Determination of the dynamics of antimicrobial resistance genes in the human and animal gut microbiome.

这项研究旨在更深入地了解抗菌素耐药性（AMR）耐药基因如何在人和动物体内生存和传播，并了解我们如何改变使用抗生素的方式，以减少AMR的数量和传播。抗生素耐药性并非在生态真空中运行，为了正确理解这一过程，我们需要更清楚地了解具有抗生素耐药性基因的细菌的潜在细菌种群和群落动态。本研究的目的是测量在患者、农场动物和环境中发现的细菌的数量和抗生素耐药性基因，以及它们随时间变化的方式（动态变化），以及对抗生素使用的反应，特别强调人类和动物疾病的临床结果。该研究将使用最先进的DNA测序技术和分析技术，研究从实验室进行的实验中获得的细菌样本以及从医院和农场采集的样本中的混合细菌种群。肠道中的许多细菌在实验室中是不可能或很难生长的，被认为是“不可培养的”。之前的研究忽略了这些问题。有待验证的总体假设是，不可培养的微生物组提供了一个AMR基因库，这些基因可能接受和捐赠AMR基因，特别是当微生物组处于抗菌选择压力下时。具体目标是：1.确定两种新型DNA测序方法的准确性和重现性，这些方法能够从粪便微生物组样本中鉴定出含有AMR基因的单个细菌菌种的DNA。2.利用这些新的基因组技术在实验条件下（小鼠和猪）研究从大肠杆菌转移AMR基因。表达超广谱β-内酰胺酶（ESBL）的大肠杆菌和在肠道微生物组内具有氟喹诺酮耐药性的肠道沙门氏菌血清型鼠伤寒沙门氏菌，这两种情况都是在用有效的抗生素治疗后以及当使用细菌对其具有耐药性的抗生素时。3.在接受抗生素治疗临床疾病的养殖猪和人类中进行肠道细菌随时间变化的研究。4.开发数学模型，捕捉细菌种群中AMR基因的通量，以确定导致耐药性积累或传播的因素。

This research aims to develop a much deeper understanding of how antimicrobial resistance (AMR) resistance genes survive and spread within people and animals and to develop an understanding of how we might change the way we use antibiotics to reduce the amount and spread of AMR. AMR does not operate in an ecological vacuum and to understand the process properly, we need to obtain a much clearer appreciation of the underlying bacterial population and community dynamics of bacteria possessing AMR genes.The aims of this research are to measure the numbers and AMR genes in bacteria found in patients, farm animals and the environment and the way they change over time (the dynamic changes), and in response to the use of antibiotics with a particular emphasis on the clinical outcomes in cases of human and animal disease. The research will use state-of-the-art DNA sequencing technology and analytical techniques to look at mixed populations of bacteria on samples of bacteria obtained from experiments performed in the laboratory and samples taken from hospitals and farms. Many of the bacteria in the gut are impossible or very difficult to grow in the laboratory and are considered to be 'unculturable'. Previous research has ignored these.The overarching hypothesis to be tested is that the unculturable microbiome provides a reservoir of AMR genes that may both receive and donate AMR genes, in particular when the microbiome is under antimicrobial selective pressure. The specific objectives are:1. To establish the accuracy and reproducibility of two novel DNA sequencing methods that enable the DNA from individual bacterial species containing AMR genes to be identified from within faecal microbiome samples. 2. To use these novel genomic techniques in experimental conditions (in mice and pigs) to investigate AMR gene transfer from E. coli expressing Extended Spectrum Beta-Lactamase (ESBL) and Salmonella enterica serovar Typhimurium with fluoroquinolone resistance within the gut microbiome both following the treatment with antibiotics that are effective and when an antibiotic is used to which the bacteria are resistant. 3. To perform studies of the gut bacteria over time in farmed pigs and humans receiving antibiotics for treatment of clinical disease. 4. To develop mathematical models that capture the flux of AMR genes in bacterial populations to identify factors that lead to the build-up or transmission of resistance.