Composting reduces the risks of resistome in beef cattle manure at the transcriptional level.
Composting reduces the risks of resistome in beef cattle manure at the transcriptional level.
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DOI：
10.1128/aem.01752-23
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发表时间：
2024-03
影响因子：
4.4
通讯作者：
Yuepeng Sun;Zachery R. Staley;Bryan. L. Woodbury;Jean‐Jack Riethoven;Xu Li
中科院分区：
文献类型：
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作者：
Yuepeng Sun;Zachery R. Staley;Bryan. L. Woodbury;Jean‐Jack Riethoven;Xu Li
需要转录组学证据来确定堆肥是否比传统储存更有效地降低畜禽粪便中抵抗组的风险。本研究的目的是比较堆肥和储存在减少肉牛粪便中抗生素耐药性风险方面的有效性。从全尺寸粪肥堆积桩和堆肥桩的中心和表面采集样本进行宏基因组和亚转录组分析。虽然在DNA水平上，储存和堆肥粪便的抗性组差异并不明显，但在转录组水平上，堆肥优于储存的优势在抗生素抗性基因（ARGs）的丰度、ARG亚型的数量和高风险ARGs（即与人畜共患病原体相关的移动ARGs）的流行程度方面是明显的。DNA和转录序列显示，高危ARGs的病原菌宿主包括大肠杆菌O157:H7和O25b:H4、肺炎克雷伯菌和肠沙门氏菌。尽管整个堆肥堆的日平均温度在整个现场研究过程中都超过了55℃，但堆肥堆中心的ARG和ARG转录本的去除量要大于表面。这项工作表明，在减少牛粪中活跃人群的ARG风险方面，堆肥比储存具有优势。在土地施用前对粪肥进行适当处理对于减轻抗生素耐药性在环境中的传播至关重要。堆存和堆肥是粪肥处理的两种常用方法。然而，堆肥在减少粪便中抗生素耐药性方面的有效性一直存在争议。本工作比较了这两种方法降低肉牛粪便中抗生素耐药性风险的能力。我们的研究结果表明，堆肥在转录组水平上比常规储存减少了更多的高风险抗性基因。这一发现不仅强调了堆肥在减少粪便中抗生素耐药性方面的有效性，而且强调了在DNA分析的同时使用RNA分析的重要性。在土地施用前对粪肥进行适当处理对于减轻抗生素耐药性在环境中的传播至关重要。堆存和堆肥是粪肥处理的两种常用方法。然而，堆肥在减少粪便中抗生素耐药性方面的有效性一直存在争议。本工作比较了这两种方法降低肉牛粪便中抗生素耐药性风险的能力。我们的研究结果表明，堆肥在转录组水平上比常规储存减少了更多的高风险抗性基因。这一发现不仅强调了堆肥在减少粪便中抗生素耐药性方面的有效性，而且强调了在DNA分析的同时使用RNA分析的重要性。
ABSTRACT Transcriptomic evidence is needed to determine whether composting is more effective than conventional stockpiling in mitigating the risk of resistome in livestock manure. The objective of this study is to compare composting and stockpiling for their effectiveness in reducing the risk of antibiotic resistance in beef cattle manure. Samples collected from the center and the surface of full-size manure stockpiling and composting piles were subject to metagenomic and metatranscriptomic analyses. While the distinctions in resistome between stockpiled and composted manure were not evident at the DNA level, the advantages of composting over stockpiling were evident at the transcriptomic level in terms of the abundance of antibiotic resistance genes (ARGs), the number of ARG subtypes, and the prevalence of high-risk ARGs (i.e., mobile ARGs associated with zoonotic pathogens). DNA and transcript contigs show that the pathogen hosts of high-risk ARGs included Escherichia coli O157:H7 and O25b:H4, Klebsiella pneumoniae, and Salmonella enterica. Although the average daily temperatures for the entire composting pile exceeded 55°C throughout the field study, more ARG and ARG transcripts were removed at the center of the composting pile than at the surface. This work demonstrates the advantage of composting over stockpiling in reducing ARG risk in active populations in beef cattle manure. IMPORTANCE Proper treatment of manure before land application is essential to mitigate the spread of antibiotic resistance in the environment. Stockpiling and composting are two commonly used methods for manure treatment. However, the effectiveness of composting in reducing antibiotic resistance in manure has been debated. This work compared the ability of these two methods to reduce the risk of antibiotic resistance in beef cattle manure. Our results demonstrate that composting reduced more high-risk resistance genes at the transcriptomic level in cattle manure than conventional stockpiling. This finding not only underscores the effectiveness of composting in reducing antibiotic resistance in manure but also highlights the importance of employing RNA analyses alongside DNA analyses. Proper treatment of manure before land application is essential to mitigate the spread of antibiotic resistance in the environment. Stockpiling and composting are two commonly used methods for manure treatment. However, the effectiveness of composting in reducing antibiotic resistance in manure has been debated. This work compared the ability of these two methods to reduce the risk of antibiotic resistance in beef cattle manure. Our results demonstrate that composting reduced more high-risk resistance genes at the transcriptomic level in cattle manure than conventional stockpiling. This finding not only underscores the effectiveness of composting in reducing antibiotic resistance in manure but also highlights the importance of employing RNA analyses alongside DNA analyses.