Rapid diagnostics and control strategies for enteric bacterial pathogens in backyard and commercial poultry production in Thailand and the Philippines

在许多低收入到中等收入国家，家禽、肉类和鸡蛋是用当地品种的禽类在小规模的鸡群中生产的。这与那些在大型商业单位生产肉类的国家形成了鲜明对比，这些国家使用专门为在高度受控的环境条件下饲养的鸡肉品种，在尽可能短的时间内最大限度地生产肉类。土著品种是杂交品种，与其商业同类品种相比，产蛋和肉类较少，但在家庭或当地社区一级是重要的食物来源。然而，由于监管实践的差异，使用抗菌素(AM)作为生长促进剂的情况很普遍，这限制了未来的商业发展，并促进了抗菌素耐药性的传播和维持。需要通过提供替代生长促进剂来减少AM的使用。商业育种计划导致肉鸡优先储存肌肉(即胸肉)，而不是将蛋白质分配给其他过程，可能包括免疫反应。在良好的生物安全性的商业条件下，在高度受控的条件下，在短时间内优化高营养饲料，商业鸟类的生产力非常高。相比之下，本土鸟类体型较小，营养需求较低，免疫力更强；然而，它们的生产力要低得多。不同的鸟类遗传背景和营养需求，以及潜在的不同免疫反应和肠道微生物群的组合，意味着家禽疾病的易感性和被人畜共患病原体定植的可能性可能在本地鸟类中有所不同。我们希望确定本地家禽品种和现代杂交禽类在遗传学、肠道微生物组和免疫学参数方面是否存在差异，并确定这些差异是否相关，以及是否可以利用这些差异进行疾病控制和管理。肠道沙门氏菌和空肠弯曲杆菌是主要的细菌性人畜共患病病原体，它们经常在家禽中定居，因此，由于肉类或鸡蛋的污染，对人类健康构成了非常重大的威胁。此外，某些类型的肠链球菌(普罗氏菌和加里纳氏菌)也对鸡构成疾病风险，影响鸡群的健康和福利。我们的目标是表征后院鸡群中本地品种鸡的感染情况，以确定感染如何调节生活在鸡肠道中的细菌群落的组成和存在的AM抗性基因。此外，我们还将描述当地鸟类对感染的免疫反应。我们将利用这些信息开发一种益生菌，以竞争性地排除沙门氏菌和/或弯曲杆菌，并开发一种廉价而简单的检测后院鸡群中是否存在不同类型沙门氏菌的方法。该项目将为商业和后院生产者提供急需的管理工具，以减少与家禽产品相关的疾病负担和健康风险。

In many Low to Middle Income Countries (LMICs) poultry meat and eggs are produced in small scale flocks using indigenous breeds of birds. This contrasts with countries that produce meat in large commercial units using chicken strains specifically bred for use in highly controlled environmental conditions with maximal meat production in as short a time as possible. Indigenous breeds are cross-bred and produce fewer eggs and less meat than their commercial equivalent but are are an important source of food at the family or local community level. However, due to differences in regulatory practices, the use of antimicrobials (AMs) as growth promoters is prevalent which limits future commercial development and promotes the spread and maintenance of antimicrobial resistance. The use of AMs needs to be reduced by the provision of alternative growth promoters. Commercial breeding programmes have resulted in broilers that preferentially deposit muscle (ie breast meat) over allocating proteins toward other processes, including, probably, the immune response. Under commercial conditions of good biosecurity, optimised high nutrient diets over short timescales in highly controlled conditions, commercial birds are very productive. In contrast, indigenous birds are smaller, have a lower nutrient demand and are immunologically more robust; they are however, far less productive. This combination of differing bird genetic background and nutritional requirements along with potentially different immunological responses and intestinal microflora means that poultry disease susceptibility and the potential for colonisation by zoonotic pathogens may be different in indigenous birds. We wish to determine if Indigenous breeds of poultry and modern hybrid birds differ in their genetics, gut microbiome and immunological parameters and establish if these differences associated and if they can be exploited for disease control and management. The major bacterial zoonotic pathogens, Salmonella enterica and Campylobacter jejuni, frequently colonise poultry and consequently present a very significant human health risk due to contamination of meat or eggs. In addition, certain types of S. enterica (the serovars Pullorum and Gallinarum) also present a disease risk to chickens, affecting the health and welfare of the flock. Our aim is to characterise the infection of an indigenous breed of chicken in backyard flocks to determine how infection modulates the composition of the bacterial community living in the chicken gut and the AM resistance genes that are present. In addition, we will characterise how the immune response of the indigenous birds responds to infection. We will use this information to develop a probiotic to competitively exclude Salmonella and/or Campylobacter and also develop a cheap and simple test for the presence of different types of Salmonella in backyard flocks. This project will provide both commercial and backyard producers with a much-needed management tool to reduce the disease burden and health risk associated with poultry products.