Abstract：
As the world\'s leading cause of human gastro-enteritis, the food- and waterborne pathogen Campylobacter needs to be intensively monitored through a One Health approach. Particularly, wild birds have been hypothesized to contribute to the spread of human clinical recurring C. jejuni genotypes across several countries. A major concern in studying epidemiological dynamics is resolving the large genomic diversity of strains circulating in the environment and various reservoirs, challenging to achieve with isolation techniques. Here, we applied a passive-filtration method to obtain isolates and in parallel recovered genotypes from metagenomic sequencing data from associated filter sweeps. For genotyping mixed strains, a reference-based computational workflow to predict allelic profiles of nine extended-MLST loci was utilized. We validated the pipeline by sequencing artificial mixtures of C. jejuni strains and observed the highest prediction accuracy when including obtained isolates as references. By analyzing metagenomic samples, we were able to detect over 20% additional genetic diversity and observed an over 50% increase in the potential to connect genotypes across wild-bird samples. With an optimized filtration method and a computational approach for genotyping strain mixtures, we provide the foundation for future studies assessing C. jejuni diversity in environmental and clinical settings at improved throughput and resolution.
摘要：
作为世界上人类胃肠炎的主要原因,食品和水传播的病原体弯曲杆菌需要通过一个健康的方法进行集中监测。特别是,据推测，野生鸟类有助于人类临床复发的空肠弯曲杆菌基因型在几个国家的传播。研究流行病学动力学的主要关注点是解决在环境和各种水库中循环的菌株的大量基因组多样性，用隔离技术实现具有挑战性。这里,我们应用被动过滤方法,从相关过滤扫描的宏基因组测序数据中获得分离株和平行回收的基因型.对于混合菌株的基因分型，利用基于参考的计算工作流程来预测9个扩展MLST基因座的等位基因谱.我们通过对空肠弯曲杆菌菌株的人工混合物进行测序来验证管道，并在包括获得的分离株作为参考时观察到最高的预测准确性。通过分析宏基因组样本，我们能够检测到超过20％的额外遗传多样性，并观察到在野生鸟类样本中连接基因型的潜力增加了50％以上。通过优化的过滤方法和对菌株混合物进行基因分型的计算方法，我们为未来评估环境和临床环境中空肠弯曲杆菌多样性的研究提供了基础,同时提高了吞吐量和分辨率.
