School of Ecology and Environment, Inner Mongolia University, Hohhot, China.
Department of Civil and Environmental Engineering, University of Nebraska-Lincoln, Lincoln, Nebraska, USA.
Appl Environ Microbiol. 2024 Apr 17;90(4):e0175223. doi: 10.1128/aem.01752-23. Epub 2024 Mar 6.
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 O157:H7 and O25b:H4, , 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.IMPORTANCEProper 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.
需要转录组学证据来确定堆肥是否比传统的堆肥更有效地降低牲畜粪便中耐药组的风险。本研究的目的是比较堆肥和堆肥在降低肉牛粪便中抗生素耐药性风险方面的效果。从大型堆肥和堆肥堆的中心和表面采集的样本进行了宏基因组学和宏转录组学分析。虽然在 DNA 水平上，堆肥和堆肥处理的粪便之间的耐药组没有明显区别，但在转录组水平上，堆肥的优势明显，表现在抗生素耐药基因（ARGs）的丰度、ARGs 亚型的数量以及高风险 ARGs（即与动物病原体相关的可移动 ARGs）的流行程度。DNA 和转录本片段表明，高风险 ARGs 的病原体宿主包括 O157：H7 和 O25b：H4， 和沙门氏菌肠。虽然整个堆肥堆的平均日温度在整个野外研究期间都超过了 55°C，但堆肥堆中心去除的 ARG 和 ARG 转录本比表面更多。这项工作表明，与堆肥相比，在减少活性牛粪便中 ARG 风险方面，堆肥具有优势。
在土地应用前对粪便进行适当处理对于减轻环境中抗生素耐药性的传播至关重要。堆肥和堆肥是两种常用的粪便处理方法。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。本研究比较了这两种方法在降低肉牛粪便中抗生素耐药风险方面的能力。我们的结果表明，与传统的堆肥相比，堆肥在转录组水平上减少了更多的高风险耐药基因。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，还强调了在 DNA 分析的基础上，同时进行 RNA 分析的重要性。
