Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Søltofts Plads, Building 221, 2800 Kgs Lyngby, Denmark.
Section for Bacteriology and Pathology, National Veterinary Institute, Technical University of Denmark, Bülowsvej 27, 1870 Frederiksberg C, Denmark.
J Antimicrob Chemother. 2017 Feb;72(2):385-392. doi: 10.1093/jac/dkw415. Epub 2016 Nov 8.
Reliable methods for monitoring antimicrobial resistance (AMR) in livestock and other reservoirs are essential to understand the trends, transmission and importance of agricultural resistance. Quantification of AMR is mostly done using culture-based techniques, but metagenomic read mapping shows promise for quantitative resistance monitoring.
We evaluated the ability of: (i) MIC determination for Escherichia coli; (ii) cfu counting of E. coli; (iii) cfu counting of aerobic bacteria; and (iv) metagenomic shotgun sequencing to predict expected tetracycline resistance based on known antimicrobial consumption in 10 Danish integrated slaughter pig herds. In addition, we evaluated whether fresh or manure floor samples constitute suitable proxies for intestinal sampling, using cfu counting, qPCR and metagenomic shotgun sequencing.
Metagenomic read-mapping outperformed cultivation-based techniques in terms of predicting expected tetracycline resistance based on antimicrobial consumption. Our metagenomic approach had sufficient resolution to detect antimicrobial-induced changes to individual resistance gene abundances. Pen floor manure samples were found to represent rectal samples well when analysed using metagenomics, as they contain the same DNA with the exception of a few contaminating taxa that proliferate in the extraintestinal environment.
We present a workflow, from sampling to interpretation, showing how resistance monitoring can be carried out in swine herds using a metagenomic approach. We propose metagenomic sequencing should be part of routine livestock resistance monitoring programmes and potentially of integrated One Health monitoring in all reservoirs.
可靠的方法来监测抗生素耐药性（AMR）在牲畜和其他储层是必不可少的，以了解趋势，传播和农业耐药的重要性。定量 AMR 主要是使用基于培养的技术，但宏基因组读映射显示出定量耐药监测的前景。
我们评估了以下方法的能力：（i）大肠杆菌 MIC 测定; （ii）大肠杆菌 CFU 计数; （iii）需氧细菌 CFU 计数; （iv）宏基因组 shotgun 测序，以根据已知的抗菌药物消耗预测 10 个丹麦综合屠宰猪群中四环素的预期耐药性。此外，我们还评估了新鲜或粪地板样本是否可以作为肠道样本的合适替代物，使用 CFU 计数，qPCR 和宏基因组 shotgun 测序。
基于宏基因组测序的读映射在预测基于抗菌药物消耗的四环素预期耐药性方面优于基于培养的技术。我们的宏基因组方法具有足够的分辨率，可以检测抗菌药物诱导的个体耐药基因丰度变化。当使用宏基因组分析时，发现猪栏粪地板样本可以很好地代表直肠样本，因为它们除了在肠外环境中增殖的少数污染类群之外，含有相同的 DNA。
我们提出了一种从采样到解释的工作流程，展示了如何使用宏基因组方法在猪群中进行耐药监测。我们建议宏基因组测序应成为常规牲畜耐药监测计划的一部分，并且可能成为所有储层综合的“One Health”监测的一部分。
