Faculty of Science and Technology, University of Tartu, Vanemuise 46, 51003 Tartu, Estonia.
BioZone Centre for Applied Biosciences and Bioengineering, Department of Chemical Engineering and Applied Chemistry, University of Toronto, 200 College Street, Toronto, ON M5S 3E5, Canada.
FEMS Microbiol Ecol. 2020 Feb 1;96(2). doi: 10.1093/femsec/fiaa006.
Solid organic waste is a significant source of antibiotic resistance genes (ARGs) and effective treatment strategies are urgently required to limit the spread of antimicrobial resistance. Here, we studied ARG diversity and abundance as well as the relationship between antibiotic resistome and microbial community structure within a lab-scale solid-state anaerobic digester treating a mixture of food waste, paper and cardboard. A total of 10 samples from digester feed and digestion products were collected for microbial community analysis including small subunit rRNA gene sequencing, total community metagenome sequencing and high-throughput quantitative PCR. We observed a significant shift in microbial community composition and a reduction in ARG diversity and abundance after 6 weeks of digestion. ARGs were identified in all samples with multidrug resistance being the most abundant ARG type. Thirty-two per cent of ARGs detected in digester feed were located on plasmids indicating potential for horizontal gene transfer. Using metagenomic assembly and binning, we detected potential bacterial hosts of ARGs in digester feed, which included Erwinia, Bifidobacteriaceae, Lactococcus lactis and Lactobacillus. Our results indicate that the process of sequential solid-state anaerobic digestion of food waste, paper and cardboard tested herein provides a significant reduction in the relative abundance of ARGs per 16S rRNA gene.
固体有机废物是抗生素耐药基因（ARGs）的重要来源，因此急需有效的处理策略来限制抗微生物耐药性的传播。在这里，我们研究了实验室规模固态厌氧消化器中处理食物垃圾、纸和纸板混合物过程中 ARG 多样性和丰度，以及抗生素耐药组与微生物群落结构之间的关系。从消化器进料和消化产物中总共收集了 10 个样本，用于微生物群落分析，包括小亚基 rRNA 基因测序、总群落宏基因组测序和高通量定量 PCR。我们观察到微生物群落组成发生了显著变化，经过 6 周的消化，ARG 多样性和丰度降低。所有样品中均检测到 ARGs，其中多药耐药性是最丰富的 ARG 类型。在消化器进料中检测到的 32%的 ARGs 位于质粒上，表明存在水平基因转移的潜力。通过宏基因组组装和分类，我们在消化器进料中检测到 ARGs 的潜在细菌宿主，包括欧文氏菌、双歧杆菌科、乳球菌和乳杆菌。我们的结果表明，本文所测试的食物垃圾、纸和纸板的连续固态厌氧消化过程，使 ARG 相对于 16S rRNA 基因的相对丰度显著降低。
