Antimicrobial resistance (AMR) has become a major concern for human and food-animal health. Key to building a better understanding of AMR selection and spread is the resistome, the collection of all antimicrobial resistance genes (ARG) and their precursors in the gut microbiome.
“When we study the microbiome, we need to have a comprehensive picture of the AMR in the gut or other compartments of the host,” said Ana Fonseca, DVM, PhD candidate in animal and microbiome sciences at Pennsylvania State University.
“Once we understand AMR, we can design strategies to prevent the possible dissemination of pathogenic bacteria and retain the long-term therapeutic potential of the antimicrobial.”
She presented the preliminary findings of her recent study at the 2024 Poultry Science Association annual meeting.
Although AMR is a natural process that occurs over time through genetic changes, antimicrobial misuse and overuse have raised the stakes. “It is a One Health problem, having significant intersectional consequences that affect the environment, humans and animals,” she noted.
Industry challenges
AMR has resulted in additional regulations for on-farm use, as well as consumer preferences for antibiotic-free products.
Fortunately, the poultry industry has antimicrobial-alternative feeding strategies that are known to improve the bird’s bodyweight. Many alternatives also have antimicrobial activities that can promote intestinal health.
“It’s well-known that such products change the bird’s microbiota. Because of that, we hypothesize that feed additives affect the abundance of resistance genes in chicken excreta,” Fonseca said.
She and her colleagues conducted a study to characterize the effects of a probiotic and an essential oils blend on the broiler resistome.
The process
Researchers allocated Cobb 500 1-day-old chicks to 32 cages with 10 broilers per cage per treatment, totaling eight replicates. The broilers were reared to 21 days. Treatments consisted of four diets:
- Basal diet (negative control)
- Basal diet with bacitracin methylene disalicylate
- Basal diet with an essential oils blend
- Basal diet with a probiotic (Bacillus subtilis)
The team collected excreta samples at 1, 10 and 21 days to characterize the broilers’ resistome. They extracted DNA from the samples to sequence for AMR analysis.
The following resistance types were evaluated: biocides (substances used to kill or control the spread of harmful organisms), drugs, metals and multi-compound. “For poultry, the most important resistant types are for drugs and biocides,” Fonseca noted.
The results
Across all samples, there were 823 unique ARGs identified, spanning a broad spectrum of treatment classes. The researchers found no major changes in the relative abundance of resistance genes in the broiler excreta among dietary treatments.
“However, looking closely into the relative abundance of resistance genes, we observed that 31% were beta-lactam resistance genes, followed by aminoglycosides, tetracyclines, and macrolides lincosamides (MLS) and streptogramins,” Fonseca said.
“Those are important antibiotics in the poultry industry. When we talk about biocides, 51% of the relative abundance are multi-biocide resistance genes,” she added.
For the relative abundance of drug resistance genes in 1-day-old chicks, 51% were beta-lactams, followed by tetracyclines (14%), and MLS and aminoglycosides (both 13%).
In 21-day-old broilers, the relative abundance of drug resistance genes declined to 33% for beta-lactams and increased to 25% for aminoglycosides and to 15% for tetracyclines and MLS.
Specifically analyzing biocides, 39% were multi-biocide resistance genes, followed by acid-resistance genes (31%) and acetate-resistance genes (15%) in 1-day-old chicks. This relative abundance shifted in the 21-day-old bird, with multi-biocide resistance increasing to 62%, acid-resistance genes declining to 14% and acetate-resistance genes declining to 7%.
Phenolic-compound resistance also shifted from 3% to 8% in 21-day-old birds.
Does bird age impact resistance? “Previously, we showed that bird age has a major effect on microbiome composition,” she noted. “Resistance composition on days 1, 10 and 21 were significantly different. We concluded that the relative abundance of drug resistance genes in broilers is created over time.”
Key takeaways
“The study tells us that feed additives did not change the excreta resistome dynamics,” Fonseca said. She noted that the controlled research setting may have influenced that outcome. “It would be interesting to observe whether the dynamic would change at the farm level.”
Study results also demonstrated that the bird’s age significantly impacts the excreta resistome. “I suggest we can correlate that with the microbiome results,” she added.
In addition, the most abundant ARG classes in the study were beta-lactams, aminoglycosides, tetracyclines and MLS. The most abundant biocide ARGs were multi-biocide and acid-resistance genes.
“This study provides valuable insights on the One Health approach by demonstrating the complexity of AMR selection pressure in poultry production,” Fonseca noted.
Looking ahead, the research team plans to evaluate different feed additives and focus more on the functionality of the microbiota and resistome, then link the metabolomics with intestinal health, she added.
