udaipur for antibiotic-resistant bacteria. Image by Namita Ashish Singh. — Researchers analysed 45 faecal samples collected over a year during each season from roosting and nesting sites in Udaipur for antibiotic-resistant bacteria. The team used DNA sequencing to identify 60 bacterial isolates representing eight genera. Image by Namita Ashish Singh.

Bacterial communities changed with the seasons

Coliform counts were the highest in winter, followed by summer and monsoon. Escherichia coli (E. coli) was the most frequently isolated bacterium, accounting for 29 of the 60 isolates, followed by Enterobacter with 16 and Klebsiella with five. The other bacteria genera identified were Citrobacter, Leclercia, Hafnia, Salmonella and Shigella.

The bacterial composition also varied between seasons. E. coli and Enterobacter were found during all three seasons. Citrobacter was detected only in winter, while no Klebsiella isolates were detected during winter. Shigella, Salmonella and Leclercia were detected only during the monsoon, and Hafnia was found only during summer. Bacterial diversity was the highest during monsoon and the lowest during summer.

The researchers identified four novel bacterial taxa that had not previously been reported from the red-naped ibis: Enterobacter mori (E. mori), Enterobacter soli (E. soli), Citrobacter freundii and Leclercia adecarboxylata. E. mori and E. soli were particularly notable because they were reported for the first time in this bird species globally. E. mori was first collected from infected roots of white mulberry, while E. soli was collected from soil.

“Their detection in ibis faeces suggests that the birds may acquire environmental bacteria while foraging. Red-naped ibises foraging in soil and wetlands, and feeding in areas influenced by garbage, soil and water could provide opportunities for contact with environmental microorganisms,” explains Koli.

Bacterial compositions among the ibises' faecal samples varied between the seasons, with coliform counts being the highest in winter. E. coli was the most frequently isolated bacterium, accounting for 29 of the 60 isolates. Image by Utkarsh Prajapati. — Bacterial compositions among the ibises’ faecal samples varied between the seasons, with coliform counts being the highest in winter. E. coli was the most frequently isolated bacterium, accounting for 29 of the 60 isolates. Image by Utkarsh Prajapati.

Resistance to multiple antibiotics

The antibiotic tests found resistance to several drugs. All the Enterobacterales isolates were resistant to linezolid and rifampicin. However, across all three seasons, all isolates were susceptible to chloramphenicol, ciprofloxacin, cefepime and ofloxacin.

Chloramphenicol is a broad-spectrum antibiotic used to treat serious bacterial infections when safer options are not suitable. Ciprofloxacin and ofloxacin are used to treat several common bacterial infections, while cefepime is used to treat severe infections, including those acquired in hospitals.

Of the 30 isolates tested, 23% showed intermediate resistance to amoxicillin, while 50% were resistant. Similarly, 30% showed intermediate resistance to ampicillin.

Ampicillin and amoxicillin are broad-spectrum penicillin antibiotics. Cefotaxime is a third-generation cephalosporin used to treat a wide range of serious bacterial infections. Trimethoprim is a prescription antibiotic mainly used to treat and prevent bacterial urinary tract infections.

“Another concerning observation was the reduced susceptibility to imipenem, a carbapenem antibiotic considered important for treating severe multidrug-resistant infections. Sixteen per cent of isolates were resistant to imipenem and another 30% showed intermediate resistance,” says Koli.

The resistance patterns also varied between bacterial groups. Overall, 40% of the tested isolates were multidrug resistant, showing non-susceptibility to at least three antibiotic classes after antibiotics to which the bacteria are intrinsically resistant were excluded. Singh notes that this is an important finding from the public health perspective.

E. coli, Klebsiella and Hafnia were not susceptible to five classes of antibiotics, while Enterobacter and Shigella were not susceptible to four.

Tests found resistance to several drugs, including ampicillin and amoxicillin, which are penicillin antibiotics; cefotaxime, which is used to treat many bacterial infections; and trimethoprim, which is used to treat bacterial urinary tract infections. Image by Namita Ashish Singh.

What are the limitations?

Previous studies have reported antibiotic-resistant and multidrug-resistant bacteria in other wild and waterbird species. “There is no reason to consider the red-naped ibis unique in this respect,” says Koli. A separate 2026 study by the same research group examined cattle egrets in Udaipur using the same number of faecal samples and a similar seasonal design. It found that about 33% of bacterial isolates were multidrug resistant, with E. coli showing the highest resistance. So, the studies do not establish that one species carries more resistant bacteria than another.

The researchers also caution against interpreting the results as evidence that the birds are transmitting resistant bacteria to people. “Our study does not establish that the ibis is a major source of antibiotic resistance or that it transmits resistant bacteria to humans or livestock. Rather, it indicates that the species can carry resistant bacteria and may potentially contribute to their environmental dispersal through faecal deposits,” says Koli.

There are other limitations. The study was conducted only in Udaipur and examined 45 faecal samples and 60 bacterial isolates, with antibiotic susceptibility testing performed on 30 representative isolates. “The resistance percentages therefore apply to the isolates tested and not to the entire red-naped ibis population. The study also focused only on culturable Enterobacterales bacteria. The study therefore does not provide a complete picture of all bacteria or antibiotic-resistance determinants present in the birds,” says Koli.

The next steps

Researchers want to move beyond documenting the presence of resistant bacteria and understand where they come from and how they move through the environment. The study authors want to study other wild bird species and regions, and compare birds living in relatively natural habitats with those that frequently use urban areas, agricultural fields, waste sites and wetlands. This could help show how habitat use affects exposure to different bacteria.

Another priority is to investigate the genetic basis of antibiotic resistance. The current study identified resistance based on how the bacteria responded to antibiotics. “Genomic analysis could identify the specific resistance genes and mobile genetic elements involved, and determine whether the same resistance mechanisms occur in bacteria from wildlife, livestock, people and the environment,” says Singh.

Ultimately, the most important question is whether there are connections among these different components, says Koli.

“Wild birds such as the red-naped ibis move across wetlands, agricultural fields and urban areas, bringing them into contact with a wide range of environmental sources of bacteria, says Alka Kumari, the lead author and a research scholar at the Mohanlal Sukhadia University. “Detecting multidrug-resistant bacteria in these birds highlights the importance of looking at antimicrobial resistance through a ‘One Health’ lens, where wildlife, livestock, humans and the environment are considered as interconnected components,” she concludes.

Banner image: A red-naped ibis in Udaipur. Image by Vijay Kumar Koli.