Modelling Campylobacter survival and spread through poultry processing: a population genomics approach.

在发达国家，弯曲杆菌是细菌性胃肠炎最常见的原因。这种微生物是鸟类和其他动物肠道微生物区系的常见组成部分，人类感染通常与食用受污染的肉类或家禽有关。在调查从根源到人类的感染方面已经做出了相当大的努力，有大量证据表明，与鸡有关的菌株是主要的疾病来源。这被认为不是因为鸡肉类型更具致病性，而是因为鸡肉在养殖场的污染水平很高，而且从加工到零售的整个过程中都保持着这种水平。弯曲杆菌是一种不太适应宿主外生存的有机体，它通过家禽加工传播并潜在地增加的机制尚不清楚。消灭养殖场中的弯曲杆菌可以解决这个问题，但这需要昂贵的生物安全干预措施，而且通过加工可能还有其他方面的干预措施在现代家禽业中可能是有效和可行的。在这个项目中，我们将使用最先进的方法来确定弯曲菌从关键阶段到家禽加工和人类疾病的整个遗传密码(基因组)。这些遗传信息将被用来检验生理特征(表型)的变异，如在特定阶段/生态位中的存活率，是如何由基因(基因型)的变化决定的。种群遗传结构的变化将被用来建立一个数学模型，该模型基于对某些基因的选择来模拟弯曲杆菌通过加工的过程，例如生物体在鸡肠道外生存所需的那些基因。通过运行具有不同参数的模型模拟，我们将调查(I)菌株在加工过程中如何变化，(Ii)负责疾病相关谱系的生存和增殖的因素，以及(Iii)加工中可以最有效地将弯曲杆菌推向灭绝的点。这种了解弯曲菌生存和传播的系统方法将为有针对性的干预提供信息。

Campylobacter is the most common cause of bacterial gastro-enteritis in the developed world. This organism is a common constituent of the gut micro-biota of birds and other animals and human infection is usually associated with the consumption of contaminated meat or poultry. Considerable effort has gone into investigating the root to human infection and there is substantial evidence that strains associated with chicken are a major source of disease. This is not thought to be because chicken types are more pathogenic but because chickens have high levels of contamination on the farm and this is maintained all the way through processing to retail. The mechanisms by which Campylobacter, an organism that is poorly adapted to survival outside of the host, spreads and potentially increases through poultry processing are poorly understood. Eliminating Campylobacter on the farm could tackle the problem but it requires expensive biosecurity interventions and there may other points through processing where interventions could be effective and practicable in the modern poultry industry. In this project we will use state-of-the-art means of determining the entire genetic code (genome) of Campylobacter strains from key stages through poultry processing and human disease. This genetic information will be used to examine how variation in the physical traits (phenotype), such as survival in a particular stage/niche, are determined by changes to the genes (genotype). Changes in the genetic structure of the population will be used to inform a mathematical model that simulates the passage of Campylobacter through processing based upon selection for certain genes, for example those required by the organism to survive outside of the chicken gut. By running model simulations with different parameters we will investigate (i) how the strains change through processing, (ii) the factors responsible for the survival and proliferation of disease associated lineages, and (iii) points in processing where Campylobacter can be most effectively pushed to extinction. This systems approach to understanding Campylobacter survival and spread will inform targeted interventions.