Metagenomic profiling uncovers microbiota and antibiotic resistance patterns across human, chicken, pig fecal, and soil environments

• Published in: The Science of the total environment 2024-10, Vol.947, p.174734, Article 174734
• Main Authors: Bai, Xue, Zhong, Hang, Cui, Xiang, Wang, Tao, Gu, Yiren, Li, Mingzhou, Miao, Xiaomeng, Li, Jing, Lu, Lizhi, Xu, Wenwu, Li, Diyan, Sun, Jing
• Format: Article
• Language: English
• Subjects: Animal gut; Animals; Anti-Bacterial Agents - pharmacology; ARGs; Bacteria - drug effects; Bacteria - genetics; Chickens - microbiology; China; Drug Resistance, Bacterial - genetics; Drug Resistance, Microbial - genetics; Feces - microbiology; Humans; Indicators; Metagenome; Metagenomics; Microbiota - drug effects; Soil; Soil Microbiology; Swine
• ISSN: 0048-9697; 1879-1026; 1879-1026
• DOI: 10.1016/j.scitotenv.2024.174734

The ongoing and progressive evolution of antibiotic resistance presents escalating challenges for the clinical management and prevention of bacterial infections. Understanding the makeup of resistance genomes and accurately quantifying the current abundance of antibiotic resistance genes (ARGs) are crucial for assessing the threat of antimicrobial resistance (AMR) to public health. This comprehensive study investigated the distribution and diversity of bacterial community composition, ARGs, and virulence factors (VFs) across human, chicken, pig fecal, and soil microbiomes in various provinces of China. As a result, multidrug resistance was identified across all samples. Core ARGs primarily related to multidrug, MLS (Macrolides-Lincosamide-Streptogramins), and tetracycline resistance were characterized. A significant correlation between ARGs and bacterial taxa was observed, especially in soil samples. Probiotic strains such as Lactobacillus harbored ARGs, potentially contributing to the dissemination of antibiotic resistance. We screened subsets of ARGs from samples from different sources as indicators to assess the level of ARGs contamination in samples, with high accuracy. These results underline the complex relationship between microbial communities, resistance mechanisms, and environmental factors, emphasizing the importance of continued research and monitoring to better understand these dynamics. [Display omitted] •Highest ARGs abundance in animal guts and soil associated to multidrug resistance•Soil (Proteobacteria) and gut (Firmicutes) phylum differences drive higher ARG level.•ARG abundance correlated with specific bacterial taxa, especially in soil•Screening subsets of ARGs to assess contamination levels of ARGs