Department of Zoology, University of Oxford, Oxford, United Kingdom.
J Clin Microbiol. 2013 Aug;51(8):2526-34. doi: 10.1128/JCM.00066-13. Epub 2013 May 22.
Sequence-based typing is essential for understanding the epidemiology of Campylobacter infections, a major worldwide cause of bacterial gastroenteritis. We demonstrate the practical and rapid exploitation of whole-genome sequencing to provide routine definitive characterization of Campylobacter jejuni and Campylobacter coli for clinical and public health purposes. Short-read data from 384 Campylobacter clinical isolates collected over 4 months in Oxford, United Kingdom, were assembled de novo. Contigs were deposited at the pubMLST.org/campylobacter website and automatically annotated for 1,667 loci. Typing and phylogenetic information was extracted and comparative analyses were performed for various subsets of loci, up to the level of the whole genome, using the Genome Comparator and Neighbor-net algorithms. The assembled sequences (for 379 isolates) were diverse and resembled collections from previous studies of human campylobacteriosis. Small subsets of very closely related isolates originated mainly from repeated sampling from the same patients and, in one case, likely laboratory contamination. Much of the within-patient variation occurred in phase-variable genes. Clinically and epidemiologically informative data can be extracted from whole-genome sequence data in real time with straightforward, publicly available tools. These analyses are highly scalable, are transparent, do not require closely related genome reference sequences, and provide improved resolution (i) among Campylobacter clonal complexes and (ii) between very closely related isolates. Additionally, these analyses rapidly differentiated unrelated isolates, allowing the detection of single-strain clusters. The approach is widely applicable to analyses of human bacterial pathogens in real time in clinical laboratories, with little specialist training required.
基于序列的分型对于了解弯曲菌感染的流行病学至关重要，弯曲菌是全球细菌性胃肠炎的主要原因。我们展示了全基因组测序的实际和快速应用，以提供用于临床和公共卫生目的的常规明确的空肠弯曲菌和大肠弯曲菌特征描述。在英国牛津进行的为期 4 个月的 384 个临床弯曲菌分离株的短读数据从头组装。将连续体提交到 pubMLST.org/campylobacter 网站，并为 1667 个基因座自动注释。提取分型和系统发育信息，并使用基因组比较器和邻居网络算法对各种基因座子集（最多到整个基因组水平）进行比较分析。组装的序列（用于 379 个分离株）是多样化的，类似于以前人类弯曲菌病研究的集合。一小部分非常密切相关的分离株主要来自同一患者的重复采样，在一种情况下，可能是实验室污染。大多数患者内的变异发生在相位可变基因中。使用简单、公开可用的工具，可以实时从全基因组序列数据中提取具有临床和流行病学意义的信息。这些分析具有高度可扩展性、透明度，不需要密切相关的基因组参考序列，并提供（i）弯曲菌克隆复合体之间和（ii）非常密切相关的分离株之间的改进分辨率。此外，这些分析可以快速区分无关的分离株，从而可以检测到单株群。该方法广泛适用于实时临床实验室中人类细菌病原体的分析，几乎不需要专门的培训。
