Real-Time Genomic Epidemiological Evaluation of Human Campylobacter Isolates by Use of Whole-Genome Multilocus Sequence Typing
Real-Time Genomic Epidemiological Evaluation of Human Campylobacter Isolates by Use of Whole-Genome Multilocus Sequence Typing
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DOI：
10.1128/jcm.00066-13
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发表时间：
2013-08-01
影响因子：
9.4
通讯作者：
Maiden, Martin C. J.
中科院分区：
文献类型：
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作者：
Cody, Alison J.;McCarthy, Noel D.;Maiden, Martin C. J.
基于序列的分型对于了解弯曲杆菌感染的流行病学是必不可少的，弯曲杆菌感染是全球细菌性胃肠炎的主要原因。我们展示了实用和快速开发的全基因组测序提供常规的明确表征空肠弯曲菌和结肠弯曲菌的临床和公共卫生目的。重新收集了在英国牛津4个月内收集的384株弯曲杆菌临床分离株的短读数据。将重叠群存放在pubMLST.org/campylobacter网站上，并自动注释1，667个基因座。分型和系统发育信息提取和比较分析进行了各种子集的位点，全基因组的水平，使用基因组比较器和邻居网络算法。组装的序列（379株）是不同的，类似的集合从以前的研究人类弯曲杆菌病。非常密切相关的分离株的小子集主要来自相同患者的重复采样，在一种情况下，可能是实验室污染。大部分患者内变异发生在相位可变基因中。临床和流行病学信息数据可以从全基因组序列数据中提取真实的时间与直接，公开可用的工具。这些分析是高度可扩展的，是透明的，不需要密切相关的基因组参考序列，并提供改进的分辨率（i）弯曲杆菌克隆复合体之间和（ii）非常密切相关的分离株之间。此外，这些分析快速区分不相关的分离株，允许检测单菌株簇。该方法广泛适用于临床实验室中真实的人类细菌病原体的分析，几乎不需要专业培训。
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.