Work

Metagenomic characterization of the resistome, bacteriome and mobilome in raw milk from intensive farming systems

Year: 2025

Type: article

Abstract: • Intensive livestock farming. Intensive livestock farming as the dominant global farming model, significantly accelerates the dissemination of antibiotic resistance genes (ARGs) among bacteria and their diffusion into the environment, primarily through its characteristics of high-density animal husbandry, routine prophylactic antibiotic use, and massive waste discharge. • A large size of samples . This is one of the few studies that has used metagenomic technology in unpre to explore the bacterial distribution and resistome in the dairy producing chain, using 539 samples of raw milk, swabs, drinking water, and forge collected from 42 dairy farms across 5 cities in China. • Drug resistance gene transfer has directionality . From the 72 culturable strains isolated from raw milk, we systematically evaluated the horizontal gene transfer risk between pathogens and found that Klebsiella pneumoniae was capable of transferring bla SHV resistance genes to Escherichia coli at a docking frequency of 8.6 × 10 −6 , though reverse transfer was not observed. • Significance of metagenomic surveillance . This study proposes a cost-effective metagenomic framework for global antimicrobial resistance surveillance, providing crucial insights for guiding policy-making and reducing risks in the food supply chain. It emphasizes the urgency of implementing region − specific interventions to curb antimicrobial resistance in dairy production. • This study provides essential insights for developing more effective strategies to mitigate bacterial contamination in dairy production. Intensive farming, as the dominant paradigm in global dairy production, exacerbates antimicrobial resistance (AMR) risks via concentrated animal operations and routine antimicrobial prophylaxis. Nevertheless, the spatiotemporal dissemination patterns of antibiotic resistance genes (ARGs) in regional intensive dairy systems remain insufficiently elucidated. Elucidating the spatiotemporal dissemination patterns of ARGs in regional intensive dairy systems by characterizing ARGs across diverse sample matrices. This investigation employed an integrated approach, combining metagenomic sequencing with comprehensive experimental validation, including bacterial isolation, antimicrobial susceptibility testing, PCR based detection of ARGs, biofilm formation assays, and conjugation experiments to characterize the antibiotic resistome across 539 samples (encompassing raw milk, forage, water, and breast swabs) collected from 42 intensive farms in Shandong, China. DY exhibited the most pronounced microbial diversity (16,347 species) and the highest ARG abundance (547 subtypes), which were predominantly β -lactamase genes (56.3 %). Multidrug-resistant determinants were pervasive across all sample types. Klebsiella pneumoniae ( K. pneumoniae ) was identified as a high-risk vector, showing 96.43 % resistance to β -lactam antibiotics and a 25 % rate of multidrug resistance (MDR). Crucially, conjugation experiments confirmed the horizontal transfer of the bla SHV gene to Escherichia coli ( E. coli ), demonstrating its potential for cross-species transmission. Furthermore, a significant correlation ( P < 0.05) was found between biofilm formation and enhanced β -lactam resistance, implicating biofilms in the maintenance of resistance. This pioneering regional ARG atlas delineates K. pneumoniae ’s epidemiological significance in Shandong’s intensive dairy continuum. Our findings advocate for precision intervention strategies and establish the utility of metagenomics for operational surveillance.

Source: Journal of Advanced Research

DOI: 10.1016/j.jare.2025.11.017