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微生物药物耐药性（AMR）耐药基因如何在人和动物体内存活和传播，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。AMR不是在生态真空中运作的，为了正确理解这一过程，我们需要更清楚地了解潜在的细菌种群和拥有AMR基因的细菌群落动态。这项研究的目的是测量在病人、农场动物和环境中发现的细菌的数量和抗菌素耐药性基因，以及它们随时间变化的方式（动态变化），并对抗生素的使用作出反应，特别强调人类和动物疾病病例的临床结果。这项研究将使用最先进的DNA测序技术和分析技术来观察从实验室实验中获得的细菌样本以及从医院和农场采集的样本上的混合细菌种群。肠道中的许多细菌是不可能或很难在实验室中生长的，被认为是“不可培养的”。之前的研究忽略了这些。需要验证的总体假设是，不可培养的微生物组提供了AMR基因的储存库，可以接受和捐赠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。建立两种新的DNA测序方法的准确性和可重复性，使含有AMR基因的单个细菌物种的DNA能够从粪便微生物组样本中鉴定出来。2. 在实验条件下（在小鼠和猪中）使用这些新的基因组技术，研究在使用有效抗生素治疗和使用细菌耐药的抗生素治疗后，肠道微生物群中表达扩展谱β -内酰胺酶（ESBL）的大肠杆菌和具有氟喹诺酮耐药性的肠沙门氏菌血清型鼠伤寒沙门氏菌的AMR基因转移。3. 对接受抗生素治疗临床疾病的养猪和人的肠道细菌进行长期研究。4. 建立数学模型，捕捉细菌种群中抗菌素耐药性基因的通量，以确定导致耐药性形成或传播的因素。

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.