A recent study published in Engineering has shed light on the quality and potential antibiotic resistance dissemination risks associated with livestock probiotics in China. The research, conducted by a team from the Jiangsu Academy of Agricultural Sciences and Yangzhou University, analyzed 95 non-duplicate commercial probiotic products for livestock from across China, revealing significant issues in labeling accuracy, strain composition, and the presence of antibiotic resistance genes (ARGs).

The study found that the labeling compliance rate for Lactobacillus was alarmingly low at just 11%, with approximately 33.3% of the products contaminated with opportunistic pathogens harboring various virulence and antibiotic resistance genes. The researchers isolated Bacillus and Enterococcus from the products and found diverse clonal types and geographical dispersion. Notably, certain Enterococcus strains exhibited close phylogenetic relationships to clones associated with human infectious diseases. The prevalence of ARGs was higher in Enterococcus compared to Bacillus and Lactobacillus. Specifically, the oxazolidine-resistance gene optrA, located on novel transferable plasmids, was identified in one isolate of Enterococcus faecium (E. faecium).

Using a chicken model, the researchers observed that optrA-positive E. faecium disrupted the normal intestinal microbiota, altering the abundance of intestinal resistome and mobile genetic elements (MGE). Metagenomic analysis revealed that the optrA gene could be transferred via the transposon IS1216E to commensal intestinal bacteria, including E. cecorum, E. gallinarum, and L. crispatus species.

The study underscores the importance of adhering to good manufacturing practice (GMP) standards in the production of livestock probiotics. The findings highlight the potential for low-quality Enterococcus strains, which contain various ARGs, to disrupt intestinal homeostasis and serve as a reservoir for ARGs. The researchers emphasize the need for careful evaluation of Enterococcus strains used as probiotics to avoid negative impacts on both livestock and human health.

The researchers conducted antimicrobial susceptibility testing on the probiotic isolates, revealing that Bacillus spp. exhibited limited and species-specific patterns of antibiotic resistance, while Enterococcus spp. showed more complex multidrug resistance patterns. Whole-genome sequencing identified a diverse array of ARGs in Enterococcus spp., including lsa(A), lnu(B), msr(C), tet(L), erm(B), lsa(E), optrA, and fexA. Phylogenetic analysis showed that the probiotic strains exhibited significant genetic diversity, with no typical geographical clustering.

The study also identified transferable plasmids carrying optrA and fexA genes in Enterococcus strains. Conjugative assays demonstrated that these plasmids could be transferred to other Enterococcus strains, conferring resistance to florfenicol and linezolid. In the chicken intestinal colonization model, the researchers found that optrA-positive E. faecium could colonize the gut and promote the transfer of the optrA gene to other Enterococcus strains, significantly altering the gut microbiota composition and increasing the abundance of ARGs and MGEs.

The findings suggest that the widespread use of multidrug-resistant Enterococcus probiotics can significantly impact the composition and abundance of resistance genes in the chicken gut microbiome. The researchers recommend rigorous molecular-level identification of probiotic strains, especially Enterococcus, to assess MGEs and transferable antimicrobial resistance (AMR) genes. They also advocate for standardized guidelines for probiotic strain usage in livestock and optimization of the manufacturing process to ensure product consistency, potency, and purity.

The study highlights the need for improved regulation and quality control of livestock probiotics in China to mitigate the risks associated with antibiotic resistance dissemination. Future work should focus on developing comprehensive guidelines and regulatory oversight to ensure the safe and effective use of probiotics in livestock farming.

The paper “Livestock Probiotics in China: Quality Analysis and Enterococcus-Associated Antibiotic Resistance Dissemination Risks,” is authored by Xing Ji, Jiayun Wang, Jun Li, Lili Zhang, Ruicheng Wei, Ran Wang, Tao He. Full text of the open access paper: https://doi.org/10.1016/j.eng.2025.03.032. For more information about Engineering, visit the website at https://www.sciencedirect.com/journal/engineering.