Campylobacter jejuni is a zoonotic pathogen that infects the human gut through the food chain mainly by consumption of undercooked chicken meat, raw chicken cross-contaminated ready-to-eat food or by raw milk. In the last decades, C. jejuni has increasingly become the most common bacterial cause for food-born infections in high income countries, costing public health systems billions of euros each year. Currently, different whole genome sequencing techniques such as short-read bridge amplification and long-read single molecule real-time sequencing techniques are applied for in-depth analysis of bacterial species, in particular, Illumina MiSeq, PacBio and MinION. In this study, we analyzed a recently isolated C. jejuni strain from chicken meat by short- and long-read data from Illumina, PacBio and MinION sequencing technologies. For comparability, this strain is used in the German PAC-CAMPY research consortium in several studies, including phenotypic analysis of biofilm formation, natural transformation and in vivo colonization models. The complete assembled genome sequence most likely consists of a chromosome of 1,645,980 bp covering 1665 coding sequences as well as a plasmid sequence with 41,772 bp that encodes for 46 genes. Multilocus sequence typing revealed that the strain belongs to the clonal complex CC-21 (ST-44) which is known to be involved in C. jejuni human infections, including outbreaks. Furthermore, we discovered resistance determinants and a point mutation in the DNA gyrase (gyrA) that render the bacterium resistant against ampicillin, tetracycline and (fluoro-)quinolones. The comparison of Illumina MiSeq, PacBio and MinION sequencing and analyses with different assembly tools enabled us to reconstruct a complete chromosome as well as a circular plasmid sequence of the C. jejuni strain BfR-CA-14430. Illumina short-read sequencing in combination with either PacBio or MinION can substantially improve the quality of the complete chromosome and epichromosomal elements on the level of mismatches and insertions/deletions, depending on the assembly program used.

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不同技术破译空肠弯曲杆菌BfR-CA-14430全基因组序列的比较

空肠弯曲杆菌是一种人畜共患病病原体，主要通过食用未煮熟的鸡肉、交叉污染的生鸡肉或生牛奶来通过食物链感染人体肠道。在过去的几十年里，空肠弯曲菌日益成为高收入国家食源性感染最常见的细菌原因，每年给公共卫生系统造成数十亿欧元的损失。目前，不同的全基因组测序技术，如短读长桥扩增和长读长单分子实时测序技术被应用于细菌物种的深入分析，特别是Illumina MiSeq、PacBio和MinION。在这项研究中，我们通过来自 Illumina、PacBio 和 MinION 测序技术的短读长和长读长数据分析了最近从鸡肉中分离出的空肠弯曲杆菌菌株。为了可比性，该菌株用于德国 PAC-CAMPY 研究联盟的多项研究，包括生物膜形成的表型分析、自然转化和体内定植模型。完整组装的基因组序列很可能包括一个 1,645,980 bp 的染色体，涵盖 1665 个编码序列，以及一个编码 46 个基因的 41,772 bp 的质粒序列。多位点序列分型显示，该菌株属于克隆复合体 CC-21 (ST-44)，已知该复合体与空肠弯曲菌人类感染有关，包括爆发。此外，我们在 DNA 旋转酶 (gyrA) 中发现了耐药性决定因素和点突变，使细菌对氨苄青霉素、四环素和（氟）喹诺酮类药物产生耐药性。Illumina MiSeq 的比较，PacBio 和 MinION 使用不同的组装工具进行测序和分析，使我们能够重建空肠弯曲杆菌 BfR-CA-14430 菌株的完整染色体和环状质粒序列。Illumina 短读长测序与 PacBio 或 MinION 相结合，可以在错配和插入/缺失水平上显着提高完整染色体和外染色体元素的质量，具体取决于所使用的组装程序。