16S rRNA gene metabarcoding of faecal samples from a production cycle on a commercial pig unit

There is considerable concern regarding the increasing threat to human health from drug resistant bacterial infections. The major driver for the development of these drug resistant infections is the use of antibiotics in humans and animals. Each time an antibiotic is used, a wide variety of bacteria including pathogenic ('bad'), commensal ('good') and environmental bacteria will be killed by the drug, however some of these bacteria will survive because they will have become resistant to the antibiotic used. Bacteria can become resistant either through a random change in their genes (mutation) or by acquiring a new gene(s) from another bacteria (horizontal gene transfer). The ability of bacteria to share antibiotic resistance genes is of considerable concern as it is possible that commensal and environmental bacteria could act as a reservoir of resistance genes that could be acquired by pathogenic bacteria. The more antibiotics that are used, the more likely it is that these resistance genes will become established within a broad range of bacteria and environments.Approximately 590 tonnes of antibiotics are used in humans and 420 tonnes in animals in the UK each year. Accurate data regarding use in animals is not available, however poultry and pig farming represent a significant proportion of this use. Whilst the use of antibiotics as growth promoters is banned in the EU, they are still used for group level treatments of farm animals. Our understanding as to how antibiotic use in farm animals relates to the levels of antibiotic resistance genes within different farming systems is very simplistic. We do not know how management decisions on farm impact on the diversity of the commensal and environmental bacteria on the farm and how this relates to the 'quantity' of antibiotic resistance genes in this system. We also do not understand what happens to these resistance genes in the face of different antibiotic treatment protocols, whether some protocols are 'worse' than others at selecting for resistance and whether the levels of resistance genes decay when antibiotic treatment is stopped. We therefore do not have a clear evidence base as to the most effective way to reduce and refine antibiotic use on farms to minimise selecting for antibiotic resistance genes.The aim of this work is therefore to demonstrate that changes in the diversity of bacteria and 'quantity' of antimicrobial resistance genes within pig faeces and their environment can be measured and related to one another, antibiotic use and management changes on the farm. The application of this work will be to develop a framework with which changes to both management practices and antibiotic use on farms can be proposed that minimise the selection for antibiotic resistance. This will benefit farmers by reducing the likelihood of selecting for resistant bacteria that infect farm animals and society more generally by reducing the likelihood that antibiotic resistant infections in humans will develop as a consequence of antibiotic use in farm animals.

当前，耐药菌感染（drug resistant bacterial infections）对人类健康构成的威胁日益加剧，引发了广泛担忧。此类耐药感染滋生的主要诱因，是人类与动物对抗生素（antibiotics）的使用。每一次抗生素施用过程中，包括致病菌（pathogenic bacteria，‘有害菌’）、共生菌（commensal bacteria，‘有益菌’）以及环境菌群在内的各类细菌，大多会被该药物杀灭，但部分细菌因已对所用抗生素产生耐药性而得以存活。细菌产生耐药性的途径主要有两种：一是自身基因发生随机突变（mutation），二是从其他细菌处获取新的基因，即水平基因转移（horizontal gene transfer）。细菌共享抗生素耐药基因（antibiotic resistance genes）的现象令人尤为担忧，因为共生菌与环境菌群可能成为耐药基因的储存库，进而被致病菌获取。抗生素使用频率越高，这些耐药基因越有可能在广泛的细菌类群与环境中定植。英国（UK）每年约有590吨抗生素用于人类医疗，420吨用于畜禽养殖。目前尚无畜禽抗生素使用的精准统计数据，但家禽与生猪养殖是抗生素使用的重要组成部分。尽管欧盟（EU）已禁止将抗生素用作生长促进剂（growth promoters），但仍将其用于畜禽的群体治疗。目前学界对畜禽养殖中抗生素使用与不同养殖系统内抗生素耐药基因水平之间的关联认知仍极为粗浅。我们尚不明确农场的管理决策如何影响农场内共生菌与环境菌群的多样性，以及这种多样性与该系统内抗生素耐药基因的‘丰度’存在何种关联；也不清楚不同抗生素治疗方案下耐药基因的变化情况，部分方案是否更易筛选出耐药菌株，以及停止抗生素治疗后耐药基因水平是否会衰减。因此，目前尚无明确的证据基础，来确定农场中减少、优化抗生素使用以最大限度降低耐药基因筛选压力的最优方案。本研究的核心目标，即验证可通过检测猪粪便（pig faeces）及其环境中细菌多样性与抗菌耐药基因（antimicrobial resistance genes）丰度的变化，将二者与农场的抗生素使用及管理变更相关联。本研究的应用价值在于，可构建一套分析框架，用于提出优化农场管理措施与抗生素使用方案的建议，从而最大限度降低耐药基因的筛选压力。此举一方面可降低感染畜禽的耐药菌出现概率，惠及养殖户；另一方面可减少因畜禽养殖抗生素使用而引发的人类耐药菌感染风险，进而惠及全社会。