Thépault Amandine, Méric Guillaume, Rivoal Katell, Pascoe Ben, Mageiros Leonardos, Touzain Fabrice, Rose Valérie, Béven Véronique, Chemaly Marianne, Sheppard Samuel K
Unit of Hygiene and Quality of Poultry & Pork Products, Laboratory of Ploufragan-Plouzané, French Agency for Food Environmental and Occupational Health & Safety (ANSES), Ploufragan, France.
University of Rennes 1, Rennes, France.
Appl Environ Microbiol. 2017 Mar 17;83(7). doi: 10.1128/AEM.03085-16. Print 2017 Apr 1.
is among the most common worldwide causes of bacterial gastroenteritis. This organism is part of the commensal microbiota of numerous host species, including livestock, and these animals constitute potential sources of human infection. Molecular typing approaches, especially multilocus sequence typing (MLST), have been used to attribute the source of human campylobacteriosis by quantifying the relative abundance of alleles at seven MLST loci among isolates from animal reservoirs and human infection, implicating chicken as a major infection source. The increasing availability of bacterial genomes provides data on allelic variation at loci across the genome, providing the potential to improve the discriminatory power of data for source attribution. Here we present a source attribution approach based on the identification of novel epidemiological markers among a reference pan-genome list of 1,810 genes identified by gene-by-gene comparison of 884 genomes of isolates from animal reservoirs, the environment, and clinical cases. Fifteen loci involved in metabolic activities, protein modification, signal transduction, and stress response or coding for hypothetical proteins were selected as host-segregating markers and used to attribute the source of 42 French and 281 United Kingdom clinical isolates. Consistent with previous studies of British campylobacteriosis, analyses performed using STRUCTURE software attributed 56.8% of British clinical cases to chicken, emphasizing the importance of this host reservoir as an infection source in the United Kingdom. However, among French clinical isolates, approximately equal proportions of isolates were attributed to chicken and ruminant reservoirs, suggesting possible differences in the relative importance of animal host reservoirs and indicating a benefit for further national-scale attribution modeling to account for differences in production, behavior, and food consumption. Accurately quantifying the relative contribution of different host reservoirs to human infection is an ongoing challenge. This study, based on the development of a novel source attribution approach, provides the first results of source attribution in in France. A systematic analysis using gene-by-gene comparison of 884 genomes of isolates, with a pan-genome list of genes, identified 15 novel epidemiological markers for source attribution. The different proportions of French and United Kingdom clinical isolates attributed to each host reservoir illustrate a potential role for local/national variations in transmission dynamics.
是全球细菌性肠胃炎最常见的病因之一。这种微生物是众多宿主物种（包括家畜）共生微生物群的一部分，而这些动物构成了人类感染的潜在来源。分子分型方法，尤其是多位点序列分型（MLST），已被用于通过量化动物宿主和人类感染分离株中七个MLST位点等位基因的相对丰度来确定人类弯曲杆菌病的来源，表明鸡肉是主要感染源。细菌基因组可用性的增加提供了全基因组位点等位基因变异的数据，为提高源归因数据的鉴别力提供了潜力。在此，我们提出了一种源归因方法，该方法基于在通过对来自动物宿主、环境和临床病例的884个分离株基因组进行逐基因比较确定的1810个基因的参考泛基因组列表中识别新的流行病学标记。选择了15个参与代谢活动、蛋白质修饰、信号转导和应激反应或编码假设蛋白质的位点作为宿主分离标记，并用于确定42株法国临床分离株和281株英国临床分离株的来源。与先前对英国弯曲杆菌病的研究一致，使用STRUCTURE软件进行的分析将56.8%的英国临床病例归因于鸡肉，强调了这种宿主作为英国感染源的重要性。然而，在法国临床分离株中，约有相同比例的分离株归因于鸡肉和反刍动物宿主，这表明动物宿主在相对重要性上可能存在差异，并表明进一步进行全国范围的源归因建模以考虑生产、行为和食物消费差异具有益处。准确量化不同宿主对人类感染的相对贡献仍然是一项持续的挑战。本研究基于一种新的源归因方法的开发，提供了法国源归因的首批结果。通过对884个分离株基因组进行逐基因比较，并结合泛基因组基因列表进行系统分析，确定了15个新的源归因流行病学标记。法国和英国临床分离株归因于每个宿主的不同比例说明了传播动态中局部/国家差异的潜在作用。
