Detailed study at the genetic level at bacteria in farm animals, human/animal sewage, sewage treatment works and rivers, to work out the complex network of transmission of important antibiotic-resistant bacteria and antibiotic resistance genes

OVERALL STUDY AIM We do not fully understand how important types (species) of bacteria and packages of genetic material (genes) coding for antibiotic resistance move between humans, animals and the environment, or where, how and why antibiotic resistance emerges. This study aims to look in detail at the genetic level at bacteria in farm animals, human/animal sewage, sewage treatment works and rivers, to work out the complex network of transmission of important antibiotic-resistant bacteria and antibiotic resistance genes. We will use this information to work out how best to slow down the spread of antibiotic resistance between humans, livestock and the environment. STUDY BACKGROUND AND AIMS IN MORE DETAIL Infections are one of the most common causes of ill-health in human and animal medicine, and are caused by a range of different micro-organisms, including viruses and bacteria. Amongst bacteria, there are some species, or types, of bacteria, which can live harmlessly in human and animal intestines, sewage, and rivers, but can also cause disease in humans and animals if they get into the wrong body space, such as the bloodstream or urine. Examples of these bacteria include E. coli, and other similar organisms, which belong to a family of bacteria called "Enterobacteriaceae".It has generally been possible to treat infections caused by bacteria using several classes of medicines, known as antibiotics. Different antibiotics kill bacteria in different ways: for example, they can switch off critical chemical processes that the bacteria need to survive, or they can break down the outer shell of the bacteria. In response to the use of antibiotics, bacteria have changed over time, finding ways to alter their structure so that antibiotics no longer have a target to act on, or by producing substances that break down the antibiotic before it has a chance to kill the bacteria. These changes to the bacteria's genetic code, so that they are no longer killed by an antibiotic, create antibiotic resistance. Bacteria can also acquire packages of genes that cause antibiotic resistance from other surrounding bacteria. This is known as horizontal gene transfer. Through these mechanisms, members of the Enterobacteriaceae family of bacteria have developed antibiotic resistance to a number of different antibiotics over a short period of time. In some cases we are no longer able to treat these infections with the antibiotics we have available.Studying antibiotic resistance and horizontal gene transfer in bacteria found in humans, animals and the environment is difficult because we cannot directly see how bacteria and their genetic material move between them. However, new "Next Generation Sequencing" (NGS) technologies allow scientists to look in great detail at the genetic code of large numbers of bacteria. Comparing this information across bacteria which have been living in the different parts of the environment (e.g. sewage treatment works, rivers) and in human and animal sewage allows us to see how bacteria have evolved to become resistant to antibiotics, and how resistance genes have been shared between them.This study will use NGS technologies to look at the genetic code of large numbers of Enterobacteriaceae bacteria found in humans, animals (pigs, sheep and poultry), sewage (pre-, during and post-treatment), and rivers. These different groups/areas will be sampled in different seasons of one calendar year to determine how antibiotic resistance genes move around between these locations and over time, and what factors might influence this movement. We will also be investigating whether various chemicals and nutrients in the water may be affecting how quickly horizontal gene transfer occurs. Understanding this is essential to work out how we might intervene more effectively to slow the spread of antibiotic resistance genes and bacteria, and keep our antibiotic medicines useful.

整体研究目标
我们尚未完全明确重要的细菌类群（物种）与编码抗生素耐药性的遗传物质包（基因）如何在人类、动物与环境之间传播，以及抗生素耐药性产生的时间、途径与机制。本研究旨在从基因层面详细分析农场动物、人类/动物污水、污水处理厂及河流中的细菌，以阐明耐药性致病菌与抗生素耐药基因传播的复杂网络。基于上述研究结果，我们将明确如何最优地减缓抗生素耐药性在人类、畜禽与环境之间的扩散。

详细研究背景与目标
感染是人类与兽医学中最常见的致病原因之一，由包括病毒、细菌在内的多种微生物引发。在细菌中，部分类群可在人类、动物肠道、污水及河流中无害定植，但当侵入血流、尿液等异常体腔时，可引发人类与动物疾病。此类细菌的代表包括大肠杆菌（E. coli）及其他隶属于肠杆菌科（Enterobacteriaceae）的相似微生物。
长期以来，临床可通过多种类别抗生素治疗细菌感染。不同抗生素通过不同机制杀灭细菌：例如，阻断细菌生存必需的关键生化过程，或破坏细菌的外膜结构。在抗生素的选择压力下，细菌逐渐演化出耐药机制：通过改变自身结构使抗生素失去作用靶点，或分泌可在抗生素发挥杀菌作用前将其降解的物质。上述细菌遗传编码的改变使其不再被抗生素杀灭，由此产生抗生素耐药性。此外，细菌还可从周围其他细菌处获得携带耐药基因的遗传物质包，这一过程被称为水平基因转移（horizontal gene transfer）。通过上述机制，肠杆菌科细菌可在短时间内对多种抗生素产生耐药性，部分菌株甚至已无可用抗生素可治疗其引发的感染。
直接研究人类、动物与环境中细菌的抗生素耐药性与水平基因转移颇具挑战，因为我们无法直接观测细菌及其遗传物质在不同宿主与环境间的传播路径。然而，新一代测序技术（Next Generation Sequencing，NGS）可让科学家详细解析大量细菌的遗传编码信息。通过对比不同环境（如污水处理厂、河流）及人类、动物污水中分离得到的细菌的基因组信息，我们可明确细菌如何演化获得抗生素耐药性，以及耐药基因如何在不同菌群间共享。
本研究将利用新一代测序技术，分析分离自人类、动物（猪、绵羊与家禽）、污水（处理前、处理中与处理后）及河流中的大量肠杆菌科细菌的基因组信息。我们将在一个日历年的不同季节对上述不同类群与环境区域进行采样，以明确抗生素耐药基因在不同地点间及随时间的传播模式，并探究影响该传播过程的潜在因素。此外，我们还将研究水体中的各类化学物质与营养盐是否会影响水平基因转移的发生速率。阐明上述机制，对于制定更有效的干预策略以减缓抗生素耐药基因与耐药菌的扩散、维持抗生素的临床使用价值至关重要。