Comparison of antibiotic resistance genes in swine manure storage pits of Iowa, USA

T. P. Neher, M. Soupir, D. Andersen, Maggie L. O’Neill, A. Howe
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Abstract

Antimicrobial resistance (AMR) can develop in deep-pit swine manure storage when bacteria are selectively pressured by unmetabolized antibiotics. Subsequent manure application on row crops is then a source of AMR into soil and downstream runoff water. Therefore, understanding the patterns of diverse antibiotic resistance genes (ARGs) in manure among different farms is important for both interpreting the results of the detection of these genes from previous studies and for the use of these genes as bioindicators of manure borne antibiotic resistance in the environment. Previous studies of manure-associated ARGs are based on limited samples of manures. To better understand the distribution of ARGs between manures, we characterized manures from 48 geographically independent swine farms across Iowa. The objectives of this study were to characterize the distribution of ARGs among these manures and to evaluate what factors in manure management may influence the presence of ARGs in manures. Our analysis included quantification of two commonly found ARGs in swine manure, ermB and tetM. Additionally, we characterized a broader suite of 31 ARGs which allowed for simultaneous assays of the presence or absence of multiple genes. We found the company integrator had a significant effect on both ermB (P=0.0007) and tetM gene concentrations (P=0.0425). Our broad analysis on ARG profiles found that the tet(36) gene was broadly present in swine manures, followed by the detection of tetT, tetM, erm(35), ermF, ermB, str, aadD, and intl3 in samples from 14 farms. Finally, we provide a comparison of methods to detect ARGs in manures, specifically comparing conventional and high-throughput qPCR and discuss their role in ARG environmental monitoring efforts. Results of this study provide insight into commonalities of ARG presence in manure holding pits and provide supporting evidence that company integrator decisions may impact ARG concentrations.
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美国爱荷华州猪粪贮存坑抗生素耐药基因比较
当细菌选择性地受到未代谢抗生素的压力时,在深坑猪粪储存中可能产生抗微生物药物耐药性(AMR)。随后对行栽作物施用粪肥会使抗菌素耐药性进入土壤和下游径流水。因此,了解不同农场粪便中各种抗生素耐药基因(ARGs)的模式对于解释先前研究中这些基因的检测结果以及将这些基因用作环境中粪便传播的抗生素耐药性的生物指标具有重要意义。以前对粪便相关ARGs的研究是基于有限的粪便样本。为了更好地了解ARGs在肥料之间的分布,我们对爱荷华州48个地理上独立的养猪场的粪便进行了表征。本研究的目的是表征这些粪肥中ARGs的分布特征,并评估粪肥管理中的哪些因素可能影响粪肥中ARGs的存在。我们的分析包括定量猪粪中两种常见的ARGs, ermB和tetM。此外,我们还鉴定了一套更广泛的31个ARGs,可以同时测定多个基因的存在或缺失。我们发现公司整合子对ermB (P=0.0007)和tetM基因浓度均有显著影响(P=0.0425)。我们对ARG谱的广泛分析发现,tet(36)基因广泛存在于猪粪便中,随后在14个农场的样本中检测到tet、tetM、erm(35)、ermF、ermB、str、aadD和intl3。最后,我们比较了检测粪便中ARG的方法,特别是比较了传统和高通量qPCR,并讨论了它们在ARG环境监测工作中的作用。本研究的结果提供了对粪池中ARG存在的共性的洞察,并提供了支持性证据,证明公司集成商的决策可能会影响ARG的浓度。
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